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free-standing single layer of MoS{math}`_2` while learning about convergence studies, parallel strategies, and GPU calculations. + +In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate. + +```{figure} img/mos2.png +:scale: 40% +``` + +*MoS{math}`_2` monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.* + +## Many-body corrections to the DFT band gap + +We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of. + +Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy {math}`\Sigma`: + +```{math} +E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle +``` + +Here {math}`\epsilon_{nk}` and {math}`\psi_{nk}` are the Kohn-Sham energies and wavefunctions, respectively, while {math}`V_{xc}` is the DFT exchange-correlation potential. + +For each electronic state {math}`nk`, the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy ({math}`\Sigma^x`), and an energy-dependent, usually gap-closing term called the correlation self-energy ({math}`\Sigma^c`). These contributions are tackled separately by the code: + +```{math} +\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega) +``` + +The energy-dependent dynamical electronic screening {math}`\varepsilon^{-1}(\omega)` is included in {math}`\Sigma^c` and must therefore be calculated as well. + +In this way, we can compute the "quasiparticle" corrections {math}`E^{QP}_{nk}` to the single-particle Kohn-Sham eigenvalues {math}`\epsilon_{nk}`. +The typical workflow for a GW calculation is: + +```{figure} img/gwflow.png +:scale: 40% +``` + +## Set up a Yambo calculation + +Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes): +```console +wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz +``` +```console +tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz +``` + +You can now enter the tutorial directory +```console +cd MoS2_HPC_tutorial_Leonardo +``` + +### Yambo `SAVE` folder + +First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo. + +The QE save folder for MoS{math}`_2` is already present at `00_QE-DFT`. We should move inside it and then run the `p2y` executable to generate the uninitialised `SAVE`. + +But first, we need to access a node interactively: +```console +srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash +``` + +Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have +```console +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 +``` + +Finally: +```console +cd 00_QE-DFT/mos2.save +mpirun -np 1 p2y +``` + +Now, we need to run the initialization step. Every Yambo run **must** start with this step. This will be automatically performed when you run Yambo on a `SAVE` directory for the first time. Just type + +```console +mpirun -np 1 yambo +``` + +and then check the yambo log called `l_setup`. The initialization step determines the {math}`G`-vector shells and the {math}`k`- and {math}`q`-point grids based on the DFT calculation. If you check inside the `SAVE` you will see two types of databases. The static ones, starting with `ns.*`, are directly converted in the `p2y` step, while the dynamical ones, `ndb.*` are generated during the initialisation. + +```console +ls SAVE/ +``` +```console +ndb.gops # info on G-vector shells, etc +ndb.kindx # info and k and q meshes +ns.db1 # info on geometry and KS bands +ns.kb_pp_pwscf # pseudopotential info +ns.wf # wave functions info +... +``` +The databases are written in netCDF format. +Yambo has produced also a human readable output, `r_setup`, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections. +```console +vim r_setup +``` +```console +[02.01] Unit cells # Lattice geometry info +================== + ... +[02.02] Symmetries # Symmetry ops. written explicitly +================== + ... +[02.03] Reciprocal space # Reciprocal lattice info +======================== +... +[02.04] K-grid lattice # k-point coords. written explicitly +====================== +... +[02.05] Energies & Occupations # Info on band gaps and occupations +============================== # DFT eigenvalues +... +[03] Transferred momenta grid and indexing # q-points (momentum transfer grid) +========================================== +``` + +Finally, let us move the `SAVE` and the report file to the directory where we will run the first GW calculation. +```console +mv SAVE r_setup ../../01_GW_first_run/ +cd ../../01_GW_first_run/ +``` + +### Yambo input file + +Now that we have a working `SAVE`, it is time to generate the input file we will be using for our first GW calculation. + +This can be done by the `yambo` executable via command-line instructions. + +If you type +```console +yambo -h +``` +You will get a list of the possibile options: + +```console + ___ __ _____ __ __ _____ _____ +| Y || _ || Y || _ \ | _ | +| | ||. | ||. ||. | / |. | | + \ _/ |. _ ||.\ / ||. _ \ |. | | + |: | |: | ||: | ||: | \|: | | + |::| |:.|:.||:.|:.||::. /|::. | + `--" `-- --"`-- --"`-----" `-----" + 'A shiny pot of fun and happiness [C.D.Hogan]' + + This is : yambo + Version : 5.1.0 Revision 21422 Hash fde6e2a07 + Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO + + Help & version: + -help (-h) : can be an option (e.g. -h optics) + -version :Code version & libraries + + Input file & Directories: + -Input (-F) :Input file + -Verbosity (-V) :Input file variables verbosity (more with -h Verbosity) + -Job (-J) :Job string + -Idir (-I) :Input directory + -Odir (-O) :I/O directory + -Cdir (-C) :Communication directory + + Parallel Control: + -parenv (-E) :Environment Parallel Variables file + -nompi :Switch off MPI support + -noopenmp :Switch off OPENMP support + + Initializations: + -setup (-i) :Initialization + -coulomb (-r) :Coulomb potential + + Response Functions: + -optics (-o) :Linear Response optical properties (more with -h optics) + -X (-d) :Inverse Dielectric Matrix (more with -h X) + -dipoles (-q) :Oscillator strenghts (or dipoles) + -kernel (-k) :Kernel (more with -h kernel) + + Self-Energy: + -hf (-x) :Hartree-Fock + -gw0 (-p) :GW approximation (more with -h gw0) + -dyson (-g) :Dyson Equation solver (more with -h dyson) + -lifetimes (-l) :GoWo Quasiparticle lifetimes + + Bethe-Salpeter Equation: + -Ksolver (-y) :BSE solver (more with -h Ksolver) + + Total Energy: + -acfdt :ACFDT Total Energy + + Utilites: + -Quiet (-Q) :Quiet input file creation + -fatlog :Verbose (fatter) log(s) + -DBlist (-D) :Databases properties + -walltime :Walltime (more with -h walltime) + -memory :Memory (more with -h memory) + -slktest :ScaLapacK test + + YAMBO developers group (http://www.yambo-code.org) +``` + +In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type: +```console +yambo -gw0 p -g n -r -V par -F gw.in +``` + +Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the `slurm` scheduler. +```console +exit +``` + +You can now inspect the input file `gw.in` and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change. + +We discuss them below step by step. + +### Parameters for a GW calculation + +We start with the runlevels: + +``` +gw0 # [R] GW approximation +ppa # [R][Xp] Plasmon Pole Approximation for the Screened Interaction +el_el_corr # [R] Electron-Electron Correlation +dyson # [R] Dyson Equation solver +rim_cut # [R] Coulomb potential +HF_and_locXC # [R] Hartree-Fock +em1d # [R][X] Dynamically Screened Interaction +``` + +```{callout} Runlevels +- The **[R]** keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have: + - `rim_cut`: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables). + - `gw0`: Yambo learns that it has to run a GW calculation (enables [GW] variables). + - `HF_and_locXC`: calculation of exchange part of the self-energy {math}`\Sigma^x` (i.e., Hartree-Fock approximation). + - `em1d`: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute {math}`\Sigma^c`. + - `ppa`: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables). + - `dyson`: Yambo will solve the Dyson-like quasiparticle equation. +``` + +Going through the file we find: + +``` +EXXRLvcs= 37965 RL # [XX] Exchange RL components +VXCRLvcs= 37965 RL # [XC] XCpotential RL components +``` + +Recall that we have, for the exchange self-energy: + +```{math} +\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q} +``` + +```{callout} Exchange self-energy +- `EXXRLvcs` controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while `VXCRLvcs` does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value). +``` + +Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have: + +```{math} +\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega') +``` + +(Here, the {math}`\rho`-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.) + +The calculation is divided in two steps. First, the response function in the plasmon pole approximation (`em1d ppa`), under the keywords `[X]` and `[Xp]`, i.e., {math}`\varepsilon^{-1}_{GG'}(q,\omega)`. + +``` +Chimod= "HARTREE" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc +% BndsRnXp + 1 | 300 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 RL # [Xp] Response block size +% LongDrXp + 1.000000 | 0.000000 | 0.000000 | # [Xp] [cc] Electric Field +% +PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy +XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze) +``` +```{callout} Response function +- `Chimod= "Hartree"` indicates that we compute the response function in the Random Phase Approximation (RPA). +- `BndsRnXp` represents the electronic states included in the response function {math}`\varepsilon`, and is a convergence parameter. +- `NGsBlkXp` is the number of G-vectors used to calculate the RPA response function {math}`\varepsilon^{-1}_{GG'}`. It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested). +- `LongDrXp` represents the direction of the long-range auxiliary external electric field used to compute {math}`\varepsilon^{-1}_{GG'}(q)` at {math}`q,G\rightarrow 0`. In general you have to be mindful of the system symmetries. In our case, we will put `1 | 1 | 1` to cover all directions. +- `PPAPntXp= 27.21138 eV` is the energy of the plasmon pole. We don't normally change this. +- `XTermKind` is used to specify a "terminator": this accelerates numerical convergence with respect to the number of bands `BndsRnXp`. +``` + +Next, we have the `[GW]` group of parameters controlling the next part of the correlation self-energy calculation: +``` +% GbndRnge + 1 | 300 | # [GW] G[W] bands range +% +GTermKind= "none" # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile) +DysSolver= "n" # [GW] Dyson Equation solver ("n","s","g") +%QPkrange # [GW] QP generalized Kpoint/Band indices +1|7|1|300| +% +``` +```{callout} Correlation self-energy +- `GbndRnge` is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator `GTermKind`. +- `DysSolver="n"` specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method `"n"`. +- `QPkrange` indicates the range of electronic (nk) states for which the GW correction {math}`\Sigma_{nk}` is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices. +``` + +We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should __edit now once and for all__. + +``` +RandQpts=1000000 # [RIM] Number of random q-points in the BZ +RandGvec= 100 RL # [RIM] Coulomb interaction RS components +CUTGeo= "slab z" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY.. +``` +```{callout} Coulomb potential +- The **[RIM]** keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to {math}`q=0` and {math}`G=0` in the {math}`q`-integration of the bare Coulomb interaction - i.e. {math}`4\pi/(q+G)^2` - for 2D systems. +- The **[CUT]** keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the {math}`z`-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic. +``` + +Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now. +``` +X_and_IO_CPU= "" # [PARALLEL] CPUs for each role +X_and_IO_ROLEs= "" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_and_IO_nCPU_LinAlg_INV=-1 # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set) +X_Threads=0 # [OPENMP/X] Number of threads for response functions +DIP_CPU= "" # [PARALLEL] CPUs for each role +DIP_ROLEs= "" # [PARALLEL] CPUs roles (k,c,v) +DIP_Threads=0 # [OPENMP/X] Number of threads for dipoles +SE_CPU= "" # [PARALLEL] CPUs for each role +SE_ROLEs= "" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads=0 # [OPENMP/GW] Number of threads for self-energy +``` + +In a GW calculation, the most important parameters to be numerically converged are: +- kpoint mesh (requires multiple nscf DFT runs) +- `BndsRnXp` +- `NGsBlkXp` +- `GbndRnge` +- [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs) + +From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations. + +--- + +## The first run + +We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file `r_setup` produced when the `SAVE` folder was initialised. Just search for the string 'Direct Gap' and you'll see that the latter occurs at k-point 7 between bands 13 and 14: +``` + [X] Filled Bands : 13 + [X] Empty Bands : 14 300 + [X] Direct Gap : 1.858370 [eV] + [X] Direct Gap localized at k : 7 +``` +In addition, we will set the number of bands in `BndsRnXp` and `GbndRnge` to a small value, just to have it run fast. Hence, we modify the input file accordingly (check `BndsRnXp`, `GbndRnge`, `LongDrXp`, `QPkrange`): +``` +rim_cut # [R] Coulomb potential +gw0 # [R] GW approximation +ppa # [R][Xp] Plasmon Pole Approximation for the Screened Interaction +dyson # [R] Dyson Equation solver +HF_and_locXC # [R] Hartree-Fock +em1d # [R][X] Dynamically Screened Interaction +X_Threads=0 # [OPENMP/X] Number of threads for response functions +DIP_Threads=0 # [OPENMP/X] Number of threads for dipoles +SE_Threads=0 # [OPENMP/GW] Number of threads for self-energy +RandQpts=1000000 # [RIM] Number of random q-points in the BZ +RandGvec= 100 RL # [RIM] Coulomb interaction RS components +CUTGeo= "slab z" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY.. +% CUTBox + 0.000000 | 0.000000 | 0.000000 | # [CUT] [au] Box sides +% +CUTRadius= 0.000000 # [CUT] [au] Sphere/Cylinder radius +CUTCylLen= 0.000000 # [CUT] [au] Cylinder length +CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified +EXXRLvcs= 37965 RL # [XX] Exchange RL components +VXCRLvcs= 37965 RL # [XC] XCpotential RL components +Chimod= "HARTREE" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc +% BndsRnXp + 1 | 20 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 RL # [Xp] Response block size +% LongDrXp + 1.000000 | 1.000000 | 1.000000 | # [Xp] [cc] Electric Field +% +PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy +XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze) +% GbndRnge + 1 | 20 | # [GW] G[W] bands range +% +GTermKind= "none" # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile) +DysSolver= "n" # [GW] Dyson Equation solver ("n","s","g") +%QPkrange # [GW] QP generalized Kpoint/Band indices +7|7|13|14| +% +``` +We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. __Modify it to suit your specific machine__. +```console +vim run_first_job.sh +``` +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=2 +#SBATCH --cpus-per-task=8 +#SBATCH --partition=boost_usr_prod +#SBATCH --time=0:05:00 +#SBATCH --gres=gpu:2 +#SBATCH --account=EUHPC_TD02_030 +#SBATCH --job-name=first_job + +export OMP_NUM_THREADS=8 +export OMP_PLACES=cores +export OMP_PROC_BIND=close + +# load yambo +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \ + yambo -F gw.in -J job_00_first_run -C out_00_first_run +``` +We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after `yambo`, it is not going to generate an input file, but rather, run the one specified by `-F`. Now, go ahead an submit this job +```console +sbatch run_first_job.sh +``` +The status of the jobs can be monitored via: +``` +squeue -u $USER # to inspect the status of jobs + # (hint: make a unix alias, if you like) +scancel # to delete jobs in the queue +``` + +The newly generated databases will be stored in the job directory, as specified by `-J`, while the report, log and output files will be stored in the communications directory (`-C`). As this is your first `yambo` run, take a moment to inspect the report and log files, which you can find inside the `-C` directory. In these report and log files, you can see the steps performed by `yambo`. For instance, the code calculates the screening at every k-point and stores it in the PPA database called `ndb.pp`. By opening the report +```console +vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa +``` +you will see +``` +[07] Dynamic Dielectric Matrix (PPA) + ==================================== + + [WR./job_00_first_run//ndb.pp]------------------------------- +``` +Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy: +```bash= +[09.01] G0W0 (W PPA) + ==================== + + [ GW ] Bands range : 1 20 + [GW/PPA] G damping : 0.100000 [eV] + + + QP @ state[ 1 ] K range: 7 7 + QP @ state[ 1 ] b range: 13 14 + + [RD./job_00_first_run//ndb.pp]------------------------------- +``` + +Now, inspect the output file +```console +vim out_00_first_run/o-job_00_first_run.qp +``` +``` +# Vxc =Slater exchange(X)+Perdew & Zunger(C) +# Vnlxc=Hartree-Fock +# +# K-point Band Eo [eV] E-Eo [eV] Sc|Eo [eV] +# + 7 13 0.000000 -0.025774 0.543987 + 7 14 1.858370 3.496193 -0.417555 +# +``` +In this file, `Eo` is our starting point (DFT) while `E-Eo` shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we'll use some simple commands. First, we get everything that is not a `#` symbol `grep -v '#'` and we pass that to another command with a "pipe" `|`. Then, `tail -n 1`/`head -n 1` will retain the first/last line, and `awk '{print $3+$4}'` will get us the sum of the third and fourth columns. Altogether, this would be as follows + +```console +grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}' +-0.025774 +grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}' +5.35456 +``` + +These two commands give us the quasiparticle energies we've calculated - their difference is the GW-corrected optical gap. + +--- + +## GW convergence + +In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse {math}`k`-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a {math}`6 \times 6 \times 1` k-point grid and without spin-orbit coupling: the `SAVE` we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let's move into the appropriate directory +```console +cd ../02_GW_convergence +``` +### Response function {math}`\varepsilon^{-1}_{GG'}` - Bands and G-vectors +We are now ready to start our convergence tests. We'll begin with the variables controlling the polarization function, i.e., `NGsBlkXp` for the number of G-vectors and `BndsRnXp` for the number of bands. For this, we will keep `GbndRnge` constant at a reasonably high value - you can inspect the input `i01-GW` +```console +vim i01-GW +``` +and check that you have: +``` +% GbndRnge + 1 | 80 | # [GW] G[W] bands range +% +``` + +Since we need to run `yambo` for several values of `NGsBlkXp` and `BndsRnXp`, it makes sense to use two nested loops. That is exactly what we did in the submission script `run01_converge_pol.sh`. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs: +```console +sbatch run01_converge_pol.sh +``` + +````{callout} Monitoring +You can monitor that the job is running by the squeue command +``` +sbatch squeue -u $USER +``` +and also by checking the files created in your folder +``` +ls -ltr +``` +```console +i01-GW_Xp_20_bands_6_Ry +job_Xp_20_bands_6_Ry +out_Xp_20_bands_6_Ry +i01-GW_Xp_20_bands_8_Ry +out_Xp_20_bands_8_Ry +job_Xp_20_bands_8_Ry +i01-GW_Xp_20_bands_10_Ry +out_Xp_20_bands_10_Ry +job_Xp_20_bands_10_Ry +i01-GW_Xp_20_bands_12_Ry +out_Xp_20_bands_12_Ry +job_Xp_20_bands_12_Ry +summary_01_20bands.txt +i01-GW_Xp_40_bands_6_Ry +... +``` +Finally you can monitor how runs are proceeding by looking into the log files +``` +tail -f out_Xp_*_bands_*/LOG/*_1 +``` +``` +==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <== + <15s> P1: [TIMING] io_WF : 1.1353s CPU (34 calls, 0.033 sec avg) + <15s> P1: [TIMING] WF_load_FFT : 1.1538s CPU ( 7 calls, 0.165 sec avg) + <15s> P1: [TIMING] io_KB_pwscf : 1.1918s CPU ( 6 calls, 0.199 sec avg) + <15s> P1: [TIMING] DIPOLE_transverse : 2.4771s CPU + <15s> P1: [TIMING] io_fragment : 2.6220s CPU (46 calls, 0.057 sec avg) + <15s> P1: [TIMING] io_X : 3.1953s CPU (19 calls, 0.168 sec avg) + <15s> P1: [TIMING] Dipoles : 4.4012s CPU + <15s> P1: [11] Memory Overview + <15s> P1: [12] Game Over & Game summary + <15s> P1: [TIMING] [Time-Profile]: 15s + +==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <== + <11s> P1: X@q[6] | | [000%] --(E) --(X) + <11s> P1: X@q[6] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%) + <11s> P1: [X-CG] R(p) Tot o/o(of R): 153 504 100 + <11s> P1: Xo@q[7] | | [000%] --(E) --(X) + <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%) + <11s> P1: X@q[7] | | [000%] --(E) --(X) + <11s> P1: X@q[7] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%) + <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock +``` +```` + +Let's now have look into the job we just submitted. +``` +vim run01_converge_pol.sh +``` +First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file `i01-GW` is used as a template for every calculation in the loops, so we assign it to a variable. +```bash +file0='i01-GW' + +for POL_BANDS in 20 40 60 80; do + +echo 'NGsBlkXp [Ry] E_vale [eV] E_cond [eV]' > summary_01_${POL_BANDS}bands.txt + +for NGsBlkXp_Ry in 6 8 10 12; do + +(...) + +done +done +``` + +Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the `sed` command, in order to generate new files in an automated way (`sed` replaces any matching string with whatever is provided by the loop variable). Next, we run `yambo` using the labels to specify different job `-J` and communication `-C` directories every time. Finally, we get the quasiparticle energies with `grep` commands as shown before and append a new line to the summary file. So, inside each loop, we have +```bash +label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry +jdir=job_${label} +cdir=out_${label} +filein=i01-GW_${label} + +sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/; + /% BndsRnXp/{n;s/.*/ 1 | ${POL_BANDS} |/}" $file0 > $filein + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir + +E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'` +E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'` + +echo ${NGsBlkXp_Ry} ' ' ${E_GW_v} ' ' ${E_GW_c} >> summary_01_${POL_BANDS}bands.txt +``` + +Finally, let us plot this data. First, check that the job has finished with +```console +squeue -u $USER +``` +```console +[$USER@login01 02_GW_convergence]$ squeue -u $USER + JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) +[$USER@login01 02_GW_convergence]$ +``` +and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven't done so yet, and then plot: +```console +module load anaconda3/2023.03 +python plot-01.py +``` +The plot will produce a `fig-01.png` file. +You can copy and open it in your local machine with something like +``` +[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH] +scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./ +``` + +You should get: +```{figure} img/convergence01.png +:scale: 80% +``` + + +For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we'll make a copy of the corresponding input file: +``` +cp i01-GW_Xp_80_bands_10_Ry i02-GW +``` + +### Self-energy {math}`\Sigma^c` - Bands + +We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., `GbndRnge`. This step is actually simpler, since it only involves one loop. This is coded in the provided script `run02_converge_Gbnds.noBG.sh`. You can look into it +``` +vim run02_converge_Gbnds.noBG.sh +``` +and go ahead and submit it. +``` +sbatch run02_converge_Gbnds.noBG.sh +``` + +````{solution} [OPTIONAL]: Use the terminator to accelerate convergence + +While that runs, we'll have a look at the so-called Bruneval-Gonze (BG) terminator, which is a method to accelerate convergence with respect to empty bands. The variable that controls this for the bands in the correlation self-energy is `GTermKind`. This is currently set to "none" in `i02-GW`, so create a new input file `i02-GW_BG` and set this variable to "BG". We can do this in the command line by simply typing +``` +sed 's/GTermKind=.*/GTermKind= "BG"/' i02-GW > i02-GW_BG +``` +Note that `XTermKind` also offers the same terminator for the sum over bands of the polarization function (we just chose not to use it in the previous section of this excercise, and we will keep it as "none"). Now, copy the last submission script and edit it to run the same convergence test using the BG terminator. +``` +cp run02_converge_Gbnds.noBG.sh run03_converge_Gbnds.BG.sh +``` +Try and do this yourself first, and then continue reading to check your understanding. +You will have to change the input file template, i.e., use `i02-GW_BG` where the terminator has been activated. Modify also the name of the newly generated input files in order to avoid overwriting. Change the name of the summary file for the same reason and, finally, modify the communications and job directories of `yambo`. Make sure you've done all the changes as outlined below. + +```bash +file0='i02-GW_BG' +summaryfile=summary_03_BG.txt + +(...) + +label=Gbands_${G_BANDS}_BG +filein=i02-GW_${G_BANDS}_Gbands_BG + +``` +Now submit your newly edited script +``` +sbatch run03_converge_Gbnds.BG.sh +``` +```` + +While this runs, check if the previous job has finished, i.e., you should have a complete `summary_02_noBG.txt` file by now. +For a visual result, proceed to plot them with +``` +python plot-02.py +``` +You should get +```{figure} img/BG_noBG.png +:scale: 80% +``` + + +```{solution} OPTIONAL +If you also did the optional step, you can compare `summary_02_noBG.txt` with `summary_03_BG.txt` once `run03_converge_Gbnds.BG.sh` has finished - you'll see the effect of the terminator immediately. +Just open the `plot-02.py` script and uncomment the line `#list_of_files = ['summary_02_noBG.txt','summary_03_BG.txt']`, then rerun it with `python plot-02.py`. +You can see that the terminator does a great job at accelerating convergence, and it allows us to use 60 bands incurring an error of only 3 meV (while the latter would have been larger than 0.1 eV had we not used the terminator). +``` + +We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication ([here](https://www.nature.com/articles/s41524-023-00989-7)). MoS{math}`_2` was one of the materials studied there, and it shows that our result, obtained with a {math}`6 \times 6 \times 1` k-grid, is simply *off the chart* (blue line). + +```{figure} img/ref-Guandalini.png +:scale: 40% +``` +_Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9_ + +````{solution} [OPTIONAL]: Use the RIM-W accelerator +However you can try to get a reasonable correction via the RIM-W approach. Create a new input file copying a suitable one: +``` +cp i02-GW_80_Gbands i04-GW_80_Gbands_rimw +vim i04-GW_80_Gbands_rimw +``` +Then, you just need to add the following two variables to the input file (for example just after the runlevel keywords) +``` +RIM_W +RandGvecW= 15 RL +``` +and prepare a submission script +``` +cp run02_converge_Gbnds.noBG.sh run04_converge_rimw.sh +vim run04_converge_rimw.sh +``` +Edit it by removing the loop and changing `summaryfile`, `label` and `filein` +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=4 +#SBATCH --cpus-per-task=8 +#SBATCH --partition=boost_usr_prod +#SBATCH --time=0:10:00 +#SBATCH --gres=gpu:4 +#SBATCH --account=EUHPC_TD02_030 +#SBATCH --job-name=mos2 + +export OMP_NUM_THREADS=8 +export OMP_PLACES=cores +export OMP_PROC_BIND=close + +# load yambo +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 + +file0='i02-GW' +summaryfile=summary_04_rimw.txt + +echo 'G bands E_vale [eV] E_cond [eV] GAP [eV]' > $summaryfile + +G_BANDS=80 + +label=Gbands_${G_BANDS}_rimw +jdir=job_${label} +cdir=out_${label} +filein=i04-GW_${G_BANDS}_Gbands_rimw + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir + +E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'` +E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'` + +GAP_GW=`echo $E_GW_c - $E_GW_v |bc` + +echo ${G_BANDS} ' ' ${E_GW_v} ' ' ${E_GW_c} ' ' ${GAP_GW} >> $summaryfile +``` +and then run +``` +sbatch run04_converge_rimw.sh +``` +How much do you get for the band gap ? +```` + +--- +## GW parallel strategies + +### MPI parallelization + +For this section, let us enter the `03_GW_parallel` directory. If you were in the `02_GW_convegence` folder just do +``` +cd ../03_GW_parallel +``` +and inspect the input `gw.in`. You will see that we set low values for most of the convergence parameters except bands: + +``` +vim gw.in +``` + +``` +FFTGvecs= 40 Ry # [FFT] Plane-waves +EXXRLvcs= 2 Ry # [XX] Exchange RL components +VXCRLvcs= 2 Ry # [XC] XCpotential RL components +% BndsRnXp + 1 | 300 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 Ry # [Xp] Response block size +% GbndRnge + 1 | 300 | # [GW] G[W] bands range +% +%QPkrange # [GW] QP generalized Kpoint/Band indices + 1| 19| 23| 30| +% +``` +Note that we also added `FFTGvecs` to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO `ecutwfc`, i.e. 60 Ry in this case). + +In addition, we have deleted all the parallel parameters since we will be setting them via the submission script. + +Actually we are now dealing with a heavier system than before: as you can see from the `QPkrange` values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized). + +For this part of the tutorial, we will be using the `slurm` submission script `job_parallel.sh`, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code: +```bash +DIP_CPU= "1 $ngpu 1" # [PARALLEL] CPUs for each role +DIP_ROLEs= "k c v" # [PARALLEL] CPUs roles (k,c,v) +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role +X_and_IO_ROLEs= "q g k c v" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_and_IO_nCPU_LinAlg_INV=1 # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set) +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +SE_CPU= "1 $ngpu 1" # [PARALLEL] CPUs for each role +SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` +The keyword `DIP` refers to the calculations of the screening matrix elements (also called "dipoles") needed for the screening function, `X` is the screening function itself (it stands for {math}`\chi` since it is a response function), `SE` the self-energy. +These three sections of the code can be parallelised independently. + +We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI _task_ is run on a single card, therefore `ntasks=ngpu`. + +```{callout} Note +- In this subsection we are mainly concerned with the **[PARALLEL]** variables which refer to MPI _tasks_ (distributed memory). +- What about **[OPENMP]** parallelisation (i.e., adding _threads_ with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are *not* run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup *for CPUs* is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later. +``` + +We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as: + +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=4 +... +#SBATCH --gres=gpu:4 +``` +and submit the job +``` +sbatch job_parallel.sh +``` + +This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report `r-*` file and the log `l-*` files, and inspect them while the calculation runs. +For simplicity you can just type +``` +tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1 +``` +to monitor the progress in the master thread (`Ctrl+c` to exit). +As you can see, the run takes some time, even though we are using minimal parameters. + +Meanwhile, we can run other jobs increasing the parallelisation. Let's employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the `job_parallel.sh` script changing + +```bash +#!/bin/bash +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=4 +... +#SBATCH --gres=gpu:4 +``` + +This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing `nodes` appropriately. Finally, you can try to produce a scaling plot. + +The timings are contained in the `r-*` report files. You can already have a look at them typing +``` +grep Time-Profile run_MPI*/r-* +``` + +The python script `parse_ytiming.py` is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided. + +If you didn't do so already, load the python module +``` +module load anaconda3/2023.03 +``` + +Then, after your jobs have finished, run the script as +``` +python parse_ytiming.py run_MPI +``` +to look for a report file in each `run_MPI*.out` folder. **Make sure you have only one report file per folder.** +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis. + +```{figure} img/gw_scaling.png +:scale: 80% +``` + +What can we learn from this plot? In particular, try to answer the following questions: +- Up to which number of MPI tasks our system scales efficiently? +- How can we decide at which point adding more nodes to the calculation becomes a waste of resources? + +```{callout} Note +Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, __Yambo has been shown to scale well up to tens of thousands of MPI tasks__! (See the next optional box for an example) +``` + +````{solution} [OPTIONAL] Comparison with CPU calculation with hybrid parallelization strategy + +We have run the same calculation using a version of Yambo compiled in order to run on CPUs. This is not the preferred approach in an accelerator-based machine like Leonardo, but it can be instructive. + +For a CPU calculation, we can use a hybrid parallel structure with threads. The OPENMP threads are controlled by modifying `cpus-per-task` and `OMP_NUM_THREADS` in the submission file. The product of the number of OpenMP threads and MPI tasks is equal to the total number of CPUs. + +For our test, we have used larger convergence parameters than in the previous run, and selected a hybrid parallel scheme with 16 MPI tasks per node, with 2 OPENMP threads (`ntasks*nthreads=ncpu=16*2=32`), since it gives the best scaling in this case. + +```{callout} Note +In general (for larger systems) we have tested that the best CPU scaling on Leonardo is actually 4 MPI tasks times 8 OPENMP threads. +``` + +Therefore, in the new CPU submission script we have: +```bash= +#!/bin/bash +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=16 +#SBATCH --cpus-per-task=2 +... +export OMP_NUM_THREADS=2 +``` + +Actually, we don't need to change the openMP-related variables appearing in the yambo input, since the value `0` means "use the value of `OMP_NUM_THREADS`" and we have now set this environment variable to our liking via the submission script. +Otherwise, any positive number can directly specify the number of threads to be used in each section of the code. + +``` +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +... +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +... +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` + +Actively looking for the best scaling on both GPU and CPU for our enlarged MoS2 system we find: + +```{figure} img/CPU_scaling.jpeg +:scale: 80% +``` + +We can see that already for this reasonably small and half-converged system run on a few nodes the GPU calculation easily reaches a speedup of 2x. The speedup vastly increases in larger systems where the calculations are more demanding, as you can see from the scaling tests below (run on the Juwels Booster machine) on a graphene-cobalt interface supercell. + +```{figure} img/grCo_scaling.png +:scale: 40% +``` +_Scaling comparison of graphene@Co(0001) interface on CPU (left, 48 cpus per node) and GPU (right, 4 GPUs per node). Tests done by Nicola Spallanzani. Data available at: http://www.gitlab.com/max-centre/Benchmarks_ + +```{callout} Note +- In real-life CPU-based calculations running on {math}`n_{cores} > 100`, as we have seen, it may be a good idea to adopt a hybrid approach. +- The most efficient scaling can depend both on your system and on the HPC facility you're running on. For a full CPU node on Leonardo (32 cores), using a large-scale system, we have found that 4 tasks times 8 threads gives the best performance. +- OpenMP can help lower memory requirements within a node. You can try to increase the OpenMP share of threads if you are getting Out Of Memory errors. +``` +```` + +. +````{solution} [OPTIONAL]: Comparing different parallelisation schemes + +Up to now we always parallelised over a single parameter, i.e. `c` or `qp`. However, Yambo allows for tuning the parallelisation scheme over several parameters broadly corresponding to "loops" (i.e., summations or discrete integrations) in the code. + +To this end you can open again the `run_parallel.sh` script and modify the section where the yambo input variables are set. + +For example, `X_CPU` sets how the MPI Tasks are distributed in the calculation of the response function. The possibilities are shown in the `X_ROLEs`. The same holds for `SE_CPU` and `SE_ROLEs` which control how MPI Tasks are distributed in the calculation of the self-energy. + +``` +X_CPU= "1 1 1 $ncpu 1" # [PARALLEL] CPUs for each role +X_ROLEs= "q g k c v" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_nCPU_LinAlg_INV= $ncpu # [PARALLEL] CPUs for Linear Algebra +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +SE_CPU= "1 $ncpu 1" # [PARALLEL] CPUs for each role +SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` + +You can try different parallelization schemes and check the performances of Yambo. In doing so, you should also change the jobname `label=MPI${ncpu}_OMP${nthreads}` in the `run_parallel.sh` script to avoid confusion with previous calculations. + +You may then check how speed, memory and load balance between the CPUs are affected. You could modify the script `parse_ytiming.py` to parse the new data, read and distinguish between more file names, new parallelisation options, etc. + +```{callout} Note +- The product of the numbers entering each variable (i.e. `X_CPU` and `SE_CPU`) times the number of threads should always match the total number of cores (unless you want to overload the cores taking advantage of multi-threads). +- Using the `X_Threads` and `SE_Threads` variables you can think about setting different hybrid schemes between the screening and the self-energy runlevels. +- Memory scales better if you parallelize on bands (`c v b`). +- Parallelization on k-points performs similarly to parallelization on bands, but requires more memory. +- Parallelization on q-points requires much less communication between the MPI tasks. It may be useful if you run on more than one node and the inter-node connection is slow. +``` +```` + +--- + +## Full GW band structure + +This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS{math}`_2`. + +This is a massive calculation, so run it right now and we'll discuss it in the meantime: +``` +cd ../04_GW_bands +sbatch gpu_job.sh +``` + +In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling. + +Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input: +``` +vim gw.in +``` + +``` +%QPkrange # [GW] QP generalized Kpoint/Band indices +1|37|25|28| +% +``` + + +After about 3 minutes the calculation should be over and the results collected in folder `GW_bnds`. The quasiparticle corrections are stored in human-readable form in the file `o-GW_bnds.QP`, and in netCDF format in the quasiparticle database `ndb.QP`. + +In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with `ypp`, the yambo pre- and post-processing executable. + +```{callout} Note +We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out [here](https://www.yambo-code.eu/wiki/index.php/First_steps_in_Yambopy) on the Yambo wiki. +``` + +Let us enter a computing node interactively + +``` +srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash +``` +and load the yambo module: +``` +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 +``` + +We can review the options with `ypp -h` and generate an input file for band structure interpolation with +``` +ypp -s b -F ypp_bands.in +``` +Let us modify the resulting input file by selecting the 'boltztrap' approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points {math}`\Gamma-M-K-\Gamma`. We also set 100 points for each high-symmetry line. +``` +electrons # [R] Electronic properties +bnds # [R] Bands +PROJECT_mode= "none" # Instruct ypp how to project the DOS. ATOM, LINE, PLANE. +INTERP_mode= "BOLTZ" # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach) +INTERP_Shell_Fac= 20.00000 # The bigger it is a higher number of shells is used +INTERP_NofNN= 1 # Number of Nearest sites in the NN method +OutputAlat= 5.90008 # [a.u.] Lattice constant used for "alat" ouput format +cooIn= "rlu" # Points coordinates (in) cc/rlu/iku/alat +cooOut= "rlu" # Points coordinates (out) cc/rlu/iku/alat +% BANDS_bands + 25 | 28 | # Number of bands +% +CIRCUIT_E_DB_path= "none" # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts) +BANDS_path= "" # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL). +BANDS_steps= 100 # Number of divisions +#BANDS_built_in # Print the bands of the generating points of the circuit using the nearest internal point +%BANDS_kpts # K points of the bands circuit + 0.00000 |0.00000 |0.00000 | + 0.00000 |0.50000 |0.00000 | + 0.33333 |0.33333 |0.00000 | + 0.00000 |0.00000 |0.00000 | +% +``` +Now, let's run ypp: +``` +mpirun -np 1 ypp -F ypp_bands.in +``` +This run will produce the file `o.bands_interpolated`. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn't tell `ypp` where to look for the quasiparticle corrections, so it went into the `SAVE` folder and interpolated the DFT data. +Let's rename the output: +``` +mv o.bands_interpolated o.DFT_bands +mkdir DFT_bands +mv o.spin* o.magn* DFT_bands/ +``` +In order to interpolate the quasiparticle database, we append its location to the `ypp` input: +``` +vim ypp_bands.in +``` +add this line at the end +``` +... +GfnQPdb= "E < ./GW_bnds/ndb.QP" +``` +and run `ypp` again. +``` +mpirun -np 1 ypp -F ypp_bands.in +``` + +When it's done, let's rename the new output as +``` +mv o.bands_interpolated o.GW_bands +mkdir GW_bands +mv o.spin* o.magn* GW_bands/ +``` + +Now we are ready to visualize the band structures. In order to do so, you can use the script `plt_bands.py` that should be already available in the directory. + +We load the python module +``` +module load anaconda3/2023.03 +``` + +and run the script as +``` +python plt_bands.py o.DFT_bands o.GW_bands 4 +``` + +Now we can also exit the computing node +``` +exit +``` + +The python script should have produced a `GW_bands.png` file containing the following visualization, which you can copy and open it in your local machine using `scp`: + +```{figure} img/gw_bands.png +:scale: 80% +``` + +You may compare this plot with a converged result from [this paper](https://doi.org/10.1016/j.surfrep.2015.10.001) (also done with Yambo): + +```{figure} img/gw_bands_ref.png +:scale: 50% +``` +_Dashed lines: DFT, thick lines: GW._ + +As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations! + +In order to learn more about Yambo, we suggest visiting the [Yambo website](https://www.yambo-code.eu/). For technical information and tutorials, you can check out the [Yambo wiki](https://www.yambo-code.eu/wiki/index.php/Main_Page). If you have issues and questions about installing and running the code, you can write about them on the [Yambo forum](https://www.yambo-code.eu/forum/index.php). diff --git a/_sources/days3+4/day3.rst.txt b/_sources/days3+4/day3.rst.txt new file mode 100644 index 0000000..8684d05 --- /dev/null +++ b/_sources/days3+4/day3.rst.txt @@ -0,0 +1,77 @@ +:sequential_nav: next + +.. _day3-siesta1: + +Day 3: SIESTA I +=============== + +SIESTA basics +------------- + +Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge). + +Slides available here: :download:`SIESTA-Intro.pdf `. + + +A first contact with SIESTA: inputs, execution and outputs +----------------------------------------------------------- + +Practical session led by Dr. Federico Pedron (ICN2). + +Tutorials covered: + +- `A First Encounter - Part 1: Running SIESTA `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/01-FirstEncounter_I + +- `A First Encounter - Part 2: Choosing your level of theory `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/02-FirstEncounter_II + +Introductory slides available here: :download:`SIESTA-First_encounter.pdf `. + +Basis sets +---------- + +Lecture by Dr. Miguel Pruneda (CINN-CSIC). + +Slides available here: :download:`SIESTA-Basis_sets.pdf `. + + +Basis set optimization +---------------------- + +Practical session led by Dr. Federico Pedron (ICN2). + +Tutorials covered: + +- `Basis set optimization `_ +- `Basis sets - Tips and tricks `_ + +Files for the tutorial:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets + +Introductory slides available here: :download:`SIESTA-Basis_set_optimization.pdf `. + +Convergence (k points, mesh, mixing) +------------------------------------ + +Practical session led by Dr. Catalina Coll (ICN2). + +Tutorials covered: + +- `The real-space grid `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04a-GridConvergence + +- `Sampling of the BZ with k-points `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04b-KPointConvergence + +- `The self-consistent-field cycle `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04c-SCF + +Introductory slides available here: :download:`SIESTA-Convergence.pdf `. + diff --git a/_sources/days3+4/day4.rst.txt b/_sources/days3+4/day4.rst.txt new file mode 100644 index 0000000..ec01043 --- /dev/null +++ b/_sources/days3+4/day4.rst.txt @@ -0,0 +1,59 @@ +:sequential_nav: next + +.. _day4-siesta2: + +Day 4: SIESTA II +================ + +Molecular Dynamics with SIESTA +------------------------------ + +Practical session led by Dr. Ernane de Freitas (ICN2). + +Tutorials covered: + +- `Molecular Dynamics `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics + +Introductory slides available here: :download:`SIESTA-MD.pdf `. + + +Analysis tools +-------------- + +Practical session led by Dr. Miguel Pruneda (CINN-CSIC). + +Tutorials covered: + +- `Analysis tools `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis + +Introductory slides available here: :download:`SIESTA-Analysis_tools.pdf `. + + +Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others +-------------------------------------------------------------------------- + +Lecture by Dr. Nick Papior (Technical University of Denmark). + +Slides available here: :download:`SIESTA-Features.pdf `. + + +Pushing the boundaries of SIESTA: accelerated and massively parallel solvers +---------------------------------------------------------------------------- + +Practical session led by Dr. Alberto García (ICMAB-CSIC). + +Tutorials covered: + +- ELSI-ELPA. +- ELSI-PEXSI. + +Files for the tutorial:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers + +Slides available here: :download:`SIESTA-Solvers.pdf `. + diff --git a/_sources/days3+4/setup.rst.txt b/_sources/days3+4/setup.rst.txt new file mode 100644 index 0000000..9c9684c --- /dev/null +++ b/_sources/days3+4/setup.rst.txt @@ -0,0 +1,67 @@ +SIESTA setup +============ + +Directory with tutorials +------------------------ +For every practical there is a folder in the shared directory +``/leonardo_work/EUHPC_TD02_030/siesta-tutorials`` that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:: + +$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I . + +Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts. + + +Running SIESTA +-------------- +You will find a sample script on how to run SIESTA in +``/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh``: :: + + #!/bin/bash + #SBATCH -J tutorialXX + #SBATCH -n 8 + #SBATCH -t 0:30:00 + #SBATCH -o %x-%j.out + #SBATCH -e %x-%j.err + #SBATCH --partition=boost_usr_prod + #SBATCH -D . + + # DO NOT CHANGE THIS LINE + source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh + + # EDIT THE CORRECT INPUT AND OUTPUT FILES. + srun -n 8 siesta < input.fdf > output.out + + +Note that ``input.fdf`` and ``output.out`` are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(``#SBATCH -J option``) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue. + + + +Suggested Software for Visualization +------------------------------------ +If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences. + +- `gnuplot `_ +- `xcrysden `_ +- `vesta `_ +- `vmd `_ +- `ovito `_ +- Python with matplotlib + + + +.. + SIESTA source code + ------------------ + If you want to try your own SIESTA compilation, have a look at this `SIESTA + compilation how-to `_ . + Be sure to have all dependencies beforehand. Note that we will not be answering + questions regarding compilation or other installations during the school. diff --git a/_sources/guide.rst.txt b/_sources/guide.rst.txt new file mode 100644 index 0000000..89553fb --- /dev/null +++ b/_sources/guide.rst.txt @@ -0,0 +1,37 @@ +Instructor's guide +================== + +Why we teach this lesson +------------------------ + + + +Intended learning outcomes +-------------------------- + + + +Timing +------ + + + +Preparing exercises +------------------- + +e.g. what to do the day before to set up common repositories. + + + +Other practical aspects +----------------------- + + + +Interesting questions you might get +----------------------------------- + + + +Typical pitfalls +---------------- diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..c5bab3f --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,326 @@ +Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo +============================================================================ + +In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential. + +This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises. + +`QUANTUM ESPRESSO `__ is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications. + +`SIESTA `__ is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a "good first approximation" to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA. + +`YAMBO `__ is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc). + +`MAX (MAterials design at the eXascale) `__ is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX's challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials' domain. + + +.. prereq:: + + - Some familiarity with density functional theory (DFT), self-consistent + field (SCF) calculations and plane wave basis sets is desirable as the + workshop will not cover the fundamental theory of these topics. + - Familiarity with working in a Linux environment and some experience with + working on an HPC system is needed to participate in the hands-on exercises. + + +Who is the course for? +---------------------- + +This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations. + + +.. toctree:: + :maxdepth: 1 + :caption: Day 1 - Quantum ESPRESSO I + + + + +.. toctree:: + :maxdepth: 1 + :caption: Day 2 - Quantum ESPRESSO II + + +.. toctree:: + :maxdepth: 1 + :caption: Days 3 and 4 - Siesta + + days3+4/setup + days3+4/day3 + days3+4/day4 + +.. toctree:: + :maxdepth: 1 + :caption: Day 5 - Yambo + + day5/yambo-tutorial + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + quick-reference + guide + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + ENCCS + + + + +About the course +---------------- + +In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties. + +Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers. + +Schedule +^^^^^^^^ + +**Day 1, QUANTUM ESPRESSO** + ++------------+-------------------------------------------------------+ +| Time | Section | ++============+=======================================================+ +|09:00-09:15 | Welcome and introduction to ENCCS | ++------------+-------------------------------------------------------+ +|09:15-09:30 | Introduction to Max-CoE and MaX flagship codes | ++------------+-------------------------------------------------------+ +|09:30-10:00 | Overview of the QE suite of codes and main features | ++------------+-------------------------------------------------------+ +|10:00-10:25 | Coffee break | ++------------+-------------------------------------------------------+ +|10:25-13:00 | PWSCF for HPC and GPU | ++------------+-------------------------------------------------------+ + + +**Day 2, QUANTUM ESPRESSO** + ++------------+----------------------------------------------------------------------+ +| Time | Section | ++============+======================================================================+ +|09:00-09:45 | Introduction to Density Functional Perturbation Theory | ++------------+----------------------------------------------------------------------+ +|09:45-10:15 | Introduction to Time Dependent Density Functional Perturbation Theory| ++------------+----------------------------------------------------------------------+ +|10:15-10:30 | Coffee break | ++------------+----------------------------------------------------------------------+ +|10:30-13:00 | Phonons and time dependent properties on HPC and GPU | ++------------+----------------------------------------------------------------------+ + + +**Day 3, SIESTA** + ++------------+-------------------------------------------------------------------------------------+ +| Time | Section | ++============+=====================================================================================+ +|09:00-09:45 | SIESTA basics | ++------------+-------------------------------------------------------------------------------------+ +|09:45-10:30 | Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs | ++------------+-------------------------------------------------------------------------------------+ +|10:30-10:45 | Break | ++------------+-------------------------------------------------------------------------------------+ +|10:45-11:15 | Basis sets | ++------------+-------------------------------------------------------------------------------------+ +|11:15-12:00 | Hands-on tutorial: Basis set optimization | ++------------+-------------------------------------------------------------------------------------+ +|12:00-13:00 | Hands-on tutorial: Convergence (k points, mesh, mixing) | ++------------+-------------------------------------------------------------------------------------+ + +**Day 4, SIESTA** + ++------------+-------------------------------------------------------------------------------------------------+ +| Time | Section | ++============+=================================================================================================+ +|09:00-10:00 | Hands-on tutorial: Moving atoms: geometry optimisation and beyond | ++------------+-------------------------------------------------------------------------------------------------+ +|10:30-11:00 | Hands-on tutorial: Analysis tools | ++------------+-------------------------------------------------------------------------------------------------+ +|11:00-11:15 | Break | ++------------+-------------------------------------------------------------------------------------------------+ +|11:15-11:45 | Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others | ++------------+-------------------------------------------------------------------------------------------------+ +|11:45-13:00 | Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers | ++------------+-------------------------------------------------------------------------------------------------+ + + +**Day 5, Yambo** + ++------------+------------------------------------------------------------------+ +| Time | Section | ++============+==================================================================+ +|09:00-09:20 | Overview of the Yambo code and its main features and performance | ++------------+------------------------------------------------------------------+ +|09:20-10:00 | Introduction to the GW approximation | ++------------+------------------------------------------------------------------+ +|10:00-10:20 | Coffee break | ++------------+------------------------------------------------------------------+ +|10:20-13:00 | Hands-on tutorial: A guided tour through GW simulations | ++------------+------------------------------------------------------------------+ + + +See also +-------- + +- ENCCS: https://enccs.se/ +- MAX-CoE: http://www.max-centre.eu/ +- Follow ENCCS on `LinkedIn `__, or `Twitter `__ +- Follow MAX-CoE on `LinkedIn `__, or `Twitter `__. + +.. math:: + + +Credits +------- + +Contributors to this workshop: + +- Pietro Davide Delugas (SISSA) +- Ivan Carnimeo (SISSA) +- Oscar Baseggio (SISSA) +- Fabrizio Ferrari Ruffino (CNR-IOM) +- Paolo Giannozzi (CNR-IOM, UniUD) +- Iurii Timrov (Paul Scherrer Institut) +- Laura Bellentani (CINECA) +- Tommaso Gorni (CINECA) +- Aurora Ponzi (CNR-IOM) +- Emilio Artacho (CIC NanoGUNE and University of Cambridge) +- Catalina Coll (ICN2) +- José Mª Escartín (ICN2) +- Roberta Farris (ICN2) +- Ernane de Freitas (ICN2) +- Alberto García (ICMAB-CSIC) +- Arnold Kole (Utrecht University) +- Nick Papior (DTU) +- Federico Pedron (ICN2) +- Miguel Pruneda (CINN-CSIC) +- José Ángel Silva Guillén (IMDEA Nanociencia) +- D. Varsano (CNR-NANO) +- A. Ferretti (CNR-NANO) +- D. Sangalli (CNR-ISM) +- A. Guandalini (Univ. of Rome, La Sapienza) +- F. Paleari (CNR-NANO) +- M. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO) +- G. Sesti (CNR-NANO) +- N. Spallanzani (CNR-NANO) + + +The lesson file structure and browsing layout is inspired by and derived from +`work `__ by `CodeRefinery +`__ licensed under the `MIT license +`__. We have copied and adapted +most of their license text. + +Licenses +-------- + +General +^^^^^^^ + +Instructional Material +~~~~~~~~~~~~~~~~~~~~~~ + +Except where otherwise noted, +this instructional material is made available under the +`Creative Commons Attribution license (CC-BY-4.0) `__. +The following is a human-readable summary of (and not a substitute for) the +`full legal text of the CC-BY-4.0 license +`__. +You are free to: + +- **share** - copy and redistribute the material in any medium or format +- **adapt** - remix, transform, and build upon the material for any purpose, + even commercially. + +The licensor cannot revoke these freedoms as long as you follow these license terms: + +- **Attribution** - You must give appropriate credit (mentioning that your work + is derived from work that is Copyright (c) ENCCS and individual contributors and, where practical, linking + to ``_), provide a `link to the license + `__, and indicate if changes were + made. You may do so in any reasonable manner, but not in any way that suggests + the licensor endorses you or your use. +- **No additional restrictions** - You may not apply legal terms or + technological measures that legally restrict others from doing anything the + license permits. + +With the understanding that: + +- You do not have to comply with the license for elements of the material in + the public domain or where your use is permitted by an applicable exception + or limitation. +- No warranties are given. The license may not give you all of the permissions + necessary for your intended use. For example, other rights such as + publicity, privacy, or moral rights may limit how you use the material. + + +Software +~~~~~~~~ + +Except where otherwise noted, the example programs and other software provided +with this repository are made available under the `OSI `__-approved +`MIT license `__. + +SIESTA +^^^^^^ + +At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved. diff --git a/_sources/quick-reference.rst.txt b/_sources/quick-reference.rst.txt new file mode 100644 index 0000000..492da1e --- /dev/null +++ b/_sources/quick-reference.rst.txt @@ -0,0 +1,2 @@ +Quick Reference +=============== diff --git a/_static/ENCCS.jpg b/_static/ENCCS.jpg new file mode 100644 index 0000000..da2355c Binary files /dev/null and b/_static/ENCCS.jpg differ diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/_static/copybutton.js b/_static/copybutton.js new file mode 100644 index 0000000..2ea7ff3 --- /dev/null +++ b/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/_static/copybutton_funcs.js b/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/_static/css/badge_only.css b/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/_static/css/badge_only.css @@ -0,0 +1 @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight 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sphinx_lesson.css with the schemes here: https://personal.sron.nl/~pault/#sec:qualitative */ + +/* instructor-note */ +.rst-content .instructor-note { + background: #DDDDDD; +} +.rst-content .instructor-note > .admonition-title { + background: #BBBBBB; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + +/* callout */ +.rst-content .callout { + background: #EEEEBB; +} +.rst-content .callout > .admonition-title { + background: #BBCC33; +} + +/* questions */ +.rst-content .questions { + background: rgba(253, 219, 199, 0.3); +} +.rst-content .questions > .admonition-title { + background: rgba(204, 51, 17, 0.5); +} + +/* discussion */ +.rst-content .discussion { + background: rgba(231, 212, 232 0.3); +} +.rst-content .discussion > .admonition-title { + background: rgba(194, 165, 207, 0.5); +} + +/* signature */ +.rst-content .signature { + background: rgba(217, 240, 211, 0.3); +} +.rst-content .signature > .admonition-title { + background: rgba(172, 211, 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} /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js new file mode 100644 index 0000000..7918c3f --- /dev/null +++ b/_static/searchtools.js @@ -0,0 +1,574 @@ +/* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * + * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/siesta/SIESTA-Analysis_tools.pdf b/_static/siesta/SIESTA-Analysis_tools.pdf new file mode 100644 index 0000000..f7045c7 Binary files /dev/null and b/_static/siesta/SIESTA-Analysis_tools.pdf differ diff --git a/_static/siesta/SIESTA-Basis_set_optimization.pdf b/_static/siesta/SIESTA-Basis_set_optimization.pdf new file mode 100644 index 0000000..f5edb26 Binary files /dev/null and b/_static/siesta/SIESTA-Basis_set_optimization.pdf differ diff --git a/_static/siesta/SIESTA-Basis_sets.pdf b/_static/siesta/SIESTA-Basis_sets.pdf new file mode 100644 index 0000000..84bfc66 Binary files /dev/null and b/_static/siesta/SIESTA-Basis_sets.pdf differ diff --git a/_static/siesta/SIESTA-Convergence.pdf b/_static/siesta/SIESTA-Convergence.pdf new file mode 100644 index 0000000..667b2fb Binary files /dev/null and b/_static/siesta/SIESTA-Convergence.pdf differ diff --git a/_static/siesta/SIESTA-Features.pdf b/_static/siesta/SIESTA-Features.pdf new file mode 100644 index 0000000..272de28 Binary files /dev/null and b/_static/siesta/SIESTA-Features.pdf differ diff --git a/_static/siesta/SIESTA-First_encounter.pdf b/_static/siesta/SIESTA-First_encounter.pdf new file mode 100644 index 0000000..627b1cd Binary files /dev/null and b/_static/siesta/SIESTA-First_encounter.pdf differ diff --git a/_static/siesta/SIESTA-Intro.pdf b/_static/siesta/SIESTA-Intro.pdf new file mode 100644 index 0000000..dcd5733 Binary files /dev/null and b/_static/siesta/SIESTA-Intro.pdf differ diff --git a/_static/siesta/SIESTA-MD.pdf b/_static/siesta/SIESTA-MD.pdf new file mode 100644 index 0000000..f7fed7f Binary files /dev/null and b/_static/siesta/SIESTA-MD.pdf differ diff --git a/_static/siesta/SIESTA-Solvers.pdf b/_static/siesta/SIESTA-Solvers.pdf new file mode 100644 index 0000000..9430066 Binary files /dev/null and b/_static/siesta/SIESTA-Solvers.pdf differ diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/_static/sphinx_lesson.css b/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/_static/sphinx_rtd_theme_ext_color_contrast.css b/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/_static/tabs.css b/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/_static/tabs.js b/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; + let nextTab = null; + if (e.keyCode === 39 || e.keyCode === 37) { + tab.setAttribute("tabindex", -1); + // Move right + if (e.keyCode === 39) { + nextTab = tab.nextElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.firstElementChild; + } + // Move left + } else if (e.keyCode === 37) { + nextTab = tab.previousElementSibling; + if (nextTab === null) { + nextTab = tab.parentNode.lastElementChild; + } + } + } + + if (nextTab !== null) { + nextTab.setAttribute("tabindex", 0); + nextTab.focus(); + } +} + +/** + * Select or deselect clicked tab. 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index 0000000..e0a1813 Binary files /dev/null and b/branch/main/_images/mos2.png differ diff --git a/branch/main/_images/ref-Guandalini.png b/branch/main/_images/ref-Guandalini.png new file mode 100644 index 0000000..cef4882 Binary files /dev/null and b/branch/main/_images/ref-Guandalini.png differ diff --git a/branch/main/_sources/day5/yambo-tutorial.md.txt b/branch/main/_sources/day5/yambo-tutorial.md.txt new file mode 100644 index 0000000..b3b677c --- /dev/null +++ b/branch/main/_sources/day5/yambo-tutorial.md.txt @@ -0,0 +1,1122 @@ +# Yambo tutorial: Quasiparticles in the GW approximation + +In this tutorial you will learn how to run a GW simulation using Yambo on a HPC machine. + +You will compute the quasiparticle corrections to the band structure of a free-standing single layer of MoS{math}`_2` while learning about convergence studies, parallel strategies, and GPU calculations. + +In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate. + +```{figure} img/mos2.png +:scale: 40% +``` + +*MoS{math}`_2` monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.* + +## Many-body corrections to the DFT band gap + +We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of. + +Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy {math}`\Sigma`: + +```{math} +E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle +``` + +Here {math}`\epsilon_{nk}` and {math}`\psi_{nk}` are the Kohn-Sham energies and wavefunctions, respectively, while {math}`V_{xc}` is the DFT exchange-correlation potential. + +For each electronic state {math}`nk`, the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy ({math}`\Sigma^x`), and an energy-dependent, usually gap-closing term called the correlation self-energy ({math}`\Sigma^c`). These contributions are tackled separately by the code: + +```{math} +\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega) +``` + +The energy-dependent dynamical electronic screening {math}`\varepsilon^{-1}(\omega)` is included in {math}`\Sigma^c` and must therefore be calculated as well. + +In this way, we can compute the "quasiparticle" corrections {math}`E^{QP}_{nk}` to the single-particle Kohn-Sham eigenvalues {math}`\epsilon_{nk}`. +The typical workflow for a GW calculation is: + +```{figure} img/gwflow.png +:scale: 40% +``` + +## Set up a Yambo calculation + +Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes): +```console +wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz +``` +```console +tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz +``` + +You can now enter the tutorial directory +```console +cd MoS2_HPC_tutorial_Leonardo +``` + +### Yambo `SAVE` folder + +First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo. + +The QE save folder for MoS{math}`_2` is already present at `00_QE-DFT`. We should move inside it and then run the `p2y` executable to generate the uninitialised `SAVE`. + +But first, we need to access a node interactively: +```console +srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash +``` + +Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have +```console +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 +``` + +Finally: +```console +cd 00_QE-DFT/mos2.save +mpirun -np 1 p2y +``` + +Now, we need to run the initialization step. Every Yambo run **must** start with this step. This will be automatically performed when you run Yambo on a `SAVE` directory for the first time. Just type + +```console +mpirun -np 1 yambo +``` + +and then check the yambo log called `l_setup`. The initialization step determines the {math}`G`-vector shells and the {math}`k`- and {math}`q`-point grids based on the DFT calculation. If you check inside the `SAVE` you will see two types of databases. The static ones, starting with `ns.*`, are directly converted in the `p2y` step, while the dynamical ones, `ndb.*` are generated during the initialisation. + +```console +ls SAVE/ +``` +```console +ndb.gops # info on G-vector shells, etc +ndb.kindx # info and k and q meshes +ns.db1 # info on geometry and KS bands +ns.kb_pp_pwscf # pseudopotential info +ns.wf # wave functions info +... +``` +The databases are written in netCDF format. +Yambo has produced also a human readable output, `r_setup`, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections. +```console +vim r_setup +``` +```console +[02.01] Unit cells # Lattice geometry info +================== + ... +[02.02] Symmetries # Symmetry ops. written explicitly +================== + ... +[02.03] Reciprocal space # Reciprocal lattice info +======================== +... +[02.04] K-grid lattice # k-point coords. written explicitly +====================== +... +[02.05] Energies & Occupations # Info on band gaps and occupations +============================== # DFT eigenvalues +... +[03] Transferred momenta grid and indexing # q-points (momentum transfer grid) +========================================== +``` + +Finally, let us move the `SAVE` and the report file to the directory where we will run the first GW calculation. +```console +mv SAVE r_setup ../../01_GW_first_run/ +cd ../../01_GW_first_run/ +``` + +### Yambo input file + +Now that we have a working `SAVE`, it is time to generate the input file we will be using for our first GW calculation. + +This can be done by the `yambo` executable via command-line instructions. + +If you type +```console +yambo -h +``` +You will get a list of the possibile options: + +```console + ___ __ _____ __ __ _____ _____ +| Y || _ || Y || _ \ | _ | +| | ||. | ||. ||. | / |. | | + \ _/ |. _ ||.\ / ||. _ \ |. | | + |: | |: | ||: | ||: | \|: | | + |::| |:.|:.||:.|:.||::. /|::. | + `--" `-- --"`-- --"`-----" `-----" + 'A shiny pot of fun and happiness [C.D.Hogan]' + + This is : yambo + Version : 5.1.0 Revision 21422 Hash fde6e2a07 + Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO + + Help & version: + -help (-h) : can be an option (e.g. -h optics) + -version :Code version & libraries + + Input file & Directories: + -Input (-F) :Input file + -Verbosity (-V) :Input file variables verbosity (more with -h Verbosity) + -Job (-J) :Job string + -Idir (-I) :Input directory + -Odir (-O) :I/O directory + -Cdir (-C) :Communication directory + + Parallel Control: + -parenv (-E) :Environment Parallel Variables file + -nompi :Switch off MPI support + -noopenmp :Switch off OPENMP support + + Initializations: + -setup (-i) :Initialization + -coulomb (-r) :Coulomb potential + + Response Functions: + -optics (-o) :Linear Response optical properties (more with -h optics) + -X (-d) :Inverse Dielectric Matrix (more with -h X) + -dipoles (-q) :Oscillator strenghts (or dipoles) + -kernel (-k) :Kernel (more with -h kernel) + + Self-Energy: + -hf (-x) :Hartree-Fock + -gw0 (-p) :GW approximation (more with -h gw0) + -dyson (-g) :Dyson Equation solver (more with -h dyson) + -lifetimes (-l) :GoWo Quasiparticle lifetimes + + Bethe-Salpeter Equation: + -Ksolver (-y) :BSE solver (more with -h Ksolver) + + Total Energy: + -acfdt :ACFDT Total Energy + + Utilites: + -Quiet (-Q) :Quiet input file creation + -fatlog :Verbose (fatter) log(s) + -DBlist (-D) :Databases properties + -walltime :Walltime (more with -h walltime) + -memory :Memory (more with -h memory) + -slktest :ScaLapacK test + + YAMBO developers group (http://www.yambo-code.org) +``` + +In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type: +```console +yambo -gw0 p -g n -r -V par -F gw.in +``` + +Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the `slurm` scheduler. +```console +exit +``` + +You can now inspect the input file `gw.in` and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change. + +We discuss them below step by step. + +### Parameters for a GW calculation + +We start with the runlevels: + +``` +gw0 # [R] GW approximation +ppa # [R][Xp] Plasmon Pole Approximation for the Screened Interaction +el_el_corr # [R] Electron-Electron Correlation +dyson # [R] Dyson Equation solver +rim_cut # [R] Coulomb potential +HF_and_locXC # [R] Hartree-Fock +em1d # [R][X] Dynamically Screened Interaction +``` + +```{callout} Runlevels +- The **[R]** keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have: + - `rim_cut`: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables). + - `gw0`: Yambo learns that it has to run a GW calculation (enables [GW] variables). + - `HF_and_locXC`: calculation of exchange part of the self-energy {math}`\Sigma^x` (i.e., Hartree-Fock approximation). + - `em1d`: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute {math}`\Sigma^c`. + - `ppa`: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables). + - `dyson`: Yambo will solve the Dyson-like quasiparticle equation. +``` + +Going through the file we find: + +``` +EXXRLvcs= 37965 RL # [XX] Exchange RL components +VXCRLvcs= 37965 RL # [XC] XCpotential RL components +``` + +Recall that we have, for the exchange self-energy: + +```{math} +\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q} +``` + +```{callout} Exchange self-energy +- `EXXRLvcs` controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while `VXCRLvcs` does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value). +``` + +Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have: + +```{math} +\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega') +``` + +(Here, the {math}`\rho`-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.) + +The calculation is divided in two steps. First, the response function in the plasmon pole approximation (`em1d ppa`), under the keywords `[X]` and `[Xp]`, i.e., {math}`\varepsilon^{-1}_{GG'}(q,\omega)`. + +``` +Chimod= "HARTREE" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc +% BndsRnXp + 1 | 300 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 RL # [Xp] Response block size +% LongDrXp + 1.000000 | 0.000000 | 0.000000 | # [Xp] [cc] Electric Field +% +PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy +XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze) +``` +```{callout} Response function +- `Chimod= "Hartree"` indicates that we compute the response function in the Random Phase Approximation (RPA). +- `BndsRnXp` represents the electronic states included in the response function {math}`\varepsilon`, and is a convergence parameter. +- `NGsBlkXp` is the number of G-vectors used to calculate the RPA response function {math}`\varepsilon^{-1}_{GG'}`. It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested). +- `LongDrXp` represents the direction of the long-range auxiliary external electric field used to compute {math}`\varepsilon^{-1}_{GG'}(q)` at {math}`q,G\rightarrow 0`. In general you have to be mindful of the system symmetries. In our case, we will put `1 | 1 | 1` to cover all directions. +- `PPAPntXp= 27.21138 eV` is the energy of the plasmon pole. We don't normally change this. +- `XTermKind` is used to specify a "terminator": this accelerates numerical convergence with respect to the number of bands `BndsRnXp`. +``` + +Next, we have the `[GW]` group of parameters controlling the next part of the correlation self-energy calculation: +``` +% GbndRnge + 1 | 300 | # [GW] G[W] bands range +% +GTermKind= "none" # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile) +DysSolver= "n" # [GW] Dyson Equation solver ("n","s","g") +%QPkrange # [GW] QP generalized Kpoint/Band indices +1|7|1|300| +% +``` +```{callout} Correlation self-energy +- `GbndRnge` is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator `GTermKind`. +- `DysSolver="n"` specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method `"n"`. +- `QPkrange` indicates the range of electronic (nk) states for which the GW correction {math}`\Sigma_{nk}` is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices. +``` + +We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should __edit now once and for all__. + +``` +RandQpts=1000000 # [RIM] Number of random q-points in the BZ +RandGvec= 100 RL # [RIM] Coulomb interaction RS components +CUTGeo= "slab z" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY.. +``` +```{callout} Coulomb potential +- The **[RIM]** keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to {math}`q=0` and {math}`G=0` in the {math}`q`-integration of the bare Coulomb interaction - i.e. {math}`4\pi/(q+G)^2` - for 2D systems. +- The **[CUT]** keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the {math}`z`-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic. +``` + +Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now. +``` +X_and_IO_CPU= "" # [PARALLEL] CPUs for each role +X_and_IO_ROLEs= "" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_and_IO_nCPU_LinAlg_INV=-1 # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set) +X_Threads=0 # [OPENMP/X] Number of threads for response functions +DIP_CPU= "" # [PARALLEL] CPUs for each role +DIP_ROLEs= "" # [PARALLEL] CPUs roles (k,c,v) +DIP_Threads=0 # [OPENMP/X] Number of threads for dipoles +SE_CPU= "" # [PARALLEL] CPUs for each role +SE_ROLEs= "" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads=0 # [OPENMP/GW] Number of threads for self-energy +``` + +In a GW calculation, the most important parameters to be numerically converged are: +- kpoint mesh (requires multiple nscf DFT runs) +- `BndsRnXp` +- `NGsBlkXp` +- `GbndRnge` +- [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs) + +From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations. + +--- + +## The first run + +We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file `r_setup` produced when the `SAVE` folder was initialised. Just search for the string 'Direct Gap' and you'll see that the latter occurs at k-point 7 between bands 13 and 14: +``` + [X] Filled Bands : 13 + [X] Empty Bands : 14 300 + [X] Direct Gap : 1.858370 [eV] + [X] Direct Gap localized at k : 7 +``` +In addition, we will set the number of bands in `BndsRnXp` and `GbndRnge` to a small value, just to have it run fast. Hence, we modify the input file accordingly (check `BndsRnXp`, `GbndRnge`, `LongDrXp`, `QPkrange`): +``` +rim_cut # [R] Coulomb potential +gw0 # [R] GW approximation +ppa # [R][Xp] Plasmon Pole Approximation for the Screened Interaction +dyson # [R] Dyson Equation solver +HF_and_locXC # [R] Hartree-Fock +em1d # [R][X] Dynamically Screened Interaction +X_Threads=0 # [OPENMP/X] Number of threads for response functions +DIP_Threads=0 # [OPENMP/X] Number of threads for dipoles +SE_Threads=0 # [OPENMP/GW] Number of threads for self-energy +RandQpts=1000000 # [RIM] Number of random q-points in the BZ +RandGvec= 100 RL # [RIM] Coulomb interaction RS components +CUTGeo= "slab z" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY.. +% CUTBox + 0.000000 | 0.000000 | 0.000000 | # [CUT] [au] Box sides +% +CUTRadius= 0.000000 # [CUT] [au] Sphere/Cylinder radius +CUTCylLen= 0.000000 # [CUT] [au] Cylinder length +CUTwsGvec= 0.700000 # [CUT] WS cutoff: number of G to be modified +EXXRLvcs= 37965 RL # [XX] Exchange RL components +VXCRLvcs= 37965 RL # [XC] XCpotential RL components +Chimod= "HARTREE" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc +% BndsRnXp + 1 | 20 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 RL # [Xp] Response block size +% LongDrXp + 1.000000 | 1.000000 | 1.000000 | # [Xp] [cc] Electric Field +% +PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy +XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze) +% GbndRnge + 1 | 20 | # [GW] G[W] bands range +% +GTermKind= "none" # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile) +DysSolver= "n" # [GW] Dyson Equation solver ("n","s","g") +%QPkrange # [GW] QP generalized Kpoint/Band indices +7|7|13|14| +% +``` +We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. __Modify it to suit your specific machine__. +```console +vim run_first_job.sh +``` +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=2 +#SBATCH --cpus-per-task=8 +#SBATCH --partition=boost_usr_prod +#SBATCH --time=0:05:00 +#SBATCH --gres=gpu:2 +#SBATCH --account=EUHPC_TD02_030 +#SBATCH --job-name=first_job + +export OMP_NUM_THREADS=8 +export OMP_PLACES=cores +export OMP_PROC_BIND=close + +# load yambo +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \ + yambo -F gw.in -J job_00_first_run -C out_00_first_run +``` +We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after `yambo`, it is not going to generate an input file, but rather, run the one specified by `-F`. Now, go ahead an submit this job +```console +sbatch run_first_job.sh +``` +The status of the jobs can be monitored via: +``` +squeue -u $USER # to inspect the status of jobs + # (hint: make a unix alias, if you like) +scancel # to delete jobs in the queue +``` + +The newly generated databases will be stored in the job directory, as specified by `-J`, while the report, log and output files will be stored in the communications directory (`-C`). As this is your first `yambo` run, take a moment to inspect the report and log files, which you can find inside the `-C` directory. In these report and log files, you can see the steps performed by `yambo`. For instance, the code calculates the screening at every k-point and stores it in the PPA database called `ndb.pp`. By opening the report +```console +vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa +``` +you will see +``` +[07] Dynamic Dielectric Matrix (PPA) + ==================================== + + [WR./job_00_first_run//ndb.pp]------------------------------- +``` +Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy: +```bash= +[09.01] G0W0 (W PPA) + ==================== + + [ GW ] Bands range : 1 20 + [GW/PPA] G damping : 0.100000 [eV] + + + QP @ state[ 1 ] K range: 7 7 + QP @ state[ 1 ] b range: 13 14 + + [RD./job_00_first_run//ndb.pp]------------------------------- +``` + +Now, inspect the output file +```console +vim out_00_first_run/o-job_00_first_run.qp +``` +``` +# Vxc =Slater exchange(X)+Perdew & Zunger(C) +# Vnlxc=Hartree-Fock +# +# K-point Band Eo [eV] E-Eo [eV] Sc|Eo [eV] +# + 7 13 0.000000 -0.025774 0.543987 + 7 14 1.858370 3.496193 -0.417555 +# +``` +In this file, `Eo` is our starting point (DFT) while `E-Eo` shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we'll use some simple commands. First, we get everything that is not a `#` symbol `grep -v '#'` and we pass that to another command with a "pipe" `|`. Then, `tail -n 1`/`head -n 1` will retain the first/last line, and `awk '{print $3+$4}'` will get us the sum of the third and fourth columns. Altogether, this would be as follows + +```console +grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}' +-0.025774 +grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}' +5.35456 +``` + +These two commands give us the quasiparticle energies we've calculated - their difference is the GW-corrected optical gap. + +--- + +## GW convergence + +In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse {math}`k`-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a {math}`6 \times 6 \times 1` k-point grid and without spin-orbit coupling: the `SAVE` we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let's move into the appropriate directory +```console +cd ../02_GW_convergence +``` +### Response function {math}`\varepsilon^{-1}_{GG'}` - Bands and G-vectors +We are now ready to start our convergence tests. We'll begin with the variables controlling the polarization function, i.e., `NGsBlkXp` for the number of G-vectors and `BndsRnXp` for the number of bands. For this, we will keep `GbndRnge` constant at a reasonably high value - you can inspect the input `i01-GW` +```console +vim i01-GW +``` +and check that you have: +``` +% GbndRnge + 1 | 80 | # [GW] G[W] bands range +% +``` + +Since we need to run `yambo` for several values of `NGsBlkXp` and `BndsRnXp`, it makes sense to use two nested loops. That is exactly what we did in the submission script `run01_converge_pol.sh`. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs: +```console +sbatch run01_converge_pol.sh +``` + +````{callout} Monitoring +You can monitor that the job is running by the squeue command +``` +sbatch squeue -u $USER +``` +and also by checking the files created in your folder +``` +ls -ltr +``` +```console +i01-GW_Xp_20_bands_6_Ry +job_Xp_20_bands_6_Ry +out_Xp_20_bands_6_Ry +i01-GW_Xp_20_bands_8_Ry +out_Xp_20_bands_8_Ry +job_Xp_20_bands_8_Ry +i01-GW_Xp_20_bands_10_Ry +out_Xp_20_bands_10_Ry +job_Xp_20_bands_10_Ry +i01-GW_Xp_20_bands_12_Ry +out_Xp_20_bands_12_Ry +job_Xp_20_bands_12_Ry +summary_01_20bands.txt +i01-GW_Xp_40_bands_6_Ry +... +``` +Finally you can monitor how runs are proceeding by looking into the log files +``` +tail -f out_Xp_*_bands_*/LOG/*_1 +``` +``` +==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <== + <15s> P1: [TIMING] io_WF : 1.1353s CPU (34 calls, 0.033 sec avg) + <15s> P1: [TIMING] WF_load_FFT : 1.1538s CPU ( 7 calls, 0.165 sec avg) + <15s> P1: [TIMING] io_KB_pwscf : 1.1918s CPU ( 6 calls, 0.199 sec avg) + <15s> P1: [TIMING] DIPOLE_transverse : 2.4771s CPU + <15s> P1: [TIMING] io_fragment : 2.6220s CPU (46 calls, 0.057 sec avg) + <15s> P1: [TIMING] io_X : 3.1953s CPU (19 calls, 0.168 sec avg) + <15s> P1: [TIMING] Dipoles : 4.4012s CPU + <15s> P1: [11] Memory Overview + <15s> P1: [12] Game Over & Game summary + <15s> P1: [TIMING] [Time-Profile]: 15s + +==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <== + <11s> P1: X@q[6] | | [000%] --(E) --(X) + <11s> P1: X@q[6] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%) + <11s> P1: [X-CG] R(p) Tot o/o(of R): 153 504 100 + <11s> P1: Xo@q[7] | | [000%] --(E) --(X) + <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%) + <11s> P1: X@q[7] | | [000%] --(E) --(X) + <11s> P1: X@q[7] |########################################| [100%] --(E) --(X) + <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%) + <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock +``` +```` + +Let's now have look into the job we just submitted. +``` +vim run01_converge_pol.sh +``` +First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file `i01-GW` is used as a template for every calculation in the loops, so we assign it to a variable. +```bash +file0='i01-GW' + +for POL_BANDS in 20 40 60 80; do + +echo 'NGsBlkXp [Ry] E_vale [eV] E_cond [eV]' > summary_01_${POL_BANDS}bands.txt + +for NGsBlkXp_Ry in 6 8 10 12; do + +(...) + +done +done +``` + +Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the `sed` command, in order to generate new files in an automated way (`sed` replaces any matching string with whatever is provided by the loop variable). Next, we run `yambo` using the labels to specify different job `-J` and communication `-C` directories every time. Finally, we get the quasiparticle energies with `grep` commands as shown before and append a new line to the summary file. So, inside each loop, we have +```bash +label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry +jdir=job_${label} +cdir=out_${label} +filein=i01-GW_${label} + +sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/; + /% BndsRnXp/{n;s/.*/ 1 | ${POL_BANDS} |/}" $file0 > $filein + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir + +E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'` +E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'` + +echo ${NGsBlkXp_Ry} ' ' ${E_GW_v} ' ' ${E_GW_c} >> summary_01_${POL_BANDS}bands.txt +``` + +Finally, let us plot this data. First, check that the job has finished with +```console +squeue -u $USER +``` +```console +[$USER@login01 02_GW_convergence]$ squeue -u $USER + JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) +[$USER@login01 02_GW_convergence]$ +``` +and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven't done so yet, and then plot: +```console +module load anaconda3/2023.03 +python plot-01.py +``` +The plot will produce a `fig-01.png` file. +You can copy and open it in your local machine with something like +``` +[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH] +scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./ +``` + +You should get: +```{figure} img/convergence01.png +:scale: 80% +``` + + +For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we'll make a copy of the corresponding input file: +``` +cp i01-GW_Xp_80_bands_10_Ry i02-GW +``` + +### Self-energy {math}`\Sigma^c` - Bands + +We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., `GbndRnge`. This step is actually simpler, since it only involves one loop. This is coded in the provided script `run02_converge_Gbnds.noBG.sh`. You can look into it +``` +vim run02_converge_Gbnds.noBG.sh +``` +and go ahead and submit it. +``` +sbatch run02_converge_Gbnds.noBG.sh +``` + +````{solution} [OPTIONAL]: Use the terminator to accelerate convergence + +While that runs, we'll have a look at the so-called Bruneval-Gonze (BG) terminator, which is a method to accelerate convergence with respect to empty bands. The variable that controls this for the bands in the correlation self-energy is `GTermKind`. This is currently set to "none" in `i02-GW`, so create a new input file `i02-GW_BG` and set this variable to "BG". We can do this in the command line by simply typing +``` +sed 's/GTermKind=.*/GTermKind= "BG"/' i02-GW > i02-GW_BG +``` +Note that `XTermKind` also offers the same terminator for the sum over bands of the polarization function (we just chose not to use it in the previous section of this excercise, and we will keep it as "none"). Now, copy the last submission script and edit it to run the same convergence test using the BG terminator. +``` +cp run02_converge_Gbnds.noBG.sh run03_converge_Gbnds.BG.sh +``` +Try and do this yourself first, and then continue reading to check your understanding. +You will have to change the input file template, i.e., use `i02-GW_BG` where the terminator has been activated. Modify also the name of the newly generated input files in order to avoid overwriting. Change the name of the summary file for the same reason and, finally, modify the communications and job directories of `yambo`. Make sure you've done all the changes as outlined below. + +```bash +file0='i02-GW_BG' +summaryfile=summary_03_BG.txt + +(...) + +label=Gbands_${G_BANDS}_BG +filein=i02-GW_${G_BANDS}_Gbands_BG + +``` +Now submit your newly edited script +``` +sbatch run03_converge_Gbnds.BG.sh +``` +```` + +While this runs, check if the previous job has finished, i.e., you should have a complete `summary_02_noBG.txt` file by now. +For a visual result, proceed to plot them with +``` +python plot-02.py +``` +You should get +```{figure} img/BG_noBG.png +:scale: 80% +``` + + +```{solution} OPTIONAL +If you also did the optional step, you can compare `summary_02_noBG.txt` with `summary_03_BG.txt` once `run03_converge_Gbnds.BG.sh` has finished - you'll see the effect of the terminator immediately. +Just open the `plot-02.py` script and uncomment the line `#list_of_files = ['summary_02_noBG.txt','summary_03_BG.txt']`, then rerun it with `python plot-02.py`. +You can see that the terminator does a great job at accelerating convergence, and it allows us to use 60 bands incurring an error of only 3 meV (while the latter would have been larger than 0.1 eV had we not used the terminator). +``` + +We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication ([here](https://www.nature.com/articles/s41524-023-00989-7)). MoS{math}`_2` was one of the materials studied there, and it shows that our result, obtained with a {math}`6 \times 6 \times 1` k-grid, is simply *off the chart* (blue line). + +```{figure} img/ref-Guandalini.png +:scale: 40% +``` +_Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9_ + +````{solution} [OPTIONAL]: Use the RIM-W accelerator +However you can try to get a reasonable correction via the RIM-W approach. Create a new input file copying a suitable one: +``` +cp i02-GW_80_Gbands i04-GW_80_Gbands_rimw +vim i04-GW_80_Gbands_rimw +``` +Then, you just need to add the following two variables to the input file (for example just after the runlevel keywords) +``` +RIM_W +RandGvecW= 15 RL +``` +and prepare a submission script +``` +cp run02_converge_Gbnds.noBG.sh run04_converge_rimw.sh +vim run04_converge_rimw.sh +``` +Edit it by removing the loop and changing `summaryfile`, `label` and `filein` +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=4 +#SBATCH --cpus-per-task=8 +#SBATCH --partition=boost_usr_prod +#SBATCH --time=0:10:00 +#SBATCH --gres=gpu:4 +#SBATCH --account=EUHPC_TD02_030 +#SBATCH --job-name=mos2 + +export OMP_NUM_THREADS=8 +export OMP_PLACES=cores +export OMP_PROC_BIND=close + +# load yambo +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 + +file0='i02-GW' +summaryfile=summary_04_rimw.txt + +echo 'G bands E_vale [eV] E_cond [eV] GAP [eV]' > $summaryfile + +G_BANDS=80 + +label=Gbands_${G_BANDS}_rimw +jdir=job_${label} +cdir=out_${label} +filein=i04-GW_${G_BANDS}_Gbands_rimw + +# run yambo +mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir + +E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'` +E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'` + +GAP_GW=`echo $E_GW_c - $E_GW_v |bc` + +echo ${G_BANDS} ' ' ${E_GW_v} ' ' ${E_GW_c} ' ' ${GAP_GW} >> $summaryfile +``` +and then run +``` +sbatch run04_converge_rimw.sh +``` +How much do you get for the band gap ? +```` + +--- +## GW parallel strategies + +### MPI parallelization + +For this section, let us enter the `03_GW_parallel` directory. If you were in the `02_GW_convegence` folder just do +``` +cd ../03_GW_parallel +``` +and inspect the input `gw.in`. You will see that we set low values for most of the convergence parameters except bands: + +``` +vim gw.in +``` + +``` +FFTGvecs= 40 Ry # [FFT] Plane-waves +EXXRLvcs= 2 Ry # [XX] Exchange RL components +VXCRLvcs= 2 Ry # [XC] XCpotential RL components +% BndsRnXp + 1 | 300 | # [Xp] Polarization function bands +% +NGsBlkXp= 1 Ry # [Xp] Response block size +% GbndRnge + 1 | 300 | # [GW] G[W] bands range +% +%QPkrange # [GW] QP generalized Kpoint/Band indices + 1| 19| 23| 30| +% +``` +Note that we also added `FFTGvecs` to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO `ecutwfc`, i.e. 60 Ry in this case). + +In addition, we have deleted all the parallel parameters since we will be setting them via the submission script. + +Actually we are now dealing with a heavier system than before: as you can see from the `QPkrange` values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized). + +For this part of the tutorial, we will be using the `slurm` submission script `job_parallel.sh`, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code: +```bash +DIP_CPU= "1 $ngpu 1" # [PARALLEL] CPUs for each role +DIP_ROLEs= "k c v" # [PARALLEL] CPUs roles (k,c,v) +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role +X_and_IO_ROLEs= "q g k c v" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_and_IO_nCPU_LinAlg_INV=1 # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set) +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +SE_CPU= "1 $ngpu 1" # [PARALLEL] CPUs for each role +SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` +The keyword `DIP` refers to the calculations of the screening matrix elements (also called "dipoles") needed for the screening function, `X` is the screening function itself (it stands for {math}`\chi` since it is a response function), `SE` the self-energy. +These three sections of the code can be parallelised independently. + +We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI _task_ is run on a single card, therefore `ntasks=ngpu`. + +```{callout} Note +- In this subsection we are mainly concerned with the **[PARALLEL]** variables which refer to MPI _tasks_ (distributed memory). +- What about **[OPENMP]** parallelisation (i.e., adding _threads_ with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are *not* run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup *for CPUs* is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later. +``` + +We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as: + +```bash +#!/bin/bash +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=4 +... +#SBATCH --gres=gpu:4 +``` +and submit the job +``` +sbatch job_parallel.sh +``` + +This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report `r-*` file and the log `l-*` files, and inspect them while the calculation runs. +For simplicity you can just type +``` +tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1 +``` +to monitor the progress in the master thread (`Ctrl+c` to exit). +As you can see, the run takes some time, even though we are using minimal parameters. + +Meanwhile, we can run other jobs increasing the parallelisation. Let's employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the `job_parallel.sh` script changing + +```bash +#!/bin/bash +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=4 +... +#SBATCH --gres=gpu:4 +``` + +This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing `nodes` appropriately. Finally, you can try to produce a scaling plot. + +The timings are contained in the `r-*` report files. You can already have a look at them typing +``` +grep Time-Profile run_MPI*/r-* +``` + +The python script `parse_ytiming.py` is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided. + +If you didn't do so already, load the python module +``` +module load anaconda3/2023.03 +``` + +Then, after your jobs have finished, run the script as +``` +python parse_ytiming.py run_MPI +``` +to look for a report file in each `run_MPI*.out` folder. **Make sure you have only one report file per folder.** +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis. + +```{figure} img/gw_scaling.png +:scale: 80% +``` + +What can we learn from this plot? In particular, try to answer the following questions: +- Up to which number of MPI tasks our system scales efficiently? +- How can we decide at which point adding more nodes to the calculation becomes a waste of resources? + +```{callout} Note +Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, __Yambo has been shown to scale well up to tens of thousands of MPI tasks__! (See the next optional box for an example) +``` + +````{solution} [OPTIONAL] Comparison with CPU calculation with hybrid parallelization strategy + +We have run the same calculation using a version of Yambo compiled in order to run on CPUs. This is not the preferred approach in an accelerator-based machine like Leonardo, but it can be instructive. + +For a CPU calculation, we can use a hybrid parallel structure with threads. The OPENMP threads are controlled by modifying `cpus-per-task` and `OMP_NUM_THREADS` in the submission file. The product of the number of OpenMP threads and MPI tasks is equal to the total number of CPUs. + +For our test, we have used larger convergence parameters than in the previous run, and selected a hybrid parallel scheme with 16 MPI tasks per node, with 2 OPENMP threads (`ntasks*nthreads=ncpu=16*2=32`), since it gives the best scaling in this case. + +```{callout} Note +In general (for larger systems) we have tested that the best CPU scaling on Leonardo is actually 4 MPI tasks times 8 OPENMP threads. +``` + +Therefore, in the new CPU submission script we have: +```bash= +#!/bin/bash +#SBATCH --nodes=4 +#SBATCH --ntasks-per-node=16 +#SBATCH --cpus-per-task=2 +... +export OMP_NUM_THREADS=2 +``` + +Actually, we don't need to change the openMP-related variables appearing in the yambo input, since the value `0` means "use the value of `OMP_NUM_THREADS`" and we have now set this environment variable to our liking via the submission script. +Otherwise, any positive number can directly specify the number of threads to be used in each section of the code. + +``` +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +... +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +... +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` + +Actively looking for the best scaling on both GPU and CPU for our enlarged MoS2 system we find: + +```{figure} img/CPU_scaling.jpeg +:scale: 80% +``` + +We can see that already for this reasonably small and half-converged system run on a few nodes the GPU calculation easily reaches a speedup of 2x. The speedup vastly increases in larger systems where the calculations are more demanding, as you can see from the scaling tests below (run on the Juwels Booster machine) on a graphene-cobalt interface supercell. + +```{figure} img/grCo_scaling.png +:scale: 40% +``` +_Scaling comparison of graphene@Co(0001) interface on CPU (left, 48 cpus per node) and GPU (right, 4 GPUs per node). Tests done by Nicola Spallanzani. Data available at: http://www.gitlab.com/max-centre/Benchmarks_ + +```{callout} Note +- In real-life CPU-based calculations running on {math}`n_{cores} > 100`, as we have seen, it may be a good idea to adopt a hybrid approach. +- The most efficient scaling can depend both on your system and on the HPC facility you're running on. For a full CPU node on Leonardo (32 cores), using a large-scale system, we have found that 4 tasks times 8 threads gives the best performance. +- OpenMP can help lower memory requirements within a node. You can try to increase the OpenMP share of threads if you are getting Out Of Memory errors. +``` +```` + +. +````{solution} [OPTIONAL]: Comparing different parallelisation schemes + +Up to now we always parallelised over a single parameter, i.e. `c` or `qp`. However, Yambo allows for tuning the parallelisation scheme over several parameters broadly corresponding to "loops" (i.e., summations or discrete integrations) in the code. + +To this end you can open again the `run_parallel.sh` script and modify the section where the yambo input variables are set. + +For example, `X_CPU` sets how the MPI Tasks are distributed in the calculation of the response function. The possibilities are shown in the `X_ROLEs`. The same holds for `SE_CPU` and `SE_ROLEs` which control how MPI Tasks are distributed in the calculation of the self-energy. + +``` +X_CPU= "1 1 1 $ncpu 1" # [PARALLEL] CPUs for each role +X_ROLEs= "q g k c v" # [PARALLEL] CPUs roles (q,g,k,c,v) +X_nCPU_LinAlg_INV= $ncpu # [PARALLEL] CPUs for Linear Algebra +X_Threads= 0 # [OPENMP/X] Number of threads for response functions +DIP_Threads= 0 # [OPENMP/X] Number of threads for dipoles +SE_CPU= "1 $ncpu 1" # [PARALLEL] CPUs for each role +SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b) +SE_Threads= 0 # [OPENMP/GW] Number of threads for self-energy +``` + +You can try different parallelization schemes and check the performances of Yambo. In doing so, you should also change the jobname `label=MPI${ncpu}_OMP${nthreads}` in the `run_parallel.sh` script to avoid confusion with previous calculations. + +You may then check how speed, memory and load balance between the CPUs are affected. You could modify the script `parse_ytiming.py` to parse the new data, read and distinguish between more file names, new parallelisation options, etc. + +```{callout} Note +- The product of the numbers entering each variable (i.e. `X_CPU` and `SE_CPU`) times the number of threads should always match the total number of cores (unless you want to overload the cores taking advantage of multi-threads). +- Using the `X_Threads` and `SE_Threads` variables you can think about setting different hybrid schemes between the screening and the self-energy runlevels. +- Memory scales better if you parallelize on bands (`c v b`). +- Parallelization on k-points performs similarly to parallelization on bands, but requires more memory. +- Parallelization on q-points requires much less communication between the MPI tasks. It may be useful if you run on more than one node and the inter-node connection is slow. +``` +```` + +--- + +## Full GW band structure + +This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS{math}`_2`. + +This is a massive calculation, so run it right now and we'll discuss it in the meantime: +``` +cd ../04_GW_bands +sbatch gpu_job.sh +``` + +In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling. + +Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input: +``` +vim gw.in +``` + +``` +%QPkrange # [GW] QP generalized Kpoint/Band indices +1|37|25|28| +% +``` + + +After about 3 minutes the calculation should be over and the results collected in folder `GW_bnds`. The quasiparticle corrections are stored in human-readable form in the file `o-GW_bnds.QP`, and in netCDF format in the quasiparticle database `ndb.QP`. + +In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with `ypp`, the yambo pre- and post-processing executable. + +```{callout} Note +We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out [here](https://www.yambo-code.eu/wiki/index.php/First_steps_in_Yambopy) on the Yambo wiki. +``` + +Let us enter a computing node interactively + +``` +srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash +``` +and load the yambo module: +``` +module load profile/chem-phys +module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1 +``` + +We can review the options with `ypp -h` and generate an input file for band structure interpolation with +``` +ypp -s b -F ypp_bands.in +``` +Let us modify the resulting input file by selecting the 'boltztrap' approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points {math}`\Gamma-M-K-\Gamma`. We also set 100 points for each high-symmetry line. +``` +electrons # [R] Electronic properties +bnds # [R] Bands +PROJECT_mode= "none" # Instruct ypp how to project the DOS. ATOM, LINE, PLANE. +INTERP_mode= "BOLTZ" # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach) +INTERP_Shell_Fac= 20.00000 # The bigger it is a higher number of shells is used +INTERP_NofNN= 1 # Number of Nearest sites in the NN method +OutputAlat= 5.90008 # [a.u.] Lattice constant used for "alat" ouput format +cooIn= "rlu" # Points coordinates (in) cc/rlu/iku/alat +cooOut= "rlu" # Points coordinates (out) cc/rlu/iku/alat +% BANDS_bands + 25 | 28 | # Number of bands +% +CIRCUIT_E_DB_path= "none" # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts) +BANDS_path= "" # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL). +BANDS_steps= 100 # Number of divisions +#BANDS_built_in # Print the bands of the generating points of the circuit using the nearest internal point +%BANDS_kpts # K points of the bands circuit + 0.00000 |0.00000 |0.00000 | + 0.00000 |0.50000 |0.00000 | + 0.33333 |0.33333 |0.00000 | + 0.00000 |0.00000 |0.00000 | +% +``` +Now, let's run ypp: +``` +mpirun -np 1 ypp -F ypp_bands.in +``` +This run will produce the file `o.bands_interpolated`. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn't tell `ypp` where to look for the quasiparticle corrections, so it went into the `SAVE` folder and interpolated the DFT data. +Let's rename the output: +``` +mv o.bands_interpolated o.DFT_bands +mkdir DFT_bands +mv o.spin* o.magn* DFT_bands/ +``` +In order to interpolate the quasiparticle database, we append its location to the `ypp` input: +``` +vim ypp_bands.in +``` +add this line at the end +``` +... +GfnQPdb= "E < ./GW_bnds/ndb.QP" +``` +and run `ypp` again. +``` +mpirun -np 1 ypp -F ypp_bands.in +``` + +When it's done, let's rename the new output as +``` +mv o.bands_interpolated o.GW_bands +mkdir GW_bands +mv o.spin* o.magn* GW_bands/ +``` + +Now we are ready to visualize the band structures. In order to do so, you can use the script `plt_bands.py` that should be already available in the directory. + +We load the python module +``` +module load anaconda3/2023.03 +``` + +and run the script as +``` +python plt_bands.py o.DFT_bands o.GW_bands 4 +``` + +Now we can also exit the computing node +``` +exit +``` + +The python script should have produced a `GW_bands.png` file containing the following visualization, which you can copy and open it in your local machine using `scp`: + +```{figure} img/gw_bands.png +:scale: 80% +``` + +You may compare this plot with a converged result from [this paper](https://doi.org/10.1016/j.surfrep.2015.10.001) (also done with Yambo): + +```{figure} img/gw_bands_ref.png +:scale: 50% +``` +_Dashed lines: DFT, thick lines: GW._ + +As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations! + +In order to learn more about Yambo, we suggest visiting the [Yambo website](https://www.yambo-code.eu/). For technical information and tutorials, you can check out the [Yambo wiki](https://www.yambo-code.eu/wiki/index.php/Main_Page). If you have issues and questions about installing and running the code, you can write about them on the [Yambo forum](https://www.yambo-code.eu/forum/index.php). diff --git a/branch/main/_sources/days3+4/day3.rst.txt b/branch/main/_sources/days3+4/day3.rst.txt new file mode 100644 index 0000000..8684d05 --- /dev/null +++ b/branch/main/_sources/days3+4/day3.rst.txt @@ -0,0 +1,77 @@ +:sequential_nav: next + +.. _day3-siesta1: + +Day 3: SIESTA I +=============== + +SIESTA basics +------------- + +Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge). + +Slides available here: :download:`SIESTA-Intro.pdf `. + + +A first contact with SIESTA: inputs, execution and outputs +----------------------------------------------------------- + +Practical session led by Dr. Federico Pedron (ICN2). + +Tutorials covered: + +- `A First Encounter - Part 1: Running SIESTA `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/01-FirstEncounter_I + +- `A First Encounter - Part 2: Choosing your level of theory `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/02-FirstEncounter_II + +Introductory slides available here: :download:`SIESTA-First_encounter.pdf `. + +Basis sets +---------- + +Lecture by Dr. Miguel Pruneda (CINN-CSIC). + +Slides available here: :download:`SIESTA-Basis_sets.pdf `. + + +Basis set optimization +---------------------- + +Practical session led by Dr. Federico Pedron (ICN2). + +Tutorials covered: + +- `Basis set optimization `_ +- `Basis sets - Tips and tricks `_ + +Files for the tutorial:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets + +Introductory slides available here: :download:`SIESTA-Basis_set_optimization.pdf `. + +Convergence (k points, mesh, mixing) +------------------------------------ + +Practical session led by Dr. Catalina Coll (ICN2). + +Tutorials covered: + +- `The real-space grid `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04a-GridConvergence + +- `Sampling of the BZ with k-points `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04b-KPointConvergence + +- `The self-consistent-field cycle `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04c-SCF + +Introductory slides available here: :download:`SIESTA-Convergence.pdf `. + diff --git a/branch/main/_sources/days3+4/day4.rst.txt b/branch/main/_sources/days3+4/day4.rst.txt new file mode 100644 index 0000000..ec01043 --- /dev/null +++ b/branch/main/_sources/days3+4/day4.rst.txt @@ -0,0 +1,59 @@ +:sequential_nav: next + +.. _day4-siesta2: + +Day 4: SIESTA II +================ + +Molecular Dynamics with SIESTA +------------------------------ + +Practical session led by Dr. Ernane de Freitas (ICN2). + +Tutorials covered: + +- `Molecular Dynamics `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics + +Introductory slides available here: :download:`SIESTA-MD.pdf `. + + +Analysis tools +-------------- + +Practical session led by Dr. Miguel Pruneda (CINN-CSIC). + +Tutorials covered: + +- `Analysis tools `_. Files available at:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis + +Introductory slides available here: :download:`SIESTA-Analysis_tools.pdf `. + + +Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others +-------------------------------------------------------------------------- + +Lecture by Dr. Nick Papior (Technical University of Denmark). + +Slides available here: :download:`SIESTA-Features.pdf `. + + +Pushing the boundaries of SIESTA: accelerated and massively parallel solvers +---------------------------------------------------------------------------- + +Practical session led by Dr. Alberto García (ICMAB-CSIC). + +Tutorials covered: + +- ELSI-ELPA. +- ELSI-PEXSI. + +Files for the tutorial:: + + /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers + +Slides available here: :download:`SIESTA-Solvers.pdf `. + diff --git a/branch/main/_sources/days3+4/setup.rst.txt b/branch/main/_sources/days3+4/setup.rst.txt new file mode 100644 index 0000000..9c9684c --- /dev/null +++ b/branch/main/_sources/days3+4/setup.rst.txt @@ -0,0 +1,67 @@ +SIESTA setup +============ + +Directory with tutorials +------------------------ +For every practical there is a folder in the shared directory +``/leonardo_work/EUHPC_TD02_030/siesta-tutorials`` that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:: + +$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I . + +Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts. + + +Running SIESTA +-------------- +You will find a sample script on how to run SIESTA in +``/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh``: :: + + #!/bin/bash + #SBATCH -J tutorialXX + #SBATCH -n 8 + #SBATCH -t 0:30:00 + #SBATCH -o %x-%j.out + #SBATCH -e %x-%j.err + #SBATCH --partition=boost_usr_prod + #SBATCH -D . + + # DO NOT CHANGE THIS LINE + source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh + + # EDIT THE CORRECT INPUT AND OUTPUT FILES. + srun -n 8 siesta < input.fdf > output.out + + +Note that ``input.fdf`` and ``output.out`` are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(``#SBATCH -J option``) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue. + + + +Suggested Software for Visualization +------------------------------------ +If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences. + +- `gnuplot `_ +- `xcrysden `_ +- `vesta `_ +- `vmd `_ +- `ovito `_ +- Python with matplotlib + + + +.. + SIESTA source code + ------------------ + If you want to try your own SIESTA compilation, have a look at this `SIESTA + compilation how-to `_ . + Be sure to have all dependencies beforehand. Note that we will not be answering + questions regarding compilation or other installations during the school. diff --git a/branch/main/_sources/guide.rst.txt b/branch/main/_sources/guide.rst.txt new file mode 100644 index 0000000..89553fb --- /dev/null +++ b/branch/main/_sources/guide.rst.txt @@ -0,0 +1,37 @@ +Instructor's guide +================== + +Why we teach this lesson +------------------------ + + + +Intended learning outcomes +-------------------------- + + + +Timing +------ + + + +Preparing exercises +------------------- + +e.g. what to do the day before to set up common repositories. + + + +Other practical aspects +----------------------- + + + +Interesting questions you might get +----------------------------------- + + + +Typical pitfalls +---------------- diff --git a/branch/main/_sources/index.rst.txt b/branch/main/_sources/index.rst.txt new file mode 100644 index 0000000..c5bab3f --- /dev/null +++ b/branch/main/_sources/index.rst.txt @@ -0,0 +1,326 @@ +Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo +============================================================================ + +In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential. + +This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises. + +`QUANTUM ESPRESSO `__ is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications. + +`SIESTA `__ is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a "good first approximation" to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA. + +`YAMBO `__ is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc). + +`MAX (MAterials design at the eXascale) `__ is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX's challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials' domain. + + +.. prereq:: + + - Some familiarity with density functional theory (DFT), self-consistent + field (SCF) calculations and plane wave basis sets is desirable as the + workshop will not cover the fundamental theory of these topics. + - Familiarity with working in a Linux environment and some experience with + working on an HPC system is needed to participate in the hands-on exercises. + + +Who is the course for? +---------------------- + +This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations. + + +.. toctree:: + :maxdepth: 1 + :caption: Day 1 - Quantum ESPRESSO I + + + + +.. toctree:: + :maxdepth: 1 + :caption: Day 2 - Quantum ESPRESSO II + + +.. toctree:: + :maxdepth: 1 + :caption: Days 3 and 4 - Siesta + + days3+4/setup + days3+4/day3 + days3+4/day4 + +.. toctree:: + :maxdepth: 1 + :caption: Day 5 - Yambo + + day5/yambo-tutorial + +.. toctree:: + :maxdepth: 1 + :caption: Reference + + quick-reference + guide + +.. toctree:: + :maxdepth: 1 + :caption: About + + All lessons + ENCCS + + + + +About the course +---------------- + +In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties. + +Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers. + +Schedule +^^^^^^^^ + +**Day 1, QUANTUM ESPRESSO** + ++------------+-------------------------------------------------------+ +| Time | Section | ++============+=======================================================+ +|09:00-09:15 | Welcome and introduction to ENCCS | ++------------+-------------------------------------------------------+ +|09:15-09:30 | Introduction to Max-CoE and MaX flagship codes | ++------------+-------------------------------------------------------+ +|09:30-10:00 | Overview of the QE suite of codes and main features | ++------------+-------------------------------------------------------+ +|10:00-10:25 | Coffee break | ++------------+-------------------------------------------------------+ +|10:25-13:00 | PWSCF for HPC and GPU | ++------------+-------------------------------------------------------+ + + +**Day 2, QUANTUM ESPRESSO** + ++------------+----------------------------------------------------------------------+ +| Time | Section | ++============+======================================================================+ +|09:00-09:45 | Introduction to Density Functional Perturbation Theory | ++------------+----------------------------------------------------------------------+ +|09:45-10:15 | Introduction to Time Dependent Density Functional Perturbation Theory| ++------------+----------------------------------------------------------------------+ +|10:15-10:30 | Coffee break | ++------------+----------------------------------------------------------------------+ +|10:30-13:00 | Phonons and time dependent properties on HPC and GPU | ++------------+----------------------------------------------------------------------+ + + +**Day 3, SIESTA** + ++------------+-------------------------------------------------------------------------------------+ +| Time | Section | ++============+=====================================================================================+ +|09:00-09:45 | SIESTA basics | ++------------+-------------------------------------------------------------------------------------+ +|09:45-10:30 | Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs | ++------------+-------------------------------------------------------------------------------------+ +|10:30-10:45 | Break | ++------------+-------------------------------------------------------------------------------------+ +|10:45-11:15 | Basis sets | ++------------+-------------------------------------------------------------------------------------+ +|11:15-12:00 | Hands-on tutorial: Basis set optimization | ++------------+-------------------------------------------------------------------------------------+ +|12:00-13:00 | Hands-on tutorial: Convergence (k points, mesh, mixing) | ++------------+-------------------------------------------------------------------------------------+ + +**Day 4, SIESTA** + ++------------+-------------------------------------------------------------------------------------------------+ +| Time | Section | ++============+=================================================================================================+ +|09:00-10:00 | Hands-on tutorial: Moving atoms: geometry optimisation and beyond | ++------------+-------------------------------------------------------------------------------------------------+ +|10:30-11:00 | Hands-on tutorial: Analysis tools | ++------------+-------------------------------------------------------------------------------------------------+ +|11:00-11:15 | Break | ++------------+-------------------------------------------------------------------------------------------------+ +|11:15-11:45 | Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others | ++------------+-------------------------------------------------------------------------------------------------+ +|11:45-13:00 | Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers | ++------------+-------------------------------------------------------------------------------------------------+ + + +**Day 5, Yambo** + ++------------+------------------------------------------------------------------+ +| Time | Section | ++============+==================================================================+ +|09:00-09:20 | Overview of the Yambo code and its main features and performance | ++------------+------------------------------------------------------------------+ +|09:20-10:00 | Introduction to the GW approximation | ++------------+------------------------------------------------------------------+ +|10:00-10:20 | Coffee break | ++------------+------------------------------------------------------------------+ +|10:20-13:00 | Hands-on tutorial: A guided tour through GW simulations | ++------------+------------------------------------------------------------------+ + + +See also +-------- + +- ENCCS: https://enccs.se/ +- MAX-CoE: http://www.max-centre.eu/ +- Follow ENCCS on `LinkedIn `__, or `Twitter `__ +- Follow MAX-CoE on `LinkedIn `__, or `Twitter `__. + +.. math:: + + +Credits +------- + +Contributors to this workshop: + +- Pietro Davide Delugas (SISSA) +- Ivan Carnimeo (SISSA) +- Oscar Baseggio (SISSA) +- Fabrizio Ferrari Ruffino (CNR-IOM) +- Paolo Giannozzi (CNR-IOM, UniUD) +- Iurii Timrov (Paul Scherrer Institut) +- Laura Bellentani (CINECA) +- Tommaso Gorni (CINECA) +- Aurora Ponzi (CNR-IOM) +- Emilio Artacho (CIC NanoGUNE and University of Cambridge) +- Catalina Coll (ICN2) +- José Mª Escartín (ICN2) +- Roberta Farris (ICN2) +- Ernane de Freitas (ICN2) +- Alberto García (ICMAB-CSIC) +- Arnold Kole (Utrecht University) +- Nick Papior (DTU) +- Federico Pedron (ICN2) +- Miguel Pruneda (CINN-CSIC) +- José Ángel Silva Guillén (IMDEA Nanociencia) +- D. Varsano (CNR-NANO) +- A. Ferretti (CNR-NANO) +- D. Sangalli (CNR-ISM) +- A. Guandalini (Univ. of Rome, La Sapienza) +- F. Paleari (CNR-NANO) +- M. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO) +- G. Sesti (CNR-NANO) +- N. Spallanzani (CNR-NANO) + + +The lesson file structure and browsing layout is inspired by and derived from +`work `__ by `CodeRefinery +`__ licensed under the `MIT license +`__. We have copied and adapted +most of their license text. + +Licenses +-------- + +General +^^^^^^^ + +Instructional Material +~~~~~~~~~~~~~~~~~~~~~~ + +Except where otherwise noted, +this instructional material is made available under the +`Creative Commons Attribution license (CC-BY-4.0) `__. +The following is a human-readable summary of (and not a substitute for) the +`full legal text of the CC-BY-4.0 license +`__. +You are free to: + +- **share** - copy and redistribute the material in any medium or format +- **adapt** - remix, transform, and build upon the material for any purpose, + even commercially. + +The licensor cannot revoke these freedoms as long as you follow these license terms: + +- **Attribution** - You must give appropriate credit (mentioning that your work + is derived from work that is Copyright (c) ENCCS and individual contributors and, where practical, linking + to ``_), provide a `link to the license + `__, and indicate if changes were + made. You may do so in any reasonable manner, but not in any way that suggests + the licensor endorses you or your use. +- **No additional restrictions** - You may not apply legal terms or + technological measures that legally restrict others from doing anything the + license permits. + +With the understanding that: + +- You do not have to comply with the license for elements of the material in + the public domain or where your use is permitted by an applicable exception + or limitation. +- No warranties are given. The license may not give you all of the permissions + necessary for your intended use. For example, other rights such as + publicity, privacy, or moral rights may limit how you use the material. + + +Software +~~~~~~~~ + +Except where otherwise noted, the example programs and other software provided +with this repository are made available under the `OSI `__-approved +`MIT license `__. + +SIESTA +^^^^^^ + +At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved. diff --git a/branch/main/_sources/quick-reference.rst.txt b/branch/main/_sources/quick-reference.rst.txt new file mode 100644 index 0000000..492da1e --- /dev/null +++ b/branch/main/_sources/quick-reference.rst.txt @@ -0,0 +1,2 @@ +Quick Reference +=============== diff --git a/branch/main/_static/ENCCS.jpg b/branch/main/_static/ENCCS.jpg new file mode 100644 index 0000000..da2355c Binary files /dev/null and b/branch/main/_static/ENCCS.jpg differ diff --git a/branch/main/_static/_sphinx_javascript_frameworks_compat.js b/branch/main/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/branch/main/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/branch/main/_static/basic.css b/branch/main/_static/basic.css new file mode 100644 index 0000000..30fee9d --- /dev/null +++ b/branch/main/_static/basic.css @@ -0,0 +1,925 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li p.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; + margin-left: auto; + margin-right: auto; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/check-solid.svg b/branch/main/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/_static/clipboard.min.js b/branch/main/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/_static/copybutton.css b/branch/main/_static/copybutton.css new file mode 100644 index 0000000..f1916ec --- /dev/null +++ b/branch/main/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/_static/copybutton.js b/branch/main/_static/copybutton.js new file mode 100644 index 0000000..2ea7ff3 --- /dev/null +++ b/branch/main/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/_static/copybutton_funcs.js b/branch/main/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/branch/main/_static/css/badge_only.css b/branch/main/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/branch/main/_static/css/badge_only.css @@ 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight 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score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/_static/siesta/SIESTA-Analysis_tools.pdf b/branch/main/_static/siesta/SIESTA-Analysis_tools.pdf new file mode 100644 index 0000000..f7045c7 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Analysis_tools.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Basis_set_optimization.pdf b/branch/main/_static/siesta/SIESTA-Basis_set_optimization.pdf new file mode 100644 index 0000000..f5edb26 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Basis_set_optimization.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Basis_sets.pdf b/branch/main/_static/siesta/SIESTA-Basis_sets.pdf new file mode 100644 index 0000000..84bfc66 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Basis_sets.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Convergence.pdf b/branch/main/_static/siesta/SIESTA-Convergence.pdf new file mode 100644 index 0000000..667b2fb Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Convergence.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Features.pdf b/branch/main/_static/siesta/SIESTA-Features.pdf new file mode 100644 index 0000000..272de28 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Features.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-First_encounter.pdf b/branch/main/_static/siesta/SIESTA-First_encounter.pdf new file mode 100644 index 0000000..627b1cd Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-First_encounter.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Intro.pdf b/branch/main/_static/siesta/SIESTA-Intro.pdf new file mode 100644 index 0000000..dcd5733 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Intro.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-MD.pdf b/branch/main/_static/siesta/SIESTA-MD.pdf new file mode 100644 index 0000000..f7fed7f Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-MD.pdf differ diff --git a/branch/main/_static/siesta/SIESTA-Solvers.pdf b/branch/main/_static/siesta/SIESTA-Solvers.pdf new file mode 100644 index 0000000..9430066 Binary files /dev/null and b/branch/main/_static/siesta/SIESTA-Solvers.pdf differ diff --git a/branch/main/_static/sphinx_highlight.js b/branch/main/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/_static/sphinx_lesson.css b/branch/main/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/_static/tabs.css b/branch/main/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/branch/main/_static/tabs.js b/branch/main/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/branch/main/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; 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By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/_static/togglebutton.js b/branch/main/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/day5/yambo-tutorial/index.html b/branch/main/day5/yambo-tutorial/index.html new file mode 100644 index 0000000..6f1d2ce --- /dev/null +++ b/branch/main/day5/yambo-tutorial/index.html @@ -0,0 +1,1193 @@ + + + + + + + Yambo tutorial: Quasiparticles in the GW approximation — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Yambo tutorial: Quasiparticles in the GW approximation
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Yambo tutorial: Quasiparticles in the GW approximation

+

In this tutorial you will learn how to run a GW simulation using Yambo on a HPC machine.

+

You will compute the quasiparticle corrections to the band structure of a free-standing single layer of MoS\(_2\) while learning about convergence studies, parallel strategies, and GPU calculations.

+

In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate.

+
+../../_images/mos2.png +
+

MoS\(_2\) monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.

+
+

Many-body corrections to the DFT band gap

+

We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of.

+

Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy \(\Sigma\):

+
+\[E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle\]
+

Here \(\epsilon_{nk}\) and \(\psi_{nk}\) are the Kohn-Sham energies and wavefunctions, respectively, while \(V_{xc}\) is the DFT exchange-correlation potential.

+

For each electronic state \(nk\), the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy (\(\Sigma^x\)), and an energy-dependent, usually gap-closing term called the correlation self-energy (\(\Sigma^c\)). These contributions are tackled separately by the code:

+
+\[\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega)\]
+

The energy-dependent dynamical electronic screening \(\varepsilon^{-1}(\omega)\) is included in \(\Sigma^c\) and must therefore be calculated as well.

+

In this way, we can compute the “quasiparticle” corrections \(E^{QP}_{nk}\) to the single-particle Kohn-Sham eigenvalues \(\epsilon_{nk}\). +The typical workflow for a GW calculation is:

+
+../../_images/gwflow.png +
+
+
+

Set up a Yambo calculation

+

Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes):

+
wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+
tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+

You can now enter the tutorial directory

+
cd MoS2_HPC_tutorial_Leonardo
+
+
+
+

Yambo SAVE folder

+

First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo.

+

The QE save folder for MoS\(_2\) is already present at 00_QE-DFT. We should move inside it and then run the p2y executable to generate the uninitialised SAVE.

+

But first, we need to access a node interactively:

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

Finally:

+
cd 00_QE-DFT/mos2.save
+mpirun -np 1 p2y
+
+
+

Now, we need to run the initialization step. Every Yambo run must start with this step. This will be automatically performed when you run Yambo on a SAVE directory for the first time. Just type

+
mpirun -np 1 yambo
+
+
+

and then check the yambo log called l_setup. The initialization step determines the \(G\)-vector shells and the \(k\)- and \(q\)-point grids based on the DFT calculation. If you check inside the SAVE you will see two types of databases. The static ones, starting with ns.*, are directly converted in the p2y step, while the dynamical ones, ndb.* are generated during the initialisation.

+
ls SAVE/
+
+
+
ndb.gops       # info on G-vector shells, etc
+ndb.kindx      # info and k and q meshes
+ns.db1         # info on geometry and KS bands
+ns.kb_pp_pwscf # pseudopotential info
+ns.wf          # wave functions info
+...
+
+
+

The databases are written in netCDF format. +Yambo has produced also a human readable output, r_setup, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections.

+
vim r_setup
+
+
+
[02.01] Unit cells # Lattice geometry info
+==================
+  ...
+[02.02] Symmetries # Symmetry ops. written explicitly
+==================
+  ...
+[02.03] Reciprocal space  # Reciprocal lattice info
+========================
+...
+[02.04] K-grid lattice # k-point coords. written explicitly
+======================
+...
+[02.05] Energies & Occupations # Info on band gaps and occupations
+============================== # DFT eigenvalues
+...
+[03] Transferred momenta grid and indexing # q-points (momentum transfer grid)
+==========================================
+
+
+

Finally, let us move the SAVE and the report file to the directory where we will run the first GW calculation.

+
mv SAVE r_setup ../../01_GW_first_run/
+cd ../../01_GW_first_run/
+
+
+
+
+

Yambo input file

+

Now that we have a working SAVE, it is time to generate the input file we will be using for our first GW calculation.

+

This can be done by the yambo executable via command-line instructions.

+

If you type

+
yambo -h
+
+
+

You will get a list of the possibile options:

+
 ___ __  _____  __ __  _____   _____
+|   Y  ||  _  ||  Y  ||  _  \ |  _  |
+|   |  ||. |  ||.    ||. |  / |. |  |
+ \   _/ |. _  ||.\ / ||. _  \ |. |  |
+  |: |  |: |  ||: |  ||: |   \|: |  |
+  |::|  |:.|:.||:.|:.||::.   /|::.  |
+  `--"  `-- --"`-- --"`-----" `-----"
+ 'A shiny pot of fun and happiness [C.D.Hogan]'
+
+ This is      : yambo
+ Version      : 5.1.0 Revision 21422 Hash fde6e2a07
+ Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO
+
+ Help & version:
+ -help            (-h) <string>   :<string> can be an option (e.g. -h optics)
+ -version                         :Code version & libraries
+
+ Input file & Directories:
+ -Input           (-F) <string>   :Input file
+ -Verbosity       (-V) <string>   :Input file variables verbosity (more with -h Verbosity)
+ -Job             (-J) <string>   :Job string
+ -Idir            (-I) <string>   :Input directory
+ -Odir            (-O) <string>   :I/O directory
+ -Cdir            (-C) <string>   :Communication directory
+
+ Parallel Control:
+ -parenv          (-E) <string>   :Environment Parallel Variables file
+ -nompi                           :Switch off MPI support
+ -noopenmp                        :Switch off OPENMP support
+
+ Initializations:
+ -setup           (-i)            :Initialization
+ -coulomb         (-r)            :Coulomb potential
+
+ Response Functions:
+ -optics          (-o) <string>   :Linear Response optical properties (more with -h optics)
+ -X               (-d) <string>   :Inverse Dielectric Matrix (more with -h X)
+ -dipoles         (-q)            :Oscillator strenghts (or dipoles)
+ -kernel          (-k) <string>   :Kernel (more with -h kernel)
+
+ Self-Energy:
+ -hf              (-x)            :Hartree-Fock
+ -gw0             (-p) <string>   :GW approximation (more with -h gw0)
+ -dyson           (-g) <string>   :Dyson Equation solver (more with -h dyson)
+ -lifetimes       (-l)            :GoWo Quasiparticle lifetimes
+
+ Bethe-Salpeter Equation:
+ -Ksolver         (-y) <string>   :BSE solver (more with -h Ksolver)
+
+ Total Energy:
+ -acfdt                           :ACFDT Total Energy
+
+ Utilites:
+ -Quiet           (-Q)            :Quiet input file creation
+ -fatlog                          :Verbose (fatter) log(s)
+ -DBlist          (-D)            :Databases properties
+ -walltime             <int>      :Walltime (more with -h walltime)
+ -memory               <int>      :Memory (more with -h memory)
+ -slktest                         :ScaLapacK test
+
+ YAMBO developers group (http://www.yambo-code.org)
+
+
+

In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type:

+
yambo -gw0 p -g n -r -V par -F gw.in
+
+
+

Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the slurm scheduler.

+
exit
+
+
+

You can now inspect the input file gw.in and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change.

+

We discuss them below step by step.

+
+
+

Parameters for a GW calculation

+

We start with the runlevels:

+
gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+el_el_corr                       # [R] Electron-Electron Correlation
+dyson                            # [R] Dyson Equation solver
+rim_cut                          # [R] Coulomb potential
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+
+
+
+

Runlevels

+
    +

  • The [R] keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have:

    +
      +

    • rim_cut: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables).

      • +

    • gw0: Yambo learns that it has to run a GW calculation (enables [GW] variables).

      • +

    • HF_and_locXC: calculation of exchange part of the self-energy \(\Sigma^x\) (i.e., Hartree-Fock approximation).

      • +

    • em1d: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute \(\Sigma^c\).

      • +

    • ppa: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables).

      • +

    • dyson: Yambo will solve the Dyson-like quasiparticle equation.

      • +
    +
    • +
+
+

Going through the file we find:

+
EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+
+
+

Recall that we have, for the exchange self-energy:

+
+\[\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q}\]
+
+

Exchange self-energy

+
    +

  • EXXRLvcs controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while VXCRLvcs does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value).

    • +
+
+

Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have:

+
+\[\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega')\]
+

(Here, the \(\rho\)-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.)

+

The calculation is divided in two steps. First, the response function in the plasmon pole approximation (em1d ppa), under the keywords [X] and [Xp], i.e., \(\varepsilon^{-1}_{GG'}(q,\omega)\).

+
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 300 |                     # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+
+
+
+

Response function

+
    +

  • Chimod= "Hartree" indicates that we compute the response function in the Random Phase Approximation (RPA).

    • +

  • BndsRnXp represents the electronic states included in the response function \(\varepsilon\), and is a convergence parameter.

    • +

  • NGsBlkXp is the number of G-vectors used to calculate the RPA response function \(\varepsilon^{-1}_{GG'}\). It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested).

    • +

  • LongDrXp represents the direction of the long-range auxiliary external electric field used to compute \(\varepsilon^{-1}_{GG'}(q)\) at \(q,G\rightarrow 0\). In general you have to be mindful of the system symmetries. In our case, we will put 1 | 1 | 1 to cover all directions.

    • +

  • PPAPntXp= 27.21138 eV is the energy of the plasmon pole. We don’t normally change this.

    • +

  • XTermKind is used to specify a “terminator”: this accelerates numerical convergence with respect to the number of bands BndsRnXp.

    • +
+
+

Next, we have the [GW] group of parameters controlling the next part of the correlation self-energy calculation:

+
% GbndRnge
+   1 | 300 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|7|1|300|
+%
+
+
+
+

Correlation self-energy

+
    +

  • GbndRnge is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator GTermKind.

    • +

  • DysSolver="n" specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method "n".

    • +

  • QPkrange indicates the range of electronic (nk) states for which the GW correction \(\Sigma_{nk}\) is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices.

    • +
+
+

We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should edit now once and for all.

+
RandQpts=1000000                       # [RIM] Number of random q-points in the BZ
+RandGvec= 100                RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+
+
+
+

Coulomb potential

+
    +

  • The [RIM] keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to \(q=0\) and \(G=0\) in the \(q\)-integration of the bare Coulomb interaction - i.e. \(4\pi/(q+G)^2\) - for 2D systems.

    • +

  • The [CUT] keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the \(z\)-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic.

    • +
+
+

Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now.

+
X_and_IO_CPU= ""                 # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= ""               # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=-1      # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_CPU= ""                      # [PARALLEL] CPUs for each role
+DIP_ROLEs= ""                    # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_CPU= ""                       # [PARALLEL] CPUs for each role
+SE_ROLEs= ""                     # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+
+
+

In a GW calculation, the most important parameters to be numerically converged are:

+
    +

  • kpoint mesh (requires multiple nscf DFT runs)

    • +

  • BndsRnXp

    • +

  • NGsBlkXp

    • +

  • GbndRnge

    • +

  • [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs)

    • +
+

From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations.

+
+
+
+
+

The first run

+

We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file r_setup produced when the SAVE folder was initialised. Just search for the string ‘Direct Gap’ and you’ll see that the latter occurs at k-point 7 between bands 13 and 14:

+
  [X] Filled Bands                                  :  13
+  [X] Empty Bands                                   :   14  300
+  [X] Direct Gap                                    :  1.858370 [eV]
+  [X] Direct Gap localized at k                     :  7
+
+
+

In addition, we will set the number of bands in BndsRnXp and GbndRnge to a small value, just to have it run fast. Hence, we modify the input file accordingly (check BndsRnXp, GbndRnge, LongDrXp, QPkrange):

+
rim_cut                          # [R] Coulomb potential
+gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+dyson                            # [R] Dyson Equation solver
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+RandQpts=1000000                 # [RIM] Number of random q-points in the BZ
+RandGvec= 100              RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+% CUTBox
+ 0.000000 | 0.000000 | 0.000000 |        # [CUT] [au] Box sides
+%
+CUTRadius= 0.000000              # [CUT] [au] Sphere/Cylinder radius
+CUTCylLen= 0.000000              # [CUT] [au] Cylinder length
+CUTwsGvec= 0.700000              # [CUT] WS cutoff: number of G to be modified
+EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 20 |                         # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 1.000000 | 1.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+% GbndRnge
+   1 | 20 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+7|7|13|14|
+%
+
+
+

We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. Modify it to suit your specific machine.

+
vim run_first_job.sh
+
+
+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=8
+#SBATCH --partition=boost_usr_prod
+#SBATCH --time=0:05:00
+#SBATCH --gres=gpu:2
+#SBATCH --account=EUHPC_TD02_030
+#SBATCH --job-name=first_job
+
+export OMP_NUM_THREADS=8
+export OMP_PLACES=cores
+export OMP_PROC_BIND=close
+
+# load yambo
+module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \
+        yambo -F gw.in -J job_00_first_run -C out_00_first_run
+
+
+

We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after yambo, it is not going to generate an input file, but rather, run the one specified by -F. Now, go ahead an submit this job

+
sbatch run_first_job.sh
+
+
+

The status of the jobs can be monitored via:

+
squeue -u $USER        # to inspect the status of jobs 
+                       # (hint: make a unix alias, if you like)
+scancel <jobid>        # to delete jobs in the queue
+
+
+

The newly generated databases will be stored in the job directory, as specified by -J, while the report, log and output files will be stored in the communications directory (-C). As this is your first yambo run, take a moment to inspect the report and log files, which you can find inside the -C directory. In these report and log files, you can see the steps performed by yambo. For instance, the code calculates the screening at every k-point and stores it in the PPA database called ndb.pp. By opening the report

+
vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa
+
+
+

you will see

+
[07] Dynamic Dielectric Matrix (PPA)
+ ====================================
+
+ [WR./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy:

+
[09.01] G0W0 (W PPA)
+  ====================
+
+  [  GW  ] Bands range     :   1  20
+  [GW/PPA] G damping       :  0.100000 [eV]
+
+
+  QP @ state[ 1 ] K range:   7   7
+  QP @ state[ 1 ] b range:  13  14
+
+  [RD./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Now, inspect the output file

+
vim out_00_first_run/o-job_00_first_run.qp 
+
+
+
# Vxc  =Slater exchange(X)+Perdew & Zunger(C)
+# Vnlxc=Hartree-Fock
+#
+#    K-point            Band               Eo [eV]            E-Eo [eV]          Sc|Eo [eV]
+#
+         7                 13                 0.000000          -0.025774           0.543987
+         7                 14                 1.858370           3.496193          -0.417555
+# 
+
+
+

In this file, Eo is our starting point (DFT) while E-Eo shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we’ll use some simple commands. First, we get everything that is not a # symbol grep -v '#' and we pass that to another command with a “pipe” |. Then, tail -n 1/head -n 1 will retain the first/last line, and awk '{print $3+$4}' will get us the sum of the third and fourth columns. Altogether, this would be as follows

+
grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}'
+-0.025774
+grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}'
+5.35456
+
+
+

These two commands give us the quasiparticle energies we’ve calculated - their difference is the GW-corrected optical gap.

+
+
+
+

GW convergence

+

In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse \(k\)-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a \(6 \times 6 \times 1\) k-point grid and without spin-orbit coupling: the SAVE we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let’s move into the appropriate directory

+
cd ../02_GW_convergence
+
+
+
+

Response function \(\varepsilon^{-1}_{GG'}\) - Bands and G-vectors

+

We are now ready to start our convergence tests. We’ll begin with the variables controlling the polarization function, i.e., NGsBlkXp for the number of G-vectors and BndsRnXp for the number of bands. For this, we will keep GbndRnge constant at a reasonably high value - you can inspect the input i01-GW

+
vim i01-GW
+
+
+

and check that you have:

+
% GbndRnge
+   1 | 80 |                         # [GW] G[W] bands range
+%
+
+
+

Since we need to run yambo for several values of NGsBlkXp and BndsRnXp, it makes sense to use two nested loops. That is exactly what we did in the submission script run01_converge_pol.sh. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs:

+
sbatch run01_converge_pol.sh
+
+
+
+

Monitoring

+

You can monitor that the job is running by the squeue command

+
sbatch squeue -u $USER
+
+
+

and also by checking the files created in your folder

+
ls -ltr
+
+
+
i01-GW_Xp_20_bands_6_Ry
+job_Xp_20_bands_6_Ry
+out_Xp_20_bands_6_Ry
+i01-GW_Xp_20_bands_8_Ry
+out_Xp_20_bands_8_Ry
+job_Xp_20_bands_8_Ry
+i01-GW_Xp_20_bands_10_Ry
+out_Xp_20_bands_10_Ry
+job_Xp_20_bands_10_Ry
+i01-GW_Xp_20_bands_12_Ry
+out_Xp_20_bands_12_Ry
+job_Xp_20_bands_12_Ry
+summary_01_20bands.txt
+i01-GW_Xp_40_bands_6_Ry
+...
+
+
+

Finally you can monitor how runs are proceeding by looking into the log files

+
tail -f out_Xp_*_bands_*/LOG/*_1
+
+
+
==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <15s> P1: [TIMING]                                          io_WF :      1.1353s CPU (34 calls,   0.033 sec avg)
+ <15s> P1: [TIMING]                                    WF_load_FFT :      1.1538s CPU ( 7 calls,   0.165 sec avg)
+ <15s> P1: [TIMING]                                    io_KB_pwscf :      1.1918s CPU ( 6 calls,   0.199 sec avg)
+ <15s> P1: [TIMING]                              DIPOLE_transverse :      2.4771s CPU
+ <15s> P1: [TIMING]                                    io_fragment :      2.6220s CPU (46 calls,   0.057 sec avg)
+ <15s> P1: [TIMING]                                           io_X :      3.1953s CPU (19 calls,   0.168 sec avg)
+ <15s> P1: [TIMING]                                        Dipoles :      4.4012s CPU
+ <15s> P1: [11] Memory Overview
+ <15s> P1: [12] Game Over & Game summary
+ <15s> P1: [TIMING]            [Time-Profile]: 15s
+
+==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <11s> P1: X@q[6] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[6] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%)
+ <11s> P1: [X-CG] R(p) Tot o/o(of R):   153   504   100
+ <11s> P1: Xo@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%)
+ <11s> P1: X@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock
+
+
+
+

Let’s now have look into the job we just submitted.

+
vim run01_converge_pol.sh
+
+
+

First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file i01-GW is used as a template for every calculation in the loops, so we assign it to a variable.

+
file0='i01-GW'
+
+for POL_BANDS in 20 40 60 80; do
+
+echo 'NGsBlkXp [Ry]   E_vale [eV]   E_cond [eV]' > summary_01_${POL_BANDS}bands.txt
+
+for NGsBlkXp_Ry in 6 8 10 12; do
+
+(...)
+
+done
+done
+
+
+

Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the sed command, in order to generate new files in an automated way (sed replaces any matching string with whatever is provided by the loop variable). Next, we run yambo using the labels to specify different job -J and communication -C directories every time. Finally, we get the quasiparticle energies with grep commands as shown before and append a new line to the summary file. So, inside each loop, we have

+
label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry
+jdir=job_${label}
+cdir=out_${label}
+filein=i01-GW_${label}
+
+sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/;
+      /% BndsRnXp/{n;s/.*/  1 |  ${POL_BANDS} |/}" $file0 > $filein
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir
+
+E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'`
+E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'`
+
+echo ${NGsBlkXp_Ry} '        ' ${E_GW_v} '        ' ${E_GW_c}  >> summary_01_${POL_BANDS}bands.txt
+
+
+

Finally, let us plot this data. First, check that the job has finished with

+
squeue -u $USER
+
+
+
[$USER@login01 02_GW_convergence]$ squeue -u $USER
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+[$USER@login01 02_GW_convergence]$ 
+
+
+

and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven’t done so yet, and then plot:

+
module load anaconda3/2023.03
+python plot-01.py
+
+
+

The plot will produce a fig-01.png file. +You can copy and open it in your local machine with something like

+
[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH]
+scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./
+
+
+

You should get:

+
+../../_images/convergence01.png +
+

For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we’ll make a copy of the corresponding input file:

+
cp i01-GW_Xp_80_bands_10_Ry i02-GW
+
+
+
+
+

Self-energy \(\Sigma^c\) - Bands

+

We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., GbndRnge. This step is actually simpler, since it only involves one loop. This is coded in the provided script run02_converge_Gbnds.noBG.sh. You can look into it

+
vim run02_converge_Gbnds.noBG.sh
+
+
+

and go ahead and submit it.

+
sbatch run02_converge_Gbnds.noBG.sh
+
+
+ +

While this runs, check if the previous job has finished, i.e., you should have a complete summary_02_noBG.txt file by now. +For a visual result, proceed to plot them with

+
python plot-02.py
+
+
+

You should get

+
+../../_images/BG_noBG.png +
+ +

We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication (here). MoS\(_2\) was one of the materials studied there, and it shows that our result, obtained with a \(6 \times 6 \times 1\) k-grid, is simply off the chart (blue line).

+
+../../_images/ref-Guandalini.png +
+

Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9

+ +
+
+
+
+

GW parallel strategies

+
+

MPI parallelization

+

For this section, let us enter the 03_GW_parallel directory. If you were in the 02_GW_convegence folder just do

+
cd ../03_GW_parallel
+
+
+

and inspect the input gw.in. You will see that we set low values for most of the convergence parameters except bands:

+
vim gw.in
+
+
+
FFTGvecs= 40       Ry    # [FFT] Plane-waves
+EXXRLvcs= 2        Ry    # [XX] Exchange RL components
+VXCRLvcs= 2        Ry    # [XC] XCpotential RL components
+% BndsRnXp
+    1 |  300 |               # [Xp] Polarization function bands
+%
+NGsBlkXp= 1            Ry    # [Xp] Response block size
+% GbndRnge
+    1 |  300 |               # [GW] G[W] bands range
+%
+%QPkrange                    # [GW] QP generalized Kpoint/Band indices
+  1| 19| 23| 30|
+%
+
+
+

Note that we also added FFTGvecs to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO ecutwfc, i.e. 60 Ry in this case).

+

In addition, we have deleted all the parallel parameters since we will be setting them via the submission script.

+

Actually we are now dealing with a heavier system than before: as you can see from the QPkrange values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized).

+

For this part of the tutorial, we will be using the slurm submission script job_parallel.sh, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code:

+
DIP_CPU= "1 $ngpu 1"          # [PARALLEL] CPUs for each role
+DIP_ROLEs= "k c v"            # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=  0               # [OPENMP/X] Number of threads for dipoles
+X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= "q g k c v"   # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=1    # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=  0                 # [OPENMP/X] Number of threads for response functions
+SE_CPU= "1 $ngpu 1"           # [PARALLEL] CPUs for each role
+SE_ROLEs= "q qp b"            # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=  0                # [OPENMP/GW] Number of threads for self-energy
+
+
+

The keyword DIP refers to the calculations of the screening matrix elements (also called “dipoles”) needed for the screening function, X is the screening function itself (it stands for \(\chi\) since it is a response function), SE the self-energy. +These three sections of the code can be parallelised independently.

+

We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI task is run on a single card, therefore ntasks=ngpu.

+
+

Note

+
    +

  • In this subsection we are mainly concerned with the [PARALLEL] variables which refer to MPI tasks (distributed memory).

    • +

  • What about [OPENMP] parallelisation (i.e., adding threads with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are not run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup for CPUs is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later.

    • +
+
+

We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as:

+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

and submit the job

+
sbatch job_parallel.sh
+
+
+

This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report r-* file and the log l-* files, and inspect them while the calculation runs. +For simplicity you can just type

+
tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1
+
+
+

to monitor the progress in the master thread (Ctrl+c to exit). +As you can see, the run takes some time, even though we are using minimal parameters.

+

Meanwhile, we can run other jobs increasing the parallelisation. Let’s employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the job_parallel.sh script changing

+
#!/bin/bash
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing nodes appropriately. Finally, you can try to produce a scaling plot.

+

The timings are contained in the r-* report files. You can already have a look at them typing

+
grep Time-Profile run_MPI*/r-*
+
+
+

The python script parse_ytiming.py is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided.

+

If you didn’t do so already, load the python module

+
module load anaconda3/2023.03
+
+
+

Then, after your jobs have finished, run the script as

+
python parse_ytiming.py run_MPI
+
+
+

to look for a report file in each run_MPI*.out folder. Make sure you have only one report file per folder. +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis.

+
+../../_images/gw_scaling.png +
+

What can we learn from this plot? In particular, try to answer the following questions:

+
    +

  • Up to which number of MPI tasks our system scales efficiently?

    • +

  • How can we decide at which point adding more nodes to the calculation becomes a waste of resources?

    • +
+
+

Note

+

Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, Yambo has been shown to scale well up to tens of thousands of MPI tasks! (See the next optional box for an example)

+
+ +

.

+ +
+
+
+
+

Full GW band structure

+

This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS\(_2\).

+

This is a massive calculation, so run it right now and we’ll discuss it in the meantime:

+
cd ../04_GW_bands
+sbatch gpu_job.sh
+
+
+

In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling.

+

Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input:

+
vim gw.in
+
+
+
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|37|25|28|
+%
+
+
+

After about 3 minutes the calculation should be over and the results collected in folder GW_bnds. The quasiparticle corrections are stored in human-readable form in the file o-GW_bnds.QP, and in netCDF format in the quasiparticle database ndb.QP.

+

In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with ypp, the yambo pre- and post-processing executable.

+
+

Note

+

We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out here on the Yambo wiki.

+
+

Let us enter a computing node interactively

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

and load the yambo module:

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

We can review the options with ypp -h and generate an input file for band structure interpolation with

+
ypp -s b -F ypp_bands.in
+
+
+

Let us modify the resulting input file by selecting the ‘boltztrap’ approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points \(\Gamma-M-K-\Gamma\). We also set 100 points for each high-symmetry line.

+
electrons                        # [R] Electronic properties
+bnds                             # [R] Bands
+PROJECT_mode= "none"             # Instruct ypp how to project the DOS. ATOM, LINE, PLANE.
+INTERP_mode= "BOLTZ"                # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach)
+INTERP_Shell_Fac= 20.00000       # The bigger it is a higher number of shells is used
+INTERP_NofNN= 1                  # Number of Nearest sites in the NN method
+OutputAlat= 5.90008             # [a.u.] Lattice constant used for "alat" ouput format
+cooIn= "rlu"                     # Points coordinates (in) cc/rlu/iku/alat
+cooOut= "rlu"                    # Points coordinates (out) cc/rlu/iku/alat
+% BANDS_bands
+   25 | 28 |                         # Number of bands
+%
+CIRCUIT_E_DB_path= "none"        # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts)
+BANDS_path= ""                   # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL).
+BANDS_steps= 100                  # Number of divisions
+#BANDS_built_in                # Print the bands of the generating points of the circuit using the nearest internal point
+%BANDS_kpts                      # K points of the bands circuit
+ 0.00000 |0.00000 |0.00000 |
+ 0.00000 |0.50000 |0.00000 |
+ 0.33333 |0.33333 |0.00000 |
+ 0.00000 |0.00000 |0.00000 |
+%
+
+
+

Now, let’s run ypp:

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

This run will produce the file o.bands_interpolated. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn’t tell ypp where to look for the quasiparticle corrections, so it went into the SAVE folder and interpolated the DFT data. +Let’s rename the output:

+
mv o.bands_interpolated o.DFT_bands
+mkdir DFT_bands
+mv o.spin* o.magn* DFT_bands/
+
+
+

In order to interpolate the quasiparticle database, we append its location to the ypp input:

+
vim ypp_bands.in
+
+
+

add this line at the end

+
...
+GfnQPdb= "E < ./GW_bnds/ndb.QP"
+
+
+

and run ypp again.

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

When it’s done, let’s rename the new output as

+
mv o.bands_interpolated o.GW_bands
+mkdir GW_bands
+mv o.spin* o.magn* GW_bands/
+
+
+

Now we are ready to visualize the band structures. In order to do so, you can use the script plt_bands.py that should be already available in the directory.

+

We load the python module

+
module load anaconda3/2023.03
+
+
+

and run the script as

+
python plt_bands.py o.DFT_bands o.GW_bands 4
+
+
+

Now we can also exit the computing node

+
exit
+
+
+

The python script should have produced a GW_bands.png file containing the following visualization, which you can copy and open it in your local machine using scp:

+
+../../_images/gw_bands.png +
+

You may compare this plot with a converged result from this paper (also done with Yambo):

+
+../../_images/gw_bands_ref.png +
+

Dashed lines: DFT, thick lines: GW.

+

As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations!

+

In order to learn more about Yambo, we suggest visiting the Yambo website. For technical information and tutorials, you can check out the Yambo wiki. If you have issues and questions about installing and running the code, you can write about them on the Yambo forum.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/days3+4/day3/index.html b/branch/main/days3+4/day3/index.html new file mode 100644 index 0000000..bcdbd0f --- /dev/null +++ b/branch/main/days3+4/day3/index.html @@ -0,0 +1,220 @@ + + + + + + + Day 3: SIESTA I — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Day 3: SIESTA I

+
+

SIESTA basics

+

Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge).

+

Slides available here: SIESTA-Intro.pdf.

+
+
+

A first contact with SIESTA: inputs, execution and outputs

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-First_encounter.pdf.

+
+
+

Basis sets

+

Lecture by Dr. Miguel Pruneda (CINN-CSIC).

+

Slides available here: SIESTA-Basis_sets.pdf.

+
+
+

Basis set optimization

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets
+
+
+

Introductory slides available here: SIESTA-Basis_set_optimization.pdf.

+
+
+

Convergence (k points, mesh, mixing)

+

Practical session led by Dr. Catalina Coll (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-Convergence.pdf.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/days3+4/day4/index.html b/branch/main/days3+4/day4/index.html new file mode 100644 index 0000000..9174f14 --- /dev/null +++ b/branch/main/days3+4/day4/index.html @@ -0,0 +1,199 @@ + + + + + + + Day 4: SIESTA II — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Day 4: SIESTA II

+
+

Molecular Dynamics with SIESTA

+

Practical session led by Dr. Ernane de Freitas (ICN2).

+

Tutorials covered:

+
    +

  • Molecular Dynamics. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-MD.pdf.

+
+
+

Analysis tools

+

Practical session led by Dr. Miguel Pruneda (CINN-CSIC).

+

Tutorials covered:

+
    +

  • Analysis tools. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-Analysis_tools.pdf.

+
+
+

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

+

Lecture by Dr. Nick Papior (Technical University of Denmark).

+

Slides available here: SIESTA-Features.pdf.

+
+
+

Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Practical session led by Dr. Alberto García (ICMAB-CSIC).

+

Tutorials covered:

+
    +

  • ELSI-ELPA.

    • +

  • ELSI-PEXSI.

    • +
+

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers
+
+
+

Slides available here: SIESTA-Solvers.pdf.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/days3+4/setup/index.html b/branch/main/days3+4/setup/index.html new file mode 100644 index 0000000..31ed90a --- /dev/null +++ b/branch/main/days3+4/setup/index.html @@ -0,0 +1,205 @@ + + + + + + + SIESTA setup — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

SIESTA setup

+
+

Directory with tutorials

+

For every practical there is a folder in the shared directory +/leonardo_work/EUHPC_TD02_030/siesta-tutorials that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:

+
$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I .
+
+
+

Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts.

+
+
+

Running SIESTA

+

You will find a sample script on how to run SIESTA in +/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh:

+
#!/bin/bash
+#SBATCH -J tutorialXX
+#SBATCH -n 8
+#SBATCH -t 0:30:00
+#SBATCH -o %x-%j.out
+#SBATCH -e %x-%j.err
+#SBATCH --partition=boost_usr_prod
+#SBATCH -D .
+
+# DO NOT CHANGE THIS LINE
+source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh
+
+# EDIT THE CORRECT INPUT AND OUTPUT FILES.
+srun -n 8 siesta < input.fdf > output.out
+
+
+

Note that input.fdf and output.out are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(#SBATCH -J option) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue.

+
+
+

Suggested Software for Visualization

+

If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences.

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/genindex/index.html b/branch/main/genindex/index.html new file mode 100644 index 0000000..65a060c --- /dev/null +++ b/branch/main/genindex/index.html @@ -0,0 +1,146 @@ + + + + + + Index — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright 2024, The contributors.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/guide/index.html b/branch/main/guide/index.html new file mode 100644 index 0000000..00ba9f1 --- /dev/null +++ b/branch/main/guide/index.html @@ -0,0 +1,177 @@ + + + + + + + Instructor’s guide — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor’s guide

+
+

Why we teach this lesson

+
+
+

Intended learning outcomes

+
+
+

Timing

+
+
+

Preparing exercises

+

e.g. what to do the day before to set up common repositories.

+
+
+

Other practical aspects

+
+
+

Interesting questions you might get

+
+
+

Typical pitfalls

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/index.html b/branch/main/index.html new file mode 100644 index 0000000..d059540 --- /dev/null +++ b/branch/main/index.html @@ -0,0 +1,505 @@ + + + + + + + Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo

+

In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential.

+

This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises.

+

QUANTUM ESPRESSO is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications.

+

SIESTA is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a “good first approximation” to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA.

+

YAMBO is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc).

+

MAX (MAterials design at the eXascale) is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX’s challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials’ domain.

+
+

Prerequisites

+
    +

  • Some familiarity with density functional theory (DFT), self-consistent +field (SCF) calculations and plane wave basis sets is desirable as the +workshop will not cover the fundamental theory of these topics.

    • +

  • Familiarity with working in a Linux environment and some experience with +working on an HPC system is needed to participate in the hands-on exercises.

    • +
+
+
+

Who is the course for?

+

This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations.

+
+
+
+
+
+

Days 3 and 4 - Siesta

+ +
+
+

Day 5 - Yambo

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+
+

About the course

+

In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties.

+

Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers.

+
+

Schedule

+

Day 1, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:15

Welcome and introduction to ENCCS

09:15-09:30

Introduction to Max-CoE and MaX flagship codes

09:30-10:00

Overview of the QE suite of codes and main features

10:00-10:25

Coffee break

10:25-13:00

PWSCF for HPC and GPU

+

Day 2, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

Introduction to Density Functional Perturbation Theory

09:45-10:15

Introduction to Time Dependent Density Functional Perturbation Theory

10:15-10:30

Coffee break

10:30-13:00

Phonons and time dependent properties on HPC and GPU

+

Day 3, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

SIESTA basics

09:45-10:30

Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs

10:30-10:45

Break

10:45-11:15

Basis sets

11:15-12:00

Hands-on tutorial: Basis set optimization

12:00-13:00

Hands-on tutorial: Convergence (k points, mesh, mixing)

+

Day 4, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-10:00

Hands-on tutorial: Moving atoms: geometry optimisation and beyond

10:30-11:00

Hands-on tutorial: Analysis tools

11:00-11:15

Break

11:15-11:45

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

11:45-13:00

Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Day 5, Yambo

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:20

Overview of the Yambo code and its main features and performance

09:20-10:00

Introduction to the GW approximation

10:00-10:20

Coffee break

10:20-13:00

Hands-on tutorial: A guided tour through GW simulations

+
+
+
+

See also

+ +
+\[\]
+
+
+

Credits

+

Contributors to this workshop:

+
    +

  • Pietro Davide Delugas (SISSA)

    • +

  • Ivan Carnimeo (SISSA)

    • +

  • Oscar Baseggio (SISSA)

    • +

  • Fabrizio Ferrari Ruffino (CNR-IOM)

    • +

  • Paolo Giannozzi (CNR-IOM, UniUD)

    • +

  • Iurii Timrov (Paul Scherrer Institut)

    • +

  • Laura Bellentani (CINECA)

    • +

  • Tommaso Gorni (CINECA)

    • +

  • Aurora Ponzi (CNR-IOM)

    • +

  • Emilio Artacho (CIC NanoGUNE and University of Cambridge)

    • +

  • Catalina Coll (ICN2)

    • +

  • José Mª Escartín (ICN2)

    • +

  • Roberta Farris (ICN2)

    • +

  • Ernane de Freitas (ICN2)

    • +

  • Alberto García (ICMAB-CSIC)

    • +

  • Arnold Kole (Utrecht University)

    • +

  • Nick Papior (DTU)

    • +

  • Federico Pedron (ICN2)

    • +

  • Miguel Pruneda (CINN-CSIC)

    • +

  • José Ángel Silva Guillén (IMDEA Nanociencia)

    • +
    • +

    1. Varsano (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Ferretti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sangalli (CNR-ISM)

      2. +
    +
    • +
    • +

    1. Guandalini (Univ. of Rome, La Sapienza)

      2. +
    +
    • +
    • +

    1. Paleari (CNR-NANO)

      2. +
    +
    • +
    • +

    1. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sesti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Spallanzani (CNR-NANO)

      2. +
    +
    • +
+

The lesson file structure and browsing layout is inspired by and derived from +work by CodeRefinery licensed under the MIT license. We have copied and adapted +most of their license text.

+
+
+

Licenses

+
+

General

+
+

Instructional Material

+

Except where otherwise noted, +this instructional material is made available under the +Creative Commons Attribution license (CC-BY-4.0). +The following is a human-readable summary of (and not a substitute for) the +full legal text of the CC-BY-4.0 license. +You are free to:

+
    +

  • share - copy and redistribute the material in any medium or format

    • +

  • adapt - remix, transform, and build upon the material for any purpose, +even commercially.

    • +
+

The licensor cannot revoke these freedoms as long as you follow these license terms:

+
    +

  • Attribution - You must give appropriate credit (mentioning that your work +is derived from work that is Copyright (c) ENCCS and individual contributors and, where practical, linking +to https://enccs.github.io/max-coe-workshop), provide a link to the license, and indicate if changes were +made. You may do so in any reasonable manner, but not in any way that suggests +the licensor endorses you or your use.

    • +

  • No additional restrictions - You may not apply legal terms or +technological measures that legally restrict others from doing anything the +license permits.

    • +
+

With the understanding that:

+
    +

  • You do not have to comply with the license for elements of the material in +the public domain or where your use is permitted by an applicable exception +or limitation.

    • +

  • No warranties are given. The license may not give you all of the permissions +necessary for your intended use. For example, other rights such as +publicity, privacy, or moral rights may limit how you use the material.

    • +
+
+
+

Software

+

Except where otherwise noted, the example programs and other software provided +with this repository are made available under the OSI-approved +MIT license.

+
+
+
+

SIESTA

+

At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/branch/main/lesson.pdf b/branch/main/lesson.pdf new file mode 100644 index 0000000..4ad4322 Binary files /dev/null and b/branch/main/lesson.pdf differ diff --git a/branch/main/objects.inv b/branch/main/objects.inv new file mode 100644 index 0000000..21a735b Binary files /dev/null and b/branch/main/objects.inv differ diff --git a/branch/main/quick-reference/index.html b/branch/main/quick-reference/index.html new file mode 100644 index 0000000..6a25b17 --- /dev/null +++ b/branch/main/quick-reference/index.html @@ -0,0 +1,148 @@ + + + + + + + Quick Reference — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Quick Reference

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+ + + + \ No newline at end of file diff --git a/branch/main/search/index.html b/branch/main/search/index.html new file mode 100644 index 0000000..e84604e --- /dev/null +++ b/branch/main/search/index.html @@ -0,0 +1,160 @@ + + + + + + Search — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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© Copyright 2024, The contributors.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+ + + + + + + + + \ No newline at end of file diff --git a/branch/main/searchindex.js b/branch/main/searchindex.js new file mode 100644 index 0000000..863fafc --- /dev/null +++ b/branch/main/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["day5/yambo-tutorial", "days3+4/day3", "days3+4/day4", "days3+4/setup", "guide", "index", "quick-reference"], "filenames": ["day5/yambo-tutorial.md", "days3+4/day3.rst", "days3+4/day4.rst", "days3+4/setup.rst", "guide.rst", "index.rst", "quick-reference.rst"], "titles": ["Yambo tutorial: Quasiparticles in the GW approximation", "Day 3: SIESTA I", "Day 4: SIESTA II", "SIESTA setup", "Instructor\u2019s guide", "Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo", "Quick Reference"], "terms": {"In": [0, 5], "thi": [0, 3, 5], "you": [0, 3, 5], "learn": [0, 5], "how": [0, 3, 5], "simul": [0, 5], "hpc": 0, "machin": 0, "comput": [0, 5], "free": [0, 5], "stand": 0, "singl": 0, "layer": 0, "mo": 0, "_2": 0, "while": [0, 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+ margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body blockquote { + -moz-hyphens: auto; + -ms-hyphens: auto; + -webkit-hyphens: auto; + hyphens: auto; +} + +a.headerlink { + visibility: hidden; +} + +a:visited { + color: #551A8B; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink, +caption:hover > a.headerlink, +p.caption:hover > a.headerlink, +div.code-block-caption:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, figure.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, figure.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, figure.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-default, figure.align-default, .figure.align-default { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-default { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar, +aside.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px; + background-color: #ffe; + width: 40%; + float: right; + clear: right; + overflow-x: auto; +} + +p.sidebar-title { + font-weight: bold; +} + +nav.contents, +aside.topic, +div.admonition, div.topic, blockquote { + clear: left; +} + +/* -- topics ---------------------------------------------------------------- */ + +nav.contents, +aside.topic, +div.topic { + border: 1px solid #ccc; + padding: 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- content of sidebars/topics/admonitions -------------------------------- */ + +div.sidebar > :last-child, +aside.sidebar > :last-child, +nav.contents > :last-child, +aside.topic > :last-child, +div.topic > :last-child, +div.admonition > :last-child { + margin-bottom: 0; +} + +div.sidebar::after, +aside.sidebar::after, +nav.contents::after, +aside.topic::after, +div.topic::after, +div.admonition::after, +blockquote::after { + display: block; + content: ''; + clear: both; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + margin-top: 10px; + margin-bottom: 10px; + border: 0; + border-collapse: collapse; +} + +table.align-center { + margin-left: auto; + margin-right: auto; +} + +table.align-default { + margin-left: auto; + margin-right: auto; +} + +table caption span.caption-number { + font-style: italic; +} + +table caption span.caption-text { +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + border-left: 0; + border-right: 0; + border-bottom: 1px solid #aaa; +} + +th { + text-align: left; + padding-right: 5px; +} + +table.citation { + border-left: solid 1px gray; + margin-left: 1px; +} + +table.citation td { + border-bottom: none; +} + +th > :first-child, +td > :first-child { + margin-top: 0px; +} + +th > :last-child, +td > :last-child { + margin-bottom: 0px; +} + +/* -- figures --------------------------------------------------------------- */ + +div.figure, figure { + margin: 0.5em; + padding: 0.5em; +} + +div.figure p.caption, figcaption { + padding: 0.3em; +} + +div.figure p.caption span.caption-number, +figcaption span.caption-number { + font-style: italic; +} + +div.figure p.caption span.caption-text, +figcaption span.caption-text { +} + +/* -- field list styles ----------------------------------------------------- */ + +table.field-list td, table.field-list th { + border: 0 !important; +} + +.field-list ul { + margin: 0; + padding-left: 1em; +} + +.field-list p { + margin: 0; +} + +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +/* -- hlist styles ---------------------------------------------------------- */ + +table.hlist { + margin: 1em 0; +} + +table.hlist td { + vertical-align: top; +} + +/* -- object description styles --------------------------------------------- */ + +.sig { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; +} + +.sig-name, code.descname { + background-color: transparent; + font-weight: bold; +} + +.sig-name { + font-size: 1.1em; +} + +code.descname { + font-size: 1.2em; +} + +.sig-prename, code.descclassname { + background-color: transparent; +} + +.optional { + font-size: 1.3em; +} + +.sig-paren { + font-size: larger; +} + +.sig-param.n { + font-style: italic; +} + +/* C++ specific styling */ + +.sig-inline.c-texpr, +.sig-inline.cpp-texpr { + font-family: unset; +} + +.sig.c .k, .sig.c .kt, +.sig.cpp .k, .sig.cpp .kt { + color: #0033B3; +} + +.sig.c .m, +.sig.cpp .m { + color: #1750EB; +} + +.sig.c .s, .sig.c .sc, +.sig.cpp .s, .sig.cpp .sc { + color: #067D17; +} + + +/* -- other body styles ----------------------------------------------------- */ + +ol.arabic { + list-style: decimal; +} + +ol.loweralpha { + list-style: lower-alpha; +} + +ol.upperalpha { + list-style: upper-alpha; +} + +ol.lowerroman { + list-style: lower-roman; +} + +ol.upperroman { + list-style: upper-roman; +} + +:not(li) > ol > li:first-child > :first-child, +:not(li) > ul > li:first-child > :first-child { + margin-top: 0px; +} + +:not(li) > ol > li:last-child > :last-child, +:not(li) > ul > li:last-child > :last-child { + margin-bottom: 0px; +} + +ol.simple ol p, +ol.simple ul p, +ul.simple ol p, +ul.simple ul p { + margin-top: 0; +} + +ol.simple > li:not(:first-child) > p, +ul.simple > li:not(:first-child) > p { + margin-top: 0; +} + +ol.simple p, +ul.simple p { + margin-bottom: 0; +} + +aside.footnote > span, +div.citation > span { + float: left; +} +aside.footnote > span:last-of-type, +div.citation > span:last-of-type { + padding-right: 0.5em; +} +aside.footnote > p { + margin-left: 2em; +} +div.citation > p { + margin-left: 4em; +} +aside.footnote > p:last-of-type, +div.citation > p:last-of-type { + margin-bottom: 0em; +} +aside.footnote > p:last-of-type:after, +div.citation > p:last-of-type:after { + content: ""; + clear: both; +} + +dl.field-list { + display: grid; + grid-template-columns: fit-content(30%) auto; +} + +dl.field-list > dt { + font-weight: bold; + word-break: break-word; + padding-left: 0.5em; + padding-right: 5px; +} + +dl.field-list > dd { + padding-left: 0.5em; + margin-top: 0em; + margin-left: 0em; + margin-bottom: 0em; +} + +dl { + margin-bottom: 15px; +} + +dd > :first-child { + margin-top: 0px; +} + +dd ul, dd table { + margin-bottom: 10px; +} + +dd { + margin-top: 3px; + margin-bottom: 10px; + margin-left: 30px; +} + +.sig dd { + margin-top: 0px; + margin-bottom: 0px; +} + +.sig dl { + margin-top: 0px; + margin-bottom: 0px; +} + +dl > dd:last-child, +dl > dd:last-child > :last-child { + margin-bottom: 0; +} + +dt:target, span.highlighted { + background-color: #fbe54e; +} + +rect.highlighted { + fill: #fbe54e; +} + +dl.glossary dt { + font-weight: bold; + font-size: 1.1em; +} + +.versionmodified { + font-style: italic; +} + +.system-message { + background-color: #fda; + padding: 5px; + border: 3px solid red; +} + +.footnote:target { + background-color: #ffa; +} + +.line-block { + display: block; + margin-top: 1em; + margin-bottom: 1em; +} + +.line-block .line-block { + margin-top: 0; + margin-bottom: 0; + margin-left: 1.5em; +} + +.guilabel, .menuselection { + font-family: sans-serif; +} + +.accelerator { + text-decoration: underline; +} + +.classifier { + font-style: oblique; +} + +.classifier:before { + font-style: normal; + margin: 0 0.5em; + content: ":"; + display: inline-block; +} + +abbr, acronym { + border-bottom: dotted 1px; + cursor: help; +} + +.translated { + background-color: rgba(207, 255, 207, 0.2) +} + +.untranslated { + background-color: rgba(255, 207, 207, 0.2) +} + +/* -- code displays --------------------------------------------------------- */ + +pre { + overflow: auto; + overflow-y: hidden; /* fixes display issues on Chrome browsers */ +} + +pre, div[class*="highlight-"] { + clear: both; +} + +span.pre { + -moz-hyphens: none; + -ms-hyphens: none; + -webkit-hyphens: none; + hyphens: none; + white-space: nowrap; +} + +div[class*="highlight-"] { + margin: 1em 0; +} + +td.linenos pre { + border: 0; + background-color: transparent; + color: #aaa; +} + +table.highlighttable { + display: block; +} + +table.highlighttable tbody { + display: block; +} + +table.highlighttable tr { + display: flex; +} + +table.highlighttable td { + margin: 0; + padding: 0; +} + +table.highlighttable td.linenos { + padding-right: 0.5em; +} + +table.highlighttable td.code { + flex: 1; + overflow: hidden; +} + +.highlight .hll { + display: block; +} + +div.highlight pre, +table.highlighttable pre { + margin: 0; +} + +div.code-block-caption + div { + margin-top: 0; +} + +div.code-block-caption { + margin-top: 1em; + padding: 2px 5px; + font-size: small; +} + +div.code-block-caption code { + background-color: transparent; +} + +table.highlighttable td.linenos, +span.linenos, +div.highlight span.gp { /* gp: Generic.Prompt */ + user-select: none; + -webkit-user-select: text; /* Safari fallback only */ + -webkit-user-select: none; /* Chrome/Safari */ + -moz-user-select: none; /* Firefox */ + -ms-user-select: none; /* IE10+ */ +} + +div.code-block-caption span.caption-number { + padding: 0.1em 0.3em; + font-style: italic; +} + +div.code-block-caption span.caption-text { +} + +div.literal-block-wrapper { + margin: 1em 0; +} + +code.xref, a code { + background-color: transparent; + font-weight: bold; +} + +h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { + background-color: transparent; +} + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + font-family: sans-serif; +} + +div.viewcode-block:target { + margin: -1px -10px; + padding: 0 10px; +} + +/* -- math display ---------------------------------------------------------- */ + +img.math { + vertical-align: middle; +} + +div.body div.math p { + text-align: center; +} + +span.eqno { + float: right; +} + +span.eqno a.headerlink { + position: absolute; + z-index: 1; +} + +div.math:hover a.headerlink { + visibility: visible; +} + +/* -- printout stylesheet --------------------------------------------------- */ + +@media print { + div.document, + div.documentwrapper, + div.bodywrapper { + margin: 0 !important; + width: 100%; + } + + div.sphinxsidebar, + div.related, + div.footer, + #top-link { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/check-solid.svg b/branch/main/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/branch/main/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/branch/main/singlehtml/_static/clipboard.min.js b/branch/main/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/branch/main/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/branch/main/singlehtml/_static/copybutton.css b/branch/main/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..f1916ec --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/branch/main/singlehtml/_static/copybutton.js b/branch/main/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..2ea7ff3 --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/branch/main/singlehtml/_static/copybutton_funcs.js b/branch/main/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/branch/main/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); + var top = secProperties['top']; + var height = secProperties['height'] + var win_height = window.innerHeight; + //console.info(top, height, win_height) + + var scroll_to = 0; + if (height >= win_height || height == 0) { + scroll_to = top; + } else { + scroll_to = top - (win_height-height)/3.; + } + //console.info(top, height, win_height, scroll_to) + + $('html, body').animate({ + scrollTop: scroll_to //+ 'px' + }, 'fast'); + +} + + +function minipres() { + /* Enable the minipres mode: + - call the hide() function + - set up the scrolling listener + */ + document.addEventListener('keydown', function (event) { + switch(event.which) { + case 37: // left + switch_slide(-1); + event.preventDefault(); + return false; + break; + //case 38: // up + case 39: // right + switch_slide(+1); + event.preventDefault(); + return false; + break; + //case 40: // down + default: + return; // exit this handler for other keys + } + }, true) + + hide() + + // Increase space between sections + //$("div .section").css('margin-bottom', '50%'); + $(sectionSelector).css('margin-top', '50%'); + + // Reduce size/color of other sections + if (hiddenSectionSelector.length > 0) { + var hideNodes = $(hiddenSectionSelector); + console.log(typeof hideNodes, hideNodes); + for (node in hideNodes) { + console.log("a", typeof node, node); + node = hideNodes[node]; // what's right way to iterate values? + console.log("b", typeof node, node); + if (node.parentNode && node.parentNode.className == "section") { + node = node.parentNode; + console.log("c", typeof node, node); + //node.css['transform'] = 'scale(.5)'; + //node.css['transform-origin'] = 'top center'; + $(node).css('color', 'lightgrey'); + //$(node).css('font-size', '20%'); + //$(node).css('visibility', 'collapse'); + //ntahousnatouhasno; + } + } + } +} + +function hide() { + /* Hide all non-essential elements on the page + */ + + // This is for sphinx_rst_theme and readthedocs + $(".wy-nav-side").remove(); + $(".wy-nav-content-wrap").css('margin-left', 0); + $('.rst-versions').remove(); // readthedocs version selector + + // Add other formats here. +} + + +var slideshow = minipres; + +if (window.location.search.match(/[?&](minipres|slideshow|pres)([=&]|$)/) ) { + //minipres() + window.addEventListener("load", minipres); +} else if (window.location.search.match(/[?&](plain)([=&]|$)/) ) { + window.addEventListener("load", hide); +} diff --git a/branch/main/singlehtml/_static/minus.png b/branch/main/singlehtml/_static/minus.png new file mode 100644 index 0000000..d96755f Binary files /dev/null and b/branch/main/singlehtml/_static/minus.png differ diff --git a/branch/main/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css b/branch/main/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css new file mode 100644 index 0000000..3356631 --- /dev/null +++ b/branch/main/singlehtml/_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css @@ -0,0 +1,2342 @@ +/* Variables */ +:root { + --mystnb-source-bg-color: #f7f7f7; + --mystnb-stdout-bg-color: #fcfcfc; + --mystnb-stderr-bg-color: #fdd; + --mystnb-traceback-bg-color: #fcfcfc; + --mystnb-source-border-color: #ccc; + --mystnb-source-margin-color: green; + --mystnb-stdout-border-color: #f7f7f7; + --mystnb-stderr-border-color: #f7f7f7; + --mystnb-traceback-border-color: #ffd6d6; + --mystnb-hide-prompt-opacity: 70%; + --mystnb-source-border-radius: .4em; + --mystnb-source-border-width: 1px; +} + +/* Whole cell */ +div.container.cell { + padding-left: 0; + margin-bottom: 1em; +} + +/* Removing all background formatting so we can control at the div level */ +.cell_input div.highlight, +.cell_output pre, +.cell_input pre, +.cell_output .output { + border: none; + box-shadow: none; +} + +.cell_output .output pre, +.cell_input pre { + margin: 0px; +} + +/* Input cells */ +div.cell div.cell_input, +div.cell details.above-input>summary { + padding-left: 0em; + padding-right: 0em; + border: var(--mystnb-source-border-width) var(--mystnb-source-border-color) solid; 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Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for translated ANSI escape sequences +Color values are copied from Jupyter Notebook +https://github.com/jupyter/notebook/blob/52581f8eda9b319eb0390ac77fe5903c38f81e3e/notebook/static/notebook/less/ansicolors.less#L14-L21 +Background colors from +https://nbsphinx.readthedocs.io/en/latest/code-cells.html#ANSI-Colors +*/ +div.highlight .-Color-Bold { + font-weight: bold; +} + +div.highlight .-Color[class*=-Black] { + color: #3E424D +} + +div.highlight .-Color[class*=-Red] { + color: #E75C58 +} + +div.highlight .-Color[class*=-Green] { + color: #00A250 +} + +div.highlight .-Color[class*=-Yellow] { + color: #DDB62B +} + +div.highlight .-Color[class*=-Blue] { + color: #208FFB +} + +div.highlight .-Color[class*=-Magenta] { + color: #D160C4 +} + +div.highlight .-Color[class*=-Cyan] { + color: #60C6C8 +} + +div.highlight .-Color[class*=-White] { + color: #C5C1B4 +} + +div.highlight .-Color[class*=-BGBlack] { + background-color: #3E424D +} + +div.highlight .-Color[class*=-BGRed] { + background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight .-Color[class*=-C145] { + color: #AFAFAF +} + +div.highlight .-Color[class*=-BGC145] { + background-color: #AFAFAF +} + +div.highlight .-Color[class*=-C146] { + color: #AFAFD7 +} + +div.highlight .-Color[class*=-BGC146] { + background-color: #AFAFD7 +} + +div.highlight .-Color[class*=-C147] { + color: #AFAFFF +} + +div.highlight .-Color[class*=-BGC147] { + background-color: #AFAFFF +} + +div.highlight .-Color[class*=-C148] { + color: #AFD700 +} + +div.highlight .-Color[class*=-BGC148] { + background-color: #AFD700 +} + +div.highlight .-Color[class*=-C149] { + color: #AFD75F +} + +div.highlight .-Color[class*=-BGC149] { + background-color: #AFD75F +} + +div.highlight .-Color[class*=-C150] { + color: #AFD787 +} + +div.highlight .-Color[class*=-BGC150] { + background-color: #AFD787 +} + +div.highlight .-Color[class*=-C151] { + color: #AFD7AF +} + +div.highlight .-Color[class*=-BGC151] { + background-color: #AFD7AF +} + +div.highlight .-Color[class*=-C152] { + color: #AFD7D7 +} + +div.highlight .-Color[class*=-BGC152] { + background-color: #AFD7D7 +} + +div.highlight .-Color[class*=-C153] { + color: #AFD7FF +} + +div.highlight .-Color[class*=-BGC153] { + background-color: #AFD7FF +} + +div.highlight .-Color[class*=-C154] { + color: #AFFF00 +} + +div.highlight .-Color[class*=-BGC154] { + background-color: #AFFF00 +} + +div.highlight .-Color[class*=-C155] { + color: #AFFF5F +} + +div.highlight .-Color[class*=-BGC155] { + background-color: #AFFF5F +} + +div.highlight .-Color[class*=-C156] { + color: #AFFF87 +} + +div.highlight .-Color[class*=-BGC156] { + background-color: #AFFF87 +} + +div.highlight .-Color[class*=-C157] { + color: #AFFFAF +} + +div.highlight .-Color[class*=-BGC157] { + background-color: #AFFFAF +} + +div.highlight .-Color[class*=-C158] { + color: #AFFFD7 +} + +div.highlight .-Color[class*=-BGC158] { + background-color: #AFFFD7 +} + +div.highlight .-Color[class*=-C159] { + color: #AFFFFF +} + +div.highlight .-Color[class*=-BGC159] { + background-color: #AFFFFF +} + +div.highlight .-Color[class*=-C160] { + color: #D70000 +} + +div.highlight .-Color[class*=-BGC160] { + background-color: #D70000 +} + +div.highlight .-Color[class*=-C161] { + color: #D7005F +} + +div.highlight .-Color[class*=-BGC161] { + background-color: #D7005F +} + +div.highlight .-Color[class*=-C162] { + color: #D70087 +} + +div.highlight .-Color[class*=-BGC162] { + background-color: #D70087 +} + +div.highlight .-Color[class*=-C163] { + color: #D700AF +} + +div.highlight .-Color[class*=-BGC163] { + background-color: #D700AF +} + +div.highlight .-Color[class*=-C164] { + color: #D700D7 +} + +div.highlight .-Color[class*=-BGC164] { + background-color: #D700D7 +} + +div.highlight .-Color[class*=-C165] { + color: #D700FF +} + +div.highlight .-Color[class*=-BGC165] { + background-color: #D700FF +} + +div.highlight .-Color[class*=-C166] { + color: #D75F00 +} + +div.highlight .-Color[class*=-BGC166] { + background-color: #D75F00 +} + +div.highlight .-Color[class*=-C167] { + color: #D75F5F +} + +div.highlight .-Color[class*=-BGC167] { + background-color: #D75F5F +} + +div.highlight .-Color[class*=-C168] { + color: #D75F87 +} + +div.highlight .-Color[class*=-BGC168] { + background-color: #D75F87 +} + +div.highlight .-Color[class*=-C169] { + color: #D75FAF +} + +div.highlight .-Color[class*=-BGC169] { + background-color: #D75FAF +} + +div.highlight .-Color[class*=-C170] { + color: #D75FD7 +} + +div.highlight .-Color[class*=-BGC170] { + background-color: #D75FD7 +} + +div.highlight .-Color[class*=-C171] { + color: #D75FFF +} + +div.highlight .-Color[class*=-BGC171] { + background-color: #D75FFF +} + +div.highlight .-Color[class*=-C172] { + color: #D78700 +} + +div.highlight .-Color[class*=-BGC172] { + background-color: #D78700 +} + +div.highlight .-Color[class*=-C173] { + color: #D7875F +} + +div.highlight .-Color[class*=-BGC173] { + background-color: #D7875F +} + +div.highlight .-Color[class*=-C174] { + color: #D78787 +} + +div.highlight .-Color[class*=-BGC174] { + background-color: #D78787 +} + +div.highlight .-Color[class*=-C175] { + color: #D787AF +} + +div.highlight .-Color[class*=-BGC175] { + background-color: #D787AF +} + +div.highlight .-Color[class*=-C176] { + color: #D787D7 +} + +div.highlight .-Color[class*=-BGC176] { + background-color: #D787D7 +} + +div.highlight .-Color[class*=-C177] { + color: #D787FF +} + +div.highlight .-Color[class*=-BGC177] { + background-color: #D787FF +} + +div.highlight .-Color[class*=-C178] { + color: #D7AF00 +} + +div.highlight .-Color[class*=-BGC178] { + background-color: #D7AF00 +} + +div.highlight .-Color[class*=-C179] { + color: #D7AF5F +} + +div.highlight .-Color[class*=-BGC179] { + background-color: #D7AF5F +} + +div.highlight .-Color[class*=-C180] { + color: #D7AF87 +} + +div.highlight .-Color[class*=-BGC180] { + background-color: #D7AF87 +} + +div.highlight .-Color[class*=-C181] { + color: #D7AFAF +} + +div.highlight .-Color[class*=-BGC181] { + background-color: #D7AFAF +} + +div.highlight .-Color[class*=-C182] { + color: #D7AFD7 +} + +div.highlight .-Color[class*=-BGC182] { + background-color: #D7AFD7 +} + +div.highlight .-Color[class*=-C183] { + color: #D7AFFF +} + +div.highlight .-Color[class*=-BGC183] { + background-color: #D7AFFF +} + +div.highlight .-Color[class*=-C184] { + color: #D7D700 +} + +div.highlight .-Color[class*=-BGC184] { + background-color: #D7D700 +} + +div.highlight .-Color[class*=-C185] { + color: #D7D75F +} + +div.highlight .-Color[class*=-BGC185] { + background-color: #D7D75F +} + +div.highlight .-Color[class*=-C186] { + color: #D7D787 +} + +div.highlight .-Color[class*=-BGC186] { + background-color: #D7D787 +} + +div.highlight .-Color[class*=-C187] { + color: #D7D7AF +} + +div.highlight .-Color[class*=-BGC187] { + background-color: #D7D7AF +} + +div.highlight .-Color[class*=-C188] { + color: #D7D7D7 +} + +div.highlight .-Color[class*=-BGC188] { + background-color: #D7D7D7 +} + +div.highlight .-Color[class*=-C189] { + color: #D7D7FF +} + +div.highlight .-Color[class*=-BGC189] { + background-color: #D7D7FF +} + +div.highlight .-Color[class*=-C190] { + color: #D7FF00 +} + +div.highlight .-Color[class*=-BGC190] { + background-color: #D7FF00 +} + +div.highlight .-Color[class*=-C191] { + color: #D7FF5F +} + +div.highlight .-Color[class*=-BGC191] { + background-color: #D7FF5F +} + +div.highlight .-Color[class*=-C192] { + color: #D7FF87 +} + +div.highlight .-Color[class*=-BGC192] { + background-color: #D7FF87 +} + +div.highlight .-Color[class*=-C193] { + color: #D7FFAF +} + +div.highlight .-Color[class*=-BGC193] { + background-color: #D7FFAF +} + +div.highlight .-Color[class*=-C194] { + color: #D7FFD7 +} + +div.highlight .-Color[class*=-BGC194] { + background-color: #D7FFD7 +} + +div.highlight .-Color[class*=-C195] { + color: #D7FFFF +} + +div.highlight .-Color[class*=-BGC195] { + background-color: #D7FFFF +} + +div.highlight .-Color[class*=-C196] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC196] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C197] { + color: #FF005F +} + +div.highlight .-Color[class*=-BGC197] { + background-color: #FF005F +} + +div.highlight .-Color[class*=-C198] { + color: #FF0087 +} + +div.highlight .-Color[class*=-BGC198] { + background-color: #FF0087 +} + +div.highlight .-Color[class*=-C199] { + color: #FF00AF +} + +div.highlight .-Color[class*=-BGC199] { + background-color: #FF00AF +} + +div.highlight .-Color[class*=-C200] { + color: #FF00D7 +} + +div.highlight .-Color[class*=-BGC200] { + background-color: #FF00D7 +} + +div.highlight .-Color[class*=-C201] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC201] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C202] { + color: #FF5F00 +} + +div.highlight .-Color[class*=-BGC202] { + background-color: #FF5F00 +} + +div.highlight .-Color[class*=-C203] { + color: #FF5F5F +} + +div.highlight .-Color[class*=-BGC203] { + background-color: #FF5F5F +} + +div.highlight .-Color[class*=-C204] { + color: #FF5F87 +} + +div.highlight .-Color[class*=-BGC204] { + background-color: #FF5F87 +} + +div.highlight .-Color[class*=-C205] { + color: #FF5FAF +} + +div.highlight .-Color[class*=-BGC205] { + background-color: #FF5FAF +} + +div.highlight .-Color[class*=-C206] { + color: #FF5FD7 +} + +div.highlight .-Color[class*=-BGC206] { + background-color: #FF5FD7 +} + +div.highlight .-Color[class*=-C207] { + color: #FF5FFF +} + +div.highlight .-Color[class*=-BGC207] { + background-color: #FF5FFF +} + +div.highlight .-Color[class*=-C208] { + color: #FF8700 +} + +div.highlight .-Color[class*=-BGC208] { + background-color: #FF8700 +} + +div.highlight .-Color[class*=-C209] { + color: #FF875F +} + +div.highlight .-Color[class*=-BGC209] { + background-color: #FF875F +} + +div.highlight .-Color[class*=-C210] { + color: #FF8787 +} + +div.highlight .-Color[class*=-BGC210] { + background-color: #FF8787 +} + +div.highlight .-Color[class*=-C211] { + color: #FF87AF +} + +div.highlight .-Color[class*=-BGC211] { + background-color: #FF87AF +} + +div.highlight .-Color[class*=-C212] { + color: #FF87D7 +} + +div.highlight .-Color[class*=-BGC212] { + background-color: #FF87D7 +} + +div.highlight .-Color[class*=-C213] { + color: #FF87FF +} + +div.highlight .-Color[class*=-BGC213] { + background-color: #FF87FF +} + +div.highlight .-Color[class*=-C214] { + color: #FFAF00 +} + +div.highlight .-Color[class*=-BGC214] { + background-color: #FFAF00 +} + +div.highlight .-Color[class*=-C215] { + color: #FFAF5F +} + +div.highlight .-Color[class*=-BGC215] { + background-color: #FFAF5F +} + +div.highlight .-Color[class*=-C216] { + color: #FFAF87 +} + +div.highlight .-Color[class*=-BGC216] { + background-color: #FFAF87 +} + +div.highlight .-Color[class*=-C217] { + color: #FFAFAF +} + +div.highlight .-Color[class*=-BGC217] { + background-color: #FFAFAF +} + +div.highlight .-Color[class*=-C218] { + color: #FFAFD7 +} + +div.highlight .-Color[class*=-BGC218] { + background-color: #FFAFD7 +} + +div.highlight .-Color[class*=-C219] { + color: #FFAFFF +} + +div.highlight .-Color[class*=-BGC219] { + background-color: #FFAFFF +} + +div.highlight .-Color[class*=-C220] { + color: #FFD700 +} + +div.highlight .-Color[class*=-BGC220] { + background-color: #FFD700 +} + +div.highlight .-Color[class*=-C221] { + color: #FFD75F +} + +div.highlight .-Color[class*=-BGC221] { + background-color: #FFD75F +} + +div.highlight .-Color[class*=-C222] { + color: #FFD787 +} + +div.highlight .-Color[class*=-BGC222] { + background-color: #FFD787 +} + +div.highlight .-Color[class*=-C223] { + color: #FFD7AF +} + +div.highlight .-Color[class*=-BGC223] { + background-color: #FFD7AF +} + +div.highlight .-Color[class*=-C224] { + color: #FFD7D7 +} + +div.highlight .-Color[class*=-BGC224] { + background-color: #FFD7D7 +} + +div.highlight .-Color[class*=-C225] { + color: #FFD7FF +} + +div.highlight .-Color[class*=-BGC225] { + background-color: #FFD7FF +} + +div.highlight .-Color[class*=-C226] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC226] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C227] { + color: #FFFF5F +} + +div.highlight .-Color[class*=-BGC227] { + background-color: #FFFF5F +} + +div.highlight .-Color[class*=-C228] { + color: #FFFF87 +} + +div.highlight .-Color[class*=-BGC228] { + background-color: #FFFF87 +} + +div.highlight .-Color[class*=-C229] { + color: #FFFFAF +} + +div.highlight .-Color[class*=-BGC229] { + background-color: #FFFFAF +} + +div.highlight .-Color[class*=-C230] { + color: #FFFFD7 +} + +div.highlight .-Color[class*=-BGC230] { + background-color: #FFFFD7 +} + +div.highlight .-Color[class*=-C231] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC231] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C232] { + color: #080808 +} + +div.highlight .-Color[class*=-BGC232] { + background-color: #080808 +} + +div.highlight .-Color[class*=-C233] { + color: #121212 +} + +div.highlight .-Color[class*=-BGC233] { + background-color: #121212 +} + +div.highlight .-Color[class*=-C234] { + color: #1C1C1C +} + +div.highlight .-Color[class*=-BGC234] { + background-color: #1C1C1C +} + +div.highlight .-Color[class*=-C235] { + color: #262626 +} + +div.highlight .-Color[class*=-BGC235] { + background-color: #262626 +} + +div.highlight .-Color[class*=-C236] { + color: #303030 +} + +div.highlight .-Color[class*=-BGC236] { + background-color: #303030 +} + +div.highlight .-Color[class*=-C237] { + color: #3A3A3A +} + +div.highlight .-Color[class*=-BGC237] { + background-color: #3A3A3A +} + +div.highlight .-Color[class*=-C238] { + color: #444444 +} + +div.highlight .-Color[class*=-BGC238] { + background-color: #444444 +} + +div.highlight .-Color[class*=-C239] { + color: #4E4E4E +} + +div.highlight .-Color[class*=-BGC239] { + background-color: #4E4E4E +} + +div.highlight .-Color[class*=-C240] { + color: #585858 +} + +div.highlight .-Color[class*=-BGC240] { + background-color: #585858 +} + +div.highlight .-Color[class*=-C241] { + color: #626262 +} + +div.highlight .-Color[class*=-BGC241] { + background-color: #626262 +} + +div.highlight .-Color[class*=-C242] { + color: #6C6C6C +} + +div.highlight .-Color[class*=-BGC242] { + background-color: #6C6C6C +} + +div.highlight .-Color[class*=-C243] { + color: #767676 +} + +div.highlight .-Color[class*=-BGC243] { + background-color: #767676 +} + +div.highlight .-Color[class*=-C244] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC244] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C245] { + color: #8A8A8A +} + +div.highlight .-Color[class*=-BGC245] { + background-color: #8A8A8A +} + +div.highlight .-Color[class*=-C246] { + color: #949494 +} + +div.highlight .-Color[class*=-BGC246] { + background-color: #949494 +} + +div.highlight .-Color[class*=-C247] { + color: #9E9E9E +} + +div.highlight .-Color[class*=-BGC247] { + background-color: #9E9E9E +} + +div.highlight .-Color[class*=-C248] { + color: #A8A8A8 +} + +div.highlight .-Color[class*=-BGC248] { + background-color: #A8A8A8 +} + +div.highlight .-Color[class*=-C249] { + color: #B2B2B2 +} + +div.highlight .-Color[class*=-BGC249] { + background-color: #B2B2B2 +} + +div.highlight .-Color[class*=-C250] { + color: #BCBCBC +} + +div.highlight .-Color[class*=-BGC250] { + background-color: #BCBCBC +} + +div.highlight .-Color[class*=-C251] { + color: #C6C6C6 +} + +div.highlight .-Color[class*=-BGC251] { + background-color: #C6C6C6 +} + +div.highlight .-Color[class*=-C252] { + color: #D0D0D0 +} + +div.highlight .-Color[class*=-BGC252] { + background-color: #D0D0D0 +} + +div.highlight .-Color[class*=-C253] { + color: #DADADA +} + +div.highlight .-Color[class*=-BGC253] { + background-color: #DADADA +} + +div.highlight .-Color[class*=-C254] { + color: #E4E4E4 +} + +div.highlight .-Color[class*=-BGC254] { + background-color: #E4E4E4 +} + +div.highlight .-Color[class*=-C255] { + color: #EEEEEE +} + +div.highlight .-Color[class*=-BGC255] { + background-color: #EEEEEE +} diff --git a/branch/main/singlehtml/_static/overrides.css b/branch/main/singlehtml/_static/overrides.css new file mode 100644 index 0000000..26a0f16 --- /dev/null +++ b/branch/main/singlehtml/_static/overrides.css @@ -0,0 +1,98 @@ +/* + * colors = ['#0271AE', '#DC2830', '#FFC438', # blue, red, light orange + * '#6E3B87', '#008D5D', '#FA902D', # purple, green, orange + * '#0095B7', '#CB0C7B', '#F7E43C', # cyan, magenta, yellow + * '#88B93B', '#444F95', '#F16232'] # pea green, dark blue, dark orange + * + * To use them in rST, you need to define a command in the epilog, see conf.py + */ +.blue {color: #0271AE;} +.red {color: #DC2830;} +.orange {color: #FFC438;} +.purple {color: #633B87;} +.green {color: #008D5D;} +.dkorange {color: #FA902D;} +.cyan {color: #0095B7;} +.magenta {color: #CB0C8B;} +.yellow {color: #F7E43C;} +.peagreen {color: #88B93B;} +.darkblue {color: 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and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf new file mode 100644 index 0000000..f7045c7 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf new file mode 100644 index 0000000..f5edb26 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf new file mode 100644 index 0000000..84bfc66 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Convergence.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Convergence.pdf new file mode 100644 index 0000000..667b2fb Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Convergence.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Features.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Features.pdf new file mode 100644 index 0000000..272de28 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Features.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-First_encounter.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-First_encounter.pdf new file mode 100644 index 0000000..627b1cd Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-First_encounter.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Intro.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Intro.pdf new file mode 100644 index 0000000..dcd5733 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Intro.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-MD.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-MD.pdf new file mode 100644 index 0000000..f7fed7f Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-MD.pdf differ diff --git a/branch/main/singlehtml/_static/siesta/SIESTA-Solvers.pdf b/branch/main/singlehtml/_static/siesta/SIESTA-Solvers.pdf new file mode 100644 index 0000000..9430066 Binary files /dev/null and b/branch/main/singlehtml/_static/siesta/SIESTA-Solvers.pdf differ diff --git a/branch/main/singlehtml/_static/sphinx_highlight.js b/branch/main/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/branch/main/singlehtml/_static/sphinx_lesson.css b/branch/main/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/branch/main/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/branch/main/singlehtml/_static/tabs.css b/branch/main/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/branch/main/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; 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If a group tab + * is selected, also select tab in other tabLists. + * @param {Node} e the element that was clicked + */ +function changeTabs(e) { + // Use this instead of the element that was clicked, in case it's a child + const notSelected = this.getAttribute("aria-selected") === "false"; + const positionBefore = this.parentNode.getBoundingClientRect().top; + const notClosable = !this.parentNode.classList.contains("closeable"); + + deselectTabList(this); + + if (notSelected || notClosable) { + selectTab(this); + const name = this.getAttribute("name"); + selectNamedTabs(name, this.id); + + if (this.classList.contains("group-tab")) { + // Persist during session + session.setItem('sphinx-tabs-last-selected', name); + } + } + + const positionAfter = this.parentNode.getBoundingClientRect().top; + const positionDelta = positionAfter - positionBefore; + // Scroll to offset content resizing + window.scrollTo(0, window.scrollY + positionDelta); +} + +/** + * Select tab and show associated panel. + * @param {Node} tab tab to select + */ +function selectTab(tab) { + tab.setAttribute("aria-selected", true); + + // Show the associated panel + document + .getElementById(tab.getAttribute("aria-controls")) + .removeAttribute("hidden"); +} + +/** + * Hide the panels associated with all tabs within the + * tablist containing this tab. + * @param {Node} tab a tab within the tablist to deselect + */ +function deselectTabList(tab) { + const parent = tab.parentNode; + const grandparent = parent.parentNode; + + Array.from(parent.children) + .forEach(t => t.setAttribute("aria-selected", false)); + + Array.from(grandparent.children) + .slice(1) // Skip tablist + .forEach(panel => panel.setAttribute("hidden", true)); +} + +/** + * Select grouped tabs with the same name, but no the tab + * with the given id. + * @param {Node} name name of grouped tab to be selected + * @param {Node} clickedId id of clicked tab + */ +function selectNamedTabs(name, clickedId=null) { + const groupedTabs = document.querySelectorAll(`.sphinx-tabs-tab[name="${name}"]`); + const tabLists = Array.from(groupedTabs).map(tab => tab.parentNode); + + tabLists + .forEach(tabList => { + // Don't want to change the tabList containing the clicked tab + const clickedTab = tabList.querySelector(`[id="${clickedId}"]`); + if (clickedTab === null ) { + // Select first tab with matching name + const tab = tabList.querySelector(`.sphinx-tabs-tab[name="${name}"]`); + deselectTabList(tab); + selectTab(tab); + } + }) +} + +if (typeof exports === 'undefined') { + exports = {}; +} + +exports.keyTabs = keyTabs; +exports.changeTabs = changeTabs; +exports.selectTab = selectTab; +exports.deselectTabList = deselectTabList; +exports.selectNamedTabs = selectNamedTabs; diff --git a/branch/main/singlehtml/_static/term_role_formatting.css b/branch/main/singlehtml/_static/term_role_formatting.css new file mode 100644 index 0000000..0b66095 --- /dev/null +++ b/branch/main/singlehtml/_static/term_role_formatting.css @@ -0,0 +1,4 @@ +/* Make terms bold */ +a.reference span.std-term { + font-weight: bold; +} diff --git a/branch/main/singlehtml/_static/togglebutton.css b/branch/main/singlehtml/_static/togglebutton.css new file mode 100644 index 0000000..54a6787 --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.css @@ -0,0 +1,160 @@ +/** + * Admonition-based toggles + */ + +/* Visibility of the target */ +.admonition.toggle .admonition-title ~ * { + transition: opacity .3s, height .3s; +} + +/* Toggle buttons inside admonitions so we see the title */ +.admonition.toggle { + position: relative; +} + +/* Titles should cut off earlier to avoid overlapping w/ button */ +.admonition.toggle .admonition-title { + padding-right: 25%; + cursor: pointer; +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:hover { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 1%); +} + +/* Hovering will cause a slight shift in color to make it feel interactive */ +.admonition.toggle .admonition-title:active { + box-shadow: inset 0 0 0px 20px rgb(0 0 0 / 3%); +} + +/* Remove extra whitespace below the admonition title when hidden */ +.admonition.toggle-hidden { + padding-bottom: 0; +} + +.admonition.toggle-hidden .admonition-title { + margin-bottom: 0; +} + +/* hides all the content of a page until de-toggled */ +.admonition.toggle-hidden .admonition-title ~ * { + height: 0; + margin: 0; + opacity: 0; + visibility: hidden; +} + +/* General button style and position*/ +button.toggle-button { + /** + * Background and shape. By default there's no background + * but users can style as they wish + */ + background: none; + border: none; + outline: none; + + /* Positioning just inside the admonition title */ + position: absolute; + right: 0.5em; + padding: 0px; + border: none; + outline: none; +} + +/* Display the toggle hint on wide screens */ +@media (min-width: 768px) { + button.toggle-button.toggle-button-hidden:before { + content: attr(data-toggle-hint); /* This will be filled in by JS */ + font-size: .8em; + align-self: center; + } +} + +/* Icon behavior */ +.tb-icon { + transition: transform .2s ease-out; + height: 1.5em; + width: 1.5em; + stroke: currentColor; /* So that we inherit the color of other text */ +} + +/* The icon should point right when closed, down when open. */ +/* Open */ +.admonition.toggle button .tb-icon { + transform: rotate(90deg); +} + +/* Closed */ +.admonition.toggle button.toggle-button-hidden .tb-icon { + transform: rotate(0deg); +} + +/* With details toggles, we don't rotate the icon so it points right */ +details.toggle-details .tb-icon { + height: 1.4em; + width: 1.4em; + margin-top: 0.1em; /* To center the button vertically */ +} + + +/** + * Details-based toggles. + * In this case, we wrap elements with `.toggle` in a details block. + */ + +/* Details blocks */ +details.toggle-details { + margin: 1em 0; +} + + +details.toggle-details summary { + display: flex; + align-items: center; + cursor: pointer; + list-style: none; + border-radius: .2em; + border-left: 3px solid #1976d2; + background-color: rgb(204 204 204 / 10%); + padding: 0.2em 0.7em 0.3em 0.5em; /* Less padding on left because the SVG has left margin */ + font-size: 0.9em; +} + +details.toggle-details summary:hover { + background-color: rgb(204 204 204 / 20%); +} + +details.toggle-details summary:active { + background: rgb(204 204 204 / 28%); +} + +.toggle-details__summary-text { + margin-left: 0.2em; +} + +details.toggle-details[open] summary { + margin-bottom: .5em; +} + +details.toggle-details[open] summary .tb-icon { + transform: rotate(90deg); +} + +details.toggle-details[open] summary ~ * { + animation: toggle-fade-in .3s ease-out; +} + +@keyframes toggle-fade-in { + from {opacity: 0%;} + to {opacity: 100%;} +} + +/* Print rules - we hide all toggle button elements at print */ +@media print { + /* Always hide the summary so the button doesn't show up */ + details.toggle-details summary { + display: none; + } +} \ No newline at end of file diff --git a/branch/main/singlehtml/_static/togglebutton.js b/branch/main/singlehtml/_static/togglebutton.js new file mode 100644 index 0000000..215a7ee --- /dev/null +++ b/branch/main/singlehtml/_static/togglebutton.js @@ -0,0 +1,187 @@ +/** + * Add Toggle Buttons to elements + */ + +let toggleChevron = ` + + + +`; + +var initToggleItems = () => { + var itemsToToggle = document.querySelectorAll(togglebuttonSelector); + console.log(`[togglebutton]: Adding toggle buttons to ${itemsToToggle.length} items`) + // Add the button to each admonition and hook up a callback to toggle visibility + itemsToToggle.forEach((item, index) => { + if (item.classList.contains("admonition")) { + // If it's an admonition block, then we'll add a button inside + // Generate unique IDs for this item + var toggleID = `toggle-${index}`; + var buttonID = `button-${toggleID}`; + + item.setAttribute('id', toggleID); + if (!item.classList.contains("toggle")){ + item.classList.add("toggle"); + } + // This is the button that will be added to each item to trigger the toggle + var collapseButton = ` + `; + + title = item.querySelector(".admonition-title") + title.insertAdjacentHTML("beforeend", collapseButton); + thisButton = document.getElementById(buttonID); + + // Add click handlers for the button + admonition title (if admonition) + admonitionTitle = document.querySelector(`#${toggleID} > .admonition-title`) + if (admonitionTitle) { + // If an admonition, then make the whole title block clickable + admonitionTitle.addEventListener('click', toggleClickHandler); + admonitionTitle.dataset.target = toggleID + admonitionTitle.dataset.button = buttonID + } else { + // If not an admonition then we'll listen for the button click + thisButton.addEventListener('click', toggleClickHandler); + } + + // Now hide the item for this toggle button unless explicitly noted to show + if (!item.classList.contains("toggle-shown")) { + toggleHidden(thisButton); + } + } else { + // If not an admonition, wrap the block in a
block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
+ + ${toggleChevron} + ${toggleHintShow} + +
`; + item.insertAdjacentHTML("beforebegin", detailsBlock); + + // Now move the toggle-able content inside of the details block + details = item.previousElementSibling + details.appendChild(item) + item.classList.add("toggle-details__container") + + // Set up a click trigger to change the text as needed + details.addEventListener('click', (click) => { + let parent = click.target.parentElement; + if (parent.tagName.toLowerCase() == "details") { + summary = parent.querySelector("summary"); + details = parent; + } else { + summary = parent; + details = parent.parentElement; + } + // Update the inner text for the proper hint + if (details.open) { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintShow; + } else { + summary.querySelector("span.toggle-details__summary-text").innerText = toggleHintHide; + } + + }); + + // If we have a toggle-shown class, open details block should be open + if (item.classList.contains("toggle-shown")) { + details.click(); + } + } + }) +}; + +// This should simply add / remove the collapsed class and change the button text +var toggleHidden = (button) => { + target = button.dataset['target'] + var itemToToggle = document.getElementById(target); + if (itemToToggle.classList.contains("toggle-hidden")) { + itemToToggle.classList.remove("toggle-hidden"); + button.classList.remove("toggle-button-hidden"); + } else { + itemToToggle.classList.add("toggle-hidden"); + button.classList.add("toggle-button-hidden"); + } +} + +var toggleClickHandler = (click) => { + // Be cause the admonition title is clickable and extends to the whole admonition + // We only look for a click event on this title to trigger the toggle. + + if (click.target.classList.contains("admonition-title")) { + button = click.target.querySelector(".toggle-button"); + } else if (click.target.classList.contains("tb-icon")) { + // We've clicked the icon and need to search up one parent for the button + button = click.target.parentElement; + } else if (click.target.tagName == "polyline") { + // We've clicked the SVG elements inside the button, need to up 2 layers + button = click.target.parentElement.parentElement; + } else if (click.target.classList.contains("toggle-button")) { + // We've clicked the button itself and so don't need to do anything + button = click.target; + } else { + console.log(`[togglebutton]: Couldn't find button for ${click.target}`) + } + target = document.getElementById(button.dataset['button']); + toggleHidden(target); +} + +// If we want to blanket-add toggle classes to certain cells +var addToggleToSelector = () => { + const selector = ""; + if (selector.length > 0) { + document.querySelectorAll(selector).forEach((item) => { + item.classList.add("toggle"); + }) + } +} + +// Helper function to run when the DOM is finished +const sphinxToggleRunWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} +sphinxToggleRunWhenDOMLoaded(addToggleToSelector) +sphinxToggleRunWhenDOMLoaded(initToggleItems) + +/** Toggle details blocks to be open when printing */ +if (toggleOpenOnPrint == "true") { + window.addEventListener("beforeprint", () => { + // Open the details + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.dataset["togglestatus"] = el.open; + el.open = true; + }); + + // Open the admonitions + document.querySelectorAll(".admonition.toggle.toggle-hidden").forEach((el) => { + console.log(el); + el.querySelector("button.toggle-button").click(); + el.dataset["toggle_after_print"] = "true"; + }); + }); + window.addEventListener("afterprint", () => { + // Re-close the details that were closed + document.querySelectorAll("details.toggle-details").forEach((el) => { + el.open = el.dataset["togglestatus"] == "true"; + delete el.dataset["togglestatus"]; + }); + + // Re-close the admonition toggle buttons + document.querySelectorAll(".admonition.toggle").forEach((el) => { + if (el.dataset["toggle_after_print"] == "true") { + el.querySelector("button.toggle-button").click(); + delete el.dataset["toggle_after_print"]; + } + }); + }); +} diff --git a/branch/main/singlehtml/index.html b/branch/main/singlehtml/index.html new file mode 100644 index 0000000..0edf156 --- /dev/null +++ b/branch/main/singlehtml/index.html @@ -0,0 +1,1701 @@ + + + + + + + Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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  • Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation
    • +
  • + Edit on GitHub +
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+

Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo

+

In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential.

+

This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises.

+

QUANTUM ESPRESSO is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications.

+

SIESTA is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a “good first approximation” to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA.

+

YAMBO is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc).

+

MAX (MAterials design at the eXascale) is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX’s challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials’ domain.

+
+

Prerequisites

+
    +

  • Some familiarity with density functional theory (DFT), self-consistent +field (SCF) calculations and plane wave basis sets is desirable as the +workshop will not cover the fundamental theory of these topics.

    • +

  • Familiarity with working in a Linux environment and some experience with +working on an HPC system is needed to participate in the hands-on exercises.

    • +
+
+
+

Who is the course for?

+

This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations.

+
+
+
+
+
+
+

SIESTA setup

+
+

Directory with tutorials

+

For every practical there is a folder in the shared directory +/leonardo_work/EUHPC_TD02_030/siesta-tutorials that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:

+
$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I .
+
+
+

Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts.

+
+
+

Running SIESTA

+

You will find a sample script on how to run SIESTA in +/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh:

+
#!/bin/bash
+#SBATCH -J tutorialXX
+#SBATCH -n 8
+#SBATCH -t 0:30:00
+#SBATCH -o %x-%j.out
+#SBATCH -e %x-%j.err
+#SBATCH --partition=boost_usr_prod
+#SBATCH -D .
+
+# DO NOT CHANGE THIS LINE
+source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh
+
+# EDIT THE CORRECT INPUT AND OUTPUT FILES.
+srun -n 8 siesta < input.fdf > output.out
+
+
+

Note that input.fdf and output.out are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(#SBATCH -J option) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue.

+
+
+

Suggested Software for Visualization

+

If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences.

+ +
+
+
+

Day 3: SIESTA I

+
+

SIESTA basics

+

Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge).

+

Slides available here: SIESTA-Intro.pdf.

+
+
+

A first contact with SIESTA: inputs, execution and outputs

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-First_encounter.pdf.

+
+
+

Basis sets

+

Lecture by Dr. Miguel Pruneda (CINN-CSIC).

+

Slides available here: SIESTA-Basis_sets.pdf.

+
+
+

Basis set optimization

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets
+
+
+

Introductory slides available here: SIESTA-Basis_set_optimization.pdf.

+
+
+

Convergence (k points, mesh, mixing)

+

Practical session led by Dr. Catalina Coll (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-Convergence.pdf.

+
+
+
+

Day 4: SIESTA II

+
+

Molecular Dynamics with SIESTA

+

Practical session led by Dr. Ernane de Freitas (ICN2).

+

Tutorials covered:

+
    +

  • Molecular Dynamics. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-MD.pdf.

+
+
+

Analysis tools

+

Practical session led by Dr. Miguel Pruneda (CINN-CSIC).

+

Tutorials covered:

+
    +

  • Analysis tools. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-Analysis_tools.pdf.

+
+
+

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

+

Lecture by Dr. Nick Papior (Technical University of Denmark).

+

Slides available here: SIESTA-Features.pdf.

+
+
+

Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Practical session led by Dr. Alberto García (ICMAB-CSIC).

+

Tutorials covered:

+
    +

  • ELSI-ELPA.

    • +

  • ELSI-PEXSI.

    • +
+

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers
+
+
+

Slides available here: SIESTA-Solvers.pdf.

+
+
+
+
+
+

Yambo tutorial: Quasiparticles in the GW approximation

+

In this tutorial you will learn how to run a GW simulation using Yambo on a HPC machine.

+

You will compute the quasiparticle corrections to the band structure of a free-standing single layer of MoS\(_2\) while learning about convergence studies, parallel strategies, and GPU calculations.

+

In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate.

+
+_images/mos2.png +
+

MoS\(_2\) monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.

+
+

Many-body corrections to the DFT band gap

+

We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of.

+

Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy \(\Sigma\):

+
+\[E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle\]
+

Here \(\epsilon_{nk}\) and \(\psi_{nk}\) are the Kohn-Sham energies and wavefunctions, respectively, while \(V_{xc}\) is the DFT exchange-correlation potential.

+

For each electronic state \(nk\), the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy (\(\Sigma^x\)), and an energy-dependent, usually gap-closing term called the correlation self-energy (\(\Sigma^c\)). These contributions are tackled separately by the code:

+
+\[\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega)\]
+

The energy-dependent dynamical electronic screening \(\varepsilon^{-1}(\omega)\) is included in \(\Sigma^c\) and must therefore be calculated as well.

+

In this way, we can compute the “quasiparticle” corrections \(E^{QP}_{nk}\) to the single-particle Kohn-Sham eigenvalues \(\epsilon_{nk}\). +The typical workflow for a GW calculation is:

+
+_images/gwflow.png +
+
+
+

Set up a Yambo calculation

+

Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes):

+
wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+
tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+

You can now enter the tutorial directory

+
cd MoS2_HPC_tutorial_Leonardo
+
+
+
+
Yambo SAVE folder
+

First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo.

+

The QE save folder for MoS\(_2\) is already present at 00_QE-DFT. We should move inside it and then run the p2y executable to generate the uninitialised SAVE.

+

But first, we need to access a node interactively:

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

Finally:

+
cd 00_QE-DFT/mos2.save
+mpirun -np 1 p2y
+
+
+

Now, we need to run the initialization step. Every Yambo run must start with this step. This will be automatically performed when you run Yambo on a SAVE directory for the first time. Just type

+
mpirun -np 1 yambo
+
+
+

and then check the yambo log called l_setup. The initialization step determines the \(G\)-vector shells and the \(k\)- and \(q\)-point grids based on the DFT calculation. If you check inside the SAVE you will see two types of databases. The static ones, starting with ns.*, are directly converted in the p2y step, while the dynamical ones, ndb.* are generated during the initialisation.

+
ls SAVE/
+
+
+
ndb.gops       # info on G-vector shells, etc
+ndb.kindx      # info and k and q meshes
+ns.db1         # info on geometry and KS bands
+ns.kb_pp_pwscf # pseudopotential info
+ns.wf          # wave functions info
+...
+
+
+

The databases are written in netCDF format. +Yambo has produced also a human readable output, r_setup, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections.

+
vim r_setup
+
+
+
[02.01] Unit cells # Lattice geometry info
+==================
+  ...
+[02.02] Symmetries # Symmetry ops. written explicitly
+==================
+  ...
+[02.03] Reciprocal space  # Reciprocal lattice info
+========================
+...
+[02.04] K-grid lattice # k-point coords. written explicitly
+======================
+...
+[02.05] Energies & Occupations # Info on band gaps and occupations
+============================== # DFT eigenvalues
+...
+[03] Transferred momenta grid and indexing # q-points (momentum transfer grid)
+==========================================
+
+
+

Finally, let us move the SAVE and the report file to the directory where we will run the first GW calculation.

+
mv SAVE r_setup ../../01_GW_first_run/
+cd ../../01_GW_first_run/
+
+
+
+
+
Yambo input file
+

Now that we have a working SAVE, it is time to generate the input file we will be using for our first GW calculation.

+

This can be done by the yambo executable via command-line instructions.

+

If you type

+
yambo -h
+
+
+

You will get a list of the possibile options:

+
 ___ __  _____  __ __  _____   _____
+|   Y  ||  _  ||  Y  ||  _  \ |  _  |
+|   |  ||. |  ||.    ||. |  / |. |  |
+ \   _/ |. _  ||.\ / ||. _  \ |. |  |
+  |: |  |: |  ||: |  ||: |   \|: |  |
+  |::|  |:.|:.||:.|:.||::.   /|::.  |
+  `--"  `-- --"`-- --"`-----" `-----"
+ 'A shiny pot of fun and happiness [C.D.Hogan]'
+
+ This is      : yambo
+ Version      : 5.1.0 Revision 21422 Hash fde6e2a07
+ Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO
+
+ Help & version:
+ -help            (-h) <string>   :<string> can be an option (e.g. -h optics)
+ -version                         :Code version & libraries
+
+ Input file & Directories:
+ -Input           (-F) <string>   :Input file
+ -Verbosity       (-V) <string>   :Input file variables verbosity (more with -h Verbosity)
+ -Job             (-J) <string>   :Job string
+ -Idir            (-I) <string>   :Input directory
+ -Odir            (-O) <string>   :I/O directory
+ -Cdir            (-C) <string>   :Communication directory
+
+ Parallel Control:
+ -parenv          (-E) <string>   :Environment Parallel Variables file
+ -nompi                           :Switch off MPI support
+ -noopenmp                        :Switch off OPENMP support
+
+ Initializations:
+ -setup           (-i)            :Initialization
+ -coulomb         (-r)            :Coulomb potential
+
+ Response Functions:
+ -optics          (-o) <string>   :Linear Response optical properties (more with -h optics)
+ -X               (-d) <string>   :Inverse Dielectric Matrix (more with -h X)
+ -dipoles         (-q)            :Oscillator strenghts (or dipoles)
+ -kernel          (-k) <string>   :Kernel (more with -h kernel)
+
+ Self-Energy:
+ -hf              (-x)            :Hartree-Fock
+ -gw0             (-p) <string>   :GW approximation (more with -h gw0)
+ -dyson           (-g) <string>   :Dyson Equation solver (more with -h dyson)
+ -lifetimes       (-l)            :GoWo Quasiparticle lifetimes
+
+ Bethe-Salpeter Equation:
+ -Ksolver         (-y) <string>   :BSE solver (more with -h Ksolver)
+
+ Total Energy:
+ -acfdt                           :ACFDT Total Energy
+
+ Utilites:
+ -Quiet           (-Q)            :Quiet input file creation
+ -fatlog                          :Verbose (fatter) log(s)
+ -DBlist          (-D)            :Databases properties
+ -walltime             <int>      :Walltime (more with -h walltime)
+ -memory               <int>      :Memory (more with -h memory)
+ -slktest                         :ScaLapacK test
+
+ YAMBO developers group (http://www.yambo-code.org)
+
+
+

In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type:

+
yambo -gw0 p -g n -r -V par -F gw.in
+
+
+

Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the slurm scheduler.

+
exit
+
+
+

You can now inspect the input file gw.in and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change.

+

We discuss them below step by step.

+
+
+
Parameters for a GW calculation
+

We start with the runlevels:

+
gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+el_el_corr                       # [R] Electron-Electron Correlation
+dyson                            # [R] Dyson Equation solver
+rim_cut                          # [R] Coulomb potential
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+
+
+
+

Runlevels

+
    +

  • The [R] keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have:

    +
      +

    • rim_cut: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables).

      • +

    • gw0: Yambo learns that it has to run a GW calculation (enables [GW] variables).

      • +

    • HF_and_locXC: calculation of exchange part of the self-energy \(\Sigma^x\) (i.e., Hartree-Fock approximation).

      • +

    • em1d: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute \(\Sigma^c\).

      • +

    • ppa: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables).

      • +

    • dyson: Yambo will solve the Dyson-like quasiparticle equation.

      • +
    +
    • +
+
+

Going through the file we find:

+
EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+
+
+

Recall that we have, for the exchange self-energy:

+
+\[\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q}\]
+
+

Exchange self-energy

+
    +

  • EXXRLvcs controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while VXCRLvcs does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value).

    • +
+
+

Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have:

+
+\[\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega')\]
+

(Here, the \(\rho\)-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.)

+

The calculation is divided in two steps. First, the response function in the plasmon pole approximation (em1d ppa), under the keywords [X] and [Xp], i.e., \(\varepsilon^{-1}_{GG'}(q,\omega)\).

+
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 300 |                     # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+
+
+
+

Response function

+
    +

  • Chimod= "Hartree" indicates that we compute the response function in the Random Phase Approximation (RPA).

    • +

  • BndsRnXp represents the electronic states included in the response function \(\varepsilon\), and is a convergence parameter.

    • +

  • NGsBlkXp is the number of G-vectors used to calculate the RPA response function \(\varepsilon^{-1}_{GG'}\). It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested).

    • +

  • LongDrXp represents the direction of the long-range auxiliary external electric field used to compute \(\varepsilon^{-1}_{GG'}(q)\) at \(q,G\rightarrow 0\). In general you have to be mindful of the system symmetries. In our case, we will put 1 | 1 | 1 to cover all directions.

    • +

  • PPAPntXp= 27.21138 eV is the energy of the plasmon pole. We don’t normally change this.

    • +

  • XTermKind is used to specify a “terminator”: this accelerates numerical convergence with respect to the number of bands BndsRnXp.

    • +
+
+

Next, we have the [GW] group of parameters controlling the next part of the correlation self-energy calculation:

+
% GbndRnge
+   1 | 300 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|7|1|300|
+%
+
+
+
+

Correlation self-energy

+
    +

  • GbndRnge is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator GTermKind.

    • +

  • DysSolver="n" specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method "n".

    • +

  • QPkrange indicates the range of electronic (nk) states for which the GW correction \(\Sigma_{nk}\) is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices.

    • +
+
+

We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should edit now once and for all.

+
RandQpts=1000000                       # [RIM] Number of random q-points in the BZ
+RandGvec= 100                RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+
+
+
+

Coulomb potential

+
    +

  • The [RIM] keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to \(q=0\) and \(G=0\) in the \(q\)-integration of the bare Coulomb interaction - i.e. \(4\pi/(q+G)^2\) - for 2D systems.

    • +

  • The [CUT] keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the \(z\)-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic.

    • +
+
+

Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now.

+
X_and_IO_CPU= ""                 # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= ""               # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=-1      # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_CPU= ""                      # [PARALLEL] CPUs for each role
+DIP_ROLEs= ""                    # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_CPU= ""                       # [PARALLEL] CPUs for each role
+SE_ROLEs= ""                     # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+
+
+

In a GW calculation, the most important parameters to be numerically converged are:

+
    +

  • kpoint mesh (requires multiple nscf DFT runs)

    • +

  • BndsRnXp

    • +

  • NGsBlkXp

    • +

  • GbndRnge

    • +

  • [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs)

    • +
+

From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations.

+
+
+
+
+

The first run

+

We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file r_setup produced when the SAVE folder was initialised. Just search for the string ‘Direct Gap’ and you’ll see that the latter occurs at k-point 7 between bands 13 and 14:

+
  [X] Filled Bands                                  :  13
+  [X] Empty Bands                                   :   14  300
+  [X] Direct Gap                                    :  1.858370 [eV]
+  [X] Direct Gap localized at k                     :  7
+
+
+

In addition, we will set the number of bands in BndsRnXp and GbndRnge to a small value, just to have it run fast. Hence, we modify the input file accordingly (check BndsRnXp, GbndRnge, LongDrXp, QPkrange):

+
rim_cut                          # [R] Coulomb potential
+gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+dyson                            # [R] Dyson Equation solver
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+RandQpts=1000000                 # [RIM] Number of random q-points in the BZ
+RandGvec= 100              RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+% CUTBox
+ 0.000000 | 0.000000 | 0.000000 |        # [CUT] [au] Box sides
+%
+CUTRadius= 0.000000              # [CUT] [au] Sphere/Cylinder radius
+CUTCylLen= 0.000000              # [CUT] [au] Cylinder length
+CUTwsGvec= 0.700000              # [CUT] WS cutoff: number of G to be modified
+EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 20 |                         # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 1.000000 | 1.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+% GbndRnge
+   1 | 20 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+7|7|13|14|
+%
+
+
+

We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. Modify it to suit your specific machine.

+
vim run_first_job.sh
+
+
+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=8
+#SBATCH --partition=boost_usr_prod
+#SBATCH --time=0:05:00
+#SBATCH --gres=gpu:2
+#SBATCH --account=EUHPC_TD02_030
+#SBATCH --job-name=first_job
+
+export OMP_NUM_THREADS=8
+export OMP_PLACES=cores
+export OMP_PROC_BIND=close
+
+# load yambo
+module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \
+        yambo -F gw.in -J job_00_first_run -C out_00_first_run
+
+
+

We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after yambo, it is not going to generate an input file, but rather, run the one specified by -F. Now, go ahead an submit this job

+
sbatch run_first_job.sh
+
+
+

The status of the jobs can be monitored via:

+
squeue -u $USER        # to inspect the status of jobs 
+                       # (hint: make a unix alias, if you like)
+scancel <jobid>        # to delete jobs in the queue
+
+
+

The newly generated databases will be stored in the job directory, as specified by -J, while the report, log and output files will be stored in the communications directory (-C). As this is your first yambo run, take a moment to inspect the report and log files, which you can find inside the -C directory. In these report and log files, you can see the steps performed by yambo. For instance, the code calculates the screening at every k-point and stores it in the PPA database called ndb.pp. By opening the report

+
vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa
+
+
+

you will see

+
[07] Dynamic Dielectric Matrix (PPA)
+ ====================================
+
+ [WR./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy:

+
[09.01] G0W0 (W PPA)
+  ====================
+
+  [  GW  ] Bands range     :   1  20
+  [GW/PPA] G damping       :  0.100000 [eV]
+
+
+  QP @ state[ 1 ] K range:   7   7
+  QP @ state[ 1 ] b range:  13  14
+
+  [RD./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Now, inspect the output file

+
vim out_00_first_run/o-job_00_first_run.qp 
+
+
+
# Vxc  =Slater exchange(X)+Perdew & Zunger(C)
+# Vnlxc=Hartree-Fock
+#
+#    K-point            Band               Eo [eV]            E-Eo [eV]          Sc|Eo [eV]
+#
+         7                 13                 0.000000          -0.025774           0.543987
+         7                 14                 1.858370           3.496193          -0.417555
+# 
+
+
+

In this file, Eo is our starting point (DFT) while E-Eo shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we’ll use some simple commands. First, we get everything that is not a # symbol grep -v '#' and we pass that to another command with a “pipe” |. Then, tail -n 1/head -n 1 will retain the first/last line, and awk '{print $3+$4}' will get us the sum of the third and fourth columns. Altogether, this would be as follows

+
grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}'
+-0.025774
+grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}'
+5.35456
+
+
+

These two commands give us the quasiparticle energies we’ve calculated - their difference is the GW-corrected optical gap.

+
+
+
+

GW convergence

+

In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse \(k\)-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a \(6 \times 6 \times 1\) k-point grid and without spin-orbit coupling: the SAVE we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let’s move into the appropriate directory

+
cd ../02_GW_convergence
+
+
+
+
Response function \(\varepsilon^{-1}_{GG'}\) - Bands and G-vectors
+

We are now ready to start our convergence tests. We’ll begin with the variables controlling the polarization function, i.e., NGsBlkXp for the number of G-vectors and BndsRnXp for the number of bands. For this, we will keep GbndRnge constant at a reasonably high value - you can inspect the input i01-GW

+
vim i01-GW
+
+
+

and check that you have:

+
% GbndRnge
+   1 | 80 |                         # [GW] G[W] bands range
+%
+
+
+

Since we need to run yambo for several values of NGsBlkXp and BndsRnXp, it makes sense to use two nested loops. That is exactly what we did in the submission script run01_converge_pol.sh. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs:

+
sbatch run01_converge_pol.sh
+
+
+
+

Monitoring

+

You can monitor that the job is running by the squeue command

+
sbatch squeue -u $USER
+
+
+

and also by checking the files created in your folder

+
ls -ltr
+
+
+
i01-GW_Xp_20_bands_6_Ry
+job_Xp_20_bands_6_Ry
+out_Xp_20_bands_6_Ry
+i01-GW_Xp_20_bands_8_Ry
+out_Xp_20_bands_8_Ry
+job_Xp_20_bands_8_Ry
+i01-GW_Xp_20_bands_10_Ry
+out_Xp_20_bands_10_Ry
+job_Xp_20_bands_10_Ry
+i01-GW_Xp_20_bands_12_Ry
+out_Xp_20_bands_12_Ry
+job_Xp_20_bands_12_Ry
+summary_01_20bands.txt
+i01-GW_Xp_40_bands_6_Ry
+...
+
+
+

Finally you can monitor how runs are proceeding by looking into the log files

+
tail -f out_Xp_*_bands_*/LOG/*_1
+
+
+
==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <15s> P1: [TIMING]                                          io_WF :      1.1353s CPU (34 calls,   0.033 sec avg)
+ <15s> P1: [TIMING]                                    WF_load_FFT :      1.1538s CPU ( 7 calls,   0.165 sec avg)
+ <15s> P1: [TIMING]                                    io_KB_pwscf :      1.1918s CPU ( 6 calls,   0.199 sec avg)
+ <15s> P1: [TIMING]                              DIPOLE_transverse :      2.4771s CPU
+ <15s> P1: [TIMING]                                    io_fragment :      2.6220s CPU (46 calls,   0.057 sec avg)
+ <15s> P1: [TIMING]                                           io_X :      3.1953s CPU (19 calls,   0.168 sec avg)
+ <15s> P1: [TIMING]                                        Dipoles :      4.4012s CPU
+ <15s> P1: [11] Memory Overview
+ <15s> P1: [12] Game Over & Game summary
+ <15s> P1: [TIMING]            [Time-Profile]: 15s
+
+==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <11s> P1: X@q[6] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[6] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%)
+ <11s> P1: [X-CG] R(p) Tot o/o(of R):   153   504   100
+ <11s> P1: Xo@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%)
+ <11s> P1: X@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock
+
+
+
+

Let’s now have look into the job we just submitted.

+
vim run01_converge_pol.sh
+
+
+

First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file i01-GW is used as a template for every calculation in the loops, so we assign it to a variable.

+
file0='i01-GW'
+
+for POL_BANDS in 20 40 60 80; do
+
+echo 'NGsBlkXp [Ry]   E_vale [eV]   E_cond [eV]' > summary_01_${POL_BANDS}bands.txt
+
+for NGsBlkXp_Ry in 6 8 10 12; do
+
+(...)
+
+done
+done
+
+
+

Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the sed command, in order to generate new files in an automated way (sed replaces any matching string with whatever is provided by the loop variable). Next, we run yambo using the labels to specify different job -J and communication -C directories every time. Finally, we get the quasiparticle energies with grep commands as shown before and append a new line to the summary file. So, inside each loop, we have

+
label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry
+jdir=job_${label}
+cdir=out_${label}
+filein=i01-GW_${label}
+
+sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/;
+      /% BndsRnXp/{n;s/.*/  1 |  ${POL_BANDS} |/}" $file0 > $filein
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir
+
+E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'`
+E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'`
+
+echo ${NGsBlkXp_Ry} '        ' ${E_GW_v} '        ' ${E_GW_c}  >> summary_01_${POL_BANDS}bands.txt
+
+
+

Finally, let us plot this data. First, check that the job has finished with

+
squeue -u $USER
+
+
+
[$USER@login01 02_GW_convergence]$ squeue -u $USER
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+[$USER@login01 02_GW_convergence]$ 
+
+
+

and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven’t done so yet, and then plot:

+
module load anaconda3/2023.03
+python plot-01.py
+
+
+

The plot will produce a fig-01.png file. +You can copy and open it in your local machine with something like

+
[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH]
+scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./
+
+
+

You should get:

+
+_images/convergence01.png +
+

For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we’ll make a copy of the corresponding input file:

+
cp i01-GW_Xp_80_bands_10_Ry i02-GW
+
+
+
+
+
Self-energy \(\Sigma^c\) - Bands
+

We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., GbndRnge. This step is actually simpler, since it only involves one loop. This is coded in the provided script run02_converge_Gbnds.noBG.sh. You can look into it

+
vim run02_converge_Gbnds.noBG.sh
+
+
+

and go ahead and submit it.

+
sbatch run02_converge_Gbnds.noBG.sh
+
+
+ +

While this runs, check if the previous job has finished, i.e., you should have a complete summary_02_noBG.txt file by now. +For a visual result, proceed to plot them with

+
python plot-02.py
+
+
+

You should get

+
+_images/BG_noBG.png +
+ +

We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication (here). MoS\(_2\) was one of the materials studied there, and it shows that our result, obtained with a \(6 \times 6 \times 1\) k-grid, is simply off the chart (blue line).

+
+_images/ref-Guandalini.png +
+

Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9

+ +
+
+
+
+

GW parallel strategies

+
+
MPI parallelization
+

For this section, let us enter the 03_GW_parallel directory. If you were in the 02_GW_convegence folder just do

+
cd ../03_GW_parallel
+
+
+

and inspect the input gw.in. You will see that we set low values for most of the convergence parameters except bands:

+
vim gw.in
+
+
+
FFTGvecs= 40       Ry    # [FFT] Plane-waves
+EXXRLvcs= 2        Ry    # [XX] Exchange RL components
+VXCRLvcs= 2        Ry    # [XC] XCpotential RL components
+% BndsRnXp
+    1 |  300 |               # [Xp] Polarization function bands
+%
+NGsBlkXp= 1            Ry    # [Xp] Response block size
+% GbndRnge
+    1 |  300 |               # [GW] G[W] bands range
+%
+%QPkrange                    # [GW] QP generalized Kpoint/Band indices
+  1| 19| 23| 30|
+%
+
+
+

Note that we also added FFTGvecs to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO ecutwfc, i.e. 60 Ry in this case).

+

In addition, we have deleted all the parallel parameters since we will be setting them via the submission script.

+

Actually we are now dealing with a heavier system than before: as you can see from the QPkrange values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized).

+

For this part of the tutorial, we will be using the slurm submission script job_parallel.sh, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code:

+
DIP_CPU= "1 $ngpu 1"          # [PARALLEL] CPUs for each role
+DIP_ROLEs= "k c v"            # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=  0               # [OPENMP/X] Number of threads for dipoles
+X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= "q g k c v"   # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=1    # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=  0                 # [OPENMP/X] Number of threads for response functions
+SE_CPU= "1 $ngpu 1"           # [PARALLEL] CPUs for each role
+SE_ROLEs= "q qp b"            # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=  0                # [OPENMP/GW] Number of threads for self-energy
+
+
+

The keyword DIP refers to the calculations of the screening matrix elements (also called “dipoles”) needed for the screening function, X is the screening function itself (it stands for \(\chi\) since it is a response function), SE the self-energy. +These three sections of the code can be parallelised independently.

+

We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI task is run on a single card, therefore ntasks=ngpu.

+
+

Note

+
    +

  • In this subsection we are mainly concerned with the [PARALLEL] variables which refer to MPI tasks (distributed memory).

    • +

  • What about [OPENMP] parallelisation (i.e., adding threads with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are not run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup for CPUs is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later.

    • +
+
+

We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as:

+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

and submit the job

+
sbatch job_parallel.sh
+
+
+

This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report r-* file and the log l-* files, and inspect them while the calculation runs. +For simplicity you can just type

+
tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1
+
+
+

to monitor the progress in the master thread (Ctrl+c to exit). +As you can see, the run takes some time, even though we are using minimal parameters.

+

Meanwhile, we can run other jobs increasing the parallelisation. Let’s employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the job_parallel.sh script changing

+
#!/bin/bash
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing nodes appropriately. Finally, you can try to produce a scaling plot.

+

The timings are contained in the r-* report files. You can already have a look at them typing

+
grep Time-Profile run_MPI*/r-*
+
+
+

The python script parse_ytiming.py is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided.

+

If you didn’t do so already, load the python module

+
module load anaconda3/2023.03
+
+
+

Then, after your jobs have finished, run the script as

+
python parse_ytiming.py run_MPI
+
+
+

to look for a report file in each run_MPI*.out folder. Make sure you have only one report file per folder. +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis.

+
+_images/gw_scaling.png +
+

What can we learn from this plot? In particular, try to answer the following questions:

+
    +

  • Up to which number of MPI tasks our system scales efficiently?

    • +

  • How can we decide at which point adding more nodes to the calculation becomes a waste of resources?

    • +
+
+

Note

+

Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, Yambo has been shown to scale well up to tens of thousands of MPI tasks! (See the next optional box for an example)

+
+ +

.

+ +
+
+
+
+

Full GW band structure

+

This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS\(_2\).

+

This is a massive calculation, so run it right now and we’ll discuss it in the meantime:

+
cd ../04_GW_bands
+sbatch gpu_job.sh
+
+
+

In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling.

+

Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input:

+
vim gw.in
+
+
+
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|37|25|28|
+%
+
+
+

After about 3 minutes the calculation should be over and the results collected in folder GW_bnds. The quasiparticle corrections are stored in human-readable form in the file o-GW_bnds.QP, and in netCDF format in the quasiparticle database ndb.QP.

+

In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with ypp, the yambo pre- and post-processing executable.

+
+

Note

+

We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out here on the Yambo wiki.

+
+

Let us enter a computing node interactively

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

and load the yambo module:

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

We can review the options with ypp -h and generate an input file for band structure interpolation with

+
ypp -s b -F ypp_bands.in
+
+
+

Let us modify the resulting input file by selecting the ‘boltztrap’ approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points \(\Gamma-M-K-\Gamma\). We also set 100 points for each high-symmetry line.

+
electrons                        # [R] Electronic properties
+bnds                             # [R] Bands
+PROJECT_mode= "none"             # Instruct ypp how to project the DOS. ATOM, LINE, PLANE.
+INTERP_mode= "BOLTZ"                # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach)
+INTERP_Shell_Fac= 20.00000       # The bigger it is a higher number of shells is used
+INTERP_NofNN= 1                  # Number of Nearest sites in the NN method
+OutputAlat= 5.90008             # [a.u.] Lattice constant used for "alat" ouput format
+cooIn= "rlu"                     # Points coordinates (in) cc/rlu/iku/alat
+cooOut= "rlu"                    # Points coordinates (out) cc/rlu/iku/alat
+% BANDS_bands
+   25 | 28 |                         # Number of bands
+%
+CIRCUIT_E_DB_path= "none"        # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts)
+BANDS_path= ""                   # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL).
+BANDS_steps= 100                  # Number of divisions
+#BANDS_built_in                # Print the bands of the generating points of the circuit using the nearest internal point
+%BANDS_kpts                      # K points of the bands circuit
+ 0.00000 |0.00000 |0.00000 |
+ 0.00000 |0.50000 |0.00000 |
+ 0.33333 |0.33333 |0.00000 |
+ 0.00000 |0.00000 |0.00000 |
+%
+
+
+

Now, let’s run ypp:

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

This run will produce the file o.bands_interpolated. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn’t tell ypp where to look for the quasiparticle corrections, so it went into the SAVE folder and interpolated the DFT data. +Let’s rename the output:

+
mv o.bands_interpolated o.DFT_bands
+mkdir DFT_bands
+mv o.spin* o.magn* DFT_bands/
+
+
+

In order to interpolate the quasiparticle database, we append its location to the ypp input:

+
vim ypp_bands.in
+
+
+

add this line at the end

+
...
+GfnQPdb= "E < ./GW_bnds/ndb.QP"
+
+
+

and run ypp again.

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

When it’s done, let’s rename the new output as

+
mv o.bands_interpolated o.GW_bands
+mkdir GW_bands
+mv o.spin* o.magn* GW_bands/
+
+
+

Now we are ready to visualize the band structures. In order to do so, you can use the script plt_bands.py that should be already available in the directory.

+

We load the python module

+
module load anaconda3/2023.03
+
+
+

and run the script as

+
python plt_bands.py o.DFT_bands o.GW_bands 4
+
+
+

Now we can also exit the computing node

+
exit
+
+
+

The python script should have produced a GW_bands.png file containing the following visualization, which you can copy and open it in your local machine using scp:

+
+_images/gw_bands.png +
+

You may compare this plot with a converged result from this paper (also done with Yambo):

+
+_images/gw_bands_ref.png +
+

Dashed lines: DFT, thick lines: GW.

+

As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations!

+

In order to learn more about Yambo, we suggest visiting the Yambo website. For technical information and tutorials, you can check out the Yambo wiki. If you have issues and questions about installing and running the code, you can write about them on the Yambo forum.

+
+
+
+
+
+

Quick Reference

+
+
+

Instructor’s guide

+
+

Why we teach this lesson

+
+
+

Intended learning outcomes

+
+
+

Timing

+
+
+

Preparing exercises

+

e.g. what to do the day before to set up common repositories.

+
+
+

Other practical aspects

+
+
+

Interesting questions you might get

+
+
+

Typical pitfalls

+
+
+
+
+
+
+
+

About the course

+

In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties.

+

Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers.

+
+

Schedule

+

Day 1, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:15

Welcome and introduction to ENCCS

09:15-09:30

Introduction to Max-CoE and MaX flagship codes

09:30-10:00

Overview of the QE suite of codes and main features

10:00-10:25

Coffee break

10:25-13:00

PWSCF for HPC and GPU

+

Day 2, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

Introduction to Density Functional Perturbation Theory

09:45-10:15

Introduction to Time Dependent Density Functional Perturbation Theory

10:15-10:30

Coffee break

10:30-13:00

Phonons and time dependent properties on HPC and GPU

+

Day 3, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

SIESTA basics

09:45-10:30

Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs

10:30-10:45

Break

10:45-11:15

Basis sets

11:15-12:00

Hands-on tutorial: Basis set optimization

12:00-13:00

Hands-on tutorial: Convergence (k points, mesh, mixing)

+

Day 4, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-10:00

Hands-on tutorial: Moving atoms: geometry optimisation and beyond

10:30-11:00

Hands-on tutorial: Analysis tools

11:00-11:15

Break

11:15-11:45

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

11:45-13:00

Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Day 5, Yambo

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:20

Overview of the Yambo code and its main features and performance

09:20-10:00

Introduction to the GW approximation

10:00-10:20

Coffee break

10:20-13:00

Hands-on tutorial: A guided tour through GW simulations

+
+
+
+

See also

+ +
+\[\]
+
+
+

Credits

+

Contributors to this workshop:

+
    +

  • Pietro Davide Delugas (SISSA)

    • +

  • Ivan Carnimeo (SISSA)

    • +

  • Oscar Baseggio (SISSA)

    • +

  • Fabrizio Ferrari Ruffino (CNR-IOM)

    • +

  • Paolo Giannozzi (CNR-IOM, UniUD)

    • +

  • Iurii Timrov (Paul Scherrer Institut)

    • +

  • Laura Bellentani (CINECA)

    • +

  • Tommaso Gorni (CINECA)

    • +

  • Aurora Ponzi (CNR-IOM)

    • +

  • Emilio Artacho (CIC NanoGUNE and University of Cambridge)

    • +

  • Catalina Coll (ICN2)

    • +

  • José Mª Escartín (ICN2)

    • +

  • Roberta Farris (ICN2)

    • +

  • Ernane de Freitas (ICN2)

    • +

  • Alberto García (ICMAB-CSIC)

    • +

  • Arnold Kole (Utrecht University)

    • +

  • Nick Papior (DTU)

    • +

  • Federico Pedron (ICN2)

    • +

  • Miguel Pruneda (CINN-CSIC)

    • +

  • José Ángel Silva Guillén (IMDEA Nanociencia)

    • +
    • +

    1. Varsano (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Ferretti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sangalli (CNR-ISM)

      2. +
    +
    • +
    • +

    1. Guandalini (Univ. of Rome, La Sapienza)

      2. +
    +
    • +
    • +

    1. Paleari (CNR-NANO)

      2. +
    +
    • +
    • +

    1. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sesti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Spallanzani (CNR-NANO)

      2. +
    +
    • +
+

The lesson file structure and browsing layout is inspired by and derived from +work by CodeRefinery licensed under the MIT license. We have copied and adapted +most of their license text.

+
+
+

Licenses

+
+

General

+
+

Instructional Material

+

Except where otherwise noted, +this instructional material is made available under the +Creative Commons Attribution license (CC-BY-4.0). +The following is a human-readable summary of (and not a substitute for) the +full legal text of the CC-BY-4.0 license. +You are free to:

+
    +

  • share - copy and redistribute the material in any medium or format

    • +

  • adapt - remix, transform, and build upon the material for any purpose, +even commercially.

    • +
+

The licensor cannot revoke these freedoms as long as you follow these license terms:

+
    +

  • Attribution - You must give appropriate credit (mentioning that your work +is derived from work that is Copyright (c) ENCCS and individual contributors and, where practical, linking +to https://enccs.github.io/max-coe-workshop), provide a link to the license, and indicate if changes were +made. You may do so in any reasonable manner, but not in any way that suggests +the licensor endorses you or your use.

    • +

  • No additional restrictions - You may not apply legal terms or +technological measures that legally restrict others from doing anything the +license permits.

    • +
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With the understanding that:

+
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  • You do not have to comply with the license for elements of the material in +the public domain or where your use is permitted by an applicable exception +or limitation.

    • +

  • No warranties are given. The license may not give you all of the permissions +necessary for your intended use. For example, other rights such as +publicity, privacy, or moral rights may limit how you use the material.

    • +
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Software

+

Except where otherwise noted, the example programs and other software provided +with this repository are made available under the OSI-approved +MIT license.

+
+
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+

SIESTA

+

At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved.

+
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© Copyright 2024, The contributors.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
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+
+ + + + \ No newline at end of file diff --git a/branch/main/singlehtml/objects.inv b/branch/main/singlehtml/objects.inv new file mode 100644 index 0000000..eb66522 Binary files /dev/null and b/branch/main/singlehtml/objects.inv differ diff --git a/day5/yambo-tutorial/index.html b/day5/yambo-tutorial/index.html new file mode 100644 index 0000000..6f1d2ce --- /dev/null +++ b/day5/yambo-tutorial/index.html @@ -0,0 +1,1193 @@ + + + + + + + Yambo tutorial: Quasiparticles in the GW approximation — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Yambo tutorial: Quasiparticles in the GW approximation
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Yambo tutorial: Quasiparticles in the GW approximation

+

In this tutorial you will learn how to run a GW simulation using Yambo on a HPC machine.

+

You will compute the quasiparticle corrections to the band structure of a free-standing single layer of MoS\(_2\) while learning about convergence studies, parallel strategies, and GPU calculations.

+

In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate.

+
+../../_images/mos2.png +
+

MoS\(_2\) monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.

+
+

Many-body corrections to the DFT band gap

+

We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of.

+

Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy \(\Sigma\):

+
+\[E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle\]
+

Here \(\epsilon_{nk}\) and \(\psi_{nk}\) are the Kohn-Sham energies and wavefunctions, respectively, while \(V_{xc}\) is the DFT exchange-correlation potential.

+

For each electronic state \(nk\), the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy (\(\Sigma^x\)), and an energy-dependent, usually gap-closing term called the correlation self-energy (\(\Sigma^c\)). These contributions are tackled separately by the code:

+
+\[\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega)\]
+

The energy-dependent dynamical electronic screening \(\varepsilon^{-1}(\omega)\) is included in \(\Sigma^c\) and must therefore be calculated as well.

+

In this way, we can compute the “quasiparticle” corrections \(E^{QP}_{nk}\) to the single-particle Kohn-Sham eigenvalues \(\epsilon_{nk}\). +The typical workflow for a GW calculation is:

+
+../../_images/gwflow.png +
+
+
+

Set up a Yambo calculation

+

Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes):

+
wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+
tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+

You can now enter the tutorial directory

+
cd MoS2_HPC_tutorial_Leonardo
+
+
+
+

Yambo SAVE folder

+

First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo.

+

The QE save folder for MoS\(_2\) is already present at 00_QE-DFT. We should move inside it and then run the p2y executable to generate the uninitialised SAVE.

+

But first, we need to access a node interactively:

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

Finally:

+
cd 00_QE-DFT/mos2.save
+mpirun -np 1 p2y
+
+
+

Now, we need to run the initialization step. Every Yambo run must start with this step. This will be automatically performed when you run Yambo on a SAVE directory for the first time. Just type

+
mpirun -np 1 yambo
+
+
+

and then check the yambo log called l_setup. The initialization step determines the \(G\)-vector shells and the \(k\)- and \(q\)-point grids based on the DFT calculation. If you check inside the SAVE you will see two types of databases. The static ones, starting with ns.*, are directly converted in the p2y step, while the dynamical ones, ndb.* are generated during the initialisation.

+
ls SAVE/
+
+
+
ndb.gops       # info on G-vector shells, etc
+ndb.kindx      # info and k and q meshes
+ns.db1         # info on geometry and KS bands
+ns.kb_pp_pwscf # pseudopotential info
+ns.wf          # wave functions info
+...
+
+
+

The databases are written in netCDF format. +Yambo has produced also a human readable output, r_setup, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections.

+
vim r_setup
+
+
+
[02.01] Unit cells # Lattice geometry info
+==================
+  ...
+[02.02] Symmetries # Symmetry ops. written explicitly
+==================
+  ...
+[02.03] Reciprocal space  # Reciprocal lattice info
+========================
+...
+[02.04] K-grid lattice # k-point coords. written explicitly
+======================
+...
+[02.05] Energies & Occupations # Info on band gaps and occupations
+============================== # DFT eigenvalues
+...
+[03] Transferred momenta grid and indexing # q-points (momentum transfer grid)
+==========================================
+
+
+

Finally, let us move the SAVE and the report file to the directory where we will run the first GW calculation.

+
mv SAVE r_setup ../../01_GW_first_run/
+cd ../../01_GW_first_run/
+
+
+
+
+

Yambo input file

+

Now that we have a working SAVE, it is time to generate the input file we will be using for our first GW calculation.

+

This can be done by the yambo executable via command-line instructions.

+

If you type

+
yambo -h
+
+
+

You will get a list of the possibile options:

+
 ___ __  _____  __ __  _____   _____
+|   Y  ||  _  ||  Y  ||  _  \ |  _  |
+|   |  ||. |  ||.    ||. |  / |. |  |
+ \   _/ |. _  ||.\ / ||. _  \ |. |  |
+  |: |  |: |  ||: |  ||: |   \|: |  |
+  |::|  |:.|:.||:.|:.||::.   /|::.  |
+  `--"  `-- --"`-- --"`-----" `-----"
+ 'A shiny pot of fun and happiness [C.D.Hogan]'
+
+ This is      : yambo
+ Version      : 5.1.0 Revision 21422 Hash fde6e2a07
+ Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO
+
+ Help & version:
+ -help            (-h) <string>   :<string> can be an option (e.g. -h optics)
+ -version                         :Code version & libraries
+
+ Input file & Directories:
+ -Input           (-F) <string>   :Input file
+ -Verbosity       (-V) <string>   :Input file variables verbosity (more with -h Verbosity)
+ -Job             (-J) <string>   :Job string
+ -Idir            (-I) <string>   :Input directory
+ -Odir            (-O) <string>   :I/O directory
+ -Cdir            (-C) <string>   :Communication directory
+
+ Parallel Control:
+ -parenv          (-E) <string>   :Environment Parallel Variables file
+ -nompi                           :Switch off MPI support
+ -noopenmp                        :Switch off OPENMP support
+
+ Initializations:
+ -setup           (-i)            :Initialization
+ -coulomb         (-r)            :Coulomb potential
+
+ Response Functions:
+ -optics          (-o) <string>   :Linear Response optical properties (more with -h optics)
+ -X               (-d) <string>   :Inverse Dielectric Matrix (more with -h X)
+ -dipoles         (-q)            :Oscillator strenghts (or dipoles)
+ -kernel          (-k) <string>   :Kernel (more with -h kernel)
+
+ Self-Energy:
+ -hf              (-x)            :Hartree-Fock
+ -gw0             (-p) <string>   :GW approximation (more with -h gw0)
+ -dyson           (-g) <string>   :Dyson Equation solver (more with -h dyson)
+ -lifetimes       (-l)            :GoWo Quasiparticle lifetimes
+
+ Bethe-Salpeter Equation:
+ -Ksolver         (-y) <string>   :BSE solver (more with -h Ksolver)
+
+ Total Energy:
+ -acfdt                           :ACFDT Total Energy
+
+ Utilites:
+ -Quiet           (-Q)            :Quiet input file creation
+ -fatlog                          :Verbose (fatter) log(s)
+ -DBlist          (-D)            :Databases properties
+ -walltime             <int>      :Walltime (more with -h walltime)
+ -memory               <int>      :Memory (more with -h memory)
+ -slktest                         :ScaLapacK test
+
+ YAMBO developers group (http://www.yambo-code.org)
+
+
+

In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type:

+
yambo -gw0 p -g n -r -V par -F gw.in
+
+
+

Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the slurm scheduler.

+
exit
+
+
+

You can now inspect the input file gw.in and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change.

+

We discuss them below step by step.

+
+
+

Parameters for a GW calculation

+

We start with the runlevels:

+
gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+el_el_corr                       # [R] Electron-Electron Correlation
+dyson                            # [R] Dyson Equation solver
+rim_cut                          # [R] Coulomb potential
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+
+
+
+

Runlevels

+
    +

  • The [R] keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have:

    +
      +

    • rim_cut: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables).

      • +

    • gw0: Yambo learns that it has to run a GW calculation (enables [GW] variables).

      • +

    • HF_and_locXC: calculation of exchange part of the self-energy \(\Sigma^x\) (i.e., Hartree-Fock approximation).

      • +

    • em1d: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute \(\Sigma^c\).

      • +

    • ppa: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables).

      • +

    • dyson: Yambo will solve the Dyson-like quasiparticle equation.

      • +
    +
    • +
+
+

Going through the file we find:

+
EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+
+
+

Recall that we have, for the exchange self-energy:

+
+\[\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q}\]
+
+

Exchange self-energy

+
    +

  • EXXRLvcs controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while VXCRLvcs does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value).

    • +
+
+

Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have:

+
+\[\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega')\]
+

(Here, the \(\rho\)-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.)

+

The calculation is divided in two steps. First, the response function in the plasmon pole approximation (em1d ppa), under the keywords [X] and [Xp], i.e., \(\varepsilon^{-1}_{GG'}(q,\omega)\).

+
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 300 |                     # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+
+
+
+

Response function

+
    +

  • Chimod= "Hartree" indicates that we compute the response function in the Random Phase Approximation (RPA).

    • +

  • BndsRnXp represents the electronic states included in the response function \(\varepsilon\), and is a convergence parameter.

    • +

  • NGsBlkXp is the number of G-vectors used to calculate the RPA response function \(\varepsilon^{-1}_{GG'}\). It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested).

    • +

  • LongDrXp represents the direction of the long-range auxiliary external electric field used to compute \(\varepsilon^{-1}_{GG'}(q)\) at \(q,G\rightarrow 0\). In general you have to be mindful of the system symmetries. In our case, we will put 1 | 1 | 1 to cover all directions.

    • +

  • PPAPntXp= 27.21138 eV is the energy of the plasmon pole. We don’t normally change this.

    • +

  • XTermKind is used to specify a “terminator”: this accelerates numerical convergence with respect to the number of bands BndsRnXp.

    • +
+
+

Next, we have the [GW] group of parameters controlling the next part of the correlation self-energy calculation:

+
% GbndRnge
+   1 | 300 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|7|1|300|
+%
+
+
+
+

Correlation self-energy

+
    +

  • GbndRnge is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator GTermKind.

    • +

  • DysSolver="n" specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method "n".

    • +

  • QPkrange indicates the range of electronic (nk) states for which the GW correction \(\Sigma_{nk}\) is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices.

    • +
+
+

We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should edit now once and for all.

+
RandQpts=1000000                       # [RIM] Number of random q-points in the BZ
+RandGvec= 100                RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+
+
+
+

Coulomb potential

+
    +

  • The [RIM] keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to \(q=0\) and \(G=0\) in the \(q\)-integration of the bare Coulomb interaction - i.e. \(4\pi/(q+G)^2\) - for 2D systems.

    • +

  • The [CUT] keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the \(z\)-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic.

    • +
+
+

Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now.

+
X_and_IO_CPU= ""                 # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= ""               # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=-1      # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_CPU= ""                      # [PARALLEL] CPUs for each role
+DIP_ROLEs= ""                    # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_CPU= ""                       # [PARALLEL] CPUs for each role
+SE_ROLEs= ""                     # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+
+
+

In a GW calculation, the most important parameters to be numerically converged are:

+
    +

  • kpoint mesh (requires multiple nscf DFT runs)

    • +

  • BndsRnXp

    • +

  • NGsBlkXp

    • +

  • GbndRnge

    • +

  • [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs)

    • +
+

From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations.

+
+
+
+
+

The first run

+

We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file r_setup produced when the SAVE folder was initialised. Just search for the string ‘Direct Gap’ and you’ll see that the latter occurs at k-point 7 between bands 13 and 14:

+
  [X] Filled Bands                                  :  13
+  [X] Empty Bands                                   :   14  300
+  [X] Direct Gap                                    :  1.858370 [eV]
+  [X] Direct Gap localized at k                     :  7
+
+
+

In addition, we will set the number of bands in BndsRnXp and GbndRnge to a small value, just to have it run fast. Hence, we modify the input file accordingly (check BndsRnXp, GbndRnge, LongDrXp, QPkrange):

+
rim_cut                          # [R] Coulomb potential
+gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+dyson                            # [R] Dyson Equation solver
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+RandQpts=1000000                 # [RIM] Number of random q-points in the BZ
+RandGvec= 100              RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+% CUTBox
+ 0.000000 | 0.000000 | 0.000000 |        # [CUT] [au] Box sides
+%
+CUTRadius= 0.000000              # [CUT] [au] Sphere/Cylinder radius
+CUTCylLen= 0.000000              # [CUT] [au] Cylinder length
+CUTwsGvec= 0.700000              # [CUT] WS cutoff: number of G to be modified
+EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 20 |                         # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 1.000000 | 1.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+% GbndRnge
+   1 | 20 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+7|7|13|14|
+%
+
+
+

We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. Modify it to suit your specific machine.

+
vim run_first_job.sh
+
+
+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=8
+#SBATCH --partition=boost_usr_prod
+#SBATCH --time=0:05:00
+#SBATCH --gres=gpu:2
+#SBATCH --account=EUHPC_TD02_030
+#SBATCH --job-name=first_job
+
+export OMP_NUM_THREADS=8
+export OMP_PLACES=cores
+export OMP_PROC_BIND=close
+
+# load yambo
+module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \
+        yambo -F gw.in -J job_00_first_run -C out_00_first_run
+
+
+

We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after yambo, it is not going to generate an input file, but rather, run the one specified by -F. Now, go ahead an submit this job

+
sbatch run_first_job.sh
+
+
+

The status of the jobs can be monitored via:

+
squeue -u $USER        # to inspect the status of jobs 
+                       # (hint: make a unix alias, if you like)
+scancel <jobid>        # to delete jobs in the queue
+
+
+

The newly generated databases will be stored in the job directory, as specified by -J, while the report, log and output files will be stored in the communications directory (-C). As this is your first yambo run, take a moment to inspect the report and log files, which you can find inside the -C directory. In these report and log files, you can see the steps performed by yambo. For instance, the code calculates the screening at every k-point and stores it in the PPA database called ndb.pp. By opening the report

+
vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa
+
+
+

you will see

+
[07] Dynamic Dielectric Matrix (PPA)
+ ====================================
+
+ [WR./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy:

+
[09.01] G0W0 (W PPA)
+  ====================
+
+  [  GW  ] Bands range     :   1  20
+  [GW/PPA] G damping       :  0.100000 [eV]
+
+
+  QP @ state[ 1 ] K range:   7   7
+  QP @ state[ 1 ] b range:  13  14
+
+  [RD./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Now, inspect the output file

+
vim out_00_first_run/o-job_00_first_run.qp 
+
+
+
# Vxc  =Slater exchange(X)+Perdew & Zunger(C)
+# Vnlxc=Hartree-Fock
+#
+#    K-point            Band               Eo [eV]            E-Eo [eV]          Sc|Eo [eV]
+#
+         7                 13                 0.000000          -0.025774           0.543987
+         7                 14                 1.858370           3.496193          -0.417555
+# 
+
+
+

In this file, Eo is our starting point (DFT) while E-Eo shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we’ll use some simple commands. First, we get everything that is not a # symbol grep -v '#' and we pass that to another command with a “pipe” |. Then, tail -n 1/head -n 1 will retain the first/last line, and awk '{print $3+$4}' will get us the sum of the third and fourth columns. Altogether, this would be as follows

+
grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}'
+-0.025774
+grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}'
+5.35456
+
+
+

These two commands give us the quasiparticle energies we’ve calculated - their difference is the GW-corrected optical gap.

+
+
+
+

GW convergence

+

In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse \(k\)-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a \(6 \times 6 \times 1\) k-point grid and without spin-orbit coupling: the SAVE we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let’s move into the appropriate directory

+
cd ../02_GW_convergence
+
+
+
+

Response function \(\varepsilon^{-1}_{GG'}\) - Bands and G-vectors

+

We are now ready to start our convergence tests. We’ll begin with the variables controlling the polarization function, i.e., NGsBlkXp for the number of G-vectors and BndsRnXp for the number of bands. For this, we will keep GbndRnge constant at a reasonably high value - you can inspect the input i01-GW

+
vim i01-GW
+
+
+

and check that you have:

+
% GbndRnge
+   1 | 80 |                         # [GW] G[W] bands range
+%
+
+
+

Since we need to run yambo for several values of NGsBlkXp and BndsRnXp, it makes sense to use two nested loops. That is exactly what we did in the submission script run01_converge_pol.sh. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs:

+
sbatch run01_converge_pol.sh
+
+
+
+

Monitoring

+

You can monitor that the job is running by the squeue command

+
sbatch squeue -u $USER
+
+
+

and also by checking the files created in your folder

+
ls -ltr
+
+
+
i01-GW_Xp_20_bands_6_Ry
+job_Xp_20_bands_6_Ry
+out_Xp_20_bands_6_Ry
+i01-GW_Xp_20_bands_8_Ry
+out_Xp_20_bands_8_Ry
+job_Xp_20_bands_8_Ry
+i01-GW_Xp_20_bands_10_Ry
+out_Xp_20_bands_10_Ry
+job_Xp_20_bands_10_Ry
+i01-GW_Xp_20_bands_12_Ry
+out_Xp_20_bands_12_Ry
+job_Xp_20_bands_12_Ry
+summary_01_20bands.txt
+i01-GW_Xp_40_bands_6_Ry
+...
+
+
+

Finally you can monitor how runs are proceeding by looking into the log files

+
tail -f out_Xp_*_bands_*/LOG/*_1
+
+
+
==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <15s> P1: [TIMING]                                          io_WF :      1.1353s CPU (34 calls,   0.033 sec avg)
+ <15s> P1: [TIMING]                                    WF_load_FFT :      1.1538s CPU ( 7 calls,   0.165 sec avg)
+ <15s> P1: [TIMING]                                    io_KB_pwscf :      1.1918s CPU ( 6 calls,   0.199 sec avg)
+ <15s> P1: [TIMING]                              DIPOLE_transverse :      2.4771s CPU
+ <15s> P1: [TIMING]                                    io_fragment :      2.6220s CPU (46 calls,   0.057 sec avg)
+ <15s> P1: [TIMING]                                           io_X :      3.1953s CPU (19 calls,   0.168 sec avg)
+ <15s> P1: [TIMING]                                        Dipoles :      4.4012s CPU
+ <15s> P1: [11] Memory Overview
+ <15s> P1: [12] Game Over & Game summary
+ <15s> P1: [TIMING]            [Time-Profile]: 15s
+
+==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <11s> P1: X@q[6] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[6] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%)
+ <11s> P1: [X-CG] R(p) Tot o/o(of R):   153   504   100
+ <11s> P1: Xo@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%)
+ <11s> P1: X@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock
+
+
+
+

Let’s now have look into the job we just submitted.

+
vim run01_converge_pol.sh
+
+
+

First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file i01-GW is used as a template for every calculation in the loops, so we assign it to a variable.

+
file0='i01-GW'
+
+for POL_BANDS in 20 40 60 80; do
+
+echo 'NGsBlkXp [Ry]   E_vale [eV]   E_cond [eV]' > summary_01_${POL_BANDS}bands.txt
+
+for NGsBlkXp_Ry in 6 8 10 12; do
+
+(...)
+
+done
+done
+
+
+

Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the sed command, in order to generate new files in an automated way (sed replaces any matching string with whatever is provided by the loop variable). Next, we run yambo using the labels to specify different job -J and communication -C directories every time. Finally, we get the quasiparticle energies with grep commands as shown before and append a new line to the summary file. So, inside each loop, we have

+
label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry
+jdir=job_${label}
+cdir=out_${label}
+filein=i01-GW_${label}
+
+sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/;
+      /% BndsRnXp/{n;s/.*/  1 |  ${POL_BANDS} |/}" $file0 > $filein
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir
+
+E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'`
+E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'`
+
+echo ${NGsBlkXp_Ry} '        ' ${E_GW_v} '        ' ${E_GW_c}  >> summary_01_${POL_BANDS}bands.txt
+
+
+

Finally, let us plot this data. First, check that the job has finished with

+
squeue -u $USER
+
+
+
[$USER@login01 02_GW_convergence]$ squeue -u $USER
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+[$USER@login01 02_GW_convergence]$ 
+
+
+

and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven’t done so yet, and then plot:

+
module load anaconda3/2023.03
+python plot-01.py
+
+
+

The plot will produce a fig-01.png file. +You can copy and open it in your local machine with something like

+
[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH]
+scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./
+
+
+

You should get:

+
+../../_images/convergence01.png +
+

For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we’ll make a copy of the corresponding input file:

+
cp i01-GW_Xp_80_bands_10_Ry i02-GW
+
+
+
+
+

Self-energy \(\Sigma^c\) - Bands

+

We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., GbndRnge. This step is actually simpler, since it only involves one loop. This is coded in the provided script run02_converge_Gbnds.noBG.sh. You can look into it

+
vim run02_converge_Gbnds.noBG.sh
+
+
+

and go ahead and submit it.

+
sbatch run02_converge_Gbnds.noBG.sh
+
+
+ +

While this runs, check if the previous job has finished, i.e., you should have a complete summary_02_noBG.txt file by now. +For a visual result, proceed to plot them with

+
python plot-02.py
+
+
+

You should get

+
+../../_images/BG_noBG.png +
+ +

We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication (here). MoS\(_2\) was one of the materials studied there, and it shows that our result, obtained with a \(6 \times 6 \times 1\) k-grid, is simply off the chart (blue line).

+
+../../_images/ref-Guandalini.png +
+

Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9

+ +
+
+
+
+

GW parallel strategies

+
+

MPI parallelization

+

For this section, let us enter the 03_GW_parallel directory. If you were in the 02_GW_convegence folder just do

+
cd ../03_GW_parallel
+
+
+

and inspect the input gw.in. You will see that we set low values for most of the convergence parameters except bands:

+
vim gw.in
+
+
+
FFTGvecs= 40       Ry    # [FFT] Plane-waves
+EXXRLvcs= 2        Ry    # [XX] Exchange RL components
+VXCRLvcs= 2        Ry    # [XC] XCpotential RL components
+% BndsRnXp
+    1 |  300 |               # [Xp] Polarization function bands
+%
+NGsBlkXp= 1            Ry    # [Xp] Response block size
+% GbndRnge
+    1 |  300 |               # [GW] G[W] bands range
+%
+%QPkrange                    # [GW] QP generalized Kpoint/Band indices
+  1| 19| 23| 30|
+%
+
+
+

Note that we also added FFTGvecs to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO ecutwfc, i.e. 60 Ry in this case).

+

In addition, we have deleted all the parallel parameters since we will be setting them via the submission script.

+

Actually we are now dealing with a heavier system than before: as you can see from the QPkrange values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized).

+

For this part of the tutorial, we will be using the slurm submission script job_parallel.sh, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code:

+
DIP_CPU= "1 $ngpu 1"          # [PARALLEL] CPUs for each role
+DIP_ROLEs= "k c v"            # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=  0               # [OPENMP/X] Number of threads for dipoles
+X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= "q g k c v"   # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=1    # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=  0                 # [OPENMP/X] Number of threads for response functions
+SE_CPU= "1 $ngpu 1"           # [PARALLEL] CPUs for each role
+SE_ROLEs= "q qp b"            # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=  0                # [OPENMP/GW] Number of threads for self-energy
+
+
+

The keyword DIP refers to the calculations of the screening matrix elements (also called “dipoles”) needed for the screening function, X is the screening function itself (it stands for \(\chi\) since it is a response function), SE the self-energy. +These three sections of the code can be parallelised independently.

+

We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI task is run on a single card, therefore ntasks=ngpu.

+
+

Note

+
    +

  • In this subsection we are mainly concerned with the [PARALLEL] variables which refer to MPI tasks (distributed memory).

    • +

  • What about [OPENMP] parallelisation (i.e., adding threads with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are not run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup for CPUs is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later.

    • +
+
+

We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as:

+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

and submit the job

+
sbatch job_parallel.sh
+
+
+

This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report r-* file and the log l-* files, and inspect them while the calculation runs. +For simplicity you can just type

+
tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1
+
+
+

to monitor the progress in the master thread (Ctrl+c to exit). +As you can see, the run takes some time, even though we are using minimal parameters.

+

Meanwhile, we can run other jobs increasing the parallelisation. Let’s employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the job_parallel.sh script changing

+
#!/bin/bash
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing nodes appropriately. Finally, you can try to produce a scaling plot.

+

The timings are contained in the r-* report files. You can already have a look at them typing

+
grep Time-Profile run_MPI*/r-*
+
+
+

The python script parse_ytiming.py is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided.

+

If you didn’t do so already, load the python module

+
module load anaconda3/2023.03
+
+
+

Then, after your jobs have finished, run the script as

+
python parse_ytiming.py run_MPI
+
+
+

to look for a report file in each run_MPI*.out folder. Make sure you have only one report file per folder. +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis.

+
+../../_images/gw_scaling.png +
+

What can we learn from this plot? In particular, try to answer the following questions:

+
    +

  • Up to which number of MPI tasks our system scales efficiently?

    • +

  • How can we decide at which point adding more nodes to the calculation becomes a waste of resources?

    • +
+
+

Note

+

Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, Yambo has been shown to scale well up to tens of thousands of MPI tasks! (See the next optional box for an example)

+
+ +

.

+ +
+
+
+
+

Full GW band structure

+

This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS\(_2\).

+

This is a massive calculation, so run it right now and we’ll discuss it in the meantime:

+
cd ../04_GW_bands
+sbatch gpu_job.sh
+
+
+

In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling.

+

Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input:

+
vim gw.in
+
+
+
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|37|25|28|
+%
+
+
+

After about 3 minutes the calculation should be over and the results collected in folder GW_bnds. The quasiparticle corrections are stored in human-readable form in the file o-GW_bnds.QP, and in netCDF format in the quasiparticle database ndb.QP.

+

In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with ypp, the yambo pre- and post-processing executable.

+
+

Note

+

We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out here on the Yambo wiki.

+
+

Let us enter a computing node interactively

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

and load the yambo module:

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

We can review the options with ypp -h and generate an input file for band structure interpolation with

+
ypp -s b -F ypp_bands.in
+
+
+

Let us modify the resulting input file by selecting the ‘boltztrap’ approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points \(\Gamma-M-K-\Gamma\). We also set 100 points for each high-symmetry line.

+
electrons                        # [R] Electronic properties
+bnds                             # [R] Bands
+PROJECT_mode= "none"             # Instruct ypp how to project the DOS. ATOM, LINE, PLANE.
+INTERP_mode= "BOLTZ"                # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach)
+INTERP_Shell_Fac= 20.00000       # The bigger it is a higher number of shells is used
+INTERP_NofNN= 1                  # Number of Nearest sites in the NN method
+OutputAlat= 5.90008             # [a.u.] Lattice constant used for "alat" ouput format
+cooIn= "rlu"                     # Points coordinates (in) cc/rlu/iku/alat
+cooOut= "rlu"                    # Points coordinates (out) cc/rlu/iku/alat
+% BANDS_bands
+   25 | 28 |                         # Number of bands
+%
+CIRCUIT_E_DB_path= "none"        # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts)
+BANDS_path= ""                   # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL).
+BANDS_steps= 100                  # Number of divisions
+#BANDS_built_in                # Print the bands of the generating points of the circuit using the nearest internal point
+%BANDS_kpts                      # K points of the bands circuit
+ 0.00000 |0.00000 |0.00000 |
+ 0.00000 |0.50000 |0.00000 |
+ 0.33333 |0.33333 |0.00000 |
+ 0.00000 |0.00000 |0.00000 |
+%
+
+
+

Now, let’s run ypp:

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

This run will produce the file o.bands_interpolated. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn’t tell ypp where to look for the quasiparticle corrections, so it went into the SAVE folder and interpolated the DFT data. +Let’s rename the output:

+
mv o.bands_interpolated o.DFT_bands
+mkdir DFT_bands
+mv o.spin* o.magn* DFT_bands/
+
+
+

In order to interpolate the quasiparticle database, we append its location to the ypp input:

+
vim ypp_bands.in
+
+
+

add this line at the end

+
...
+GfnQPdb= "E < ./GW_bnds/ndb.QP"
+
+
+

and run ypp again.

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

When it’s done, let’s rename the new output as

+
mv o.bands_interpolated o.GW_bands
+mkdir GW_bands
+mv o.spin* o.magn* GW_bands/
+
+
+

Now we are ready to visualize the band structures. In order to do so, you can use the script plt_bands.py that should be already available in the directory.

+

We load the python module

+
module load anaconda3/2023.03
+
+
+

and run the script as

+
python plt_bands.py o.DFT_bands o.GW_bands 4
+
+
+

Now we can also exit the computing node

+
exit
+
+
+

The python script should have produced a GW_bands.png file containing the following visualization, which you can copy and open it in your local machine using scp:

+
+../../_images/gw_bands.png +
+

You may compare this plot with a converged result from this paper (also done with Yambo):

+
+../../_images/gw_bands_ref.png +
+

Dashed lines: DFT, thick lines: GW.

+

As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations!

+

In order to learn more about Yambo, we suggest visiting the Yambo website. For technical information and tutorials, you can check out the Yambo wiki. If you have issues and questions about installing and running the code, you can write about them on the Yambo forum.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/days3+4/day3/index.html b/days3+4/day3/index.html new file mode 100644 index 0000000..bcdbd0f --- /dev/null +++ b/days3+4/day3/index.html @@ -0,0 +1,220 @@ + + + + + + + Day 3: SIESTA I — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Day 3: SIESTA I

+
+

SIESTA basics

+

Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge).

+

Slides available here: SIESTA-Intro.pdf.

+
+
+

A first contact with SIESTA: inputs, execution and outputs

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-First_encounter.pdf.

+
+
+

Basis sets

+

Lecture by Dr. Miguel Pruneda (CINN-CSIC).

+

Slides available here: SIESTA-Basis_sets.pdf.

+
+
+

Basis set optimization

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets
+
+
+

Introductory slides available here: SIESTA-Basis_set_optimization.pdf.

+
+
+

Convergence (k points, mesh, mixing)

+

Practical session led by Dr. Catalina Coll (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-Convergence.pdf.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/days3+4/day4/index.html b/days3+4/day4/index.html new file mode 100644 index 0000000..9174f14 --- /dev/null +++ b/days3+4/day4/index.html @@ -0,0 +1,199 @@ + + + + + + + Day 4: SIESTA II — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Day 4: SIESTA II

+
+

Molecular Dynamics with SIESTA

+

Practical session led by Dr. Ernane de Freitas (ICN2).

+

Tutorials covered:

+
    +

  • Molecular Dynamics. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-MD.pdf.

+
+
+

Analysis tools

+

Practical session led by Dr. Miguel Pruneda (CINN-CSIC).

+

Tutorials covered:

+
    +

  • Analysis tools. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-Analysis_tools.pdf.

+
+
+

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

+

Lecture by Dr. Nick Papior (Technical University of Denmark).

+

Slides available here: SIESTA-Features.pdf.

+
+
+

Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Practical session led by Dr. Alberto García (ICMAB-CSIC).

+

Tutorials covered:

+
    +

  • ELSI-ELPA.

    • +

  • ELSI-PEXSI.

    • +
+

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers
+
+
+

Slides available here: SIESTA-Solvers.pdf.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/days3+4/setup/index.html b/days3+4/setup/index.html new file mode 100644 index 0000000..31ed90a --- /dev/null +++ b/days3+4/setup/index.html @@ -0,0 +1,205 @@ + + + + + + + SIESTA setup — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

SIESTA setup

+
+

Directory with tutorials

+

For every practical there is a folder in the shared directory +/leonardo_work/EUHPC_TD02_030/siesta-tutorials that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:

+
$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I .
+
+
+

Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts.

+
+
+

Running SIESTA

+

You will find a sample script on how to run SIESTA in +/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh:

+
#!/bin/bash
+#SBATCH -J tutorialXX
+#SBATCH -n 8
+#SBATCH -t 0:30:00
+#SBATCH -o %x-%j.out
+#SBATCH -e %x-%j.err
+#SBATCH --partition=boost_usr_prod
+#SBATCH -D .
+
+# DO NOT CHANGE THIS LINE
+source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh
+
+# EDIT THE CORRECT INPUT AND OUTPUT FILES.
+srun -n 8 siesta < input.fdf > output.out
+
+
+

Note that input.fdf and output.out are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(#SBATCH -J option) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue.

+
+
+

Suggested Software for Visualization

+

If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences.

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex/index.html b/genindex/index.html new file mode 100644 index 0000000..65a060c --- /dev/null +++ b/genindex/index.html @@ -0,0 +1,146 @@ + + + + + + Index — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ + +

Index

+ +
+ +
+ + +
+
+
+ +
+ +
+

© Copyright 2024, The contributors.

+
+ + Built with Sphinx using a + theme + provided by Read the Docs. + + +
+
+
+
+
+ + + + \ No newline at end of file diff --git a/guide/index.html b/guide/index.html new file mode 100644 index 0000000..00ba9f1 --- /dev/null +++ b/guide/index.html @@ -0,0 +1,177 @@ + + + + + + + Instructor’s guide — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Instructor’s guide

+
+

Why we teach this lesson

+
+
+

Intended learning outcomes

+
+
+

Timing

+
+
+

Preparing exercises

+

e.g. what to do the day before to set up common repositories.

+
+
+

Other practical aspects

+
+
+

Interesting questions you might get

+
+
+

Typical pitfalls

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..d059540 --- /dev/null +++ b/index.html @@ -0,0 +1,505 @@ + + + + + + + Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo
    • +
  • + Edit on GitHub +
    • +
+
+
+
+
+ +
+

Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo

+

In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential.

+

This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises.

+

QUANTUM ESPRESSO is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications.

+

SIESTA is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a “good first approximation” to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA.

+

YAMBO is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc).

+

MAX (MAterials design at the eXascale) is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX’s challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials’ domain.

+
+

Prerequisites

+
    +

  • Some familiarity with density functional theory (DFT), self-consistent +field (SCF) calculations and plane wave basis sets is desirable as the +workshop will not cover the fundamental theory of these topics.

    • +

  • Familiarity with working in a Linux environment and some experience with +working on an HPC system is needed to participate in the hands-on exercises.

    • +
+
+
+

Who is the course for?

+

This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations.

+
+
+
+
+
+

Days 3 and 4 - Siesta

+ +
+
+

Day 5 - Yambo

+ +
+
+

Reference

+ +
+
+

About

+ +
+
+
+

About the course

+

In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties.

+

Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers.

+
+

Schedule

+

Day 1, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:15

Welcome and introduction to ENCCS

09:15-09:30

Introduction to Max-CoE and MaX flagship codes

09:30-10:00

Overview of the QE suite of codes and main features

10:00-10:25

Coffee break

10:25-13:00

PWSCF for HPC and GPU

+

Day 2, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

Introduction to Density Functional Perturbation Theory

09:45-10:15

Introduction to Time Dependent Density Functional Perturbation Theory

10:15-10:30

Coffee break

10:30-13:00

Phonons and time dependent properties on HPC and GPU

+

Day 3, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

SIESTA basics

09:45-10:30

Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs

10:30-10:45

Break

10:45-11:15

Basis sets

11:15-12:00

Hands-on tutorial: Basis set optimization

12:00-13:00

Hands-on tutorial: Convergence (k points, mesh, mixing)

+

Day 4, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-10:00

Hands-on tutorial: Moving atoms: geometry optimisation and beyond

10:30-11:00

Hands-on tutorial: Analysis tools

11:00-11:15

Break

11:15-11:45

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

11:45-13:00

Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Day 5, Yambo

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:20

Overview of the Yambo code and its main features and performance

09:20-10:00

Introduction to the GW approximation

10:00-10:20

Coffee break

10:20-13:00

Hands-on tutorial: A guided tour through GW simulations

+
+
+
+

See also

+ +
+\[\]
+
+
+

Credits

+

Contributors to this workshop:

+
    +

  • Pietro Davide Delugas (SISSA)

    • +

  • Ivan Carnimeo (SISSA)

    • +

  • Oscar Baseggio (SISSA)

    • +

  • Fabrizio Ferrari Ruffino (CNR-IOM)

    • +

  • Paolo Giannozzi (CNR-IOM, UniUD)

    • +

  • Iurii Timrov (Paul Scherrer Institut)

    • +

  • Laura Bellentani (CINECA)

    • +

  • Tommaso Gorni (CINECA)

    • +

  • Aurora Ponzi (CNR-IOM)

    • +

  • Emilio Artacho (CIC NanoGUNE and University of Cambridge)

    • +

  • Catalina Coll (ICN2)

    • +

  • José Mª Escartín (ICN2)

    • +

  • Roberta Farris (ICN2)

    • +

  • Ernane de Freitas (ICN2)

    • +

  • Alberto García (ICMAB-CSIC)

    • +

  • Arnold Kole (Utrecht University)

    • +

  • Nick Papior (DTU)

    • +

  • Federico Pedron (ICN2)

    • +

  • Miguel Pruneda (CINN-CSIC)

    • +

  • José Ángel Silva Guillén (IMDEA Nanociencia)

    • +
    • +

    1. Varsano (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Ferretti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sangalli (CNR-ISM)

      2. +
    +
    • +
    • +

    1. Guandalini (Univ. of Rome, La Sapienza)

      2. +
    +
    • +
    • +

    1. Paleari (CNR-NANO)

      2. +
    +
    • +
    • +

    1. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sesti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Spallanzani (CNR-NANO)

      2. +
    +
    • +
+

The lesson file structure and browsing layout is inspired by and derived from +work by CodeRefinery licensed under the MIT license. We have copied and adapted +most of their license text.

+
+
+

Licenses

+
+

General

+
+

Instructional Material

+

Except where otherwise noted, +this instructional material is made available under the +Creative Commons Attribution license (CC-BY-4.0). +The following is a human-readable summary of (and not a substitute for) the +full legal text of the CC-BY-4.0 license. +You are free to:

+
    +

  • share - copy and redistribute the material in any medium or format

    • +

  • adapt - remix, transform, and build upon the material for any purpose, +even commercially.

    • +
+

The licensor cannot revoke these freedoms as long as you follow these license terms:

+
    +

  • Attribution - You must give appropriate credit (mentioning that your work +is derived from work that is Copyright (c) ENCCS and individual contributors and, where practical, linking +to https://enccs.github.io/max-coe-workshop), provide a link to the license, and indicate if changes were +made. You may do so in any reasonable manner, but not in any way that suggests +the licensor endorses you or your use.

    • +

  • No additional restrictions - You may not apply legal terms or +technological measures that legally restrict others from doing anything the +license permits.

    • +
+

With the understanding that:

+
    +

  • You do not have to comply with the license for elements of the material in +the public domain or where your use is permitted by an applicable exception +or limitation.

    • +

  • No warranties are given. The license may not give you all of the permissions +necessary for your intended use. For example, other rights such as +publicity, privacy, or moral rights may limit how you use the material.

    • +
+
+
+

Software

+

Except where otherwise noted, the example programs and other software provided +with this repository are made available under the OSI-approved +MIT license.

+
+
+
+

SIESTA

+

At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved.

+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lesson.pdf b/lesson.pdf new file mode 100644 index 0000000..4ad4322 Binary files /dev/null and b/lesson.pdf differ diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..21a735b Binary files /dev/null and b/objects.inv differ diff --git a/quick-reference/index.html b/quick-reference/index.html new file mode 100644 index 0000000..6a25b17 --- /dev/null +++ b/quick-reference/index.html @@ -0,0 +1,148 @@ + + + + + + + Quick Reference — Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
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+ } +} \ No newline at end of file diff --git a/singlehtml/_static/check-solid.svg b/singlehtml/_static/check-solid.svg new file mode 100644 index 0000000..92fad4b --- /dev/null +++ b/singlehtml/_static/check-solid.svg @@ -0,0 +1,4 @@ + + + + diff --git a/singlehtml/_static/clipboard.min.js b/singlehtml/_static/clipboard.min.js new file mode 100644 index 0000000..54b3c46 --- /dev/null +++ b/singlehtml/_static/clipboard.min.js @@ -0,0 +1,7 @@ +/*! + * clipboard.js v2.0.8 + * https://clipboardjs.com/ + * + * Licensed MIT © Zeno Rocha + */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 + + + + diff --git a/singlehtml/_static/copybutton.css b/singlehtml/_static/copybutton.css new file mode 100644 index 0000000..f1916ec --- /dev/null +++ b/singlehtml/_static/copybutton.css @@ -0,0 +1,94 @@ +/* Copy buttons */ +button.copybtn { + position: absolute; + display: flex; + top: .3em; + right: .3em; + width: 1.7em; + height: 1.7em; + opacity: 0; + transition: opacity 0.3s, border .3s, background-color .3s; + user-select: none; + padding: 0; + border: none; + outline: none; + border-radius: 0.4em; + /* The colors that GitHub uses */ + border: #1b1f2426 1px solid; + background-color: #f6f8fa; + color: #57606a; +} + +button.copybtn.success { + border-color: #22863a; + color: #22863a; +} + +button.copybtn svg { + stroke: currentColor; + width: 1.5em; + height: 1.5em; + padding: 0.1em; +} + +div.highlight { + position: relative; +} + +/* Show the copybutton */ +.highlight:hover button.copybtn, button.copybtn.success { + opacity: 1; +} + +.highlight button.copybtn:hover { + background-color: rgb(235, 235, 235); +} + +.highlight button.copybtn:active { + background-color: rgb(187, 187, 187); +} + +/** + * A minimal CSS-only tooltip copied from: + * https://codepen.io/mildrenben/pen/rVBrpK + * + * To use, write HTML like the following: + * + *

Short

+ */ + .o-tooltip--left { + position: relative; + } + + .o-tooltip--left:after { + opacity: 0; + visibility: hidden; + position: absolute; + content: attr(data-tooltip); + padding: .2em; + font-size: .8em; + left: -.2em; + background: grey; + color: white; + white-space: nowrap; + z-index: 2; + border-radius: 2px; + transform: translateX(-102%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); +} + +.o-tooltip--left:hover:after { + display: block; + opacity: 1; + visibility: visible; + transform: translateX(-100%) translateY(0); + transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); + transition-delay: .5s; +} + +/* By default the copy button shouldn't show up when printing a page */ +@media print { + button.copybtn { + display: none; + } +} diff --git a/singlehtml/_static/copybutton.js b/singlehtml/_static/copybutton.js new file mode 100644 index 0000000..2ea7ff3 --- /dev/null +++ b/singlehtml/_static/copybutton.js @@ -0,0 +1,248 @@ +// Localization support +const messages = { + 'en': { + 'copy': 'Copy', + 'copy_to_clipboard': 'Copy to clipboard', + 'copy_success': 'Copied!', + 'copy_failure': 'Failed to copy', + }, + 'es' : { + 'copy': 'Copiar', + 'copy_to_clipboard': 'Copiar al portapapeles', + 'copy_success': '¡Copiado!', + 'copy_failure': 'Error al copiar', + }, + 'de' : { + 'copy': 'Kopieren', + 'copy_to_clipboard': 'In die Zwischenablage kopieren', + 'copy_success': 'Kopiert!', + 'copy_failure': 'Fehler beim Kopieren', + }, + 'fr' : { + 'copy': 'Copier', + 'copy_to_clipboard': 'Copier dans le presse-papier', + 'copy_success': 'Copié !', + 'copy_failure': 'Échec de la copie', + }, + 'ru': { + 'copy': 'Скопировать', + 'copy_to_clipboard': 'Скопировать в буфер', + 'copy_success': 'Скопировано!', + 'copy_failure': 'Не удалось скопировать', + }, + 'zh-CN': { + 'copy': '复制', + 'copy_to_clipboard': '复制到剪贴板', + 'copy_success': '复制成功!', + 'copy_failure': '复制失败', + }, + 'it' : { + 'copy': 'Copiare', + 'copy_to_clipboard': 'Copiato negli appunti', + 'copy_success': 'Copiato!', + 'copy_failure': 'Errore durante la copia', + } +} + +let locale = 'en' +if( document.documentElement.lang !== undefined + && messages[document.documentElement.lang] !== undefined ) { + locale = document.documentElement.lang +} + +let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; +if (doc_url_root == '#') { + doc_url_root = ''; +} + +/** + * SVG files for our copy buttons + */ +let iconCheck = ` + ${messages[locale]['copy_success']} + + +` + +// If the user specified their own SVG use that, otherwise use the default +let iconCopy = ``; +if (!iconCopy) { + iconCopy = ` + ${messages[locale]['copy_to_clipboard']} + + + +` +} + +/** + * Set up copy/paste for code blocks + */ + +const runWhenDOMLoaded = cb => { + if (document.readyState != 'loading') { + cb() + } else if (document.addEventListener) { + document.addEventListener('DOMContentLoaded', cb) + } else { + document.attachEvent('onreadystatechange', function() { + if (document.readyState == 'complete') cb() + }) + } +} + +const codeCellId = index => `codecell${index}` + +// Clears selected text since ClipboardJS will select the text when copying +const clearSelection = () => { + if (window.getSelection) { + window.getSelection().removeAllRanges() + } else if (document.selection) { + document.selection.empty() + } +} + +// Changes tooltip text for a moment, then changes it back +// We want the timeout of our `success` class to be a bit shorter than the +// tooltip and icon change, so that we can hide the icon before changing back. +var timeoutIcon = 2000; +var timeoutSuccessClass = 1500; + +const temporarilyChangeTooltip = (el, oldText, newText) => { + el.setAttribute('data-tooltip', newText) + el.classList.add('success') + // Remove success a little bit sooner than we change the tooltip + // So that we can use CSS to hide the copybutton first + setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) + setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) +} + +// Changes the copy button icon for two seconds, then changes it back +const temporarilyChangeIcon = (el) => { + el.innerHTML = iconCheck; + setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) +} + +const addCopyButtonToCodeCells = () => { + // If ClipboardJS hasn't loaded, wait a bit and try again. This + // happens because we load ClipboardJS asynchronously. + if (window.ClipboardJS === undefined) { + setTimeout(addCopyButtonToCodeCells, 250) + return + } + + // Add copybuttons to all of our code cells + const COPYBUTTON_SELECTOR = 'div.highlight pre'; + const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + codeCells.forEach((codeCell, index) => { + const id = codeCellId(index) + codeCell.setAttribute('id', id) + + const clipboardButton = id => + `` + codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) + }) + +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} + + +var copyTargetText = (trigger) => { + var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); + + // get filtered text + let exclude = '.linenos'; + + let text = filterText(target, exclude); + return formatCopyText(text, '', false, true, true, true, '', '') +} + + // Initialize with a callback so we can modify the text before copy + const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) + + // Update UI with error/success messages + clipboard.on('success', event => { + clearSelection() + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) + temporarilyChangeIcon(event.trigger) + }) + + clipboard.on('error', event => { + temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) + }) +} + +runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/singlehtml/_static/copybutton_funcs.js b/singlehtml/_static/copybutton_funcs.js new file mode 100644 index 0000000..dbe1aaa --- /dev/null +++ b/singlehtml/_static/copybutton_funcs.js @@ -0,0 +1,73 @@ +function escapeRegExp(string) { + return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string +} + +/** + * Removes excluded text from a Node. + * + * @param {Node} target Node to filter. + * @param {string} exclude CSS selector of nodes to exclude. + * @returns {DOMString} Text from `target` with text removed. + */ +export function filterText(target, exclude) { + const clone = target.cloneNode(true); // clone as to not modify the live DOM + if (exclude) { + // remove excluded nodes + clone.querySelectorAll(exclude).forEach(node => node.remove()); + } + return clone.innerText; +} + +// Callback when a copy button is clicked. Will be passed the node that was clicked +// should then grab the text and replace pieces of text that shouldn't be used in output +export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; + var match; + + // Do we check for line continuation characters and "HERE-documents"? + var useLineCont = !!lineContinuationChar + var useHereDoc = !!hereDocDelim + + // create regexp to capture prompt and remaining line + if (isRegexp) { + regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') + } else { + regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') + } + + const outputLines = []; + var promptFound = false; + var gotLineCont = false; + var gotHereDoc = false; + const lineGotPrompt = []; + for (const line of textContent.split('\n')) { + match = line.match(regexp) + if (match || gotLineCont || gotHereDoc) { + promptFound = regexp.test(line) + lineGotPrompt.push(promptFound) + if (removePrompts && promptFound) { + outputLines.push(match[2]) + } else { + outputLines.push(line) + } + gotLineCont = line.endsWith(lineContinuationChar) & useLineCont + if (line.includes(hereDocDelim) & useHereDoc) + gotHereDoc = !gotHereDoc + } else if (!onlyCopyPromptLines) { + outputLines.push(line) + } else if (copyEmptyLines && line.trim() === '') { + outputLines.push(line) + } + } + + // If no lines with the prompt were found then just use original lines + if (lineGotPrompt.some(v => v === true)) { + textContent = outputLines.join('\n'); + } + + // Remove a trailing newline to avoid auto-running when pasting + if (textContent.endsWith("\n")) { + textContent = textContent.slice(0, -1) + } + return textContent +} diff --git a/singlehtml/_static/css/badge_only.css b/singlehtml/_static/css/badge_only.css new file mode 100644 index 0000000..c718cee --- /dev/null +++ b/singlehtml/_static/css/badge_only.css @@ -0,0 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+ return this; // for chaining... + } +})(jQuery); + +// NO good way to do this!. Copy a hack from here +// https://stackoverflow.com/questions/901115/how-can-i-get-query-string-values-in-javascript +// https://stackoverflow.com/a/2880929 +var urlParams; +(window.onpopstate = function () { + var match, + pl = /\+/g, // Regex for replacing addition symbol with a space + search = /([^&=]+)=?([^&]*)/g, + decode = function (s) { return decodeURIComponent(s.replace(pl, " ")); }, + query = window.location.search.substring(1); + urlParams = {}; + while (match = search.exec(query)) + urlParams[decode(match[1])] = decode(match[2]); +})(); + +// Select heading levels +var maxHeading = urlParams['h'] +if (maxHeading === undefined) maxHeading = 2 +var headingLevels = []; +for (h=2 ; h (sections.length-1) ) { + // if we would scroll past bottom, or above top, do nothing + return; + } + + console.log('xxxxxx'); + var targetSection = sections[targetPos]; + console.log(targetSection, typeof(targetSection)); + + // Return targetSection top and height + var secProperties = section_top_and_height(targetSection); 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+} + +/* Pandas tables. Pulled from the Jupyter / nbsphinx CSS */ +div.cell_output table { + border: none; + border-collapse: collapse; + border-spacing: 0; + color: black; + font-size: 1em; + table-layout: fixed; +} + +div.cell_output thead { + border-bottom: 1px solid black; + vertical-align: bottom; +} + +div.cell_output tr, +div.cell_output th, +div.cell_output td { + text-align: right; + vertical-align: middle; + padding: 0.5em 0.5em; + line-height: normal; + white-space: normal; + max-width: none; + border: none; +} + +div.cell_output th { + font-weight: bold; +} + +div.cell_output tbody tr:nth-child(odd) { + background: #f5f5f5; +} + +div.cell_output tbody tr:hover { + background: rgba(66, 165, 245, 0.2); +} + +/** source code line numbers **/ +span.linenos { + opacity: 0.5; +} + +/* Inline text from `paste` operation */ + +span.pasted-text { + font-weight: bold; +} + +span.pasted-inline img { + max-height: 2em; +} + +tbody span.pasted-inline img { + max-height: none; +} + +/* Font colors for 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background-color: #E75C58 +} + +div.highlight .-Color[class*=-BGGreen] { + background-color: #00A250 +} + +div.highlight .-Color[class*=-BGYellow] { + background-color: #DDB62B +} + +div.highlight .-Color[class*=-BGBlue] { + background-color: #208FFB +} + +div.highlight .-Color[class*=-BGMagenta] { + background-color: #D160C4 +} + +div.highlight .-Color[class*=-BGCyan] { + background-color: #60C6C8 +} + +div.highlight .-Color[class*=-BGWhite] { + background-color: #C5C1B4 +} + +/* Font colors for 8-bit ANSI */ + +div.highlight .-Color[class*=-C0] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC0] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C1] { + color: #800000 +} + +div.highlight .-Color[class*=-BGC1] { + background-color: #800000 +} + +div.highlight .-Color[class*=-C2] { + color: #008000 +} + +div.highlight .-Color[class*=-BGC2] { + background-color: #008000 +} + +div.highlight .-Color[class*=-C3] { + color: #808000 +} + +div.highlight .-Color[class*=-BGC3] { + background-color: #808000 +} + +div.highlight .-Color[class*=-C4] { + color: #000080 +} + +div.highlight .-Color[class*=-BGC4] { + background-color: #000080 +} + +div.highlight .-Color[class*=-C5] { + color: #800080 +} + +div.highlight .-Color[class*=-BGC5] { + background-color: #800080 +} + +div.highlight .-Color[class*=-C6] { + color: #008080 +} + +div.highlight .-Color[class*=-BGC6] { + background-color: #008080 +} + +div.highlight .-Color[class*=-C7] { + color: #C0C0C0 +} + +div.highlight .-Color[class*=-BGC7] { + background-color: #C0C0C0 +} + +div.highlight .-Color[class*=-C8] { + color: #808080 +} + +div.highlight .-Color[class*=-BGC8] { + background-color: #808080 +} + +div.highlight .-Color[class*=-C9] { + color: #FF0000 +} + +div.highlight .-Color[class*=-BGC9] { + background-color: #FF0000 +} + +div.highlight .-Color[class*=-C10] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC10] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C11] { + color: #FFFF00 +} + +div.highlight .-Color[class*=-BGC11] { + background-color: #FFFF00 +} + +div.highlight .-Color[class*=-C12] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC12] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C13] { + color: #FF00FF +} + +div.highlight .-Color[class*=-BGC13] { + background-color: #FF00FF +} + +div.highlight .-Color[class*=-C14] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC14] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C15] { + color: #FFFFFF +} + +div.highlight .-Color[class*=-BGC15] { + background-color: #FFFFFF +} + +div.highlight .-Color[class*=-C16] { + color: #000000 +} + +div.highlight .-Color[class*=-BGC16] { + background-color: #000000 +} + +div.highlight .-Color[class*=-C17] { + color: #00005F +} + +div.highlight .-Color[class*=-BGC17] { + background-color: #00005F +} + +div.highlight .-Color[class*=-C18] { + color: #000087 +} + +div.highlight .-Color[class*=-BGC18] { + background-color: #000087 +} + +div.highlight .-Color[class*=-C19] { + color: #0000AF +} + +div.highlight .-Color[class*=-BGC19] { + background-color: #0000AF +} + +div.highlight .-Color[class*=-C20] { + color: #0000D7 +} + +div.highlight .-Color[class*=-BGC20] { + background-color: #0000D7 +} + +div.highlight .-Color[class*=-C21] { + color: #0000FF +} + +div.highlight .-Color[class*=-BGC21] { + background-color: #0000FF +} + +div.highlight .-Color[class*=-C22] { + color: #005F00 +} + +div.highlight .-Color[class*=-BGC22] { + background-color: #005F00 +} + +div.highlight .-Color[class*=-C23] { + color: #005F5F +} + +div.highlight .-Color[class*=-BGC23] { + background-color: #005F5F +} + +div.highlight .-Color[class*=-C24] { + color: #005F87 +} + +div.highlight .-Color[class*=-BGC24] { + background-color: #005F87 +} + +div.highlight .-Color[class*=-C25] { + color: #005FAF +} + +div.highlight .-Color[class*=-BGC25] { + background-color: #005FAF +} + +div.highlight .-Color[class*=-C26] { + color: #005FD7 +} + +div.highlight .-Color[class*=-BGC26] { + background-color: #005FD7 +} + +div.highlight .-Color[class*=-C27] { + color: #005FFF +} + +div.highlight .-Color[class*=-BGC27] { + background-color: #005FFF +} + +div.highlight .-Color[class*=-C28] { + color: #008700 +} + +div.highlight .-Color[class*=-BGC28] { + background-color: #008700 +} + +div.highlight .-Color[class*=-C29] { + color: #00875F +} + +div.highlight .-Color[class*=-BGC29] { + background-color: #00875F +} + +div.highlight .-Color[class*=-C30] { + color: #008787 +} + +div.highlight .-Color[class*=-BGC30] { + background-color: #008787 +} + +div.highlight .-Color[class*=-C31] { + color: #0087AF +} + +div.highlight .-Color[class*=-BGC31] { + background-color: #0087AF +} + +div.highlight .-Color[class*=-C32] { + color: #0087D7 +} + +div.highlight .-Color[class*=-BGC32] { + background-color: #0087D7 +} + +div.highlight .-Color[class*=-C33] { + color: #0087FF +} + +div.highlight .-Color[class*=-BGC33] { + background-color: #0087FF +} + +div.highlight .-Color[class*=-C34] { + color: #00AF00 +} + +div.highlight .-Color[class*=-BGC34] { + background-color: #00AF00 +} + +div.highlight .-Color[class*=-C35] { + color: #00AF5F +} + +div.highlight .-Color[class*=-BGC35] { + background-color: #00AF5F +} + +div.highlight .-Color[class*=-C36] { + color: #00AF87 +} + +div.highlight .-Color[class*=-BGC36] { + background-color: #00AF87 +} + +div.highlight .-Color[class*=-C37] { + color: #00AFAF +} + +div.highlight .-Color[class*=-BGC37] { + background-color: #00AFAF +} + +div.highlight .-Color[class*=-C38] { + color: #00AFD7 +} + +div.highlight .-Color[class*=-BGC38] { + background-color: #00AFD7 +} + +div.highlight .-Color[class*=-C39] { + color: #00AFFF +} + +div.highlight .-Color[class*=-BGC39] { + background-color: #00AFFF +} + +div.highlight .-Color[class*=-C40] { + color: #00D700 +} + +div.highlight .-Color[class*=-BGC40] { + background-color: #00D700 +} + +div.highlight .-Color[class*=-C41] { + color: #00D75F +} + +div.highlight .-Color[class*=-BGC41] { + background-color: #00D75F +} + +div.highlight .-Color[class*=-C42] { + color: #00D787 +} + +div.highlight .-Color[class*=-BGC42] { + background-color: #00D787 +} + +div.highlight .-Color[class*=-C43] { + color: #00D7AF +} + +div.highlight .-Color[class*=-BGC43] { + background-color: #00D7AF +} + +div.highlight .-Color[class*=-C44] { + color: #00D7D7 +} + +div.highlight .-Color[class*=-BGC44] { + background-color: #00D7D7 +} + +div.highlight .-Color[class*=-C45] { + color: #00D7FF +} + +div.highlight .-Color[class*=-BGC45] { + background-color: #00D7FF +} + +div.highlight .-Color[class*=-C46] { + color: #00FF00 +} + +div.highlight .-Color[class*=-BGC46] { + background-color: #00FF00 +} + +div.highlight .-Color[class*=-C47] { + color: #00FF5F +} + +div.highlight .-Color[class*=-BGC47] { + background-color: #00FF5F +} + +div.highlight .-Color[class*=-C48] { + color: #00FF87 +} + +div.highlight .-Color[class*=-BGC48] { + background-color: #00FF87 +} + +div.highlight .-Color[class*=-C49] { + color: #00FFAF +} + +div.highlight .-Color[class*=-BGC49] { + background-color: #00FFAF +} + +div.highlight .-Color[class*=-C50] { + color: #00FFD7 +} + +div.highlight .-Color[class*=-BGC50] { + background-color: #00FFD7 +} + +div.highlight .-Color[class*=-C51] { + color: #00FFFF +} + +div.highlight .-Color[class*=-BGC51] { + background-color: #00FFFF +} + +div.highlight .-Color[class*=-C52] { + color: #5F0000 +} + +div.highlight .-Color[class*=-BGC52] { + background-color: #5F0000 +} + +div.highlight .-Color[class*=-C53] { + color: #5F005F +} + +div.highlight .-Color[class*=-BGC53] { + background-color: #5F005F +} + +div.highlight .-Color[class*=-C54] { + color: #5F0087 +} + +div.highlight .-Color[class*=-BGC54] { + background-color: #5F0087 +} + +div.highlight .-Color[class*=-C55] { + color: #5F00AF +} + +div.highlight .-Color[class*=-BGC55] { + background-color: #5F00AF +} + +div.highlight .-Color[class*=-C56] { + color: #5F00D7 +} + +div.highlight .-Color[class*=-BGC56] { + background-color: #5F00D7 +} + +div.highlight .-Color[class*=-C57] { + color: #5F00FF +} + +div.highlight .-Color[class*=-BGC57] { + background-color: #5F00FF +} + +div.highlight .-Color[class*=-C58] { + color: #5F5F00 +} + +div.highlight .-Color[class*=-BGC58] { + background-color: #5F5F00 +} + +div.highlight .-Color[class*=-C59] { + color: #5F5F5F +} + +div.highlight .-Color[class*=-BGC59] { + background-color: #5F5F5F +} + +div.highlight .-Color[class*=-C60] { + color: #5F5F87 +} + +div.highlight .-Color[class*=-BGC60] { + background-color: #5F5F87 +} + +div.highlight .-Color[class*=-C61] { + color: #5F5FAF +} + +div.highlight .-Color[class*=-BGC61] { + background-color: #5F5FAF +} + +div.highlight .-Color[class*=-C62] { + color: #5F5FD7 +} + +div.highlight .-Color[class*=-BGC62] { + background-color: #5F5FD7 +} + +div.highlight .-Color[class*=-C63] { + color: #5F5FFF +} + +div.highlight .-Color[class*=-BGC63] { + background-color: #5F5FFF +} + +div.highlight .-Color[class*=-C64] { + color: #5F8700 +} + +div.highlight .-Color[class*=-BGC64] { + background-color: #5F8700 +} + +div.highlight .-Color[class*=-C65] { + color: #5F875F +} + +div.highlight .-Color[class*=-BGC65] { + background-color: #5F875F +} + +div.highlight .-Color[class*=-C66] { + color: #5F8787 +} + +div.highlight .-Color[class*=-BGC66] { + background-color: #5F8787 +} + +div.highlight .-Color[class*=-C67] { + color: #5F87AF +} + +div.highlight .-Color[class*=-BGC67] { + background-color: #5F87AF +} + +div.highlight .-Color[class*=-C68] { + color: #5F87D7 +} + +div.highlight .-Color[class*=-BGC68] { + background-color: #5F87D7 +} + +div.highlight .-Color[class*=-C69] { + color: #5F87FF +} + +div.highlight .-Color[class*=-BGC69] { + background-color: #5F87FF +} + +div.highlight .-Color[class*=-C70] { + color: #5FAF00 +} + +div.highlight .-Color[class*=-BGC70] { + background-color: #5FAF00 +} + +div.highlight .-Color[class*=-C71] { + color: #5FAF5F +} + +div.highlight .-Color[class*=-BGC71] { + background-color: #5FAF5F +} + +div.highlight .-Color[class*=-C72] { + color: #5FAF87 +} + +div.highlight .-Color[class*=-BGC72] { + background-color: #5FAF87 +} + +div.highlight .-Color[class*=-C73] { + color: #5FAFAF +} + +div.highlight .-Color[class*=-BGC73] { + background-color: #5FAFAF +} + +div.highlight .-Color[class*=-C74] { + color: #5FAFD7 +} + +div.highlight .-Color[class*=-BGC74] { + background-color: #5FAFD7 +} + +div.highlight .-Color[class*=-C75] { + color: #5FAFFF +} + +div.highlight .-Color[class*=-BGC75] { + background-color: #5FAFFF +} + +div.highlight .-Color[class*=-C76] { + color: #5FD700 +} + +div.highlight .-Color[class*=-BGC76] { + background-color: #5FD700 +} + +div.highlight .-Color[class*=-C77] { + color: #5FD75F +} + +div.highlight .-Color[class*=-BGC77] { + background-color: #5FD75F +} + +div.highlight .-Color[class*=-C78] { + color: #5FD787 +} + +div.highlight .-Color[class*=-BGC78] { + background-color: #5FD787 +} + +div.highlight .-Color[class*=-C79] { + color: #5FD7AF +} + +div.highlight .-Color[class*=-BGC79] { + background-color: #5FD7AF +} + +div.highlight .-Color[class*=-C80] { + color: #5FD7D7 +} + +div.highlight .-Color[class*=-BGC80] { + background-color: #5FD7D7 +} + +div.highlight .-Color[class*=-C81] { + color: #5FD7FF +} + +div.highlight .-Color[class*=-BGC81] { + background-color: #5FD7FF +} + +div.highlight .-Color[class*=-C82] { + color: #5FFF00 +} + +div.highlight .-Color[class*=-BGC82] { + background-color: #5FFF00 +} + +div.highlight .-Color[class*=-C83] { + color: #5FFF5F +} + +div.highlight .-Color[class*=-BGC83] { + background-color: #5FFF5F +} + +div.highlight .-Color[class*=-C84] { + color: #5FFF87 +} + +div.highlight .-Color[class*=-BGC84] { + background-color: #5FFF87 +} + +div.highlight .-Color[class*=-C85] { + color: #5FFFAF +} + +div.highlight .-Color[class*=-BGC85] { + background-color: #5FFFAF +} + +div.highlight .-Color[class*=-C86] { + color: #5FFFD7 +} + +div.highlight .-Color[class*=-BGC86] { + background-color: #5FFFD7 +} + +div.highlight .-Color[class*=-C87] { + color: #5FFFFF +} + +div.highlight .-Color[class*=-BGC87] { + background-color: #5FFFFF +} + +div.highlight .-Color[class*=-C88] { + color: #870000 +} + +div.highlight .-Color[class*=-BGC88] { + background-color: #870000 +} + +div.highlight .-Color[class*=-C89] { + color: #87005F +} + +div.highlight .-Color[class*=-BGC89] { + background-color: #87005F +} + +div.highlight .-Color[class*=-C90] { + color: #870087 +} + +div.highlight .-Color[class*=-BGC90] { + background-color: #870087 +} + +div.highlight .-Color[class*=-C91] { + color: #8700AF +} + +div.highlight .-Color[class*=-BGC91] { + background-color: #8700AF +} + +div.highlight .-Color[class*=-C92] { + color: #8700D7 +} + +div.highlight .-Color[class*=-BGC92] { + background-color: #8700D7 +} + +div.highlight .-Color[class*=-C93] { + color: #8700FF +} + +div.highlight .-Color[class*=-BGC93] { + background-color: #8700FF +} + +div.highlight .-Color[class*=-C94] { + color: #875F00 +} + +div.highlight .-Color[class*=-BGC94] { + background-color: #875F00 +} + +div.highlight .-Color[class*=-C95] { + color: #875F5F +} + +div.highlight .-Color[class*=-BGC95] { + background-color: #875F5F +} + +div.highlight .-Color[class*=-C96] { + color: #875F87 +} + +div.highlight .-Color[class*=-BGC96] { + background-color: #875F87 +} + +div.highlight .-Color[class*=-C97] { + color: #875FAF +} + +div.highlight .-Color[class*=-BGC97] { + background-color: #875FAF +} + +div.highlight .-Color[class*=-C98] { + color: #875FD7 +} + +div.highlight .-Color[class*=-BGC98] { + background-color: #875FD7 +} + +div.highlight .-Color[class*=-C99] { + color: #875FFF +} + +div.highlight .-Color[class*=-BGC99] { + background-color: #875FFF +} + +div.highlight .-Color[class*=-C100] { + color: #878700 +} + +div.highlight .-Color[class*=-BGC100] { + background-color: #878700 +} + +div.highlight .-Color[class*=-C101] { + color: #87875F +} + +div.highlight .-Color[class*=-BGC101] { + background-color: #87875F +} + +div.highlight .-Color[class*=-C102] { + color: #878787 +} + +div.highlight .-Color[class*=-BGC102] { + background-color: #878787 +} + +div.highlight .-Color[class*=-C103] { + color: #8787AF +} + +div.highlight .-Color[class*=-BGC103] { + background-color: #8787AF +} + +div.highlight .-Color[class*=-C104] { + color: #8787D7 +} + +div.highlight .-Color[class*=-BGC104] { + background-color: #8787D7 +} + +div.highlight .-Color[class*=-C105] { + color: #8787FF +} + +div.highlight .-Color[class*=-BGC105] { + background-color: #8787FF +} + +div.highlight .-Color[class*=-C106] { + color: #87AF00 +} + +div.highlight .-Color[class*=-BGC106] { + background-color: #87AF00 +} + +div.highlight .-Color[class*=-C107] { + color: #87AF5F +} + +div.highlight .-Color[class*=-BGC107] { + background-color: #87AF5F +} + +div.highlight .-Color[class*=-C108] { + color: #87AF87 +} + +div.highlight .-Color[class*=-BGC108] { + background-color: #87AF87 +} + +div.highlight .-Color[class*=-C109] { + color: #87AFAF +} + +div.highlight .-Color[class*=-BGC109] { + background-color: #87AFAF +} + +div.highlight .-Color[class*=-C110] { + color: #87AFD7 +} + +div.highlight .-Color[class*=-BGC110] { + background-color: #87AFD7 +} + +div.highlight .-Color[class*=-C111] { + color: #87AFFF +} + +div.highlight .-Color[class*=-BGC111] { + background-color: #87AFFF +} + +div.highlight .-Color[class*=-C112] { + color: #87D700 +} + +div.highlight .-Color[class*=-BGC112] { + background-color: #87D700 +} + +div.highlight .-Color[class*=-C113] { + color: #87D75F +} + +div.highlight .-Color[class*=-BGC113] { + background-color: #87D75F +} + +div.highlight .-Color[class*=-C114] { + color: #87D787 +} + +div.highlight .-Color[class*=-BGC114] { + background-color: #87D787 +} + +div.highlight .-Color[class*=-C115] { + color: #87D7AF +} + +div.highlight .-Color[class*=-BGC115] { + background-color: #87D7AF +} + +div.highlight .-Color[class*=-C116] { + color: #87D7D7 +} + +div.highlight .-Color[class*=-BGC116] { + background-color: #87D7D7 +} + +div.highlight .-Color[class*=-C117] { + color: #87D7FF +} + +div.highlight .-Color[class*=-BGC117] { + background-color: #87D7FF +} + +div.highlight .-Color[class*=-C118] { + color: #87FF00 +} + +div.highlight .-Color[class*=-BGC118] { + background-color: #87FF00 +} + +div.highlight .-Color[class*=-C119] { + color: #87FF5F +} + +div.highlight .-Color[class*=-BGC119] { + background-color: #87FF5F +} + +div.highlight .-Color[class*=-C120] { + color: #87FF87 +} + +div.highlight .-Color[class*=-BGC120] { + background-color: #87FF87 +} + +div.highlight .-Color[class*=-C121] { + color: #87FFAF +} + +div.highlight .-Color[class*=-BGC121] { + background-color: #87FFAF +} + +div.highlight .-Color[class*=-C122] { + color: #87FFD7 +} + +div.highlight .-Color[class*=-BGC122] { + background-color: #87FFD7 +} + +div.highlight .-Color[class*=-C123] { + color: #87FFFF +} + +div.highlight .-Color[class*=-BGC123] { + background-color: #87FFFF +} + +div.highlight .-Color[class*=-C124] { + color: #AF0000 +} + +div.highlight .-Color[class*=-BGC124] { + background-color: #AF0000 +} + +div.highlight .-Color[class*=-C125] { + color: #AF005F +} + +div.highlight .-Color[class*=-BGC125] { + background-color: #AF005F +} + +div.highlight .-Color[class*=-C126] { + color: #AF0087 +} + +div.highlight .-Color[class*=-BGC126] { + background-color: #AF0087 +} + +div.highlight .-Color[class*=-C127] { + color: #AF00AF +} + +div.highlight .-Color[class*=-BGC127] { + background-color: #AF00AF +} + +div.highlight .-Color[class*=-C128] { + color: #AF00D7 +} + +div.highlight .-Color[class*=-BGC128] { + background-color: #AF00D7 +} + +div.highlight .-Color[class*=-C129] { + color: #AF00FF +} + +div.highlight .-Color[class*=-BGC129] { + background-color: #AF00FF +} + +div.highlight .-Color[class*=-C130] { + color: #AF5F00 +} + +div.highlight .-Color[class*=-BGC130] { + background-color: #AF5F00 +} + +div.highlight .-Color[class*=-C131] { + color: #AF5F5F +} + +div.highlight .-Color[class*=-BGC131] { + background-color: #AF5F5F +} + +div.highlight .-Color[class*=-C132] { + color: #AF5F87 +} + +div.highlight .-Color[class*=-BGC132] { + background-color: #AF5F87 +} + +div.highlight .-Color[class*=-C133] { + color: #AF5FAF +} + +div.highlight .-Color[class*=-BGC133] { + background-color: #AF5FAF +} + +div.highlight .-Color[class*=-C134] { + color: #AF5FD7 +} + +div.highlight .-Color[class*=-BGC134] { + background-color: #AF5FD7 +} + +div.highlight .-Color[class*=-C135] { + color: #AF5FFF +} + +div.highlight .-Color[class*=-BGC135] { + background-color: #AF5FFF +} + +div.highlight .-Color[class*=-C136] { + color: #AF8700 +} + +div.highlight .-Color[class*=-BGC136] { + background-color: #AF8700 +} + +div.highlight .-Color[class*=-C137] { + color: #AF875F +} + +div.highlight .-Color[class*=-BGC137] { + background-color: #AF875F +} + +div.highlight .-Color[class*=-C138] { + color: #AF8787 +} + +div.highlight .-Color[class*=-BGC138] { + background-color: #AF8787 +} + +div.highlight .-Color[class*=-C139] { + color: #AF87AF +} + +div.highlight .-Color[class*=-BGC139] { + background-color: #AF87AF +} + +div.highlight .-Color[class*=-C140] { + color: #AF87D7 +} + +div.highlight .-Color[class*=-BGC140] { + background-color: #AF87D7 +} + +div.highlight .-Color[class*=-C141] { + color: #AF87FF +} + +div.highlight .-Color[class*=-BGC141] { + background-color: #AF87FF +} + +div.highlight .-Color[class*=-C142] { + color: #AFAF00 +} + +div.highlight .-Color[class*=-BGC142] { + background-color: #AFAF00 +} + +div.highlight .-Color[class*=-C143] { + color: #AFAF5F +} + +div.highlight .-Color[class*=-BGC143] { + background-color: #AFAF5F +} + +div.highlight .-Color[class*=-C144] { + color: #AFAF87 +} + +div.highlight .-Color[class*=-BGC144] { + background-color: #AFAF87 +} + +div.highlight 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+ +/* override colors in sphinx_lesson.css with the schemes here: https://personal.sron.nl/~pault/#sec:qualitative */ + +/* instructor-note */ +.rst-content .instructor-note { + background: #DDDDDD; +} +.rst-content .instructor-note > .admonition-title { + background: #BBBBBB; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + +/* callout */ +.rst-content .callout { + background: #EEEEBB; +} +.rst-content .callout > .admonition-title { + background: #BBCC33; +} + +/* questions */ +.rst-content .questions { + background: rgba(253, 219, 199, 0.3); +} +.rst-content .questions > .admonition-title { + background: rgba(204, 51, 17, 0.5); +} + +/* discussion */ +.rst-content .discussion { + background: rgba(231, 212, 232 0.3); +} +.rst-content .discussion > .admonition-title { + background: rgba(194, 165, 207, 0.5); +} + +/* signature */ +.rst-content .signature { + background: rgba(217, 240, 211, 0.3); +} +.rst-content .signature > .admonition-title { + background: rgba(172, 211, 158, 0.5); +} +.rst-content .signature > .admonition-title::before { + content: "\01F527"; +} + +/* parameters */ +.rst-content .parameters { + background: rgba(217, 240, 211, 0.0); +} +.rst-content .parameters > .admonition-title { + background: rgba(172, 211, 158, 0.5); +} +.rst-content .parameters > .admonition-title::before { + content: "\01F4BB"; +} + +/* typealong */ +.rst-content .typealong { + background: rgba(221, 221, 221, 0.3); +} +.rst-content .typealong > .admonition-title { + background: rgba(187, 187, 187, 1.0); +} +.rst-content .typealong > .admonition-title::before { + content: "\02328"; +} + +/* Equation numbers to the right */ +.math { + text-align: left; +} +.eqno { + float: right; +} diff --git a/singlehtml/_static/plus.png b/singlehtml/_static/plus.png new file mode 100644 index 0000000..7107cec Binary files /dev/null and b/singlehtml/_static/plus.png differ diff --git a/singlehtml/_static/pygments.css b/singlehtml/_static/pygments.css 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// query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf b/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf new file mode 100644 index 0000000..f7045c7 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Analysis_tools.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf b/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf new file mode 100644 index 0000000..f5edb26 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Basis_set_optimization.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf b/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf new file mode 100644 index 0000000..84bfc66 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Basis_sets.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Convergence.pdf b/singlehtml/_static/siesta/SIESTA-Convergence.pdf new file mode 100644 index 0000000..667b2fb Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Convergence.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Features.pdf b/singlehtml/_static/siesta/SIESTA-Features.pdf new file mode 100644 index 0000000..272de28 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Features.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-First_encounter.pdf b/singlehtml/_static/siesta/SIESTA-First_encounter.pdf new file mode 100644 index 0000000..627b1cd Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-First_encounter.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Intro.pdf b/singlehtml/_static/siesta/SIESTA-Intro.pdf new file mode 100644 index 0000000..dcd5733 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Intro.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-MD.pdf b/singlehtml/_static/siesta/SIESTA-MD.pdf new file mode 100644 index 0000000..f7fed7f Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-MD.pdf differ diff --git a/singlehtml/_static/siesta/SIESTA-Solvers.pdf b/singlehtml/_static/siesta/SIESTA-Solvers.pdf new file mode 100644 index 0000000..9430066 Binary files /dev/null and b/singlehtml/_static/siesta/SIESTA-Solvers.pdf differ diff --git a/singlehtml/_static/sphinx_highlight.js b/singlehtml/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/singlehtml/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/singlehtml/_static/sphinx_lesson.css b/singlehtml/_static/sphinx_lesson.css new file mode 100644 index 0000000..14b20c6 --- /dev/null +++ b/singlehtml/_static/sphinx_lesson.css @@ -0,0 +1,51 @@ +/* sphinx_lesson.css */ + +body.wy-body-for-nav img.with-border { + border: 2px solid; +} + +.rst-content .admonition-no-content { + padding-bottom: 0px; +} + +.rst-content .demo > .admonition-title::before { + content: "\01F440"; /* Eyes */ } +.rst-content .type-along > .admonition-title::before { + content: "\02328\0FE0F"; /* Keyboard */ } +.rst-content .exercise > .admonition-title::before { + content: "\0270D\0FE0F"; /* Hand */ } +.rst-content .solution > .admonition-title::before { + content: "\02714\0FE0E"; /* Check mark */ } +.rst-content .homework > .admonition-title::before { + content: "\01F4DD"; /* Memo */ } +.rst-content .discussion > .admonition-title::before { + content: "\01F4AC"; /* Speech balloon */ } +.rst-content .questions > .admonition-title::before { + content: "\02753\0FE0E"; /* Question mark */ } +.rst-content .prerequisites > .admonition-title::before { + content: "\02699"; /* Gear */ } +.rst-content .seealso > .admonition-title::before { + content: "\027A1\0FE0E"; /* Question mark */ } + + +/* instructor-note */ +.rst-content .instructor-note { + background: #e7e7e7; +} +.rst-content .instructor-note > .admonition-title { + background: #6a6a6a; +} +.rst-content .instructor-note > .admonition-title::before { + content: ""; +} + + +/* sphinx_toggle_button, make the font white */ +.rst-content .toggle.admonition button.toggle-button { + color: white; +} + +/* sphinx-togglebutton, remove underflow when toggled to hidden mode */ +.rst-content .admonition.toggle-hidden { + padding-bottom: 0px; +} diff --git a/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css new file mode 100644 index 0000000..e68feb8 --- /dev/null +++ b/singlehtml/_static/sphinx_rtd_theme_ext_color_contrast.css @@ -0,0 +1,47 @@ +/* The following are for web accessibility of sphinx_rtd_theme: they + * solve some of the most frequent contrast issues. Remove when this + * solved: + * https://github.com/readthedocs/sphinx_rtd_theme/issues/971 + */ +/* background: #fcfcfc, note boxes #E7F2FA */ +a { color: #2573A7; } /* original #2980B9, #1F5C84; */ +body { color: #242424; } /* original #404040, #383838 */ +.wy-side-nav-search>a, .wy-side-nav-search .wy-dropdown>a { + color: #ffffff; +} /* original #fcfcfc */ +footer { color: #737373; } /* original gray=#808080*/ +footer span.commit code, footer span.commit .rst-content tt, .rst-content footer span.commit tt { + color: #737373; +} /* original gray=#808080*/ +.rst-content tt.literal, .rst-content tt.literal, .rst-content code.literal { + color: #AB2314; +} +/* Sidebar background */ +.wy-side-nav-search { background-color: #277CB4;} + +/* Same, but for pygments */ +.highlight .ch { color: #3E7A89; } /* #! line */ +.highlight .c1 { color: #3E7A89; } /* also comments */ +.highlight .nv { color: #AD3ECC; } /* variable */ +.highlight .gp { color: #B45608; } /* prompt character, $*/ +.highlight .si { color: #3975B1; } /* ${} variable text */ +.highlight .nc { color: #0C78A7; } + +/* Sphinx admonitions */ +/* warning */ +.wy-alert.wy-alert-warning .wy-alert-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .attention .wy-alert-title, .rst-content .caution .wy-alert-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .attention .admonition-title, .rst-content .caution .admonition-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .warning .admonition-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .admonition-todo .admonition-title, .rst-content .wy-alert-warning.admonition .admonition-title { + background: #B15E16; } +/* important */ +.wy-alert.wy-alert-success .wy-alert-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .hint .wy-alert-title, .rst-content .important .wy-alert-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .hint .admonition-title, .rst-content .important .admonition-title, .rst-content .tip .admonition-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition .admonition-title { + background: #12826C; } +/* seealso, note, etc */ +.wy-alert.wy-alert-info .wy-alert-title, .rst-content .note .wy-alert-title, .rst-content .wy-alert-info.attention .wy-alert-title, .rst-content .wy-alert-info.caution .wy-alert-title, .rst-content .wy-alert-info.danger .wy-alert-title, .rst-content .wy-alert-info.error .wy-alert-title, .rst-content .wy-alert-info.hint .wy-alert-title, .rst-content .wy-alert-info.important .wy-alert-title, .rst-content .wy-alert-info.tip .wy-alert-title, .rst-content .wy-alert-info.warning .wy-alert-title, .rst-content .seealso .wy-alert-title, .rst-content .wy-alert-info.admonition-todo .wy-alert-title, .rst-content .wy-alert-info.admonition .wy-alert-title, .wy-alert.wy-alert-info .rst-content .admonition-title, .rst-content .wy-alert.wy-alert-info .admonition-title, .rst-content .note .admonition-title, .rst-content .wy-alert-info.attention .admonition-title, .rst-content .wy-alert-info.caution .admonition-title, .rst-content .wy-alert-info.danger .admonition-title, .rst-content .wy-alert-info.error .admonition-title, .rst-content .wy-alert-info.hint .admonition-title, .rst-content .wy-alert-info.important .admonition-title, .rst-content .wy-alert-info.tip .admonition-title, .rst-content .wy-alert-info.warning .admonition-title, .rst-content .seealso .admonition-title, .rst-content .wy-alert-info.admonition-todo .admonition-title, .rst-content .wy-alert-info.admonition .admonition-title { + background: #277CB4; } +/* error, danger */ +.rst-content .danger .admonition-title, .rst-content .danger .wy-alert-title, .rst-content .error .admonition-title, .rst-content .error .wy-alert-title, .rst-content .wy-alert-danger.admonition-todo .admonition-title, .rst-content .wy-alert-danger.admonition-todo .wy-alert-title, .rst-content .wy-alert-danger.admonition .admonition-title, .rst-content .wy-alert-danger.admonition .wy-alert-title, .rst-content .wy-alert-danger.attention .admonition-title, .rst-content .wy-alert-danger.attention .wy-alert-title, .rst-content .wy-alert-danger.caution .admonition-title, .rst-content .wy-alert-danger.caution .wy-alert-title, .rst-content .wy-alert-danger.hint .admonition-title, .rst-content .wy-alert-danger.hint .wy-alert-title, .rst-content .wy-alert-danger.important .admonition-title, .rst-content .wy-alert-danger.important .wy-alert-title, .rst-content .wy-alert-danger.note .admonition-title, .rst-content .wy-alert-danger.note .wy-alert-title, .rst-content .wy-alert-danger.seealso .admonition-title, .rst-content .wy-alert-danger.seealso .wy-alert-title, .rst-content .wy-alert-danger.tip .admonition-title, .rst-content .wy-alert-danger.tip .wy-alert-title, .rst-content .wy-alert-danger.warning .admonition-title, .rst-content .wy-alert-danger.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-danger .admonition-title, .wy-alert.wy-alert-danger .rst-content .admonition-title, .wy-alert.wy-alert-danger .wy-alert-title { + background: #e31704; +} + +/* Generic admonition titles */ +.wy-alert-title, .rst-content .admonition-title { + background: #277CB4; } diff --git a/singlehtml/_static/tabs.css b/singlehtml/_static/tabs.css new file mode 100644 index 0000000..957ba60 --- /dev/null +++ b/singlehtml/_static/tabs.css @@ -0,0 +1,89 @@ +.sphinx-tabs { + margin-bottom: 1rem; +} + +[role="tablist"] { + border-bottom: 1px solid #a0b3bf; +} + +.sphinx-tabs-tab { + position: relative; + font-family: Lato,'Helvetica Neue',Arial,Helvetica,sans-serif; + color: #1D5C87; + line-height: 24px; + margin: 0; + font-size: 16px; + font-weight: 400; + background-color: rgba(255, 255, 255, 0); + border-radius: 5px 5px 0 0; + border: 0; + padding: 1rem 1.5rem; + margin-bottom: 0; +} + +.sphinx-tabs-tab[aria-selected="true"] { + font-weight: 700; + border: 1px solid #a0b3bf; + border-bottom: 1px solid white; + margin: -1px; + background-color: white; +} + +.sphinx-tabs-tab:focus { + z-index: 1; + outline-offset: 1px; +} + +.sphinx-tabs-panel { + position: relative; + padding: 1rem; + border: 1px solid #a0b3bf; + margin: 0px -1px -1px -1px; + border-radius: 0 0 5px 5px; + border-top: 0; + background: white; +} + +.sphinx-tabs-panel.code-tab { + padding: 0.4rem; +} + +.sphinx-tab img { + margin-bottom: 24 px; +} + +/* Dark theme preference styling */ + +@media (prefers-color-scheme: dark) { + body[data-theme="auto"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); + } + + body[data-theme="auto"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); + } + + body[data-theme="auto"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 1px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); + } +} + +/* Explicit dark theme styling */ + +body[data-theme="dark"] .sphinx-tabs-panel { + color: white; + background-color: rgb(50, 50, 50); +} + +body[data-theme="dark"] .sphinx-tabs-tab { + color: white; + background-color: rgba(255, 255, 255, 0.05); +} + +body[data-theme="dark"] .sphinx-tabs-tab[aria-selected="true"] { + border-bottom: 2px solid rgb(50, 50, 50); + background-color: rgb(50, 50, 50); +} diff --git a/singlehtml/_static/tabs.js b/singlehtml/_static/tabs.js new file mode 100644 index 0000000..48dc303 --- /dev/null +++ b/singlehtml/_static/tabs.js @@ -0,0 +1,145 @@ +try { + var session = window.sessionStorage || {}; +} catch (e) { + var session = {}; +} + +window.addEventListener("DOMContentLoaded", () => { + const allTabs = document.querySelectorAll('.sphinx-tabs-tab'); + const tabLists = document.querySelectorAll('[role="tablist"]'); + + allTabs.forEach(tab => { + tab.addEventListener("click", changeTabs); + }); + + tabLists.forEach(tabList => { + tabList.addEventListener("keydown", keyTabs); + }); + + // Restore group tab selection from session + const lastSelected = session.getItem('sphinx-tabs-last-selected'); + if (lastSelected != null) selectNamedTabs(lastSelected); +}); + +/** + * Key focus left and right between sibling elements using arrows + * @param {Node} e the element in focus when key was pressed + */ +function keyTabs(e) { + const tab = e.target; 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block + // Define the structure of the details block and insert it as a sibling + var detailsBlock = ` +
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  • Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo documentation
    • +
  • + Edit on GitHub +
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+ +
+

Efficient materials modelling on HPC with Quantum ESPRESSO, Siesta and Yambo

+

In recent years, computing technologies underlying materials modelling and +electronic structure calculation have evolved rapidly. High-performance +computing (HPC) is transitioning from petascale to exascale, while individual +compute nodes are increasingly based on heterogeneous architectures that every +year become more diversified due to different vendor choices. In this environment, +electronic structure codes also have to evolve fast in order to adapt to new +hardware facilities. Nowadays, state-of-the-art electronic structure codes based +on modern density functional theory (DFT) methods allow treating realistic +molecular systems with a very high accuracy. However, due to the increased +complexity of the codes, some extra skills are required from users in order to +fully exploit their potential.

+

This training material gives a broad overview of important fundamental concepts +for molecular and materials modelling on HPC, with a focus on three of the most +modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). +Theory sections are interleaved with practical demonstrations and hands-on exercises.

+

QUANTUM ESPRESSO is one of the most +popular suites of computer codes for electronic-structure calculations and +materials modelling at the nanoscale, based on density-functional theory, plane +waves, and pseudopotentials. It is able to predict and give fundamental insights +about many properties of materials, molecular systems, micro and nanodevices, +biological systems, in many fields, providing a huge amount of data for +data-driven science applications.

+

SIESTA is a pseudopotential-based +DFT software whose strength lies in its use of atomic-like strictly-localised +basis sets: the use of a “good first approximation” to the full problem +decreases the number of basis functions needed to achieve a given accuracy, and +the finite support of the orbitals leads to sparsity in the Hamiltonian and +overlap matrices, thus enabling the use of reduced-scaling methods. The +functionalities of SIESTA include, amongst others, the calculation of energies +and forces, molecular-dynamics simulations, band structures, densities of +states, spin-orbit couplings, van der Waals functionals, DFT+U for correlated +systems, real-time TDDFT, and non-equilibrium calculations with TranSIESTA.

+

YAMBO is an open-source code implementing +first-principles methods based on Green’s function (GF) theory to describe +excited-state properties of realistic materials. These methods include the GW +approximation, the Bethe Salpeter equation, nonequilibrium GF (NEGF) and TDDFT, +allowing for the prediction of accurate quasiparticle energies (e.g. ARPES band +structures), linear and non-linear optical properties, capturing the physics of +excitons, plasmons, and magnons. It is also possible to calculate +temperature-dependent electronic and optical properties via electron-phonon +coupling and nonequilibrium and non-linear optical properties via NEGF real-time +simulations (pump-probe experiments, etc).

+

MAX (MAterials design at the eXascale) is a +European Centre of Excellence which enables materials modelling, simulations, +discovery and design at the frontiers of the current and future High-Performance +Computing (HPC), High Throughput Computing (HTC) and data analytics technologies. +MaX’s challenge lies in bringing the most successful and widely used open-source, +community codes in quantum simulations of materials towards exascale and extreme +scaling performance and make them available for a large and growing base of +researchers in the materials’ domain.

+
+

Prerequisites

+
    +

  • Some familiarity with density functional theory (DFT), self-consistent +field (SCF) calculations and plane wave basis sets is desirable as the +workshop will not cover the fundamental theory of these topics.

    • +

  • Familiarity with working in a Linux environment and some experience with +working on an HPC system is needed to participate in the hands-on exercises.

    • +
+
+
+

Who is the course for?

+

This workshop is aimed towards researchers and engineers who already have some +previous experience with materials modelling and electronic structure calculations.

+
+
+
+
+
+
+

SIESTA setup

+
+

Directory with tutorials

+

For every practical there is a folder in the shared directory +/leonardo_work/EUHPC_TD02_030/siesta-tutorials that contains all the files +you will need for said practical. At the start of every tutorial, please copy +the required files from that shared directory to your scratch folder. For +example, for the first tutorial:

+
$ cp -pr /leonardo_work/EUHPC_TD02_030/siesta-tutorials/01-FirstEncounter_I .
+
+
+

Please do NOT copy these files before the start of the practical, in case they +are updated shortly before the practical starts.

+
+
+

Running SIESTA

+

You will find a sample script on how to run SIESTA in +/leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/runsample.sh:

+
#!/bin/bash
+#SBATCH -J tutorialXX
+#SBATCH -n 8
+#SBATCH -t 0:30:00
+#SBATCH -o %x-%j.out
+#SBATCH -e %x-%j.err
+#SBATCH --partition=boost_usr_prod
+#SBATCH -D .
+
+# DO NOT CHANGE THIS LINE
+source /leonardo_work/EUHPC_TD02_030/softwares/siesta-5.0beta1/siestarc.sh
+
+# EDIT THE CORRECT INPUT AND OUTPUT FILES.
+srun -n 8 siesta < input.fdf > output.out
+
+
+

Note that input.fdf and output.out are generic input and output file names, for +each execution of siesta you will need to change them to the actual names of +your input and output files. It is also convenient to change the name of the job +(#SBATCH -J option) to something that allows you to identify (vs. your other +submissions) when checking the status of the queue.

+
+
+

Suggested Software for Visualization

+

If you run visualizations in your own PC, you may want to have a few of these +installed. Some are redundant, and will depend on your own preferences.

+ +
+
+
+

Day 3: SIESTA I

+
+

SIESTA basics

+

Lecture by Prof. Emilio Artacho (CIC NanoGUNE, Ikerbasque, and University of Cambridge).

+

Slides available here: SIESTA-Intro.pdf.

+
+
+

A first contact with SIESTA: inputs, execution and outputs

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-First_encounter.pdf.

+
+
+

Basis sets

+

Lecture by Dr. Miguel Pruneda (CINN-CSIC).

+

Slides available here: SIESTA-Basis_sets.pdf.

+
+
+

Basis set optimization

+

Practical session led by Dr. Federico Pedron (ICN2).

+

Tutorials covered:

+ +

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets
+
+
+

Introductory slides available here: SIESTA-Basis_set_optimization.pdf.

+
+
+

Convergence (k points, mesh, mixing)

+

Practical session led by Dr. Catalina Coll (ICN2).

+

Tutorials covered:

+ +

Introductory slides available here: SIESTA-Convergence.pdf.

+
+
+
+

Day 4: SIESTA II

+
+

Molecular Dynamics with SIESTA

+

Practical session led by Dr. Ernane de Freitas (ICN2).

+

Tutorials covered:

+
    +

  • Molecular Dynamics. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-MD.pdf.

+
+
+

Analysis tools

+

Practical session led by Dr. Miguel Pruneda (CINN-CSIC).

+

Tutorials covered:

+
    +

  • Analysis tools. Files available at:

    +
    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis
+
    +
    +
    • +
+

Introductory slides available here: SIESTA-Analysis_tools.pdf.

+
+
+

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

+

Lecture by Dr. Nick Papior (Technical University of Denmark).

+

Slides available here: SIESTA-Features.pdf.

+
+
+

Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Practical session led by Dr. Alberto García (ICMAB-CSIC).

+

Tutorials covered:

+
    +

  • ELSI-ELPA.

    • +

  • ELSI-PEXSI.

    • +
+

Files for the tutorial:

+
/leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers
+
+
+

Slides available here: SIESTA-Solvers.pdf.

+
+
+
+
+
+

Yambo tutorial: Quasiparticles in the GW approximation

+

In this tutorial you will learn how to run a GW simulation using Yambo on a HPC machine.

+

You will compute the quasiparticle corrections to the band structure of a free-standing single layer of MoS\(_2\) while learning about convergence studies, parallel strategies, and GPU calculations.

+

In the end, you will obtain a quasiparticle band structure based on the simulations, the first step towards the reproduction of an ARPES spectrum. Beware: we will not use fully converged parameters, so the final result should not be considered very accurate.

+
+_images/mos2.png +
+

MoS\(_2\) monolayer (top and side views). Gray: Mo atoms, yellow: S atoms.

+
+

Many-body corrections to the DFT band gap

+

We want to describe the electronic energy levels using a better description of electron-electron interactions than DFT is capable of.

+

Essentially, we want to solve the non-linear quasiparticle equation at first order in the GW self-energy \(\Sigma\):

+
+\[E^{QP}_{nk}=\epsilon_{nk}+Z_{nk}[\Sigma]\langle\psi_{nk}|\Sigma(\epsilon_{nk})-V_{xc}|\psi_{nk}\rangle\]
+

Here \(\epsilon_{nk}\) and \(\psi_{nk}\) are the Kohn-Sham energies and wavefunctions, respectively, while \(V_{xc}\) is the DFT exchange-correlation potential.

+

For each electronic state \(nk\), the self-energy can be separated into two components: a static, gap-opening term called the exchange self-energy (\(\Sigma^x\)), and an energy-dependent, usually gap-closing term called the correlation self-energy (\(\Sigma^c\)). These contributions are tackled separately by the code:

+
+\[\Sigma_{nk}(\omega)=\Sigma_{nk}^x+\Sigma^c_{nk}(\omega)\]
+

The energy-dependent dynamical electronic screening \(\varepsilon^{-1}(\omega)\) is included in \(\Sigma^c\) and must therefore be calculated as well.

+

In this way, we can compute the “quasiparticle” corrections \(E^{QP}_{nk}\) to the single-particle Kohn-Sham eigenvalues \(\epsilon_{nk}\). +The typical workflow for a GW calculation is:

+
+_images/gwflow.png +
+
+
+

Set up a Yambo calculation

+

Go to your user work directory and download the materials for the tutorial (1.2GB, it may take a couple of minutes):

+
wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+
tar -xvzf MoS2_HPC_tutorial_Leonardo.tar.gz
+
+
+

You can now enter the tutorial directory

+
cd MoS2_HPC_tutorial_Leonardo
+
+
+
+
Yambo SAVE folder
+

First of all, we need to convert some of the data produced in a previous non-self-consistent DFT calculation (in this case using Quantum ESPRESSO) into a convenient format for Yambo.

+

The QE save folder for MoS\(_2\) is already present at 00_QE-DFT. We should move inside it and then run the p2y executable to generate the uninitialised SAVE.

+

But first, we need to access a node interactively:

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

Then we need to load the yambo-specific modules in in the cluster. On Leonardo Booster, we have

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

Finally:

+
cd 00_QE-DFT/mos2.save
+mpirun -np 1 p2y
+
+
+

Now, we need to run the initialization step. Every Yambo run must start with this step. This will be automatically performed when you run Yambo on a SAVE directory for the first time. Just type

+
mpirun -np 1 yambo
+
+
+

and then check the yambo log called l_setup. The initialization step determines the \(G\)-vector shells and the \(k\)- and \(q\)-point grids based on the DFT calculation. If you check inside the SAVE you will see two types of databases. The static ones, starting with ns.*, are directly converted in the p2y step, while the dynamical ones, ndb.* are generated during the initialisation.

+
ls SAVE/
+
+
+
ndb.gops       # info on G-vector shells, etc
+ndb.kindx      # info and k and q meshes
+ns.db1         # info on geometry and KS bands
+ns.kb_pp_pwscf # pseudopotential info
+ns.wf          # wave functions info
+...
+
+
+

The databases are written in netCDF format. +Yambo has produced also a human readable output, r_setup, reporting relevant information such as lattice parameters, symmetries, atomic positions, k-points, DFT eigenvalues and band gaps. We can have a quick look at the sections.

+
vim r_setup
+
+
+
[02.01] Unit cells # Lattice geometry info
+==================
+  ...
+[02.02] Symmetries # Symmetry ops. written explicitly
+==================
+  ...
+[02.03] Reciprocal space  # Reciprocal lattice info
+========================
+...
+[02.04] K-grid lattice # k-point coords. written explicitly
+======================
+...
+[02.05] Energies & Occupations # Info on band gaps and occupations
+============================== # DFT eigenvalues
+...
+[03] Transferred momenta grid and indexing # q-points (momentum transfer grid)
+==========================================
+
+
+

Finally, let us move the SAVE and the report file to the directory where we will run the first GW calculation.

+
mv SAVE r_setup ../../01_GW_first_run/
+cd ../../01_GW_first_run/
+
+
+
+
+
Yambo input file
+

Now that we have a working SAVE, it is time to generate the input file we will be using for our first GW calculation.

+

This can be done by the yambo executable via command-line instructions.

+

If you type

+
yambo -h
+
+
+

You will get a list of the possibile options:

+
 ___ __  _____  __ __  _____   _____
+|   Y  ||  _  ||  Y  ||  _  \ |  _  |
+|   |  ||. |  ||.    ||. |  / |. |  |
+ \   _/ |. _  ||.\ / ||. _  \ |. |  |
+  |: |  |: |  ||: |  ||: |   \|: |  |
+  |::|  |:.|:.||:.|:.||::.   /|::.  |
+  `--"  `-- --"`-- --"`-----" `-----"
+ 'A shiny pot of fun and happiness [C.D.Hogan]'
+
+ This is      : yambo
+ Version      : 5.1.0 Revision 21422 Hash fde6e2a07
+ Configuration: MPI+OpenMP+SLK+HDF5_MPI_IO
+
+ Help & version:
+ -help            (-h) <string>   :<string> can be an option (e.g. -h optics)
+ -version                         :Code version & libraries
+
+ Input file & Directories:
+ -Input           (-F) <string>   :Input file
+ -Verbosity       (-V) <string>   :Input file variables verbosity (more with -h Verbosity)
+ -Job             (-J) <string>   :Job string
+ -Idir            (-I) <string>   :Input directory
+ -Odir            (-O) <string>   :I/O directory
+ -Cdir            (-C) <string>   :Communication directory
+
+ Parallel Control:
+ -parenv          (-E) <string>   :Environment Parallel Variables file
+ -nompi                           :Switch off MPI support
+ -noopenmp                        :Switch off OPENMP support
+
+ Initializations:
+ -setup           (-i)            :Initialization
+ -coulomb         (-r)            :Coulomb potential
+
+ Response Functions:
+ -optics          (-o) <string>   :Linear Response optical properties (more with -h optics)
+ -X               (-d) <string>   :Inverse Dielectric Matrix (more with -h X)
+ -dipoles         (-q)            :Oscillator strenghts (or dipoles)
+ -kernel          (-k) <string>   :Kernel (more with -h kernel)
+
+ Self-Energy:
+ -hf              (-x)            :Hartree-Fock
+ -gw0             (-p) <string>   :GW approximation (more with -h gw0)
+ -dyson           (-g) <string>   :Dyson Equation solver (more with -h dyson)
+ -lifetimes       (-l)            :GoWo Quasiparticle lifetimes
+
+ Bethe-Salpeter Equation:
+ -Ksolver         (-y) <string>   :BSE solver (more with -h Ksolver)
+
+ Total Energy:
+ -acfdt                           :ACFDT Total Energy
+
+ Utilites:
+ -Quiet           (-Q)            :Quiet input file creation
+ -fatlog                          :Verbose (fatter) log(s)
+ -DBlist          (-D)            :Databases properties
+ -walltime             <int>      :Walltime (more with -h walltime)
+ -memory               <int>      :Memory (more with -h memory)
+ -slktest                         :ScaLapacK test
+
+ YAMBO developers group (http://www.yambo-code.org)
+
+
+

In order to build our input, we need to use the options for a GW calculation. We want to use the plasmon pole approximation for the dynamical screening, solve the quasiparticle equation with the Newton method, and add a truncation of the Coulomb potential which is useful for 2D systems. In addition, we want to set up explicitly the parameters for parallel runs. Therefore we type:

+
yambo -gw0 p -g n -r -V par -F gw.in
+
+
+

Now we can exit the computing node, since all remaining calculations will be run by submitting jobs with the slurm scheduler.

+
exit
+
+
+

You can now inspect the input file gw.in and try to familiarize with some of the parameters. The input will come with default values for many parameters that we might need to change.

+

We discuss them below step by step.

+
+
+
Parameters for a GW calculation
+

We start with the runlevels:

+
gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+el_el_corr                       # [R] Electron-Electron Correlation
+dyson                            # [R] Dyson Equation solver
+rim_cut                          # [R] Coulomb potential
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+
+
+
+

Runlevels

+
    +

  • The [R] keyword refers to the runlevels: these flag tell Yambo which parts of the code should be executed. Each runlevel enables its own set of input variables. In particular here we have:

    +
      +

    • rim_cut: Coulomb potential random integration method and cutoff (enables [RIM] and [CUT] variables).

      • +

    • gw0: Yambo learns that it has to run a GW calculation (enables [GW] variables).

      • +

    • HF_and_locXC: calculation of exchange part of the self-energy \(\Sigma^x\) (i.e., Hartree-Fock approximation).

      • +

    • em1d: enables the calculation of the dynamical screening of the electrons, i.e. the dielectric matrix ([X] variables). In this way Yambo can go beyond Hartree-Fock and compute \(\Sigma^c\).

      • +

    • ppa: tells Yambo that the dynamical screening should be computed in the plasmon pole approximation ([Xp] variables).

      • +

    • dyson: Yambo will solve the Dyson-like quasiparticle equation.

      • +
    +
    • +
+
+

Going through the file we find:

+
EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+
+
+

Recall that we have, for the exchange self-energy:

+
+\[\Sigma^x_{nk} = - \sum_G\sum_v \int \frac{d^3q}{2\pi^3} v(q+G)|\rho_{nv}(k,q,G)|^2f_{vk-q}\]
+
+

Exchange self-energy

+
    +

  • EXXRLvcs controls the number of Reciprocal Lattice vectors (i.e., G-vectors) used to build the exchange self-energy, while VXCRLvcs does the same for the exchange-correlation potential reconstructed from DFT. Since these two quantities are to be subtracted, it is important to keep the same values here (and possibly not change the default maximum value).

    • +
+
+

Let us now have a look at the parameters for the calculation of the correlation part of the self-energy. Recall that we have:

+
+\[\Sigma^c_{nk} = i \sum_m \int \frac{d^3q}{2\pi^3} \sum_{GG'} v(q+G) \rho_{nmk}(q,G) \rho^*_{nmk}(q,G') \int d\omega' G^0_{mk-q}(\omega-\omega')\varepsilon^{-1}_{GG'}(q,\omega')\]
+

(Here, the \(\rho\)-terms represent the screening matrix elements which are computed separately by yambo and stored in their own database.)

+

The calculation is divided in two steps. First, the response function in the plasmon pole approximation (em1d ppa), under the keywords [X] and [Xp], i.e., \(\varepsilon^{-1}_{GG'}(q,\omega)\).

+
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 300 |                     # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+
+
+
+

Response function

+
    +

  • Chimod= "Hartree" indicates that we compute the response function in the Random Phase Approximation (RPA).

    • +

  • BndsRnXp represents the electronic states included in the response function \(\varepsilon\), and is a convergence parameter.

    • +

  • NGsBlkXp is the number of G-vectors used to calculate the RPA response function \(\varepsilon^{-1}_{GG'}\). It is a convergence parameter and can be expressed in number of reciprocal lattice vectors (RL) or energy (Ry, suggested).

    • +

  • LongDrXp represents the direction of the long-range auxiliary external electric field used to compute \(\varepsilon^{-1}_{GG'}(q)\) at \(q,G\rightarrow 0\). In general you have to be mindful of the system symmetries. In our case, we will put 1 | 1 | 1 to cover all directions.

    • +

  • PPAPntXp= 27.21138 eV is the energy of the plasmon pole. We don’t normally change this.

    • +

  • XTermKind is used to specify a “terminator”: this accelerates numerical convergence with respect to the number of bands BndsRnXp.

    • +
+
+

Next, we have the [GW] group of parameters controlling the next part of the correlation self-energy calculation:

+
% GbndRnge
+   1 | 300 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|7|1|300|
+%
+
+
+
+

Correlation self-energy

+
    +

  • GbndRnge is the number of bands used to build the correlation self-energy. It is a convergence parameter and can be accelerated with the terminator GTermKind.

    • +

  • DysSolver="n" specifies the method used to solve the linearised quasiparticle equation. In most cases, we use the Newton method "n".

    • +

  • QPkrange indicates the range of electronic (nk) states for which the GW correction \(\Sigma_{nk}\) is computed. The first pair of numbers represents the range of k-point indices, the second pair the range of band indices.

    • +
+
+

We now take a look at the parameters relative to the Coulomb interaction at small momenta and for 2D systems, which we should edit now once and for all.

+
RandQpts=1000000                       # [RIM] Number of random q-points in the BZ
+RandGvec= 100                RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+
+
+
+

Coulomb potential

+
    +

  • The [RIM] keyword refers to a Monte Carlo random integration method performed to avoid numerical instabilities close to \(q=0\) and \(G=0\) in the \(q\)-integration of the bare Coulomb interaction - i.e. \(4\pi/(q+G)^2\) - for 2D systems.

    • +

  • The [CUT] keyword refers to the truncation of the Coulomb interaction to avoid spurious interaction between periodically repeated copies of the simulation supercell along the \(z\)-direction (we are working with a plane-wave code). Keep in mind that the vacuum space between two copies of the system should be converged: here we are using 20 bohr but a value of 40 bohr would be more realistic.

    • +
+
+

Finally, we have the parallel parameters. We are going to discuss them at the end of the parallel section, we can skip them for now.

+
X_and_IO_CPU= ""                 # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= ""               # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=-1      # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_CPU= ""                      # [PARALLEL] CPUs for each role
+DIP_ROLEs= ""                    # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_CPU= ""                       # [PARALLEL] CPUs for each role
+SE_ROLEs= ""                     # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+
+
+

In a GW calculation, the most important parameters to be numerically converged are:

+
    +

  • kpoint mesh (requires multiple nscf DFT runs)

    • +

  • BndsRnXp

    • +

  • NGsBlkXp

    • +

  • GbndRnge

    • +

  • [2D system]: vacuum separation with Coulomb cutoff (requires multiple scf+nscf DFT runs)

    • +
+

From the above discussion you can easily guess that many-body perturbation theory calculations are much more numerically expensive than DFT calculations.

+
+
+
+
+

The first run

+

We will start by running a single GW calculation. Here we will focus on the magnitude of the quasiparticle gap. This means that we only need to calculate two quasi-particle corrections, i.e., valence and conduction bands at the k-point where the minimum gap occurs. This information can be found by inspecting the report file r_setup produced when the SAVE folder was initialised. Just search for the string ‘Direct Gap’ and you’ll see that the latter occurs at k-point 7 between bands 13 and 14:

+
  [X] Filled Bands                                  :  13
+  [X] Empty Bands                                   :   14  300
+  [X] Direct Gap                                    :  1.858370 [eV]
+  [X] Direct Gap localized at k                     :  7
+
+
+

In addition, we will set the number of bands in BndsRnXp and GbndRnge to a small value, just to have it run fast. Hence, we modify the input file accordingly (check BndsRnXp, GbndRnge, LongDrXp, QPkrange):

+
rim_cut                          # [R] Coulomb potential
+gw0                              # [R] GW approximation
+ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
+dyson                            # [R] Dyson Equation solver
+HF_and_locXC                     # [R] Hartree-Fock
+em1d                             # [R][X] Dynamically Screened Interaction
+X_Threads=0                      # [OPENMP/X] Number of threads for response functions
+DIP_Threads=0                    # [OPENMP/X] Number of threads for dipoles
+SE_Threads=0                     # [OPENMP/GW] Number of threads for self-energy
+RandQpts=1000000                 # [RIM] Number of random q-points in the BZ
+RandGvec= 100              RL    # [RIM] Coulomb interaction RS components
+CUTGeo= "slab z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
+% CUTBox
+ 0.000000 | 0.000000 | 0.000000 |        # [CUT] [au] Box sides
+%
+CUTRadius= 0.000000              # [CUT] [au] Sphere/Cylinder radius
+CUTCylLen= 0.000000              # [CUT] [au] Cylinder length
+CUTwsGvec= 0.700000              # [CUT] WS cutoff: number of G to be modified
+EXXRLvcs=  37965           RL    # [XX] Exchange    RL components
+VXCRLvcs=  37965           RL    # [XC] XCpotential RL components
+Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
+% BndsRnXp
+   1 | 20 |                         # [Xp] Polarization function bands
+%
+NGsBlkXp= 1                RL    # [Xp] Response block size
+% LongDrXp
+ 1.000000 | 1.000000 | 1.000000 |        # [Xp] [cc] Electric Field
+%
+PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
+XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
+% GbndRnge
+   1 | 20 |                         # [GW] G[W] bands range
+%
+GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
+DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
+%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+7|7|13|14|
+%
+
+
+

We are now ready to run this calculation. Since you should never run a Yambo calculation on the login node, we will need a submission script to add our job to the queue. A submission script optimized for Leonardo Booster (running on GPUs) is provided as an example. Modify it to suit your specific machine.

+
vim run_first_job.sh
+
+
+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=2
+#SBATCH --cpus-per-task=8
+#SBATCH --partition=boost_usr_prod
+#SBATCH --time=0:05:00
+#SBATCH --gres=gpu:2
+#SBATCH --account=EUHPC_TD02_030
+#SBATCH --job-name=first_job
+
+export OMP_NUM_THREADS=8
+export OMP_PLACES=cores
+export OMP_PROC_BIND=close
+
+# load yambo
+module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core \
+        yambo -F gw.in -J job_00_first_run -C out_00_first_run
+
+
+

We will ignore all details regarding parallelization, as it will be covered in the next section. Since there are no lowercase flags after yambo, it is not going to generate an input file, but rather, run the one specified by -F. Now, go ahead an submit this job

+
sbatch run_first_job.sh
+
+
+

The status of the jobs can be monitored via:

+
squeue -u $USER        # to inspect the status of jobs 
+                       # (hint: make a unix alias, if you like)
+scancel <jobid>        # to delete jobs in the queue
+
+
+

The newly generated databases will be stored in the job directory, as specified by -J, while the report, log and output files will be stored in the communications directory (-C). As this is your first yambo run, take a moment to inspect the report and log files, which you can find inside the -C directory. In these report and log files, you can see the steps performed by yambo. For instance, the code calculates the screening at every k-point and stores it in the PPA database called ndb.pp. By opening the report

+
vim out_00_first_run/r-job_00_first_run_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa
+
+
+

you will see

+
[07] Dynamic Dielectric Matrix (PPA)
+ ====================================
+
+ [WR./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Then, the actual GW section will use this calculated dielectric screening to construct the correlation part of the self-energy:

+
[09.01] G0W0 (W PPA)
+  ====================
+
+  [  GW  ] Bands range     :   1  20
+  [GW/PPA] G damping       :  0.100000 [eV]
+
+
+  QP @ state[ 1 ] K range:   7   7
+  QP @ state[ 1 ] b range:  13  14
+
+  [RD./job_00_first_run//ndb.pp]-------------------------------
+
+
+

Now, inspect the output file

+
vim out_00_first_run/o-job_00_first_run.qp 
+
+
+
# Vxc  =Slater exchange(X)+Perdew & Zunger(C)
+# Vnlxc=Hartree-Fock
+#
+#    K-point            Band               Eo [eV]            E-Eo [eV]          Sc|Eo [eV]
+#
+         7                 13                 0.000000          -0.025774           0.543987
+         7                 14                 1.858370           3.496193          -0.417555
+# 
+
+
+

In this file, Eo is our starting point (DFT) while E-Eo shows the GW correction one should apply to obtain the quasi-particle energies. In order to calculate the gap (automatically from the command line), we’ll use some simple commands. First, we get everything that is not a # symbol grep -v '#' and we pass that to another command with a “pipe” |. Then, tail -n 1/head -n 1 will retain the first/last line, and awk '{print $3+$4}' will get us the sum of the third and fourth columns. Altogether, this would be as follows

+
grep -v '#' out_00_first_run/o-job_00_first_run.qp|head -n 1| awk '{print $3+$4}'
+-0.025774
+grep -v '#' out_00_first_run/o-job_00_first_run.qp|tail -n 1| awk '{print $3+$4}'
+5.35456
+
+
+

These two commands give us the quasiparticle energies we’ve calculated - their difference is the GW-corrected optical gap.

+
+
+
+

GW convergence

+

In this part of the tutorial, we will study convergence with respect to some of the parameters mentioned above. In order to complete this tutorial within a single hands-on session, we will restrict ourselves to a very coarse \(k\)-point grid. +Hence, we will perform our convergence studies on top of a DFT calculation done with a \(6 \times 6 \times 1\) k-point grid and without spin-orbit coupling: the SAVE we generated earlier. +While this will speed up calculations and could be run even on a single GPU card, you should be aware that such coarse sampling of the BZ is significantly underconverged and should only be used for educational purposes. In addition, spin-orbit interaction is extremely relevant for the valley physics of MoS2 and should not be neglected in realistic calculations. +Let’s move into the appropriate directory

+
cd ../02_GW_convergence
+
+
+
+
Response function \(\varepsilon^{-1}_{GG'}\) - Bands and G-vectors
+

We are now ready to start our convergence tests. We’ll begin with the variables controlling the polarization function, i.e., NGsBlkXp for the number of G-vectors and BndsRnXp for the number of bands. For this, we will keep GbndRnge constant at a reasonably high value - you can inspect the input i01-GW

+
vim i01-GW
+
+
+

and check that you have:

+
% GbndRnge
+   1 | 80 |                         # [GW] G[W] bands range
+%
+
+
+

Since we need to run yambo for several values of NGsBlkXp and BndsRnXp, it makes sense to use two nested loops. That is exactly what we did in the submission script run01_converge_pol.sh. Since this will take a few minutes, save time by submitting it straight away and we will have a look at it while it runs:

+
sbatch run01_converge_pol.sh
+
+
+
+

Monitoring

+

You can monitor that the job is running by the squeue command

+
sbatch squeue -u $USER
+
+
+

and also by checking the files created in your folder

+
ls -ltr
+
+
+
i01-GW_Xp_20_bands_6_Ry
+job_Xp_20_bands_6_Ry
+out_Xp_20_bands_6_Ry
+i01-GW_Xp_20_bands_8_Ry
+out_Xp_20_bands_8_Ry
+job_Xp_20_bands_8_Ry
+i01-GW_Xp_20_bands_10_Ry
+out_Xp_20_bands_10_Ry
+job_Xp_20_bands_10_Ry
+i01-GW_Xp_20_bands_12_Ry
+out_Xp_20_bands_12_Ry
+job_Xp_20_bands_12_Ry
+summary_01_20bands.txt
+i01-GW_Xp_40_bands_6_Ry
+...
+
+
+

Finally you can monitor how runs are proceeding by looking into the log files

+
tail -f out_Xp_*_bands_*/LOG/*_1
+
+
+
==> out_Xp_20_bands_6_Ry/LOG/l-job_Xp_20_bands_6_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <15s> P1: [TIMING]                                          io_WF :      1.1353s CPU (34 calls,   0.033 sec avg)
+ <15s> P1: [TIMING]                                    WF_load_FFT :      1.1538s CPU ( 7 calls,   0.165 sec avg)
+ <15s> P1: [TIMING]                                    io_KB_pwscf :      1.1918s CPU ( 6 calls,   0.199 sec avg)
+ <15s> P1: [TIMING]                              DIPOLE_transverse :      2.4771s CPU
+ <15s> P1: [TIMING]                                    io_fragment :      2.6220s CPU (46 calls,   0.057 sec avg)
+ <15s> P1: [TIMING]                                           io_X :      3.1953s CPU (19 calls,   0.168 sec avg)
+ <15s> P1: [TIMING]                                        Dipoles :      4.4012s CPU
+ <15s> P1: [11] Memory Overview
+ <15s> P1: [12] Game Over & Game summary
+ <15s> P1: [TIMING]            [Time-Profile]: 15s
+
+==> out_Xp_20_bands_8_Ry/LOG/l-job_Xp_20_bands_8_Ry_HF_and_locXC_gw0_dyson_rim_cut_em1d_ppa_CPU_1 <==
+ <11s> P1: X@q[6] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[6] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):18975/64009(30%)
+ <11s> P1: [X-CG] R(p) Tot o/o(of R):   153   504   100
+ <11s> P1: Xo@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: Xo@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for X Frequencies on 1 CPU] Loaded/Total (Percentual):2/2(100%)
+ <11s> P1: X@q[7] |                                        | [000%] --(E) --(X)
+ <11s> P1: X@q[7] |########################################| [100%] --(E) --(X)
+ <11s> P1: [PARALLEL distribution for RL vectors(X) on 2 CPU] Loaded/Total (Percentual):31878/64009(50%)
+ <11s> P1: [08] Local Exchange-Correlation + Non-Local Fock
+
+
+
+

Let’s now have look into the job we just submitted.

+
vim run01_converge_pol.sh
+
+
+

First, we defined the double loop and we intialize a summary file for each iteration of the outer loop by printing a header to it. The input file i01-GW is used as a template for every calculation in the loops, so we assign it to a variable.

+
file0='i01-GW'
+
+for POL_BANDS in 20 40 60 80; do
+
+echo 'NGsBlkXp [Ry]   E_vale [eV]   E_cond [eV]' > summary_01_${POL_BANDS}bands.txt
+
+for NGsBlkXp_Ry in 6 8 10 12; do
+
+(...)
+
+done
+done
+
+
+

Inside the loops, we generate some useful labels which will come in handy to distinguish between runs. Then, we pass the variables from the loops to the sed command, in order to generate new files in an automated way (sed replaces any matching string with whatever is provided by the loop variable). Next, we run yambo using the labels to specify different job -J and communication -C directories every time. Finally, we get the quasiparticle energies with grep commands as shown before and append a new line to the summary file. So, inside each loop, we have

+
label=Xp_${POL_BANDS}_bands_${NGsBlkXp_Ry}_Ry
+jdir=job_${label}
+cdir=out_${label}
+filein=i01-GW_${label}
+
+sed "s/NGsBlkXp=.*/NGsBlkXp=${NGsBlkXp_Ry} Ry/;
+      /% BndsRnXp/{n;s/.*/  1 |  ${POL_BANDS} |/}" $file0 > $filein
+
+# run yambo
+mpirun -np ${SLURM_NTASKS} --map-by socket:PE=8 --rank-by core yambo -F $filein -J $jdir -C $cdir
+
+E_GW_v=`grep -v '#' ${cdir}/o-${jdir}.qp|head -n 1| awk '{print $3+$4}'`
+E_GW_c=`grep -v '#' ${cdir}/o-${jdir}.qp|tail -n 1| awk '{print $3+$4}'`
+
+echo ${NGsBlkXp_Ry} '        ' ${E_GW_v} '        ' ${E_GW_c}  >> summary_01_${POL_BANDS}bands.txt
+
+
+

Finally, let us plot this data. First, check that the job has finished with

+
squeue -u $USER
+
+
+
[$USER@login01 02_GW_convergence]$ squeue -u $USER
+             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
+[$USER@login01 02_GW_convergence]$ 
+
+
+

and verify that the energies were extracted correctly by inspecting the summary files. Remember to load the python module if you haven’t done so yet, and then plot:

+
module load anaconda3/2023.03
+python plot-01.py
+
+
+

The plot will produce a fig-01.png file. +You can copy and open it in your local machine with something like

+
[Run this on another terminal in your local machine, fixing $USER, $LOGIN and $TUTORIALPATH]
+scp $USER@$LOGIN:$TUTORIALPATH/MoS2_HPC_tutorial_Leonardo/02_GW_convergence/fig-01.png ./
+
+
+

You should get:

+
+_images/convergence01.png +
+

For the purpose of the tutorial, we will choose 80 bands and 10 Ry as our converged parameters and move on. An error within 10 meV is usually acceptable. To retain the chosen variables, we’ll make a copy of the corresponding input file:

+
cp i01-GW_Xp_80_bands_10_Ry i02-GW
+
+
+
+
+
Self-energy \(\Sigma^c\) - Bands
+

We will now proceed to converge the number of bands for the correlation part of the self-energy, i.e., GbndRnge. This step is actually simpler, since it only involves one loop. This is coded in the provided script run02_converge_Gbnds.noBG.sh. You can look into it

+
vim run02_converge_Gbnds.noBG.sh
+
+
+

and go ahead and submit it.

+
sbatch run02_converge_Gbnds.noBG.sh
+
+
+ +

While this runs, check if the previous job has finished, i.e., you should have a complete summary_02_noBG.txt file by now. +For a visual result, proceed to plot them with

+
python plot-02.py
+
+
+

You should get

+
+_images/BG_noBG.png +
+ +

We will end the convergence part of the tutorial with an important consideration about k-points convergence. The latter is the most cumbersome and computationally intensive among the various convergence tests, and it involves re-running the DFT step. For this reason (and for this reason only) it was ignored in this tutorial. However, it absolutely cannot be overlooked since it is crucial for the accuracy of the calculated GW corrections. You can read about k-points convergence in GW and, importantly, a very efficient workaround for 2D systems in a recent publication (here). MoS\(_2\) was one of the materials studied there, and it shows that our result, obtained with a \(6 \times 6 \times 1\) k-grid, is simply off the chart (blue line).

+
+_images/ref-Guandalini.png +
+

Guandalini, D’Amico, Ferretti & Varsano. npj Comput Mater 9

+ +
+
+
+
+

GW parallel strategies

+
+
MPI parallelization
+

For this section, let us enter the 03_GW_parallel directory. If you were in the 02_GW_convegence folder just do

+
cd ../03_GW_parallel
+
+
+

and inspect the input gw.in. You will see that we set low values for most of the convergence parameters except bands:

+
vim gw.in
+
+
+
FFTGvecs= 40       Ry    # [FFT] Plane-waves
+EXXRLvcs= 2        Ry    # [XX] Exchange RL components
+VXCRLvcs= 2        Ry    # [XC] XCpotential RL components
+% BndsRnXp
+    1 |  300 |               # [Xp] Polarization function bands
+%
+NGsBlkXp= 1            Ry    # [Xp] Response block size
+% GbndRnge
+    1 |  300 |               # [GW] G[W] bands range
+%
+%QPkrange                    # [GW] QP generalized Kpoint/Band indices
+  1| 19| 23| 30|
+%
+
+
+

Note that we also added FFTGvecs to reduce the size of the Fourier transforms (the default corresponds to Quantum ESPRESSO ecutwfc, i.e. 60 Ry in this case).

+

In addition, we have deleted all the parallel parameters since we will be setting them via the submission script.

+

Actually we are now dealing with a heavier system than before: as you can see from the QPkrange values, we have switched to a 12x12x1 k-point grid - having 19 points in the irreducible Brillouin zone - and turned spin-orbit coupling on in the DFT calculation (now the top valence band is number 26 instead of 13 because the bands are spin-polarized).

+

For this part of the tutorial, we will be using the slurm submission script job_parallel.sh, which is available in the calculation directory. +If you inspect it, you will see that the script adds additional variables to the yambo input file. +These variables control the parallel execution of the code:

+
DIP_CPU= "1 $ngpu 1"          # [PARALLEL] CPUs for each role
+DIP_ROLEs= "k c v"            # [PARALLEL] CPUs roles (k,c,v)
+DIP_Threads=  0               # [OPENMP/X] Number of threads for dipoles
+X_and_IO_CPU= "1 1 1 $ngpu 1" # [PARALLEL] CPUs for each role
+X_and_IO_ROLEs= "q g k c v"   # [PARALLEL] CPUs roles (q,g,k,c,v)
+X_and_IO_nCPU_LinAlg_INV=1    # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
+X_Threads=  0                 # [OPENMP/X] Number of threads for response functions
+SE_CPU= "1 $ngpu 1"           # [PARALLEL] CPUs for each role
+SE_ROLEs= "q qp b"            # [PARALLEL] CPUs roles (q,qp,b)
+SE_Threads=  0                # [OPENMP/GW] Number of threads for self-energy
+
+
+

The keyword DIP refers to the calculations of the screening matrix elements (also called “dipoles”) needed for the screening function, X is the screening function itself (it stands for \(\chi\) since it is a response function), SE the self-energy. +These three sections of the code can be parallelised independently.

+

We are running on GPUs. In particular, each node hosts four GPU cards. Yambo is coded in such a way that each MPI task is run on a single card, therefore ntasks=ngpu.

+
+

Note

+
    +

  • In this subsection we are mainly concerned with the [PARALLEL] variables which refer to MPI tasks (distributed memory).

    • +

  • What about [OPENMP] parallelisation (i.e., adding threads with shared memory)? When Yambo is run on GPUs, the explicit threading that you can set in the input and submission script only applies to the very few sections of the code that are not run on GPU cards, but stay on the CPUs. Therefore, in a GPU calculation, CPU-only threads are not going to be a relevant factor in the performance of the code. We keep them fixed to 8 since on Leonardo Booster (32 CPUs and 4 GPUs per node) the best hybrid parallel setup for CPUs is 4 tasks times 8 threads. We will see an example of the impact of threads in a CPU-only calculation later.

    • +
+
+

We start by calculating the QP corrections using 4 MPI tasks / GPUs. We leave the number of openMP threads at 8, the optimized value for Yambo on Leonardo. Therefore, edit the submission script as:

+
#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

and submit the job

+
sbatch job_parallel.sh
+
+
+

This will create a new input file and run it. The calculation databases and the human-readable files will be put in separate directories. Check the location of the report r-* file and the log l-* files, and inspect them while the calculation runs. +For simplicity you can just type

+
tail -f run_MPI4_OMP8.out/LOG/l-*_CPU_1
+
+
+

to monitor the progress in the master thread (Ctrl+c to exit). +As you can see, the run takes some time, even though we are using minimal parameters.

+

Meanwhile, we can run other jobs increasing the parallelisation. Let’s employ 16 MPI tasks / GPUs (i.e., 4 nodes on Leonardo). To this end modify the job_parallel.sh script changing

+
#!/bin/bash
+#SBATCH --nodes=4
+#SBATCH --ntasks-per-node=4
+...
+#SBATCH --gres=gpu:4
+
+
+

This time the code should be much faster. Once the run is over, try to run the simulation also on 8 MPI tasks by changing nodes appropriately. Finally, you can try to produce a scaling plot.

+

The timings are contained in the r-* report files. You can already have a look at them typing

+
grep Time-Profile run_MPI*/r-*
+
+
+

The python script parse_ytiming.py is useful for the post-processing of report files. You can already find it in the directory, together with the reports for the longer calculations with 1 and 2 MPI tasks which have been provided.

+

If you didn’t do so already, load the python module

+
module load anaconda3/2023.03
+
+
+

Then, after your jobs have finished, run the script as

+
python parse_ytiming.py run_MPI
+
+
+

to look for a report file in each run_MPI*.out folder. Make sure you have only one report file per folder. +You can also play with the script to make it print detailed timing information, however you should already see that it produced a png plot showing times-to-completion on y axis against number of MPI tasks (i.e., GPUs in this case) on the x axis.

+
+_images/gw_scaling.png +
+

What can we learn from this plot? In particular, try to answer the following questions:

+
    +

  • Up to which number of MPI tasks our system scales efficiently?

    • +

  • How can we decide at which point adding more nodes to the calculation becomes a waste of resources?

    • +
+
+

Note

+

Keep in mind that the MPI scaling we are seeing here is not the true Yambo scaling, but depends on the small size of our tutorial system. In a realistic calculation for a large-sized system, Yambo has been shown to scale well up to tens of thousands of MPI tasks! (See the next optional box for an example)

+
+ +

.

+ +
+
+
+
+

Full GW band structure

+

This is the final section of the tutorial, in which we want to compute the full correction to the band structure of single-layer MoS\(_2\).

+

This is a massive calculation, so run it right now and we’ll discuss it in the meantime:

+
cd ../04_GW_bands
+sbatch gpu_job.sh
+
+
+

In order to get somewhat realistic results, we will use the larger values for the convergence parameters we have identified in the convergence section. In addition, we also increased the vacuum separation (to 30 au) and the k-point mesh (to 18x18x1) in the DFT calculation, and of course we consider spin-orbit coupling.

+

Now we have a heavier calculation, and we have to do it not just for the band gap, but the entire band structure which includes 37 kpoints in the irreducible Brillouin zone, two spin-orbit-split valence bands, and two spin-orbit-split conduction bands. Let us check the new input:

+
vim gw.in
+
+
+
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
+1|37|25|28|
+%
+
+
+

After about 3 minutes the calculation should be over and the results collected in folder GW_bnds. The quasiparticle corrections are stored in human-readable form in the file o-GW_bnds.QP, and in netCDF format in the quasiparticle database ndb.QP.

+

In order to visualize the results in the form of a GW band structure, we will first interpolate the calculated points - recall that we have just 37 points, few of which lie on high-symmetry lines - with ypp, the yambo pre- and post-processing executable.

+
+

Note

+

We also have a python-based interface for advanced treatment of all the Yambo databases, called Yambopy. You can check it out here on the Yambo wiki.

+
+

Let us enter a computing node interactively

+
srun --nodes=1 --ntasks-per-node=1 --gres=gpu:1 --cpus-per-task=8 --mem=490000 --account=EUHPC_TD02_030 --partition=boost_usr_prod --qos=boost_qos_dbg --time=0:30:00 --pty /bin/bash
+
+
+

and load the yambo module:

+
module load profile/chem-phys
+module load yambo/5.2.0--openmpi--4.1.4--nvhpc--23.1
+
+
+

We can review the options with ypp -h and generate an input file for band structure interpolation with

+
ypp -s b -F ypp_bands.in
+
+
+

Let us modify the resulting input file by selecting the ‘boltztrap’ approach to interpolation, the last two valence and first two conduction bands, and a path in the Brillouin zone along the the points \(\Gamma-M-K-\Gamma\). We also set 100 points for each high-symmetry line.

+
electrons                        # [R] Electronic properties
+bnds                             # [R] Bands
+PROJECT_mode= "none"             # Instruct ypp how to project the DOS. ATOM, LINE, PLANE.
+INTERP_mode= "BOLTZ"                # Interpolation mode (NN=nearest point, BOLTZ=boltztrap aproach)
+INTERP_Shell_Fac= 20.00000       # The bigger it is a higher number of shells is used
+INTERP_NofNN= 1                  # Number of Nearest sites in the NN method
+OutputAlat= 5.90008             # [a.u.] Lattice constant used for "alat" ouput format
+cooIn= "rlu"                     # Points coordinates (in) cc/rlu/iku/alat
+cooOut= "rlu"                    # Points coordinates (out) cc/rlu/iku/alat
+% BANDS_bands
+   25 | 28 |                         # Number of bands
+%
+CIRCUIT_E_DB_path= "none"        # SAVE obtained from the QE `bands` run (alternative to %BANDS_kpts)
+BANDS_path= ""                   # High-Symmetry points labels (G,M,K,L...) also using composed positions (0.5xY+0.5xL).
+BANDS_steps= 100                  # Number of divisions
+#BANDS_built_in                # Print the bands of the generating points of the circuit using the nearest internal point
+%BANDS_kpts                      # K points of the bands circuit
+ 0.00000 |0.00000 |0.00000 |
+ 0.00000 |0.50000 |0.00000 |
+ 0.33333 |0.33333 |0.00000 |
+ 0.00000 |0.00000 |0.00000 |
+%
+
+
+

Now, let’s run ypp:

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

This run will produce the file o.bands_interpolated. You can inspect it and see that it contains a plottable band structure, but beware: these are the DFT eigevalues! We didn’t tell ypp where to look for the quasiparticle corrections, so it went into the SAVE folder and interpolated the DFT data. +Let’s rename the output:

+
mv o.bands_interpolated o.DFT_bands
+mkdir DFT_bands
+mv o.spin* o.magn* DFT_bands/
+
+
+

In order to interpolate the quasiparticle database, we append its location to the ypp input:

+
vim ypp_bands.in
+
+
+

add this line at the end

+
...
+GfnQPdb= "E < ./GW_bnds/ndb.QP"
+
+
+

and run ypp again.

+
mpirun -np 1 ypp -F ypp_bands.in
+
+
+

When it’s done, let’s rename the new output as

+
mv o.bands_interpolated o.GW_bands
+mkdir GW_bands
+mv o.spin* o.magn* GW_bands/
+
+
+

Now we are ready to visualize the band structures. In order to do so, you can use the script plt_bands.py that should be already available in the directory.

+

We load the python module

+
module load anaconda3/2023.03
+
+
+

and run the script as

+
python plt_bands.py o.DFT_bands o.GW_bands 4
+
+
+

Now we can also exit the computing node

+
exit
+
+
+

The python script should have produced a GW_bands.png file containing the following visualization, which you can copy and open it in your local machine using scp:

+
+_images/gw_bands.png +
+

You may compare this plot with a converged result from this paper (also done with Yambo):

+
+_images/gw_bands_ref.png +
+

Dashed lines: DFT, thick lines: GW.

+

As you can see, the general result is not too bad, but there are some differences both at the DFT and GW levels. The magnitude of the band gap is too large, and the relative energy of the two conduction band minima is not correct. One obvious issue is the lack of convergence of our tutorial calculations. As we know, we should include more vacuum space and many, many more k-points. Additionally, this is a transition metal dichalcogenide: for this class of systems, the details of the band structure can strongly depend on small variations in the lattice parameters and on the type of pseudopotential used. A great deal of care must be taken when performing these calculations!

+

In order to learn more about Yambo, we suggest visiting the Yambo website. For technical information and tutorials, you can check out the Yambo wiki. If you have issues and questions about installing and running the code, you can write about them on the Yambo forum.

+
+
+
+
+
+

Quick Reference

+
+
+

Instructor’s guide

+
+

Why we teach this lesson

+
+
+

Intended learning outcomes

+
+
+

Timing

+
+
+

Preparing exercises

+

e.g. what to do the day before to set up common repositories.

+
+
+

Other practical aspects

+
+
+

Interesting questions you might get

+
+
+

Typical pitfalls

+
+
+
+
+
+
+
+

About the course

+

In this workshop, participants will learn how to launch the most common +types of calculations (e.g. scf, phonons, quasi-particle energies, +time-dependent properties) using QE, SIESTA and Yambo, how to prepare input +files and how to read output files in order to extract the desired properties.

+

Best practices for efficient exploitation of HPC resources will be discussed. +On the QE days, there will be particular emphasis on how to use the different schemes of data +distribution (e.g. plane waves, pools, images) in combination with the different +parallelization and acceleration schemes (MPI, OpenMP, GPU-offload) available. +Regarding SIESTA, participants will learn about its algorithmic efficiency, +and they will be able to explore its accelerated and massively parallel solvers.

+
+

Schedule

+

Day 1, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:15

Welcome and introduction to ENCCS

09:15-09:30

Introduction to Max-CoE and MaX flagship codes

09:30-10:00

Overview of the QE suite of codes and main features

10:00-10:25

Coffee break

10:25-13:00

PWSCF for HPC and GPU

+

Day 2, QUANTUM ESPRESSO

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

Introduction to Density Functional Perturbation Theory

09:45-10:15

Introduction to Time Dependent Density Functional Perturbation Theory

10:15-10:30

Coffee break

10:30-13:00

Phonons and time dependent properties on HPC and GPU

+

Day 3, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:45

SIESTA basics

09:45-10:30

Hands-on tutorial: A first contact with SIESTA: inputs, execution and outputs

10:30-10:45

Break

10:45-11:15

Basis sets

11:15-12:00

Hands-on tutorial: Basis set optimization

12:00-13:00

Hands-on tutorial: Convergence (k points, mesh, mixing)

+

Day 4, SIESTA

+ + + + + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-10:00

Hands-on tutorial: Moving atoms: geometry optimisation and beyond

10:30-11:00

Hands-on tutorial: Analysis tools

11:00-11:15

Break

11:15-11:45

Features available in SIESTA: spin-orbit couplings, TranSIESTA, and others

11:45-13:00

Hands-on tutorial: Pushing the boundaries of SIESTA: accelerated and massively parallel solvers

+

Day 5, Yambo

+ + + + + + + + + + + + + + + + + + + + +

Time

Section

09:00-09:20

Overview of the Yambo code and its main features and performance

09:20-10:00

Introduction to the GW approximation

10:00-10:20

Coffee break

10:20-13:00

Hands-on tutorial: A guided tour through GW simulations

+
+
+
+

See also

+ +
+\[\]
+
+
+

Credits

+

Contributors to this workshop:

+
    +

  • Pietro Davide Delugas (SISSA)

    • +

  • Ivan Carnimeo (SISSA)

    • +

  • Oscar Baseggio (SISSA)

    • +

  • Fabrizio Ferrari Ruffino (CNR-IOM)

    • +

  • Paolo Giannozzi (CNR-IOM, UniUD)

    • +

  • Iurii Timrov (Paul Scherrer Institut)

    • +

  • Laura Bellentani (CINECA)

    • +

  • Tommaso Gorni (CINECA)

    • +

  • Aurora Ponzi (CNR-IOM)

    • +

  • Emilio Artacho (CIC NanoGUNE and University of Cambridge)

    • +

  • Catalina Coll (ICN2)

    • +

  • José Mª Escartín (ICN2)

    • +

  • Roberta Farris (ICN2)

    • +

  • Ernane de Freitas (ICN2)

    • +

  • Alberto García (ICMAB-CSIC)

    • +

  • Arnold Kole (Utrecht University)

    • +

  • Nick Papior (DTU)

    • +

  • Federico Pedron (ICN2)

    • +

  • Miguel Pruneda (CINN-CSIC)

    • +

  • José Ángel Silva Guillén (IMDEA Nanociencia)

    • +
    • +

    1. Varsano (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Ferretti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sangalli (CNR-ISM)

      2. +
    +
    • +
    • +

    1. Guandalini (Univ. of Rome, La Sapienza)

      2. +
    +
    • +
    • +

    1. Paleari (CNR-NANO)

      2. +
    +
    • +
    • +

    1. D’Alessio (Univ. Modena and Reggio Emilia, CNR-NANO)

      2. +
    +
    • +
    • +

    1. Sesti (CNR-NANO)

      2. +
    +
    • +
    • +

    1. Spallanzani (CNR-NANO)

      2. +
    +
    • +
+

The lesson file structure and browsing layout is inspired by and derived from +work by CodeRefinery licensed under the MIT license. We have copied and adapted +most of their license text.

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Software

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Except where otherwise noted, the example programs and other software provided +with this repository are made available under the OSI-approved +MIT license.

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SIESTA

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At the moment, unless otherwise stated, the contents of the SIESTA tutorials are +copyrighted - all rights reserved.

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© Copyright 2024, The contributors.

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