Siesta updates

content/day3/index.rst → content/days3+4/day3.rst

@@ -20,18 +20,22 @@ Practical session led by Dr. Federico Pedron (ICN2).
 
 Tutorials covered:
 
-- `A First Encounter - Part 1: Running SIESTA <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/first-encounter/index.html>`_
-- `A First Encounter - Part 2: Choosing your level of theory <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/first-encounter-theorylevel/index.html>`_
+- `A First Encounter - Part 1: Running SIESTA <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/first-encounter/index.html>`_.  Files available at::
 
-Introductory slides available here: (TBA).
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/01-FirstEncounter_I
+
+- `A First Encounter - Part 2: Choosing your level of theory <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/first-encounter-theorylevel/index.html>`_. Files available at::
 
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/02-FirstEncounter_II
+
+Introductory slides available here: (TBA).
 
 Basis sets
 ----------
 
 Lecture by Dr. Miguel Pruneda (CINN-CSIC).
 
-Slides available here: (TBA).
+Slides available here: :download:`Basis_sets.pdf </_static/siesta/SIESTA-Basis_sets.pdf>`
 
 
 Basis set optimization
@@ -44,8 +48,11 @@ Tutorials covered:
 - `Basis set optimization <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/basis-optimization/index.html>`_
 - `Basis sets - Tips and tricks <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/basis-sets/index.html>`_
 
-Introductory slides available here: (TBA).
+Files for the tutorial::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/03-BasisSets
 
+Introductory slides available here: (TBA).
 
 Convergence (k points, mesh, mixing)
 ------------------------------------
@@ -54,8 +61,17 @@ Practical session led by Dr. Catalina Coll (ICN2).
 
 Tutorials covered:
 
-- `The real-space grid <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/grid-convergence/index.html>`_
-- `Sampling of the BZ with k-points <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/kpoint-convergence/index.html>`_
-- `The self-consistent-field cycle <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/scf-convergence/index.html>`_
+- `The real-space grid <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/grid-convergence/index.html>`_. Files available at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04a-GridConvergence
+
+- `Sampling of the BZ with k-points <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/kpoint-convergence/index.html>`_. Files available at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04b-KPointConvergence
+
+- `The self-consistent-field cycle <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/scf-convergence/index.html>`_. Files available at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day3-Wed/04c-SCF
 
 Introductory slides available here: (TBA).
+

content/day4/index.rst → content/days3+4/day4.rst

@@ -2,18 +2,19 @@
 
 ..  _day4-siesta2:
 
-Day 4: SIESTA I
-===============
+Day 4: SIESTA II
+================
 
-A first contact with SIESTA: inputs, execution and outputs
------------------------------------------------------------
+Molecular Dynamics with SIESTA
+------------------------------
 
 Practical session led by Dr. Ernane de Freitas (ICN2).
 
 Tutorials covered:
 
-- `Structural optimization using forces and stresses <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/structure-optimization/index.html>`_
-- `Molecular Dynamics <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/advanced/molecular-dynamics/index.html>`_
+- `Molecular Dynamics <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/advanced/molecular-dynamics/index.html>`_. Files available at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/01-MolecularDynamics
 
 Introductory slides available here: (TBA).
 
@@ -25,7 +26,9 @@ Practical session led by Dr. Miguel Pruneda (CINN-CSIC).
 
 Tutorials covered:
 
-- TBA
+- `Analysis tools <https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/analysis-tools/index.html>`_. Files available at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/02-Analysis
 
 Introductory slides available here: (TBA).
 
@@ -45,6 +48,9 @@ Practical session led by Dr. Alberto García (ICMAB-CSIC)
 
 Tutorials covered:
 
-- TBA
+- TBA. Files avilable at::
+
+    /leonardo_work/EUHPC_TD02_030/siesta-tutorials/day4-Thu/03-SiestaSolvers
 
 Introductory slides available here: (TBA).
+

content/days3+4/setup.rst

@@ -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 <http://www.gnuplot.info/>`_
+- `xcrysden <http://www.xcrysden.org/>`_
+- `vesta <https://jp-minerals.org/vesta/en/>`_
+- `vmd <https://www.ks.uiuc.edu/Research/vmd/>`_
+- `ovito <https://www.ovito.org/about/>`_
+- Python with matplotlib
+
+
+
+..
+  SIESTA source code
+  ------------------
+  If you want to try your own SIESTA compilation, have a look at this `SIESTA
+  compilation how-to <https://docs.siesta-project.org/projects/siesta/en/latest/installation/quick-install.html>`_ .
+  Be sure to have all dependencies beforehand. Note that we will not be answering
+  questions regarding compilation or other installations during the school.

content/index.rst

@@ -88,17 +88,11 @@ previous experience with materials modelling and electronic structure calculatio
 
 .. toctree::
    :maxdepth: 1
-   :caption: Day 3 - Siesta I
-
-   day3/index
-
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Day 4 - Siesta II
-
-   day4/index
+   :caption: Days 3 and 4 - Siesta
 
+   days3+4/setup
+   days3+4/day3
+   days3+4/day4
 
 .. toctree::
    :maxdepth: 1