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Merge pull request easybuilders#20846 from WilleBell/20240618143525_n…
…ew_pr_VASPKIT151
{tools}[foss/2023a] VASPKIT v1.5.1- Loading branch information
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easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1-foss-2023a.eb
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| easyblock = 'Tarball' | ||
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| name = 'VASPKIT' | ||
| version = '1.5.1' | ||
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| homepage = 'https://vaspkit.com/' | ||
| description = """ | ||
| VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput | ||
| analysis of various material properties from the raw calculated data using the widely-used | ||
| VASP code. | ||
| """ | ||
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| toolchain = {'name': 'foss', 'version': '2023a'} | ||
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| dependencies = [ | ||
| ('Python', '3.11.3'), | ||
| ('matplotlib', '3.7.2'), | ||
| ] | ||
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| source_urls = [SOURCEFORGE_SOURCE] | ||
| sources = ['%(namelower)s.%(version)s.linux.x64.tar.gz'] | ||
| patches = ['%(name)s-1.5.1_fix-envvars.patch'] | ||
| checksums = [ | ||
| {'vaspkit.1.5.1.linux.x64.tar.gz': '41bbdc0759f72cd43ef7e2f541d228a639bd95dba2a549398b28f47d760d72b1'}, | ||
| {'VASPKIT-1.5.1_fix-envvars.patch': '952e2530b53e4632c3f8ab2ec24f88c61d76e263d9a377772c44c3ad071c1970'}, | ||
| ] | ||
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| sanity_check_paths = { | ||
| 'files': ["bin/vaspkit", "how_to_set_environment_variables"], | ||
| 'dirs': ["bin"], | ||
| } | ||
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| # remove setup.sh to avoid users to run it | ||
| postinstallcmds = ['rm %(installdir)s/setup.sh'] | ||
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| modloadmsg = """ | ||
| When using this module for the first time run: | ||
| cp $EBROOTVASPKIT/how_to_set_environment_variables ~/.vaspkit | ||
| and modify paths set in ~/.vaspkit as needed. | ||
| """ | ||
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| moduleclass = 'tools' |
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easybuild/easyconfigs/v/VASPKIT/VASPKIT-1.5.1_fix-envvars.patch
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| Set correct environment variables, add instructions to set POTCAR paths, translate example job script to slurm | ||
| Author: Cintia Willemyns (Vrije Universiteit Brussel) | ||
| diff -Naur vaspkit.1.5.1.orig/how_to_set_auto_plot vaspkit.1.5.1/how_to_set_auto_plot | ||
| --- vaspkit.1.5.1.orig/how_to_set_auto_plot 2024-06-18 10:57:18.521696013 +0200 | ||
| +++ vaspkit.1.5.1/how_to_set_auto_plot 2024-06-18 11:55:12.298424299 +0200 | ||
| @@ -1,7 +1,7 @@ | ||
| (1) Make sure you have installed python3, numpy, scipy, matplotlib, etc. | ||
| (2) Add the following parameters in the ~/.vaspkit file; | ||
| ####################################################################### | ||
| - PYTHON_BIN ~/anaconda3/bin/python3 | ||
| + PYTHON_BIN $EBROOTPYTHON/bin/python3 | ||
| AUTO_PLOT .TRUE. | ||
| ####################################################################### | ||
| (3) Copy the plot presets from the vaspkit/how_to_set_environment_variable file to the ~/.vaspkit file. Must copy the block from #BEGIN_CUSTOMIZE_PLOT to #END_CUSTOMIZE_PLOT. | ||
| diff -Naur vaspkit.1.5.1.orig/how_to_set_environment_variables vaspkit.1.5.1/how_to_set_environment_variables | ||
| --- vaspkit.1.5.1.orig/how_to_set_environment_variables 2024-06-18 10:57:17.784058000 +0200 | ||
| +++ vaspkit.1.5.1/how_to_set_environment_variables 2024-06-18 13:59:20.120174533 +0200 | ||
| @@ -1,11 +1,13 @@ | ||
| # cp how_to_set_environment_variables ~/.vaspkit and modify the ~/.vaspkit file based on the settings in your supercomputer! | ||
| +# Modify paths as needed, e.g if you want to make PBE-POTCAR file, use POTCAR_TYPE = PBE and set the PBE_PATH to where you unzipped the VASP PAW_PBE pseudo potentials. | ||
| +# Do not modify VASPKIT_UTILITIES_PATH or PYTHON_BIN paths! | ||
| # All environment variables are case sensitive. | ||
| VASP5 = .TRUE. # .TRUE. or .FALSE.; Set .FALSE. if you are using vasp.4.x | ||
| -LDA_PATH = ~/POTCAR/LDA # Path of LDA potential | ||
| -PBE_PATH = ~/POTCAR/PBE # Path of PBE potential | ||
| -GGA_PATH = ~/POTCAR/GGA # Path of PW91 potential | ||
| -VASPKIT_UTILITIES_PATH = ~/vaspkit/utilities # Path of VASPKIT | ||
| -PYTHON_BIN = ~/anaconda3/bin/python3 # Python executable program with its installation path. Recommend Anaconda package | ||
| +LDA_PATH = <path/to/LDA/potential> # Path of LDA potential | ||
| +PBE_PATH = <path/to/PBE/potential> # Path of PBE potential | ||
| +GGA_PATH = <path/to/PW91/potential> # Path of PW91 potential | ||
| +VASPKIT_UTILITIES_PATH = $EBROOTVASPKIT/utilities # Path of VASPKIT | ||
| +PYTHON_BIN = $EBROOTPYTHON/bin/python3 # Python executable program with its installation path. Recommend Anaconda package | ||
| POTCAR_TYPE = PBE # PBE, PW91 or LDA; Set PBE if you want to make PBE-POTCAR file | ||
| GW_POTCAR = .FALSE. # .TRUE. or .FALSE.; For example, H_GW, O_GW will be chose when POTCAR_GW set to .TRUE. | ||
| RECOMMENDED_POTCAR = .TRUE. # .TRUE. or .FALSE.; The recommended PAW potential will be chose when RECOMMENDED_POTCAR set to .TRUE. | ||
| @@ -42,7 +44,7 @@ | ||
| INTERPOLATION_SPACING = 0.04 # Determines the number of interpolation grids, in unit of A in real-space or 1/A in reciprocal space (default: 0.04) | ||
| INTERPOLATION_METHOD = 'cubic' # 'linear', 'cubic' (3rd order-spline interpolation), quartic (4th order-spline interpolation), or FFT available only for 2D and 3D grids (default method: 'cubic') | ||
| AUTO_SUBMIT_JOB = .FALSE. # .TRUE. or .FALSE. (default: .FASLE.). Whether to auto-submit vaspkit or vasp job or not. | ||
| -SUBMIT_JOB_COMMAND = 'qsub job.sh' # The command line to submit job | ||
| +SUBMIT_JOB_COMMAND = 'sbatch job.sh' # The command line to submit job | ||
| AUTO_PLOT = .FALSE. # TRUE. or .FALSE. (default: .FASLE.). Whether to auto-plot data graphs in the post-processing. | ||
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| # New added in Version 1.4.1 | ||
| @@ -69,12 +71,14 @@ | ||
| #| Must copy the block from #BEGIN_CUSTOMIZE_JOB_SCRIPT to #END_CUSTOMIZE_JOB_SCRIPT | | ||
| #+------------------------------------------------------------------------------------------------------------------+ | ||
| #BEGIN_CUSTOMIZE_JOB_SCRIPT | ||
| -#PBS -N name | ||
| -#PBS -o out | ||
| -#PBS -e err | ||
| -#PBS -l nodes=2:ppn=4 | ||
| -#PBS -r y | ||
| -cd $PBS_O_WORKDIR | ||
| +#!/bin/bash | ||
| +#SBATCH --job-name=name # Job name | ||
| +#SBATCH --output=out # Standard output | ||
| +#SBATCH --error=err # Standard error | ||
| +#SBATCH --nodes=2 # Number of nodes | ||
| +#SBATCH --ntasks-per-node=4 # Number of tasks per node | ||
| +#SBATCH --requeue # Requeue the job if it fails | ||
| +cd $SLURM_SUBMIT_DIR | ||
| mpirun -np 8 vasp_std > vasp-out | ||
| #END_CUSTOMIZE_JOB_SCRIPT | ||
| #+------------------------------------------------------------------------------------------------------------------+ |