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doku:molecular_dynamics [2020/04/23 08:14]
ir 		doku:molecular_dynamics [2021/10/22 09:02] (current)
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 ====== Molecular Dynamics ====== ====== Molecular Dynamics ======
  
-[[https://wiki.vsc.ac.at/doku.php?id=pandoc:introduction-to-mul-cluster:01_introduction:05_user_software&s[]=fluent|VASP, ...]]+COMSOL, LAMMPS, VASP,  Wien2k 
 + 
 +====== VASP ====== 
 + 
 +===== VASP ===== 
 + 
 +==== Modules ==== 
 + 
 +<code> 
 +module purge 
 +module load autotools  
 +module load gnu7/7.2.0  
 +module load openmpi3/3.0.0  
 +module load openblas/0.2.20 
 +module load scalapack/2.0.2  
 +module load fftw/3.3.6  
 +module load prun 
 + 
 +</code> 
 + 
 +---- 
 + 
 +===== VASP ===== 
 + 
 +==== vasp.5.lib ==== 
 + 
 +<code> 
 +ln -s makefile.linux_gfortran makefile 
 +export CC=gcc 
 +make 
 +</code> 
 + 
 +---- 
 + 
 +===== VASP 5.4.1/5.4.4 ===== 
 + 
 +==== makefile.include ==== 
 + 
 +<code> 
 +OFLAG      = -O2 -march=broadwell 
 + 
 +LIBDIR     = /opt/ohpc/pub/libs/gnu7/openblas/0.2.20/lib 
 + 
 +BLAS       = -L$(LIBDIR) -lopenblas 
 + 
 +LAPACK     = 
 + 
 +BLACS      = 
 + 
 +SCALAPACK  = -L$(LIBDIR) -lscalapack $(BLACS) 
 + 
 +FFTW       ?= /opt/ohpc/pub/libs/gnu7/openmpi3/fftw/3.3.6 
 + 
 +</code> 
 + 
 +---- 
 + 
 +===== VASP 5.4.1/5.4.4 ===== 
 + 
 +==== Compile ==== 
 + 
 +<code> 
 +make all 
 +</code> 
 +==== If you have to recompile ==== 
 + 
 +<code> 
 +make veryclean 
 +make all 
 +</code> 
 +==== To build only specific version ==== 
 + 
 +<code> 
 +make std 
 +</code> 
 + 
 +---- 
 + 
 +===== VASP 5.4.1/5.4.4 ===== 
 + 
 +==== Job script ==== 
 + 
 +''%%/opt/ohpc/pub/examples/slurm/mul/vasp%%'' 
 + 
 +<code> 
 +#!/bin/bash 
 +# 
 +#SBATCH -J vasp 
 +#SBATCH -N 2 
 +#SBATCH -o job.%j.out 
 +#SBATCH -p E5-2690v4 
 +#SBATCH -q E5-2690v4-batch 
 +#SBATCH --ntasks-per-node=28 
 +#SBATCH --threads-per-core=1 
 +#SBATCH --mem=16G 
 + 
 +export OMP_NUM_THREADS=1 
 + 
 +exe=/path/to/my/vasp/vasp.5.4.4/bin/vasp_std 
 + 
 +time mpirun -np $SLURM_NPROCS $exe 
 + 
 +</code> 
 + 
 +---- 
 + 
 +====== LAMMPS ====== 
 + 
 +===== LAMMPS ===== 
 + 
 +''%%/opt/ohpc/pub/examples/slurm/mul/lammps%%'' 
 + 
 +<code> 
 +#!/bin/bash 
 +# 
 +#SBATCH -J lammps  
 +#SBATCH -N 2 
 +#SBATCH -o job.%j.out 
 +#SBATCH -p E5-2690v4 
 +#SBATCH -q E5-2690v4-batch 
 +#SBATCH --ntasks-per-node=28 
 +#SBATCH --threads-per-core=1 
 +#SBATCH --mem=16G 
 + 
 +module purge 
 +module load lammps 
 + 
 +mpirun -np $SLURM_NTASKS lmp_mul -in ./in.put 
 +</code> 
 + 
 +---- 
 + 
 +====== Wien2k ====== 
 + 
 + 
 +---- 
 + 
 +===== Wien2k ===== 
 + 
 +Example job script in: 
 + 
 +<code> 
 +/opt/ohpc/pub/examples/slurm/mul/wien2k 
 +</code> 
 + 
 +---- 
 + 
  • doku/molecular_dynamics.1587629693.txt.gz
  • Last modified: 2020/04/23 08:14
  • by ir