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doku:molecular_dynamics [2020/04/23 08:45]
ir 		doku:molecular_dynamics [2021/10/22 09:02] (current)
ir
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 COMSOL, LAMMPS, VASP,  Wien2k 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>
 +
 +----
 +
 +
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