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Molecular Dynamics

COMSOL, LAMMPS, VASP, Wien2k

VASP

VASP

Modules

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

VASP

vasp.5.lib

ln -s makefile.linux_gfortran makefile
export CC=gcc
make

VASP 5.4.1/5.4.4

makefile.include

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

VASP 5.4.1/5.4.4

Compile

make all

If you have to recompile

make veryclean
make all

To build only specific version

make std

VASP 5.4.1/5.4.4

Job script

/opt/ohpc/pub/examples/slurm/mul/vasp

#!/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

LAMMPS

LAMMPS

/opt/ohpc/pub/examples/slurm/mul/lammps

#!/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

Wien2k


Wien2k

Example job script in:

/opt/ohpc/pub/examples/slurm/mul/wien2k

doku/molecular_dynamics.txt · Last modified: 2021/10/22 09:02 by ir