IMD is a software package for classical molecular dynamics simulations. Several types of interactions are supported, such as central pair potentials, EAM potentials for metals, Stillinger-Weber and Tersoff potentials for covalent systems, and Gay-Berne potentials for liquid crystals. A rich choice of simulation options is available: different integrators for the simulation of the various thermodynamic ensembles, options that allow to shear and deform the sample during the simulation, and many more. There is no restriction on the number of particle types. (http://imd.itap.physik.uni-stuttgart.de/)
The latest versions of IMD are released under GPL-3.0.
Availability / Target HPC systems
IMD is currently not centrally installed, but can be installed locally in users’ home folder. Follow the instruction on http://imd.itap.physik.uni-stuttgart.de/userguide/compiling.html. While compiling at RRZE, first load “
intel64” module. It is recommended to clean the compilation before initiating a new compiling process, i.e.
gmake clean. Specify
IMDSYS=lima on any of RRZE’s cluster; however, only use the resulting binary on the cluster where you produced it, i.e. recompile again with
IMDSYS=lima when moving to a different cluster.
If there is enough demand, RRZE might also provide a module for IMD.
Sample job scripts
parallel IMD job on Emmy
#!/bin/bash -l #PBS -l nodes=2:ppn=40,walltime=01:00:00 #PBS -N myJobName #PBS -M myEmailAdress@fau.de #PBS -j oe module load intel64 # specify the full path of the IMD executable IMDCMD=$HOME/bin/imd_mpi_eam4point_fire_fnorm_homdef_stress_nbl_mono_hpo # input parameter file name PARAM=myJob.param # run your job mpirun -n 40 $IMDCMD -p $PARAM
parallel IMD job on Meggie
#!/bin/bash -l # # allocate 4 nodes with 20 cores per node = 4*20 = 80 MPI tasks #SBATCH --nodes=4 #SBATCH --tasks-per-node=20 # # allocate nodes for 6 hours #SBATCH --time=06:00:00 # job name #SBATCH --job-name=my-IMD # do not export environment variables #SBATCH --export=NONE # # first non-empty non-comment line ends SBATCH options # do not export environment variables unset SLURM_EXPORT_ENV # jobs always start in submit directory module load intel64 # specify the full path of the IMD executable IMDCMD=$HOME/bin/imd_mpi_eam4point_fire_fnorm_homdef_stress_nbl_mono_hpo # input parameter file name PARAM=myJob.param # run srun $IMDCMD -p $PARAM
- AG Bitzek (WW1 – I: General Materials Properties)