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Molecular Dynamics Simulation Sofware

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

For further information, please visit LAMMPS website.

  • Module:
  • intel/composer/2013_4_183
  • fftw/3.3.4/intel/composer2013-4.183/interlagos
  • mpi/intelmpi/5.1.0.079
  • software/lammps/7Dec15
  • Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

For further information, please visit LAMMPS website.

  • Binaries: lmp_mpi and lmp_serial plus those in the module's tools directory.
  • URL(s): lammps
  • Docs:
  • Example call(s):

#

   # To run lammps, you need to provide an input script for example "in.script" and also a a data file that your input script needs to read to start the simulation. In the following example, "16" is the number of cores requested.

mpirun -n 16 -envall lmp_mpi < in.script

<code bash>

</code>

  • LSF considerations (e.g. bsub example): an example of a script for job submission
  • #!/bin/bash
  • #BSUB -J lammps-test #jobname
  • #BSUB -o test.log

#BSUB -e test.err ##BSUB -q short #BSUB -q nodeshort #BSUB -W 300 #runtime in min #BSUB -n 64

# Store working directory to be safe SAVEDPWD=`pwd`

# We define a bash function to do the cleaning when the signal is caught

cp ${SAVEDPWD}/in.fene1000x10 /jobdir/${LSB_JOBID}/ cp ${SAVEDPWD}/data.file /jobdir/${LSB_JOBID}/

cd /jobdir/${LSB_JOBID}

mpirun -n 64 -envall lmp_mpi <in.fene1000x10

mv -f *.* ${SAVEDPWD} you can submit the job as bsub < lammps_job.sh * Please download all the required modules, before starting to run lammps. * contact: sjabbari (Institut für Physik) ==== HOOMD ==== * Modules: * software/hoomd/1.0.5/gcc-4.6.2_cuda-6.5.14/nompi * software/hoomd/1.0.5/gcc-4.6.2_cuda-6.5.14/openmpi-1.8.7 * software/hoomd/1.3.2/gcc-4.6.2_cuda-6.5.14/nompi * Description: * Binaries: hoomd and hoomd-config.sh plus those in the module's tools directory. * URL(s): HOOMD * Docs: HOOMD-Tutorial * Example call(s): <code bash> </code> * LSF considerations (e.g. bsub example): * contact: milchev'' (Institut für Physik)

  • md_software.1456422559.txt.gz
  • Last modified: 2016/02/25 18:49
  • by sjabbari