LAMMPSA. DescriptionLAMMPS is a classical molecular dynamics code. It can be applied to metals, semiconductors, biomolecules, polymers in all-atom or coarse-grained models. The source code is distributed under the terms of GPL by Sandia National Laboratories. See LAMMPS home page http://lammps.sandia.gov/ for additional information. B. How to download LAMMPSThere are several different mechanisms to download LAMMPS. See complete instructions for downloading the code. You can download a recent stable version from the LAMMPS github repository https://github.com/lammps/lammps using wget. For example, the October, 2020 stable release can be obtained by running wget https://github.com/lammps/lammps/archive/stable_29Oct2020.zip C. How to build LAMMPSOn Blue Waters, LAMMPS can be built under the GNU environment. Building under other compiler environments may be possible. Please contact help+bw@ncsa.illinois.edu if you need to use another environment. C.1 Building under GNU environmentmodule swap PrgEnv-cray PrgEnv-gnu module add fftw module add cmake/3.17.3 mkdir ~/lammps cd ~/lammps wget https://github.com/lammps/lammps/archive/stable_29Oct2020.zip unzip stable_29Oct2020.zip cd lammps-stable_29Oct2020 mkdir build cd build cmake -D CMAKE_CXX_COMPILER=CC -D CMAKE_C_COMPILER=cc -D CMAKE_Fortran_COMPILER=ftn \ -D CMAKE_INSTALL_PREFIX=$HOME/lammps -D PKG_MOLECULE=yes ../cmake make make install D. Sample testLAMMPS comes with an extensive suit of tests. To make sure that the compiled code works, we wil run one of the supplied tests. cd ../examples/micelle Create run.pbs file having the following content: #!/bin/bash #PBS -l nodes=1:ppn=32:xe #PBS -l walltime=00:05:00 #PBS -q debug cd $PBS_O_WORKDIR export OMP_NUM_THREADS=8 aprun -n 4 -N 4 -d 8 $HOME/lammps/bin/lmp -in in.micelle -log job.out -screen none Submit the job qsub run.pbs Open the file job.out with text editor and make sure that line "Loop time of 0.121433 on 4 procs for 1000 steps with 1200 atoms" is present near the end of the file. It indicates that the job performed 1,000 dynamics steps on 4 processors. Timing of 0.121433 will be different on different machines and may somewhat vary from run to run, which is normal. E. How to download older versions of LAMMPSThere are several different mechanisms to download older versions of LAMMPS. See complete instructions for downloading the code. To download a stable version of the code to local directory mylammps by using svn tool, use the following command svn co -r N svn://svn.lammps.org/lammps-ro/trunk mylammps where N is SVN tag. For the recent stable version 1 Feb 2014, the tag N is 11423. The LAMMPS web site supplies the list of a few stable versions. To download the latest version, use svn co svn://svn.lammps.org/lammps-ro/trunk mylammps F. How to build LAMMPS (1 Feb 2014 version)On Cray XE6 platform, LAMMPS can be built under GNU or PGI environments. Following instructions are tested on 1 Feb 2014 release. F.1 Building under GNU environment
Successful compilation will create lmp_xe6 binary file. A few comments should be made. Althought the February 1, 2014 release comes with Makefile.xe6 for Cray XE6 pltaform included into the distribution, that Makefile.xe6 is not functional. We made following changes to correct it:
The compilation was conducted under the following environment:
F.2 Building under PGI environment
Successful compilation will create lmp_xe6 binary file. Again, as in the previous case, Makefile.xe6 needs a few corrections:
The compilation was conducted under the following environment:
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