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OpenMP support in miniMD
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apawloski/miniMD-omp
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/* ---------------------------------------------------------------------- miniMD is a simple, parallel molecular dynamics (MD) code. miniMD is an MD microapplication in the Mantevo project at Sandia National Laboratories ( http://software.sandia.gov/mantevo/ ). The primary authors of miniMD are Steve Plimpton and Paul Crozier ([email protected]). Copyright (2008) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this software; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. See also: http://www.gnu.org/licenses/lgpl.txt . For questions, contact Paul S. Crozier ([email protected]). Please read the accompanying README and LICENSE files. ---------------------------------------------------------------------- */ ------------------------------------------------ Description: ------------------------------------------------ miniMD is a simple, parallel molecular dynamics (MD) code. Authors: Steve Plimpton and Paul Crozier ([email protected]). This simple benchmark code is a self-contained piece of C++ software that performs parallel molecular dynamics simulation of a Lennard-Jones system and gives timing information. It is implemented to be very scalable (in a weak sense). Any reasonable parallel computer should be able to achieve excellent scaled speedup (weak scaling). miniMD uses a spatial decomposition parallelism and has many other similarities to the much more complicated LAMMPS MD code: http://lammps.sandia.gov ------------------------------------------------ Compiling the code: ------------------------------------------------ There is a simple Makefile that should be easily modified for most Unix-like environments. There are also one or more Makefiles with extensions that indicate the target machine and compilers. Read the Makefile for further instructions. If you generate a Makefile for your platform and care to share it, please send it to Paul Crozier: [email protected] . By default the code compiles with MPI support and can be run on one or more processors. To remove all output files, type: make clean_<platform> ------------------------------------------------ Running the code: ------------------------------------------------ Usage: miniMD (serial mode) mpirun -np numproc miniMD (MPI mode) Example: mpirun -np 16 ./miniMD You will also need to provide a simple input script, which you can model after the lj.in input script included in this directory. The format and parameter description is as follows: Lennard-Jones input file for MD benchmark 10 10 10 size of problem 100 timesteps 10 10 10 neighbor bins in each direction 0.00462 timestep size (reduced units) 1.444 initial temperature (reduced units) 0.8442 density (reduced units) 20 reneighboring every this many steps 2.5 2.8 inner and outer cutoff (reduced units) 1 thermo calculation every this many steps (0 = start,end)
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