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README
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README
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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
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)