/* ----------------------------------------------------------------------
   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 
   (pscrozi@sandia.gov).

   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 (pscrozi@sandia.gov). 

   Please read the accompanying README and LICENSE files.
---------------------------------------------------------------------- */


------------------------------------------------
Description:
------------------------------------------------
miniMD is a simple, parallel molecular dynamics (MD) code.

Authors: Steve Plimpton and Paul Crozier (pscrozi@sandia.gov).        

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:
pscrozi@sandia.gov . 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)