lammps/examples/COUPLE/lammps_spparks

This directory has an application that models grain growth in the
presence of strain.  The grain growth is simulated by a Potts model in
a kinetic Monte Carlo code SPPARKS.  Clusters of like spins on a
lattice represent grains.  The Hamiltonian for the energy due of a
collection of spins includes a strain term and is described on this
page in the SPPARKS documentation:

http://www.sandia.gov/~sjplimp/spparks/doc/app_potts_strain.html.

The strain is computed by LAMMPS as a particle displacement where
pairs of atoms across a grain boundary are of different types and thus
push off from each other due to a Lennard-Jones sigma between
particles of different types that is larger than the sigma between
particles of the same type (interior to grains).

lmpspk.cpp	    main program
		    it links LAMMPS and SPPARKS as libraries
in.spparks	    SPPARKS input script, without the run command
lmppath.h	    contains path to LAMMPS home directory
spkpath.h	    contains path to SPPARKS home directory

After editing the Makefile, lmppath.h, and spkpath.h to make them
suitable for your box, type:

g++ -f Makefile.g++

and you should get the lmpspk executable.

NOTE: To build and run this coupled application, you must of course,
have SPPARKS built on your system.  It's WWW site is
http://www.sandia.gov/~sjplimp/spparks.html.  It is an open-source
code, written by two of the LAMMPS authors.

You can run lmpspk in serial or parallel as:

% lmpspk Niter Ndelta Sfactor in.spparks
% mpirun -np 4 lmpspk Niter Ndelta Sfactor in.spparks

where

Niter = # of outer iterations
Ndelta = time to run MC in each iteration
Sfactor = multiplier on strain effect
in.spparks = SPPARKS input script

The log files are for this run:

% lmpspk 20 10.0 1 in.spparks

This application is an example of a coupling where the driver code
(lmpspk) alternates back and forth between the 2 applications (LAMMPS
and SPPARKS).  Each outer timestep in the driver code, the following
tasks are performed.  One code (SPPARKS) is invoked for a few Monte
Carlo steps.  Some of its output (spin state) is passed to the other
code (LAMMPS) as input (atom type).  The the other code (LAMMPS) is
invoked for a few timesteps.  Some of its output (atom coords) is
massaged to become an input (per-atom strain) for the original code
(SPPARKS).

The driver code launches both SPPARKS and LAMMPS in parallel and they
both decompose their spatial domains in the same manner.  The datums
in SPPARKS (lattice sites) are the same as the datums in LAMMPS
(coarse-grained particles).  If this were not the case, more
sophisticated inter-code communication could be performed.

You can look at the log files in the directory to see sample LAMMPS
and SPPARKS output for this simulation.  Dump files produced by the
run are stored as dump.mc and dump.md.  The image*.png files show
snapshots from both the LAMMPS and SPPARKS output.  Note that the
in.lammps and data.lammps files are not inputs; they are generated by
the lmpspk driver.