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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4806 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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examples/COUPLE/README deleted 100644 → 0
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This directory has a C and C++ code that shows how LAMMPS can be
linked to a driver application as a library. The purpose is to
illustrate how another code could perform computations while using
LAMMPS to perform MD, or how an umbrella code or script could call
both LAMMPS and some other code to perform a coupled calculation.
c_driver.c is the C driver
c++_driver.c is the C++ driver
The 2 codes do the same thing, so you can compare them to see how to
drive LAMMPS in this manner. The C driver is similar in spirit to
what one could use from a Fortran program or scripting language.
LAMMPS must first be built as a library. See the "Making LAMMPS"
section of Section_start.html in the documentation for info on how to
do this. Basically, you type something like
make makelib
make -f Makefile.lib g++
in the LAMMPS src directory to create liblmp_g++.a
You can then build either driver code with a compile line something
like this, which includes paths to the LAMMPS library interface, MPI,
and FFTW.
This builds the C++ driver with the LAMMPS library using a C++ compiler:
g++ -I/home/sjplimp/lammps/src -c c++_driver.cpp
g++ -L/home/sjplimp/lammps/src c++_driver.o \
-llmp_g++ -lfftw -lmpich -lpthread -o c++_driver
This builds the C driver with the LAMMPS library using a C compiler:
gcc -I/home/sjplimp/lammps/src -c c_driver.cpp
gcc -L/home/sjplimp/lammps/src c_driver.o \
-llmp_g++ -lfftw -lmpich -lpthread -lstdc++ -o c_driver
You then run c++_driver or c_driver on a parallel machine on some
number of processors Q with 2 arguments:
mpirun -np Q c_driver P in.lj
P is the number of procs you want LAMMPS to run on (must be <= Q).
In.lj is a LAMMPS input script.
The driver will launch LAMMPS on P procs, read the input script a line
at a time, and pass each command line to LAMMPS. The final line of
the script is a "run" command, so LAMMPS will run the problem.
The driver then requests all the atom coordinates from LAMMPS, moves
one of the atoms a small amount "epsilon", passes the coordinates back
to LAMMPS, and runs LAMMPS again. If you look at the output, you
should see a small energy change between runs, due to the moved atom.
The C driver is calling C-style routines in the src/library.cpp file
of LAMMPS. You could add any functions you wish to this file to
manipulate LAMMPS data however you wish.
The C++ driver does the same thing, except that it instantiates LAMMPS
as an object first. Some of the functions in src/library.cpp can be
invoked directly as methods within appropriate LAMMPS classes, which
is what the driver does. Any public LAMMPS class method could be
called from the driver this way. However the get/put functions are
only implemented in src/library.cpp, so the C++ driver calls them as
C-style functions.
examples/COUPLE/c++_driver.cpp deleted 100644 → 0
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// c++_driver = simple example of how an umbrella program
// can invoke LAMMPS as a library on some subset of procs
// Syntax: c++_driver P in.lammps
// P = # of procs to run LAMMPS on
// must be <= # of procs the driver code itself runs on
// in.lammps = LAMMPS input script
// See README for compilation instructions
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "mpi.h"
#include "lammps.h" // these are LAMMPS include files
#include "input.h"
#include "atom.h"
#include "library.h"
using namespace LAMMPS_NS;
int main(int narg, char **arg)
{
// setup MPI and various communicators
// driver runs on all procs in MPI_COMM_WORLD
// comm_lammps only has 1st P procs (could be all or any subset)
MPI_Init(&narg,&arg);
if (narg != 3) {
printf("Syntax: c++_driver P in.lammps\n");
exit(1);
}
int me,nprocs;
MPI_Comm_rank(MPI_COMM_WORLD,&me);
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
int nprocs_lammps = atoi(arg[1]);
if (nprocs_lammps > nprocs) {
if (me == 0)
printf("ERROR: LAMMPS cannot use more procs than available\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
int lammps;
if (me < nprocs_lammps) lammps = 1;
else lammps = MPI_UNDEFINED;
MPI_Comm comm_lammps;
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
// open LAMMPS input script
FILE *fp;
if (me == 0) {
fp = fopen(arg[2],"r");
if (fp == NULL) {
printf("ERROR: Could not open LAMMPS input script\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
}
// run the input script thru LAMMPS one line at a time until end-of-file
// driver proc 0 reads a line, Bcasts it to all procs
// (could just send it to proc 0 of comm_lammps and let it Bcast)
// all LAMMPS procs call input->one() on the line
LAMMPS *lmp;
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
int n;
char line[1024];
while (1) {
if (me == 0) {
if (fgets(line,1024,fp) == NULL) n = 0;
else n = strlen(line) + 1;
if (n == 0) fclose(fp);
}
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
if (n == 0) break;
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
if (lammps == 1) lmp->input->one(line);
}
// run 10 more steps
// get coords from LAMMPS
// change coords of 1st atom
// put coords back into LAMMPS
// run a single step with changed coords
if (lammps == 1) {
lmp->input->one("run 10");
int natoms = static_cast<int> (lmp->atom->natoms);
double *x = new double[3*natoms];
lammps_get_coords(lmp,x); // no LAMMPS class function for this
double epsilon = 0.1;
x[0] += epsilon;
lammps_put_coords(lmp,x); // no LAMMPS class function for this
delete [] x;
lmp->input->one("run 1");
}
if (lammps == 1) delete lmp;
// close down MPI
MPI_Finalize();
}
examples/COUPLE/c_driver.c deleted 100644 → 0
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* c_driver = simple example of how an umbrella program
can invoke LAMMPS as a library on some subset of procs
Syntax: c_driver P in.lammps
P = # of procs to run LAMMPS on
must be <= # of procs the driver code itself runs on
in.lammps = LAMMPS input script
See README for compilation instructions */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "mpi.h"
#include "library.h" /* this is a LAMMPS include file */
int main(int narg, char **arg)
{
/* setup MPI and various communicators
driver runs on all procs in MPI_COMM_WORLD
comm_lammps only has 1st P procs (could be all or any subset) */
MPI_Init(&narg,&arg);
if (narg != 3) {
printf("Syntax: c_driver P in.lammps\n");
exit(1);
}
int me,nprocs;
MPI_Comm_rank(MPI_COMM_WORLD,&me);
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
int nprocs_lammps = atoi(arg[1]);
if (nprocs_lammps > nprocs) {
if (me == 0)
printf("ERROR: LAMMPS cannot use more procs than available\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
int lammps;
if (me < nprocs_lammps) lammps = 1;
else lammps = MPI_UNDEFINED;
MPI_Comm comm_lammps;
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
/* open LAMMPS input script */
FILE *fp;
if (me == 0) {
fp = fopen(arg[2],"r");
if (fp == NULL) {
printf("ERROR: Could not open LAMMPS input script\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
}
/* run the input script thru LAMMPS one line at a time until end-of-file
driver proc 0 reads a line, Bcasts it to all procs
(could just send it to proc 0 of comm_lammps and let it Bcast)
all LAMMPS procs call lammps_command() on the line */
void *ptr;
if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
int n;
char line[1024];
while (1) {
if (me == 0) {
if (fgets(line,1024,fp) == NULL) n = 0;
else n = strlen(line) + 1;
if (n == 0) fclose(fp);
}
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
if (n == 0) break;
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
if (lammps == 1) lammps_command(ptr,line);
}
/* run 10 more steps
get coords from LAMMPS
change coords of 1st atom
put coords back into LAMMPS
run a single step with changed coords */
if (lammps == 1) {
lammps_command(ptr,"run 10");
int natoms = lammps_get_natoms(ptr);
double *x = (double *) malloc(3*natoms*sizeof(double));
lammps_get_coords(ptr,x);
double epsilon = 0.1;
x[0] += epsilon;
lammps_put_coords(ptr,x);
free(x);
lammps_command(ptr,"run 1");
}
if (lammps == 1) lammps_close(ptr);
/* close down MPI */
MPI_Finalize();
}
examples/COUPLE/in.lj deleted 100644 → 0
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# 3d Lennard-Jones melt
units lj
atom_style atomic
atom_modify map array
lattice fcc 0.8442
region box block 0 4 0 4 0 4
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
run 10
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