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sjplimp
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This directory has a C and C++ code that shows how LAMMPS can be
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linked to a driver application as a library. The purpose is to
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illustrate how another code could perform computations while using
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LAMMPS to perform MD, or how an umbrella code or script could call
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both LAMMPS and some other code to perform a coupled calculation.
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c_driver.c is the C driver
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c++_driver.c is the C++ driver
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The 2 codes do the same thing, so you can compare them to see how to
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drive LAMMPS in this manner. The C driver is similar in spirit to
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what one could use from a Fortran program or scripting language.
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LAMMPS must first be built as a library. See the "Making LAMMPS"
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section of Section_start.html in the documentation for info on how to
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do this. Basically, you type something like
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make makelib
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make -f Makefile.lib g++
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in the LAMMPS src directory to create liblmp_g++.a
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You can then build either driver code with a compile line something
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like this, which includes paths to the LAMMPS library interface, MPI,
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and FFTW.
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This builds the C++ driver with the LAMMPS library using a C++ compiler:
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g++ -I/home/sjplimp/lammps/src -c c++_driver.cpp
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g++ -L/home/sjplimp/lammps/src c++_driver.o \
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-llmp_g++ -lfftw -lmpich -lpthread -o c++_driver
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This builds the C driver with the LAMMPS library using a C compiler:
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gcc -I/home/sjplimp/lammps/src -c c_driver.cpp
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gcc -L/home/sjplimp/lammps/src c_driver.o \
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-llmp_g++ -lfftw -lmpich -lpthread -lstdc++ -o c_driver
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You then run c++_driver or c_driver on a parallel machine on some
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number of processors Q with 2 arguments:
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mpirun -np Q c_driver P in.lj
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P is the number of procs you want LAMMPS to run on (must be <= Q).
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In.lj is a LAMMPS input script.
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The driver will launch LAMMPS on P procs, read the input script a line
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at a time, and pass each command line to LAMMPS. The final line of
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the script is a "run" command, so LAMMPS will run the problem.
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The driver then requests all the atom coordinates from LAMMPS, moves
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one of the atoms a small amount "epsilon", passes the coordinates back
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to LAMMPS, and runs LAMMPS again. If you look at the output, you
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should see a small energy change between runs, due to the moved atom.
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The C driver is calling C-style routines in the src/library.cpp file
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of LAMMPS. You could add any functions you wish to this file to
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manipulate LAMMPS data however you wish.
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The C++ driver does the same thing, except that it instantiates LAMMPS
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as an object first. Some of the functions in src/library.cpp can be
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invoked directly as methods within appropriate LAMMPS classes, which
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is what the driver does. Any public LAMMPS class method could be
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called from the driver this way. However the get/put functions are
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only implemented in src/library.cpp, so the C++ driver calls them as
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C-style functions.
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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// c++_driver = simple example of how an umbrella program
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// can invoke LAMMPS as a library on some subset of procs
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// Syntax: c++_driver P in.lammps
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// P = # of procs to run LAMMPS on
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// must be <= # of procs the driver code itself runs on
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// in.lammps = LAMMPS input script
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// See README for compilation instructions
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "mpi.h"
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#include "lammps.h" // these are LAMMPS include files
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#include "input.h"
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#include "atom.h"
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#include "library.h"
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using namespace LAMMPS_NS;
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int main(int narg, char **arg)
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{
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// setup MPI and various communicators
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// driver runs on all procs in MPI_COMM_WORLD
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// comm_lammps only has 1st P procs (could be all or any subset)
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MPI_Init(&narg,&arg);
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if (narg != 3) {
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printf("Syntax: c++_driver P in.lammps\n");
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exit(1);
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}
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int me,nprocs;
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MPI_Comm_rank(MPI_COMM_WORLD,&me);
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MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
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int nprocs_lammps = atoi(arg[1]);
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if (nprocs_lammps > nprocs) {
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if (me == 0)
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printf("ERROR: LAMMPS cannot use more procs than available\n");
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MPI_Abort(MPI_COMM_WORLD,1);
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}
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int lammps;
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if (me < nprocs_lammps) lammps = 1;
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else lammps = MPI_UNDEFINED;
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MPI_Comm comm_lammps;
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MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
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// open LAMMPS input script
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FILE *fp;
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if (me == 0) {
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fp = fopen(arg[2],"r");
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if (fp == NULL) {
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printf("ERROR: Could not open LAMMPS input script\n");
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MPI_Abort(MPI_COMM_WORLD,1);
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}
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}
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// run the input script thru LAMMPS one line at a time until end-of-file
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// driver proc 0 reads a line, Bcasts it to all procs
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// (could just send it to proc 0 of comm_lammps and let it Bcast)
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// all LAMMPS procs call input->one() on the line
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LAMMPS *lmp;
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if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
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int n;
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char line[1024];
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while (1) {
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if (me == 0) {
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if (fgets(line,1024,fp) == NULL) n = 0;
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else n = strlen(line) + 1;
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if (n == 0) fclose(fp);
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}
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MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
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if (n == 0) break;
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MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
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if (lammps == 1) lmp->input->one(line);
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}
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// run 10 more steps
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// get coords from LAMMPS
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// change coords of 1st atom
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// put coords back into LAMMPS
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// run a single step with changed coords
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if (lammps == 1) {
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lmp->input->one("run 10");
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int natoms = static_cast<int> (lmp->atom->natoms);
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double *x = new double[3*natoms];
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lammps_get_coords(lmp,x); // no LAMMPS class function for this
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double epsilon = 0.1;
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x[0] += epsilon;
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lammps_put_coords(lmp,x); // no LAMMPS class function for this
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delete [] x;
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lmp->input->one("run 1");
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}
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if (lammps == 1) delete lmp;
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// close down MPI
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MPI_Finalize();
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}
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@ -1,116 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* c_driver = simple example of how an umbrella program
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can invoke LAMMPS as a library on some subset of procs
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Syntax: c_driver P in.lammps
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P = # of procs to run LAMMPS on
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must be <= # of procs the driver code itself runs on
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in.lammps = LAMMPS input script
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See README for compilation instructions */
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "mpi.h"
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#include "library.h" /* this is a LAMMPS include file */
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int main(int narg, char **arg)
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{
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/* setup MPI and various communicators
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driver runs on all procs in MPI_COMM_WORLD
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comm_lammps only has 1st P procs (could be all or any subset) */
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MPI_Init(&narg,&arg);
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if (narg != 3) {
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printf("Syntax: c_driver P in.lammps\n");
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exit(1);
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}
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int me,nprocs;
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MPI_Comm_rank(MPI_COMM_WORLD,&me);
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MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
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int nprocs_lammps = atoi(arg[1]);
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if (nprocs_lammps > nprocs) {
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if (me == 0)
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printf("ERROR: LAMMPS cannot use more procs than available\n");
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MPI_Abort(MPI_COMM_WORLD,1);
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}
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int lammps;
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if (me < nprocs_lammps) lammps = 1;
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else lammps = MPI_UNDEFINED;
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MPI_Comm comm_lammps;
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MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
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/* open LAMMPS input script */
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FILE *fp;
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if (me == 0) {
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fp = fopen(arg[2],"r");
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if (fp == NULL) {
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printf("ERROR: Could not open LAMMPS input script\n");
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MPI_Abort(MPI_COMM_WORLD,1);
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}
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}
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/* run the input script thru LAMMPS one line at a time until end-of-file
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driver proc 0 reads a line, Bcasts it to all procs
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(could just send it to proc 0 of comm_lammps and let it Bcast)
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all LAMMPS procs call lammps_command() on the line */
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void *ptr;
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if (lammps == 1) lammps_open(0,NULL,comm_lammps,&ptr);
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int n;
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char line[1024];
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while (1) {
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if (me == 0) {
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if (fgets(line,1024,fp) == NULL) n = 0;
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else n = strlen(line) + 1;
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if (n == 0) fclose(fp);
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}
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MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
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if (n == 0) break;
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MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
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if (lammps == 1) lammps_command(ptr,line);
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}
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/* run 10 more steps
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get coords from LAMMPS
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change coords of 1st atom
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put coords back into LAMMPS
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run a single step with changed coords */
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if (lammps == 1) {
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lammps_command(ptr,"run 10");
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int natoms = lammps_get_natoms(ptr);
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double *x = (double *) malloc(3*natoms*sizeof(double));
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lammps_get_coords(ptr,x);
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double epsilon = 0.1;
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x[0] += epsilon;
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lammps_put_coords(ptr,x);
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free(x);
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lammps_command(ptr,"run 1");
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}
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if (lammps == 1) lammps_close(ptr);
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/* close down MPI */
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MPI_Finalize();
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}
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@ -1,24 +0,0 @@
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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atom_modify map array
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lattice fcc 0.8442
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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run 10
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