forked from lijiext/lammps
add example to COUPLE folder demonstrating loading LAMMPS as a plugin.
This commit is contained in:
Axel Kohlmeyer
parent
7434267f57
commit
4180b4a7d6
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This directory has a simple C code that shows how
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LAMMPS can be linked to a driver application as a library. The purpose
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is to illustrate how another code could perform computations while
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using LAMMPS to perform MD on all or a subset of the processors, or
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how an umbrella code or script could call both LAMMPS and some other
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code to perform a coupled calculation.
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simple.c is the C driver
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liblammpsplugin.c is the LAMMPS library plugin loader
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The 3 codes do the same thing, so you can compare them to see how to
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drive LAMMPS from each language. See lammps/python/example/simple.py
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to do something similar from Python. The Fortran driver requires an
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additional wrapper library that interfaces the C interface of the
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LAMMPS library to Fortran and also translates the MPI communicator
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from Fortran to C.
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First build LAMMPS as a library (see examples/COUPLE/README), e.g.
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cd $HOME/lammps/src
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make mode=shlib mpi
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or
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cd $HOME/lammps
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mkdir build-shared
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cd build-shared
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cmake -D BUILD_LIB=on -D BUILD_SHARED_LIBS=on ../cmake
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make
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You can then build any of the driver codes with compile lines like
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these, which include paths to the LAMMPS library interface, and
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linking with FFTW (only needed if you built LAMMPS as a library with
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its PPPM solver).
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mpicc -c simple.c
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mpicc simple.o -llammps -lfftw -o simpleC
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You then run simpleC on a parallel machine
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on some number of processors Q with 3 arguments:
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% mpirun -np Q simpleC P in.lj $HOME/lammps/src/liblammps.so
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or
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% mpirun -np Q simpleC P in.lj $HOME/lammps/build-shared/liblammps.so
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P is the number of procs you want LAMMPS to run on (must be <= Q) and
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in.lj is a LAMMPS input script and the last argument is the path to
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the LAMMPS shared library. This either has to be an absolute path, or
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liblammps.so has to be in a folder that is included in the environment
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variable LD_LIBRARY_PATH so it will be found by the dynamic object loader.
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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 through the function pointers in the liblammpsplugin_t struct.
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This has the benefit that your binary is not linked to liblammps.so directly
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and thus you can change the name of the shared library (e.g. to have
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different variants compiled, or to load a different LAMMPS versions without
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having to update your executable).
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@ -0,0 +1,25 @@
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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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variable fx atom fx
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run 10
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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/*
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Variant of the C style library interface to LAMMPS
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that uses a shared library and dynamically opens it,
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so this can be used as a prototype code to integrate
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a LAMMPS plugin to some other software.
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*/
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#include "library.h"
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#include "liblammpsplugin.h"
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#include <stdlib.h>
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#include <dlfcn.h>
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liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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{
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liblammpsplugin_t *lmp;
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void *handle;
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if (lib == NULL) return NULL;
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handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
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if (handle == NULL) return NULL;
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lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
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lmp->handle = handle;
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#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
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ADDSYM(open);
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ADDSYM(open_no_mpi);
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ADDSYM(close);
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ADDSYM(version);
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ADDSYM(file);
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ADDSYM(command);
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ADDSYM(commands_list);
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ADDSYM(commands_string);
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ADDSYM(free);
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ADDSYM(extract_setting);
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ADDSYM(extract_global);
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ADDSYM(extract_box);
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ADDSYM(extract_atom);
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ADDSYM(extract_compute);
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ADDSYM(extract_fix);
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ADDSYM(extract_variable);
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ADDSYM(get_thermo);
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ADDSYM(get_natoms);
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ADDSYM(set_variable);
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ADDSYM(reset_box);
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ADDSYM(gather_atoms);
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ADDSYM(gather_atoms_concat);
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ADDSYM(gather_atoms_subset);
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ADDSYM(scatter_atoms);
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ADDSYM(scatter_atoms_subset);
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ADDSYM(set_fix_external_callback);
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ADDSYM(config_has_package);
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ADDSYM(config_package_count);
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ADDSYM(config_package_name);
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ADDSYM(config_has_gzip_support);
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ADDSYM(config_has_png_support);
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ADDSYM(config_has_jpeg_support);
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ADDSYM(config_has_ffmpeg_support);
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ADDSYM(config_has_exceptions);
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ADDSYM(create_atoms);
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#ifdef LAMMPS_EXCEPTIONS
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lmp->has_exceptions = 1;
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ADDSYM(has_error);
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ADDSYM(get_last_error_message);
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#else
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lmp->has_exceptions = 0;
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lmp->has_error = NULL;
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lmp->get_last_error_message = NULL;
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#endif
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return lmp;
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}
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int liblammpsplugin_release(liblammpsplugin_t *lmp)
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{
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if (lmp == NULL) return 1;
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if (lmp->handle == NULL) return 2;
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dlclose(lmp->handle);
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free((void *)lmp);
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return 0;
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}
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@ -0,0 +1,126 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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#ifndef LIBLAMMPSPLUGIN_H
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#define LIBLAMMPSPLUGIN_H
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/*
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Variant of the C style library interface to LAMMPS
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that uses a shared library and dynamically opens it,
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so this can be used as a prototype code to integrate
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a LAMMPS plugin to some other software.
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*/
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/*
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* Follow the behavior of regular LAMMPS compilation and assume
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* -DLAMMPS_SMALLBIG when no define is set.
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*/
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#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
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#define LAMMPS_SMALLBIG
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#endif
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#include <mpi.h>
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#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
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#include <inttypes.h> /* for int64_t */
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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#if defined(LAMMPS_BIGBIG)
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typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
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#elif defined(LAMMPS_SMALLBIG)
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typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
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#else
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typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
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#endif
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struct _liblammpsplugin {
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int abiversion;
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int has_exceptions;
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void *handle;
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void (*open)(int, char **, MPI_Comm, void **);
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void (*open_no_mpi)(int, char **, void **);
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void (*close)(void *);
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int (*version)(void *);
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void (*file)(void *, char *);
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char *(*command)(void *, char *);
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void (*commands_list)(void *, int, char **);
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void (*commands_string)(void *, char *);
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void (*free)(void *);
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int (*extract_setting)(void *, char *);
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void *(*extract_global)(void *, char *);
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void (*extract_box)(void *, double *, double *,
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double *, double *, double *, int *, int *);
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void *(*extract_atom)(void *, char *);
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void *(*extract_compute)(void *, char *, int, int);
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void *(*extract_fix)(void *, char *, int, int, int, int);
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void *(*extract_variable)(void *, char *, char *);
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double (*get_thermo)(void *, char *);
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int (*get_natoms)(void *);
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int (*set_variable)(void *, char *, char *);
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void (*reset_box)(void *, double *, double *, double, double, double);
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void (*gather_atoms)(void *, char *, int, int, void *);
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void (*gather_atoms_concat)(void *, char *, int, int, void *);
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void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
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void (*scatter_atoms)(void *, char *, int, int, void *);
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void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
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void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);
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int (*config_has_package)(char * package_name);
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int (*config_package_count)();
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int (*config_package_name)(int index, char * buffer, int max_size);
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int (*config_has_gzip_support)();
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int (*config_has_png_support)();
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int (*config_has_jpeg_support)();
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int (*config_has_ffmpeg_support)();
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int (*config_has_exceptions)();
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int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);
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int (*find_fix_neighlist)(void* ptr, char * id, int request);
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int (*find_compute_neighlist)(void* ptr, char * id, int request);
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int (*neighlist_num_elements)(void* ptr, int idx);
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void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
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// lammps_create_atoms() takes tagint and imageint as args
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// ifdef insures they are compatible with rest of LAMMPS
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// caller must match to how LAMMPS library is built
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#ifdef LAMMPS_BIGBIG
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void (*create_atoms)(void *, int, int64_t *, int *,
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double *, double *, int64_t *, int);
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#else
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void (*create_atoms)(void *, int, int *, int *,
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double *, double *, int *, int);
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#endif
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int (*has_error)(void *);
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int (*get_last_error_message)(void *, char *, int);
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};
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typedef struct _liblammpsplugin liblammpsplugin_t;
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liblammpsplugin_t *liblammpsplugin_load(const char *);
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int liblammpsplugin_release(liblammpsplugin_t *);
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#undef LAMMPS
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#ifdef __cplusplus
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}
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#endif
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#endif
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@ -0,0 +1,294 @@
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LAMMPS (18 Feb 2020)
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
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1 by 1 by 1 MPI processor grid
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Created 256 atoms
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create_atoms CPU = 0.000297844 secs
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Setting up Verlet run ...
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Unit style : lj
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Current step : 0
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Time step : 0.005
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Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6218056 -5.0244179
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10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
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Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms
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Performance: 2629719.113 tau/day, 6087.313 timesteps/s
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93.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0014956 | 0.0014956 | 0.0014956 | 0.0 | 91.04
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 8.045e-05 | 8.045e-05 | 8.045e-05 | 0.0 | 4.90
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Output | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 | 0.0 | 0.69
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Modify | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 | 0.0 | 2.28
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Other | | 1.789e-05 | | | 1.09
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Nlocal: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1431 ave 1431 max 1431 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9984 ave 9984 max 9984 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9984
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Ave neighs/atom = 39
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Neighbor list builds = 0
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Dangerous builds not checked
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Setting up Verlet run ...
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Unit style : lj
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Current step : 10
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Time step : 0.005
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Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
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Step Temp E_pair E_mol TotEng Press
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10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
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20 0.6239063 -5.557644 0 -4.6254403 0.97451173
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Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms
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Performance: 2162504.180 tau/day, 5005.797 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0018518 | 0.0018518 | 0.0018518 | 0.0 | 92.70
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 | 0.0 | 3.99
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Output | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 | 0.0 | 0.57
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Modify | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 | 0.0 | 1.85
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Other | | 1.773e-05 | | | 0.89
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Nlocal: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1431 ave 1431 max 1431 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9952 ave 9952 max 9952 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9952
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Ave neighs/atom = 38.875
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Neighbor list builds = 0
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Dangerous builds not checked
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Setting up Verlet run ...
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Unit style : lj
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Current step : 20
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Time step : 0.005
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Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
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Step Temp E_pair E_mol TotEng Press
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20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
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21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
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Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms
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Performance: 1419553.695 tau/day, 3286.004 timesteps/s
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98.9% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.00027815 | 0.00027815 | 0.00027815 | 0.0 | 91.40
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 8.321e-06 | 8.321e-06 | 8.321e-06 | 0.0 | 2.73
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Output | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 | 0.0 | 3.45
|
||||
Modify | 3.968e-06 | 3.968e-06 | 3.968e-06 | 0.0 | 1.30
|
||||
Other | | 3.365e-06 | | | 1.11
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9705 ave 9705 max 9705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Force on 1 atom via extract_atom: 26.9581
|
||||
Force on 1 atom via extract_variable: 26.9581
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 21
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2203779.175 tau/day, 5101.341 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018146 | 0.0018146 | 0.0018146 | 0.0 | 92.57
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 | 0.0 | 4.09
|
||||
Output | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 | 0.0 | 0.56
|
||||
Modify | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 | 0.0 | 1.88
|
||||
Other | | 1.756e-05 | | | 0.90
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9688 ave 9688 max 9688 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9688
|
||||
Ave neighs/atom = 37.8438
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 31
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 1995088.941 tau/day, 4618.261 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035121 | 0.0035121 | 0.0035121 | 0.0 | 81.10
|
||||
Neigh | 0.00050258 | 0.00050258 | 0.00050258 | 0.0 | 11.61
|
||||
Comm | 0.00019444 | 0.00019444 | 0.00019444 | 0.0 | 4.49
|
||||
Output | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 | 0.0 | 0.28
|
||||
Modify | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 | 0.0 | 1.68
|
||||
Other | | 3.647e-05 | | | 0.84
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1421 ave 1421 max 1421 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9700 ave 9700 max 9700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 51
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2197727.285 tau/day, 5087.332 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018222 | 0.0018222 | 0.0018222 | 0.0 | 92.70
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 | 0.0 | 3.98
|
||||
Output | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 | 0.0 | 0.55
|
||||
Modify | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 | 0.0 | 1.87
|
||||
Other | | 1.764e-05 | | | 0.90
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1421 ave 1421 max 1421 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9700 ave 9700 max 9700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 61
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
|
||||
Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 2006838.581 tau/day, 4645.460 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 81.13
|
||||
Neigh | 0.00050437 | 0.00050437 | 0.00050437 | 0.0 | 11.72
|
||||
Comm | 0.0001868 | 0.0001868 | 0.0001868 | 0.0 | 4.34
|
||||
Output | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 | 0.0 | 0.27
|
||||
Modify | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 | 0.0 | 1.70
|
||||
Other | | 3.604e-05 | | | 0.84
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1405 ave 1405 max 1405 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9701 ave 9701 max 9701 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9701
|
||||
Ave neighs/atom = 37.8945
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Deleted 256 atoms, new total = 0
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 81
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
|
||||
Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2205851.941 tau/day, 5106.139 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018143 | 0.0018143 | 0.0018143 | 0.0 | 92.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 | 0.0 | 4.01
|
||||
Output | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 | 0.0 | 0.55
|
||||
Modify | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 | 0.0 | 1.89
|
||||
Other | | 1.762e-05 | | | 0.90
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9705 ave 9705 max 9705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,296 @@
|
|||
LAMMPS (18 Feb 2020)
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000265157 secs
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
Loop time of 0.00115264 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3747912.946 tau/day, 8675.724 timesteps/s
|
||||
94.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00074885 | 0.00075021 | 0.00075156 | 0.0 | 65.09
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00031829 | 0.00031943 | 0.00032056 | 0.0 | 27.71
|
||||
Output | 9.306e-06 | 2.6673e-05 | 4.4041e-05 | 0.0 | 2.31
|
||||
Modify | 2.0684e-05 | 2.0891e-05 | 2.1098e-05 | 0.0 | 1.81
|
||||
Other | | 3.544e-05 | | | 3.07
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1109 ave 1109 max 1109 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4992 ave 4992 max 4992 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 10
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
Loop time of 0.00120443 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3586761.860 tau/day, 8302.689 timesteps/s
|
||||
95.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00087798 | 0.00091359 | 0.0009492 | 0.0 | 75.85
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016739 | 0.00020368 | 0.00023997 | 0.0 | 16.91
|
||||
Output | 1.0124e-05 | 3.0513e-05 | 5.0901e-05 | 0.0 | 2.53
|
||||
Modify | 1.89e-05 | 1.9812e-05 | 2.0725e-05 | 0.0 | 1.64
|
||||
Other | | 3.683e-05 | | | 3.06
|
||||
|
||||
Nlocal: 128 ave 134 max 122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1115 max 1103 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4976 ave 5205 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 20
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
Loop time of 0.000206062 on 2 procs for 1 steps with 256 atoms
|
||||
|
||||
Performance: 2096456.406 tau/day, 4852.908 timesteps/s
|
||||
94.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00012947 | 0.00013524 | 0.00014101 | 0.0 | 65.63
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.858e-05 | 2.4113e-05 | 2.9647e-05 | 0.0 | 11.70
|
||||
Output | 8.699e-06 | 2.4204e-05 | 3.9708e-05 | 0.0 | 11.75
|
||||
Modify | 2.34e-06 | 2.3705e-06 | 2.401e-06 | 0.0 | 1.15
|
||||
Other | | 2.013e-05 | | | 9.77
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4852.5 ave 5106 max 4599 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Force on 1 atom via extract_atom: -18.109
|
||||
Force on 1 atom via extract_variable: -18.109
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Force on 1 atom via extract_atom: 26.9581
|
||||
Force on 1 atom via extract_variable: 26.9581
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 21
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
Loop time of 0.00119048 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3628802.105 tau/day, 8400.005 timesteps/s
|
||||
98.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00085276 | 0.00089699 | 0.00094123 | 0.0 | 75.35
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016896 | 0.00021444 | 0.00025992 | 0.0 | 18.01
|
||||
Output | 9.413e-06 | 2.5939e-05 | 4.2465e-05 | 0.0 | 2.18
|
||||
Modify | 1.8977e-05 | 2.0009e-05 | 2.1042e-05 | 0.0 | 1.68
|
||||
Other | | 3.31e-05 | | | 2.78
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4844 ave 5096 max 4592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9688
|
||||
Ave neighs/atom = 37.8438
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 31
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
Loop time of 0.00252603 on 2 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 3420382.192 tau/day, 7917.551 timesteps/s
|
||||
99.2% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016245 | 0.0017014 | 0.0017784 | 0.2 | 67.36
|
||||
Neigh | 0.00025359 | 0.0002563 | 0.00025901 | 0.0 | 10.15
|
||||
Comm | 0.00036863 | 0.00045124 | 0.00053385 | 0.0 | 17.86
|
||||
Output | 9.839e-06 | 2.8031e-05 | 4.6223e-05 | 0.0 | 1.11
|
||||
Modify | 3.7027e-05 | 3.9545e-05 | 4.2063e-05 | 0.0 | 1.57
|
||||
Other | | 4.948e-05 | | | 1.96
|
||||
|
||||
Nlocal: 128 ave 132 max 124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1100 ave 1101 max 1099 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850 ave 4953 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 51
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
Loop time of 0.00115444 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3742065.976 tau/day, 8662.190 timesteps/s
|
||||
96.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00087346 | 0.00089311 | 0.00091275 | 0.0 | 77.36
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016192 | 0.0001823 | 0.00020269 | 0.0 | 15.79
|
||||
Output | 9.49e-06 | 2.6234e-05 | 4.2978e-05 | 0.0 | 2.27
|
||||
Modify | 1.9095e-05 | 1.9843e-05 | 2.0591e-05 | 0.0 | 1.72
|
||||
Other | | 3.296e-05 | | | 2.85
|
||||
|
||||
Nlocal: 128 ave 132 max 124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1100 ave 1101 max 1099 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850 ave 4953 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 61
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
|
||||
Loop time of 0.00244325 on 2 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 3536279.919 tau/day, 8185.833 timesteps/s
|
||||
99.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016916 | 0.0017038 | 0.001716 | 0.0 | 69.73
|
||||
Neigh | 0.00025229 | 0.00025512 | 0.00025795 | 0.0 | 10.44
|
||||
Comm | 0.00035772 | 0.00036918 | 0.00038064 | 0.0 | 15.11
|
||||
Output | 1.0858e-05 | 2.7875e-05 | 4.4891e-05 | 0.0 | 1.14
|
||||
Modify | 3.817e-05 | 3.9325e-05 | 4.048e-05 | 0.0 | 1.61
|
||||
Other | | 4.796e-05 | | | 1.96
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1088.5 ave 1092 max 1085 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850.5 ave 4851 max 4850 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9701
|
||||
Ave neighs/atom = 37.8945
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Deleted 256 atoms, new total = 0
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 81
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
|
||||
Loop time of 0.00118092 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3658158.625 tau/day, 8467.960 timesteps/s
|
||||
98.6% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0008476 | 0.00089265 | 0.00093771 | 0.0 | 75.59
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016335 | 0.00020946 | 0.00025557 | 0.0 | 17.74
|
||||
Output | 8.87e-06 | 2.5733e-05 | 4.2595e-05 | 0.0 | 2.18
|
||||
Modify | 1.8755e-05 | 1.9814e-05 | 2.0872e-05 | 0.0 | 1.68
|
||||
Other | | 3.326e-05 | | | 2.82
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4852.5 ave 5106 max 4599 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,175 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: simpleC 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 "liblammpsplugin.h" /* this is the include for the plugin loader */
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
int n,me,nprocs;
|
||||
int nprocs_lammps, lammps;
|
||||
char line[1024];
|
||||
MPI_Comm comm_lammps;
|
||||
FILE *fp = NULL;
|
||||
liblammpsplugin_t *plugin = NULL;
|
||||
void *lmp = NULL;
|
||||
double *x = NULL;
|
||||
double *v = NULL;
|
||||
char *strtwo;
|
||||
char *cmds[2];
|
||||
int *type = NULL;
|
||||
|
||||
/* 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 != 4) {
|
||||
printf("Syntax: simpleC P in.lammps /path/to/liblammps.so\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
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);
|
||||
}
|
||||
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
/* open LAMMPS input script */
|
||||
|
||||
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 */
|
||||
|
||||
if (lammps == 1) {
|
||||
plugin = liblammpsplugin_load(arg[3]);
|
||||
if (plugin == NULL) {
|
||||
if (me == 0) printf("ERROR: Could not load shared LAMMPS library\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
if (lammps == 1) plugin->open(0,NULL,comm_lammps,&lmp);
|
||||
|
||||
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) plugin->command(lmp,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) {
|
||||
plugin->command(lmp,"run 10");
|
||||
|
||||
int natoms = plugin->get_natoms(lmp);
|
||||
x = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"x",1,3,x);
|
||||
v = (double *) malloc(3*natoms*sizeof(double));
|
||||
plugin->gather_atoms(lmp,"v",1,3,v);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
plugin->scatter_atoms(lmp,"x",1,3,x);
|
||||
|
||||
plugin->command(lmp,"run 1");
|
||||
}
|
||||
|
||||
// extract force on single atom two different ways
|
||||
|
||||
if (lammps == 1) {
|
||||
double **f = (double **) plugin->extract_atom(lmp,"f");
|
||||
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
|
||||
|
||||
double *fx = (double *) plugin->extract_variable(lmp,"fx","all");
|
||||
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
|
||||
}
|
||||
|
||||
/* use commands_string() and commands_list() to invoke more commands */
|
||||
|
||||
strtwo = (char *)"run 10\nrun 20";
|
||||
if (lammps == 1) plugin->commands_string(lmp,strtwo);
|
||||
|
||||
cmds[0] = (char *)"run 10";
|
||||
cmds[1] = (char *)"run 20";
|
||||
if (lammps == 1) plugin->commands_list(lmp,2,cmds);
|
||||
|
||||
/* delete all atoms
|
||||
create_atoms() to create new ones with old coords, vels
|
||||
initial thermo should be same as step 20 */
|
||||
|
||||
if (lammps == 1) {
|
||||
int natoms = plugin->get_natoms(lmp);
|
||||
type = (int *) malloc(natoms*sizeof(double));
|
||||
int i;
|
||||
for (i = 0; i < natoms; i++) type[i] = 1;
|
||||
|
||||
plugin->command(lmp,"delete_atoms group all");
|
||||
plugin->create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
|
||||
plugin->command(lmp,"run 10");
|
||||
}
|
||||
|
||||
if (x) free(x);
|
||||
if (v) free(v);
|
||||
if (type) free(type);
|
||||
|
||||
// close down LAMMPS
|
||||
|
||||
if (lammps == 1) {
|
||||
plugin->close(lmp);
|
||||
liblammpsplugin_release(plugin);
|
||||
}
|
||||
|
||||
/* close down MPI */
|
||||
|
||||
if (lammps == 1) MPI_Comm_free(&comm_lammps);
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
|
@ -11,6 +11,9 @@
|
|||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LAMMPS_LIBRARY_H
|
||||
#define LAMMPS_LIBRARY_H
|
||||
|
||||
/*
|
||||
C or Fortran style library interface to LAMMPS
|
||||
new LAMMPS-specific functions can be added
|
||||
|
|
@ -114,6 +117,7 @@ int lammps_get_last_error_message(void *, char *, int);
|
|||
}
|
||||
#endif
|
||||
|
||||
#endif /* LAMMPS_LIBRARY_H */
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Library error: issuing LAMMPS command during run
|
||||
|
|
|
|||
Loading…
Reference in New Issue