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45fab72fdcf38c71dbeb0dae156ba67dc08cfaa6
lammps/src/lammps.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#include "lammps.h"
#include "style_angle.h" // IWYU pragma: keep
#include "style_atom.h" // IWYU pragma: keep
#include "style_bond.h" // IWYU pragma: keep
#include "style_command.h" // IWYU pragma: keep
#include "style_compute.h" // IWYU pragma: keep
#include "style_dihedral.h" // IWYU pragma: keep
#include "style_dump.h" // IWYU pragma: keep
#include "style_fix.h" // IWYU pragma: keep
#include "style_improper.h" // IWYU pragma: keep
#include "style_integrate.h" // IWYU pragma: keep
#include "style_kspace.h" // IWYU pragma: keep
#include "style_minimize.h" // IWYU pragma: keep
#include "style_pair.h" // IWYU pragma: keep
#include "style_region.h" // IWYU pragma: keep
#include "universe.h"
#include "input.h"
#include "info.h"
#include "atom.h" // IWYU pragma: keep
#include "update.h"
#include "neighbor.h" // IWYU pragma: keep
#include "comm.h"
#include "comm_brick.h"
#include "domain.h" // IWYU pragma: keep
#include "force.h"
#include "modify.h"
#include "group.h"
#include "output.h"
#include "citeme.h"
#include "accelerator_kokkos.h"
#include "accelerator_omp.h" // IWYU pragma: keep
#include "timer.h"
#include "lmppython.h"
#include "version.h"
#include "memory.h"
#include "error.h"
#include <cctype>
#include <cmath>
#include <cstring>
#include <map>
#include "lmpinstalledpkgs.h"
#include "lmpgitversion.h"
static void print_style(FILE *fp, const char *str, int &pos);
struct LAMMPS_NS::package_styles_lists {
std::map<std::string,std::string> angle_styles;
std::map<std::string,std::string> atom_styles;
std::map<std::string,std::string> body_styles;
std::map<std::string,std::string> bond_styles;
std::map<std::string,std::string> command_styles;
std::map<std::string,std::string> compute_styles;
std::map<std::string,std::string> dihedral_styles;
std::map<std::string,std::string> dump_styles;
std::map<std::string,std::string> fix_styles;
std::map<std::string,std::string> improper_styles;
std::map<std::string,std::string> integrate_styles;
std::map<std::string,std::string> kspace_styles;
std::map<std::string,std::string> minimize_styles;
std::map<std::string,std::string> pair_styles;
std::map<std::string,std::string> reader_styles;
std::map<std::string,std::string> region_styles;
};
using namespace LAMMPS_NS;
/** \class LAMMPS_NS::LAMMPS
* \brief LAMMPS simulation instance
*
* The LAMMPS class contains pointers of all constituent class instances
* and global variables that are used by a LAMMPS simulation. Its contents
* represent the entire state of the simulation.
*
* The LAMMPS class manages the components of an MD simulation by creating,
* deleting, and initializing instances of the classes it is composed of,
* processing command line flags, and providing access to some global properties.
* The specifics of setting up and running a simulation are handled by the
* individual component class instances. */
/** Create a LAMMPS simulation instance
*
* The LAMMPS constructor starts up a simulation by allocating all
* fundamental classes in the necessary order, parses input switches
* and their arguments, initializes communicators, screen and logfile
* output FILE pointers.
*
* \param narg number of arguments
* \param arg list of arguments
* \param communicator MPI communicator used by this LAMMPS instance
*/
LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
memory(nullptr), error(nullptr), universe(nullptr), input(nullptr), atom(nullptr),
update(nullptr), neighbor(nullptr), comm(nullptr), domain(nullptr), force(nullptr),
modify(nullptr), group(nullptr), output(nullptr), timer(nullptr), kokkos(nullptr),
atomKK(nullptr), memoryKK(nullptr), python(nullptr), citeme(nullptr)
{
memory = new Memory(this);
error = new Error(this);
universe = new Universe(this,communicator);
version = (const char *) LAMMPS_VERSION;
num_ver = utils::date2num(version);
clientserver = 0;
cslib = nullptr;
cscomm = 0;
screen = nullptr;
logfile = nullptr;
infile = nullptr;
initclock = MPI_Wtime();
init_pkg_lists();
// check if -mpi is first arg
// if so, then 2 apps were launched with one mpirun command
// this means passed communicator (e.g. MPI_COMM_WORLD) is bigger than LAMMPS
// e.g. for client/server coupling with another code
// in the future LAMMPS might leverage this in other ways
// universe communicator needs to shrink to be just LAMMPS
// syntax: -mpi color
// color = integer for this app, different than other app(s)
// do the following:
// perform an MPI_Comm_split() to create a new LAMMPS-only subcomm
// NOTE: this assumes other app(s) does same thing, else will hang!
// re-create universe with subcomm
// store full multi-app comm in cscomm
// cscomm is used by CSLIB package to exchange messages w/ other app
int iarg = 1;
if (narg-iarg >= 2 && (strcmp(arg[iarg],"-mpi") == 0 ||
strcmp(arg[iarg],"-m") == 0)) {
int me,nprocs;
MPI_Comm_rank(communicator,&me);
MPI_Comm_size(communicator,&nprocs);
int color = atoi(arg[iarg+1]);
MPI_Comm subcomm;
MPI_Comm_split(communicator,color,me,&subcomm);
cscomm = communicator;
communicator = subcomm;
delete universe;
universe = new Universe(this,communicator);
}
// parse input switches
int inflag = 0;
int screenflag = 0;
int logflag = 0;
int partscreenflag = 0;
int partlogflag = 0;
int kokkosflag = 0;
int restart2data = 0;
int restart2dump = 0;
int restartremap = 0;
int citeflag = 1;
int helpflag = 0;
suffix = suffix2 = suffixp = nullptr;
suffix_enable = 0;
if (arg) exename = arg[0];
else exename = nullptr;
packargs = nullptr;
num_package = 0;
char *restartfile = nullptr;
int wfirst,wlast;
int kkfirst,kklast;
int npack = 0;
int *pfirst = nullptr;
int *plast = nullptr;
iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"-echo") == 0 ||
strcmp(arg[iarg],"-e") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-help") == 0 ||
strcmp(arg[iarg],"-h") == 0) {
if (iarg+1 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
helpflag = 1;
citeflag = 0;
iarg += 1;
} else if (strcmp(arg[iarg],"-in") == 0 ||
strcmp(arg[iarg],"-i") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
inflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-kokkos") == 0 ||
strcmp(arg[iarg],"-k") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (strcmp(arg[iarg+1],"on") == 0) kokkosflag = 1;
else if (strcmp(arg[iarg+1],"off") == 0) kokkosflag = 0;
else error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
// delimit any extra args for the Kokkos instantiation
kkfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
kklast = iarg;
} else if (strcmp(arg[iarg],"-log") == 0 ||
strcmp(arg[iarg],"-l") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
logflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-mpi") == 0 ||
strcmp(arg[iarg],"-m") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (iarg != 1) error->universe_all(FLERR,"Invalid command-line argument");
iarg += 2;
} else if (strcmp(arg[iarg],"-nocite") == 0 ||
strcmp(arg[iarg],"-nc") == 0) {
citeflag = 0;
iarg++;
} else if (strcmp(arg[iarg],"-package") == 0 ||
strcmp(arg[iarg],"-pk") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
memory->grow(pfirst,npack+1,"lammps:pfirst");
memory->grow(plast,npack+1,"lammps:plast");
// delimit args for package command invocation
// any package arg with leading "-" will be followed by numeric digit
iarg++;
pfirst[npack] = iarg;
while (iarg < narg) {
if (arg[iarg][0] != '-') iarg++;
else if (isdigit(arg[iarg][1])) iarg++;
else break;
}
plast[npack++] = iarg;
} else if (strcmp(arg[iarg],"-partition") == 0 ||
strcmp(arg[iarg],"-p") == 0) {
universe->existflag = 1;
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg++;
while (iarg < narg && arg[iarg][0] != '-') {
universe->add_world(arg[iarg]);
iarg++;
}
} else if (strcmp(arg[iarg],"-plog") == 0 ||
strcmp(arg[iarg],"-pl") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partlogflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-pscreen") == 0 ||
strcmp(arg[iarg],"-ps") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
partscreenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-reorder") == 0 ||
strcmp(arg[iarg],"-ro") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (universe->existflag)
error->universe_all(FLERR,"Cannot use -reorder after -partition");
universe->reorder(arg[iarg+1],arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg],"-restart2data") == 0 ||
strcmp(arg[iarg],"-r2data") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (restart2dump)
error->universe_all(FLERR,
"Cannot use both -restart2data and -restart2dump");
restart2data = 1;
restartfile = arg[iarg+1];
// check for restart remap flag
if (strcmp(arg[iarg+2],"remap") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartremap = 1;
iarg++;
}
iarg += 2;
// delimit args for the write_data command
wfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wlast = iarg;
} else if (strcmp(arg[iarg],"-restart2dump") == 0 ||
strcmp(arg[iarg],"-r2dump") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
if (restart2data)
error->universe_all(FLERR,
"Cannot use both -restart2data and -restart2dump");
restart2dump = 1;
restartfile = arg[iarg+1];
// check for restart remap flag
if (strcmp(arg[iarg+2],"remap") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
restartremap = 1;
iarg++;
}
iarg += 2;
// delimit args for the write_dump command
wfirst = iarg;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
wlast = iarg;
} else if (strcmp(arg[iarg],"-screen") == 0 ||
strcmp(arg[iarg],"-sc") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
screenflag = iarg + 1;
iarg += 2;
} else if (strcmp(arg[iarg],"-suffix") == 0 ||
strcmp(arg[iarg],"-sf") == 0) {
if (iarg+2 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
delete [] suffix;
delete [] suffix2;
suffix = suffix2 = nullptr;
suffix_enable = 1;
// hybrid option to set fall-back for suffix2
if (strcmp(arg[iarg+1],"hybrid") == 0) {
if (iarg+4 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
int n = strlen(arg[iarg+2]) + 1;
suffix = new char[n];
strcpy(suffix,arg[iarg+2]);
n = strlen(arg[iarg+3]) + 1;
suffix2 = new char[n];
strcpy(suffix2,arg[iarg+3]);
iarg += 4;
} else {
int n = strlen(arg[iarg+1]) + 1;
suffix = new char[n];
strcpy(suffix,arg[iarg+1]);
iarg += 2;
}
} else if (strcmp(arg[iarg],"-var") == 0 ||
strcmp(arg[iarg],"-v") == 0) {
if (iarg+3 > narg)
error->universe_all(FLERR,"Invalid command-line argument");
iarg += 3;
while (iarg < narg && arg[iarg][0] != '-') iarg++;
} else error->universe_all(FLERR,"Invalid command-line argument");
}
// if no partition command-line switch, universe is one world with all procs
if (universe->existflag == 0) universe->add_world(nullptr);
// sum of procs in all worlds must equal total # of procs
if (!universe->consistent())
error->universe_all(FLERR,"Processor partitions do not match "
"number of allocated processors");
// universe cannot use stdin for input file
if (universe->existflag && inflag == 0)
error->universe_all(FLERR,"Must use -in switch with multiple partitions");
// if no partition command-line switch, cannot use -pscreen option
if (universe->existflag == 0 && partscreenflag)
error->universe_all(FLERR,"Can only use -pscreen with multiple partitions");
// if no partition command-line switch, cannot use -plog option
if (universe->existflag == 0 && partlogflag)
error->universe_all(FLERR,"Can only use -plog with multiple partitions");
// set universe screen and logfile
if (universe->me == 0) {
if (screenflag == 0)
universe->uscreen = stdout;
else if (strcmp(arg[screenflag],"none") == 0)
universe->uscreen = nullptr;
else {
universe->uscreen = fopen(arg[screenflag],"w");
if (universe->uscreen == nullptr)
error->universe_one(FLERR,fmt::format("Cannot open universe screen "
"file {}: {}",arg[screenflag],
utils::getsyserror()));
}
if (logflag == 0) {
if (helpflag == 0) {
universe->ulogfile = fopen("log.lammps","w");
if (universe->ulogfile == nullptr)
error->universe_warn(FLERR,"Cannot open log.lammps for writing: "
+ utils::getsyserror());
}
} else if (strcmp(arg[logflag],"none") == 0)
universe->ulogfile = nullptr;
else {
universe->ulogfile = fopen(arg[logflag],"w");
if (universe->ulogfile == nullptr)
error->universe_one(FLERR,fmt::format("Cannot open universe log "
"file {}: {}",arg[logflag],
utils::getsyserror()));
}
}
if (universe->me > 0) {
if (screenflag == 0) universe->uscreen = stdout;
else universe->uscreen = nullptr;
universe->ulogfile = nullptr;
}
// make universe and single world the same, since no partition switch
// world inherits settings from universe
// set world screen, logfile, communicator, infile
// open input script if from file
if (universe->existflag == 0) {
screen = universe->uscreen;
logfile = universe->ulogfile;
world = universe->uworld;
if (universe->me == 0) {
if (inflag == 0) infile = stdin;
else if (strcmp(arg[inflag], "none") == 0) infile = stdin;
else infile = fopen(arg[inflag],"r");
if (infile == nullptr)
error->one(FLERR,fmt::format("Cannot open input script {}: {}",
arg[inflag], utils::getsyserror()));
}
if ((universe->me == 0) && !helpflag)
utils::logmesg(this,fmt::format("LAMMPS ({})\n",version));
// universe is one or more worlds, as setup by partition switch
// split universe communicator into separate world communicators
// set world screen, logfile, communicator, infile
// open input script
} else {
int me;
MPI_Comm_split(universe->uworld,universe->iworld,0,&world);
MPI_Comm_rank(world,&me);
screen = logfile = infile = nullptr;
if (me == 0) {
std::string str;
if (partscreenflag == 0) {
if (screenflag == 0) {
str = fmt::format("screen.{}",universe->iworld);
screen = fopen(str.c_str(),"w");
if (screen == nullptr)
error->one(FLERR,fmt::format("Cannot open screen file {}: {}",
str,utils::getsyserror()));
} else if (strcmp(arg[screenflag],"none") == 0) {
screen = nullptr;
} else {
str = fmt::format("{}.{}",arg[screenflag],universe->iworld);
screen = fopen(str.c_str(),"w");
if (screen == nullptr)
error->one(FLERR,fmt::format("Cannot open screen file {}: {}",
arg[screenflag],utils::getsyserror()));
}
} else if (strcmp(arg[partscreenflag],"none") == 0) {
screen = nullptr;
} else {
str = fmt::format("{}.{}",arg[partscreenflag],universe->iworld);
screen = fopen(str.c_str(),"w");
if (screen == nullptr)
error->one(FLERR,fmt::format("Cannot open screen file {}: {}",
str,utils::getsyserror()));
}
if (partlogflag == 0) {
if (logflag == 0) {
str = fmt::format("log.lammps.{}",universe->iworld);
logfile = fopen(str.c_str(),"w");
if (logfile == nullptr)
error->one(FLERR,fmt::format("Cannot open logfile {}: {}",
str, utils::getsyserror()));
} else if (strcmp(arg[logflag],"none") == 0) {
logfile = nullptr;
} else {
str = fmt::format("{}.{}",arg[logflag],universe->iworld);
logfile = fopen(str.c_str(),"w");
if (logfile == nullptr)
error->one(FLERR,fmt::format("Cannot open logfile {}: {}",
str, utils::getsyserror()));
}
} else if (strcmp(arg[partlogflag],"none") == 0) {
logfile = nullptr;
} else {
str = fmt::format("{}.{}",arg[partlogflag],universe->iworld);
logfile = fopen(str.c_str(),"w");
if (logfile == nullptr)
error->one(FLERR,fmt::format("Cannot open logfile {}: {}",
str, utils::getsyserror()));
}
if (strcmp(arg[inflag], "none") != 0) {
infile = fopen(arg[inflag],"r");
if (infile == nullptr)
error->one(FLERR,fmt::format("Cannot open input script {}: {}",
arg[inflag], utils::getsyserror()));
}
}
// screen and logfile messages for universe and world
if ((universe->me == 0) && (!helpflag)) {
const char fmt[] = "LAMMPS ({})\nRunning on {} partitions of processors\n";
if (universe->uscreen)
fmt::print(universe->uscreen,fmt,version,universe->nworlds);
if (universe->ulogfile)
fmt::print(universe->ulogfile,fmt,version,universe->nworlds);
}
if ((me == 0) && (!helpflag))
utils::logmesg(this,fmt::format("LAMMPS ({})\nProcessor partition = {}\n",
version, universe->iworld));
}
// check consistency of datatype settings in lmptype.h
if (sizeof(smallint) != sizeof(int))
error->all(FLERR,"Smallint setting in lmptype.h is invalid");
if (sizeof(imageint) < sizeof(smallint))
error->all(FLERR,"Imageint setting in lmptype.h is invalid");
if (sizeof(tagint) < sizeof(smallint))
error->all(FLERR,"Tagint setting in lmptype.h is invalid");
if (sizeof(bigint) < sizeof(imageint) || sizeof(bigint) < sizeof(tagint))
error->all(FLERR,"Bigint setting in lmptype.h is invalid");
int mpisize;
MPI_Type_size(MPI_LMP_TAGINT,&mpisize);
if (mpisize != sizeof(tagint))
error->all(FLERR,"MPI_LMP_TAGINT and tagint in "
"lmptype.h are not compatible");
MPI_Type_size(MPI_LMP_BIGINT,&mpisize);
if (mpisize != sizeof(bigint))
error->all(FLERR,"MPI_LMP_BIGINT and bigint in "
"lmptype.h are not compatible");
#ifdef LAMMPS_SMALLBIG
if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 8)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_BIGBIG
if (sizeof(smallint) != 4 || sizeof(imageint) != 8 ||
sizeof(tagint) != 8 || sizeof(bigint) != 8)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
#ifdef LAMMPS_SMALLSMALL
if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
sizeof(tagint) != 4 || sizeof(bigint) != 4)
error->all(FLERR,"Small to big integers are not sized correctly");
#endif
// create Kokkos class if KOKKOS installed, unless explicitly switched off
// instantiation creates dummy Kokkos class if KOKKOS is not installed
// add args between kkfirst and kklast to Kokkos instantiation
kokkos = nullptr;
if (kokkosflag == 1) {
kokkos = new KokkosLMP(this,kklast-kkfirst,&arg[kkfirst]);
if (!kokkos->kokkos_exists)
error->all(FLERR,"Cannot use -kokkos on without KOKKOS installed");
}
// allocate CiteMe class if enabled
if (citeflag) citeme = new CiteMe(this);
else citeme = nullptr;
// allocate input class now that MPI is fully setup
input = new Input(this,narg,arg);
// copy package cmdline arguments
if (npack > 0) {
num_package = npack;
packargs = new char**[npack];
for (int i=0; i < npack; ++i) {
int n = plast[i] - pfirst[i];
packargs[i] = new char*[n+1];
for (int j=0; j < n; ++j)
packargs[i][j] = strdup(arg[pfirst[i]+j]);
packargs[i][n] = nullptr;
}
memory->destroy(pfirst);
memory->destroy(plast);
}
// if helpflag set, print help and quit with "success" status
// otherwise allocate top level classes.
if (helpflag) {
if (universe->me == 0 && screen) help();
error->done(0);
} else {
create();
post_create();
}
// if either restart conversion option was used, invoke 2 commands and quit
// add args between wfirst and wlast to write_data or write_data command
// add "noinit" to write_data to prevent a system init
// write_dump will just give a warning message about no init
if (restart2data || restart2dump) {
std::string cmd = fmt::format("read_restart {}",restartfile);
if (restartremap) cmd += " remap\n";
input->one(cmd);
if (restart2data) cmd = "write_data ";
else cmd = "write_dump";
for (iarg = wfirst; iarg < wlast; iarg++)
cmd += fmt::format(" {}", arg[iarg]);
if (restart2data) cmd += " noinit";
input->one(cmd);
error->done(0);
}
}
/** Shut down a LAMMPS simulation instance
*
* The LAMMPS destructor shuts down the simulation by deleting top-level class
* instances, closing screen and log files for the global instance (aka "world")
* and files and MPI communicators in sub-partitions ("universes"). Then it
* deletes the fundamental class instances and copies of data inside the class.
*/
LAMMPS::~LAMMPS()
{
const int me = comm->me;
destroy();
delete citeme;
if (num_package) {
for (int i = 0; i < num_package; i++) {
for (char **ptr = packargs[i]; *ptr != nullptr; ++ptr)
free(*ptr);
delete[] packargs[i];
}
delete[] packargs;
}
num_package = 0;
packargs = nullptr;
double totalclock = MPI_Wtime() - initclock;
if ((me == 0) && (screen || logfile)) {
int seconds = fmod(totalclock,60.0);
totalclock = (totalclock - seconds) / 60.0;
int minutes = fmod(totalclock,60.0);
int hours = (totalclock - minutes) / 60.0;
utils::logmesg(this,fmt::format("Total wall time: {}:{:02d}:{:02d}\n",
hours, minutes, seconds));
}
if (universe->nworlds == 1) {
if (screen && screen != stdout) fclose(screen);
if (logfile) fclose(logfile);
logfile = nullptr;
if (screen != stdout) screen = nullptr;
} else {
if (screen && screen != stdout) fclose(screen);
if (logfile) fclose(logfile);
if (universe->ulogfile) fclose(universe->ulogfile);
logfile = nullptr;
if (screen != stdout) screen = nullptr;
}
if (infile && infile != stdin) fclose(infile);
if (world != universe->uworld) MPI_Comm_free(&world);
delete python;
delete kokkos;
delete [] suffix;
delete [] suffix2;
delete [] suffixp;
// free the MPI comm created by -mpi command-line arg processed in constructor
// it was passed to universe as if original universe world
// may have been split later by partitions, universe will free the splits
// free a copy of uorig here, so check in universe destructor will still work
MPI_Comm copy = universe->uorig;
if (cscomm) MPI_Comm_free(&copy);
delete input;
delete universe;
delete error;
delete memory;
delete pkg_lists;
}
/* ----------------------------------------------------------------------
allocate single instance of top-level classes
fundamental classes are allocated in constructor
some classes have package variants
------------------------------------------------------------------------- */
void LAMMPS::create()
{
force = nullptr; // Domain->Lattice checks if Force exists
// Comm class must be created before Atom class
// so that nthreads is defined when create_avec invokes grow()
if (kokkos) comm = new CommKokkos(this);
else comm = new CommBrick(this);
if (kokkos) neighbor = new NeighborKokkos(this);
else neighbor = new Neighbor(this);
if (kokkos) domain = new DomainKokkos(this);
#ifdef LMP_USER_OMP
else domain = new DomainOMP(this);
#else
else domain = new Domain(this);
#endif
if (kokkos) atom = new AtomKokkos(this);
else atom = new Atom(this);
if (kokkos)
atom->create_avec("atomic/kk",0,nullptr,1);
else
atom->create_avec("atomic",0,nullptr,1);
group = new Group(this);
force = new Force(this); // must be after group, to create temperature
if (kokkos) modify = new ModifyKokkos(this);
else modify = new Modify(this);
output = new Output(this); // must be after group, so "all" exists
// must be after modify so can create Computes
update = new Update(this); // must be after output, force, neighbor
timer = new Timer(this);
python = new Python(this);
}
/* ----------------------------------------------------------------------
check suffix consistency with installed packages
invoke package-specific default package commands
only invoke if suffix is set and enabled
also check if suffix2 is set
called from LAMMPS constructor and after clear() command
so that package-specific core classes have been instantiated
------------------------------------------------------------------------- */
void LAMMPS::post_create()
{
// default package command triggered by "-k on"
if (kokkos && kokkos->kokkos_exists) input->one("package kokkos");
// suffix will always be set if suffix_enable = 1
// check that KOKKOS package classes were instantiated
// check that GPU, INTEL, USER-OMP fixes were compiled with LAMMPS
if (suffix_enable) {
if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU"))
error->all(FLERR,"Using suffix gpu without GPU package installed");
if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL"))
error->all(FLERR,"Using suffix intel without USER-INTEL package installed");
if (strcmp(suffix,"kk") == 0 &&
(kokkos == nullptr || kokkos->kokkos_exists == 0))
error->all(FLERR,"Using suffix kk without KOKKOS package enabled");
if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP"))
error->all(FLERR,"Using suffix omp without USER-OMP package installed");
if (strcmp(suffix,"gpu") == 0) input->one("package gpu 1");
if (strcmp(suffix,"intel") == 0) input->one("package intel 1");
if (strcmp(suffix,"omp") == 0) input->one("package omp 0");
if (suffix2) {
if (strcmp(suffix2,"gpu") == 0) input->one("package gpu 1");
if (strcmp(suffix2,"intel") == 0) input->one("package intel 1");
if (strcmp(suffix2,"omp") == 0) input->one("package omp 0");
}
}
// invoke any command-line package commands
if (num_package) {
char str[256];
for (int i = 0; i < num_package; i++) {
strcpy(str,"package");
for (char **ptr = packargs[i]; *ptr != nullptr; ++ptr) {
if (strlen(str) + strlen(*ptr) + 2 > 256)
error->all(FLERR,"Too many -pk arguments in command line");
strcat(str," ");
strcat(str,*ptr);
}
input->one(str);
}
}
}
/* ----------------------------------------------------------------------
initialize top-level classes
do not initialize Timer class, other classes like Run() do that explicitly
------------------------------------------------------------------------- */
void LAMMPS::init()
{
update->init();
force->init(); // pair must come after update due to minimizer
domain->init();
atom->init(); // atom must come after force and domain
// atom deletes extra array
// used by fix shear_history::unpack_restart()
// when force->pair->gran_history creates fix
// atom_vec init uses deform_vremap
modify->init(); // modify must come after update, force, atom, domain
neighbor->init(); // neighbor must come after force, modify
comm->init(); // comm must come after force, modify, neighbor, atom
output->init(); // output must come after domain, force, modify
}
/* ----------------------------------------------------------------------
delete single instance of top-level classes
fundamental classes are deleted in destructor
------------------------------------------------------------------------- */
void LAMMPS::destroy()
{
delete update;
update = nullptr;
delete neighbor;
neighbor = nullptr;
delete force;
force = nullptr;
delete group;
group = nullptr;
delete output;
output = nullptr;
delete modify; // modify must come after output, force, update
// since they delete fixes
modify = nullptr;
delete comm; // comm must come after modify
// since fix destructors may access comm
comm = nullptr;
delete domain; // domain must come after modify
// since fix destructors access domain
domain = nullptr;
delete atom; // atom must come after modify, neighbor
// since fixes delete callbacks in atom
atom = nullptr;
delete timer;
timer = nullptr;
delete python;
python = nullptr;
}
/* ----------------------------------------------------------------------
initialize lists of styles in packages
------------------------------------------------------------------------- */
void _noopt LAMMPS::init_pkg_lists()
{
pkg_lists = new package_styles_lists;
#define PACKAGE "UNKNOWN"
#define ANGLE_CLASS
#define AngleStyle(key,Class) \
pkg_lists->angle_styles[#key] = PACKAGE;
#include "packages_angle.h"
#undef AngleStyle
#undef ANGLE_CLASS
#define ATOM_CLASS
#define AtomStyle(key,Class) \
pkg_lists->atom_styles[#key] = PACKAGE;
#include "packages_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
#define BODY_CLASS
#define BodyStyle(key,Class) \
pkg_lists->body_styles[#key] = PACKAGE;
#include "packages_body.h"
#undef BodyStyle
#undef BODY_CLASS
#define BOND_CLASS
#define BondStyle(key,Class) \
pkg_lists->bond_styles[#key] = PACKAGE;
#include "packages_bond.h"
#undef BondStyle
#undef BOND_CLASS
#define COMMAND_CLASS
#define CommandStyle(key,Class) \
pkg_lists->command_styles[#key] = PACKAGE;
#include "packages_command.h"
#undef CommandStyle
#undef COMMAND_CLASS
#define COMPUTE_CLASS
#define ComputeStyle(key,Class) \
pkg_lists->compute_styles[#key] = PACKAGE;
#include "packages_compute.h"
#undef ComputeStyle
#undef COMPUTE_CLASS
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) \
pkg_lists->dihedral_styles[#key] = PACKAGE;
#include "packages_dihedral.h"
#undef DihedralStyle
#undef DIHEDRAL_CLASS
#define DUMP_CLASS
#define DumpStyle(key,Class) \
pkg_lists->dump_styles[#key] = PACKAGE;
#include "packages_dump.h"
#undef DumpStyle
#undef DUMP_CLASS
#define FIX_CLASS
#define FixStyle(key,Class) \
pkg_lists->fix_styles[#key] = PACKAGE;
#include "packages_fix.h"
#undef FixStyle
#undef FIX_CLASS
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) \
pkg_lists->improper_styles[#key] = PACKAGE;
#include "packages_improper.h"
#undef ImproperStyle
#undef IMPROPER_CLASS
#define INTEGRATE_CLASS
#define IntegrateStyle(key,Class) \
pkg_lists->integrate_styles[#key] = PACKAGE;
#include "packages_integrate.h"
#undef IntegrateStyle
#undef INTEGRATE_CLASS
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) \
pkg_lists->kspace_styles[#key] = PACKAGE;
#include "packages_kspace.h"
#undef KSpaceStyle
#undef KSPACE_CLASS
#define MINIMIZE_CLASS
#define MinimizeStyle(key,Class) \
pkg_lists->minimize_styles[#key] = PACKAGE;
#include "packages_minimize.h"
#undef MinimizeStyle
#undef MINIMIZE_CLASS
#define PAIR_CLASS
#define PairStyle(key,Class) \
pkg_lists->pair_styles[#key] = PACKAGE;
#include "packages_pair.h"
#undef PairStyle
#undef PAIR_CLASS
#define READER_CLASS
#define ReaderStyle(key,Class) \
pkg_lists->reader_styles[#key] = PACKAGE;
#include "packages_reader.h"
#undef ReaderStyle
#undef READER_CLASS
#define REGION_CLASS
#define RegionStyle(key,Class) \
pkg_lists->region_styles[#key] = PACKAGE;
#include "packages_region.h"
#undef RegionStyle
#undef REGION_CLASS
}
/** Return true if a LAMMPS package is enabled in this binary
*
* \param pkg name of package
* \return true if yes, else false
*/
bool LAMMPS::is_installed_pkg(const char *pkg)
{
for (int i=0; installed_packages[i] != nullptr; ++i)
if (strcmp(installed_packages[i],pkg) == 0) return true;
return false;
}
#define check_for_match(style,list,name) \
if (strcmp(list,#style) == 0) { \
std::map<std::string,std::string> &styles(pkg_lists-> style ## _styles); \
if (styles.find(name) != styles.end()) { \
return styles[name].c_str(); \
} \
}
/** \brief Return name of package that a specific style belongs to
*
* This function checks the given name against all list of styles
* for all type of styles and if the name and the style match, it
* returns which package this style belongs to.
*
* \param style Type of style (e.g. atom, pair, fix, etc.)
* \param name Name of style
* \return Name of the package this style is part of
*/
const char *LAMMPS::match_style(const char *style, const char *name)
{
check_for_match(angle,style,name);
check_for_match(atom,style,name);
check_for_match(body,style,name);
check_for_match(bond,style,name);
check_for_match(command,style,name);
check_for_match(compute,style,name);
check_for_match(dump,style,name);
check_for_match(fix,style,name);
check_for_match(compute,style,name);
check_for_match(improper,style,name);
check_for_match(integrate,style,name);
check_for_match(kspace,style,name);
check_for_match(minimize,style,name);
check_for_match(pair,style,name);
check_for_match(reader,style,name);
check_for_match(region,style,name);
return nullptr;
}
/* ----------------------------------------------------------------------
help message for command line options and styles present in executable
------------------------------------------------------------------------- */
void _noopt LAMMPS::help()
{
FILE *fp = screen;
const char *pager = nullptr;
// if output is "stdout", use a pipe to a pager for paged output.
// this will avoid the most important help text to rush past the
// user. scrollback buffers are often not large enough. this is most
// beneficial to windows users, who are not used to command line.
if (fp == stdout) {
pager = getenv("PAGER");
if (pager == nullptr) pager = "more";
#if defined(_WIN32)
fp = _popen(pager,"w");
#else
fp = popen(pager,"w");
#endif
// reset to original state, if pipe command failed
if (fp == nullptr) {
fp = stdout;
pager = nullptr;
}
}
// general help message about command line and flags
if (has_git_info) {
fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - "
LAMMPS_VERSION "\nGit info (%s / %s)\n\n",git_branch, git_descriptor);
} else {
fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - "
LAMMPS_VERSION "\n\n");
}
fprintf(fp,
"Usage example: %s -var t 300 -echo screen -in in.alloy\n\n"
"List of command line options supported by this LAMMPS executable:\n\n"
"-echo none/screen/log/both : echoing of input script (-e)\n"
"-help : print this help message (-h)\n"
"-in none/filename : read input from file or stdin (default) (-i)\n"
"-kokkos on/off ... : turn KOKKOS mode on or off (-k)\n"
"-log none/filename : where to send log output (-l)\n"
"-mpicolor color : which exe in a multi-exe mpirun cmd (-m)\n"
"-nocite : disable writing log.cite file (-nc)\n"
"-package style ... : invoke package command (-pk)\n"
"-partition size1 size2 ... : assign partition sizes (-p)\n"
"-plog basename : basename for partition logs (-pl)\n"
"-pscreen basename : basename for partition screens (-ps)\n"
"-restart2data rfile dfile ... : convert restart to data file (-r2data)\n"
"-restart2dump rfile dgroup dstyle dfile ... \n"
" : convert restart to dump file (-r2dump)\n"
"-reorder topology-specs : processor reordering (-r)\n"
"-screen none/filename : where to send screen output (-sc)\n"
"-suffix gpu/intel/opt/omp : style suffix to apply (-sf)\n"
"-var varname value : set index style variable (-v)\n\n",
exename);
print_config(fp);
fprintf(fp,"List of individual style options included in this LAMMPS executable\n\n");
int pos = 80;
fprintf(fp,"* Atom styles:\n");
#define ATOM_CLASS
#define AtomStyle(key,Class) print_style(fp,#key,pos);
#include "style_atom.h"
#undef ATOM_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Integrate styles:\n");
#define INTEGRATE_CLASS
#define IntegrateStyle(key,Class) print_style(fp,#key,pos);
#include "style_integrate.h"
#undef INTEGRATE_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Minimize styles:\n");
#define MINIMIZE_CLASS
#define MinimizeStyle(key,Class) print_style(fp,#key,pos);
#include "style_minimize.h"
#undef MINIMIZE_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Pair styles:\n");
#define PAIR_CLASS
#define PairStyle(key,Class) print_style(fp,#key,pos);
#include "style_pair.h"
#undef PAIR_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Bond styles:\n");
#define BOND_CLASS
#define BondStyle(key,Class) print_style(fp,#key,pos);
#include "style_bond.h"
#undef BOND_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Angle styles:\n");
#define ANGLE_CLASS
#define AngleStyle(key,Class) print_style(fp,#key,pos);
#include "style_angle.h"
#undef ANGLE_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Dihedral styles:\n");
#define DIHEDRAL_CLASS
#define DihedralStyle(key,Class) print_style(fp,#key,pos);
#include "style_dihedral.h"
#undef DIHEDRAL_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Improper styles:\n");
#define IMPROPER_CLASS
#define ImproperStyle(key,Class) print_style(fp,#key,pos);
#include "style_improper.h"
#undef IMPROPER_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* KSpace styles:\n");
#define KSPACE_CLASS
#define KSpaceStyle(key,Class) print_style(fp,#key,pos);
#include "style_kspace.h"
#undef KSPACE_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Fix styles\n");
#define FIX_CLASS
#define FixStyle(key,Class) print_style(fp,#key,pos);
#include "style_fix.h"
#undef FIX_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Compute styles:\n");
#define COMPUTE_CLASS
#define ComputeStyle(key,Class) print_style(fp,#key,pos);
#include "style_compute.h"
#undef COMPUTE_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Region styles:\n");
#define REGION_CLASS
#define RegionStyle(key,Class) print_style(fp,#key,pos);
#include "style_region.h"
#undef REGION_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Dump styles:\n");
#define DUMP_CLASS
#define DumpStyle(key,Class) print_style(fp,#key,pos);
#include "style_dump.h"
#undef DUMP_CLASS
fprintf(fp,"\n\n");
pos = 80;
fprintf(fp,"* Command styles\n");
#define COMMAND_CLASS
#define CommandStyle(key,Class) print_style(fp,#key,pos);
#include "style_command.h"
#undef COMMAND_CLASS
fprintf(fp,"\n\n");
// close pipe to pager, if active
if (pager != nullptr) pclose(fp);
}
/* ----------------------------------------------------------------------
print style names in columns
skip any style that starts with upper-case letter, since internal
------------------------------------------------------------------------- */
void print_style(FILE *fp, const char *str, int &pos)
{
if (isupper(str[0])) return;
int len = strlen(str);
if (pos+len > 80) {
fprintf(fp,"\n");
pos = 0;
}
if (len < 16) {
fprintf(fp,"%-16s",str);
pos += 16;
} else if (len < 32) {
fprintf(fp,"%-32s",str);
pos += 32;
} else if (len < 48) {
fprintf(fp,"%-48s",str);
pos += 48;
} else if (len < 64) {
fprintf(fp,"%-64s",str);
pos += 64;
} else {
fprintf(fp,"%-80s",str);
pos += 80;
}
}
void LAMMPS::print_config(FILE *fp)
{
const char *pkg;
int ncword, ncline = 0;
fmt::print(fp,"OS: {}\n\n",Info::get_os_info());
fmt::print(fp,"Compiler: {} with {}\nC++ standard: {}\n",
Info::get_compiler_info(),Info::get_openmp_info(),
Info::get_cxx_info());
int major,minor;
std::string infobuf = Info::get_mpi_info(major,minor);
fmt::print(fp,"MPI v{}.{}: {}\n\n",major,minor,infobuf);
fputs("Active compile time flags:\n\n",fp);
if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp);
if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp);
if (Info::has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",fp);
if (Info::has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",fp);
if (Info::has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",fp);
#if defined(LAMMPS_BIGBIG)
fputs("-DLAMMPS_BIGBIG\n",fp);
#elif defined(LAMMPS_SMALLBIG)
fputs("-DLAMMPS_SMALLBIG\n",fp);
#else // defined(LAMMPS_SMALLSMALL)
fputs("-DLAMMPS_SMALLSMALL\n",fp);
#endif
fmt::print(fp,"sizeof(smallint): {}-bit\n"
"sizeof(imageint): {}-bit\n"
"sizeof(tagint): {}-bit\n"
"sizeof(bigint): {}-bit\n",
sizeof(smallint)*8, sizeof(imageint)*8,
sizeof(tagint)*8, sizeof(bigint)*8);
fputs("\nInstalled packages:\n\n",fp);
for (int i = 0; nullptr != (pkg = installed_packages[i]); ++i) {
ncword = strlen(pkg);
if (ncline + ncword > 78) {
ncline = 0;
fputs("\n",fp);
}
fprintf(fp,"%s ",pkg);
ncline += ncword + 1;
}
fputs("\n\n",fp);
}
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