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rerun.cpp
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Tue, May 28, 16:37

rerun.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://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 <stdlib.h>
#include <string.h>
#include "rerun.h"
#include "read_dump.h"
#include "domain.h"
#include "update.h"
#include "integrate.h"
#include "modify.h"
#include "output.h"
#include "finish.h"
#include "timer.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Rerun::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Rerun command before simulation box is defined");
if (narg < 2) error->all(FLERR,"Illegal rerun command");
// list of dump files = args until a keyword
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"first") == 0) break;
if (strcmp(arg[iarg],"last") == 0) break;
if (strcmp(arg[iarg],"every") == 0) break;
if (strcmp(arg[iarg],"skip") == 0) break;
if (strcmp(arg[iarg],"start") == 0) break;
if (strcmp(arg[iarg],"stop") == 0) break;
if (strcmp(arg[iarg],"dump") == 0) break;
iarg++;
}
int nfile = iarg;
if (nfile == 0 || nfile == narg) error->all(FLERR,"Illegal rerun command");
// parse optional args up until "dump"
// user MAXBIGINT -1 so Output can add 1 to it and still be a big int
bigint first = 0;
bigint last = MAXBIGINT - 1;
int nevery = 0;
int nskip = 1;
int startflag = 0;
int stopflag = 0;
bigint start = -1;
bigint stop = -1;
while (iarg < narg) {
if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
first = force->bnumeric(FLERR,arg[iarg+1]);
if (first < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"last") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
last = force->bnumeric(FLERR,arg[iarg+1]);
if (last < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"skip") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
nskip = force->inumeric(FLERR,arg[iarg+1]);
if (nskip <= 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
startflag = 1;
start = force->bnumeric(FLERR,arg[iarg+1]);
if (start < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"stop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
stopflag = 1;
stop = force->bnumeric(FLERR,arg[iarg+1]);
if (stop < 0) error->all(FLERR,"Illegal rerun command");
iarg += 2;
} else if (strcmp(arg[iarg],"dump") == 0) {
break;
} else error->all(FLERR,"Illegal rerun command");
}
int nremain = narg - iarg - 1;
if (nremain <= 0) error->all(FLERR,"Illegal rerun command");
if (first > last) error->all(FLERR,"Illegal rerun command");
if (startflag && stopflag && start > stop)
error->all(FLERR,"Illegal rerun command");
// pass list of filenames to ReadDump
// along with post-"dump" args and post-"format" args
ReadDump *rd = new ReadDump(lmp);
rd->store_files(nfile,arg);
if (nremain)
nremain = rd->fields_and_keywords(nremain,&arg[narg-nremain]);
else nremain = rd->fields_and_keywords(0,NULL);
if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
else rd->setup_reader(0,NULL);
// perform the pseudo run
// invoke lmp->init() only once
// read all relevant snapshots
// use setup_minimal() since atoms are already owned by correct procs
// addstep_compute_all() insures energy/virial computed on every snapshot
update->whichflag = 1;
if (startflag) update->beginstep = update->firststep = start;
else update->beginstep = update->firststep = first;
if (stopflag) update->endstep = update->laststep = stop;
else update->endstep = update->laststep = last;
int firstflag = 1;
int ndump = 0;
lmp->init();
timer->init();
timer->barrier_start();
bigint ntimestep = rd->seek(first,0);
if (ntimestep < 0)
error->all(FLERR,"Rerun dump file does not contain requested snapshot");
while (1) {
ndump++;
rd->header(firstflag);
update->reset_timestep(ntimestep);
rd->atoms();
modify->init();
update->integrate->setup_minimal(1);
modify->end_of_step();
if (firstflag) output->setup();
else if (output->next) output->write(ntimestep);
firstflag = 0;
ntimestep = rd->next(ntimestep,last,nevery,nskip);
if (stopflag && ntimestep > stop)
error->all(FLERR,"Read rerun dump file timestep > specified stop");
if (ntimestep < 0) break;
}
// insure thermo output on last dump timestep
output->next_thermo = update->ntimestep;
output->write(update->ntimestep);
timer->barrier_stop();
update->integrate->cleanup();
// set update->nsteps to ndump for Finish stats to print
update->nsteps = ndump;
Finish finish(lmp);
finish.end(1);
update->whichflag = 0;
update->firststep = update->laststep = 0;
update->beginstep = update->endstep = 0;
// clean-up
delete rd;
}

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