forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8236 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
2bc8b55c79
commit
78f8f69895
|
|
@ -49,7 +49,7 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
|
|||
dimension = domain->dimension;
|
||||
triclinic = domain->triclinic;
|
||||
|
||||
nfiles = 0;
|
||||
nfile = 0;
|
||||
files = NULL;
|
||||
|
||||
nfield = 0;
|
||||
|
|
@ -59,13 +59,14 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp)
|
|||
uflag = ucflag = ucflag_all = NULL;
|
||||
|
||||
reader = NULL;
|
||||
fp = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ReadDump::~ReadDump()
|
||||
{
|
||||
for (int i = 0; i < nfiles; i++) delete [] files[i];
|
||||
for (int i = 0; i < nfile; i++) delete [] files[i];
|
||||
delete [] files;
|
||||
for (int i = 0; i < nfield; i++) delete [] fieldlabel[i];
|
||||
delete [] fieldlabel;
|
||||
|
|
@ -113,7 +114,6 @@ void ReadDump::command(int narg, char **arg)
|
|||
bigint natoms_prev = atom->natoms;
|
||||
atoms();
|
||||
|
||||
// NOTE: this logic is not yet right
|
||||
if (me == 0) close();
|
||||
|
||||
// print out stats
|
||||
|
|
@ -158,10 +158,10 @@ void ReadDump::command(int narg, char **arg)
|
|||
|
||||
void ReadDump::store_files(int nstr, char **str)
|
||||
{
|
||||
nfiles = nstr;
|
||||
files = new char*[nfiles];
|
||||
nfile = nstr;
|
||||
files = new char*[nfile];
|
||||
|
||||
for (int i = 0; i < nfiles; i++) {
|
||||
for (int i = 0; i < nfile; i++) {
|
||||
int n = strlen(str[i]) + 1;
|
||||
files[i] = new char[n];
|
||||
strcpy(files[i],str[i]);
|
||||
|
|
@ -184,7 +184,6 @@ void ReadDump::setup_reader()
|
|||
|
||||
/* ----------------------------------------------------------------------
|
||||
seek Nrequest timestep in one or more dump files
|
||||
Nrequest can be a timestamp or -1 to match first step with exact = 0
|
||||
if exact = 1, must find exactly Nrequest
|
||||
if exact = 0, find first step >= Nrequest
|
||||
return matching ntimestep or -1 if did not find a match
|
||||
|
|
@ -196,7 +195,11 @@ bigint ReadDump::seek(bigint nrequest, int exact)
|
|||
bigint ntimestep;
|
||||
|
||||
if (me == 0) {
|
||||
for (ifile = 0; ifile < nfiles; ifile++) {
|
||||
|
||||
// exit file loop when dump timestep >= nrequest
|
||||
// or files exhausted
|
||||
|
||||
for (ifile = 0; ifile < nfile; ifile++) {
|
||||
ntimestep = -1;
|
||||
open(files[ifile]);
|
||||
reader->file(fp);
|
||||
|
|
@ -211,9 +214,9 @@ bigint ReadDump::seek(bigint nrequest, int exact)
|
|||
}
|
||||
|
||||
currentfile = ifile;
|
||||
if (ntimestep < nrequest) close();
|
||||
if (ntimestep < nrequest) ntimestep = -1;
|
||||
if (exact && ntimestep != nrequest) ntimestep = -1;
|
||||
if (ntimestep < 0) close();
|
||||
}
|
||||
|
||||
MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
|
||||
|
|
@ -223,34 +226,48 @@ bigint ReadDump::seek(bigint nrequest, int exact)
|
|||
/* ----------------------------------------------------------------------
|
||||
find next matching snapshot in one or more dump files
|
||||
Ncurrent = current timestep from last snapshot
|
||||
Nstop = match no timestep bigger than Nstop
|
||||
Nlast = match no timestep bigger than Nlast
|
||||
Nevery = only match timesteps that are a multiple of Nevery
|
||||
Nskip = skip every this many timesteps
|
||||
return matching ntimestep or -1 if did not find a match
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint ReadDump::next(bigint ncurrent, bigint nstop, int nevery, int nskip)
|
||||
bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip)
|
||||
{
|
||||
int ifile,eofflag;
|
||||
bigint ntimestep;
|
||||
|
||||
// NOTE: this logic is not yet right
|
||||
|
||||
if (me == 0) {
|
||||
for (ifile = currentfile; ifile < nfiles; ifile++) {
|
||||
|
||||
// exit file loop when dump timestep matches all criteria
|
||||
// or files exhausted
|
||||
|
||||
int iskip = 0;
|
||||
|
||||
for (ifile = currentfile; ifile < nfile; ifile++) {
|
||||
ntimestep = -1;
|
||||
if (ifile != currentfile) open(files[ifile]);
|
||||
reader->file(fp);
|
||||
while (1) {
|
||||
eofflag = reader->read_time(ntimestep);
|
||||
if (eofflag) ntimestep = -1;
|
||||
break;
|
||||
if (iskip == nskip) iskip = 0;
|
||||
iskip++;
|
||||
if (eofflag) break;
|
||||
if (ntimestep <= ncurrent) break;
|
||||
if (ntimestep > nlast) break;
|
||||
if (nevery && ntimestep % nevery) reader->skip();
|
||||
else if (iskip < nskip) reader->skip();
|
||||
else break;
|
||||
}
|
||||
if (ntimestep > ncurrent) break;
|
||||
close();
|
||||
if (eofflag) close();
|
||||
else break;
|
||||
}
|
||||
|
||||
currentfile = ifile;
|
||||
if (eofflag) ntimestep = -1;
|
||||
if (ntimestep <= ncurrent) ntimestep = -1;
|
||||
if (ntimestep > nlast) ntimestep = -1;
|
||||
if (ntimestep < 0) close();
|
||||
}
|
||||
|
||||
MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world);
|
||||
|
|
@ -860,6 +877,8 @@ void ReadDump::open(char *file)
|
|||
|
||||
void ReadDump::close()
|
||||
{
|
||||
if (fp == NULL) return;
|
||||
if (compressed) pclose(fp);
|
||||
else fclose(fp);
|
||||
fp = NULL;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ private:
|
|||
int dimension;
|
||||
int triclinic;
|
||||
|
||||
int nfiles; // # of dump files to process
|
||||
int nfile; // # of dump files to process
|
||||
char **files; // list of file names
|
||||
int currentfile; // currently open file
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,177 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 "lmptype.h"
|
||||
#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"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void Rerun::command(int narg, char **arg)
|
||||
{
|
||||
if (narg < 2) error->all(FLERR,"Illegal rerun command");
|
||||
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,"Rerun command before simulation box is defined");
|
||||
|
||||
// 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"
|
||||
|
||||
bigint first = 0;
|
||||
bigint last = MAXBIGINT;
|
||||
int nevery = 0;
|
||||
int nskip = 1;
|
||||
int startflag = 0;
|
||||
int stopflag = 0;
|
||||
bigint start,stop;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"first") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
|
||||
first = ATOBIGINT(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 = ATOBIGINT(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 = atoi(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 = atoi(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 = ATOBIGINT(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 = ATOBIGINT(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");
|
||||
}
|
||||
|
||||
if (strcmp(arg[iarg],"dump") != 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
|
||||
|
||||
ReadDump *rd = new ReadDump(lmp);
|
||||
|
||||
rd->store_files(nfile,arg);
|
||||
rd->fields_and_keywords(narg-iarg-1,&arg[iarg+1]);
|
||||
rd->setup_reader();
|
||||
|
||||
// perform the psuedo run
|
||||
// invoke lmp->init() only once
|
||||
// read all relevant snapshots
|
||||
// uset setup_minimal() since atoms are already owned by correct procs
|
||||
// addstep_compute_all() insures energy/virial computed on every snapshot
|
||||
// set update->nsteps to ndump for Finish stats to print
|
||||
|
||||
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(TIME_LOOP);
|
||||
|
||||
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->addstep_compute_all(ntimestep);
|
||||
update->integrate->setup_minimal(1);
|
||||
output->setup(firstflag,firstflag);
|
||||
firstflag = 0;
|
||||
|
||||
ntimestep = rd->next(ntimestep,last,nevery,nskip);
|
||||
if (ntimestep < 0) break;
|
||||
}
|
||||
|
||||
timer->barrier_stop(TIME_LOOP);
|
||||
|
||||
update->integrate->cleanup();
|
||||
|
||||
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;
|
||||
}
|
||||
|
|
@ -0,0 +1,36 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
|
||||
CommandStyle(rerun,Rerun)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_RERUN_H
|
||||
#define LMP_RERUN_H
|
||||
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class Rerun : protected Pointers {
|
||||
public:
|
||||
Rerun(class LAMMPS *);
|
||||
void command(int, char **);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue