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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8236 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-07 17:19:17 +00:00
parent 2bc8b55c79
commit 78f8f69895
4 changed files with 251 additions and 19 deletions
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55
src/read_dump.cpp
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@ -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;
}