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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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46
src/dump_dcd.cpp
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@ -5,7 +5,7 @@
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
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.
@ -64,7 +64,7 @@ DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
unwrap_flag = 0;
format_default = NULL;
// allocate global array for atom coords
bigint n = group->count(igroup);
@ -162,11 +162,11 @@ void DumpDCD::write_header(bigint n)
dim[5] = domain->zprd;
dim[1] = dim[3] = dim[4] = 0.0;
}
if (me == 0) {
uint32_t out_integer = 48;
fwrite_int32(fp,out_integer);
fwrite(dim,out_integer,1,fp);
fwrite(dim,out_integer,1,fp);
fwrite_int32(fp,out_integer);
if (flush_flag) fflush(fp);
}
@ -195,30 +195,30 @@ void DumpDCD::pack(int *ids)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (domain->triclinic) {
buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
buf[m++] = x[i][1] + iy * yprd + iz * yz;
buf[m++] = x[i][2] + iz * zprd;
} else {
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
}
ids[n++] = tag[i];
if (domain->triclinic) {
buf[m++] = x[i][0] + ix * xprd + iy * xy + iz * xz;
buf[m++] = x[i][1] + iy * yprd + iz * yz;
buf[m++] = x[i][2] + iz * zprd;
} else {
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
}
ids[n++] = tag[i];
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
ids[n++] = tag[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
ids[n++] = tag[i];
}
}
}
@ -286,7 +286,7 @@ void DumpDCD::write_frame()
fwrite_int32(fp,out_integer);
fwrite(zf,out_integer,1,fp);
fwrite_int32(fp,out_integer);
// update NFILE and NSTEP fields in DCD header
nframes++;
@ -319,7 +319,7 @@ void DumpDCD::write_dcd_header(const char *remarks)
fwrite_int32(fp,ntimestep); // START = timestep of first snapshot
fwrite_int32(fp,nevery_save); // SKIP = interval between snapshots
fwrite_int32(fp,ntimestep); // NSTEP = timestep of last snapshot
fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
fwrite_int32(fp,0); // NAMD writes NSTEP or ISTART
fwrite_int32(fp,0);
fwrite_int32(fp,0);
fwrite_int32(fp,0);