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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4405 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-07-20 18:17:24 +00:00
parent 71fa7dbfd9
commit c4f3b2fe6d
3 changed files with 69 additions and 30 deletions
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52
src/XTC/dump_xtc.cpp
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@ -53,8 +53,6 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump xtc command");
if (igroup != group->find("all")) error->all("Dump xtc must use group all");
if (domain->triclinic)
error->all("Dump xtc does not yet support triclinic simulation boxes");
if (binary || compressed || multifile || multiproc)
error->all("Invalid dump xtc filename");
@ -175,15 +173,28 @@ void DumpXTC::write_header(int n)
xdr_float(&xd,&time_value);
// cell basis vectors
if (domain->triclinic) {
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
float xy = sfactor * domain->xy;
float xz = sfactor * domain->xz;
float yz = sfactor * domain->yz;
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&xy ); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&xz ); xdr_float(&xd,&yz ); xdr_float(&xd,&zdim);
} else {
float zero = 0.0;
float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim);
xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim);
}
}
/* ---------------------------------------------------------------------- */
@ -209,14 +220,27 @@ int DumpXTC::pack()
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double xy = domain->xy;
double xz = domain->xz;
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];
buf[m++] = sfactor*(x[i][0] + ((image[i] & 1023) - 512) * xprd);
buf[m++] = sfactor*(x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd);
buf[m++] = sfactor*(x[i][2] + ((image[i] >> 20) - 512) * zprd);
}
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (domain->triclinic) {
buf[m++] = tag[i];
buf[m++] = sfactor * (x[i][0] + ix * xprd + iy * xy + iz * xz);
buf[m++] = sfactor * (x[i][1] + iy * yprd + iz * yz);
buf[m++] = sfactor * (x[i][2] + iz * zprd);
} else {
buf[m++] = tag[i];
buf[m++] = sfactor * (x[i][0] + ix * xprd);
buf[m++] = sfactor * (x[i][1] + iy * yprd);
buf[m++] = sfactor * (x[i][2] + iz * zprd);
}
}
} else {
for (int i = 0; i < nlocal; i++) {
buf[m++] = tag[i];