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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4795 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-09-15 22:16:20 +00:00
parent 1d3b37782f
commit ded8b22c19
19 changed files with 909 additions and 747 deletions
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145
src/dump_dcd.cpp
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@ -13,6 +13,7 @@
/* ----------------------------------------------------------------------
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
Axel Kohlmeyer (Temple U), support for groups
------------------------------------------------------------------------- */
#include "math.h"
@ -54,20 +55,22 @@ static inline void fwrite_int32(FILE* fd, uint32_t i)
DumpDCD::DumpDCD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal dump dcd command");
if (igroup != group->find("all")) error->all("Dump dcd must use group all");
if (binary || compressed || multifile || multiproc)
error->all("Invalid dump dcd filename");
size_one = 4;
size_one = 3;
sort_flag = 1;
sortcol = 0;
unwrap_flag = 0;
format_default = NULL;
// allocate global array for atom coords
natoms = static_cast<int> (atom->natoms);
if (igroup == 0) natoms = static_cast<int> (atom->natoms);
else natoms = static_cast<int> (group->count(igroup));
if (natoms <= 0) error->all("Invalid natoms for dump dcd");
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for dump dcd");
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
xf = &coords[0*natoms];
yf = &coords[1*natoms];
@ -88,8 +91,11 @@ DumpDCD::~DumpDCD()
/* ---------------------------------------------------------------------- */
void DumpDCD::init()
void DumpDCD::init_style()
{
if (sort_flag == 0 || sortcol != 0)
error->all("Dump dcd requires sorting by atom ID");
// check that dump frequency has not changed and is not a variable
int idump;
@ -105,31 +111,6 @@ void DumpDCD::init()
/* ---------------------------------------------------------------------- */
int DumpDCD::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"unwrap") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
else error->all("Illegal dump_modify command");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
double DumpDCD::memory_usage()
{
double bytes = maxbuf * sizeof(double);
bytes += 3*natoms * sizeof(float);
return bytes;
}
/* ---------------------------------------------------------------------- */
void DumpDCD::openfile()
{
if (me == 0) {
@ -193,21 +174,30 @@ void DumpDCD::write_header(int n)
int DumpDCD::count()
{
return atom->nlocal;
if (igroup == 0) return atom->nlocal;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int m = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) m++;
return m;
}
/* ---------------------------------------------------------------------- */
int DumpDCD::pack()
void DumpDCD::pack(int *ids)
{
int m,n;
int *tag = atom->tag;
double **x = atom->x;
int *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// assume group all, so no need to perform mask check
int m = 0;
m = n = 0;
if (unwrap_flag) {
double xprd = domain->xprd;
double yprd = domain->yprd;
@ -217,53 +207,51 @@ int DumpDCD::pack()
double yz = domain->yz;
for (int i = 0; i < nlocal; i++) {
int ix = (image[i] & 1023) - 512;
int iy = (image[i] >> 10 & 1023) - 512;
int iz = (image[i] >> 20) - 512;
if (mask[i] & groupbit) {
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++] = 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++] = tag[i];
buf[m++] = x[i][0] + ix * xprd;
buf[m++] = x[i][1] + iy * yprd;
buf[m++] = x[i][2] + iz * zprd;
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++) {
buf[m++] = tag[i];
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
}
}
return m;
} 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];
}
}
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_data(int n, double *mybuf)
{
// spread buf atom coords into global arrays
// copy buf atom coords into 3 global arrays
int tag;
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (mybuf[m]) - 1;
xf[tag] = mybuf[m+1];
yf[tag] = mybuf[m+2];
zf[tag] = mybuf[m+3];
m += size_one;
xf[ntotal] = mybuf[m++];
yf[ntotal] = mybuf[m++];
zf[ntotal] = mybuf[m++];
ntotal++;
}
// if last chunk of atoms in this snapshot, write global arrays to file
ntotal += n;
if (ntotal == natoms) {
write_frame();
ntotal = 0;
@ -272,6 +260,31 @@ void DumpDCD::write_data(int n, double *mybuf)
/* ---------------------------------------------------------------------- */
int DumpDCD::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"unwrap") == 0) {
if (narg < 2) error->all("Illegal dump_modify command");
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
else error->all("Illegal dump_modify command");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
double DumpDCD::memory_usage()
{
double bytes = Dump::memory_usage();
bytes += 3*natoms * sizeof(float);
return bytes;
}
/* ---------------------------------------------------------------------- */
void DumpDCD::write_frame()
{
// write coords