ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

113
src/dump_xyz.cpp
View File

@ -28,39 +28,18 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
if (binary || multiproc) error->all("Invalid dump xyz filename");
size_one = 5;
sort_flag = 1;
sortcol = 0;
char *str = (char *) "%d %g %g %g";
int n = strlen(str) + 1;
format_default = new char[n];
strcpy(format_default,str);
// allocate global array for atom coords if group is all
if (igroup == 0) {
natoms = static_cast<int> (atom->natoms);
if (natoms <= 0) error->all("Invalid natoms for dump xyz");
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for dump xyz");
types = (int *) memory->smalloc(natoms*sizeof(int),"dump:types");
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
}
ntotal = 0;
}
/* ---------------------------------------------------------------------- */
DumpXYZ::~DumpXYZ()
{
if (igroup == 0) {
memory->sfree(types);
memory->sfree(coords);
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::init()
void DumpXYZ::init_style()
{
delete [] format;
char *str;
@ -77,41 +56,10 @@ void DumpXYZ::init()
if (multifile == 0) openfile();
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory in buf and global coords array
------------------------------------------------------------------------- */
double DumpXYZ::memory_usage()
{
double bytes = maxbuf * sizeof(double);
if (igroup == 0) {
bytes += natoms * sizeof(int);
bytes += 3*natoms * sizeof(float);
}
return bytes;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_header(int n)
{
// check bounds of atom IDs if group is all
// all procs realloc types & coords if necessary
if (igroup == 0) {
if (atom->tag_consecutive() == 0)
error->all("Atom IDs must be consecutive for dump xyz all");
if (n != natoms) {
memory->sfree(types);
memory->sfree(coords);
natoms = n;
types = (int *) memory->smalloc(natoms*sizeof(int),"dump:types");
coords = (float *) memory->smalloc(3*natoms*sizeof(float),"dump:coords");
}
}
// only proc 0 writes header
if (me == 0) {
fprintf(fp,"%d\n",n);
fprintf(fp,"Atoms\n");
@ -135,15 +83,17 @@ int DumpXYZ::count()
/* ---------------------------------------------------------------------- */
int DumpXYZ::pack()
void DumpXYZ::pack(int *ids)
{
int m,n;
int *tag = atom->tag;
int *type = atom->type;
int *mask = atom->mask;
double **x = atom->x;
int nlocal = atom->nlocal;
int m = 0;
m = n = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
buf[m++] = tag[i];
@ -151,57 +101,18 @@ int DumpXYZ::pack()
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
if (ids) ids[n++] = tag[i];
}
return m;
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_data(int n, double *mybuf)
{
// for group = all, spread buf atom coords into global arrays
// if last chunk of atoms in this snapshot, write global arrays to file
if (igroup == 0) {
int j,tag;
int m = 0;
for (int i = 0; i < n; i++) {
tag = static_cast<int> (mybuf[m]) - 1;
types[tag] = static_cast<int> (mybuf[m+1]);
j = 3*tag;
coords[j++] = mybuf[m+2];
coords[j++] = mybuf[m+3];
coords[j] = mybuf[m+4];
m += size_one;
}
ntotal += n;
if (ntotal == natoms) {
write_frame();
ntotal = 0;
}
// for group != all, write unsorted type,x,y,z to file
} else {
int m = 0;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}
}
/* ---------------------------------------------------------------------- */
void DumpXYZ::write_frame()
{
int m = 0;
for (int i = 0; i < natoms; i++) {
fprintf(fp,format,types[i],coords[m],coords[m+1],coords[m+2]);
m += 3;
for (int i = 0; i < n; i++) {
fprintf(fp,format,
static_cast<int> (mybuf[m+1]),mybuf[m+2],mybuf[m+3],mybuf[m+4]);
m += size_one;
}
}