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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10611 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-08-20 20:44:10 +00:00
parent c0a36bf823
commit c2fd1c17b2
7 changed files with 176 additions and 10 deletions
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87
src/fix_property_atom.cpp
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@ -33,6 +33,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
restart_peratom = 1;
wd_section = 1;
int iarg = 3;
nvalue = narg-iarg;
@ -150,7 +151,7 @@ void FixPropertyAtom::init()
}
/* ----------------------------------------------------------------------
unpack section of data file
unpack N lines in buf from section of data file labeled by keyword
------------------------------------------------------------------------- */
void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
@ -209,13 +210,95 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
delete [] values;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
return # of lines in section of data file labeled by keyword
------------------------------------------------------------------------- */
bigint FixPropertyAtom::read_data_skip_lines(char *keyword)
{
return atom->natoms;
}
/* ----------------------------------------------------------------------
return size I own for Mth data section
# of data sections = 1 for this fix
nx = # of local atoms
ny = columns = tag + nvalues
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_size(int mth, int &nx, int &ny)
{
nx = atom->nlocal;
ny = nvalue + 1;
}
/* ----------------------------------------------------------------------
pack values for Mth data section into buf
buf allocated by caller as Nlocal by Nvalues+1
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
{
int i;
// 1st column = atom tag
// rest of columns = per-atom values
int *tag = atom->tag;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) buf[i][0] = tag[i];
for (int m = 0; m < nvalue; m++) {
int mp1 = m+1;
if (style[m] == MOLECULE) {
int *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) buf[i][mp1] = molecule[i];
} else if (style[m] == INTEGER) {
int *vec = atom->ivector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
} else if (style[m] == DOUBLE) {
double *vec = atom->dvector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
}
}
}
/* ----------------------------------------------------------------------
write section keyword for Mth data section to file
use MOLECULE if that is only field, else use fix ID
only called by proc 0
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section_keyword(int mth, FILE *fp)
{
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecule\n\n");
else fprintf(fp,"\n%s\n\n",id);
}
/* ----------------------------------------------------------------------
write N lines from buf to file
convert buf fields to int or double depending on styles
index can be used to prepend global numbering
only called by proc 0
------------------------------------------------------------------------- */
void FixPropertyAtom::write_data_section(int mth, FILE *fp,
int n, double **buf, int index)
{
int m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT,static_cast<int> (buf[i][0]));
for (m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE || style[m] == INTEGER)
fprintf(fp," " TAGINT_FORMAT,static_cast<int> (buf[i][m+1]));
else fprintf(fp," %g",buf[i][m+1]);
}
fprintf(fp,"\n");
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */