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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10350 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-07-25 19:47:41 +00:00
parent 856f78e50a
commit 48510d047b
4 changed files with 166 additions and 26 deletions
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78
src/fix_property_atom.cpp
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@ -25,11 +25,6 @@ using namespace FixConst;
enum{MOLECULE,INTEGER,DOUBLE};
// NOTE: how to prevent atom style being changed after this fix defined?
// e.g. what if replicate happens, will it wipe out molecule_flag
// will it copy ivectors in atom.h ??
// maybe setting of atom->mol_flag should happen in fix init
/* ---------------------------------------------------------------------- */
FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
@ -42,6 +37,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
nvalue = narg-iarg;
style = new int[nvalue];
index = new int[nvalue];
molecule_flag = 0;
@ -58,9 +54,19 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
nvalue++;
} else if (strstr(arg[iarg],"i_") == arg[iarg]) {
style[nvalue] = INTEGER;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],0);
nvalue++;
} else if (strstr(arg[iarg],"d_") == arg[iarg]) {
style[nvalue] = DOUBLE;
int tmp;
index[nvalue] = atom->find_custom(&arg[iarg][2],tmp);
if (index[nvalue] >= 0)
error->all(FLERR,"Fix property/atom vector name already exists");
index[nvalue] = atom->add_custom(&arg[iarg][2],1);
nvalue++;
} else break;
@ -111,11 +117,14 @@ FixPropertyAtom::~FixPropertyAtom()
memory->destroy(atom->molecule);
atom->molecule = NULL;
} else if (style[m] == INTEGER) {
atom->remove_custom(0,index[m]);
} else if (style[m] == DOUBLE) {
atom->remove_custom(1,index[m]);
}
}
delete [] style;
delete [] index;
}
/* ---------------------------------------------------------------------- */
@ -187,8 +196,10 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf)
if ((m = atom->map(tagdata)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) atom->molecule[m] = atoi(values[j+1]);
else if (style[j] == INTEGER) atom->molecule[m] = atoi(values[j+1]);
else if (style[j] == DOUBLE) atom->molecule[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
else if (style[j] == DOUBLE)
atom->dvector[index[j]][m] = atof(values[j+1]);
}
}
@ -235,13 +246,13 @@ void FixPropertyAtom::grow_arrays(int nmax)
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (style[m] == INTEGER) {
memory->grow(atom->molecule,nmax,"atom:molecule");
memory->grow(atom->ivector[index[m]],nmax,"atom:ivector");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->molecule[nmax_old],0,nbytes);
memset(&atom->ivector[index[m]][nmax_old],0,nbytes);
} else if (style[m] == DOUBLE) {
memory->grow(atom->molecule,nmax,"atom:molecule");
memory->grow(atom->dvector[index[m]],nmax,"atom:dvector");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->molecule[nmax_old],0,nbytes);
memset(&atom->dvector[index[m]][nmax_old],0,nbytes);
}
}
@ -258,9 +269,9 @@ void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
if (style[m] == MOLECULE)
atom->molecule[j] = atom->molecule[i];
else if (style[m] == INTEGER)
atom->molecule[j] = atom->molecule[i];
atom->ivector[index[m]][j] = atom->ivector[index[m]][i];
else if (style[m] == DOUBLE)
atom->molecule[j] = atom->molecule[i];
atom->dvector[index[m]][j] = atom->dvector[index[m]][i];
}
}
@ -281,11 +292,20 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
buf[m++] = molecule[j];
}
} else if (style[j] == INTEGER) {
int *ivector = atom->ivector[index[k]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ivector[j];
}
} else if (style[j] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = dvector[j];
}
}
}
printf("PBORDER %ld %d\n",update->ntimestep,m);
return m;
}
@ -304,9 +324,17 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
last = first + n;
for (i = first; i < last; i++)
molecule[i] = static_cast<int> (buf[m++]);
} else if (style[k] == INTEGER) {
} else if (style[k] == DOUBLE) {
}
} else if (style[k] == INTEGER) {
int *ivector = atom->ivector[index[k]];
last = first + n;
for (i = first; i < last; i++)
ivector[i] = static_cast<int> (buf[m++]);
} else if (style[k] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
last = first + n;
for (i = first; i < last; i++)
dvector[i] = buf[m++];
}
}
return m;
@ -320,8 +348,8 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) buf[m] = atom->molecule[i];
else if (style[m] == INTEGER) buf[m] = atom->molecule[i];
else if (style[m] == DOUBLE) buf[m] = atom->molecule[i];
else if (style[m] == INTEGER) buf[m] = atom->ivector[index[m]][i];
else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
}
return nvalue;
}
@ -336,9 +364,9 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
if (style[m] == MOLECULE)
atom->molecule[nlocal] = static_cast<int> (buf[m]);
else if (style[m] == INTEGER)
atom->molecule[nlocal] = static_cast<int> (buf[m]);
atom->ivector[index[m]][nlocal] = static_cast<int> (buf[m]);
else if (style[m] == DOUBLE)
atom->molecule[nlocal] = buf[m];
atom->dvector[index[m]][nlocal] = buf[m];
}
return nvalue;
}
@ -352,8 +380,8 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
buf[0] = nvalue+1;
for (int m = 1; m <= nvalue; m++) {
if (style[m] == MOLECULE) buf[m] = atom->molecule[i];
else if (style[m] == INTEGER) buf[m] = atom->molecule[i];
else if (style[m] == DOUBLE) buf[m] = atom->molecule[i];
else if (style[m] == INTEGER) buf[m] = atom->ivector[index[m]][i];
else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
}
return nvalue+1;
}
@ -376,9 +404,9 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
if (style[i] == MOLECULE)
atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
else if (style[m] == INTEGER)
atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
atom->ivector[index[m]][nlocal] = static_cast<int> (extra[nlocal][m++]);
else if (style[m] == DOUBLE)
atom->molecule[nlocal] = extra[nlocal][m++];
atom->dvector[index[m]][nlocal] = extra[nlocal][m++];
}
}