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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11223 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-11 00:29:03 +00:00
parent 4f6a55e71b
commit d9a32bfaa8
3 changed files with 95 additions and 32 deletions
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5
src/atom.h
View File

@ -49,7 +49,7 @@ class Atom : protected Pointers {
tagint *image;
double **x,**v,**f;
int *molecule;
int *molecule,*molindex,*molatom;
double *q,**mu;
double **omega,**angmom,**torque;
double *radius,*rmass,*vfrac,*s0;
@ -104,7 +104,8 @@ class Atom : protected Pointers {
int ecp_flag;
int wavepacket_flag,sph_flag;
int molecule_flag,q_flag,mu_flag;
int molecule_flag,molindex_flag,molatom_flag;
int q_flag,mu_flag;
int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;

105
src/fix_property_atom.cpp
View File

@ -23,7 +23,7 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum{MOLECULE,INTEGER,DOUBLE};
enum{MOLECULE,CHARGE,INTEGER,DOUBLE};
/* ---------------------------------------------------------------------- */
@ -41,6 +41,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
index = new int[nvalue];
molecule_flag = 0;
q_flag = 0;
nvalue = 0;
while (iarg < narg) {
@ -53,6 +54,15 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
style[nvalue] = MOLECULE;
atom->molecule_flag = molecule_flag = 1;
nvalue++;
} else if (strcmp(arg[iarg],"q") == 0) {
if (atom->q_flag)
error->all(FLERR,"Fix property/atom q when atom_style "
"already has charge attribute");
if (q_flag)
error->all(FLERR,"Fix property/atom cannot specify q twice");
style[nvalue] = CHARGE;
atom->q_flag = q_flag = 1;
nvalue++;
} else if (strstr(arg[iarg],"i_") == arg[iarg]) {
style[nvalue] = INTEGER;
int tmp;
@ -89,6 +99,12 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (border) comm_border = nvalue;
// store current atom style
int n = strlen(atom->atom_style) + 1;
astyle = new char[n];
strcpy(astyle,atom->atom_style);
// perform initial allocation of atom-based array
// register with Atom class
@ -117,6 +133,10 @@ FixPropertyAtom::~FixPropertyAtom()
atom->molecule_flag = 0;
memory->destroy(atom->molecule);
atom->molecule = NULL;
} else if (style[m] == CHARGE) {
atom->q_flag = 0;
memory->destroy(atom->q);
atom->q = NULL;
} else if (style[m] == INTEGER) {
atom->remove_custom(0,index[m]);
} else if (style[m] == DOUBLE) {
@ -126,6 +146,7 @@ FixPropertyAtom::~FixPropertyAtom()
delete [] style;
delete [] index;
delete [] astyle;
}
/* ---------------------------------------------------------------------- */
@ -140,14 +161,11 @@ int FixPropertyAtom::setmask()
void FixPropertyAtom::init()
{
// check again if atom style already defines molecule vector
// based on molecular setting
// this could happen if script changed atom_style
// after this fix was already in place
// error if atom style has changed since fix was defined
// don't allow this b/c user could change to style that defines molecule,q
if (molecule_flag && atom->molecular)
error->all(FLERR,"Fix property/atom mol when atom_style "
"already has molecule attribute");
if (strcmp(astyle,atom->atom_style) != 0)
error->all(FLERR,"Atom style was redefined after using fix property/atom");
}
/* ----------------------------------------------------------------------
@ -201,6 +219,7 @@ 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] == CHARGE) atom->q[m] = atof(values[j+1]);
else if (style[j] == INTEGER)
atom->ivector[index[j]][m] = atoi(values[j+1]);
else if (style[j] == DOUBLE)
@ -251,32 +270,36 @@ void FixPropertyAtom::write_data_section_pack(int mth, double **buf)
int *tag = atom->tag;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) buf[i][0] = tag[i];
for (i = 0; i < nlocal; i++) buf[i][0] = ubuf(tag[i]).d;
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];
for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(molecule[i]).d;
} else if (style[m] == CHARGE) {
double *q = atom->q;
for (i = 0; i < nlocal; i++) buf[i][mp1] = q[i];
} else if (style[m] == INTEGER) {
int *vec = atom->ivector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
int *ivec = atom->ivector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = ubuf(ivec[i]).d;
} else if (style[m] == DOUBLE) {
double *vec = atom->dvector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = vec[i];
double *dvec = atom->dvector[index[m]];
for (i = 0; i < nlocal; i++) buf[i][mp1] = dvec[i];
}
}
}
/* ----------------------------------------------------------------------
write section keyword for Mth data section to file
use MOLECULE if that is only field, else use fix ID
use Molecules or Charges 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,"\nMolecules\n\n");
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
else fprintf(fp,"\n%s\n\n",id);
}
@ -293,10 +316,10 @@ void FixPropertyAtom::write_data_section(int mth, FILE *fp,
int m;
for (int i = 0; i < n; i++) {
fprintf(fp,TAGINT_FORMAT,static_cast<int> (buf[i][0]));
fprintf(fp,"%d",(int) ubuf(buf[i][0]).i);
for (m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE || style[m] == INTEGER)
fprintf(fp," " TAGINT_FORMAT,static_cast<int> (buf[i][m+1]));
fprintf(fp," %d",(int) ubuf(buf[i][m+1]).i);
else fprintf(fp," %g",buf[i][m+1]);
}
fprintf(fp,"\n");
@ -312,6 +335,7 @@ double FixPropertyAtom::memory_usage()
double bytes = 0.0;
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(int);
else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double);
else if (style[m] == INTEGER) bytes = atom->nmax * sizeof(int);
else if (style[m] == DOUBLE) bytes = atom->nmax * sizeof(double);
}
@ -332,6 +356,10 @@ void FixPropertyAtom::grow_arrays(int nmax)
memory->grow(atom->molecule,nmax,"atom:molecule");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (style[m] == CHARGE) {
memory->grow(atom->q,nmax,"atom:q");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->q[nmax_old],0,nbytes);
} else if (style[m] == INTEGER) {
memory->grow(atom->ivector[index[m]],nmax,"atom:ivector");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
@ -355,6 +383,8 @@ void FixPropertyAtom::copy_arrays(int i, int j, int delflag)
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
atom->molecule[j] = atom->molecule[i];
else if (style[m] == CHARGE)
atom->q[j] = atom->q[i];
else if (style[m] == INTEGER)
atom->ivector[index[m]][j] = atom->ivector[index[m]][i];
else if (style[m] == DOUBLE)
@ -376,13 +406,19 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
int *molecule = atom->molecule;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = molecule[j];
buf[m++] = ubuf(molecule[j]).d;
}
} else if (style[k] == CHARGE) {
double *q = atom->q;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = q[j];
}
} else if (style[k] == INTEGER) {
int *ivector = atom->ivector[index[k]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ivector[j];
buf[m++] = ubuf(ivector[j]).i;
}
} else if (style[k] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
@ -410,12 +446,17 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
int *molecule = atom->molecule;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = static_cast<int> (buf[m++]);
molecule[i] = (int) ubuf(buf[m++]).i;
} else if (style[k] == CHARGE) {
double *q = atom->q;
last = first + n;
for (i = first; i < last; i++)
q[i] = buf[m++];
} 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++]);
ivector[i] = (int) ubuf(buf[m++]).i;
} else if (style[k] == DOUBLE) {
double *dvector = atom->dvector[index[k]];
last = first + n;
@ -434,8 +475,9 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
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->ivector[index[m]][i];
if (style[m] == MOLECULE) buf[m] = ubuf(atom->molecule[i]).d;
else if (style[m] == CHARGE) buf[m] = atom->q[i];
else if (style[m] == INTEGER) buf[m] = ubuf(atom->ivector[index[m]][i]).d;
else if (style[m] == DOUBLE) buf[m] = atom->dvector[index[m]][i];
}
return nvalue;
@ -449,9 +491,11 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE)
atom->molecule[nlocal] = static_cast<int> (buf[m]);
atom->molecule[nlocal] = (int) ubuf(buf[m]).i;
else if (style[m] == CHARGE)
atom->q[nlocal] = buf[m];
else if (style[m] == INTEGER)
atom->ivector[index[m]][nlocal] = static_cast<int> (buf[m]);
atom->ivector[index[m]][nlocal] = (int) ubuf(buf[m]).i;
else if (style[m] == DOUBLE)
atom->dvector[index[m]][nlocal] = buf[m];
}
@ -468,8 +512,9 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
int m = 1;
for (int j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) buf[m++] = atom->molecule[i];
else if (style[j] == INTEGER) buf[m++] = atom->ivector[index[m]][i];
if (style[j] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (style[j] == CHARGE) buf[m++] = atom->q[i];
else if (style[j] == INTEGER) buf[m++] = ubuf(atom->ivector[index[m]][i]).d;
else if (style[j] == DOUBLE) buf[m++] = atom->dvector[index[m]][i];
}
@ -492,9 +537,11 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
for (int i = 0; i < nvalue; i++) {
if (style[i] == MOLECULE)
atom->molecule[nlocal] = static_cast<int> (extra[nlocal][m++]);
atom->molecule[nlocal] = (int) ubuf(extra[nlocal][m++]).i;
else if (style[i] == CHARGE)
atom->q[nlocal] = extra[nlocal][m++];
else if (style[i] == INTEGER)
atom->ivector[index[m]][nlocal] = static_cast<int> (extra[nlocal][m++]);
atom->ivector[index[m]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
else if (style[i] == DOUBLE)
atom->dvector[index[m]][nlocal] = extra[nlocal][m++];
}

17
src/fix_property_atom.h
View File

@ -51,9 +51,24 @@ class FixPropertyAtom : public Fix {
double memory_usage();
private:
int nvalue,border,molecule_flag;
int nvalue,border;
int molecule_flag,q_flag;
int *style,*index;
char *astyle;
int nmax_old; // length of peratom arrays the last time they grew
// union data struct for packing 32-bit and 64-bit ints into double bufs
// see atom_vec.h for documentation
union ubuf {
double d;
int64_t i;
ubuf(double arg) : d(arg) {}
ubuf(int64_t arg) : i(arg) {}
ubuf(int arg) : i(arg) {}
};
};
}