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Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

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# Resolved Conflicts:
#	doc/Manual.html
#	doc/Manual.txt
#	src/USER-SMTBQ/pair_smtbq.cpp
This commit is contained in:
Axel Kohlmeyer
2016-01-12 07:02:29 -05:00
parent f5cf3008dd 05240f9467
commit 607c4aa2a3
48 changed files with 1769 additions and 321 deletions
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64
src/atom.cpp
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@ -1318,45 +1318,51 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
tagint id_offset)
{
int j,m,tagdata,ninteger,ndouble;
int j,m,nvalues,tagdata,ninteger,ndouble;
int maxint = 0;
int maxdouble = 0;
char **ivalues = NULL;
char **dvalues = NULL;
int *ivalues = NULL;
double *dvalues = NULL;
// loop over lines of body data
// tokenize the lines into ivalues and dvalues
// if I own atom tag, unpack its values
// if I own atom tag, tokenize lines into ivalues/dvalues, call data_body()
// else skip values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f")) + id_offset;
ninteger = atoi(strtok(NULL," \t\n\r\f"));
ndouble = atoi(strtok(NULL," \t\n\r\f"));
if (ninteger > maxint) {
delete [] ivalues;
maxint = ninteger;
ivalues = new char*[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
maxdouble = ndouble;
dvalues = new char*[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = strtok(NULL," \t\n\r\f");
for (j = 0; j < ndouble; j++)
dvalues[j] = strtok(NULL," \t\n\r\f");
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
if ((m = map(tagdata)) >= 0)
ninteger = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
ndouble = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
delete [] ivalues;
maxint = ninteger;
ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
for (j = 0; j < ndouble; j++)
dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
strtok(NULL," \t\n\r\f");
}
}
delete [] ivalues;
@ -1588,7 +1594,13 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom,
else if (rmass_flag)
rmass[ilocal] = 4.0*MY_PI/3.0 *
radius[ilocal]*radius[ilocal]*radius[ilocal];
if (onemol->bodyflag) {
body[ilocal] = 0; // as if a body read from data file
onemol->avec_body->data_body(ilocal,onemol->nibody,onemol->ndbody,
onemol->ibodyparams,onemol->dbodyparams);
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
if (molecular != 1) return;
// add bond topology info