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

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# Conflicts:
#	doc/Manual.html
#	doc/Manual.txt
#	doc/info.txt
#	src/atom.cpp
#	src/info.cpp
This commit is contained in:
Axel Kohlmeyer
2015-07-17 06:56:56 -04:00
parent 622497a3e9 21727b3892
commit 6bd45c6681
37 changed files with 1677 additions and 163 deletions
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29
src/atom.cpp
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@ -1414,20 +1414,27 @@ int Atom::shape_consistency(int itype,
void Atom::add_molecule(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal molecule command");
if (find_molecule(arg[0]) >= 0)
if (narg < 1) error->all(FLERR,"Illegal molecule command");
if (find_molecule(arg[0]) >= 0)
error->all(FLERR,"Reuse of molecule template ID");
int nprevious = nmolecule;
nmolecule += narg-1;
molecules = (Molecule **)
memory->srealloc(molecules,nmolecule*sizeof(Molecule *),"atom::molecules");
// may over-allocate if not all args are mol files, but OK for srealloc
for (int i = 1; i < narg; i++) {
molecules[nprevious] = new Molecule(lmp,arg[0],arg[i]);
if (i == 1) molecules[nprevious]->nset = narg-1;
else molecules[nprevious]->nset = 0;
nprevious++;
molecules = (Molecule **)
memory->srealloc(molecules,(nmolecule+narg-1)*sizeof(Molecule *),
"atom::molecules");
// 1st molecule in set stores nset = # of mols, others store nset = 0
int ifile = 1;
while (1) {
molecules[nmolecule] = new Molecule(lmp,narg,arg,ifile);
molecules[nmolecule]->nset = 0;
molecules[nmolecule-ifile+1]->nset++;
nmolecule++;
if (molecules[nmolecule-1]->last) break;
ifile++;
}
}