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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11300 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-22 18:33:55 +00:00
parent b7eb7f3301
commit 41c5be7a8e
9 changed files with 54 additions and 34 deletions
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29
src/atom.cpp
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@ -42,7 +42,6 @@ using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 1
#define DELTA_MOLECULE 1
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
#define CUDA_CHUNK 3000
@ -117,7 +116,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// user-defined molecules
nmolecule = maxmol = 0;
nmolecule = 0;
molecules = NULL;
// custom atom arrays
@ -1293,27 +1292,30 @@ int Atom::shape_consistency(int itype,
}
/* ----------------------------------------------------------------------
add a new molecule template
add a new molecule template = set of molecules
------------------------------------------------------------------------- */
void Atom::add_molecule(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal molecule command");
if (find_molecule(arg[0]) >= 0) error->all(FLERR,"Reuse of molecule ID");
if (narg < 2) error->all(FLERR,"Illegal molecule command");
if (find_molecule(arg[0]) >= 0)
error->all(FLERR,"Reuse of molecule template ID");
// extend molecule list if necessary
int nprevious = nmolecule;
nmolecule += narg-1;
molecules = (Molecule **)
memory->srealloc(molecules,nmolecule*sizeof(Molecule *),"atom::molecules");
if (nmolecule == maxmol) {
maxmol += DELTA_MOLECULE;
molecules = (Molecule **)
memory->srealloc(molecules,maxmol*sizeof(Molecule *),"atom::molecules");
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[nmolecule++] = new Molecule(lmp,narg,arg);
}
/* ----------------------------------------------------------------------
find which molecule has molecule ID
find first molecule in set with template ID
return -1 if does not exist
------------------------------------------------------------------------- */
@ -1328,6 +1330,7 @@ int Atom::find_molecule(char *id)
/* ----------------------------------------------------------------------
add info to current atom ilocal from molecule template onemol and its iatom
offset = atom ID preceeding IDs of atoms in this molecule
called by fixes and commands that add molecules
------------------------------------------------------------------------- */
void Atom::add_molecule_atom(Molecule *onemol, int iatom,