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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11328 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-01-25 22:46:08 +00:00
parent 2f6a46a2be
commit 0ce16af78b
63 changed files with 2943 additions and 798 deletions
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81
src/create_atoms.cpp
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@ -160,11 +160,12 @@ void CreateAtoms::command(int narg, char **arg)
error->all(FLERR,"Create_atoms molecule must have coordinates");
if (onemol->typeflag == 0)
error->all(FLERR,"Create_atoms molecule must have atom types");
if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
if (ntype+onemol->ntypes <= 0 || ntype+onemol->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in create_atoms mol command");
if (onemol->tag_require && !atom->tag_enable)
error->all(FLERR,
"Create_atoms molecule has atom IDs, but system does not");
onemol->check_attributes(0);
// create_atoms uses geoemetric center of molecule for insertion
@ -291,6 +292,19 @@ void CreateAtoms::command(int narg, char **arg)
int molcreate = (atom->nlocal - nlocal_previous) / onemol->natoms;
// for atom style template systems, increment total bonds,angles,etc
if (atom->molecular == 2) {
bigint nmolme = molcreate;
bigint nmoltotal;
MPI_Allreduce(&nmolme,&nmoltotal,1,MPI_LMP_BIGINT,MPI_SUM,world);
atom->nbonds += nmoltotal * onemol->nbonds;
atom->nangles += nmoltotal * onemol->nangles;
atom->ndihedrals += nmoltotal * onemol->ndihedrals;
atom->nimpropers += nmoltotal * onemol->nimpropers;
}
// if atom style template
// maxmol = max molecule ID across all procs, for previous atoms
// moloffset = max molecule ID for all molecules owned by previous procs
// including molecules existing before this creation
@ -332,38 +346,44 @@ void CreateAtoms::command(int narg, char **arg)
tagint **improper_atom4 = atom->improper_atom4;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int molecular = atom->molecular;
int ilocal = nlocal_previous;
for (int i = 0; i < molcreate; i++) {
if (tag) offset = tag[ilocal]-1;
for (int m = 0; m < natoms; m++) {
if (molecule) molecule[ilocal] = moloffset + i+1;
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
if (onemol->angleflag)
for (int j = 0; j < num_angle[ilocal]; j++) {
angle_atom1[ilocal][j] += offset;
angle_atom2[ilocal][j] += offset;
angle_atom3[ilocal][j] += offset;
}
if (onemol->dihedralflag)
for (int j = 0; j < num_dihedral[ilocal]; j++) {
dihedral_atom1[ilocal][j] += offset;
dihedral_atom2[ilocal][j] += offset;
dihedral_atom3[ilocal][j] += offset;
dihedral_atom4[ilocal][j] += offset;
}
if (onemol->improperflag)
for (int j = 0; j < num_improper[ilocal]; j++) {
improper_atom1[ilocal][j] += offset;
improper_atom2[ilocal][j] += offset;
improper_atom3[ilocal][j] += offset;
improper_atom4[ilocal][j] += offset;
}
if (onemol->specialflag)
for (int j = 0; j < nspecial[ilocal][2]; j++)
special[ilocal][j] += offset;
if (molecular) molecule[ilocal] = moloffset + i+1;
if (molecular == 2) {
atom->molindex[ilocal] = 0;
atom->molatom[ilocal] = m;
} else if (molecular) {
if (onemol->bondflag)
for (int j = 0; j < num_bond[ilocal]; j++)
bond_atom[ilocal][j] += offset;
if (onemol->angleflag)
for (int j = 0; j < num_angle[ilocal]; j++) {
angle_atom1[ilocal][j] += offset;
angle_atom2[ilocal][j] += offset;
angle_atom3[ilocal][j] += offset;
}
if (onemol->dihedralflag)
for (int j = 0; j < num_dihedral[ilocal]; j++) {
dihedral_atom1[ilocal][j] += offset;
dihedral_atom2[ilocal][j] += offset;
dihedral_atom3[ilocal][j] += offset;
dihedral_atom4[ilocal][j] += offset;
}
if (onemol->improperflag)
for (int j = 0; j < num_improper[ilocal]; j++) {
improper_atom1[ilocal][j] += offset;
improper_atom2[ilocal][j] += offset;
improper_atom3[ilocal][j] += offset;
improper_atom4[ilocal][j] += offset;
}
if (onemol->specialflag)
for (int j = 0; j < nspecial[ilocal][2]; j++)
special[ilocal][j] += offset;
}
ilocal++;
}
}
@ -400,11 +420,12 @@ void CreateAtoms::command(int narg, char **arg)
}
// for MOLECULE mode:
// create special bond lists for molecular systems
// create special bond lists for molecular systems,
// but not for atom style template
// only if onemol added bonds but not special info
if (mode == MOLECULE) {
if (atom->molecular && onemol->bondflag && !onemol->specialflag) {
if (atom->molecular == 1 && onemol->bondflag && !onemol->specialflag) {
Special special(lmp);
special.build();
}