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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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90
src/atom.cpp
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@ -74,6 +74,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
x = v = f = NULL;
molecule = NULL;
molindex = molatom = NULL;
q = NULL;
mu = NULL;
omega = angmom = torque = NULL;
@ -215,6 +216,8 @@ Atom::~Atom()
memory->destroy(erforce);
memory->destroy(molecule);
memory->destroy(molindex);
memory->destroy(molatom);
memory->destroy(nspecial);
memory->destroy(special);
@ -321,7 +324,8 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
int sflag;
avec = new_avec(style,suffix,sflag);
avec->settings(narg,arg);
avec->store_args(narg,arg);
avec->process_args(narg,arg);
avec->grow(1);
nmax = 0;
avec->reset();
@ -1336,59 +1340,53 @@ int Atom::find_molecule(char *id)
void Atom::add_molecule_atom(Molecule *onemol, int iatom,
int ilocal, tagint offset)
{
if (onemol->qflag) q[ilocal] = onemol->q[iatom];
if (onemol->radiusflag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag) rmass[ilocal] = onemol->rmass[iatom];
if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
else if (rmass_flag)
rmass[ilocal] = 4.0*MY_PI/3.0 *
radius[ilocal]*radius[ilocal]*radius[ilocal];
if (onemol->bondflag) {
num_bond[ilocal] = onemol->num_bond[iatom];
for (int i = 0; i < num_bond[ilocal]; i++) {
bond_type[ilocal][i] = onemol->bond_type[iatom][i];
bond_atom[ilocal][i] = onemol->bond_atom[iatom][i] + offset;
}
}
if (onemol->angleflag) {
num_angle[ilocal] = onemol->num_angle[iatom];
for (int i = 0; i < num_angle[ilocal]; i++) {
angle_type[ilocal][i] = onemol->angle_type[iatom][i];
angle_atom1[ilocal][i] = onemol->angle_atom1[iatom][i] + offset;
angle_atom2[ilocal][i] = onemol->angle_atom2[iatom][i] + offset;
angle_atom3[ilocal][i] = onemol->angle_atom3[iatom][i] + offset;
}
}
if (onemol->dihedralflag) {
num_dihedral[ilocal] = onemol->num_dihedral[iatom];
for (int i = 0; i < num_dihedral[ilocal]; i++) {
dihedral_type[ilocal][i] = onemol->dihedral_type[iatom][i];
dihedral_atom1[ilocal][i] = onemol->dihedral_atom1[iatom][i] + offset;
dihedral_atom2[ilocal][i] = onemol->dihedral_atom2[iatom][i] + offset;
dihedral_atom3[ilocal][i] = onemol->dihedral_atom3[iatom][i] + offset;
dihedral_atom4[ilocal][i] = onemol->dihedral_atom4[iatom][i] + offset;
}
}
if (onemol->improperflag) {
num_improper[ilocal] = onemol->num_improper[iatom];
for (int i = 0; i < num_improper[ilocal]; i++) {
improper_type[ilocal][i] = onemol->improper_type[iatom][i];
improper_atom1[ilocal][i] = onemol->improper_atom1[iatom][i] + offset;
improper_atom2[ilocal][i] = onemol->improper_atom2[iatom][i] + offset;
improper_atom3[ilocal][i] = onemol->improper_atom3[iatom][i] + offset;
improper_atom4[ilocal][i] = onemol->improper_atom4[iatom][i] + offset;
}
if (molecular != 1) return;
// add bond topology info
// for molecular atom styles, but not atom style template
if (avec->bonds_allow) num_bond[ilocal] = onemol->num_bond[iatom];
for (int i = 0; i < num_bond[ilocal]; i++) {
bond_type[ilocal][i] = onemol->bond_type[iatom][i];
bond_atom[ilocal][i] = onemol->bond_atom[iatom][i] + offset;
}
// error check against maxspecial in case user has not done one of these:
// create_box extra/special/per/atom N
// read_data extra special per atom N
// special_bonds extra N
// if explicitly used special_bonds, may not have maintained extra
if (avec->angles_allow) num_angle[ilocal] = onemol->num_angle[iatom];
for (int i = 0; i < num_angle[ilocal]; i++) {
angle_type[ilocal][i] = onemol->angle_type[iatom][i];
angle_atom1[ilocal][i] = onemol->angle_atom1[iatom][i] + offset;
angle_atom2[ilocal][i] = onemol->angle_atom2[iatom][i] + offset;
angle_atom3[ilocal][i] = onemol->angle_atom3[iatom][i] + offset;
}
if (avec->dihedrals_allow)
num_dihedral[ilocal] = onemol->num_dihedral[iatom];
for (int i = 0; i < num_dihedral[ilocal]; i++) {
dihedral_type[ilocal][i] = onemol->dihedral_type[iatom][i];
dihedral_atom1[ilocal][i] = onemol->dihedral_atom1[iatom][i] + offset;
dihedral_atom2[ilocal][i] = onemol->dihedral_atom2[iatom][i] + offset;
dihedral_atom3[ilocal][i] = onemol->dihedral_atom3[iatom][i] + offset;
dihedral_atom4[ilocal][i] = onemol->dihedral_atom4[iatom][i] + offset;
}
if (avec->impropers_allow)
num_improper[ilocal] = onemol->num_improper[iatom];
for (int i = 0; i < num_improper[ilocal]; i++) {
improper_type[ilocal][i] = onemol->improper_type[iatom][i];
improper_atom1[ilocal][i] = onemol->improper_atom1[iatom][i] + offset;
improper_atom2[ilocal][i] = onemol->improper_atom2[iatom][i] + offset;
improper_atom3[ilocal][i] = onemol->improper_atom3[iatom][i] + offset;
improper_atom4[ilocal][i] = onemol->improper_atom4[iatom][i] + offset;
}
if (onemol->specialflag) {
if (onemol->maxspecial > maxspecial)
error->one(FLERR,"Molecule file special bond counts are too large");
nspecial[ilocal][0] = onemol->nspecial[iatom][0];
nspecial[ilocal][1] = onemol->nspecial[iatom][1];
int n = nspecial[ilocal][2] = onemol->nspecial[iatom][2];