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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-05-07 16:15:31 +00:00
parent 4ab16d5388
commit 4c9bba90f1
34 changed files with 146 additions and 215 deletions
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53
src/read_data.cpp
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@ -206,9 +206,9 @@ void ReadData::command(int narg, char **arg)
domain->box_exist = 1;
update->ntimestep = 0;
// insure extra settings are applied before grow(),
// even if no topology in file
// if topology is in file, realloc and another grow() is done below
// apply extra settings before grow(), even if no topology in file
// deallocate() insures new settings are used for topology arrays
// if per-atom topology is in file, another grow() is done below
atom->bond_per_atom = atom->extra_bond_per_atom;
atom->angle_per_atom = atom->extra_angle_per_atom;
@ -220,6 +220,7 @@ void ReadData::command(int narg, char **arg)
else n = static_cast<int> (LB_FACTOR * atom->natoms / comm->nprocs);
atom->allocate_type_arrays();
atom->deallocate_topology();
atom->avec->grow(n);
domain->print_box(" ");
@ -497,49 +498,11 @@ void ReadData::command(int narg, char **arg)
firstpass = 0;
// reallocate bond,angle,diehdral,improper arrays via grow()
// use new bond,angle,dihedral,improper per-atom values from 1st pass
// should leave other atom arrays unchanged, since already nmax in length
// if bonds/etc not in data file, initialize per-atom size
// with extra settings before grow() of these topology arrays
if (bondflag) {
memory->destroy(atom->bond_type);
memory->destroy(atom->bond_atom);
atom->bond_type = NULL;
atom->bond_atom = NULL;
}
if (angleflag) {
memory->destroy(atom->angle_type);
memory->destroy(atom->angle_atom1);
memory->destroy(atom->angle_atom2);
memory->destroy(atom->angle_atom3);
atom->angle_type = NULL;
atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
}
if (dihedralflag) {
memory->destroy(atom->dihedral_type);
memory->destroy(atom->dihedral_atom1);
memory->destroy(atom->dihedral_atom2);
memory->destroy(atom->dihedral_atom3);
memory->destroy(atom->dihedral_atom4);
atom->dihedral_type = NULL;
atom->dihedral_atom1 = atom->dihedral_atom2 =
atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
}
if (improperflag) {
memory->destroy(atom->improper_type);
memory->destroy(atom->improper_atom1);
memory->destroy(atom->improper_atom2);
memory->destroy(atom->improper_atom3);
memory->destroy(atom->improper_atom4);
atom->improper_type = NULL;
atom->improper_atom1 = atom->improper_atom2 =
atom->improper_atom3 = atom->improper_atom4 = NULL;
}
// will use new bond,angle,dihedral,improper per-atom values from 1st pass
// will also observe extra settings even if bond/etc topology not in file
// leaves other atom arrays unchanged, since already nmax in length
atom->deallocate_topology();
atom->avec->grow(atom->nmax);
}