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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@622 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-06-20 13:17:59 +00:00
parent bde732bced
commit aaed6ebc33
131 changed files with 4277 additions and 2222 deletions
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105
src/MOLECULE/atom_vec_molecular.cpp
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@ -146,75 +146,9 @@ void AtomVecMolecular::grow(int n)
/* ---------------------------------------------------------------------- */
void AtomVecMolecular::reset_ptrs()
void AtomVecMolecular::reset_special()
{
tag = atom->tag;
type = atom->type;
mask = atom->mask;
image = atom->image;
x = atom->x;
v = atom->v;
f = atom->f;
molecule = atom->molecule;
nspecial = atom->nspecial;
special = atom->special;
num_bond = atom->num_bond;
bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
num_angle = atom->num_angle;
angle_type = atom->angle_type;
angle_atom1 = atom->angle_atom1;
angle_atom2 = atom->angle_atom2;
angle_atom3 = atom->angle_atom3;
num_dihedral = atom->num_dihedral;
dihedral_type = atom->dihedral_type;
dihedral_atom1 = atom->dihedral_atom1;
dihedral_atom2 = atom->dihedral_atom2;
dihedral_atom3 = atom->dihedral_atom3;
dihedral_atom4 = atom->dihedral_atom4;
num_improper = atom->num_improper;
improper_type = atom->improper_type;
improper_atom1 = atom->improper_atom1;
improper_atom2 = atom->improper_atom2;
improper_atom3 = atom->improper_atom3;
improper_atom4 = atom->improper_atom4;
}
/* ----------------------------------------------------------------------
zero auxiliary data for owned atom I
data in copy(), not including tag,type,mask,image,x,v
------------------------------------------------------------------------- */
void AtomVecMolecular::zero_owned(int i)
{
molecule[i] = 0;
num_bond[i] = 0;
num_angle[i] = 0;
num_dihedral[i] = 0;
num_improper[i] = 0;
nspecial[i][0] = 0;
nspecial[i][1] = 0;
nspecial[i][2] = 0;
}
/* ----------------------------------------------------------------------
zero auxiliary data for n ghost atoms
data in border(), not including x,tag,type,mask
grow() is here since zero_ghost called first in hybrid::unpack_border()
------------------------------------------------------------------------- */
void AtomVecMolecular::zero_ghost(int n, int first)
{
int last = first + n;
for (int i = first; i < last; i++) {
if (i == nmax) atom->avec->grow(0);
molecule[i] = 0;
}
}
/* ---------------------------------------------------------------------- */
@ -601,18 +535,6 @@ int AtomVecMolecular::size_restart()
return n;
}
/* ----------------------------------------------------------------------
size of restart data for atom I
do not include extra data stored by fixes, included by caller
------------------------------------------------------------------------- */
int AtomVecMolecular::size_restart_one(int i)
{
int n = 16 + 2*num_bond[i] + 4*num_angle[i] +
5*num_dihedral[i] + 5*num_improper[i];
return n;
}
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
@ -755,7 +677,7 @@ int AtomVecMolecular::unpack_restart(double *buf)
set other values to defaults
------------------------------------------------------------------------- */
void AtomVecMolecular::create_atom(int itype, double *coord, int ihybrid)
void AtomVecMolecular::create_atom(int itype, double *coord)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -785,8 +707,7 @@ void AtomVecMolecular::create_atom(int itype, double *coord, int ihybrid)
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecMolecular::data_atom(double *coord, int imagetmp, char **values,
int ihybrid)
void AtomVecMolecular::data_atom(double *coord, int imagetmp, char **values)
{
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
@ -819,6 +740,26 @@ void AtomVecMolecular::data_atom(double *coord, int imagetmp, char **values,
atom->nlocal++;
}
/* ----------------------------------------------------------------------
unpack hybrid quantities from one line in Atoms section of data file
initialize other atom quantities for this sub-style
------------------------------------------------------------------------- */
int AtomVecMolecular::data_atom_hybrid(int nlocal, char **values)
{
molecule[nlocal] = atoi(values[0]);
v[nlocal][0] = 0.0;
v[nlocal][1] = 0.0;
v[nlocal][2] = 0.0;
num_bond[nlocal] = 0;
num_angle[nlocal] = 0;
num_dihedral[nlocal] = 0;
num_improper[nlocal] = 0;
return 1;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */