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lammps/src/atom_molecular.cpp
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atom_molecular.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom_molecular.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
/* ---------------------------------------------------------------------- */
AtomMolecular::AtomMolecular(int narg, char **arg) : Atom(narg, arg) {}
/* ---------------------------------------------------------------------- */
void AtomMolecular::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
num_angle[j] = num_angle[i];
num_dihedral[j] = num_dihedral[i];
num_improper[j] = num_improper[i];
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
for (k = 0; k < num_angle[j]; k++) {
angle_type[j][k] = angle_type[i][k];
angle_atom1[j][k] = angle_atom1[i][k];
angle_atom2[j][k] = angle_atom2[i][k];
angle_atom3[j][k] = angle_atom3[i][k];
}
for (k = 0; k < num_dihedral[j]; k++) {
dihedral_type[j][k] = dihedral_type[i][k];
dihedral_atom1[j][k] = dihedral_atom1[i][k];
dihedral_atom2[j][k] = dihedral_atom2[i][k];
dihedral_atom3[j][k] = dihedral_atom3[i][k];
dihedral_atom4[j][k] = dihedral_atom4[i][k];
}
for (k = 0; k < num_improper[j]; k++) {
improper_type[j][k] = improper_type[i][k];
improper_atom1[j][k] = improper_atom1[i][k];
improper_atom2[j][k] = improper_atom2[i][k];
improper_atom3[j][k] = improper_atom3[i][k];
improper_atom4[j][k] = improper_atom4[i][k];
}
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
modify->fix[extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::pack_comm(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
}
}
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::pack_border(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = molecule[j];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomMolecular::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomMolecular::pack_exchange(int i, double *buf)
{
int k;
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = molecule[i];
buf[m++] = num_bond[i];
for (k = 0; k < num_bond[i]; k++) {
buf[m++] = bond_type[i][k];
buf[m++] = bond_atom[i][k];
}
buf[m++] = num_angle[i];
for (k = 0; k < num_angle[i]; k++) {
buf[m++] = angle_type[i][k];
buf[m++] = angle_atom1[i][k];
buf[m++] = angle_atom2[i][k];
buf[m++] = angle_atom3[i][k];
}
buf[m++] = num_dihedral[i];
for (k = 0; k < num_dihedral[i]; k++) {
buf[m++] = dihedral_type[i][k];
buf[m++] = dihedral_atom1[i][k];
buf[m++] = dihedral_atom2[i][k];
buf[m++] = dihedral_atom3[i][k];
buf[m++] = dihedral_atom4[i][k];
}
buf[m++] = num_improper[i];
for (k = 0; k < num_improper[i]; k++) {
buf[m++] = improper_type[i][k];
buf[m++] = improper_atom1[i][k];
buf[m++] = improper_atom2[i][k];
buf[m++] = improper_atom3[i][k];
buf[m++] = improper_atom4[i][k];
}
buf[m++] = nspecial[i][0];
buf[m++] = nspecial[i][1];
buf[m++] = nspecial[i][2];
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomMolecular::unpack_exchange(double *buf)
{
int k;
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
molecule[nlocal] = static_cast<int> (buf[m++]);
num_bond[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_bond[nlocal]; k++) {
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
}
num_angle[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_angle[nlocal]; k++) {
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
}
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_dihedral[nlocal]; k++) {
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
num_improper[nlocal] = static_cast<int> (buf[m++]);
for (k = 0; k < num_improper[nlocal]; k++) {
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
}
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
for (k = 0; k < nspecial[nlocal][2]; k++)
special[nlocal][k] = static_cast<int> (buf[m++]);
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->unpack_exchange(nlocal,&buf[m]);
nlocal++;
return m;
}
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