Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/neigh_bond.cpp
2041f82bc4bcefficient_neuronet

Last Change
Raw File

neigh_bond.cpp
View Options

/* ----------------------------------------------------------------------
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 "neighbor.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#define BONDDELTA 10000
/* ---------------------------------------------------------------------- */
void Neighbor::bond_all()
{
int i,m,atom1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *tag = atom->tag;
int newton_bond = force->newton_bond;
nbondlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_bond[i]; m++) {
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
char str[128];
sprintf(str,"Bond atoms %d %d missing on proc %d at step %d",
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(str);
}
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::bond_partial()
{
int i,m,atom1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
int **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *tag = atom->tag;
int newton_bond = force->newton_bond;
nbondlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_bond[i]; m++) {
if (bond_type[i][m] <= 0) continue;
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
char str[128];
sprintf(str,"Bond atoms %d %d missing on proc %d at step %d",
tag[i],bond_atom[i][m],me,update->ntimestep);
error->one(str);
}
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[i][m];
nbondlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::angle_all()
{
int i,m,atom1,atom2,atom3;
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
nanglelist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_angle[i]; m++) {
atom1 = atom->map(angle_atom1[i][m]);
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,"Angle atoms %d %d %d missing on proc %d at step %d",
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::angle_partial()
{
int i,m,atom1,atom2,atom3;
int nlocal = atom->nlocal;
int *num_angle = atom->num_angle;
int **angle_atom1 = atom->angle_atom1;
int **angle_atom2 = atom->angle_atom2;
int **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int newton_bond = force->newton_bond;
nanglelist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_angle[i]; m++) {
if (angle_type[i][m] <= 0) continue;
atom1 = atom->map(angle_atom1[i][m]);
atom2 = atom->map(angle_atom2[i][m]);
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
char str[128];
sprintf(str,"Angle atoms %d %d %d missing on proc %d at step %d",
angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
anglelist[nanglelist][2] = atom3;
anglelist[nanglelist][3] = angle_type[i][m];
nanglelist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::dihedral_all()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_dihedral[i]; m++) {
atom1 = atom->map(dihedral_atom1[i][m]);
atom2 = atom->map(dihedral_atom2[i][m]);
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Dihedral atoms %d %d %d %d missing on proc %d at step %d",
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
dihedrallist =
memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::dihedral_partial()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_dihedral = atom->num_dihedral;
int **dihedral_atom1 = atom->dihedral_atom1;
int **dihedral_atom2 = atom->dihedral_atom2;
int **dihedral_atom3 = atom->dihedral_atom3;
int **dihedral_atom4 = atom->dihedral_atom4;
int **dihedral_type = atom->dihedral_type;
int newton_bond = force->newton_bond;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_dihedral[i]; m++) {
if (dihedral_type[i][m] <= 0) continue;
atom1 = atom->map(dihedral_atom1[i][m]);
atom2 = atom->map(dihedral_atom2[i][m]);
atom3 = atom->map(dihedral_atom3[i][m]);
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Dihedral atoms %d %d %d %d missing on proc %d at step %d",
dihedral_atom1[i][m],dihedral_atom2[i][m],
dihedral_atom3[i][m],dihedral_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
dihedrallist =
memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
ndihedrallist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::improper_all()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
nimproperlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_improper[i]; m++) {
atom1 = atom->map(improper_atom1[i][m]);
atom2 = atom->map(improper_atom2[i][m]);
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Improper atoms %d %d %d %d missing on proc %d at step %d",
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
improperlist =
memory->grow_2d_int_array(improperlist,maximproper,5,
"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
}
}
/* ---------------------------------------------------------------------- */
void Neighbor::improper_partial()
{
int i,m,atom1,atom2,atom3,atom4;
int nlocal = atom->nlocal;
int *num_improper = atom->num_improper;
int **improper_atom1 = atom->improper_atom1;
int **improper_atom2 = atom->improper_atom2;
int **improper_atom3 = atom->improper_atom3;
int **improper_atom4 = atom->improper_atom4;
int **improper_type = atom->improper_type;
int newton_bond = force->newton_bond;
nimproperlist = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < num_improper[i]; m++) {
if (improper_type[i][m] <= 0) continue;
atom1 = atom->map(improper_atom1[i][m]);
atom2 = atom->map(improper_atom2[i][m]);
atom3 = atom->map(improper_atom3[i][m]);
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
char str[128];
sprintf(str,"Improper atoms %d %d %d %d missing on proc %d at step %d",
improper_atom1[i][m],improper_atom2[i][m],
improper_atom3[i][m],improper_atom4[i][m],
me,update->ntimestep);
error->one(str);
}
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
improperlist =
memory->grow_2d_int_array(improperlist,maximproper,5,
"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
improperlist[nimproperlist][2] = atom3;
improperlist[nimproperlist][3] = atom4;
improperlist[nimproperlist][4] = improper_type[i][m];
nimproperlist++;
}
}
}
c4science · Help