555 lines
18 KiB
C++
555 lines
18 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "neighbor.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "domain.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define BONDDELTA 10000
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// bondlist, anglelist, dihedrallist, improperlist
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// no longer store atom->map() of the bond partners
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// instead store domain->closest_image() of the bond partners of atom I
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// this enables distances between list atoms to be calculated
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// w/out invoking domain->minimium_image(), e.g. in bond->compute()
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/* ---------------------------------------------------------------------- */
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void Neighbor::bond_all()
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{
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int i,m,atom1;
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int nlocal = atom->nlocal;
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int *num_bond = atom->num_bond;
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int **bond_atom = atom->bond_atom;
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int **bond_type = atom->bond_type;
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int *tag = atom->tag;
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int newton_bond = force->newton_bond;
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nbondlist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_bond[i]; m++) {
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atom1 = atom->map(bond_atom[i][m]);
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if (atom1 == -1) {
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char str[128];
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sprintf(str,
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"Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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tag[i],bond_atom[i][m],me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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if (newton_bond || i < atom1) {
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if (nbondlist == maxbond) {
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maxbond += BONDDELTA;
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memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
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}
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bondlist[nbondlist][0] = i;
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bondlist[nbondlist][1] = atom1;
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bondlist[nbondlist][2] = bond_type[i][m];
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nbondlist++;
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}
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}
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if (cluster_check) bond_check();
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::bond_partial()
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{
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int i,m,atom1;
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int nlocal = atom->nlocal;
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int *num_bond = atom->num_bond;
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int **bond_atom = atom->bond_atom;
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int **bond_type = atom->bond_type;
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int *tag = atom->tag;
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int newton_bond = force->newton_bond;
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nbondlist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_bond[i]; m++) {
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if (bond_type[i][m] <= 0) continue;
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atom1 = atom->map(bond_atom[i][m]);
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if (atom1 == -1) {
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char str[128];
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sprintf(str,
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"Bond atoms %d %d missing on proc %d at step " BIGINT_FORMAT,
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tag[i],bond_atom[i][m],me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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if (newton_bond || i < atom1) {
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if (nbondlist == maxbond) {
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maxbond += BONDDELTA;
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memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
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}
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bondlist[nbondlist][0] = i;
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bondlist[nbondlist][1] = atom1;
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bondlist[nbondlist][2] = bond_type[i][m];
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nbondlist++;
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}
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}
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if (cluster_check) bond_check();
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::bond_check()
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{
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int i,j;
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double dx,dy,dz,dxstart,dystart,dzstart;
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double **x = atom->x;
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int flag = 0;
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for (int m = 0; m < nbondlist; m++) {
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i = bondlist[m][0];
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j = bondlist[m][1];
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dxstart = dx = x[i][0] - x[j][0];
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dystart = dy = x[i][1] - x[j][1];
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dzstart = dz = x[i][2] - x[j][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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}
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int flag_all;
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MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
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if (flag_all) error->all(FLERR,"Bond extent > half of periodic box length");
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::angle_all()
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{
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int i,m,atom1,atom2,atom3;
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int nlocal = atom->nlocal;
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int *num_angle = atom->num_angle;
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int **angle_atom1 = atom->angle_atom1;
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int **angle_atom2 = atom->angle_atom2;
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int **angle_atom3 = atom->angle_atom3;
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int **angle_type = atom->angle_type;
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int newton_bond = force->newton_bond;
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nanglelist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_angle[i]; m++) {
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atom1 = atom->map(angle_atom1[i][m]);
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atom2 = atom->map(angle_atom2[i][m]);
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atom3 = atom->map(angle_atom3[i][m]);
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if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
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char str[128];
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sprintf(str,
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"Angle atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
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me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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atom2 = domain->closest_image(i,atom2);
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atom3 = domain->closest_image(i,atom3);
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if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
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if (nanglelist == maxangle) {
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maxangle += BONDDELTA;
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memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
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}
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anglelist[nanglelist][0] = atom1;
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anglelist[nanglelist][1] = atom2;
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anglelist[nanglelist][2] = atom3;
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anglelist[nanglelist][3] = angle_type[i][m];
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nanglelist++;
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}
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}
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if (cluster_check) angle_check();
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::angle_partial()
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{
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int i,m,atom1,atom2,atom3;
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int nlocal = atom->nlocal;
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int *num_angle = atom->num_angle;
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int **angle_atom1 = atom->angle_atom1;
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int **angle_atom2 = atom->angle_atom2;
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int **angle_atom3 = atom->angle_atom3;
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int **angle_type = atom->angle_type;
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int newton_bond = force->newton_bond;
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nanglelist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_angle[i]; m++) {
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if (angle_type[i][m] <= 0) continue;
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atom1 = atom->map(angle_atom1[i][m]);
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atom2 = atom->map(angle_atom2[i][m]);
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atom3 = atom->map(angle_atom3[i][m]);
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if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
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char str[128];
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sprintf(str,
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"Angle atoms %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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angle_atom1[i][m],angle_atom2[i][m],angle_atom3[i][m],
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me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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atom2 = domain->closest_image(i,atom2);
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atom3 = domain->closest_image(i,atom3);
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if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
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if (nanglelist == maxangle) {
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maxangle += BONDDELTA;
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memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
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}
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anglelist[nanglelist][0] = atom1;
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anglelist[nanglelist][1] = atom2;
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anglelist[nanglelist][2] = atom3;
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anglelist[nanglelist][3] = angle_type[i][m];
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nanglelist++;
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}
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}
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if (cluster_check) angle_check();
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::angle_check()
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{
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int i,j,k;
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double dx,dy,dz,dxstart,dystart,dzstart;
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double **x = atom->x;
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int flag = 0;
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// check all 3 distances
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// in case angle potential computes any of them
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for (int m = 0; m < nanglelist; m++) {
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i = anglelist[m][0];
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j = anglelist[m][1];
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k = anglelist[m][2];
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dxstart = dx = x[i][0] - x[j][0];
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dystart = dy = x[i][1] - x[j][1];
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dzstart = dz = x[i][2] - x[j][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[i][0] - x[k][0];
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dystart = dy = x[i][1] - x[k][1];
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dzstart = dz = x[i][2] - x[k][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[j][0] - x[k][0];
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dystart = dy = x[j][1] - x[k][1];
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dzstart = dz = x[j][2] - x[k][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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}
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int flag_all;
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MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
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if (flag_all) error->all(FLERR,"Angle extent > half of periodic box length");
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::dihedral_all()
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{
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int i,m,atom1,atom2,atom3,atom4;
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int nlocal = atom->nlocal;
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_atom1 = atom->dihedral_atom1;
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int **dihedral_atom2 = atom->dihedral_atom2;
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int **dihedral_atom3 = atom->dihedral_atom3;
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int **dihedral_atom4 = atom->dihedral_atom4;
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int **dihedral_type = atom->dihedral_type;
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int newton_bond = force->newton_bond;
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ndihedrallist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_dihedral[i]; m++) {
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atom1 = atom->map(dihedral_atom1[i][m]);
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atom2 = atom->map(dihedral_atom2[i][m]);
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atom3 = atom->map(dihedral_atom3[i][m]);
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atom4 = atom->map(dihedral_atom4[i][m]);
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if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
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char str[128];
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sprintf(str,
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"Dihedral atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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dihedral_atom1[i][m],dihedral_atom2[i][m],
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dihedral_atom3[i][m],dihedral_atom4[i][m],
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me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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atom2 = domain->closest_image(i,atom2);
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atom3 = domain->closest_image(i,atom3);
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atom4 = domain->closest_image(i,atom4);
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if (newton_bond ||
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(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
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if (ndihedrallist == maxdihedral) {
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maxdihedral += BONDDELTA;
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memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
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}
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dihedrallist[ndihedrallist][0] = atom1;
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dihedrallist[ndihedrallist][1] = atom2;
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dihedrallist[ndihedrallist][2] = atom3;
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dihedrallist[ndihedrallist][3] = atom4;
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dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
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ndihedrallist++;
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}
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}
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if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::dihedral_partial()
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{
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int i,m,atom1,atom2,atom3,atom4;
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int nlocal = atom->nlocal;
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_atom1 = atom->dihedral_atom1;
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int **dihedral_atom2 = atom->dihedral_atom2;
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int **dihedral_atom3 = atom->dihedral_atom3;
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int **dihedral_atom4 = atom->dihedral_atom4;
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int **dihedral_type = atom->dihedral_type;
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int newton_bond = force->newton_bond;
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ndihedrallist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_dihedral[i]; m++) {
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if (dihedral_type[i][m] <= 0) continue;
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atom1 = atom->map(dihedral_atom1[i][m]);
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atom2 = atom->map(dihedral_atom2[i][m]);
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atom3 = atom->map(dihedral_atom3[i][m]);
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atom4 = atom->map(dihedral_atom4[i][m]);
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if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
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char str[128];
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sprintf(str,
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"Dihedral atoms %d %d %d %d missing on proc %d at step "
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BIGINT_FORMAT,
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dihedral_atom1[i][m],dihedral_atom2[i][m],
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dihedral_atom3[i][m],dihedral_atom4[i][m],
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me,update->ntimestep);
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error->one(FLERR,str);
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}
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atom1 = domain->closest_image(i,atom1);
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atom2 = domain->closest_image(i,atom2);
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atom3 = domain->closest_image(i,atom3);
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atom4 = domain->closest_image(i,atom4);
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if (newton_bond ||
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(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
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if (ndihedrallist == maxdihedral) {
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maxdihedral += BONDDELTA;
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memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
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}
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dihedrallist[ndihedrallist][0] = atom1;
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dihedrallist[ndihedrallist][1] = atom2;
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dihedrallist[ndihedrallist][2] = atom3;
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dihedrallist[ndihedrallist][3] = atom4;
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dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
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ndihedrallist++;
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}
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}
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if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::dihedral_check(int nlist, int **list)
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{
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int i,j,k,l;
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double dx,dy,dz,dxstart,dystart,dzstart;
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double **x = atom->x;
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int flag = 0;
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// check all 6 distances
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// in case dihedral/improper potential computes any of them
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for (int m = 0; m < nlist; m++) {
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i = list[m][0];
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j = list[m][1];
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k = list[m][2];
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l = list[m][3];
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dxstart = dx = x[i][0] - x[j][0];
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dystart = dy = x[i][1] - x[j][1];
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dzstart = dz = x[i][2] - x[j][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[i][0] - x[k][0];
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dystart = dy = x[i][1] - x[k][1];
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dzstart = dz = x[i][2] - x[k][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[i][0] - x[l][0];
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dystart = dy = x[i][1] - x[l][1];
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dzstart = dz = x[i][2] - x[l][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[j][0] - x[k][0];
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dystart = dy = x[j][1] - x[k][1];
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dzstart = dz = x[j][2] - x[k][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[j][0] - x[l][0];
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dystart = dy = x[j][1] - x[l][1];
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dzstart = dz = x[j][2] - x[l][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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dxstart = dx = x[k][0] - x[l][0];
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dystart = dy = x[k][1] - x[l][1];
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dzstart = dz = x[k][2] - x[l][2];
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domain->minimum_image(dx,dy,dz);
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if (dx != dxstart || dy != dystart || dz != dzstart) flag = 1;
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}
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int flag_all;
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MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
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if (flag_all)
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error->all(FLERR,"Dihedral/improper extent > half of periodic box length");
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}
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/* ---------------------------------------------------------------------- */
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void Neighbor::improper_all()
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{
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int i,m,atom1,atom2,atom3,atom4;
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int nlocal = atom->nlocal;
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int *num_improper = atom->num_improper;
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int **improper_atom1 = atom->improper_atom1;
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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 "
|
|
BIGINT_FORMAT,
|
|
improper_atom1[i][m],improper_atom2[i][m],
|
|
improper_atom3[i][m],improper_atom4[i][m],
|
|
me,update->ntimestep);
|
|
error->one(FLERR,str);
|
|
}
|
|
atom1 = domain->closest_image(i,atom1);
|
|
atom2 = domain->closest_image(i,atom2);
|
|
atom3 = domain->closest_image(i,atom3);
|
|
atom4 = domain-> closest_image(i,atom4);
|
|
if (newton_bond ||
|
|
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
|
|
if (nimproperlist == maximproper) {
|
|
maximproper += BONDDELTA;
|
|
memory->grow(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++;
|
|
}
|
|
}
|
|
|
|
if (cluster_check) dihedral_check(nimproperlist,improperlist);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
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 "
|
|
BIGINT_FORMAT,
|
|
improper_atom1[i][m],improper_atom2[i][m],
|
|
improper_atom3[i][m],improper_atom4[i][m],
|
|
me,update->ntimestep);
|
|
error->one(FLERR,str);
|
|
}
|
|
atom1 = domain->closest_image(i,atom1);
|
|
atom2 = domain->closest_image(i,atom2);
|
|
atom3 = domain->closest_image(i,atom3);
|
|
atom4 = domain->closest_image(i,atom4);
|
|
if (newton_bond ||
|
|
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
|
|
if (nimproperlist == maximproper) {
|
|
maximproper += BONDDELTA;
|
|
memory->grow(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++;
|
|
}
|
|
}
|
|
|
|
if (cluster_check) dihedral_check(nimproperlist,improperlist);
|
|
}
|