Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/USER-OPENMP/pair_dipole_cut_omp.cpp
8ba2e16c14e0lammm-master-deprecated

Last Change
Raw File

pair_dipole_cut_omp.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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 "math.h"
#include "stdlib.h"
#include "pair_dipole_cut_omp.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairDipoleCutOMP::PairDipoleCutOMP(LAMMPS *lmp) : PairOMP(lmp)
{
single_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairDipoleCutOMP::~PairDipoleCutOMP()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut_lj);
memory->destroy_2d_double_array(cut_ljsq);
memory->destroy_2d_double_array(cut_coul);
memory->destroy_2d_double_array(cut_coulsq);
memory->destroy_2d_double_array(epsilon);
memory->destroy_2d_double_array(sigma);
memory->destroy_2d_double_array(lj1);
memory->destroy_2d_double_array(lj2);
memory->destroy_2d_double_array(lj3);
memory->destroy_2d_double_array(lj4);
memory->destroy_2d_double_array(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairDipoleCutOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
// ev_setup_thr(eflag,vflag);
} else evflag = vflag_fdotr = 0;
if (evflag) {
if (eflag) {
if (force->newton_pair) return eval<1,1,1>();
else return eval<1,1,0>();
} else {
if (force->newton_pair) return eval<1,0,1>();
else return eval<1,0,0>();
}
} else {
if (force->newton_pair) return eval<0,0,1>();
else return eval<0,0,0>();
}
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairDipoleCutOMP::eval()
{
#if defined(_OPENMP)
#pragma omp parallel default(shared)
#endif
{
int i,j,ii,jj,inum,jnum,itype,jtype,tid;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fx,fy,fz;
double rsq,rinv,r2inv,r6inv,r3inv,r5inv,r7inv;
double forcecoulx,forcecouly,forcecoulz,crossx,crossy,crossz;
double tixcoul,tiycoul,tizcoul,tjxcoul,tjycoul,tjzcoul;
double fq,pdotp,pidotr,pjdotr,pre1,pre2,pre3,pre4;
double forcelj,factor_coul,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
double **x = atom->x;
double *q = atom->q;
double **mu = atom->mu;
int *type = atom->type;
double *dipole = atom->dipole;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int nthreads = comm->nthreads;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
int iifrom, iito;
double **f = loop_setup_thr(atom->f,iifrom,iito,tid,inum,nall,nthreads);
double **torque = atom->torque + tid*nall;
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j = j % nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
if (rsq < cut_coulsq[itype][jtype]) {
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
if (qtmp != 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
pre1 = qtmp*q[j]*r3inv;
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
forcecoulz += pre1*delz;
}
if (dipole[itype] > 0.0 && dipole[jtype] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
r7inv = r5inv*r2inv;
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
pre2 = 3.0*r5inv*pjdotr;
pre3 = 3.0*r5inv*pidotr;
pre4 = -1.0*r3inv;
forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
}
if (dipole[itype] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pre1 = 3.0*q[j]*r5inv * pidotr;
pre2 = q[j]*r3inv;
forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
}
if (dipole[jtype] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pre1 = 3.0*qtmp*r5inv * pjdotr;
pre2 = qtmp*r3inv;
forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
}
}
// LJ interaction
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= factor_lj * r2inv;
} else forcelj = 0.0;
// total force
fq = factor_coul*qqrd2e;
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
// force & torque accumulation
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
torque[i][0] += fq*tixcoul;
torque[i][1] += fq*tiycoul;
torque[i][2] += fq*tizcoul;
if (NEWTON_PAIR || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
torque[j][0] += fq*tjxcoul;
torque[j][1] += fq*tjycoul;
torque[j][2] += fq*tjzcoul;
}
if (EFLAG) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = qtmp*q[j]*rinv;
if (dipole[itype] > 0.0 && dipole[jtype] > 0.0)
ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
if (dipole[itype] > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv*pidotr;
if (dipole[jtype] > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv*pjdotr;
ecoul *= factor_coul*qqrd2e;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (EVFLAG) ev_tally_xyz(i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fx,fy,fz,delx,dely,delz);
}
}
}
// reduce per thread forces and torques into global force/torque arrays.
force_reduce_thr(atom->f, nall, nthreads, tid);
force_reduce_thr(atom->torque, nall, nthreads, tid);
}
ev_reduce_thr();
if (vflag_fdotr) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairDipoleCutOMP::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj");
cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq");
cut_coul = memory->create_2d_double_array(n+1,n+1,"pair:cut_coul");
cut_coulsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_coulsq");
epsilon = memory->create_2d_double_array(n+1,n+1,"pair:epsilon");
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairDipoleCutOMP::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2)
error->all("Incorrect args in pair_style command");
cut_lj_global = force->numeric(arg[0]);
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = force->numeric(arg[1]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairDipoleCutOMP::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 6)
error->all("Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(arg[2]);
double sigma_one = force->numeric(arg[3]);
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(arg[4]);
if (narg == 6) cut_coul_one = force->numeric(arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
cut_lj[i][j] = cut_lj_one;
cut_coul[i][j] = cut_coul_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairDipoleCutOMP::init_style()
{
if (!atom->q_flag || !atom->mu_flag ||
!atom->torque_flag || atom->dipole == NULL)
error->all("Pair dipole/cut requires atom attributes "
"q, mu, torque, dipole");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairDipoleCutOMP::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
}
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDipoleCutOMP::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDipoleCutOMP::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairDipoleCutOMP::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairDipoleCutOMP::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
c4science · Help