diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index 072a6c994..b88f72bac 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -1,621 +1,642 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mario Orsi (QMUL), m.orsi@qmul.ac.uk
Samuel Genheden (University of Southampton)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include "pair_lj_sf_dipole_sf.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include <string.h>
using namespace LAMMPS_NS;
+static int warn_single = 0;
+
/* ---------------------------------------------------------------------- */
PairLJSFDipoleSF::PairLJSFDipoleSF(LAMMPS *lmp) : Pair(lmp)
{
}
/* ---------------------------------------------------------------------- */
PairLJSFDipoleSF::~PairLJSFDipoleSF()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
memory->destroy(cut_coul);
memory->destroy(cut_coulsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(scale);
}
}
/* ---------------------------------------------------------------------- */
void PairLJSFDipoleSF::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fx,fy,fz;
double rsq,rinv,r2inv,r6inv,r3inv,r5inv;
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;
double presf,afac,bfac,pqfac,qpfac,forceljcut,forceljsf;
double aforcecoulx,aforcecouly,aforcecoulz;
double bforcecoulx,bforcecouly,bforcecoulz;
double rcutlj2inv, rcutcoul2inv,rcutlj6inv;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
double **mu = atom->mu;
double **torque = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
-// The global scaling parameters aren't used anymore
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; 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];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
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
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-rcutcoul2inv);
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
forcecoulz += pre1*delz;
}
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*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;
afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
aforcecoulx = pre1*delx;
aforcecouly = pre1*dely;
aforcecoulz = pre1*delz;
bfac = 1.0 - 4.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
presf = 2.0 * r2inv * pidotr * pjdotr;
bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);
forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
pre2 = 3.0 * bfac * r5inv * pjdotr;
pre3 = 3.0 * bfac * r5inv * pidotr;
pre4 = -bfac * r3inv;
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 (mu[i][3] > 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 * (1-rsq*rcutcoul2inv);
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = q[j] * r3inv * pqfac;
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 (mu[j][3] > 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 * (1-rsq*rcutcoul2inv);
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = qtmp * r3inv * qpfac;
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;
forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
rcutlj6inv * rcutlj2inv;
forcelj = factor_lj * (forceljcut - forceljsf);
} else forcelj = 0.0;
// total force
fq = factor_coul*qqrd2e*scale[itype][jtype];
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 = (1.0-sqrt(rsq/cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
ecoul *= factor_coul*qqrd2e*scale[itype][jtype];
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
rsq*rcutlj2inv+
rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[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);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(scale,n+1,n+1,"pair:scale");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2)
error->all(FLERR,"Incorrect args in pair_style command");
if (strcmp(update->unit_style,"electron") == 0)
error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles");
cut_lj_global = force->numeric(FLERR,arg[0]);
if (narg == 1) cut_coul_global = cut_lj_global;
else cut_coul_global = force->numeric(FLERR,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 PairLJSFDipoleSF::coeff(int narg, char **arg)
{
- if (narg < 4 || narg > 7)
+ if (narg < 4 || narg > 8)
error->all(FLERR,"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(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
- double scale_one = 1.0;
- if (narg >= 5) scale_one = force->numeric(FLERR,arg[4]);
-
double cut_lj_one = cut_lj_global;
double cut_coul_one = cut_coul_global;
- if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]);
- if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]);
+ double scale_one = 1.0;
+ int iarg = 4;
+
+ if ((narg > iarg) && (strcmp(arg[iarg],"scale") != 0)) {
+ cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[iarg]);
+ ++iarg;
+ }
+ if ((narg > iarg) && (strcmp(arg[iarg],"scale") != 0)) {
+ cut_coul_one = force->numeric(FLERR,arg[iarg]);
+ ++iarg;
+ }
+ if (narg > iarg) {
+ if (strcmp(arg[iarg],"scale") == 0) {
+ scale_one = force->numeric(FLERR,arg[iarg+1]);
+ iarg += 2;
+ } else error->all(FLERR,"Incorrect args for pair coefficients");
+ }
+ if (iarg != narg)
+ error->all(FLERR,"Incorrect args for pair coefficients");
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;
scale[i][j] = scale_one;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::init_style()
{
if (!atom->q_flag || !atom->mu_flag || !atom->torque_flag)
error->all(FLERR,"Pair dipole/sf requires atom attributes q, mu, torque");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJSFDipoleSF::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);
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];
scale[j][i] = scale[i][j];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::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);
fwrite(&scale[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::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);
fread(&scale[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);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul_global,sizeof(double),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJSFDipoleSF::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(&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(&mix_flag,1,MPI_INT,0,world);
}
// PairLJSFDipoleSF: calculation of force is missing (to be implemented)
double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv;
double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
double **x = atom->x;
double *q = atom->q;
double **mu = atom->mu;
+ if (!warn_single) {
+ warn_single = 1;
+ if (comm->me == 0) {
+ error->warning(FLERR,"Single method for lj/sf/dipole/sf does not compute forces");
+ }
+ }
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
fforce = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
// if (qtmp != 0.0 && q[j] != 0.0) {
// pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);
// forcecoulx += pre1*delx;
// forcecouly += pre1*dely;
// forcecoulz += pre1*delz;
// }
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
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;
bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
}
if (mu[i][3] > 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;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
}
}
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
}
double eng = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
ecoul *= factor_coul*force->qqrd2e*scale[itype][jtype];
eng += ecoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
rsq*rcutlj2inv+
rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
eng += evdwl*factor_lj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJSFDipoleSF::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"scale") == 0) return (void *) scale;
return NULL;
}
diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
index 1eadfe3d1..29250b09f 100644
--- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
@@ -1,317 +1,317 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_lj_sf_dipole_sf_omp.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "suffix.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJSFDipoleSFOMP::PairLJSFDipoleSFOMP(LAMMPS *lmp) :
PairLJSFDipoleSF(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
void PairLJSFDipoleSFOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (evflag) {
if (eflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
void PairLJSFDipoleSFOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul;
double rsq,rinv,r2inv,r6inv,r3inv,r5inv,fx,fy,fz;
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;
double presf,afac,bfac,pqfac,qpfac,forceljcut,forceljsf;
double aforcecoulx,aforcecouly,aforcecoulz;
double bforcecoulx,bforcecouly,bforcecoulz;
double rcutlj2inv, rcutcoul2inv,rcutlj6inv;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
double * const * const torque = thr->get_torque();
const double * _noalias const q = atom->q;
const dbl4_t * _noalias const mu = (dbl4_t *) atom->mu[0];
const int * _noalias const type = atom->type;
const int nlocal = atom->nlocal;
const double * _noalias const special_coul = force->special_coul;
const double * _noalias const special_lj = force->special_lj;
const double qqrd2e = force->qqrd2e;
double fxtmp,fytmp,fztmp,t1tmp,t2tmp,t3tmp;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++ii) {
i = ilist[ii];
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
qtmp = q[i];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
fxtmp=fytmp=fztmp=t1tmp=t2tmp=t3tmp=0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
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
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
if (qtmp != 0.0 && q[j] != 0.0) {
pre1 = qtmp*q[j]*rinv*(r2inv-rcutcoul2inv);
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
forcecoulz += pre1*delz;
}
if (mu[i].w > 0.0 && mu[j].w > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pdotp = mu[i].x*mu[j].x + mu[i].y*mu[j].y + mu[i].z*mu[j].z;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
aforcecoulx = pre1*delx;
aforcecouly = pre1*dely;
aforcecoulz = pre1*delz;
bfac = 1.0 - 4.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv +
3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
presf = 2.0 * r2inv * pidotr * pjdotr;
bforcecoulx = bfac * (pjdotr*mu[i].x+pidotr*mu[j].x-presf*delx);
bforcecouly = bfac * (pjdotr*mu[i].y+pidotr*mu[j].y-presf*dely);
bforcecoulz = bfac * (pjdotr*mu[i].z+pidotr*mu[j].z-presf*delz);
forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );
pre2 = 3.0 * bfac * r5inv * pjdotr;
pre3 = 3.0 * bfac * r5inv * pidotr;
pre4 = -bfac * r3inv;
crossx = pre4 * (mu[i].y*mu[j].z - mu[i].z*mu[j].y);
crossy = pre4 * (mu[i].z*mu[j].x - mu[i].x*mu[j].z);
crossz = pre4 * (mu[i].x*mu[j].y - mu[i].y*mu[j].x);
tixcoul += crossx + pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += crossy + pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += crossz + pre2 * (mu[i].x*dely - mu[i].y*delx);
tjxcoul += -crossx + pre3 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -crossy + pre3 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -crossz + pre3 * (mu[j].x*dely - mu[j].y*delx);
}
if (mu[i].w > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i].x*delx + mu[i].y*dely + mu[i].z*delz;
pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = q[j] * r3inv * pqfac;
forcecoulx += pre2*mu[i].x - pre1*delx;
forcecouly += pre2*mu[i].y - pre1*dely;
forcecoulz += pre2*mu[i].z - pre1*delz;
tixcoul += pre2 * (mu[i].y*delz - mu[i].z*dely);
tiycoul += pre2 * (mu[i].z*delx - mu[i].x*delz);
tizcoul += pre2 * (mu[i].x*dely - mu[i].y*delx);
}
if (mu[j].w > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j].x*delx + mu[j].y*dely + mu[j].z*delz;
pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
2.0*rsq*sqrt(rsq*rcutcoul2inv)*rcutcoul2inv;
pre2 = qtmp * r3inv * qpfac;
forcecoulx += pre1*delx - pre2*mu[j].x;
forcecouly += pre1*dely - pre2*mu[j].y;
forcecoulz += pre1*delz - pre2*mu[j].z;
tjxcoul += -pre2 * (mu[j].y*delz - mu[j].z*dely);
tjycoul += -pre2 * (mu[j].z*delx - mu[j].x*delz);
tjzcoul += -pre2 * (mu[j].x*dely - mu[j].y*delx);
}
}
// LJ interaction
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;
rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
rcutlj6inv * rcutlj2inv;
forcelj = factor_lj * (forceljcut - forceljsf);
} else forcelj = 0.0;
// total force
- fq = factor_coul*qqrd2e;
+ fq = factor_coul*qqrd2e*scale[itype][jtype];
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
// force & torque accumulation
fxtmp += fx;
fytmp += fy;
fztmp += fz;
t1tmp += fq*tixcoul;
t2tmp += fq*tiycoul;
t3tmp += fq*tizcoul;
if (NEWTON_PAIR || j < nlocal) {
f[j].x -= fx;
f[j].y -= fy;
f[j].z -= 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 = (1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype]));
+ ecoul = (1.0-sqrt(rsq/cut_coulsq[itype][jtype]));
ecoul *= ecoul;
ecoul *= qtmp * q[j] * rinv;
if (mu[i].w > 0.0 && mu[j].w > 0.0)
ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
if (mu[i].w > 0.0 && q[j] != 0.0)
ecoul += -q[j] * r3inv * pqfac * pidotr;
if (mu[j].w > 0.0 && qtmp != 0.0)
ecoul += qtmp * r3inv * qpfac * pjdotr;
- ecoul *= factor_coul*qqrd2e;
+ ecoul *= factor_coul*qqrd2e*scale[itype][jtype];
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype])+
rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
rsq*rcutlj2inv+
rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,
evdwl,ecoul,fx,fy,fz,delx,dely,delz,thr);
}
}
f[i].x += fxtmp;
f[i].y += fytmp;
f[i].z += fztmp;
torque[i][0] += t1tmp;
torque[i][1] += t2tmp;
torque[i][2] += t3tmp;
}
}
/* ---------------------------------------------------------------------- */
double PairLJSFDipoleSFOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairLJSFDipoleSF::memory_usage();
return bytes;
}