Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/DIPOLE/pair_lj_cut_dipole_long.cpp
677b11428e37lammm-master-deprecated

Last Change
Raw File

pair_lj_cut_dipole_long.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 "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_dipole_long.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "force.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include "string.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairLJCutDipoleLong::PairLJCutDipoleLong(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
ewaldflag = dipoleflag = 1;
respa_enable = 0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutDipoleLong::~PairLJCutDipoleLong()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutDipoleLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r,rinv,r2inv,r6inv;
double forcecoulx,forcecouly,forcecoulz,fforce;
double tixcoul,tiycoul,tizcoul,tjxcoul,tjycoul,tjzcoul;
double fx,fy,fz,fdx,fdy,fdz,fax,fay,faz;
double pdotp,pidotr,pjdotr,pre1,pre2,pre3;
double grij,expm2,t,erfc;
double g0,g1,g2,b0,b1,b2,b3,d0,d1,d2,d3;
double zdix,zdiy,zdiz,zdjx,zdjy,zdjz,zaix,zaiy,zaiz,zajx,zajy,zajz;
double g0b1_g1b2_g2b3,g0d1_g1d2_g2d3;
double forcelj,factor_coul,factor_lj,facm1;
double evdwl,ecoul;
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;
int nall = atom->nlocal + atom->nghost;
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;
pre1 = 2.0 * g_ewald / MY_PIS;
pre2 = 4.0 * pow(g_ewald,3.0) / MY_PIS;
pre3 = 8.0 * pow(g_ewald,5.0) / MY_PIS;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = atom->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);
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
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;
g0 = qtmp*q[j];
g1 = qtmp*pjdotr - q[j]*pidotr + pdotp;
g2 = -pidotr*pjdotr;
if (factor_coul > 0.0) {
b0 = erfc * rinv;
b1 = (b0 + pre1*expm2) * r2inv;
b2 = (3.0*b1 + pre2*expm2) * r2inv;
b3 = (5.0*b2 + pre3*expm2) * r2inv;
g0b1_g1b2_g2b3 = g0*b1 + g1*b2 + g2*b3;
fdx = delx * g0b1_g1b2_g2b3 -
b1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
b2 * (pjdotr*mu[i][0] + pidotr*mu[j][0]);
fdy = dely * g0b1_g1b2_g2b3 -
b1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
b2 * (pjdotr*mu[i][1] + pidotr*mu[j][1]);
fdz = delz * g0b1_g1b2_g2b3 -
b1 * (qtmp*mu[j][2] - q[j]*mu[i][2]) +
b2 * (pjdotr*mu[i][2] + pidotr*mu[j][2]);
zdix = delx * (q[j]*b1 + b2*pjdotr) - b1*mu[j][0];
zdiy = dely * (q[j]*b1 + b2*pjdotr) - b1*mu[j][1];
zdiz = delz * (q[j]*b1 + b2*pjdotr) - b1*mu[j][2];
zdjx = delx * (-qtmp*b1 + b2*pidotr) - b1*mu[i][0];
zdjy = dely * (-qtmp*b1 + b2*pidotr) - b1*mu[i][1];
zdjz = delz * (-qtmp*b1 + b2*pidotr) - b1*mu[i][2];
if (factor_coul < 1.0) {
fdx *= factor_coul;
fdy *= factor_coul;
fdz *= factor_coul;
zdix *= factor_coul;
zdiy *= factor_coul;
zdiz *= factor_coul;
zdjx *= factor_coul;
zdjy *= factor_coul;
zdjz *= factor_coul;
}
} else {
fdx = fdy = fdz = 0.0;
zdix = zdiy = zdiz = 0.0;
zdjx = zdjy = zdjz = 0.0;
}
if (factor_coul < 1.0) {
d0 = (erfc - 1.0) * rinv;
d1 = (d0 + pre1*expm2) * r2inv;
d2 = (3.0*d1 + pre2*expm2) * r2inv;
d3 = (5.0*d2 + pre3*expm2) * r2inv;
g0d1_g1d2_g2d3 = g0*d1 + g1*d2 + g2*d3;
fax = delx * g0d1_g1d2_g2d3 -
d1 * (qtmp*mu[j][0] - q[j]*mu[i][0]) +
d2 * (pjdotr*mu[i][0] + pidotr*mu[j][0]);
fay = dely * g0d1_g1d2_g2d3 -
d1 * (qtmp*mu[j][1] - q[j]*mu[i][1]) +
d2 * (pjdotr*mu[i][1] + pidotr*mu[j][1]);
faz = delz * g0d1_g1d2_g2d3 -
d1 * (qtmp*mu[j][2] - q[j]*mu[i][2]) +
d2 * (pjdotr*mu[i][2] + pidotr*mu[j][2]);
zaix = delx * (q[j]*d1 + d2*pjdotr) - d1*mu[j][0];
zaiy = dely * (q[j]*d1 + d2*pjdotr) - d1*mu[j][1];
zaiz = delz * (q[j]*d1 + d2*pjdotr) - d1*mu[j][2];
zajx = delx * (-qtmp*d1 + d2*pidotr) - d1*mu[i][0];
zajy = dely * (-qtmp*d1 + d2*pidotr) - d1*mu[i][1];
zajz = delz * (-qtmp*d1 + d2*pidotr) - d1*mu[i][2];
if (factor_coul > 0.0) {
facm1 = 1.0 - factor_coul;
fax *= facm1;
fay *= facm1;
faz *= facm1;
zaix *= facm1;
zaiy *= facm1;
zaiz *= facm1;
zajx *= facm1;
zajy *= facm1;
zajz *= facm1;
}
} else {
fax = fay = faz = 0.0;
zaix = zaiy = zaiz = 0.0;
zajx = zajy = zajz = 0.0;
}
forcecoulx = fdx + fax;
forcecouly = fdy + fay;
forcecoulz = fdz + faz;
tixcoul = mu[i][1]*(zdiz + zaiz) - mu[i][2]*(zdiy + zaiy);
tiycoul = mu[i][2]*(zdix + zaix) - mu[i][0]*(zdiz + zaiz);
tizcoul = mu[i][0]*(zdiy + zaiy) - mu[i][1]*(zdix + zaix);
tjxcoul = mu[j][1]*(zdjz + zajz) - mu[j][2]*(zdjy + zajy);
tjycoul = mu[j][2]*(zdjx + zajx) - mu[j][0]*(zdjz + zajz);
tjzcoul = mu[j][0]*(zdjy + zajy) - mu[j][1]*(zdjx + zajx);
} else {
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
}
// LJ interaction
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj * forcelj*r2inv;
} else fforce = 0.0;
// total force
fx = qqrd2e*forcecoulx + delx*fforce;
fy = qqrd2e*forcecouly + dely*fforce;
fz = qqrd2e*forcecoulz + delz*fforce;
// force & torque accumulation
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
torque[i][0] += qqrd2e*tixcoul;
torque[i][1] += qqrd2e*tiycoul;
torque[i][2] += qqrd2e*tizcoul;
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
torque[j][0] += qqrd2e*tjxcoul;
torque[j][1] += qqrd2e*tjycoul;
torque[j][2] += qqrd2e*tjzcoul;
}
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = qqrd2e*(b0*g0 + b1*g1 + b2*g2);
if (factor_coul < 1.0) {
ecoul *= factor_coul;
ecoul += (1-factor_coul) * qqrd2e * (d0*g0 + d1*g1 + d2*g2);
}
} 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);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::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(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(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2)
error->all(FLERR,"Incorrect args in pair_style command");
cut_lj_global = force->numeric(FLERR,arg[0]);
if (narg == 1) cut_coul = cut_lj_global;
else cut_coul = 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;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
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 cut_lj_one = cut_lj_global;
if (narg == 5) cut_lj_one = force->numeric(FLERR,arg[4]);
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;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCutDipoleLong::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]);
}
double cut = MAX(cut_lj[i][j],cut_coul);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[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];
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;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::init_style()
{
if (!atom->q_flag || !atom->mu_flag || !atom->torque_flag)
error->all(FLERR,"Pair dipole/long requires atom attributes q, mu, torque");
if (strcmp(update->unit_style,"electron") == 0)
error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles");
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
cut_coulsq = cut_coul * cut_coul;
neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::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);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::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);
}
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);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutDipoleLong::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul,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 PairLJCutDipoleLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,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,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void *PairLJCutDipoleLong::extract(const char *str, int &dim)
{
if (strcmp(str,"cut_coul") == 0) {
dim = 0;
return (void *) &cut_coul;
} else if (strcmp(str,"ewald_order") == 0) {
ewald_order = 0;
ewald_order |= 1<<1;
ewald_order |= 1<<3;
dim = 0;
return (void *) &ewald_order;
} else if (strcmp(str,"ewald_mix") == 0) {
dim = 0;
return (void *) &mix_flag;
}
return NULL;
}
c4science · Help