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pair_lj_cut_coul_long.cpp
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Tue, Feb 18, 23:40

pair_lj_cut_coul_long.cpp
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_coul_long.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#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
/* ---------------------------------------------------------------------- */
PairLJCutCoulLong::PairLJCutCoulLong()
{
respa_enable = 1;
ftable = NULL;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairLJCutCoulLong::~PairLJCutCoulLong()
{
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(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);
}
if (ftable) free_tables();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::compute(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj;
int *neighs;
double **f;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
if (vflag == 2) f = update->f_pair;
else f = atom->f;
double **x = atom->x;
double *q = atom->q;
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;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
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;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrtf(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;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
itable = *int_rsq & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
if (eflag) {
if (newton_pair || j < nlocal) factor = 1.0;
else factor = 0.5;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng_coul += factor*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng_vdwl += factor*factor_lj*philj;
}
}
if (vflag == 1) {
if (newton_pair || j < nlocal) {
virial[0] += delx*delx*fforce;
virial[1] += dely*dely*fforce;
virial[2] += delz*delz*fforce;
virial[3] += delx*dely*fforce;
virial[4] += delx*delz*fforce;
virial[5] += dely*delz*fforce;
} else {
virial[0] += 0.5*delx*delx*fforce;
virial[1] += 0.5*dely*dely*fforce;
virial[2] += 0.5*delz*delz*fforce;
virial[3] += 0.5*delx*dely*fforce;
virial[4] += 0.5*delx*delz*fforce;
virial[5] += 0.5*dely*delz*fforce;
}
}
}
}
}
if (vflag == 2) virial_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::compute_inner()
{
int i,j,k,numneigh,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double rsw;
int *neighs;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
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;
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
double cut_out_diff = cut_out_off - cut_out_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_inner[i];
numneigh = neighbor->numneigh_inner[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq) {
r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::compute_middle()
{
int i,j,k,numneigh,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double rsw;
int *neighs;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
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;
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
double cut_out_off = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_out_diff = cut_out_off - cut_out_on;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
double cut_out_on_sq = cut_out_on*cut_out_on;
double cut_out_off_sq = cut_out_off*cut_out_off;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh_middle[i];
numneigh = neighbor->numneigh_middle[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
r2inv = 1.0/rsq;
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
jtype = type[j];
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fforce *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fforce *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::compute_outer(int eflag, int vflag)
{
int i,j,k,numneigh,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double factor,phicoul,philj;
double rsw;
int *neighs;
float rsq;
int *int_rsq = (int *) &rsq;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
double **f = atom->f;
double **x = atom->x;
double *q = atom->q;
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;
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
double cut_in_diff = cut_in_on - cut_in_off;
double cut_in_off_sq = cut_in_off*cut_in_off;
double cut_in_on_sq = cut_in_on*cut_in_on;
// loop over neighbors of my atoms
for (i = 0; i < nlocal; i++) {
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
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;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrtf(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;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - 1.0);
if (rsq > cut_in_off_sq) {
if (rsq < cut_in_on_sq) {
rsw = (r - cut_in_off)/cut_in_diff;
forcecoul += prefactor*rsw*rsw*(3 - 2*rsw);
if (factor_coul < 1.0)
forcecoul -= (1.0-factor_coul)*prefactor*rsw*rsw*(3 - 2*rsw);
} else {
forcecoul += prefactor;
if (factor_coul < 1.0)
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else {
itable = *int_rsq & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype] && rsq > cut_in_off_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq < cut_in_on_sq) {
rsw = (sqrtf(rsq) - cut_in_off)/cut_in_diff;
forcelj *= rsw*rsw*(3 - 2*rsw);
}
} else forcelj = 0.0;
fforce = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fforce;
f[i][1] += dely*fforce;
f[i][2] += delz*fforce;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fforce;
f[j][1] -= dely*fforce;
f[j][2] -= delz*fforce;
}
if (eflag) {
if (newton_pair || j < nlocal) factor = 1.0;
else factor = 0.5;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
} else {
table = etable[itable] + fraction*detable[itable];
phicoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ptable[itable] + fraction*dptable[itable];
prefactor = qtmp*q[j] * table;
phicoul -= (1.0-factor_coul)*prefactor;
}
}
eng_coul += factor*phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng_vdwl += factor*factor_lj*philj;
}
}
if (vflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
table = vtable[itable] + fraction*dvtable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ptable[itable] + fraction*dptable[itable];
prefactor = qtmp*q[j] * table;
phicoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq <= cut_in_off_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else if (rsq <= cut_in_on_sq)
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (newton_pair || j < nlocal) {
virial[0] += delx*delx*fforce;
virial[1] += dely*dely*fforce;
virial[2] += delz*delz*fforce;
virial[3] += delx*dely*fforce;
virial[4] += delx*delz*fforce;
virial[5] += dely*delz*fforce;
} else {
virial[0] += 0.5*delx*delx*fforce;
virial[1] += 0.5*dely*dely*fforce;
virial[2] += 0.5*delz*delz*fforce;
virial[3] += 0.5*delx*dely*fforce;
virial[4] += 0.5*delx*delz*fforce;
virial[5] += 0.5*dely*delz*fforce;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCutCoulLong::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");
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 PairLJCutCoulLong::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all("Illegal pair_style command");
cut_lj_global = atof(arg[0]);
if (narg == 1) cut_coul = cut_lj_global;
else cut_coul = atof(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 PairLJCutCoulLong::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5) 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 = atof(arg[2]);
double sigma_one = atof(arg[3]);
double cut_lj_one = cut_lj_global;
if (narg == 5) cut_lj_one = atof(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("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCutCoulLong::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];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double PI = 4.0*atan(1.0);
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
}
return cut;
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutCoulLong::init_style()
{
int i,j;
// require an atom style with charge defined
if (atom->charge_allow == 0)
error->all("Must use charged atom style with this pair style");
cut_coulsq = cut_coul * cut_coul;
// set & error check interior rRESPA cutoffs
if (strcmp(update->integrate_style,"respa") == 0) {
if (((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
error->all("Pair cutoff < Respa interior cutoff");
}
} else cut_respa = NULL;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all("Pair style is incompatible with KSpace style");
else if (strcmp(force->kspace_style,"ewald") == 0)
g_ewald = force->kspace->g_ewald;
else if (strcmp(force->kspace_style,"pppm") == 0)
g_ewald = force->kspace->g_ewald;
else error->all("Pair style is incompatible with KSpace style");
// setup force tables
if (ncoultablebits) init_tables();
}
/* ----------------------------------------------------------------------
setup force tables used in compute routines
------------------------------------------------------------------------- */
void PairLJCutCoulLong::init_tables()
{
int masklo,maskhi;
double r,grij,expm2,derfc,rsw;
double qqrd2e = force->qqrd2e;
tabinnersq = tabinner*tabinner;
init_bitmap(tabinner,cut_coul,ncoultablebits,
masklo,maskhi,ncoulmask,ncoulshiftbits);
int ntable = 1;
for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
// linear lookup tables of length N = 2^ncoultablebits
// stored value = value at lower edge of bin
// d values = delta from lower edge to upper edge of bin
if (ftable) free_tables();
rtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:rtable");
ftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ftable");
ctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ctable");
etable = (double *) memory->smalloc(ntable*sizeof(double),"pair:etable");
drtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:drtable");
dftable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dftable");
dctable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dctable");
detable = (double *) memory->smalloc(ntable*sizeof(double),"pair:detable");
if (cut_respa == NULL) {
vtable = ptable = dvtable = dptable = NULL;
} else {
vtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:vtable");
ptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:ptable");
dvtable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dvtable");
dptable = (double *) memory->smalloc(ntable*sizeof(double),"pair:dptable");
}
float rsq;
int *int_rsq = (int *) &rsq;
float minrsq;
int *int_minrsq = (int *) &minrsq;
int itablemin;
*int_minrsq = 0 << ncoulshiftbits;
*int_minrsq = *int_minrsq | maskhi;
for (int i = 0; i < ntable; i++) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | masklo;
if (rsq < tabinnersq) {
*int_rsq = i << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
}
r = sqrtf(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
etable[i] = qqrd2e/r * derfc;
} else {
rtable[i] = rsq;
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
ctable[i] = 0.0;
etable[i] = qqrd2e/r * derfc;
ptable[i] = qqrd2e/r;
vtable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
ftable[i] += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
ctable[i] = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
ftable[i] = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
ctable[i] = qqrd2e/r;
}
}
}
minrsq = MIN(minrsq,rsq);
}
tabinnersq = minrsq;
int ntablem1 = ntable - 1;
for (int i = 0; i < ntablem1; i++) {
drtable[i] = 1.0/(rtable[i+1] - rtable[i]);
dftable[i] = ftable[i+1] - ftable[i];
dctable[i] = ctable[i+1] - ctable[i];
detable[i] = etable[i+1] - etable[i];
}
if (cut_respa) {
for (int i = 0; i < ntablem1; i++) {
dvtable[i] = vtable[i+1] - vtable[i];
dptable[i] = ptable[i+1] - ptable[i];
}
}
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
drtable[ntablem1] = 1.0/(rtable[0] - rtable[ntablem1]);
dftable[ntablem1] = ftable[0] - ftable[ntablem1];
dctable[ntablem1] = ctable[0] - ctable[ntablem1];
detable[ntablem1] = etable[0] - etable[ntablem1];
if (cut_respa) {
dvtable[ntablem1] = vtable[0] - vtable[ntablem1];
dptable[ntablem1] = ptable[0] - ptable[ntablem1];
}
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
double f_tmp,c_tmp,e_tmp,p_tmp,v_tmp;
itablemin = *int_minrsq & ncoulmask;
itablemin >>= ncoulshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
*int_rsq = itablemax << ncoulshiftbits;
*int_rsq = *int_rsq | maskhi;
if (rsq < cut_coulsq) {
rsq = cut_coulsq;
r = sqrtf(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
derfc = erfc(grij);
if (cut_respa == NULL) {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
e_tmp = qqrd2e/r * derfc;
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2 - 1.0);
c_tmp = 0.0;
e_tmp = qqrd2e/r * derfc;
p_tmp = qqrd2e/r;
v_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
if (rsq > cut_respa[2]*cut_respa[2]) {
if (rsq < cut_respa[3]*cut_respa[3]) {
rsw = (r - cut_respa[2])/(cut_respa[3] - cut_respa[2]);
f_tmp += qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
c_tmp = qqrd2e/r * rsw*rsw*(3.0 - 2.0*rsw);
} else {
f_tmp = qqrd2e/r * (derfc + EWALD_F*grij*expm2);
c_tmp = qqrd2e/r;
}
}
}
drtable[itablemax] = 1.0/(rsq - rtable[itablemax]);
dftable[itablemax] = f_tmp - ftable[itablemax];
dctable[itablemax] = c_tmp - ctable[itablemax];
detable[itablemax] = e_tmp - etable[itablemax];
if (cut_respa) {
dvtable[itablemax] = v_tmp - vtable[itablemax];
dptable[itablemax] = p_tmp - ptable[itablemax];
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutCoulLong::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 PairLJCutCoulLong::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 PairLJCutCoulLong::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 PairLJCutCoulLong::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);
}
/* ----------------------------------------------------------------------
free memory for tables used in pair computations
------------------------------------------------------------------------- */
void PairLJCutCoulLong::free_tables()
{
memory->sfree(rtable);
memory->sfree(drtable);
memory->sfree(ftable);
memory->sfree(dftable);
memory->sfree(ctable);
memory->sfree(dctable);
memory->sfree(etable);
memory->sfree(detable);
memory->sfree(vtable);
memory->sfree(dvtable);
memory->sfree(ptable);
memory->sfree(dptable);
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
int eflag, One &one)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double fraction,table,forcecoul,forcelj,phicoul,philj;
int itable;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
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;
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
float rsq_single = rsq;
int *int_rsq = (int *) &rsq_single;
itable = *int_rsq & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_single - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
one.fforce = (forcecoul + factor_lj*forcelj) * r2inv;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
one.eng_coul = phicoul;
} else one.eng_coul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
one.eng_vdwl = factor_lj*philj;
} else one.eng_vdwl = 0.0;
}
}

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