Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
7dfc6b7eab71master

Last Change
Raw File

pair_lj_charmm_coul_long_soft.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_charmm_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#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
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongSoft::PairLJCharmmCoulLongSoft(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ewaldflag = pppmflag = 1;
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongSoft::~PairLJCharmmCoulLongSoft()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lambda);
memory->destroy(eps14);
memory->destroy(sigma14);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(lj14_1);
memory->destroy(lj14_2);
memory->destroy(lj14_3);
memory->destroy(lj14_4);
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double r,rsq,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
double denc, denlj, r4sig6;
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;
int *type = atom->type;
int nlocal = atom->nlocal;
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 < cut_bothsq) {
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;
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fpair = forcecoul + factor_lj*forcelj;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::compute_inner()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,forcecoul,forcelj,factor_coul,factor_lj;
double rsw;
double denc, denlj, r4sig6;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
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_inner;
ilist = list->ilist_inner;
numneigh = list->numneigh_inner;
firstneigh = list->firstneigh_inner;
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 (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;
if (rsq < cut_out_off_sq) {
jtype = type[j];
denc = sqrt(lj4[itype][jtype] + rsq);
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
fpair = forcecoul + factor_lj*forcelj;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw-3.0);
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::compute_middle()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,forcecoul,forcelj,factor_coul,factor_lj;
double philj,switch1,switch2;
double rsw;
double denc, denlj, r4sig6;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
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_middle;
ilist = list->ilist_middle;
numneigh = list->numneigh_middle;
firstneigh = list->firstneigh_middle;
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 (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;
if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
jtype = type[j];
denc = sqrt(lj4[itype][jtype] + rsq);
forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*forcecoul;
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
fpair = forcecoul + factor_lj*forcelj;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double r,rsq,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,fprefactor,eprefactor,t,erfc;
double philj,switch1,switch2;
double rsw;
double denc, denlj, r4sig6;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
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;
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 (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;
if (rsq < cut_bothsq) {
jtype = type[j];
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;
denc = sqrt(lj4[itype][jtype] + rsq);
fprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] /
(denc*denc*denc);
forcecoul = fprefactor * (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 += fprefactor*rsw*rsw*(3.0 - 2.0*rsw);
if (factor_coul < 1.0)
forcecoul -=
(1.0-factor_coul)*fprefactor*rsw*rsw*(3.0 - 2.0*rsw);
} else {
forcecoul += fprefactor;
if (factor_coul < 1.0)
forcecoul -= (1.0-factor_coul)*fprefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq && rsq > cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
forcelj *= rsw*rsw*(3.0 - 2.0*rsw);
}
} else forcelj = 0.0;
fpair = forcecoul + forcelj;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
eprefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc;
ecoul = eprefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*eprefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
evdwl = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (vflag) {
if (rsq < cut_coulsq) {
forcecoul = fprefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*fprefactor;
} else forcecoul = 0.0;
if (rsq <= cut_in_off_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
}
fpair = forcecoul + factor_lj*forcelj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::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(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lambda,n+1,n+1,"pair:lambda");
memory->create(eps14,n+1,n+1,"pair:eps14");
memory->create(sigma14,n+1,n+1,"pair:sigma14");
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(lj14_1,n+1,n+1,"pair:lj14_1");
memory->create(lj14_2,n+1,n+1,"pair:lj14_2");
memory->create(lj14_3,n+1,n+1,"pair:lj14_3");
memory->create(lj14_4,n+1,n+1,"pair:lj14_4");
}
/* ----------------------------------------------------------------------
global settings
unlike other pair styles,
there are no individual pair settings that these override
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::settings(int narg, char **arg)
{
if (narg != 5 && narg != 6) error->all(FLERR,"Illegal pair_style command");
nlambda = force->numeric(FLERR,arg[0]);
alphalj = force->numeric(FLERR,arg[1]);
alphac = force->numeric(FLERR,arg[2]);
cut_lj_inner = force->numeric(FLERR,arg[3]);
cut_lj = force->numeric(FLERR,arg[4]);
if (narg == 5) cut_coul = cut_lj;
else cut_coul = force->numeric(FLERR,arg[5]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::coeff(int narg, char **arg)
{
if (narg != 5 && narg != 7) error->all(FLERR,"Illegal pair_coeff command");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double lambda_one = force->numeric(FLERR,arg[4]);
double eps14_one = epsilon_one;
double sigma14_one = sigma_one;
if (narg == 7) {
eps14_one = force->numeric(FLERR,arg[5]);
sigma14_one = force->numeric(FLERR,arg[6]);
}
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;
lambda[i][j] = lambda_one;
eps14[i][j] = eps14_one;
sigma14[i][j] = sigma14_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
"Pair style lj/charmm/coul/long/soft requires atom attribute q");
// request regular or rRESPA neighbor lists
int irequest;
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
int respa = 0;
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
if (respa == 0) irequest = neighbor->request(this,instance_me);
else if (respa == 1) {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
} else {
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respainner = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 2;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respamiddle = 1;
irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->id = 3;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->respaouter = 1;
}
} else irequest = neighbor->request(this,instance_me);
// require cut_lj_inner < cut_lj
if (cut_lj_inner >= cut_lj)
error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff");
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
cut_ljsq = cut_lj * cut_lj;
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
if (MIN(cut_lj,cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
if (cut_lj_inner < cut_respa[1])
error->all(FLERR,"Pair inner cutoff < Respa interior cutoff");
} else cut_respa = NULL;
// 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;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCharmmCoulLongSoft::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]);
if (lambda[i][i] != lambda[j][j])
error->all(FLERR,"Pair lj/charmm/coul/long/soft different lambda values in mix");
lambda[i][j] = lambda[i][i];
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
sigma14[i][i],sigma14[j][j]);
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
}
double cut = MAX(cut_lj,cut_coul);
lj1[i][j] = pow(lambda[i][j], nlambda);
lj2[i][j] = pow(sigma[i][j], 6.0);
lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
// 1-4 interactions unaffected (they're part of the dihedral term)
lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
epsilon[j][i] = epsilon[i][j];
sigma[j][i] = sigma[i][j];
lambda[j][i] = lambda[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];
lj14_1[j][i] = lj14_1[i][j];
lj14_2[j][i] = lj14_2[i][j];
lj14_3[j][i] = lj14_3[i][j];
lj14_4[j][i] = lj14_4[i][j];
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp);
fwrite(&eps14[i][j],sizeof(double),1,fp);
fwrite(&sigma14[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp);
fread(&eps14[i][j],sizeof(double),1,fp);
fread(&sigma14[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(&lambda[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::write_restart_settings(FILE *fp)
{
fwrite(&nlambda,sizeof(double),1,fp);
fwrite(&alphalj,sizeof(double),1,fp);
fwrite(&alphac,sizeof(double),1,fp);
fwrite(&cut_lj_inner,sizeof(double),1,fp);
fwrite(&cut_lj,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 PairLJCharmmCoulLongSoft::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&nlambda,sizeof(double),1,fp);
fread(&alphalj,sizeof(double),1,fp);
fread(&alphac,sizeof(double),1,fp);
fread(&cut_lj_inner,sizeof(double),1,fp);
fread(&cut_lj,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(&nlambda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj,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);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g %g\n",i,epsilon[i][i],sigma[i][i],
lambda[i][i],eps14[i][i],sigma14[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLongSoft::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],
lambda[i][j],eps14[i][j],sigma14[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulLongSoft::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r,grij,expm2,t,erfc,prefactor;
double switch1,switch2,forcecoul,forcelj,phicoul,philj;
double denc, denlj, r4sig6;
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;
denc = sqrt(lj4[itype][jtype] + rsq);
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] /
(denc*denc*denc);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r4sig6 = rsq*rsq / lj2[itype][jtype];
denlj = lj3[itype][jtype] + rsq*r4sig6;
forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
(48.0*r4sig6/(denlj*denlj*denlj) - 24.0*r4sig6/(denlj*denlj));
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0 * (cut_ljsq-rsq) * (rsq-cut_lj_innersq) / denom_lj;
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fforce = forcecoul + factor_lj*forcelj;
double eng = 0.0;
if (rsq < cut_coulsq) {
prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
eng += phicoul;
}
if (rsq < cut_ljsq) {
philj = lj1[itype][jtype] * 4.0 * epsilon[itype][jtype] *
(1.0/(denlj*denlj) - 1.0/denlj);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
philj *= switch1;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJCharmmCoulLongSoft::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"lj14_1") == 0) return (void *) lj14_1;
if (strcmp(str,"lj14_2") == 0) return (void *) lj14_2;
if (strcmp(str,"lj14_3") == 0) return (void *) lj14_3;
if (strcmp(str,"lj14_4") == 0) return (void *) lj14_4;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"lambda") == 0) return (void *) lambda;
dim = 0;
if (strcmp(str,"implicit") == 0) return (void *) &implicit;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
return NULL;
}
c4science · Help