Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80871968
pair_lj_charmm_coul_long.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Sep 3, 00:38
Size
33 KB
Mime Type
text/x-c
Expires
Thu, Sep 5, 00:38 (2 d)
Engine
blob
Format
Raw Data
Handle
20468813
Attached To
rLAMMPS lammps
pair_lj_charmm_coul_long.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)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_charmm_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 "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
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ewaldflag = pppmflag = 1;
ftable = NULL;
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLong::~PairLJCharmmCoulLong()
{
if (!copymode) {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(epsilon);
memory->destroy(sigma);
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);
memory->destroy(offset);
}
if (ftable) free_tables();
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
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;
if (rsq < cut_bothsq) {
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 = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - 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) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
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) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
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 PairLJCharmmCoulLong::compute_inner()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double rsw;
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 = listinner->inum;
ilist = listinner->ilist;
numneigh = listinner->numneigh;
firstneigh = listinner->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;
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;
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv;
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 PairLJCharmmCoulLong::compute_middle()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair;
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double philj,switch1,switch2;
double rsw;
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 = listmiddle->inum;
ilist = listmiddle->ilist;
numneigh = listmiddle->numneigh;
firstneigh = listmiddle->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;
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;
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (rsq < cut_in_on_sq) {
rsw = (sqrt(rsq) - cut_in_off)*cut_in_diff_inv;
fpair *= rsw*rsw*(3.0 - 2.0*rsw);
}
if (rsq > cut_out_on_sq) {
rsw = (sqrt(rsq) - cut_out_on)*cut_out_diff_inv;
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 PairLJCharmmCoulLong::compute_outer(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double philj,switch1,switch2;
double rsw;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
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 = listouter->inum;
ilist = listouter->ilist;
numneigh = listouter->numneigh;
firstneigh = listouter->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) {
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 = 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*(3.0 - 2.0*rsw);
if (factor_coul < 1.0)
forcecoul -=
(1.0-factor_coul)*prefactor*rsw*rsw*(3.0 - 2.0*rsw);
} else {
forcecoul += prefactor;
if (factor_coul < 1.0)
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - 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 && rsq > cut_in_off_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
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) * r2inv;
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) {
if (!ncoultablebits || rsq <= tabinnersq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ptable[itable] + fraction*dptable[itable];
prefactor = qtmp*q[j] * table;
ecoul -= (1.0-factor_coul)*prefactor;
}
}
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
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;
forcecoul -= (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]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else if (rsq <= cut_in_on_sq) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
}
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::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(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");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
unlike other pair styles,
there are no individual pair settings that these override
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::settings(int narg, char **arg)
{
if (narg != 2 && narg != 3) error->all(FLERR,"Illegal pair_style command");
cut_lj_inner = force->numeric(FLERR,arg[0]);
cut_lj = force->numeric(FLERR,arg[1]);
if (narg == 2) cut_coul = cut_lj;
else cut_coul = force->numeric(FLERR,arg[2]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::coeff(int narg, char **arg)
{
if (narg != 4 && narg != 6) error->all(FLERR,"Illegal pair_coeff command");
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 eps14_one = epsilon_one;
double sigma14_one = sigma_one;
if (narg == 6) {
eps14_one = force->numeric(FLERR,arg[4]);
sigma14_one = force->numeric(FLERR,arg[5]);
}
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
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 PairLJCharmmCoulLong::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
"Pair style lj/charmm/coul/long 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) );
denom_lj_inv = 1.0 / denom_lj;
// set & error check interior rRESPA cutoffs
if (strstr(update->integrate_style,"respa") &&
((Respa *) update->integrate)->level_inner >= 0) {
cut_respa = ((Respa *) update->integrate)->cutoff;
cut_in_off = cut_respa[0];
cut_in_on = cut_respa[1];
cut_out_on = cut_respa[2];
cut_out_off = cut_respa[3];
cut_in_diff = cut_in_on - cut_in_off;
cut_out_diff = cut_out_off - cut_out_on;
cut_in_diff_inv = 1.0 / (cut_in_diff);
cut_out_diff_inv = 1.0 / (cut_out_diff);
cut_in_off_sq = cut_in_off*cut_in_off;
cut_in_on_sq = cut_in_on*cut_in_on;
cut_out_on_sq = cut_out_on*cut_out_on;
cut_out_off_sq = cut_out_off*cut_out_off;
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;
// setup force tables
if (ncoultablebits) init_tables(cut_coul,cut_respa);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
else if (id == 1) listinner = ptr;
else if (id == 2) listmiddle = ptr;
else if (id == 3) listouter = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCharmmCoulLong::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]);
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] = 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);
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);
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 PairLJCharmmCoulLong::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(&eps14[i][j],sizeof(double),1,fp);
fwrite(&sigma14[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::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(&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(&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 PairLJCharmmCoulLong::write_restart_settings(FILE *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);
fwrite(&ncoultablebits,sizeof(int),1,fp);
fwrite(&tabinner,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
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);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
}
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);
MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",
i,epsilon[i][i],sigma[i][i],eps14[i][i],sigma14[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCharmmCoulLong::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\n",i,j,
epsilon[i][j],sigma[i][j],eps14[i][j],sigma14[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor;
double switch1,switch2,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 {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - 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) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) * denom_lj_inv;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
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;
eng += phicoul;
}
if (rsq < cut_ljsq) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) * denom_lj_inv;
philj *= switch1;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJCharmmCoulLong::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;
dim = 0;
if (strcmp(str,"implicit") == 0) return (void *) &implicit;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
return NULL;
}
Event Timeline
Log In to Comment