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pair_lj_charmmfsw_coul_charmmfsh.cpp
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Tue, Feb 18, 23:17

pair_lj_charmmfsw_coul_charmmfsh.cpp
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/* ----------------------------------------------------------------------
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)
The lj-fsw/coul-fsh (force-switched and force-shifted) sections
were provided by Robert Meissner
and Lucio Colombi Ciacchi of Bremen University, Bremen, Germany,
with additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lj_charmmfsw_coul_charmmfsh.h"
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
Pair(lmp)
{
implicit = 0;
mix_flag = ARITHMETIC;
writedata = 1;
// short-range/long-range flag accessed by DihedralCharmmfsw
dihedflag = 0;
// switch qqr2e from LAMMPS value to CHARMM value
if (strcmp(update->unit_style,"real") == 0) {
if ((comm->me == 0) && (force->qqr2e != force->qqr2e_charmm_real))
error->message(FLERR,"Switching to CHARMM coulomb energy"
" conversion constant");
force->qqr2e = force->qqr2e_charmm_real;
}
}
/* ---------------------------------------------------------------------- */
PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh()
{
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);
}
}
// switch qqr2e back from CHARMM value to LAMMPS value
if (update && strcmp(update->unit_style,"real") == 0) {
if ((comm->me == 0) && (force->qqr2e == force->qqr2e_charmm_real))
error->message(FLERR,"Restoring original LAMMPS coulomb energy"
" conversion constant");
force->qqr2e = force->qqr2e_lammps_real;
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl12,evdwl6,ecoul,fpair;
double r,rinv,r3inv,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double switch1;
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;
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
forcecoul = qqrd2e * qtmp*q[j]*
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
} 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;
forcelj = forcelj*switch1;
}
} else forcelj = 0.0;
fpair = (factor_coul*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) {
ecoul = qqrd2e * qtmp*q[j]*
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
ecoul *= factor_coul;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
if (rsq > cut_lj_innersq) {
rinv = 1.0/r;
r3inv = rinv*rinv*rinv;
evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
evdwl = evdwl12 + evdwl6;
} else {
evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
evdwl6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
evdwl = evdwl12 + evdwl6;
}
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();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::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");
}
/* ----------------------------------------------------------------------
global settings
unlike other pair styles,
there are no individual pair settings that these override
------------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::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 PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg)
{
if (narg != 4 && narg != 6)
error->all(FLERR,"Incorrect args for pair coefficients");
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 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 PairLJCharmmfswCoulCharmmfsh::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/charmmfsw/coul/charmmfsh "
"requires atom attribute q");
neighbor->request(this,instance_me);
// require cut_lj_inner < cut_lj
if (cut_lj_inner >= cut_lj)
error->all(FLERR,"Pair inner lj cutoff >= Pair outer lj cutoff");
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
cut_ljsq = cut_lj * cut_lj;
cut_ljinv = 1.0/cut_lj;
cut_lj_innerinv = 1.0/cut_lj_inner;
cut_lj3 = cut_lj * cut_lj * cut_lj;
cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv;
cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv;
cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner;
cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq;
cut_lj6inv = cut_lj3inv * cut_lj3inv;
cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv;
cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq;
cut_coulsq = cut_coul * cut_coul;
cut_coulinv = 1.0/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_lj12 = 1.0/(cut_lj6 - cut_lj_inner6);
denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCharmmfswCoulCharmmfsh::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 data file
------------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::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 PairLJCharmmfswCoulCharmmfsh::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]);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::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 PairLJCharmmfswCoulCharmmfsh::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 PairLJCharmmfswCoulCharmmfsh::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);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCharmmfswCoulCharmmfsh::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);
}
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);
}
/* ---------------------------------------------------------------------- */
double PairLJCharmmfswCoulCharmmfsh::
single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj, double &fforce)
{
double r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj;
double phicoul,philj,philj12,philj6;
double switch1;
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
if (rsq < cut_coulsq) {
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j] *
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
r3inv = rinv*rinv*rinv;
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;
forcelj = forcelj*switch1;
}
} else forcelj = 0.0;
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq) {
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] *
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
eng += factor_coul*phicoul;
}
if (rsq < cut_ljsq) {
if (rsq > cut_lj_innersq) {
philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
philj = philj12 + philj6;
} else {
philj12 = r6inv*lj3[itype][jtype]*r6inv -
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
philj6 = -lj4[itype][jtype]*r6inv +
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
philj = philj12 + philj6;
}
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJCharmmfswCoulCharmmfsh::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;
// info extracted by dihedral_charmmfsw
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner;
if (strcmp(str,"cut_lj") == 0) return (void *) &cut_lj;
if (strcmp(str,"dihedflag") == 0) return (void *) &dihedflag;
return NULL;
}

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