Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F91593161
pair_lj_charmmfsw_coul_charmmfsh.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, Nov 12, 13:28
Size
17 KB
Mime Type
text/x-c
Expires
Thu, Nov 14, 13:28 (2 d)
Engine
blob
Format
Raw Data
Handle
22289887
Attached To
rLAMMPS lammps
pair_lj_charmmfsw_coul_charmmfsh.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)
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;
}
Event Timeline
Log In to Comment