Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-FEP/pair_coul_long_soft.cpp
354e20f43157efficient_neuronet

Last Change
Raw File

pair_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_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
#include "integrate.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
/* ---------------------------------------------------------------------- */
PairCoulLongSoft::PairCoulLongSoft(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
qdist = 0.0;
}
/* ---------------------------------------------------------------------- */
PairCoulLongSoft::~PairCoulLongSoft()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(scale);
memory->destroy(lambda);
memory->destroy(lam1);
memory->destroy(lam2);
}
}
/* ---------------------------------------------------------------------- */
void PairCoulLongSoft::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double r,rsq,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
double denc;
int *ilist,*jlist,*numneigh,**firstneigh;
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;
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_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_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(lam2[itype][jtype] + rsq);
prefactor = qqrd2e * lam1[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;
fpair = forcecoul;
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) {
prefactor = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / denc;
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairCoulLongSoft::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(scale,n+1,n+1,"pair:scale");
memory->create(lambda,n+1,n+1,"pair:lambda");
memory->create(lam1,n+1,n+1,"pair:lam1");
memory->create(lam2,n+1,n+1,"pair:lam2");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulLongSoft::settings(int narg, char **arg)
{
if (narg != 3) error->all(FLERR,"Illegal pair_style command");
nlambda = force->numeric(FLERR,arg[0]);
alphac = force->numeric(FLERR,arg[1]);
cut_coul = force->numeric(FLERR,arg[2]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulLongSoft::coeff(int narg, char **arg)
{
if (narg != 3)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double lambda_one = force->numeric(FLERR,arg[2]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
lambda[i][j] = lambda_one;
scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulLongSoft::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/long requires atom attribute q");
neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
// 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 PairCoulLongSoft::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
if (lambda[i][i] != lambda[j][j])
error->all(FLERR,"Pair coul/cut/soft different lambda values in mix");
lambda[i][j] = lambda[i][i];
}
lam1[i][j] = pow(lambda[i][j], nlambda);
lam2[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
scale[j][i] = scale[i][j];
lambda[j][i] = lambda[i][j];
lam1[j][i] = lam1[i][j];
lam2[j][i] = lam2[i][j];
return cut_coul+2.0*qdist;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulLongSoft::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(&lambda[i][j],sizeof(double),1,fp);
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulLongSoft::write_restart_settings(FILE *fp)
{
fwrite(&nlambda,sizeof(double),1,fp);
fwrite(&alphac,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 PairCoulLongSoft::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&nlambda,sizeof(double),1,fp);
fread(&alphac,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(&alphac,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 PairCoulLongSoft::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 forcecoul,phicoul;
double denc;
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(lam2[itype][jtype] + rsq);
prefactor = force->qqrd2e * lam1[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;
fforce = forcecoul;
if (rsq < cut_coulsq) {
prefactor = force->qqrd2e * lam1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
phicoul = prefactor*erfc;
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
} else phicoul = 0.0;
return phicoul;
}
/* ---------------------------------------------------------------------- */
void *PairCoulLongSoft::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
dim = 2;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"lambda") == 0) return (void *) lambda;
return NULL;
}
c4science · Help