Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F91642868
pair_coul_cut_soft.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
Wed, Nov 13, 00:40
Size
10 KB
Mime Type
text/x-c
Expires
Fri, Nov 15, 00:40 (2 d)
Engine
blob
Format
Raw Data
Handle
22269443
Attached To
rLAMMPS lammps
pair_coul_cut_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_coul_cut_soft.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCoulCutSoft::PairCoulCutSoft(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairCoulCutSoft::~PairCoulCutSoft()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(lambda);
memory->destroy(lam1);
memory->destroy(lam2);
}
}
/* ---------------------------------------------------------------------- */
void PairCoulCutSoft::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 rsq,forcecoul,factor_coul;
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 < cutsq[itype][jtype]) {
denc = sqrt(lam2[itype][jtype] + rsq);
forcecoul = qqrd2e * lam1[itype][jtype] * qtmp*q[j] / (denc*denc*denc);
fpair = factor_coul*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)
ecoul = factor_coul * qqrd2e * lam1[itype][jtype] * qtmp*q[j] / denc;
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 PairCoulCutSoft::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(cut,n+1,n+1,"pair:cut");
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 PairCoulCutSoft::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_global = force->numeric(FLERR,arg[2]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulCutSoft::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 4)
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]);
double cut_one = cut_global;
if (narg == 4) cut_one = force->numeric(FLERR,arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
lambda[i][j] = lambda_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulCutSoft::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/cut/soft requires atom attribute q");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulCutSoft::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];
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
lam1[i][j] = pow(lambda[i][j], nlambda);
lam2[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
cut[j][i] = cut[i][j];
lambda[j][i] = lambda[i][j];
lam1[j][i] = lam1[i][j];
lam2[j][i] = lam2[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulCutSoft::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);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulCutSoft::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);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulCutSoft::write_restart_settings(FILE *fp)
{
fwrite(&nlambda,sizeof(double),1,fp);
fwrite(&alphac,sizeof(double),1,fp);
fwrite(&cut_global,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 PairCoulCutSoft::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&nlambda,sizeof(double),1,fp);
fread(&alphac,sizeof(double),1,fp);
fread(&cut_global,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_global,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 PairCoulCutSoft::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g\n",i,lambda[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairCoulCutSoft::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\n",i,j,lambda[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairCoulCutSoft::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double forcecoul,phicoul;
double denc;
if (rsq < cutsq[itype][jtype]) {
denc = sqrt(lam2[itype][jtype] + rsq);
forcecoul = force->qqrd2e * lam1[itype][jtype] * atom->q[i]*atom->q[j] /
(denc*denc*denc);
} else forcecoul = 0.0;
fforce = factor_coul*forcecoul;
if (rsq < cutsq[itype][jtype])
phicoul = force->qqrd2e * lam1[itype][jtype] * atom->q[i]*atom->q[j] / denc;
else phicoul = 0.0;
return factor_coul*phicoul;
}
/* ---------------------------------------------------------------------- */
void *PairCoulCutSoft::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"lambda") == 0) return (void *) lambda;
return NULL;
}
Event Timeline
Log In to Comment