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lammps/src/MISC/pair_nm_cut.cpp
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pair_nm_cut.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: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_nm_cut.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairNMCut::PairNMCut(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairNMCut::~PairNMCut()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(e0);
memory->destroy(r0);
memory->destroy(nn);
memory->destroy(mm);
memory->destroy(nm);
memory->destroy(e0nm);
memory->destroy(r0n);
memory->destroy(r0m);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairNMCut::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,factor_lj;
double r,forcenm,rminv,rninv;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
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];
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)];
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]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rminv = pow(r2inv,mm[itype][jtype]/2.0);
rninv = pow(r2inv,nn[itype][jtype]/2.0);
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
fpair = factor_lj*forcenm*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) {
evdwl = e0nm[itype][jtype] *
(mm[itype][jtype]*r0n[itype][jtype]*rninv -
nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairNMCut::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(e0,n+1,n+1,"pair:e0");
memory->create(r0,n+1,n+1,"pair:r0");
memory->create(nn,n+1,n+1,"pair:nn");
memory->create(mm,n+1,n+1,"pair:mm");
memory->create(nm,n+1,n+1,"pair:nm");
memory->create(e0nm,n+1,n+1,"pair:e0nm");
memory->create(r0n,n+1,n+1,"pair:r0n");
memory->create(r0m,n+1,n+1,"pair:r0m");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairNMCut::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// 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 PairNMCut::coeff(int narg, char **arg)
{
if (narg < 6 || narg > 7)
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 e0_one = force->numeric(FLERR,arg[2]);
double r0_one = force->numeric(FLERR,arg[3]);
double nn_one = force->numeric(FLERR,arg[4]);
double mm_one = force->numeric(FLERR,arg[5]);
double cut_one = cut_global;
if (narg == 7) cut_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
e0[i][j] = e0_one;
r0[i][j] = r0_one;
nn[i][j] = nn_one;
mm[i][j] = mm_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairNMCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
nm[i][j] = nn[i][j]*mm[i][j];
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
r0n[i][j] = pow(r0[i][j],nn[i][j]);
r0m[i][j] = pow(r0[i][j],mm[i][j]);
if (offset_flag) {
offset[i][j] = e0nm[i][j] *
((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) -
(nn[i][j]*r0m[i][j] / pow(cut[i][j],mm[i][j])));
} else offset[i][j] = 0.0;
e0[j][i] = e0[i][j];
nn[j][i] = nn[i][j];
mm[j][i] = mm[i][j];
nm[j][i] = nm[i][j];
r0[j][i] = r0[i][j];
e0nm[j][i] = e0nm[i][j];
r0n[j][i] = r0n[i][j];
r0m[j][i] = r0m[i][j];
offset[j][i] = offset[i][j];
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
double p1 = 1-nn[i][j];
double p2 = 1-mm[i][j];
double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
(rr1*pow(cut[i][j],p1)-rr2*pow(cut[i][j],p2));
ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
nn[i][j]*mm[i][j]*(rrr1*pow(cut[i][j],p1)-rrr2*pow(cut[i][j],p2));
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairNMCut::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(&e0[i][j],sizeof(double),1,fp);
fwrite(&r0[i][j],sizeof(double),1,fp);
fwrite(&nn[i][j],sizeof(double),1,fp);
fwrite(&mm[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairNMCut::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(&e0[i][j],sizeof(double),1,fp);
fread(&r0[i][j],sizeof(double),1,fp);
fread(&nn[i][j],sizeof(double),1,fp);
fread(&mm[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&mm[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairNMCut::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairNMCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
}
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);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairNMCut::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairNMCut::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 %g\n",i,j,
e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairNMCut::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,forcenm,phinm;
r2inv = 1.0/rsq;
r = sqrt(rsq);
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
fforce = factor_lj*forcenm*r2inv;
phinm = e0nm[itype][jtype] *
(mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) -
offset[itype][jtype];
return factor_lj*phinm;
}
/* ---------------------------------------------------------------------- */
void *PairNMCut::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"e0") == 0) return (void *) e0;
if (strcmp(str,"r0") == 0) return (void *) r0;
if (strcmp(str,"nn") == 0) return (void *) nn;
if (strcmp(str,"mm") == 0) return (void *) mm;
return NULL;
}
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