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added the pair files

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Simon_nimbus
2020-10-20 11:50:57 +01:00
parent a77bb30730
commit 09f6d1fa57
2 changed files with 479 additions and 0 deletions
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src/pair_wf.cpp Normal file
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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 Authors: Xipeng Wang, Simon Ramirez-Hinestrosa
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_wf.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;
/* ---------------------------------------------------------------------- */
PairWF::PairWF(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
PairWF::~PairWF()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(nu);
memory->destroy(mu);
memory->destroy(nm);
memory->destroy(e0nm); //Alpha * epsilon
memory->destroy(rcmu);
memory->destroy(sigma_mu);
memory->destroy(offset);
}
}
/* ---------------------------------------------------------------------- */
void PairWF::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, rm, rn;
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,mu[itype][jtype]);
rm = sigma_mu[itype][jtype]*rminv - 1.0;
rn = rcmu[itype][jtype]*rminv - 1.0;
forcenm = 2.0*mu[itype][jtype] *sigma_mu[itype][jtype]*pow(rn,2.0*nu[itype][jtype])
+ 4.0*nm[itype][jtype] *rcmu[itype][jtype]*rm*pow(rn,2.0*nu[itype][jtype]-1.0);
fpair = factor_lj*e0nm[itype][jtype]*forcenm*pow(r2inv,mu[itype][jtype]+1.0);
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] *
(rm*pow(rn,2.0*nu[itype][jtype])) - 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 PairWF::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(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(nu,n+1,n+1,"pair:nu");
memory->create(mu,n+1,n+1,"pair:mu");
memory->create(nm,n+1,n+1,"pair:nm");
memory->create(e0nm,n+1,n+1,"pair:e0nm");
memory->create(rcmu,n+1,n+1,"pair:rcmu");
memory->create(sigma_mu,n+1,n+1,"pair:sigma_mu");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairWF::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; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairWF::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(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 nu_one = force->numeric(FLERR,arg[4]);
double mu_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++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
nu[i][j] = nu_one;
mu[i][j] = mu_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 PairWF::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
nm[i][j] = nu[i][j]*mu[i][j];
e0nm[i][j] = epsilon[i][j]*2.0*nu[i][j]*pow(cut[i][j]/sigma[i][j],2.0*mu[i][j])
*pow((1+2.0*nu[i][j])/(2.0*nu[i][j])/(pow(cut[i][j]/sigma[i][j],2.0*mu[i][j])-1.0),
2.0*nu[i][j]+1.0);
rcmu[i][j] = pow(cut[i][j],2.0*mu[i][j]);
sigma_mu[i][j] = pow(sigma[i][j], 2.0*mu[i][j]);
if (offset_flag && (cut[i][j] > 0.0)) {
offset[i][j] = 0.0;
} else offset[i][j] = 0.0;
epsilon[j][i] = epsilon[i][j];
nu[j][i] = nu[i][j];
mu[j][i] = mu[i][j];
nm[j][i] = nm[i][j];
sigma[j][i] = sigma[i][j];
e0nm[j][i] = e0nm[i][j];
rcmu[j][i] = rcmu[i][j];
sigma_mu[j][i] = sigma_mu[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairWF::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(&nu[i][j],sizeof(double),1,fp);
fwrite(&mu[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairWF::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(&nu[i][j],sizeof(double),1,fp);
fread(&mu[i][j],sizeof(double),1,fp);
fread(&cut[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(&nu[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&mu[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairWF::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 PairWF::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 PairWF::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],nu[i][i],mu[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairWF::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,
epsilon[i][j],sigma[i][j],nu[i][j],mu[i][j],cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairWF::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r2inv,r, rminv, rm, rn, forcenm,phinm;
r2inv = 1.0/rsq;
r = sqrt(rsq);
r2inv = 1.0/rsq;
r = sqrt(rsq);
rminv = pow(r2inv,mu[itype][jtype]);
rm = sigma_mu[itype][jtype]*rminv - 1.0;
rn = rcmu[itype][jtype]*rminv - 1.0;
forcenm = 2.0*mu[itype][jtype] *sigma_mu[itype][jtype]*pow(rn,2.0*nu[itype][jtype])
+ 4.0*nm[itype][jtype] *rcmu[itype][jtype]*rm*pow(rn,2.0*nu[itype][jtype]-1.0);
fforce = factor_lj*e0nm[itype][jtype]*forcenm*pow(r2inv,mu[itype][jtype]+1.0);
phinm = e0nm[itype][jtype] * rm*pow(rn,2.0*nu[itype][jtype]) -
offset[itype][jtype];
return factor_lj*phinm;
}
/* ---------------------------------------------------------------------- */
void *PairWF::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"nu") == 0) return (void *) nu;
if (strcmp(str,"mu") == 0) return (void *) mu;
return NULL;
}

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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(wf,PairWF)
#else
#ifndef LMP_PAIR_WF
#define LMP_PAIR_WF
#include "pair.h"
namespace LAMMPS_NS {
class PairWF : public Pair {
public:
PairWF(class LAMMPS *);
virtual ~PairWF();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
protected:
double cut_global;
double **cut;
double **epsilon,**sigma,**nu, **mu;
double **nm,**e0nm,**rcmu,**sigma_mu,**offset;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/