mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7254 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
e2d5ab683f
commit
0dacc993ae
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "pair_coul_diel.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairCoulDiel::PairCoulDiel(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairCoulDiel::~PairCoulDiel()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(sigmae);
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memory->destroy(rme);
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memory->destroy(offset);
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memory->destroy(cutsq);
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memory->destroy(cut);
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allocated = 0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulDiel::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
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double rsq,r,rarg,th,depsdr,epsr,forcecoul,factor_coul;
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int *ilist,*jlist,*numneigh,**firstneigh;
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ecoul = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_coul = force->special_coul;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r = sqrt(rsq);
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rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
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th=tanh(rarg);
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epsr=a_eps+b_eps*th;
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depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
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forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
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fpair = factor_coul*forcecoul/r;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (eflag) {
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ecoul = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
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ecoul *= factor_coul;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,
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ecoul,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairCoulDiel::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(cut,n+1,n+1,"pair:cut");
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memory->create(sigmae,n+1,n+1,"pair:sigmae");
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memory->create(rme,n+1,n+1,"pair:rme");
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memory->create(offset,n+1,n+1,"pair:offset");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairCoulDiel::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(arg[0]);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairCoulDiel::coeff(int narg, char **arg)
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{
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if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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eps_s = force->numeric(arg[2]);
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double rme_one =force->numeric(arg[3]);
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double sigmae_one = force->numeric(arg[4]);
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double cut_one = cut_global;
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if (narg == 6) cut_one = force->numeric(arg[5]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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sigmae[i][j] = sigmae_one;
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rme[i][j] = rme_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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a_eps = 0.5*(5.2+eps_s);
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b_eps = 0.5*(eps_s-5.2);
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairCoulDiel::init_style()
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{
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if (!atom->q_flag)
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error->all(FLERR,"Pair style coul/diel requires atom attribute q");
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int irequest = neighbor->request(this);
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairCoulDiel::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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error->all(FLERR,"for pair style coul/diel, parameters need to be set explicitly for all pairs.");
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}
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double *q = atom->q;
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double qqrd2e = force->qqrd2e;
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if (offset_flag) {
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double rarg = (cut[i][j]-rme[i][j])/sigmae[i][j];
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double epsr=a_eps+b_eps*tanh(rarg);
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offset[i][j] = qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/cut[i][j];
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} else offset[i][j] = 0.0;
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sigmae[j][i] = sigmae[i][j];
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rme[j][i] = rme[i][j];
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offset[j][i] = offset[i][j];
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cut[j][i] = cut[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairCoulDiel::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&rme[i][j],sizeof(double),1,fp);
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fwrite(&sigmae[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairCoulDiel::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (setflag[i][j]) {
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if (me == 0) {
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fread(&rme[i][j],sizeof(double),1,fp);
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fread(&sigmae[i][j],sizeof(double),1,fp);
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fread(&cut[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairCoulDiel::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairCoulDiel::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&cut_global,sizeof(double),1,fp);
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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}
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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double PairCoulDiel::single(int i, int j, int itype, int jtype,
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double rsq, double factor_coul, double factor_lj,
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double &fforce)
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{
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double r, rarg,forcedielec,phidielec;
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double th,epsr,depsdr;
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double *q = atom->q;
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double qqrd2e = force->qqrd2e;
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r=sqrt(rsq);
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rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
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th = tanh(rarg);
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epsr=a_eps+b_eps*th;
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depsdr=b_eps*(1.-th*th)/sigmae[itype][jtype];
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forcedielec = qqrd2e*q[i]*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
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fforce = factor_coul*forcedielec/r;
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phidielec = (qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/r)- offset[itype][jtype];
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return factor_coul*phidielec;
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}
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@ -0,0 +1,57 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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|
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Copyright (2003) Sandia Corporation. Under the terms of Contract
|
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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.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(coul/diel,PairCoulDiel)
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#else
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#ifndef LMP_PAIR_COUL_DIEL_H
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#define LMP_PAIR_COUL_DIEL_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairCoulDiel : public Pair {
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public:
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PairCoulDiel(class LAMMPS *);
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virtual ~PairCoulDiel();
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virtual void compute(int, int);
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virtual void settings(int, char **);
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virtual void coeff(int, char **);
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virtual void init_style();
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virtual double init_one(int, int);
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virtual void write_restart(FILE *);
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virtual void read_restart(FILE *);
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virtual void write_restart_settings(FILE *);
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virtual void read_restart_settings(FILE *);
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virtual double single(int, int, int, int, double, double, double, double &);
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protected:
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double cut_global;
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double **cut;
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double **sigmae, **rme, **offset;
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double a_eps, b_eps, eps_s;
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void allocate();
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};
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}
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#endif
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#endif
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@ -0,0 +1,371 @@
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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: Arben Jusufi, Axel Kohlmeyer (Temple U.)
|
||||
------------------------------------------------------------------------- */
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|
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "pair_gauss_cut.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "update.h"
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#include "integrate.h"
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#include "memory.h"
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#include "error.h"
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#include "math_const.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairGaussCut::PairGaussCut(LAMMPS *lmp) : Pair(lmp)
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{
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respa_enable = 0;
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}
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||||
/* ---------------------------------------------------------------------- */
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||||
PairGaussCut::~PairGaussCut()
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{
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if (allocated) {
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memory->destroy(setflag);
|
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memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
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memory->destroy(hgauss);
|
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memory->destroy(sigmah);
|
||||
memory->destroy(rmh);
|
||||
memory->destroy(pgauss);
|
||||
memory->destroy(offset);
|
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}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::compute(int eflag, int vflag)
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{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r,rexp,ugauss,factor_lj;
|
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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]) {
|
||||
r = sqrt(rsq);
|
||||
rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
|
||||
ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
|
||||
fpair = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
|
||||
|
||||
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 = ugauss - 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 PairGaussCut::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(hgauss,n+1,n+1,"pair:hgauss");
|
||||
memory->create(sigmah,n+1,n+1,"pair:sigmah");
|
||||
memory->create(rmh,n+1,n+1,"pair:rmh");
|
||||
memory->create(pgauss,n+1,n+1,"pair:pgauss");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_global = force->numeric(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 PairGaussCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 5 || narg > 6) 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 hgauss_one = force->numeric(arg[2]);
|
||||
double rmh_one = force->numeric(arg[3]);
|
||||
double sigmah_one = force->numeric(arg[4]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 6) cut_one = force->numeric(arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
hgauss[i][j] = hgauss_one;
|
||||
sigmah[i][j] = sigmah_one;
|
||||
rmh[i][j] = rmh_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 PairGaussCut::init_one(int i, int j)
|
||||
{
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all(FLERR,"for gauss/cut pair style, parameters need to be set explicitly for all pairs.");
|
||||
}
|
||||
pgauss[i][j] = hgauss[i][j] / sqrt(MY_2PI)/ sigmah[i][j];
|
||||
|
||||
|
||||
if (offset_flag) {
|
||||
double rexp = (cut[i][j]-rmh[i][j])/sigmah[i][j];
|
||||
offset[i][j] = pgauss[i][j] * exp(-0.5*rexp*rexp);
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
hgauss[j][i] = hgauss[i][j];
|
||||
sigmah[j][i] = sigmah[i][j];
|
||||
rmh[j][i] = rmh[i][j];
|
||||
pgauss[j][i] = pgauss[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
cut[j][i] = cut[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);
|
||||
}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::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(&hgauss[i][j],sizeof(double),1,fp);
|
||||
fwrite(&rmh[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigmah[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::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(&hgauss[i][j],sizeof(double),1,fp);
|
||||
fread(&rmh[i][j],sizeof(double),1,fp);
|
||||
fread(&sigmah[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&hgauss[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&rmh[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigmah[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::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);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGaussCut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_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);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGaussCut::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r, rexp,ugauss,phigauss;
|
||||
|
||||
r=sqrt(rsq);
|
||||
rexp = (r-rmh[itype][jtype])/sigmah[itype][jtype];
|
||||
ugauss = pgauss[itype][jtype]*exp(-0.5*rexp*rexp);
|
||||
|
||||
fforce = factor_lj*rexp/r*ugauss/sigmah[itype][jtype];
|
||||
|
||||
phigauss = ugauss - offset[itype][jtype];
|
||||
return factor_lj*phigauss;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
double PairGaussCut::memory_usage()
|
||||
{
|
||||
const int n=atom->ntypes;
|
||||
|
||||
double bytes = Pair::memory_usage();
|
||||
|
||||
bytes += 7*((n+1)*(n+1) * sizeof(double) + (n+1)*sizeof(double *));
|
||||
bytes += 1*((n+1)*(n+1) * sizeof(int) + (n+1)*sizeof(int *));
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
/* -*- 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(gauss/cut,PairGaussCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_GAUSS_CUT_H
|
||||
#define LMP_PAIR_GAUSS_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairGaussCut : public Pair {
|
||||
public:
|
||||
PairGaussCut(class LAMMPS *);
|
||||
~PairGaussCut();
|
||||
|
||||
virtual void compute(int, int);
|
||||
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
virtual void settings(int, char **);
|
||||
virtual void coeff(int, char **);
|
||||
|
||||
virtual double init_one(int, int);
|
||||
|
||||
virtual void write_restart(FILE *);
|
||||
virtual void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
|
||||
virtual double memory_usage();
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **hgauss,**sigmah,**rmh;
|
||||
double **pgauss,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,96 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Luca Ferraro (CASPUR)
|
||||
email: luca.ferraro@caspur.it
|
||||
|
||||
Tersoff Potential
|
||||
References:
|
||||
1) Tersoff, Phys. Rev. B 39, 5566 (1988)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tersoff/table,PairTersoffTable)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_Tersoff_H
|
||||
#define LMP_PAIR_Tersoff_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTersoffTable : public Pair {
|
||||
public:
|
||||
PairTersoffTable(class LAMMPS *);
|
||||
virtual ~PairTersoffTable();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void init_style();
|
||||
|
||||
protected:
|
||||
struct Param {
|
||||
double lam1,lam2,lam3;
|
||||
double c,d,h;
|
||||
double gamma,powerm;
|
||||
double powern,beta;
|
||||
double biga,bigb,cutoffR, cutoffS;
|
||||
double cut,cutsq;
|
||||
int ielement,jelement,kelement;
|
||||
int powermint;
|
||||
};
|
||||
|
||||
|
||||
double cutmax; // max cutoff for all elements
|
||||
int nelements; // # of unique elements
|
||||
char **elements; // names of unique elements
|
||||
int ***elem2param; // mapping from element triplets to parameters
|
||||
int *map; // mapping from atom types to elements
|
||||
int nparams; // # of stored parameter sets
|
||||
int maxparam; // max # of parameter sets
|
||||
Param *params; // parameter set for an I-J-K interaction
|
||||
|
||||
void allocate();
|
||||
|
||||
void read_file(char *);
|
||||
void setup();
|
||||
|
||||
// max number of interaction per atom for environment potential
|
||||
static const int leadingDimensionInteractionList = 64;
|
||||
// pre-loop coordination functions
|
||||
double **preGtetaFunction, **preGtetaFunctionDerived;
|
||||
double *preCutoffFunction, *preCutoffFunctionDerived;
|
||||
void allocatePreLoops(void);
|
||||
void deallocatePreLoops(void);
|
||||
// grids
|
||||
static const double GRIDSTART = 0.1;
|
||||
static const int GRIDDENSITY_FCUTOFF = 5000;
|
||||
static const int GRIDDENSITY_EXP = 12000;
|
||||
static const int GRIDDENSITY_GTETA = 12000;
|
||||
static const int GRIDDENSITY_BIJ = 7500;
|
||||
double minArgumentExponential;
|
||||
double *exponential, ***cutoffFunction, ***cutoffFunctionDerived;
|
||||
double **gtetaFunction, **gtetaFunctionDerived, **betaZetaPower, **betaZetaPowerDerived;
|
||||
void allocateGrids(void);
|
||||
void deallocateGrids(void);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue