forked from lijiext/lammps
376 lines
11 KiB
C++
376 lines
11 KiB
C++
/* -*- 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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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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Contributing author:
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Rodolfo Paula Leite (Unicamp/Brazil) - pl.rodolfo@gmail.com
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Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
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------------------------------------------------------------------------- */
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#include "pair_ufm.h"
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#include <cmath>
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#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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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 "neigh_request.h"
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#include "update.h"
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#include "integrate.h"
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#include "respa.h"
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#include "math_const.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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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairUFM::PairUFM(LAMMPS *lmp) : Pair(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairUFM::~PairUFM()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(cut);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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memory->destroy(scale);
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memory->destroy(uf1);
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memory->destroy(uf2);
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memory->destroy(uf3);
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memory->destroy(uf4);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairUFM::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 xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq, expuf, factor;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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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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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 = special_lj[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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expuf = exp(- rsq * uf2[itype][jtype]);
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fpair = factor * scale[itype][jtype] * uf1[itype][jtype] * expuf /(1.0 - expuf);
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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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evdwl = -uf3[itype][jtype] * log(1.0 - expuf) - offset[itype][jtype];
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evdwl *= factor;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,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 PairUFM::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(epsilon,n+1,n+1,"pair:epsilon");
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memory->create(sigma,n+1,n+1,"pair:sigma");
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memory->create(scale,n+1,n+1,"pair:scale");
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memory->create(uf1,n+1,n+1,"pair:uf1");
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memory->create(uf2,n+1,n+1,"pair:uf2");
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memory->create(uf3,n+1,n+1,"pair:uf3");
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memory->create(uf4,n+1,n+1,"pair:uf4");
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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 PairUFM::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(FLERR,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 PairUFM::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 5)
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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(FLERR,arg[0],atom->ntypes,ilo,ihi);
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force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
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double epsilon_one = force->numeric(FLERR,arg[2]);
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double sigma_one = force->numeric(FLERR,arg[3]);
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double cut_one = cut_global;
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if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
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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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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_one;
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scale[i][j] = 1.0;
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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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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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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 PairUFM::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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uf1[i][j] = 2.0 * epsilon[i][j] / pow(sigma[i][j],2.0);
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uf2[i][j] = 1.0 / pow(sigma[i][j],2.0);
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uf3[i][j] = epsilon[i][j];
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uf4[i][j] = sigma[i][j];
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if (offset_flag) {
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double ratio = pow(cut[i][j] / sigma[i][j],2.0);
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offset[i][j] = - epsilon[i][j] * log ( 1.0 - exp( -ratio )) ;
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} else offset[i][j] = 0.0;
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uf1[j][i] = uf1[i][j];
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uf2[j][i] = uf2[i][j];
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uf3[j][i] = uf3[i][j];
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uf4[j][i] = uf4[i][j];
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scale[j][i] = scale[i][j];
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offset[j][i] = offset[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 PairUFM::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(&epsilon[i][j],sizeof(double),1,fp);
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fwrite(&sigma[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 PairUFM::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 (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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fread(&epsilon[i][j],sizeof(double),1,fp);
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fread(&sigma[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(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[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 PairUFM::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 PairUFM::read_restart_settings(FILE *fp)
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{
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int me = comm->me;
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if (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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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void PairUFM::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes all pairs to data file
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------------------------------------------------------------------------- */
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void PairUFM::write_data_all(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = i; j <= atom->ntypes; j++)
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fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairUFM::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
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double /*factor_coul*/, double factor_lj,
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double &fforce)
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{
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double expuf,phiuf;
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expuf = exp(- rsq * uf2[itype][jtype]);
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fforce = factor_lj * uf1[itype][jtype] * expuf /(1.0 - expuf);
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phiuf = - uf3[itype][jtype] * log(1.0 - expuf) - offset[itype][jtype];
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return factor_lj * phiuf;
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}
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/* ---------------------------------------------------------------------- */
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void *PairUFM::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
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if (strcmp(str,"sigma") == 0) return (void *) sigma;
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if (strcmp(str,"scale") == 0) return (void *) scale;
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return NULL;
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}
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