438 lines
14 KiB
C++
438 lines
14 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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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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#include "pair_lj_class2_soft.h"
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#include <cmath>
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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 "neigh_list.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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PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp)
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{
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writedata = 1;
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centroidstressflag = CENTROID_SAME;
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}
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/* ---------------------------------------------------------------------- */
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PairLJClass2Soft::~PairLJClass2Soft()
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{
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if (copymode) return;
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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(lambda);
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memory->destroy(lj1);
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJClass2Soft::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,forcelj,factor_lj;
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double denlj, r4sig6;
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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_lj = 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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denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
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r4sig6 = rsq*rsq / lj2[itype][jtype];
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forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
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(18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2));
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fpair = factor_lj*forcelj;
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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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denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0);
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evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
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offset[itype][jtype];
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evdwl *= factor_lj;
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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 PairLJClass2Soft::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(lambda,n+1,n+1,"pair:lambda");
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memory->create(lj1,n+1,n+1,"pair:lj1");
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memory->create(lj2,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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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 PairLJClass2Soft::settings(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR,"Illegal pair_style command");
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nlambda = utils::numeric(FLERR,arg[0],false,lmp);
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alphalj = utils::numeric(FLERR,arg[1],false,lmp);
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cut_global = utils::numeric(FLERR,arg[2],false,lmp);
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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; 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 PairLJClass2Soft::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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utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
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utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
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double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp);
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double sigma_one = utils::numeric(FLERR,arg[3],false,lmp);
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double lambda_one = utils::numeric(FLERR,arg[4],false,lmp);
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if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients");
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double cut_one = cut_global;
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if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
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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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lambda[i][j] = lambda_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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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 PairLJClass2Soft::init_one(int i, int j)
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{
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// always mix epsilon,sigma via sixthpower rules
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// mix distance via user-defined rule
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if (setflag[i][j] == 0) {
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epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
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pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
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(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
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sigma[i][j] =
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pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
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if (lambda[i][i] != lambda[j][j])
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error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix");
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lambda[i][j] = lambda[i][i];
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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lj1[i][j] = pow(lambda[i][j], nlambda);
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lj2[i][j] = pow(sigma[i][j], 6.0);
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lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]);
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if (offset_flag && (cut[i][j] > 0.0)) {
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double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0);
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offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj);
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} else offset[i][j] = 0.0;
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epsilon[j][i] = epsilon[i][j];
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sigma[j][i] = sigma[i][j];
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lambda[j][i] = lambda[i][j];
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lj1[j][i] = lj1[i][j];
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lj2[j][i] = lj2[i][j];
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lj3[j][i] = lj3[i][j];
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offset[j][i] = offset[i][j];
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// compute I,J contribution to long-range tail correction
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// count total # of atoms of type I and J via Allreduce
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if (tail_flag) {
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double count[2],all[2];
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count[0] = count[1] = 0.0;
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for (int k = 0; k < nlocal; k++) {
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if (type[k] == i) count[0] += 1.0;
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if (type[k] == j) count[1] += 1.0;
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}
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MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
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double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
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double sig6 = sig3*sig3;
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double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
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double rc6 = rc3*rc3;
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// check the following expressions for etail_lj & ptail_ij they are not correct !
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etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
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sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
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ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] *
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sig6 * (sig3 - 2.0*rc3) / rc6;
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}
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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 PairLJClass2Soft::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(&lambda[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 PairLJClass2Soft::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
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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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utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&lambda[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
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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(&lambda[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 PairLJClass2Soft::write_restart_settings(FILE *fp)
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{
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fwrite(&nlambda,sizeof(double),1,fp);
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fwrite(&alphalj,sizeof(double),1,fp);
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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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fwrite(&tail_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 PairLJClass2Soft::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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utils::sfread(FLERR,&nlambda,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&alphalj,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
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utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
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utils::sfread(FLERR,&tail_flag,sizeof(int),1,fp,nullptr,error);
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}
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MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world);
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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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MPI_Bcast(&tail_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 PairLJClass2Soft::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 %g\n",i,epsilon[i][i],sigma[i][i],lambda[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 PairLJClass2Soft::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 %g\n",i,j,epsilon[i][j],sigma[i][j],
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lambda[i][j],cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairLJClass2Soft::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 forcelj,philj;
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double r4sig6, denlj;
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if (rsq < cutsq[itype][jtype]) {
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r4sig6 = rsq*rsq / lj2[itype][jtype];
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denlj = lj3[itype][jtype] + rsq*r4sig6;
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forcelj = lj1[itype][jtype] * epsilon[itype][jtype] *
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(18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj));
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} else forcelj = 0.0;
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fforce = factor_lj*forcelj;
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if (rsq < cutsq[itype][jtype]) {
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denlj = lj3[itype][jtype] + rsq*rsq*rsq / lj2[itype][jtype];
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philj = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) -
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offset[itype][jtype];
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} else philj = 0.0;
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return factor_lj*philj;
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}
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/* ---------------------------------------------------------------------- */
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void *PairLJClass2Soft::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,"lambda") == 0) return (void *) lambda;
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return nullptr;
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}
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