423 lines
13 KiB
C++
423 lines
13 KiB
C++
/* ----------------------------------------------------------------------
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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_expand.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "math_const.h"
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#include "memory.h"
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#include "neigh_list.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairLJExpand::PairLJExpand(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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PairLJExpand::~PairLJExpand()
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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(shift);
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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(lj4);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJExpand::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, r2inv, r6inv, forcelj, factor_lj;
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double r, rshift, rshiftsq;
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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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r = sqrt(rsq);
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rshift = r - shift[itype][jtype];
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rshiftsq = rshift * rshift;
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r2inv = 1.0 / rshiftsq;
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r6inv = r2inv * r2inv * r2inv;
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forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
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fpair = factor_lj * forcelj / rshift / 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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evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - 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, 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 PairLJExpand::allocate()
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{
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allocated = 1;
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int np1 = atom->ntypes + 1;
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memory->create(setflag, np1, np1, "pair:setflag");
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for (int i = 1; i < np1; i++)
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for (int j = i; j < np1; j++) setflag[i][j] = 0;
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memory->create(cutsq, np1, np1, "pair:cutsq");
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memory->create(cut, np1, np1, "pair:cut");
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memory->create(epsilon, np1, np1, "pair:epsilon");
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memory->create(sigma, np1, np1, "pair:sigma");
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memory->create(shift, np1, np1, "pair:shift");
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memory->create(lj1, np1, np1, "pair:lj1");
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memory->create(lj2, np1, np1, "pair:lj2");
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memory->create(lj3, np1, np1, "pair:lj3");
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memory->create(lj4, np1, np1, "pair:lj4");
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memory->create(offset, np1, np1, "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 PairLJExpand::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 = utils::numeric(FLERR, arg[0], 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 PairLJExpand::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 shift_one = utils::numeric(FLERR, arg[4], false, lmp);
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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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shift[i][j] = shift_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 PairLJExpand::init_one(int i, int j)
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{
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// always mix shift arithmetically
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], 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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shift[i][j] = 0.5 * (shift[i][i] + shift[j][j]);
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}
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
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if (offset_flag && (cut[i][j] > 0.0)) {
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double ratio = sigma[i][j] / (cut[i][j] + shift[i][j]);
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offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0));
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} else
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offset[i][j] = 0.0;
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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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lj4[j][i] = lj4[i][j];
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shift[j][i] = shift[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 sig2 = sigma[i][j] * sigma[i][j];
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double sig6 = sig2 * sig2 * sig2;
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double rc1 = cut[i][j];
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double rc2 = rc1 * rc1;
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double rc3 = rc2 * rc1;
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double rc9 = rc3 * rc3 * rc3;
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double shift1 = shift[i][j];
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double shift2 = shift1 * shift1;
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double shift3 = shift2 * shift1;
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etail_ij = 8.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 *
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((1.0 / 9.0 + 2.0 * shift1 / (10.0 * rc1) + shift2 / (11.0 * rc2)) * sig6 / rc9 -
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(1.0 / 3.0 + 2.0 * shift1 / (4.0 * rc1) + shift2 / (5.0 * rc2)) / rc3);
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ptail_ij = 16.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 *
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((1.0 / 9.0 + 3.0 * shift1 / (10.0 * rc1) + 3.0 * shift2 / (11.0 * rc2) +
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shift3 / (12.0 * rc3)) *
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2.0 * sig6 / rc9 -
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(1.0 / 3.0 + 3.0 * shift1 / (4.0 * rc1) + 3.0 * shift2 / (5.0 * rc2) +
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shift3 / (6.0 * rc3)) /
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rc3);
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}
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return cut[i][j] + shift[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 PairLJExpand::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(&shift[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 PairLJExpand::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, &shift[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(&shift[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 PairLJExpand::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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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 PairLJExpand::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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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(&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 PairLJExpand::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], shift[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 PairLJExpand::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], shift[i][j], cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
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double /*factor_coul*/, double factor_lj, double &fforce)
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{
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double r, rshift, rshiftsq, r2inv, r6inv, forcelj, philj;
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r = sqrt(rsq);
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rshift = r - shift[itype][jtype];
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rshiftsq = rshift * rshift;
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r2inv = 1.0 / rshiftsq;
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r6inv = r2inv * r2inv * r2inv;
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forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
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fforce = factor_lj * forcelj / rshift / r;
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philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
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return factor_lj * philj;
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}
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/* ---------------------------------------------------------------------- */
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void *PairLJExpand::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, "delta") == 0) return (void *) shift;
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return nullptr;
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}
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