add new pair styles harmonic/cut and harmonic/cut/omp
This commit is contained in:
Axel Kohlmeyer
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -1489,6 +1489,8 @@
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/pair_dpd_fdt.h
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/pair_dpd_fdt_energy.cpp
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/pair_dpd_fdt_energy.h
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/pair_harmonic_cut.cpp
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/pair_harmonic_cut.h
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/pair_lennard_mdf.cpp
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/pair_lennard_mdf.h
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/pair_lj_cut_coul_long_cs.cpp
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314
src/EXTRA-PAIR/pair_harmonic_cut.cpp
Normal file
314
src/EXTRA-PAIR/pair_harmonic_cut.cpp
Normal file
@ -0,0 +1,314 @@
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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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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: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "pair_harmonic_cut.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 "neighbor.h"
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#include "update.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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PairHarmonicCut::PairHarmonicCut(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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PairHarmonicCut::~PairHarmonicCut()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(cut);
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memory->destroy(cutsq);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairHarmonicCut::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, fxtmp, fytmp, fztmp;
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double delx, dely, delz, rsq, factor_lj;
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int *ilist, *jlist, *numneigh, **firstneigh;
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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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fxtmp = fytmp = fztmp = 0.0;
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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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const double r = sqrt(rsq);
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const double delta = cut[itype][jtype] - r;
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const double philj = factor_lj * delta * k[itype][jtype];
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const double fpair = delta * philj / r;
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fxtmp += delx * fpair;
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fytmp += dely * fpair;
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fztmp += 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 (evflag) ev_tally(i, j, nlocal, newton_pair, philj, 0.0, fpair, delx, dely, delz);
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}
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}
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f[i][0] += fxtmp;
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f[i][1] += fytmp;
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f[i][2] += fztmp;
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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 PairHarmonicCut::allocate()
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{
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allocated = 1;
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int n = atom->ntypes + 1;
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memory->create(setflag, n, n, "pair:setflag");
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for (int i = 1; i < n; i++)
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for (int j = i; j < n; j++) setflag[i][j] = 0;
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memory->create(k, n, n, "pair:k");
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memory->create(cut, n, n, "pair:cut");
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memory->create(cutsq, n, n, "pair:cutsq");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairHarmonicCut::settings(int narg, char **arg)
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{
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if (narg > 0) error->all(FLERR, "Illegal pair_style command");
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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 PairHarmonicCut::coeff(int narg, char **arg)
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{
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if (narg != 4) 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 k_one = utils::numeric(FLERR, arg[2], false, lmp);
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double cut_one = utils::numeric(FLERR, arg[3], 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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k[i][j] = k_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 PairHarmonicCut::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
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cut[j][i] = cut[i][j];
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k[i][j] = mix_energy(k[i][i], k[j][j], cut[i][i], cut[j][j]);
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k[j][i] = k[i][j];
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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 PairHarmonicCut::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(&k[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 PairHarmonicCut::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, &k[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(&k[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 PairHarmonicCut::write_restart_settings(FILE *fp)
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{
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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 PairHarmonicCut::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, &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(&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 PairHarmonicCut::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g %g\n", i, k[i][i], cut[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 PairHarmonicCut::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++) fprintf(fp, "%d %d %g %g\n", i, j, k[i][j], cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairHarmonicCut::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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if (rsq >= cutsq[itype][jtype]) {
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fforce = 0.0;
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return 0.0;
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}
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const double r = sqrt(rsq);
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const double delta = cut[itype][jtype] - r;
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const double philj = factor_lj * delta * k[itype][jtype];
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fforce = delta * philj / r;
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return philj;
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}
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/* ---------------------------------------------------------------------- */
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void *PairHarmonicCut::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str, "k") == 0) return (void *) k;
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if (strcmp(str, "cut") == 0) return (void *) cut;
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return nullptr;
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}
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72
src/EXTRA-PAIR/pair_harmonic_cut.h
Normal file
72
src/EXTRA-PAIR/pair_harmonic_cut.h
Normal file
@ -0,0 +1,72 @@
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/* -*- 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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Steve Plimpton, sjplimp@sandia.gov
|
||||
|
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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.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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// clang-format off
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PairStyle(harmonic/cut,PairHarmonicCut);
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// clang-format on
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#else
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#ifndef LMP_PAIR_HARMONIC_CUT_H
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#define LMP_PAIR_HARMONIC_CUT_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairHarmonicCut : public Pair {
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public:
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PairHarmonicCut(class LAMMPS *);
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virtual ~PairHarmonicCut();
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virtual void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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double init_one(int, int);
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void write_restart(FILE *);
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void read_restart(FILE *);
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void write_restart_settings(FILE *);
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void read_restart_settings(FILE *);
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void write_data(FILE *);
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void write_data_all(FILE *);
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double single(int, int, int, int, double, double, double, double &);
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void *extract(const char *, int &);
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protected:
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double **k, **cut;
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virtual void allocate();
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Incorrect args for pair coefficients
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Self-explanatory. Check the input script or data file.
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E: Pair cutoff < Respa interior cutoff
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One or more pairwise cutoffs are too short to use with the specified
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rRESPA cutoffs.
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*/
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152
src/OPENMP/pair_harmonic_cut_omp.cpp
Normal file
152
src/OPENMP/pair_harmonic_cut_omp.cpp
Normal file
@ -0,0 +1,152 @@
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/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
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------------------------------------------------------------------------- */
|
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|
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#include "pair_harmonic_cut_omp.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 "neigh_list.h"
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#include "suffix.h"
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#include "omp_compat.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairHarmonicCutOMP::PairHarmonicCutOMP(LAMMPS *lmp) : PairHarmonicCut(lmp), ThrOMP(lmp, THR_PAIR)
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{
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suffix_flag |= Suffix::OMP;
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}
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/* ---------------------------------------------------------------------- */
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void PairHarmonicCutOMP::compute(int eflag, int vflag)
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{
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ev_init(eflag, vflag);
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const int nall = atom->nlocal + atom->nghost;
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const int nthreads = comm->nthreads;
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const int inum = list->inum;
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#if defined(_OPENMP)
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#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(eflag, vflag)
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#endif
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{
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int ifrom, ito, tid;
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loop_setup_thr(ifrom, ito, tid, inum, nthreads);
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ThrData *thr = fix->get_thr(tid);
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thr->timer(Timer::START);
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ev_setup_thr(eflag, vflag, nall, eatom, vatom, nullptr, thr);
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if (evflag) {
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if (eflag) {
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if (force->newton_pair)
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eval<1, 1, 1>(ifrom, ito, thr);
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else
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eval<1, 1, 0>(ifrom, ito, thr);
|
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} else {
|
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if (force->newton_pair)
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eval<1, 0, 1>(ifrom, ito, thr);
|
||||
else
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||||
eval<1, 0, 0>(ifrom, ito, thr);
|
||||
}
|
||||
} else {
|
||||
if (force->newton_pair)
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eval<0, 0, 1>(ifrom, ito, thr);
|
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else
|
||||
eval<0, 0, 0>(ifrom, ito, thr);
|
||||
}
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||||
thr->timer(Timer::PAIR);
|
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reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
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template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void PairHarmonicCutOMP::eval(int iifrom, int iito, ThrData *const thr)
|
||||
{
|
||||
const dbl3_t *_noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t *_noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const int *_noalias const type = atom->type;
|
||||
const double *_noalias const special_lj = force->special_lj;
|
||||
const int *_noalias const ilist = list->ilist;
|
||||
const int *_noalias const numneigh = list->numneigh;
|
||||
const int *const *const firstneigh = list->firstneigh;
|
||||
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fxtmp, fytmp, fztmp;
|
||||
double rsq, factor_lj;
|
||||
|
||||
const int nlocal = atom->nlocal;
|
||||
int j, jj, jnum, jtype;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (int ii = iifrom; ii < iito; ++ii) {
|
||||
const int i = ilist[ii];
|
||||
const int itype = type[i];
|
||||
const int *_noalias const jlist = firstneigh[i];
|
||||
const double *_noalias const cutsqi = cutsq[itype];
|
||||
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
jnum = numneigh[i];
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsqi[jtype]) {
|
||||
const double r = sqrt(rsq);
|
||||
const double delta = cut[itype][jtype] - r;
|
||||
const double philj = factor_lj * delta * k[itype][jtype];
|
||||
const double fpair = delta * philj / r;
|
||||
|
||||
fxtmp += delx * fpair;
|
||||
fytmp += dely * fpair;
|
||||
fztmp += delz * fpair;
|
||||
if (NEWTON_PAIR || j < nlocal) {
|
||||
f[j].x -= delx * fpair;
|
||||
f[j].y -= dely * fpair;
|
||||
f[j].z -= delz * fpair;
|
||||
}
|
||||
|
||||
if (EVFLAG)
|
||||
ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, philj, 0.0, fpair, delx, dely, delz, thr);
|
||||
}
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairHarmonicCutOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairHarmonicCut::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
48
src/OPENMP/pair_harmonic_cut_omp.h
Normal file
48
src/OPENMP/pair_harmonic_cut_omp.h
Normal file
@ -0,0 +1,48 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, 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: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
// clang-format off
|
||||
PairStyle(harmonic/cut/omp,PairHarmonicCutOMP);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_HARMONIC_CUT_OMP_H
|
||||
#define LMP_PAIR_HARMONIC_CUT_OMP_H
|
||||
|
||||
#include "pair_harmonic_cut.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairHarmonicCutOMP : public PairHarmonicCut, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairHarmonicCutOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int NEWTON_PAIR>
|
||||
void eval(int ifrom, int ito, ThrData *const thr);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Reference in New Issue
Block a user