459 lines
14 KiB
C++
459 lines
14 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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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "pair_lepton.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 "memory.h"
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#include "neigh_list.h"
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#include "Lepton.h"
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#include "lepton_utils.h"
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#include <cmath>
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#include <exception>
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#include <map>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairLepton::PairLepton(LAMMPS *lmp) :
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Pair(lmp), cut(nullptr), type2expression(nullptr), offset(nullptr)
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{
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respa_enable = 0;
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single_enable = 1;
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writedata = 1;
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restartinfo = 1;
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reinitflag = 0;
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cut_global = 0.0;
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centroidstressflag = CENTROID_SAME;
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functions["zbl"] = new Lepton::ZBLFunction(force->qqr2e, force->angstrom, force->qelectron);
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}
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/* ---------------------------------------------------------------------- */
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PairLepton::~PairLepton()
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{
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for (auto &f : functions) delete f.second;
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if (allocated) {
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memory->destroy(cut);
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memory->destroy(cutsq);
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memory->destroy(setflag);
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memory->destroy(type2expression);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLepton::compute(int eflag, int vflag)
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{
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ev_init(eflag, vflag);
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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>();
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else
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eval<1, 1, 0>();
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} else {
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if (force->newton_pair)
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eval<1, 0, 1>();
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else
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eval<1, 0, 0>();
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}
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} else {
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if (force->newton_pair)
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eval<0, 0, 1>();
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else
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eval<0, 0, 0>();
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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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template <int EVFLAG, int EFLAG, int NEWTON_PAIR> void PairLepton::eval()
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{
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const double *const *const x = atom->x;
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double *const *const f = atom->f;
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const int *const type = atom->type;
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const int nlocal = atom->nlocal;
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const double *const special_lj = force->special_lj;
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const int inum = list->inum;
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const int *const ilist = list->ilist;
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const int *const numneigh = list->numneigh;
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const int *const *const firstneigh = list->firstneigh;
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double fxtmp, fytmp, fztmp;
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std::vector<Lepton::CompiledExpression> pairforce;
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std::vector<Lepton::CompiledExpression> pairpot;
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std::vector<bool> has_ref;
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try {
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for (const auto &expr : expressions) {
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auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp), functions);
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pairforce.emplace_back(parsed.differentiate("r").createCompiledExpression());
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has_ref.push_back(true);
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try {
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pairforce.back().getVariableReference("r");
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} catch (Lepton::Exception &) {
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has_ref.back() = false;
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}
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if (EFLAG) pairpot.emplace_back(parsed.createCompiledExpression());
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}
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} catch (std::exception &e) {
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error->all(FLERR, e.what());
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}
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// loop over neighbors of my atoms
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for (int ii = 0; ii < inum; ii++) {
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const int i = ilist[ii];
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const double xtmp = x[i][0];
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const double ytmp = x[i][1];
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const double ztmp = x[i][2];
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const int itype = type[i];
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const int *jlist = firstneigh[i];
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const int jnum = numneigh[i];
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fxtmp = fytmp = fztmp = 0.0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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const double factor_lj = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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const int jtype = type[j];
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx * delx + dely * dely + delz * delz;
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if (rsq < cutsq[itype][jtype]) {
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const double r = sqrt(rsq);
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const int idx = type2expression[itype][jtype];
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if (has_ref[idx]) pairforce[idx].getVariableReference("r") = r;
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const double fpair = -pairforce[idx].evaluate() / r * factor_lj;
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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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double evdwl = 0.0;
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if (EFLAG) {
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try {
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pairpot[idx].getVariableReference("r") = r;
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} catch (Lepton::Exception &) {
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; // ignore -> constant potential
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}
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evdwl = pairpot[idx].evaluate() - 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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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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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLepton::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(cut, np1, np1, "pair:cut");
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memory->create(cutsq, np1, np1, "pair:cutsq");
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memory->create(type2expression, np1, np1, "pair:type2expression");
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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 PairLepton::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR, "Incorrect number of arguments for pair_style lepton command");
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cut_global = utils::numeric(FLERR, arg[0], false, lmp);
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}
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/* ----------------------------------------------------------------------
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set coeffs for all type pairs
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------------------------------------------------------------------------- */
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void PairLepton::coeff(int narg, char **arg)
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{
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if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect number of 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 cut_one = cut_global;
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if (narg == 4) {
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if (pppmflag || ewaldflag || msmflag || dispersionflag || tip4pflag) {
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error->all(FLERR, "Only a global cutoff is allowed with Kspace compatibility enabled");
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} else {
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cut_one = utils::numeric(FLERR, arg[3], false, lmp);
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}
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}
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// remove whitespace and quotes from expression string and then
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// check if the expression can be parsed and evaluated without error
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auto exp_one = LeptonUtils::condense(arg[2]);
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try {
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auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(exp_one, lmp), functions);
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auto pairforce = parsed.differentiate("r").createCompiledExpression();
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auto pairpot = parsed.createCompiledExpression();
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try {
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pairpot.getVariableReference("r") = 1.0;
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pairforce.getVariableReference("r") = 1.0;
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} catch (Lepton::Exception &) {
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; // ignore -> constant potential or force
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}
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pairpot.evaluate();
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pairforce.evaluate();
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} catch (std::exception &e) {
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error->all(FLERR, e.what());
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}
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std::size_t idx = 0;
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for (const auto &exp : expressions) {
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if (exp == exp_one) break;
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++idx;
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}
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// not found, add to list
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if ((expressions.size() == 0) || (idx == expressions.size())) expressions.push_back(exp_one);
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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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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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type2expression[i][j] = idx;
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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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double PairLepton::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
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offset[i][j] = 0.0;
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if (offset_flag) {
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try {
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auto expr = LeptonUtils::substitute(expressions[type2expression[i][j]], lmp);
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auto pairpot = Lepton::Parser::parse(expr, functions).createCompiledExpression();
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try {
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pairpot.getVariableReference("r") = cut[i][j];
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} catch (Lepton::Exception &) {
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; // ignore -> constant potential
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}
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offset[i][j] = pairpot.evaluate();
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} catch (std::exception &) {
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}
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}
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cut[j][i] = cut[i][j];
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type2expression[j][i] = type2expression[i][j];
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offset[j][i] = offset[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairLepton::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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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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fwrite(&setflag[i][j], sizeof(int), 1, fp);
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if (setflag[i][j]) {
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fwrite(&cut[i][j], sizeof(double), 1, fp);
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fwrite(&type2expression[i][j], sizeof(int), 1, fp);
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}
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}
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int num = expressions.size();
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int maxlen = 0;
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for (const auto &exp : expressions) maxlen = MAX(maxlen, (int) exp.size());
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++maxlen;
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fwrite(&num, sizeof(int), 1, fp);
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fwrite(&maxlen, sizeof(int), 1, fp);
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for (const auto &exp : expressions) {
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int n = exp.size() + 1;
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fwrite(&n, sizeof(int), 1, fp);
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fwrite(exp.c_str(), sizeof(char), n, fp);
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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 PairLepton::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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expressions.clear();
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const int me = comm->me;
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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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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, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
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utils::sfread(FLERR, &type2expression[i][j], sizeof(int), 1, fp, nullptr, error);
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}
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MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&type2expression[i][j], 1, MPI_INT, 0, world);
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}
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}
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int num, maxlen, len;
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if (me == 0) {
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utils::sfread(FLERR, &num, sizeof(int), 1, fp, nullptr, error);
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utils::sfread(FLERR, &maxlen, sizeof(int), 1, fp, nullptr, error);
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}
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MPI_Bcast(&num, 1, MPI_INT, 0, world);
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MPI_Bcast(&maxlen, 1, MPI_INT, 0, world);
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char *buf = new char[maxlen];
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for (int i = 0; i < num; ++i) {
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if (me == 0) {
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utils::sfread(FLERR, &len, sizeof(int), 1, fp, nullptr, error);
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utils::sfread(FLERR, buf, sizeof(char), len, fp, nullptr, error);
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}
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MPI_Bcast(buf, maxlen, MPI_CHAR, 0, world);
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expressions.emplace_back(buf);
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}
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delete[] buf;
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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 PairLepton::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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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairLepton::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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}
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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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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void PairLepton::write_data(FILE *fp)
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{
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if (pppmflag || ewaldflag || msmflag || dispersionflag || tip4pflag) {
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp, "%d %s\n", i, expressions[type2expression[i][i]].c_str());
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} else {
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp, "%d %s %g\n", i, expressions[type2expression[i][i]].c_str(), cut[i][i]);
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}
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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 PairLepton::write_data_all(FILE *fp)
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{
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if (pppmflag || ewaldflag || msmflag || dispersionflag || tip4pflag) {
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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 %s\n", i, j, expressions[type2expression[i][j]].c_str());
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} else {
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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 %s %g\n", i, j, expressions[type2expression[i][j]].c_str(), cut[i][j]);
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}
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}
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/* ---------------------------------------------------------------------- */
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double PairLepton::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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const auto &expr = expressions[type2expression[itype][jtype]];
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auto parsed = Lepton::Parser::parse(LeptonUtils::substitute(expr, lmp), functions);
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auto pairpot = parsed.createCompiledExpression();
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auto pairforce = parsed.differentiate("r").createCompiledExpression();
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const double r = sqrt(rsq);
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try {
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pairpot.getVariableReference("r") = r;
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pairforce.getVariableReference("r") = r;
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} catch (Lepton::Exception &) {
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; // ignore -> constant potential or force
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}
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fforce = -pairforce.evaluate() / r * factor_lj;
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return (pairpot.evaluate() - offset[itype][jtype]) * factor_lj;
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}
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