rename USER-PACE to ML-PACE
This commit is contained in:
Axel Kohlmeyer
388
src/ML-PACE/pair_pace.cpp
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388
src/ML-PACE/pair_pace.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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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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Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
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Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
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Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1
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^1: Ruhr-University Bochum, Bochum, Germany
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^2: University of Cambridge, Cambridge, United Kingdom
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^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
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^4: University of British Columbia, Vancouver, BC, Canada
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*/
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//
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// Created by Lysogorskiy Yury on 27.02.20.
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//
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#include "pair_pace.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 "neigh_request.h"
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#include "neighbor.h"
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#include "update.h"
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#include <cstring>
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#include "ace_evaluator.h"
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#include "ace_recursive.h"
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#include "ace_c_basis.h"
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#include "ace_version.h"
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namespace LAMMPS_NS {
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struct ACEImpl {
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ACEImpl() : basis_set(nullptr), ace(nullptr){}
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~ACEImpl() {delete basis_set; delete ace;}
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ACECTildeBasisSet *basis_set;
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ACERecursiveEvaluator *ace;
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};
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}
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define MAXLINE 1024
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#define DELTA 4
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//added YL
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//keywords for ACE evaluator style
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#define RECURSIVE_KEYWORD "recursive"
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#define PRODUCT_KEYWORD "product"
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static int elements_num_pace = 104;
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static char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na",
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"Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn",
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"Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr",
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"Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb",
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"Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd",
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"Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir",
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"Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th",
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"Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr"
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};
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static int AtomicNumberByName_pace(char *elname) {
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for (int i = 1; i < elements_num_pace; i++)
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if (strcmp(elname, elements_pace[i]) == 0)
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return i;
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return -1;
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}
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/* ---------------------------------------------------------------------- */
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PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) {
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single_enable = 0;
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restartinfo = 0;
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one_coeff = 1;
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manybody_flag = 1;
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aceimpl = new ACEImpl;
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recursive = false;
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scale = nullptr;
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}
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/* ----------------------------------------------------------------------
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check if allocated, since class can be destructed when incomplete
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------------------------------------------------------------------------- */
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PairPACE::~PairPACE() {
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if (copymode) return;
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delete aceimpl;
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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(scale);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairPACE::compute(int eflag, int vflag) {
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int i, j, ii, jj, inum, jnum;
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double delx, dely, delz, evdwl;
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double fij[3];
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int *ilist, *jlist, *numneigh, **firstneigh;
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ev_init(eflag, vflag);
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// downwards modified by YL
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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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// number of atoms in cell
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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// inum: length of the neighborlists list
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inum = list->inum;
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// ilist: list of "i" atoms for which neighbor lists exist
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ilist = list->ilist;
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//numneigh: the length of each these neigbor list
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numneigh = list->numneigh;
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// the pointer to the list of neighbors of "i"
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firstneigh = list->firstneigh;
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if (inum != nlocal)
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error->all(FLERR,"inum: {} nlocal: {} are different",inum, nlocal);
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// Aidan Thompson told RD (26 July 2019) that practically always holds:
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// inum = nlocal
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// i = ilist(ii) < inum
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// j = jlist(jj) < nall
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// neighborlist contains neighbor atoms plus skin atoms,
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// skin atoms can be removed by setting skin to zero but here
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// they are disregarded anyway
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//determine the maximum number of neighbours
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int max_jnum = -1;
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int nei = 0;
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for (ii = 0; ii < list->inum; ii++) {
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i = ilist[ii];
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jnum = numneigh[i];
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nei = nei + jnum;
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if (jnum > max_jnum)
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max_jnum = jnum;
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}
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aceimpl->ace->resize_neighbours_cache(max_jnum);
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//loop over atoms
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for (ii = 0; ii < list->inum; ii++) {
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i = list->ilist[ii];
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const int itype = type[i];
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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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jlist = firstneigh[i];
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jnum = numneigh[i];
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// checking if neighbours are actually within cutoff range is done inside compute_atom
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// mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom
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// by using 'aceimpl->ace->element_type_mapping' array
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// x: [r0 ,r1, r2, ..., r100]
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// i = 0 ,1
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// jnum(0) = 50
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// jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total]
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try {
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aceimpl->ace->compute_atom(i, x, type, jnum, jlist);
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} catch (exception &e) {
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error->one(FLERR, e.what());
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}
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// 'compute_atom' will update the `aceimpl->ace->e_atom` and `aceimpl->ace->neighbours_forces(jj, alpha)` arrays
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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const int jtype = type[j];
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j &= NEIGHMASK;
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delx = x[j][0] - xtmp;
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dely = x[j][1] - ytmp;
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delz = x[j][2] - ztmp;
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fij[0] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 0);
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fij[1] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 1);
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fij[2] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 2);
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f[i][0] += fij[0];
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f[i][1] += fij[1];
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f[i][2] += fij[2];
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f[j][0] -= fij[0];
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f[j][1] -= fij[1];
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f[j][2] -= fij[2];
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// tally per-atom virial contribution
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if (vflag)
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ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0,
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fij[0], fij[1], fij[2],
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-delx, -dely, -delz);
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}
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// tally energy contribution
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if (eflag) {
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// evdwl = energy of atom I
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evdwl = scale[1][1]*aceimpl->ace->e_atom;
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ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0);
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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// end modifications YL
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}
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/* ---------------------------------------------------------------------- */
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void PairPACE::allocate() {
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag, n + 1, n + 1, "pair:setflag");
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memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
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memory->create(scale, n + 1, n + 1,"pair:scale");
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map = new int[n+1];
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairPACE::settings(int narg, char **arg) {
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if (narg > 1)
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error->all(FLERR,"Illegal pair_style command.");
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// ACE potentials are parameterized in metal units
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if (strcmp("metal",update->unit_style) != 0)
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error->all(FLERR,"ACE potentials require 'metal' units");
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recursive = true; // default evaluator style: RECURSIVE
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if (narg > 0) {
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if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0)
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recursive = true;
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else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) {
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recursive = false;
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} else error->all(FLERR,"Illegal pair_style command");
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}
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if (comm->me == 0) {
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utils::logmesg(lmp,"ACE version: {}.{}.{}\n",
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VERSION_YEAR, VERSION_MONTH, VERSION_DAY);
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if (recursive) utils::logmesg(lmp,"Recursive evaluator is used\n");
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else utils::logmesg(lmp,"Product evaluator is used\n");
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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 PairPACE::coeff(int narg, char **arg) {
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if (!allocated) allocate();
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map_element2type(narg-3,arg+3);
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auto potential_file_name = utils::get_potential_file_path(arg[2]);
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char **elemtypes = &arg[3];
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//load potential file
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delete aceimpl->basis_set;
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aceimpl->basis_set = new ACECTildeBasisSet();
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if (comm->me == 0)
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utils::logmesg(lmp,"Loading {}\n", potential_file_name);
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aceimpl->basis_set->load(potential_file_name);
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if (comm->me == 0) {
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utils::logmesg(lmp,"Total number of basis functions\n");
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for (SPECIES_TYPE mu = 0; mu < aceimpl->basis_set->nelements; mu++) {
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int n_r1 = aceimpl->basis_set->total_basis_size_rank1[mu];
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int n = aceimpl->basis_set->total_basis_size[mu];
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utils::logmesg(lmp,"\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n);
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}
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}
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// read args that map atom types to pACE elements
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// map[i] = which element the Ith atom type is, -1 if not mapped
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// map[0] is not used
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delete aceimpl->ace;
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aceimpl->ace = new ACERecursiveEvaluator();
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aceimpl->ace->set_recursive(recursive);
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aceimpl->ace->element_type_mapping.init(atom->ntypes + 1);
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const int n = atom->ntypes;
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for (int i = 1; i <= n; i++) {
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char *elemname = elemtypes[i - 1];
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int atomic_number = AtomicNumberByName_pace(elemname);
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if (atomic_number == -1)
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error->all(FLERR,"'{}' is not a valid element\n", elemname);
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SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname);
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if (mu != -1) {
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if (comm->me == 0)
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utils::logmesg(lmp,"Mapping LAMMPS atom type #{}({}) -> "
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"ACE species type #{}\n", i, elemname, mu);
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map[i] = mu;
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aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator
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} else {
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error->all(FLERR,"Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name);
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}
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}
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// initialize scale factor
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for (int i = 1; i <= n; i++) {
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for (int j = i; j <= n; j++) {
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scale[i][j] = 1.0;
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}
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}
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aceimpl->ace->set_basis(*aceimpl->basis_set, 1);
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairPACE::init_style() {
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if (atom->tag_enable == 0)
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error->all(FLERR, "Pair style pACE requires atom IDs");
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if (force->newton_pair == 0)
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error->all(FLERR, "Pair style pACE requires newton pair on");
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// request a full neighbor list
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int irequest = neighbor->request(this, instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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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 PairPACE::init_one(int i, int j) {
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if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
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//cutoff from the basis set's radial functions settings
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scale[j][i] = scale[i][j];
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return aceimpl->basis_set->radial_functions->cut(map[i], map[j]);
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}
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/* ----------------------------------------------------------------------
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extract method for extracting value of scale variable
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---------------------------------------------------------------------- */
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void *PairPACE::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str,"scale") == 0) return (void *) scale;
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return nullptr;
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}
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