lammps/src/USER-PACE/pair_pace.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://lammps.sandia.gov/, 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.
------------------------------------------------------------------------- */

/*
Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1,
 Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
 Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1

^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
*/


//
// Created by Lysogorskiy Yury on 27.02.20.
//

#include "pair_pace.h"

#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "update.h"

#include <cstring>

#include "ace_evaluator.h"
#include "ace_recursive.h"
#include "ace_c_basis.h"
#include "ace_version.h"

namespace LAMMPS_NS {
  struct ACEImpl {
    ACECTildeBasisSet *basis_set;
    ACERecursiveEvaluator *ace;
  };
}

using namespace LAMMPS_NS;
using namespace MathConst;

#define MAXLINE 1024
#define DELTA 4

//added YL

//keywords for ACE evaluator style
#define RECURSIVE_KEYWORD "recursive"
#define PRODUCT_KEYWORD "product"

static int elements_num_pace = 104;
static char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na",
                                        "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn",
                                        "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr",
                                        "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb",
                                        "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd",
                                        "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir",
                                        "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th",
                                        "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr"
};

static int AtomicNumberByName_pace(char *elname) {
  for (int i = 1; i < elements_num_pace; i++)
    if (strcmp(elname, elements_pace[i]) == 0)
      return i;
  return -1;
}

/* ---------------------------------------------------------------------- */
PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) {
  single_enable = 0;
  restartinfo = 0;
  one_coeff = 1;
  manybody_flag = 1;

  aceimpl = new ACEImpl;
  aceimpl->ace = nullptr;
  aceimpl->basis_set = nullptr;
  recursive = false;

  scale = nullptr;
}

/* ----------------------------------------------------------------------
   check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */

PairPACE::~PairPACE() {
  if (copymode) return;

  delete aceimpl->basis_set;
  delete aceimpl->ace;
  delete aceimpl;

  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);
    memory->destroy(scale);
  }
}

/* ---------------------------------------------------------------------- */

void PairPACE::compute(int eflag, int vflag) {
  int i, j, ii, jj, inum, jnum;
  double delx, dely, delz, evdwl;
  double fij[3];
  int *ilist, *jlist, *numneigh, **firstneigh;

  ev_init(eflag, vflag);

  // downwards modified by YL

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;

  // number of atoms in cell
  int nlocal = atom->nlocal;

  int newton_pair = force->newton_pair;

  // inum: length of the neighborlists list
  inum = list->inum;

  // ilist: list of "i" atoms for which neighbor lists exist
  ilist = list->ilist;

  //numneigh: the length of each these neigbor list
  numneigh = list->numneigh;

  // the pointer to the list of neighbors of "i"
  firstneigh = list->firstneigh;

  if (inum != nlocal)
    error->all(FLERR,"inum: {} nlocal: {} are different",inum, nlocal);

  // Aidan Thompson told RD (26 July 2019) that practically always holds:
  // inum = nlocal
  // i = ilist(ii) < inum
  // j = jlist(jj) < nall
  // neighborlist contains neighbor atoms plus skin atoms,
  //       skin atoms can be removed by setting skin to zero but here
  //       they are disregarded anyway


  //determine the maximum number of neighbours
  int max_jnum = -1;
  int nei = 0;
  for (ii = 0; ii < list->inum; ii++) {
    i = ilist[ii];
    jnum = numneigh[i];
    nei = nei + jnum;
    if (jnum > max_jnum)
      max_jnum = jnum;
  }

  aceimpl->ace->resize_neighbours_cache(max_jnum);

  //loop over atoms
  for (ii = 0; ii < list->inum; ii++) {
    i = list->ilist[ii];
    const int itype = type[i];

    const double xtmp = x[i][0];
    const double ytmp = x[i][1];
    const double ztmp = x[i][2];

    jlist = firstneigh[i];
    jnum = numneigh[i];

    // checking if neighbours are actually within cutoff range is done inside compute_atom
    // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom
    //      by using 'aceimpl->ace->element_type_mapping' array
    // x: [r0 ,r1, r2, ..., r100]
    // i = 0 ,1
    // jnum(0) = 50
    // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total]

    try {
      aceimpl->ace->compute_atom(i, x, type, jnum, jlist);
    } catch (exception &e) {
      error->one(FLERR, e.what());
    }
    // 'compute_atom' will update the `aceimpl->ace->e_atom` and `aceimpl->ace->neighbours_forces(jj, alpha)` arrays

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      const int jtype = type[j];
      j &= NEIGHMASK;
      delx = x[j][0] - xtmp;
      dely = x[j][1] - ytmp;
      delz = x[j][2] - ztmp;

      fij[0] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 0);
      fij[1] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 1);
      fij[2] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 2);

      f[i][0] += fij[0];
      f[i][1] += fij[1];
      f[i][2] += fij[2];
      f[j][0] -= fij[0];
      f[j][1] -= fij[1];
      f[j][2] -= fij[2];

      // tally per-atom virial contribution
      if (vflag)
        ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0,
                     fij[0], fij[1], fij[2],
                     -delx, -dely, -delz);
    }

    // tally energy contribution
    if (eflag) {
      // evdwl = energy of atom I
      evdwl = scale[1][1]*aceimpl->ace->e_atom;
      ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0);
    }
  }

  if (vflag_fdotr) virial_fdotr_compute();

  // end modifications YL
}

/* ---------------------------------------------------------------------- */

void PairPACE::allocate() {
  allocated = 1;
  int n = atom->ntypes;

  memory->create(setflag, n + 1, n + 1, "pair:setflag");
  memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
  memory->create(scale, n + 1, n + 1,"pair:scale");
  map = new int[n+1];
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void PairPACE::settings(int narg, char **arg) {
  if (narg > 1)
    error->all(FLERR,"Illegal pair_style command.");

  // ACE potentials are parameterized in metal units
  if (strcmp("metal",update->unit_style) != 0)
    error->all(FLERR,"ACE potentials require 'metal' units");

  recursive = true; // default evaluator style: RECURSIVE
  if (narg > 0) {
    if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0)
      recursive = true;
    else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) {
      recursive = false;
    } else error->all(FLERR,"Illegal pair_style command");
  }

  if (comm->me == 0) {
    utils::logmesg(lmp,"ACE version: {}.{}.{}\n",
                   VERSION_YEAR, VERSION_MONTH, VERSION_DAY);
    if (recursive) utils::logmesg(lmp,"Recursive evaluator is used\n");
    else utils::logmesg(lmp,"Product evaluator is used\n");
  }
}

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairPACE::coeff(int narg, char **arg) {

  if (!allocated) allocate();

  map_element2type(narg-3,arg+3);

  auto potential_file_name = utils::get_potential_file_path(arg[2]);
  char **elemtypes = &arg[3];

  //load potential file
  aceimpl->basis_set = new ACECTildeBasisSet();
  if (comm->me == 0)
    utils::logmesg(lmp,"Loading {}\n", potential_file_name);
  aceimpl->basis_set->load(potential_file_name);

  if (comm->me == 0) {
    utils::logmesg(lmp,"Total number of basis functions\n");

    for (SPECIES_TYPE mu = 0; mu < aceimpl->basis_set->nelements; mu++) {
      int n_r1 = aceimpl->basis_set->total_basis_size_rank1[mu];
      int n = aceimpl->basis_set->total_basis_size[mu];
      utils::logmesg(lmp,"\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n);
    }
  }

  // read args that map atom types to pACE elements
  // map[i] = which element the Ith atom type is, -1 if not mapped
  // map[0] is not used

  aceimpl->ace = new ACERecursiveEvaluator();
  aceimpl->ace->set_recursive(recursive);
  aceimpl->ace->element_type_mapping.init(atom->ntypes + 1);

  const int n = atom->ntypes;
  for (int i = 1; i <= n; i++) {
    char *elemname = elemtypes[i - 1];
    int atomic_number = AtomicNumberByName_pace(elemname);
    if (atomic_number == -1)
      error->all(FLERR,"'{}' is not a valid element\n", elemname);

    SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname);
    if (mu != -1) {
      if (comm->me == 0)
        utils::logmesg(lmp,"Mapping LAMMPS atom type #{}({}) -> "
                       "ACE species type #{}\n", i, elemname, mu);
      map[i] = mu;
      aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species  mapping for ace evaluator
    } else {
      error->all(FLERR,"Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name);
    }
  }

  // initialize scale factor
  for (int i = 1; i <= n; i++) {
    for (int j = i; j <= n; j++) {
      scale[i][j] = 1.0;
    }
  }

  aceimpl->ace->set_basis(*aceimpl->basis_set, 1);
}

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairPACE::init_style() {
  if (atom->tag_enable == 0)
    error->all(FLERR, "Pair style pACE requires atom IDs");
  if (force->newton_pair == 0)
    error->all(FLERR, "Pair style pACE requires newton pair on");

  // request a full neighbor list
  int irequest = neighbor->request(this, instance_me);
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;
}

/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairPACE::init_one(int i, int j) {
  if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
  //cutoff from the basis set's radial functions settings
  scale[j][i] = scale[i][j];
  return aceimpl->basis_set->radial_functions->cut(map[i], map[j]);
}

/* ----------------------------------------------------------------------
    extract method for extracting value of scale variable
 ---------------------------------------------------------------------- */
void *PairPACE::extract(const char *str, int &dim)
{
  dim = 2;
  if (strcmp(str,"scale") == 0) return (void *) scale;
  return nullptr;
}