rename SNAP package to ML-SNAP and fix up some remaining MLIAP to ML-IAP issues
This commit is contained in:
Axel Kohlmeyer
423
src/ML-SNAP/compute_snav_atom.cpp
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423
src/ML-SNAP/compute_snav_atom.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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#include "compute_snav_atom.h"
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#include <cstring>
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#include "sna.h"
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snav(nullptr),
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radelem(nullptr), wjelem(nullptr)
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{
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
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radelem = nullptr;
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wjelem = nullptr;
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int ntypes = atom->ntypes;
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int nargmin = 6+2*ntypes;
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if (narg < nargmin) error->all(FLERR,"Illegal compute snav/atom command");
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// default values
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rmin0 = 0.0;
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switchflag = 1;
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bzeroflag = 1;
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bnormflag = 0;
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quadraticflag = 0;
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chemflag = 0;
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bnormflag = 0;
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wselfallflag = 0;
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nelements = 1;
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// process required arguments
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memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
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memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
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rcutfac = atof(arg[3]);
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rfac0 = atof(arg[4]);
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twojmax = atoi(arg[5]);
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for (int i = 0; i < ntypes; i++)
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radelem[i+1] = atof(arg[6+i]);
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for (int i = 0; i < ntypes; i++)
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wjelem[i+1] = atof(arg[6+ntypes+i]);
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// construct cutsq
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double cut;
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memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq");
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for (int i = 1; i <= ntypes; i++) {
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cut = 2.0*radelem[i]*rcutfac;
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cutsq[i][i] = cut*cut;
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for (int j = i+1; j <= ntypes; j++) {
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cut = (radelem[i]+radelem[j])*rcutfac;
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cutsq[i][j] = cutsq[j][i] = cut*cut;
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}
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}
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// process optional args
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int iarg = nargmin;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"rmin0") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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rmin0 = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"switchflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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switchflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"bzeroflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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bzeroflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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quadraticflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"chem") == 0) {
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if (iarg+2+ntypes > narg)
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error->all(FLERR,"Illegal compute sna/atom command");
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chemflag = 1;
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memory->create(map,ntypes+1,"compute_sna_atom:map");
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nelements = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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for (int i = 0; i < ntypes; i++) {
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int jelem = utils::inumeric(FLERR,arg[iarg+2+i],false,lmp);
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if (jelem < 0 || jelem >= nelements)
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error->all(FLERR,"Illegal compute snav/atom command");
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map[i+1] = jelem;
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}
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iarg += 2+ntypes;
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} else if (strcmp(arg[iarg],"bnormflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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bnormflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"wselfallflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snav/atom command");
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wselfallflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else error->all(FLERR,"Illegal compute snav/atom command");
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}
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snaptr = new SNA(lmp, rfac0, twojmax,
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rmin0, switchflag, bzeroflag,
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chemflag, bnormflag, wselfallflag, nelements);
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ncoeff = snaptr->ncoeff;
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nperdim = ncoeff;
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if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
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size_peratom_cols = 6*nperdim*atom->ntypes;
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comm_reverse = size_peratom_cols;
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peratom_flag = 1;
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nmax = 0;
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snav = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSNAVAtom::~ComputeSNAVAtom()
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{
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memory->destroy(snav);
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memory->destroy(radelem);
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memory->destroy(wjelem);
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memory->destroy(cutsq);
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delete snaptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAVAtom::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute snav/atom requires a pair style be defined");
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// TODO: Not sure what to do with this error check since cutoff radius is not
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// a single number
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//if (sqrt(cutsq) > force->pair->cutforce)
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// error->all(FLERR,"Compute snav/atom cutoff is longer than pairwise cutoff");
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// need an occasional full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->compute = 1;
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->occasional = 1;
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style,"snav/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute snav/atom");
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snaptr->init();
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAVAtom::init_list(int /*id*/, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAVAtom::compute_peratom()
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{
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int ntotal = atom->nlocal + atom->nghost;
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invoked_peratom = update->ntimestep;
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// grow snav array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(snav);
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nmax = atom->nmax;
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memory->create(snav,nmax,size_peratom_cols,
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"snav/atom:snav");
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array_atom = snav;
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}
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// clear local array
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for (int i = 0; i < ntotal; i++)
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for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++) {
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snav[i][icoeff] = 0.0;
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}
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// invoke full neighbor list (will copy or build if necessary)
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neighbor->build_one(list);
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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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int** const firstneigh = list->firstneigh;
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int * const type = atom->type;
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// compute sna derivatives for each atom in group
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// use full neighbor list to count atoms less than cutoff
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double** const x = atom->x;
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const int* const mask = atom->mask;
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for (int ii = 0; ii < inum; ii++) {
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const int i = ilist[ii];
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if (mask[i] & groupbit) {
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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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int ielem = 0;
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if (chemflag)
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ielem = map[itype];
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const double radi = radelem[itype];
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const int* const jlist = firstneigh[i];
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const int jnum = numneigh[i];
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const int typeoffset = 6*nperdim*(atom->type[i]-1);
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// insure rij, inside, and typej are of size jnum
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snaptr->grow_rij(jnum);
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// rij[][3] = displacements between atom I and those neighbors
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// inside = indices of neighbors of I within cutoff
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// typej = types of neighbors of I within cutoff
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// note Rij sign convention => dU/dRij = dU/dRj = -dU/dRi
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int ninside = 0;
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for (int jj = 0; jj < jnum; jj++) {
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int j = jlist[jj];
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j &= NEIGHMASK;
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const double delx = x[j][0] - xtmp;
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const double dely = x[j][1] - ytmp;
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const double delz = x[j][2] - ztmp;
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const double rsq = delx*delx + dely*dely + delz*delz;
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int jtype = type[j];
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int jelem = 0;
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if (chemflag)
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jelem = map[jtype];
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if (rsq < cutsq[itype][jtype]&&rsq>1e-20) {
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snaptr->rij[ninside][0] = delx;
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snaptr->rij[ninside][1] = dely;
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snaptr->rij[ninside][2] = delz;
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snaptr->inside[ninside] = j;
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snaptr->wj[ninside] = wjelem[jtype];
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snaptr->rcutij[ninside] = (radi+radelem[jtype])*rcutfac;
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snaptr->element[ninside] = jelem; // element index for multi-element snap
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ninside++;
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}
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}
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snaptr->compute_ui(ninside, ielem);
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snaptr->compute_zi();
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if (quadraticflag) {
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snaptr->compute_bi(ielem);
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}
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for (int jj = 0; jj < ninside; jj++) {
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const int j = snaptr->inside[jj];
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snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
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snaptr->rcutij[jj], jj, snaptr->element[jj]);
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snaptr->compute_dbidrj();
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// Accumulate -dBi/dRi*Ri, -dBi/dRj*Rj
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double *snavi = snav[i]+typeoffset;
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double *snavj = snav[j]+typeoffset;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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snavi[icoeff] += snaptr->dblist[icoeff][0]*xtmp;
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snavi[icoeff+nperdim] += snaptr->dblist[icoeff][1]*ytmp;
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snavi[icoeff+2*nperdim] += snaptr->dblist[icoeff][2]*ztmp;
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snavi[icoeff+3*nperdim] += snaptr->dblist[icoeff][1]*ztmp;
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snavi[icoeff+4*nperdim] += snaptr->dblist[icoeff][0]*ztmp;
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snavi[icoeff+5*nperdim] += snaptr->dblist[icoeff][0]*ytmp;
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snavj[icoeff] -= snaptr->dblist[icoeff][0]*x[j][0];
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snavj[icoeff+nperdim] -= snaptr->dblist[icoeff][1]*x[j][1];
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snavj[icoeff+2*nperdim] -= snaptr->dblist[icoeff][2]*x[j][2];
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snavj[icoeff+3*nperdim] -= snaptr->dblist[icoeff][1]*x[j][2];
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snavj[icoeff+4*nperdim] -= snaptr->dblist[icoeff][0]*x[j][2];
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snavj[icoeff+5*nperdim] -= snaptr->dblist[icoeff][0]*x[j][1];
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}
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if (quadraticflag) {
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const int quadraticoffset = ncoeff;
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snavi += quadraticoffset;
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snavj += quadraticoffset;
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int ncount = 0;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bi = snaptr->blist[icoeff];
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double bix = snaptr->dblist[icoeff][0];
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double biy = snaptr->dblist[icoeff][1];
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double biz = snaptr->dblist[icoeff][2];
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// diagonal element of quadratic matrix
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double dbxtmp = bi*bix;
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double dbytmp = bi*biy;
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double dbztmp = bi*biz;
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snavi[ncount] += dbxtmp*xtmp;
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snavi[ncount+nperdim] += dbytmp*ytmp;
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snavi[ncount+2*nperdim] += dbztmp*ztmp;
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snavi[ncount+3*nperdim] += dbytmp*ztmp;
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snavi[ncount+4*nperdim] += dbxtmp*ztmp;
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snavi[ncount+5*nperdim] += dbxtmp*ytmp;
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snavj[ncount] -= dbxtmp*x[j][0];
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snavj[ncount+nperdim] -= dbytmp*x[j][1];
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snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
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snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
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snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
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snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
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ncount++;
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// upper-triangular elements of quadratic matrix
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
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double dbxtmp = bi*snaptr->dblist[jcoeff][0]
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+ bix*snaptr->blist[jcoeff];
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double dbytmp = bi*snaptr->dblist[jcoeff][1]
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+ biy*snaptr->blist[jcoeff];
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double dbztmp = bi*snaptr->dblist[jcoeff][2]
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+ biz*snaptr->blist[jcoeff];
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snavi[ncount] += dbxtmp*xtmp;
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snavi[ncount+nperdim] += dbytmp*ytmp;
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snavi[ncount+2*nperdim] += dbztmp*ztmp;
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snavi[ncount+3*nperdim] += dbytmp*ztmp;
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snavi[ncount+4*nperdim] += dbxtmp*ztmp;
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snavi[ncount+5*nperdim] += dbxtmp*ytmp;
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snavj[ncount] -= dbxtmp*x[j][0];
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snavj[ncount+nperdim] -= dbytmp*x[j][1];
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snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
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snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
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snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
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snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
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ncount++;
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}
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}
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}
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}
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}
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}
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// communicate snav contributions between neighbor procs
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comm->reverse_comm_compute(this);
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}
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/* ---------------------------------------------------------------------- */
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int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf)
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{
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int i,m,last,icoeff;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++)
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for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
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buf[m++] = snav[i][icoeff];
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSNAVAtom::unpack_reverse_comm(int n, int *list, double *buf)
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{
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int i,j,m,icoeff;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
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snav[j][icoeff] += buf[m++];
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}
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double ComputeSNAVAtom::memory_usage()
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{
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double bytes = (double)nmax*size_peratom_cols * sizeof(double); // snav
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bytes += snaptr->memory_usage(); // SNA object
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return bytes;
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}
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