575 lines
18 KiB
C++
575 lines
18 KiB
C++
// 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_snap.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 "pair.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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enum{SCALAR,VECTOR,ARRAY};
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ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(nullptr), list(nullptr), snap(nullptr),
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snapall(nullptr), snap_peratom(nullptr), radelem(nullptr), wjelem(nullptr),
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snaptr(nullptr), rinnerelem(nullptr), drinnerelem(nullptr)
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{
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array_flag = 1;
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extarray = 0;
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag, bnormflag, wselfallflag;
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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 snap 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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quadraticflag = 0;
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bikflag = 0;
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chemflag = 0;
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bnormflag = 0;
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wselfallflag = 0;
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switchinnerflag = 0;
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nelements = 1;
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// process required arguments
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memory->create(radelem,ntypes+1,"snap:radelem"); // offset by 1 to match up with types
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memory->create(wjelem,ntypes+1,"snap: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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cutmax = 0.0;
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memory->create(cutsq,ntypes+1,ntypes+1,"snap: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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if (cut > cutmax) cutmax = cut;
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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 snap 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],"bzeroflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap 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],"switchflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap 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],"quadraticflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap 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 > narg)
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error->all(FLERR,"Illegal compute snap command");
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chemflag = 1;
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memory->create(map,ntypes+1,"compute_snap: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 snap 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 snap 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 snap command");
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wselfallflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"bikflag") == 0) {
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if (iarg+2 > narg)
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error->all(FLERR,"Illegal compute snap command");
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bikflag = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"switchinnerflag") == 0) {
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if (iarg+1+2*ntypes > narg)
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error->all(FLERR,"Illegal compute snap command");
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switchinnerflag = 1;
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iarg++;
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memory->create(rinnerelem,ntypes+1,"snap:rinnerelem");
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memory->create(drinnerelem,ntypes+1,"snap:drinnerelem");
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for (int i = 0; i < ntypes; i++)
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rinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
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iarg += ntypes;
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for (int i = 0; i < ntypes; i++)
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drinnerelem[i+1] = utils::numeric(FLERR,arg[iarg+i],false,lmp);
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iarg += ntypes;
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} else error->all(FLERR,"Illegal compute snap 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,
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nelements, switchinnerflag);
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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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ndims_force = 3;
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ndims_virial = 6;
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yoffset = nperdim;
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zoffset = 2*nperdim;
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natoms = atom->natoms;
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bik_rows = 1;
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if (bikflag) bik_rows = natoms;
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size_array_rows = bik_rows+ndims_force*natoms+ndims_virial;
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size_array_cols = nperdim*atom->ntypes+1;
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lastcol = size_array_cols-1;
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ndims_peratom = ndims_force;
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size_peratom = ndims_peratom*nperdim*atom->ntypes;
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nmax = 0;
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}
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/* ---------------------------------------------------------------------- */
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ComputeSnap::~ComputeSnap()
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{
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memory->destroy(snap);
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memory->destroy(snapall);
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memory->destroy(snap_peratom);
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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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if (chemflag) memory->destroy(map);
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if (switchinnerflag) {
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memory->destroy(rinnerelem);
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memory->destroy(drinnerelem);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::init()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Compute snap requires a pair style be defined");
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if (cutmax > force->pair->cutforce)
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error->all(FLERR,"Compute snap 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,"snap") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning(FLERR,"More than one compute snap");
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snaptr->init();
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// allocate memory for global array
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memory->create(snap,size_array_rows,size_array_cols,
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"snap:snap");
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memory->create(snapall,size_array_rows,size_array_cols,
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"snap:snapall");
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array = snapall;
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// find compute for reference energy
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std::string id_pe = std::string("thermo_pe");
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int ipe = modify->find_compute(id_pe);
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if (ipe == -1)
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error->all(FLERR,"compute thermo_pe does not exist.");
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c_pe = modify->compute[ipe];
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// add compute for reference virial tensor
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std::string id_virial = std::string("snap_press");
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std::string pcmd = id_virial + " all pressure NULL virial";
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modify->add_compute(pcmd);
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int ivirial = modify->find_compute(id_virial);
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if (ivirial == -1)
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error->all(FLERR,"compute snap_press does not exist.");
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c_virial = modify->compute[ivirial];
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::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 ComputeSnap::compute_array()
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{
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int ntotal = atom->nlocal + atom->nghost;
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invoked_array = update->ntimestep;
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// grow snap_peratom array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(snap_peratom);
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nmax = atom->nmax;
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memory->create(snap_peratom,nmax,size_peratom,
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"snap:snap_peratom");
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}
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// clear global array
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for (int irow = 0; irow < size_array_rows; irow++)
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for (int icoeff = 0; icoeff < size_array_cols; icoeff++)
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snap[irow][icoeff] = 0.0;
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// clear local peratom array
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for (int i = 0; i < ntotal; i++)
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for (int icoeff = 0; icoeff < size_peratom; icoeff++) {
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snap_peratom[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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int irow = 0;
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if (bikflag) irow = atom->tag[ilist[ii] & NEIGHMASK]-1;
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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_local = ndims_peratom*nperdim*(itype-1);
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const int typeoffset_global = nperdim*(itype-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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if (switchinnerflag) {
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snaptr->rinnerij[ninside] = 0.5*(rinnerelem[itype]+rinnerelem[jtype]);
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snaptr->drinnerij[ninside] = 0.5*(drinnerelem[itype]+drinnerelem[jtype]);
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}
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if (chemflag) snaptr->element[ninside] = jelem;
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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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snaptr->compute_bi(ielem);
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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(jj);
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snaptr->compute_dbidrj();
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// Accumulate dBi/dRi, -dBi/dRj
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double *snadi = snap_peratom[i]+typeoffset_local;
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double *snadj = snap_peratom[j]+typeoffset_local;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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snadi[icoeff] += snaptr->dblist[icoeff][0];
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snadi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
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snadi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
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snadj[icoeff] -= snaptr->dblist[icoeff][0];
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snadj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
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snadj[icoeff+zoffset] -= snaptr->dblist[icoeff][2];
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}
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if (quadraticflag) {
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const int quadraticoffset = ncoeff;
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snadi += quadraticoffset;
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snadj += 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 elements 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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snadi[ncount] += dbxtmp;
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snadi[ncount+yoffset] += dbytmp;
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snadi[ncount+zoffset] += dbztmp;
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snadj[ncount] -= dbxtmp;
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snadj[ncount+yoffset] -= dbytmp;
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snadj[ncount+zoffset] -= dbztmp;
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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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snadi[ncount] += dbxtmp;
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snadi[ncount+yoffset] += dbytmp;
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snadi[ncount+zoffset] += dbztmp;
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snadj[ncount] -= dbxtmp;
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snadj[ncount+yoffset] -= dbytmp;
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snadj[ncount+zoffset] -= dbztmp;
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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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// Accumulate Bi
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// linear contributions
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int k = typeoffset_global;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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snap[irow][k++] += snaptr->blist[icoeff];
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// quadratic contributions
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if (quadraticflag) {
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bveci = snaptr->blist[icoeff];
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snap[irow][k++] += 0.5*bveci*bveci;
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
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double bvecj = snaptr->blist[jcoeff];
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snap[irow][k++] += bveci*bvecj;
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}
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}
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}
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}
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}
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// accumulate bispectrum force contributions to global array
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for (int itype = 0; itype < atom->ntypes; itype++) {
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const int typeoffset_local = ndims_peratom*nperdim*itype;
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const int typeoffset_global = nperdim*itype;
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for (int icoeff = 0; icoeff < nperdim; icoeff++) {
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for (int i = 0; i < ntotal; i++) {
|
|
double *snadi = snap_peratom[i]+typeoffset_local;
|
|
int iglobal = atom->tag[i];
|
|
int irow = 3*(iglobal-1)+bik_rows;
|
|
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff];
|
|
snap[irow++][icoeff+typeoffset_global] += snadi[icoeff+yoffset];
|
|
snap[irow][icoeff+typeoffset_global] += snadi[icoeff+zoffset];
|
|
}
|
|
}
|
|
}
|
|
|
|
// accumulate forces to global array
|
|
|
|
for (int i = 0; i < atom->nlocal; i++) {
|
|
int iglobal = atom->tag[i];
|
|
int irow = 3*(iglobal-1)+bik_rows;
|
|
snap[irow++][lastcol] = atom->f[i][0];
|
|
snap[irow++][lastcol] = atom->f[i][1];
|
|
snap[irow][lastcol] = atom->f[i][2];
|
|
}
|
|
|
|
// accumulate bispectrum virial contributions to global array
|
|
|
|
dbdotr_compute();
|
|
|
|
// sum up over all processes
|
|
|
|
MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
|
|
|
|
// assign energy to last column
|
|
for (int i = 0; i < bik_rows; i++) snapall[i][lastcol] = 0;
|
|
int irow = 0;
|
|
double reference_energy = c_pe->compute_scalar();
|
|
snapall[irow][lastcol] = reference_energy;
|
|
|
|
// assign virial stress to last column
|
|
// switch to Voigt notation
|
|
|
|
c_virial->compute_vector();
|
|
irow += 3*natoms+bik_rows;
|
|
snapall[irow++][lastcol] = c_virial->vector[0];
|
|
snapall[irow++][lastcol] = c_virial->vector[1];
|
|
snapall[irow++][lastcol] = c_virial->vector[2];
|
|
snapall[irow++][lastcol] = c_virial->vector[5];
|
|
snapall[irow++][lastcol] = c_virial->vector[4];
|
|
snapall[irow][lastcol] = c_virial->vector[3];
|
|
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
compute global virial contributions via summing r_i.dB^j/dr_i over
|
|
own & ghost atoms
|
|
------------------------------------------------------------------------- */
|
|
|
|
void ComputeSnap::dbdotr_compute()
|
|
{
|
|
double **x = atom->x;
|
|
int irow0 = bik_rows+ndims_force*natoms;
|
|
|
|
// sum over bispectrum contributions to forces
|
|
// on all particles including ghosts
|
|
|
|
int nall = atom->nlocal + atom->nghost;
|
|
for (int i = 0; i < nall; i++)
|
|
for (int itype = 0; itype < atom->ntypes; itype++) {
|
|
const int typeoffset_local = ndims_peratom*nperdim*itype;
|
|
const int typeoffset_global = nperdim*itype;
|
|
double *snadi = snap_peratom[i]+typeoffset_local;
|
|
for (int icoeff = 0; icoeff < nperdim; icoeff++) {
|
|
double dbdx = snadi[icoeff];
|
|
double dbdy = snadi[icoeff+yoffset];
|
|
double dbdz = snadi[icoeff+zoffset];
|
|
int irow = irow0;
|
|
snap[irow++][icoeff+typeoffset_global] += dbdx*x[i][0];
|
|
snap[irow++][icoeff+typeoffset_global] += dbdy*x[i][1];
|
|
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][2];
|
|
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][1];
|
|
snap[irow++][icoeff+typeoffset_global] += dbdz*x[i][0];
|
|
snap[irow][icoeff+typeoffset_global] += dbdy*x[i][0];
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage
|
|
------------------------------------------------------------------------- */
|
|
|
|
double ComputeSnap::memory_usage()
|
|
{
|
|
|
|
double bytes = (double)size_array_rows*size_array_cols *
|
|
sizeof(double); // snap
|
|
bytes += (double)size_array_rows*size_array_cols *
|
|
sizeof(double); // snapall
|
|
bytes += (double)nmax*size_peratom * sizeof(double); // snap_peratom
|
|
bytes += snaptr->memory_usage(); // SNA object
|
|
int n = atom->ntypes+1;
|
|
bytes += (double)n*sizeof(int); // map
|
|
|
|
return bytes;
|
|
}
|