307 lines
8.4 KiB
C++
307 lines
8.4 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, 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 "pair_grid.h"
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#include "pair_sna_grid.h"
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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 "domain.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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#include "tokenizer.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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PairSNAGrid::PairSNAGrid(LAMMPS *lmp) :
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PairGrid(lmp),
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radelem(nullptr), wjelem(nullptr)
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{
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snaptr = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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PairSNAGrid::~PairSNAGrid()
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{
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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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}
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/* ---------------------------------------------------------------------- */
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void PairSNAGrid::init_style()
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{
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if (force->pair == nullptr)
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error->all(FLERR,"Pair sna/grid requires a pair style be defined");
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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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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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ndesc = ndesc_base + snaptr->ncoeff;
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printf("ndesc = %d\n", ndesc);
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snaptr->init();
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}
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/* ---------------------------------------------------------------------- */
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void PairSNAGrid::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 PairSNAGrid::compute(int eflag, int vflag)
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{
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// compute sna for each gridpoint
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double** const x = atom->x;
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const int* const mask = atom->mask;
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int * const type = atom->type;
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const int ntotal = atom->nlocal + atom->nghost;
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// insure rij, inside, and typej are of size jnum
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snaptr->grow_rij(ntotal);
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for (int iz = nzlo; iz <= nzhi; iz++)
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for (int iy = nylo; iy <= nyhi; iy++)
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for (int ix = nxlo; ix <= nxhi; ix++) {
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double xgrid[3];
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grid2x(ix, iy, iz, xgrid);
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const double xtmp = xgrid[0];
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const double ytmp = xgrid[1];
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const double ztmp = xgrid[2];
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// currently, all grid points are type 1
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const int itype = 1;
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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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// 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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int ninside = 0;
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for (int j = 0; j < ntotal; j++) {
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const double delx = xtmp - x[j][0];
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const double dely = ytmp - x[j][1];
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const double delz = ztmp - x[j][2];
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const double rsq = delx*delx + dely*dely + delz*delz;
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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[jtype][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] = 2.0*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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snaptr->compute_bi(ielem);
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// linear contributions
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for (int icoeff = 0; icoeff < ncoeff; icoeff++)
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gridlocal[ndesc_base+icoeff][iz][iy][ix] =
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snaptr->blist[icoeff];
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// quadratic contributions
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if (quadraticflag) {
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int ncount = ncoeff;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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double bveci = snaptr->blist[icoeff];
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gridlocal[ndesc_base+ncount++][iz][iy][ix] =
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0.5*bveci*bveci;
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for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
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gridlocal[ndesc_base+ncount++][iz][iy][ix] =
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bveci*snaptr->blist[jcoeff];
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairSNAGrid::settings(int narg, char ** arg)
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{
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// call base class first
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PairGrid::settings(narg, arg);
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// skip over arguments used by base class
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// so that argument positions are identical to
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// regular per-atom compute
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arg += nargbase;
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narg -= nargbase;
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int ntypes = atom->ntypes;
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int nargmin = 3+2*ntypes;
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if (narg < nargmin) error->all(FLERR,"Illegal pair sna/grid 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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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,"pair:sna/grid:radelem"); // offset by 1 to match up with types
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memory->create(wjelem,ntypes+1,"pair:sna/grid:wjelem");
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rcutfac = atof(arg[0]);
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rfac0 = atof(arg[1]);
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twojmax = atoi(arg[2]);
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for(int i = 0; i < ntypes; i++)
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radelem[i+1] = atof(arg[3+i]);
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for(int i = 0; i < ntypes; i++)
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wjelem[i+1] = atof(arg[3+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,"pair:sna/grid: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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printf("settings cutmax = %g \n",cutmax);
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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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printf("%d %d %d %s\n",iarg,narg,nargbase,arg[iarg]);
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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 pair sna/grid 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 pair sna/grid 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 pair sna/grid 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 pair sna/grid 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 pair sna/grid command");
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chemflag = 1;
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memory->create(map,ntypes+1,"pair:sna/grid: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 pair sna/grid 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 pair sna/grid 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 pair sna/grid 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 pair sna/grid command");
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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 PairSNAGrid::memory_usage()
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{
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double nbytes = snaptr->memory_usage(); // SNA object
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int n = atom->ntypes+1;
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nbytes += (double)n*sizeof(int); // map
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return nbytes;
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}
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