forked from lijiext/lammps
Started on ComputeSnap
This commit is contained in:
Aidan Thompson
parent
2e6b19ea5f
commit
58bbbc3d8b
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@ -0,0 +1,377 @@
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/* ----------------------------------------------------------------------
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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 "compute_snap.h"
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#include <cstring>
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#include <cstdlib>
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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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ComputeSnap::ComputeSnap(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg), cutsq(NULL), list(NULL), snap(NULL),
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radelem(NULL), wjelem(NULL)
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{
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double rfac0, rmin0;
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int twojmax, switchflag, bzeroflag;
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radelem = NULL;
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wjelem = NULL;
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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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// 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 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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ncoeff = snaptr->ncoeff;
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nperdim = ncoeff;
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if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
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yoffset = nperdim;
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zoffset = 2*nperdim;
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size_peratom_cols = 3*nperdim*atom->ntypes;
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comm_reverse = size_peratom_cols;
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nmax = 0;
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snap = NULL;
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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(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 ComputeSnap::init()
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{
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if (force->pair == NULL)
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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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}
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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()
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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 snap array if necessary
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if (atom->nmax > nmax) {
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memory->destroy(snap);
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nmax = atom->nmax;
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memory->create(snap,nmax,size_peratom_cols,
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"snap:snap");
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array = snap;
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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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snap[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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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 = threencoeff*(atom->type[i]-1);
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// const int quadraticoffset = threencoeff*atom->ntypes +
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// threencoeffq*(atom->type[i]-1);
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const int typeoffset = 3*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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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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ninside++;
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}
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}
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snaptr->compute_ui(ninside);
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snaptr->compute_zi();
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if (quadraticflag) {
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snaptr->compute_bi();
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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],
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snaptr->wj[jj],
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snaptr->rcutij[jj],jj);
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snaptr->compute_dbidrj();
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// Accumulate -dBi/dRi, -dBi/dRj
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double *snapi = snap[i]+typeoffset;
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double *snapj = snap[j]+typeoffset;
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for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
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snapi[icoeff] += snaptr->dblist[icoeff][0];
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snapi[icoeff+yoffset] += snaptr->dblist[icoeff][1];
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snapi[icoeff+zoffset] += snaptr->dblist[icoeff][2];
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snapj[icoeff] -= snaptr->dblist[icoeff][0];
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snapj[icoeff+yoffset] -= snaptr->dblist[icoeff][1];
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snapj[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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snapi += quadraticoffset;
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snapj += 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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snapi[ncount] += dbxtmp;
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snapi[ncount+yoffset] += dbytmp;
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snapi[ncount+zoffset] += dbztmp;
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snapj[ncount] -= dbxtmp;
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snapj[ncount+yoffset] -= dbytmp;
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snapj[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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snapi[ncount] += dbxtmp;
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snapi[ncount+yoffset] += dbytmp;
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snapi[ncount+zoffset] += dbztmp;
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snapj[ncount] -= dbxtmp;
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snapj[ncount+yoffset] -= dbytmp;
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snapj[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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}
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}
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// communicate snap 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 ComputeSnap::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++] = snap[i][icoeff];
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeSnap::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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snap[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 ComputeSnap::memory_usage()
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{
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double bytes = nmax*size_peratom_cols * sizeof(double); // snap
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bytes += snaptr->memory_usage(); // SNA object
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return bytes;
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}
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@ -0,0 +1,77 @@
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/* -*- 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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#ifdef COMPUTE_CLASS
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ComputeStyle(snap,ComputeSnap)
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#else
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#ifndef LMP_COMPUTE_SNAP_H
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#define LMP_COMPUTE_SNAP_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeSnap : public Compute {
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public:
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ComputeSnap(class LAMMPS *, int, char **);
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~ComputeSnap();
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void init();
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void init_list(int, class NeighList *);
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void compute();
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int pack_reverse_comm(int, int, double *);
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void unpack_reverse_comm(int, int *, double *);
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double memory_usage();
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private:
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int nmax;
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int ncoeff, nperdim, yoffset, zoffset;
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double **cutsq;
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class NeighList *list;
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double **snap;
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double rcutfac;
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double *radelem;
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double *wjelem;
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class SNA* snaptr;
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double cutmax;
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int quadraticflag;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Compute snap requires a pair style be defined
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Self-explanatory.
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E: Compute snap cutoff is longer than pairwise cutoff
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UNDOCUMENTED
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W: More than one compute snad/atom
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Self-explanatory.
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*/
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