lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "compute_coord_atom.h"
#include <cmath>
#include <cstring>
#include "compute_orientorder_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#define INVOKED_PERATOM 8

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

ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
  Compute(lmp, narg, arg),
  typelo(NULL), typehi(NULL), cvec(NULL), carray(NULL),
  group2(NULL), id_orientorder(NULL), normv(NULL)
{
  if (narg < 5) error->all(FLERR,"Illegal compute coord/atom command");

  jgroup = group->find("all");
  jgroupbit = group->bitmask[jgroup];
  cstyle = NONE;

  if (strcmp(arg[3],"cutoff") == 0) {
    cstyle = CUTOFF;
    double cutoff = force->numeric(FLERR,arg[4]);
    cutsq = cutoff*cutoff;

    int iarg = 5;
    if ((narg > 6) && (strcmp(arg[5],"group") == 0)) {
      int len = strlen(arg[6])+1;
      group2 = new char[len];
      strcpy(group2,arg[6]);
      iarg += 2;
      jgroup = group->find(group2);
      if (jgroup == -1)
        error->all(FLERR,"Compute coord/atom group2 ID does not exist");
      jgroupbit = group->bitmask[jgroup];
    }

    ncol = narg-iarg + 1;
    int ntypes = atom->ntypes;
    typelo = new int[ncol];
    typehi = new int[ncol];

    if (narg == iarg) {
      ncol = 1;
      typelo[0] = 1;
      typehi[0] = ntypes;
    } else {
      ncol = 0;
      while (iarg < narg) {
        force->bounds(FLERR,arg[iarg],ntypes,typelo[ncol],typehi[ncol]);
        if (typelo[ncol] > typehi[ncol])
          error->all(FLERR,"Illegal compute coord/atom command");
        ncol++;
        iarg++;
      }
    }

  } else if (strcmp(arg[3],"orientorder") == 0) {
    cstyle = ORIENT;
    if (narg != 6) error->all(FLERR,"Illegal compute coord/atom command");

    int n = strlen(arg[4]) + 1;
    id_orientorder = new char[n];
    strcpy(id_orientorder,arg[4]);

    int iorientorder = modify->find_compute(id_orientorder);
    if (iorientorder < 0)
      error->all(FLERR,"Could not find compute coord/atom compute ID");
    if (strcmp(modify->compute[iorientorder]->style,"orientorder/atom") != 0)
      error->all(FLERR,"Compute coord/atom compute ID is not orientorder/atom");

    threshold = force->numeric(FLERR,arg[5]);
    if (threshold <= -1.0 || threshold >= 1.0)
      error->all(FLERR,"Compute coord/atom threshold not between -1 and 1");

    ncol = 1;
    typelo = new int[ncol];
    typehi = new int[ncol];
    typelo[0] = 1;
    typehi[0] = atom->ntypes;

  } else error->all(FLERR,"Invalid cstyle in compute coord/atom");

  peratom_flag = 1;
  if (ncol == 1) size_peratom_cols = 0;
  else size_peratom_cols = ncol;

  nmax = 0;
}

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

ComputeCoordAtom::~ComputeCoordAtom()
{
  delete [] group2;
  delete [] typelo;
  delete [] typehi;
  memory->destroy(cvec);
  memory->destroy(carray);
  delete [] id_orientorder;
}

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

void ComputeCoordAtom::init()
{
  if (cstyle == ORIENT) {
    int iorientorder = modify->find_compute(id_orientorder);
    c_orientorder = (ComputeOrientOrderAtom*)(modify->compute[iorientorder]);
    cutsq = c_orientorder->cutsq;
    l = c_orientorder->qlcomp;
    //  communicate real and imaginary 2*l+1 components of the normalized vector
    comm_forward = 2*(2*l+1);
    if (c_orientorder->iqlcomp < 0)
      error->all(FLERR,"Compute coord/atom requires components "
                 "option in compute orientorder/atom");
  }

  if (force->pair == NULL)
    error->all(FLERR,"Compute coord/atom requires a pair style be defined");
  if (sqrt(cutsq) > force->pair->cutforce)
    error->all(FLERR,
               "Compute coord/atom cutoff is longer than pairwise cutoff");

  // need an occasional full neighbor list

  int irequest = neighbor->request(this,instance_me);
  neighbor->requests[irequest]->pair = 0;
  neighbor->requests[irequest]->compute = 1;
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;
  neighbor->requests[irequest]->occasional = 1;
}

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

void ComputeCoordAtom::init_list(int /*id*/, NeighList *ptr)
{
  list = ptr;
}

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

void ComputeCoordAtom::compute_peratom()
{
  int i,j,m,ii,jj,inum,jnum,jtype,n;
  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
  int *ilist,*jlist,*numneigh,**firstneigh;
  double *count;

  invoked_peratom = update->ntimestep;

  // grow coordination array if necessary

  if (atom->nmax > nmax) {
    if (ncol == 1) {
      memory->destroy(cvec);
      nmax = atom->nmax;
      memory->create(cvec,nmax,"coord/atom:cvec");
      vector_atom = cvec;
    } else {
      memory->destroy(carray);
      nmax = atom->nmax;
      memory->create(carray,nmax,ncol,"coord/atom:carray");
      array_atom = carray;
    }
  }

  if (cstyle == ORIENT) {
    if (!(c_orientorder->invoked_flag & INVOKED_PERATOM)) {
      c_orientorder->compute_peratom();
      c_orientorder->invoked_flag |= INVOKED_PERATOM;
    }
    nqlist = c_orientorder->nqlist;
    normv = c_orientorder->array_atom;
    comm->forward_comm_compute(this);
  }

  // invoke full neighbor list (will copy or build if necessary)

  neighbor->build_one(list);

  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  // compute coordination number(s) for each atom in group
  // use full neighbor list to count atoms less than cutoff

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

  if (cstyle == CUTOFF) {

    if (ncol == 1) {

      for (ii = 0; ii < inum; ii++) {
        i = ilist[ii];
        if (mask[i] & groupbit) {
          xtmp = x[i][0];
          ytmp = x[i][1];
          ztmp = x[i][2];
          jlist = firstneigh[i];
          jnum = numneigh[i];

          n = 0;
          for (jj = 0; jj < jnum; jj++) {
            j = jlist[jj];
            j &= NEIGHMASK;

            if (mask[j] & jgroupbit) {
              jtype = type[j];
              delx = xtmp - x[j][0];
              dely = ytmp - x[j][1];
              delz = ztmp - x[j][2];
              rsq = delx*delx + dely*dely + delz*delz;
              if (rsq < cutsq && jtype >= typelo[0] && jtype <= typehi[0])
                n++;
            }
          }

          cvec[i] = n;
        } else cvec[i] = 0.0;
      }

    } else {
      for (ii = 0; ii < inum; ii++) {
        i = ilist[ii];
        count = carray[i];
        for (m = 0; m < ncol; m++) count[m] = 0.0;

        if (mask[i] & groupbit) {
          xtmp = x[i][0];
          ytmp = x[i][1];
          ztmp = x[i][2];
          jlist = firstneigh[i];
          jnum = numneigh[i];


          for (jj = 0; jj < jnum; jj++) {
            j = jlist[jj];
            j &= NEIGHMASK;

            jtype = type[j];
            delx = xtmp - x[j][0];
            dely = ytmp - x[j][1];
            delz = ztmp - x[j][2];
            rsq = delx*delx + dely*dely + delz*delz;
            if (rsq < cutsq) {
              for (m = 0; m < ncol; m++)
                if (jtype >= typelo[m] && jtype <= typehi[m])
                  count[m] += 1.0;
            }
          }
        }
      }
    }

  } else if (cstyle == ORIENT) {

    for (ii = 0; ii < inum; ii++) {
      i = ilist[ii];
      if (mask[i] & groupbit) {
        xtmp = x[i][0];
        ytmp = x[i][1];
        ztmp = x[i][2];
        jlist = firstneigh[i];
        jnum = numneigh[i];

        n = 0;
        for (jj = 0; jj < jnum; jj++) {
          j = jlist[jj];
          j &= NEIGHMASK;
          delx = xtmp - x[j][0];
          dely = ytmp - x[j][1];
          delz = ztmp - x[j][2];
          rsq = delx*delx + dely*dely + delz*delz;
          if (rsq < cutsq) {
            double dot_product = 0.0;
            for (int m=0; m < 2*(2*l+1); m++) {
              dot_product += normv[i][nqlist+m]*normv[j][nqlist+m];
            }
            if (dot_product > threshold) n++;
          }
        }
        cvec[i] = n;
      } else cvec[i] = 0.0;
    }
  }
}

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

int ComputeCoordAtom::pack_forward_comm(int n, int *list, double *buf,
                                        int /*pbc_flag*/, int * /*pbc*/)
{
  int i,m=0,j;
  for (i = 0; i < n; ++i) {
    for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
      buf[m++] = normv[list[i]][j];
    }
  }

  return m;
}

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

void ComputeCoordAtom::unpack_forward_comm(int n, int first, double *buf)
{
  int i,last,m=0,j;
  last = first + n;
  for (i = first; i < last; ++i) {
    for (j = nqlist; j < nqlist + 2*(2*l+1); ++j) {
      normv[i][j] = buf[m++];
    }
  }
}

/* ----------------------------------------------------------------------
   memory usage of local atom-based array
------------------------------------------------------------------------- */

double ComputeCoordAtom::memory_usage()
{
  double bytes = ncol*nmax * sizeof(double);
  return bytes;
}