Commit 3e9a18b5 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14533 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 9cf43f2a

src/neigh_shardlow.cpp

0 → 100644
+471 −0
Original line number Diff line number Diff line 
/* ----------------------------------------------------------------------

   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.

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



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

   Contributing authors: 

   James Larentzos and Timothy I. Mattox (Engility Corporation)

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



#include "neighbor.h"

#include "neigh_list.h"

#include "neigh_request.h"

#include "atom.h"

#include "atom_vec.h"

#include "molecule.h"

#include "domain.h"

#include "group.h"

#include "memory.h"

#include "error.h"

#include "update.h"



using namespace LAMMPS_NS;



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

   convert atom coords into the ssa active interaction region number

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



int Neighbor::coord2ssa_airnum(double *x)

{

  int ix, iy, iz;



  ix = iy = iz = 0;

  if (x[2] < domain->sublo[2]) iz = -1;

  if (x[2] > domain->subhi[2]) iz = 1;

  if (x[1] < domain->sublo[1]) iy = -1;

  if (x[1] > domain->subhi[1]) iy = 1;

  if (x[0] < domain->sublo[0]) ix = -1;

  if (x[0] > domain->subhi[0]) ix = 1;



  if(iz < 0) return 0;



  if(iz == 0){

    if( iy<0 ) return 0; // bottom left/middle/right

    if( (iy==0) && (ix<0)  ) return 0; // left atoms

    if( (iy==0) && (ix==0) ) return 1; // Locally owned atoms

    if( (iy==0) && (ix>0)  ) return 3; // Right atoms

    if( (iy>0)  && (ix==0) ) return 2; // Top-middle atoms

    if( (iy>0)  && (ix!=0) ) return 4; // Top-right and top-left atoms

  } else if(iz > 0) {

    if((ix==0) && (iy==0)) return 5; // Back atoms

    if((ix==0) && (iy!=0)) return 6; // Top-back and bottom-back atoms

    if((ix!=0) && (iy==0)) return 7; // Left-back and right-back atoms

    if((ix!=0) && (iy!=0)) return 8; // Back corner atoms

  }



  return 0;

}



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

 *    assign owned and ghost atoms their ssa active interaction region numbers

 *    Called in the pre_neighbor and setup_pre_neighbor fix stages

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



void Neighbor::assign_ssa_airnums()

{

  int i,ibin;

  double **x = atom->x;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  int nall = nlocal + atom->nghost;



  if (nall > len_ssa_airnum) {

    len_ssa_airnum = nall;

    memory->destroy(ssa_airnum);

    memory->create(ssa_airnum,len_ssa_airnum,"ssa_airnum");

  }



  // bin in reverse order so linked list will be in forward order



  if (includegroup) {

    int bitmask = group->bitmask[includegroup];

    for (i = nall-1; i >= nlocal; i--) {

      if (mask[i] & bitmask) {

        ibin = coord2ssa_airnum(x[i]);

      } else {

        ibin = 0;

      }

      ssa_airnum[i] = ibin;

    }

    // All the local excluded atoms are in the zero airnum

    ibin = 0;

    for (i = atom->nlocal-1; i >= atom->nfirst; i--) {

      ssa_airnum[i] = ibin;

    }

  } else {

    for (i = nall-1; i >= nlocal; i--) {

      ibin = coord2ssa_airnum(x[i]);

      ssa_airnum[i] = ibin;

    }

  }



  // All the local included atoms are in the same airnum (#1)

  if (i >= 0) {

    ibin = coord2ssa_airnum(x[i]);

    do {

      ssa_airnum[i] = ibin;

    } while (--i >= 0);

  }

}



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

   routines to create a stencil = list of bin offsets

   stencil = bins whose closest corner to central bin is within cutoff

   sx,sy,sz = bin bounds = furthest the stencil could possibly extend

   3d creates xyz stencil, 2d creates xy stencil

   for half list with newton on:

     stencil is bins to the "upper right" of central bin

     stencil does not include self

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



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



void Neighbor::stencil_half_bin_2d_ssa(NeighList *list,

                                   int sx, int sy, int sz)

{

  int i,j;

  int *stencil = list->stencil;

  int nstencil = 0;



  for (j = 0; j <= sy; j++)

    for (i = -sx; i <= sx; i++)

      if (j > 0 || (j == 0 && i > 0))

        if (bin_distance(i,j,0) < cutneighmaxsq)

          stencil[nstencil++] = j*mbinx + i;



  list->nstencil = nstencil;



  // Now include additional bins for AIR ghosts only

  for (j = -sy; j <= 0; j++)

    for (i = -sx; i <= sx; i++) {

      if (j == 0 && i > 0) continue;

      if (bin_distance(i,j,0) < cutneighmaxsq)

        stencil[nstencil++] = j*mbinx + i;

    }



  while (nstencil < list->maxstencil) {

    stencil[nstencil++] = INT_MAX;

  }

}



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



void Neighbor::stencil_half_bin_3d_ssa(NeighList *list,

                                   int sx, int sy, int sz)

{

  int i,j,k;

  int *stencil = list->stencil;

  int nstencil = 0;



  for (k = 0; k <= sz; k++)

    for (j = -sy; j <= sy; j++)

      for (i = -sx; i <= sx; i++)

        if (k > 0 || j > 0 || (j == 0 && i > 0))

          if (bin_distance(i,j,k) < cutneighmaxsq)

            stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;



  list->nstencil = nstencil;



  // Now include additional bins for AIR ghosts only

  for (k = -sz; k < 0; k++)

    for (j = -sy; j <= sy; j++)

      for (i = -sx; i <= sx; i++)

        if (bin_distance(i,j,k) < cutneighmaxsq)

          stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;

  k = 0; // skip already included bins at k == 0

  for (j = -sy; j <= 0; j++)

    for (i = -sx; i <= sx; i++) {

      if (j == 0 && i > 0) continue;

      if (bin_distance(i,j,k) < cutneighmaxsq)

        stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;

    }



  while (nstencil < list->maxstencil) {

    stencil[nstencil++] = INT_MAX;

  }

}



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

   build half list from full list for use by Shardlow Spliting Algorithm

   pair stored once if i,j are both owned and i < j

   if j is ghost, only store if j coords are "above and to the right" of i

   works if full list is a skip list

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



void Neighbor::half_from_full_newton_ssa(NeighList *list)

{

  int i,j,ii,jj,n,jnum,joriginal;

  int *neighptr,*jlist;



  int nlocal = atom->nlocal;



  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  MyPage<int> *ipage = list->ipage;



  int *ilist_full = list->listfull->ilist;

  int *numneigh_full = list->listfull->numneigh;

  int **firstneigh_full = list->listfull->firstneigh;

  int inum_full = list->listfull->inum;



  int inum = 0;

  ipage->reset();



  // loop over parent full list



  for (ii = 0; ii < inum_full; ii++) {

    n = 0;

    neighptr = ipage->vget();



    i = ilist_full[ii];



    // loop over full neighbor list



    jlist = firstneigh_full[i];

    jnum = numneigh_full[i];



    for (jj = 0; jj < jnum; jj++) {

      joriginal = jlist[jj];

      j = joriginal & NEIGHMASK;

      if (j < nlocal) {

        if (i > j) continue;

      } else {

        if (ssa_airnum[j] <= 0) continue;

      }

      neighptr[n++] = joriginal;

    }



    ilist[inum++] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    ipage->vgot(n);

    if (ipage->status())

      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

  }



  list->inum = inum;

}



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

   for Shardlow Spliting Algorithm:

   binned neighbor list construction with full Newton's 3rd law

   each owned atom i checks its own bin and other bins in Newton stencil

   every pair stored exactly once by some processor

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



void Neighbor::half_bin_newton_ssa(NeighList *list)

{

  int i,j,k,n,itype,jtype,ibin,which,imol,iatom,moltemplate;

  tagint tagprev;

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;

  int *neighptr;



  double **x = atom->x;

  int *type = atom->type;

  int *mask = atom->mask;

  tagint *tag = atom->tag;

  tagint *molecule = atom->molecule;

  tagint **special = atom->special;

  int **nspecial = atom->nspecial;

  int nlocal = atom->nlocal;

  int nall = nlocal + atom->nghost;



  int *molindex = atom->molindex;

  int *molatom = atom->molatom;

  Molecule **onemols = atom->avec->onemols;

  int molecular = atom->molecular;

  if (molecular == 2) moltemplate = 1;

  else moltemplate = 0;



  int *ilist = list->ilist;

  int *numneigh = list->numneigh;

  int **firstneigh = list->firstneigh;

  int nstencil = list->nstencil;

  int maxstencil = list->maxstencil;

  int *stencil = list->stencil;

  MyPage<int> *ipage = list->ipage;



  int inum = 0;



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

   bin owned and ghost atoms for use by Shardlow Splitting Algorithm

    exclude ghost atoms that are not in the Active Interaction Regions (AIR)

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



  if (mbins > maxhead_ssa) {

    maxhead_ssa = mbins;

    memory->destroy(gbinhead_ssa);

    memory->destroy(binhead_ssa);

    memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa");

    memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa");

  }

  for (i = 0; i < mbins; i++) {

    gbinhead_ssa[i] = -1;

    binhead_ssa[i] = -1;

  }



  if (maxbin > maxbin_ssa) {

    maxbin_ssa = maxbin;

    memory->destroy(bins_ssa);

    memory->create(bins_ssa,maxbin_ssa,"bins_ssa");

  }



  // bin in reverse order so linked list will be in forward order



  if (includegroup) {

    int bitmask = group->bitmask[includegroup];

    for (i = nall-1; i >= nlocal; i--) {

      if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR

      if (mask[i] & bitmask) {

        ibin = coord2bin(x[i]);

        bins_ssa[i] = gbinhead_ssa[ibin];

        gbinhead_ssa[ibin] = i;

      }

    }

    nlocal = atom->nfirst; // This is important for the code that follows!

  } else {

    for (i = nall-1; i >= nlocal; i--) {

      if (ssa_airnum[i] <= 0) continue; // skip ghost atoms not in AIR

      ibin = coord2bin(x[i]);

      bins_ssa[i] = gbinhead_ssa[ibin];

      gbinhead_ssa[ibin] = i;

    }

  }

  for (i = nlocal-1; i >= 0; i--) {

    ibin = coord2bin(x[i]);

    bins_ssa[i] = binhead_ssa[ibin];

    binhead_ssa[ibin] = i;

  }



  ipage->reset();



  // loop over owned atoms, storing half of the neighbors



  for (i = 0; i < nlocal; i++) {

    n = 0;

    neighptr = ipage->vget();



    itype = type[i];

    xtmp = x[i][0];

    ytmp = x[i][1];

    ztmp = x[i][2];

    if (moltemplate) {

      imol = molindex[i];

      iatom = molatom[i];

      tagprev = tag[i] - iatom - 1;

    }



    // loop over rest of local atoms in i's bin

    // just store them, since j is beyond i in linked list



    for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) {



      jtype = type[j];

      if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;



      delx = xtmp - x[j][0];

      dely = ytmp - x[j][1];

      delz = ztmp - x[j][2];

      rsq = delx*delx + dely*dely + delz*delz;



      if (rsq <= cutneighsq[itype][jtype]) {

        if (molecular) {

          if (!moltemplate)

            which = find_special(special[i],nspecial[i],tag[j]);

          else if (imol >= 0)

            which = find_special(onemols[imol]->special[iatom],

                                 onemols[imol]->nspecial[iatom],

                                 tag[j]-tagprev);

          else which = 0;

          if (which == 0) neighptr[n++] = j;

          else if (domain->minimum_image_check(delx,dely,delz))

            neighptr[n++] = j;

          else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);

        } else neighptr[n++] = j;

      }

    }



    ibin = coord2bin(x[i]);



    // loop over all local atoms in other bins in "half" stencil

    for (k = 0; k < nstencil; k++) {

      for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {



        jtype = type[j];

        if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;



        delx = xtmp - x[j][0];

        dely = ytmp - x[j][1];

        delz = ztmp - x[j][2];

        rsq = delx*delx + dely*dely + delz*delz;



        if (rsq <= cutneighsq[itype][jtype]) {

          if (molecular) {

            if (!moltemplate)

              which = find_special(special[i],nspecial[i],tag[j]);

            else if (imol >= 0)

              which = find_special(onemols[imol]->special[iatom],

                                   onemols[imol]->nspecial[iatom],

                                   tag[j]-tagprev);

            else which = 0;

            if (which == 0) neighptr[n++] = j;

            else if (domain->minimum_image_check(delx,dely,delz))

              neighptr[n++] = j;

            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);

          } else neighptr[n++] = j;

        }

      }

    }



    // loop over AIR ghost atoms in all bins in "full" stencil

    // Note: the non-AIR ghost atoms have already been filtered out

    for (k = 0; k < maxstencil; k++) {

      if (stencil[k] > mbins) break; /* Check if ghost stencil bins are exhausted */

      for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) {



        jtype = type[j];

        if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;



        delx = xtmp - x[j][0];

        dely = ytmp - x[j][1];

        delz = ztmp - x[j][2];

        rsq = delx*delx + dely*dely + delz*delz;



        if (rsq <= cutneighsq[itype][jtype]) {

          if (molecular) {

            if (!moltemplate)

              which = find_special(special[i],nspecial[i],tag[j]);

            else if (imol >= 0)

              which = find_special(onemols[imol]->special[iatom],

                                   onemols[imol]->nspecial[iatom],

                                   tag[j]-tagprev);

            else which = 0;

            if (which == 0) neighptr[n++] = j;

            else if (domain->minimum_image_check(delx,dely,delz))

              neighptr[n++] = j;

            else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);

          } else neighptr[n++] = j;

        }

      }

    }



    ilist[inum++] = i;

    firstneigh[i] = neighptr;

    numneigh[i] = n;

    ipage->vgot(n);

    if (ipage->status())

      error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");

  }



  list->inum = inum;

}

src/neighbor.cpp

+0 −6
Original line number Diff line number Diff line
@@ -162,7 +162,6 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp) 
  improperlist = NULL;



  copymode = 0;

  last_binning_timestep = -1;

}



/* ---------------------------------------------------------------------- */
@@ -2015,11 +2014,6 @@ void Neighbor::bin_atoms() 
{

  int i,ibin;



  // NOTE: added for USER-DPD, why do we need this?



  //if (last_binning_timestep == update->ntimestep) return;

  //last_binning_timestep = update->ntimestep;



  for (i = 0; i < mbins; i++) binhead[i] = -1;



  // bin in reverse order so linked list will be in forward order

src/neighbor.h

+13 −9
Original line number Diff line number Diff line
@@ -71,7 +71,7 @@ class Neighbor : protected Pointers { 


  int cluster_check;               // 1 if check bond/angle/etc satisfies minimg



  // USER-DPD package - better to make this private?

  // USER-DPD package



  int *ssa_airnum;              // AIR number of each atom for SSA in USER-DPD
@@ -121,7 +121,6 @@ class Neighbor : protected Pointers { 


  int binatomflag;                 // bin atoms or not when build neigh list

                                   // turned off by build_one()

  bigint last_binning_timestep;	   // last step neighbor binning was done



  int nbinx,nbiny,nbinz;           // # of global bins

  int *bins;                       // ptr to next atom in each bin
@@ -181,6 +180,11 @@ class Neighbor : protected Pointers { 
  // USER-DPD package



  int len_ssa_airnum;        // length of ssa_airnum array

  int *bins_ssa;             // ptr to next atom in each bin used by SSA

  int maxbin_ssa;            // size of bins array used by SSA

  int *binhead_ssa;          // ptr to 1st atom in each bin used by SSA

  int *gbinhead_ssa;         // ptr to 1st ghost atom in each bin used by SSA

  int maxhead_ssa;           // size of binhead array used by SSA



  // methods
@@ -320,13 +324,13 @@ class Neighbor : protected Pointers { 


  // SSA neighboring for USER-DPD



  //int coord2ssa_airnum(double *);  // map atom coord to an AIR number

  //void assign_ssa_airnums();       // set ssa_airnum values

  int coord2ssa_airnum(double *);  // map atom coord to an AIR number

  void assign_ssa_airnums();       // set ssa_airnum values



  void half_bin_newton_ssa(NeighList *) {}

  void half_from_full_newton_ssa(class NeighList *) {}

  void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {}

  void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {}

  void half_bin_newton_ssa(NeighList *);

  void half_from_full_newton_ssa(class NeighList *);

  void stencil_half_bin_2d_ssa(class NeighList *, int, int, int);

  void stencil_half_bin_3d_ssa(class NeighList *, int, int, int);



  // find_special: determine if atom j is in special list of atom i

  // if it is not, return 0

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