xref: /dports/science/plumed/plumed2-2.7.2/src/tools/LinkCells.cpp

/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2014-2021 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed.org for more information.

   This file is part of plumed, version 2.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "LinkCells.h"
#include "Communicator.h"
#include "Tools.h"

namespace PLMD {

LinkCells::LinkCells( Communicator& cc ) :
  comm(cc),
  cutoffwasset(false),
  link_cutoff(0.0),
  ncells(3),
  nstride(3)
{
}

void LinkCells::setCutoff( const double& lcut ) {
  cutoffwasset=true; link_cutoff=lcut;
}

double LinkCells::getCutoff() const {
  plumed_assert( cutoffwasset ); return link_cutoff;
}

void LinkCells::buildCellLists( const std::vector<Vector>& pos, const std::vector<unsigned>& indices, const Pbc& pbc ) {
  plumed_assert( cutoffwasset && pos.size()==indices.size() );

  // Must be able to check that pbcs are not nonsensical in some way?? -- GAT

  // Setup the pbc object by copying it from action
  mypbc.setBox( pbc.getBox() );

  // Setup the lists
  if( pos.size()!=allcells.size() ) {
    allcells.resize( pos.size() ); lcell_lists.resize( pos.size() );
  }

  {
// This is the reciprocal lattice
// notice that reciprocal.getRow(0) is a vector that is orthogonal to b and c
// This allows to use linked cells in non orthorhomic boxes
    Tensor reciprocal(transpose(mypbc.getInvBox()));
    ncells[0] = std::floor( 1.0/ reciprocal.getRow(0).modulo() / link_cutoff );
    if( ncells[0]==0 ) ncells[0]=1;
    ncells[1] = std::floor( 1.0/ reciprocal.getRow(1).modulo() / link_cutoff );
    if( ncells[1]==0 ) ncells[1]=1;
    ncells[2] = std::floor( 1.0/ reciprocal.getRow(2).modulo() / link_cutoff );
    if( ncells[2]==0 ) ncells[2]=1;
  }
  // Setup the strides
  nstride[0]=1; nstride[1]=ncells[0]; nstride[2]=ncells[0]*ncells[1];

  // Setup the storage for link cells
  unsigned ncellstot=ncells[0]*ncells[1]*ncells[2];
  if( lcell_tots.size()!=ncellstot ) {
    lcell_tots.resize( ncellstot ); lcell_starts.resize( ncellstot );
  }
  // Clear nlcells
  for(unsigned i=0; i<ncellstot; ++i) lcell_tots[i]=0;
  // Clear allcells
  allcells.assign( allcells.size(), 0 );

  // Find out what cell everyone is in
  unsigned rank=comm.Get_rank(), size=comm.Get_size();
  for(unsigned i=rank; i<pos.size(); i+=size) {
    allcells[i]=findCell( pos[i] );
    lcell_tots[allcells[i]]++;
  }
  // And gather all this information on every node
  comm.Sum( allcells ); comm.Sum( lcell_tots );

  // Now prepare the link cell lists
  unsigned tot=0;
  for(unsigned i=0; i<lcell_tots.size(); ++i) { lcell_starts[i]=tot; tot+=lcell_tots[i]; lcell_tots[i]=0; }
  plumed_assert( tot==pos.size() );

  // And setup the link cells properly
  for(unsigned j=0; j<pos.size(); ++j) {
    unsigned myind = lcell_starts[ allcells[j] ] + lcell_tots[ allcells[j] ];
    lcell_lists[ myind ] = indices[j];
    lcell_tots[allcells[j]]++;
  }
}

#define LINKC_MIN(n) ((n<2)? 0 : -1)
#define LINKC_MAX(n) ((n<3)? 1 : 2)
#define LINKC_PBC(n,num) ((n<0)? num-1 : n%num )

void LinkCells::addRequiredCells( const std::array<unsigned,3>& celn, unsigned& ncells_required,
                                  std::vector<unsigned>& cells_required ) const {
  unsigned nnew_cells=0;
  for(int nx=LINKC_MIN(ncells[0]); nx<LINKC_MAX(ncells[0]); ++nx) {
    int xval = celn[0] + nx;
    xval=LINKC_PBC(xval,ncells[0])*nstride[0];
    for(int ny=LINKC_MIN(ncells[1]); ny<LINKC_MAX(ncells[1]); ++ny) {
      int yval = celn[1] + ny;
      yval=LINKC_PBC(yval,ncells[1])*nstride[1];
      for(int nz=LINKC_MIN(ncells[2]); nz<LINKC_MAX(ncells[2]); ++nz) {
        int zval = celn[2] + nz;
        zval=LINKC_PBC(zval,ncells[2])*nstride[2];

        unsigned mybox=xval+yval+zval; bool added=false;
        for(unsigned k=0; k<ncells_required; ++k) {
          if( mybox==cells_required[k] ) { added=true; break; }
        }
        if( !added ) { cells_required[ncells_required+nnew_cells]=mybox; nnew_cells++; }
      }
    }
  }
  ncells_required += nnew_cells;
}

void LinkCells::retrieveNeighboringAtoms( const Vector& pos, std::vector<unsigned>& cell_list,
    unsigned& natomsper, std::vector<unsigned>& atoms ) const {
  if( cell_list.size()!=getNumberOfCells() ) cell_list.resize( getNumberOfCells() );
  unsigned ncellt=0; addRequiredCells( findMyCell( pos ), ncellt, cell_list );
  retrieveAtomsInCells( ncellt, cell_list, natomsper, atoms );
}

void LinkCells::retrieveAtomsInCells( const unsigned& ncells_required,
                                      const std::vector<unsigned>& cells_required,
                                      unsigned& natomsper, std::vector<unsigned>& atoms ) const {
  plumed_assert( natomsper==1 || natomsper==2 );  // This is really a bug. If you are trying to reuse this ask GAT for help
  for(unsigned i=0; i<ncells_required; ++i) {
    unsigned mybox=cells_required[i];
    for(unsigned k=0; k<lcell_tots[mybox]; ++k) {
      unsigned myatom = lcell_lists[lcell_starts[mybox]+k];
      if( myatom!=atoms[0] ) { // Ideally would provide an option to not do this
        atoms[natomsper]=myatom;
        natomsper++;
      }
    }
  }
}

std::array<unsigned,3> LinkCells::findMyCell( const Vector& pos ) const {
  Vector fpos=mypbc.realToScaled( pos );
  std::array<unsigned,3> celn;
  for(unsigned j=0; j<3; ++j) {
    celn[j] = std::floor( ( Tools::pbc(fpos[j]) + 0.5 ) * ncells[j] );
    plumed_assert( celn[j]>=0 && celn[j]<ncells[j] ); // Check that atom is in box
  }
  return celn;
}

unsigned LinkCells::convertIndicesToIndex( const unsigned& nx, const unsigned& ny, const unsigned& nz ) const {
  return nx*nstride[0] + ny*nstride[1] + nz*nstride[2];
}

unsigned LinkCells::findCell( const Vector& pos ) const {
  std::array<unsigned,3> celn( findMyCell(pos ) );
  return convertIndicesToIndex( celn[0], celn[1], celn[2] );
}


}