Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #ifndef __PLUMED_tools_LinkCells_h
      23             : #define __PLUMED_tools_LinkCells_h
      24             : 
      25             : #include <vector>
      26             : #include "Vector.h"
      27             : #include "Pbc.h"
      28             : 
      29             : namespace PLMD {
      30             : 
      31             : class Communicator;
      32             : 
      33             : /// \ingroup TOOLBOX
      34             : /// A class for doing link cells
      35             : class LinkCells {
      36             : private:
      37             : /// Symbolic link to plumed communicator
      38             :   Communicator & comm;
      39             : /// Check that the link cells were set up correctly
      40             :   bool cutoffwasset;
      41             : /// Are there periodic boundary conditions setup
      42             :   bool nopbc;
      43             : /// The cutoff to use for the sizes of the cells
      44             :   double link_cutoff;
      45             : /// The pbc we are using for link cells
      46             :   Pbc mypbc;
      47             : /// The location of the origin if we are not using periodic boundary conditions
      48             :   Vector origin;
      49             : /// The number of cells in each direction
      50             :   std::vector<unsigned> ncells;
      51             : /// The number of cells to stride through to get the link cells
      52             :   std::vector<unsigned> nstride;
      53             : /// The list of cells each atom is inside
      54             :   std::vector<unsigned> allcells;
      55             : /// The start of each block corresponding to each link cell
      56             :   std::vector<unsigned> lcell_starts;
      57             : /// The number of atoms in each link cell
      58             :   std::vector<unsigned> lcell_tots;
      59             : /// The atoms ordered by link cells
      60             :   std::vector<unsigned> lcell_lists;
      61             : public:
      62             : ///
      63             :   explicit LinkCells( Communicator& comm );
      64             : /// Have the link cells been enabled
      65             :   bool enabled() const ;
      66             : /// Set the value of the cutoff
      67             :   void setCutoff( const double& lcut );
      68             : /// Get the value of the cutoff
      69             :   double getCutoff() const ;
      70             : /// Get the total number of link cells
      71             :   unsigned getNumberOfCells() const ;
      72             : /// Get the nuumber of atoms in the cell that contains the most atoms
      73             :   unsigned getMaxInCell() const ;
      74             : /// Build the link cell lists
      75             :   void buildCellLists( const std::vector<Vector>& pos, const std::vector<unsigned>& indices, const Pbc& pbc );
      76             : /// Take three indices and return the index of the corresponding cell
      77             :   unsigned convertIndicesToIndex( const unsigned& nx, const unsigned& ny, const unsigned& nz ) const ;
      78             : /// Find the cell index in which this position is contained
      79             :   unsigned findCell( const Vector& pos ) const ;
      80             : /// Find the cell in which this position is contained
      81             :   std::array<unsigned,3> findMyCell( const Vector& pos ) const ;
      82             : /// Get the list of cells we need to surround the a particular cell
      83             :   void addRequiredCells( const std::array<unsigned,3>& celn, unsigned& ncells_required,
      84             :                          std::vector<unsigned>& cells_required ) const ;
      85             : /// Retrieve the atoms in a list of cells
      86             :   void retrieveAtomsInCells( const unsigned& ncells_required,
      87             :                              const std::vector<unsigned>& cells_required,
      88             :                              unsigned& natomsper, std::vector<unsigned>& atoms ) const ;
      89             : /// Retrieve the atoms we need to consider
      90             :   void retrieveNeighboringAtoms( const Vector& pos, std::vector<unsigned>& cell_list, unsigned& natomsper, std::vector<unsigned>& atoms ) const ;
      91             : };
      92             : 
      93             : inline
      94             : bool LinkCells::enabled() const {
      95             :   return cutoffwasset;
      96             : }
      97             : 
      98             : inline
      99             : unsigned LinkCells::getNumberOfCells() const {
     100        8670 :   return ncells[0]*ncells[1]*ncells[2];
     101             : }
     102             : 
     103             : }
     104             : 
     105             : #endif