Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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_NeighborList_h //{
      23             : #define __PLUMED_tools_NeighborList_h
      24             : 
      25             : #include "Vector.h"
      26             : #include "AtomNumber.h"
      27             : 
      28             : #include <vector>
      29             : 
      30             : namespace PLMD {
      31             : 
      32             : class Pbc;
      33             : class Communicator;
      34             : 
      35             : /// \ingroup TOOLBOX
      36             : /// A class that implements neighbor lists from two lists or a single list of atoms
      37             : class NeighborList {
      38             : public:
      39             :   using pairIDs=std::pair<unsigned,unsigned>;
      40             :   using pairAtomNumbers=std::pair<PLMD::AtomNumber,PLMD::AtomNumber>;
      41             : private:
      42             :   bool reduced=false;
      43             :   bool serial_;
      44             :   bool do_pair_;
      45             :   bool do_pbc_;
      46             :   bool twolists_;
      47             :   const PLMD::Pbc* pbc_;
      48             :   Communicator& comm;
      49             :   std::vector<PLMD::AtomNumber> fullatomlist_{};
      50             :   std::vector<PLMD::AtomNumber> requestlist_{};
      51             :   std::vector<pairIDs > neighbors_{};
      52             :   double distance_;
      53             :   size_t nlist0_=0;
      54             :   size_t nlist1_=0;
      55             :   size_t nallpairs_;
      56             :   unsigned stride_=0;
      57             :   unsigned lastupdate_=0;
      58             : /// Initialize the neighbor list with all possible pairs
      59             :   void initialize();
      60             : /// Return the pair of indexes in the positions array
      61             : /// of the two atoms forming the i-th pair among all possible pairs
      62             :   pairIDs getIndexPair(unsigned i);
      63             : /// Extract the list of atoms from the current list of close pairs
      64             :   void setRequestList();
      65             : public:
      66             :   NeighborList(const std::vector<PLMD::AtomNumber>& list0,
      67             :                const std::vector<PLMD::AtomNumber>& list1,
      68             :                const bool& serial,
      69             :                const bool& do_pair,
      70             :                const bool& do_pbc,
      71             :                const PLMD::Pbc& pbc,
      72             :                Communicator &cm,
      73         456 :                const double& distance=1.0e+30,
      74         456 :                const unsigned& stride=0);
      75             :   NeighborList(const std::vector<PLMD::AtomNumber>& list0,
      76             :                const bool& serial,
      77             :                const bool& do_pbc,
      78             :                const PLMD::Pbc& pbc,
      79             :                Communicator &cm,
      80          22 :                const double& distance=1.0e+30,
      81          22 :                const unsigned& stride=0);
      82             :   ~NeighborList();
      83             : /// Return the list of all atoms. These are needed to rebuild the neighbor list.
      84             :   std::vector<PLMD::AtomNumber>& getFullAtomList();
      85             : /// Update the indexes in the neighbor list to match the
      86             : /// ordering in the new positions array
      87             : /// and return the new list of atoms that must be requested to the main code
      88             :   std::vector<PLMD::AtomNumber>& getReducedAtomList();
      89             : /// Update the neighbor list and prepare the new
      90             : /// list of atoms that will be requested to the main code
      91             :   void update(const std::vector<PLMD::Vector>& positions);
      92             : /// Get the update stride of the neighbor list
      93             :   unsigned getStride() const;
      94             : /// Get the last step in which the neighbor list was updated
      95             :   unsigned getLastUpdate() const;
      96             : /// Set the step of the last update
      97             :   void setLastUpdate(unsigned step);
      98             : /// Get the size of the neighbor list
      99             :   unsigned size() const;
     100             : /// Get the distance used to create the neighbor list
     101             :   double distance() const;
     102             : /// Get the i-th pair of the neighbor list
     103             :   pairIDs getClosePair(unsigned i) const;
     104             : /// Get the list of neighbors of the i-th atom
     105             :   std::vector<unsigned> getNeighbors(unsigned i);
     106             : /// Get the i-th pair of AtomNumbers from the neighbor list
     107             :   pairAtomNumbers getClosePairAtomNumber(unsigned i) const;
     108             : };
     109             : 
     110             : } // namespace PLMD
     111             : 
     112             : #endif //__PLUMED_tools_NeighborList_h }