Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 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_clusters_ClusteringBase_h
      23             : #define __PLUMED_clusters_ClusteringBase_h
      24             : 
      25             : #include "matrixtools/MatrixOperationBase.h"
      26             : #include "tools/Matrix.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace clusters {
      30             : 
      31             : class ClusteringBase : public matrixtools::MatrixOperationBase {
      32             : protected:
      33             : /// Vector that stores the sizes of the current set of clusters
      34             :   std::vector< std::pair<unsigned,unsigned> > cluster_sizes;
      35             : /// Used to identify the cluster we are working on
      36             :   int number_of_cluster;
      37             : /// Vector that identifies the cluster each atom belongs to
      38             :   std::vector<unsigned> which_cluster;
      39             : /// Get the number of nodes
      40             :   unsigned getNumberOfNodes() const ;
      41             : /// Get the neighbour list based on the adjacency matrix
      42             :   void retrieveAdjacencyLists( std::vector<unsigned>& nneigh, Matrix<unsigned>& adj_list );
      43             : public:
      44             : /// Create manual
      45             :   static void registerKeywords( Keywords& keys );
      46             : /// Constructor
      47             :   explicit ClusteringBase(const ActionOptions&);
      48             : ///
      49          24 :   unsigned getNumberOfDerivatives() override { return 0; }
      50             : ///
      51             :   void calculate() override;
      52             : ///
      53             :   virtual void performClustering()=0;
      54             : /// Cannot apply forces on a clustering object
      55             :   void apply() override ;
      56           0 :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override { plumed_error(); }
      57             : };
      58             : 
      59             : inline
      60             : unsigned ClusteringBase::getNumberOfNodes() const {
      61       20929 :   return getPntrToArgument(0)->getShape()[0];
      62             : }
      63             : 
      64             : }
      65             : }
      66             : #endif