Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2019 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_adjmat_ClusterAnalysisBase_h
      23             : #define __PLUMED_adjmat_ClusterAnalysisBase_h
      24             : 
      25             : #include "ClusteringBase.h"
      26             : #include "multicolvar/MultiColvarBase.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace adjmat {
      30             : 
      31         108 : class ClusterAnalysisBase : public multicolvar::MultiColvarBase {
      32             : private:
      33             :   MultiValue myfvals;
      34             :   multicolvar::AtomValuePack myfatoms;
      35             :   ClusteringBase* myclusters;
      36             : protected:
      37             :   unsigned getNumberOfNodes() const ;
      38             :   unsigned getNumberOfClusters() const ;
      39             :   void retrieveAtomsInCluster( const unsigned& clust, std::vector<unsigned>& myatoms ) const ;
      40             :   bool nodeIsActive( const unsigned& ind ) const ;
      41             :   double getCutoffForConnection() const ;
      42             :   bool areConnected( const unsigned& ind1, const unsigned& ind2 ) const ;
      43             :   void getPropertiesOfNode( const unsigned& ind, std::vector<double>& vals ) const ;
      44             :   void getNodePropertyDerivatives( const unsigned& ind, MultiValue& myvals ) const ;
      45             : public:
      46             :   static void registerKeywords( Keywords& keys );
      47             :   explicit ClusterAnalysisBase(const ActionOptions&);
      48             :   unsigned getNumberOfQuantities() const ;
      49             :   bool isPeriodic();
      50             :   void turnOnDerivatives();
      51             :   void setupActiveTaskSet( std::vector<unsigned>& active_tasks, const std::string& input_label ) {}
      52             :   Vector getPositionOfAtomForLinkCells( const unsigned& ) const ;
      53           0 :   double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const { plumed_error(); }
      54             : };
      55             : 
      56             : }
      57             : }
      58             : #endif
      59             : 
      60             :