Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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_analysis_LandmarkSelectionBase_h
      23             : #define __PLUMED_analysis_LandmarkSelectionBase_h
      24             : 
      25             : #include "AnalysisBase.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace analysis {
      29             : 
      30             : class LandmarkSelectionBase : public AnalysisBase {
      31             :   friend class ReselectLandmarks;
      32             : private:
      33             : /// The number of landmarks we are selecting
      34             :   unsigned nlandmarks;
      35             : /// The weights of the landmark points
      36             :   std::vector<double> lweights;
      37             : /// The indices of the landmarks in the original data set
      38             :   std::vector<unsigned> landmark_indices;
      39             : /// How do we treat weights
      40             :   bool novoronoi, noweights;
      41             : protected:
      42             : /// Transfer frame i in the underlying action to the object we are going to analyze
      43             :   void selectFrame( const unsigned& );
      44             : /// Do a voronoi analysis
      45             :   void voronoiAnalysis( const std::vector<unsigned>& myindices, std::vector<double>& lweights, std::vector<unsigned>& assignments ) const ;
      46             : public:
      47             :   static void registerKeywords( Keywords& keys );
      48             :   explicit LandmarkSelectionBase( const ActionOptions& ao );
      49             : /// Return the number of data points
      50             :   unsigned getNumberOfDataPoints() const override;
      51             : /// Return the index of the data point in the base class
      52             :   unsigned getDataPointIndexInBase( const unsigned& idata ) const override;
      53             : /// Get the weight
      54             :   double getWeight( const unsigned& idata ) override;
      55             : /// Get a reference configuration
      56             :   DataCollectionObject& getStoredData( const unsigned& idat, const bool& calcdist ) override;
      57             : /// Select landmark configurations
      58             :   void performAnalysis() override;
      59             :   virtual void selectLandmarks()=0;
      60             : /// Get the squared dissimilarity between two reference configurations
      61             :   double getDissimilarity( const unsigned& i, const unsigned& j ) override;
      62             : /// This does nothing - it just ensures the final class is not abstract
      63           0 :   void performTask( const unsigned&, const unsigned&, MultiValue& ) const override { plumed_error(); }
      64             : };
      65             : 
      66             : inline
      67      126447 : unsigned LandmarkSelectionBase::getNumberOfDataPoints() const {
      68      126447 :   return nlandmarks;
      69             : }
      70             : 
      71             : inline
      72      125002 : unsigned LandmarkSelectionBase::getDataPointIndexInBase( const unsigned& idata ) const {
      73      125002 :   return AnalysisBase::getDataPointIndexInBase( landmark_indices[idata] );
      74             : }
      75             : 
      76             : inline
      77     8361301 : double LandmarkSelectionBase::getWeight( const unsigned& idata ) {
      78     8361301 :   return lweights[idata];
      79             : }
      80             : 
      81             : inline
      82         531 : DataCollectionObject& LandmarkSelectionBase::getStoredData( const unsigned& idat, const bool& calcdist ) {
      83         531 :   return AnalysisBase::getStoredData( landmark_indices[idat], calcdist );
      84             : }
      85             : 
      86             : inline
      87       62329 : double LandmarkSelectionBase::getDissimilarity( const unsigned& i, const unsigned& j ) {
      88       62329 :   return AnalysisBase::getDissimilarity( landmark_indices[i], landmark_indices[j] );
      89             : }
      90             : 
      91             : }
      92             : }
      93             : #endif