Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2019 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_analysis_LandmarkSelectionBase_h
      23             : #define __PLUMED_analysis_LandmarkSelectionBase_h
      24             : 
      25             : #include "reference/ReferenceConfiguration.h"
      26             : #include "AnalysisWithLandmarks.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace analysis {
      30             : 
      31           1 : class LandmarkSelectionOptions {
      32             :   friend class LandmarkRegister;
      33             :   friend class LandmarkSelectionBase;
      34             : private:
      35             :   std::vector<std::string> words;
      36             :   AnalysisWithLandmarks* action;
      37             : public:
      38             :   LandmarkSelectionOptions( const std::vector<std::string>& input, AnalysisWithLandmarks* myanalysis );
      39             : };
      40             : 
      41             : class LandmarkSelectionBase {
      42             :   friend class AnalysisWithLandmarks;
      43             :   friend class CopyAllFrames;
      44             : private:
      45             : /// Name of the method we are using for landmark selection
      46             :   std::string style;
      47             : /// The number of landmarks we are selecting
      48             :   unsigned nlandmarks;
      49             : /// The input to the landmark selection object
      50             :   std::vector<std::string> input;
      51             : /// A pointer to the underlying action
      52             :   AnalysisWithLandmarks* action;
      53             : /// How do we treat weights
      54             :   bool novoronoi, noweights;
      55             : protected:
      56             : /// Return the numbe of landmarks
      57             :   unsigned getNumberOfLandmarks() const ;
      58             : /// Return the communicator
      59             :   Communicator& getCommunicator();
      60             : /// Read a keywords from the input
      61             :   template <class T>
      62             :   void parse(const std::string&,T& );
      63             : /// Read a flag from the input
      64             :   void parseFlag(const std::string& key, bool& t);
      65             : /// Get the number of frames in the underlying action
      66             :   unsigned getNumberOfFrames() const;
      67             : /// Get the weight of the ith frame
      68             :   double getWeightOfFrame( const unsigned& );
      69             : /// Calculate the distance between the ith and jth frames
      70             :   double getDistanceBetweenFrames( const unsigned&, const unsigned&  );
      71             : /// Transfer frame i in the underlying action to the object we are going to analyze
      72             :   void selectFrame( const unsigned&, MultiReferenceBase* );
      73             : public:
      74             :   explicit LandmarkSelectionBase( const LandmarkSelectionOptions& lo );
      75             :   virtual ~LandmarkSelectionBase();
      76             : /// Check everything was read in
      77             :   void checkRead() const ;
      78             : /// Return a description of the landmark selection protocol
      79             :   std::string description();
      80             : /// Overwrite this to have a more descriptive output
      81           0 :   virtual std::string rest_of_description() { return ""; };
      82             : /// Actually do landmark selection
      83             :   void selectLandmarks( MultiReferenceBase* );
      84             :   virtual void select( MultiReferenceBase* )=0;
      85             : };
      86             : 
      87             : inline
      88             : unsigned LandmarkSelectionBase::getNumberOfLandmarks() const {
      89           0 :   return nlandmarks;
      90             : }
      91             : 
      92             : inline
      93             : Communicator& LandmarkSelectionBase::getCommunicator() {
      94             :   return action->comm;
      95             : }
      96             : 
      97             : inline
      98         202 : unsigned LandmarkSelectionBase::getNumberOfFrames() const {
      99         404 :   return action->getNumberOfDataPoints();
     100             : }
     101             : 
     102             : template <class T>
     103           0 : void LandmarkSelectionBase::parse( const std::string& key, T& t ) {
     104           0 :   bool found=Tools::parse(input,key,t);
     105           0 :   if(!found) plumed_merror("landmark seleciton style " + style + " requires " + key + " keyword");
     106           0 : }
     107             : 
     108             : }
     109             : }
     110             : #endif