Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2023 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_dimred_PCA_h
      23             : #define __PLUMED_dimred_PCA_h
      24             : 
      25             : #include "DimensionalityReductionBase.h"
      26             : #include "reference/ReferenceConfiguration.h"
      27             : #include "reference/Direction.h"
      28             : #include "tools/PDB.h"
      29             : 
      30             : namespace PLMD {
      31             : namespace dimred {
      32             : 
      33             : class PCA : public DimensionalityReductionBase {
      34             :   friend class OutputPCAProjection;
      35             : private:
      36             : /// The way we are measuring distances
      37             :   std::string mtype;
      38             : /// The position of the reference configuration (the one we align to)
      39             :   PDB mypdb;
      40             : /// The eigenvectors for the displacements in argument space
      41             :   std::string ofilename, fmt;
      42             : /// The eigenvectors that we are using
      43             :   std::unique_ptr<ReferenceConfiguration> myref;
      44             :   std::vector<Direction> directions;
      45             : public:
      46             :   static void registerKeywords( Keywords& keys );
      47             :   explicit PCA(const ActionOptions&ao);
      48             :   void performAnalysis() override;
      49             :   void getProjection( const unsigned& idata, std::vector<double>& point, double& weight ) override;
      50             :   void getProjection( analysis::DataCollectionObject& myidata, std::vector<double>& point );
      51           0 :   void calculateProjections( const Matrix<double>&, Matrix<double>& ) override { plumed_error(); }
      52           0 :   void setTargetDistance( const unsigned&, const double& ) override { plumed_error(); }
      53           0 :   double calculateStress( const std::vector<double>& pp, std::vector<double>& der ) override { plumed_error(); }
      54             : };
      55             : 
      56             : }
      57             : }
      58             : #endif