Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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_SketchMapBase_h
      23             : #define __PLUMED_dimred_SketchMapBase_h
      24             : 
      25             : #include "tools/SwitchingFunction.h"
      26             : #include "DimensionalityReductionBase.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace dimred {
      30             : 
      31             : class SketchMapBase : public DimensionalityReductionBase {
      32             : private:
      33             : /// To save us retyping switching functions many times the code will reuse the
      34             : /// ones from previous sketch-map objects
      35             :   bool reuse_hd, reuse_ld;
      36             : /// Was previous action in chain a sketch-map action
      37             :   SketchMapBase* smapbase;
      38             : /// Switching functions for low and high dimensional space
      39             :   SwitchingFunction lowdf, highdf;
      40             : /// This is used within calculate stress to hold the target distances and the
      41             : /// target values for the high dimensional switching function
      42             :   std::vector<double> dtargets, ftargets, pweights;
      43             : /// Stress normalization (sum_ij w_i w_j)
      44             :   double normw;
      45             : protected:
      46             : /// This holds the target distances and target transformed distances
      47             :   Matrix<double> distances, transformed;
      48             : /// The fraction of pure distances to mix in when optimising
      49             :   double mixparam;
      50             : public:
      51             :   static void registerKeywords( Keywords& keys );
      52             :   explicit SketchMapBase( const ActionOptions& );
      53             : /// This starts the process of calculating the projections
      54             :   void calculateProjections( const Matrix<double>&, Matrix<double>& ) override;
      55             : /// This finishes the process of calculating the prjections
      56             :   virtual void minimise( Matrix<double>& )=0;
      57             : /// Apply the low dimensional switching function to the value val
      58             :   double transformLowDimensionalDistance( const double& val, double& df ) const ;
      59             : /// Apply the high dimensional switching function to the value val
      60             :   double transformHighDimensionalDistance( const double& val, double& df ) const ;
      61             : /// Set the target distance and from it calculate the target value for the switching function
      62             : /// This target vector is used when we use calculateStress when finding the projections of individual points.
      63             : /// For example this function is used in PLMD::dimred::ProjectOutOfSample
      64             :   void setTargetDistance( const unsigned& idata, const double& dist ) override;
      65             : /// Calculate the pointwise stress on one point when it is located at p.
      66             : /// This function makes use of the distance data in dtargets and ftargets
      67             : /// It is used in PLMD::dimred::ProjectOutOfSample and in pointwise optimisation
      68             :   double calculateStress( const std::vector<double>& p, std::vector<double>& d ) override;
      69             : /// Calculate the total stress when the projections are placed at point p.  Notice
      70             : /// this is a vectorized version of the matrix of projections
      71             :   double calculateFullStress( const std::vector<double>& p, std::vector<double>& d );
      72             : };
      73             : 
      74             : inline
      75    26384110 : double SketchMapBase::transformLowDimensionalDistance( const double& val, double& df ) const {
      76    26384110 :   if( reuse_ld ) return smapbase->transformLowDimensionalDistance( val, df );
      77    21473710 :   double ans=1.0 - lowdf.calculate( val, df ); df*=-val; return ans;
      78             : }
      79             : 
      80             : inline
      81      341661 : double SketchMapBase::transformHighDimensionalDistance( const double& val, double& df ) const {
      82      341661 :   if( reuse_hd ) return smapbase->transformHighDimensionalDistance( val, df );
      83      316711 :   double ans=1.0 - highdf.calculate( val, df ); df*=-val; return ans;
      84             : }
      85             : 
      86             : inline
      87      145000 : void SketchMapBase::setTargetDistance( const unsigned& idata, const double& dist ) {
      88      145000 :   double df; dtargets[idata]=dist; ftargets[idata]=transformHighDimensionalDistance( dist, df );
      89      145000 : }
      90             : 
      91             : }
      92             : }
      93             : #endif