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             : #include "DimensionalityReductionBase.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "SMACOF.h"
      25             : 
      26             : //+PLUMEDOC DIMRED SMACOF_MDS
      27             : /*
      28             : Optimize the multidimensional scaling stress function using the SMACOF algorithm.
      29             : 
      30             : \par Examples
      31             : 
      32             : */
      33             : //+ENDPLUMEDOC
      34             : 
      35             : namespace PLMD {
      36             : namespace dimred {
      37             : 
      38             : class SmacofMDS : public DimensionalityReductionBase {
      39             : private:
      40             :   unsigned maxloops;
      41             :   double tol;
      42             : public:
      43             :   static void registerKeywords( Keywords& keys );
      44             :   explicit SmacofMDS( const ActionOptions& );
      45             :   void calculateProjections( const Matrix<double>&, Matrix<double>& ) override;
      46             : };
      47             : 
      48       10419 : PLUMED_REGISTER_ACTION(SmacofMDS,"SMACOF_MDS")
      49             : 
      50           1 : void SmacofMDS::registerKeywords( Keywords& keys ) {
      51           1 :   DimensionalityReductionBase::registerKeywords( keys );
      52           1 :   keys.remove("NLOW_DIM");
      53           2 :   keys.add("compulsory","SMACOF_TOL","1E-4","tolerance for the SMACOF optimization algorithm");
      54           2 :   keys.add("compulsory","SMACOF_MAXCYC","1000","maximum number of optimization cycles for SMACOF algorithm");
      55           1 : }
      56             : 
      57           0 : SmacofMDS::SmacofMDS( const ActionOptions& ao):
      58             :   Action(ao),
      59           0 :   DimensionalityReductionBase(ao)
      60             : {
      61           0 :   if( !dimredbase ) error("SMACOF must be initialized using output from dimensionality reduction object");
      62             : 
      63           0 :   parse("SMACOF_TOL",tol); parse("SMACOF_MAXCYC",maxloops);
      64           0 :   log.printf("  running smacof to convergence at %f or for a maximum of %u steps \n",tol,maxloops);
      65           0 : }
      66             : 
      67           0 : void SmacofMDS::calculateProjections( const Matrix<double>& targets, Matrix<double>& projections ) {
      68             :   // Take the square root of all the distances and the weights
      69             :   Matrix<double> weights( targets.nrows(), targets.ncols() );
      70             :   Matrix<double> distances( targets.nrows(), targets.ncols() );
      71           0 :   for(unsigned i=1; i<distances.ncols(); ++i) {
      72           0 :     for(unsigned j=0; j<i; ++j) {
      73           0 :       distances(i,j)=distances(j,i)=std::sqrt( targets(i,j) );
      74           0 :       weights(i,j)=weights(j,i)=getWeight(i)*getWeight(j);
      75             :     }
      76             :   }
      77             :   // And run SMACOF
      78           0 :   SMACOF::run( weights, targets, tol, maxloops, projections );
      79           0 : }
      80             : 
      81             : }
      82             : }