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             : #include "ClassicalScaling.h"
      23             : #include "reference/PointWiseMapping.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace analysis {
      27             : 
      28           2 : void ClassicalScaling::run( PointWiseMapping* mymap ) {
      29             :   // Retrieve the distances from the dimensionality reduction object
      30           2 :   double half=(-0.5); Matrix<double> distances( half*mymap->modifyDmat() );
      31             : 
      32             :   // Apply centering transtion
      33             :   unsigned n=distances.nrows(); double sum;
      34             :   // First HM
      35         402 :   for(unsigned i=0; i<n; ++i) {
      36       40200 :     sum=0; for(unsigned j=0; j<n; ++j) sum+=distances(i,j);
      37       40200 :     for(unsigned j=0; j<n; ++j) distances(i,j) -= sum/n;
      38             :   }
      39             :   // Now (HM)H
      40         402 :   for(unsigned i=0; i<n; ++i) {
      41       40200 :     sum=0; for(unsigned j=0; j<n; ++j) sum+=distances(j,i);
      42       40200 :     for(unsigned j=0; j<n; ++j) distances(j,i) -= sum/n;
      43             :   }
      44             : 
      45             :   // Diagonalize matrix
      46           2 :   std::vector<double> eigval(n); Matrix<double> eigvec(n,n);
      47           2 :   diagMat( distances, eigval, eigvec );
      48             : 
      49             :   // Pass final projections to map object
      50         402 :   for(unsigned i=0; i<n; ++i) {
      51        1800 :     for(unsigned j=0; j<mymap->getNumberOfProperties(); ++j) mymap->setProjectionCoordinate( i, j, sqrt(eigval[n-1-j])*eigvec(n-1-j,i) );
      52             :   }
      53           2 : }
      54             : 
      55             : }
      56        4839 : }