Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 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_SMACOF_h
      23             : #define __PLUMED_dimred_SMACOF_h
      24             : 
      25             : #include <vector>
      26             : #include "core/Value.h"
      27             : #include "tools/Matrix.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace dimred {
      31             : 
      32           1 : class SMACOF {
      33             : private:
      34             :   Matrix<double> Distances, Weights;
      35             :   double calculateSigma( const Matrix<double>& InitialZ, Matrix<double>& dists );
      36             : public:
      37             :   explicit SMACOF( const Value* mysquaredists );
      38             :   void optimize( const double& tol, const unsigned& maxloops, std::vector<double>& proj);
      39             :   double getDistance( const unsigned& i, const unsigned& j ) const ;
      40             :   void setWeight( const unsigned& i, const unsigned& j, const double& ww );
      41             : };
      42             : 
      43             : inline
      44             : double SMACOF::getDistance( const unsigned& i, const unsigned& j ) const {
      45      249500 :   return Distances( i, j );
      46             : }
      47             : 
      48             : inline
      49      499000 : void SMACOF::setWeight( const unsigned& i, const unsigned& j, const double& ww ) {
      50      499000 :   Weights(i,j) = Weights(j,i ) = ww;
      51      499000 : }
      52             : 
      53             : }
      54             : }
      55             : #endif