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 "LandmarkSelectionBase.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "tools/Random.h"
      25             : #include <iostream>
      26             : 
      27             : //+PLUMEDOC LANDMARKS LANDMARK_SELECT_STAGED
      28             : /*
      29             : Select a set of landmarks using the staged algorithm.
      30             : 
      31             : \par Examples
      32             : 
      33             : */
      34             : //+ENDPLUMEDOC
      35             : 
      36             : 
      37             : namespace PLMD {
      38             : namespace analysis {
      39             : 
      40             : class LandmarkStaged : public LandmarkSelectionBase {
      41             : private:
      42             :   unsigned seed;
      43             :   double gamma;
      44             : public:
      45             :   static void registerKeywords( Keywords& keys );
      46             :   explicit LandmarkStaged( const ActionOptions& ao );
      47             :   void selectLandmarks() override;
      48             : };
      49             : 
      50       10419 : PLUMED_REGISTER_ACTION(LandmarkStaged,"LANDMARK_SELECT_STAGED")
      51             : 
      52           1 : void LandmarkStaged::registerKeywords( Keywords& keys ) {
      53           1 :   LandmarkSelectionBase::registerKeywords(keys);
      54           2 :   keys.add("compulsory","GAMMA","the gamma parameter to be used in weights");
      55           2 :   keys.add("compulsory","SEED","1234","a random number seed");
      56           1 : }
      57             : 
      58           0 : LandmarkStaged::LandmarkStaged( const ActionOptions& ao ):
      59             :   Action(ao),
      60           0 :   LandmarkSelectionBase(ao)
      61             : {
      62           0 :   parse("SEED",seed); parse("GAMMA",gamma);
      63           0 :   log.printf("  probability of selecting voronoi polyhedra equal to exp(-weight/%f) \n", gamma );
      64           0 : }
      65             : 
      66           0 : void LandmarkStaged::selectLandmarks() {
      67           0 :   unsigned int n = getNumberOfDataPoints(); // The number of landmarks to pick
      68           0 :   unsigned int N = my_input_data->getNumberOfDataPoints();  // The total number of frames we can choose from
      69           0 :   unsigned int m = static_cast<int>( std::sqrt(n*N) );
      70           0 :   std::vector<unsigned> fpslandmarks(m);
      71             :   // Select first point at random
      72           0 :   Random random; random.setSeed(-seed); double rand=random.RandU01();
      73           0 :   fpslandmarks[0] = std::floor( N*rand );
      74             : 
      75             :   // using FPS we want to find m landmarks where m = sqrt(nN)
      76             :   // Now find distance to all other points
      77             :   Matrix<double> distances( m, N );
      78           0 :   for(unsigned int i=0; i<N; ++i) {
      79           0 :     distances(0,i) = my_input_data->getDissimilarity( fpslandmarks[0], i );
      80             :   }
      81             : 
      82             :   // Now find all other landmarks
      83           0 :   for(unsigned i=1; i<m; ++i) {
      84             :     // Find point that has the largest minimum distance from the landmarks selected thus far
      85             :     double maxd=0;
      86           0 :     for(unsigned j=0; j<N; ++j) {
      87           0 :       double mind=distances(0,j);
      88           0 :       for(unsigned k=1; k<i; ++k) {
      89           0 :         if( distances(k,j)<mind ) { mind=distances(k,j); }
      90             :       }
      91           0 :       if( mind>maxd ) { maxd=mind; fpslandmarks[i]=j; }
      92             :     }
      93           0 :     for(unsigned k=0; k<N; ++k) distances(i,k) = my_input_data->getDissimilarity( fpslandmarks[i], k );
      94             :   }
      95             : 
      96             :   // Initial FPS selection of m landmarks completed
      97             :   // Now find voronoi weights of these m points
      98           0 :   std::vector<unsigned> poly_assign( N );
      99           0 :   std::vector<double> weights( m, 0 );
     100           0 :   voronoiAnalysis( fpslandmarks, weights, poly_assign );
     101             : 
     102             :   //Calculate total weight of voronoi polyhedras
     103           0 :   double vweight=0; for(unsigned i=0; i<m; i++) vweight += std::exp( -weights[i] / gamma );
     104             : 
     105           0 :   std::vector<bool> selected(N, false); unsigned ncount=0;
     106           0 :   while ( ncount<n) {
     107             : //  generate random number and check which point it belongs to. select only it was not selected before
     108           0 :     double rand = vweight*random.RandU01();
     109             :     double running_vweight=0;
     110           0 :     for(unsigned jpoly=0; jpoly<m; ++jpoly) {
     111           0 :       running_vweight+=std::exp( -weights[jpoly] / gamma );
     112           0 :       if( running_vweight>=rand ) {
     113             :         double tweight=0;
     114           0 :         for(unsigned i=0; i<poly_assign.size(); ++i) {
     115           0 :           if( poly_assign[i]==jpoly ) tweight += getWeight( i );
     116             :         }
     117           0 :         double rand_poly = tweight*random.RandU01();
     118             :         double running_tweight=0;
     119           0 :         for(unsigned i=0; i<N; ++i) {
     120           0 :           if( poly_assign[i]==jpoly ) {
     121           0 :             running_tweight += getWeight( i );
     122           0 :             if( running_tweight>=rand_poly && !selected[i] ) {
     123           0 :               selectFrame(i); selected[i]=true; ncount++; break;
     124           0 :             } else if( running_tweight>=rand_poly ) {
     125             :               break;
     126             :             }
     127             :           }
     128             :         }
     129             :       }
     130             :     }
     131             :   }
     132           0 : }
     133             : 
     134             : }
     135             : }