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 "AnalysisBase.h"
      23             : #include "ReadAnalysisFrames.h"
      24             : #include "reference/ReferenceConfiguration.h"
      25             : #include "reference/MetricRegister.h"
      26             : #include "core/PlumedMain.h"
      27             : #include "core/ActionSet.h"
      28             : #include "core/ActionRegister.h"
      29             : #include "core/ActionSetup.h"
      30             : #include "tools/IFile.h"
      31             : 
      32             : //+PLUMEDOC ANALYSIS READ_DISSIMILARITY_MATRIX
      33             : /*
      34             : Read a matrix of dissimilarities between a trajectory of atomic configurations from a file.
      35             : 
      36             : \par Examples
      37             : 
      38             : */
      39             : //+ENDPLUMEDOC
      40             : 
      41             : namespace PLMD {
      42             : namespace analysis {
      43             : 
      44             : class ReadDissimilarityMatrix : public AnalysisBase {
      45             : private:
      46             :   unsigned nnodes;
      47             :   std::vector<DataCollectionObject> fake_data;
      48             :   std::string fname, wfile;
      49             : //  Matrix<double> dissimilarities;
      50             :   std::vector<std::vector<double> > dissimilarities;
      51             :   std::vector<double> weights;
      52             : public:
      53             :   static void registerKeywords( Keywords& keys );
      54             :   explicit ReadDissimilarityMatrix( const ActionOptions& ao );
      55             :   unsigned getNumberOfDataPoints() const override;
      56             : // Return the index of the data point in the base class
      57             :   unsigned getDataPointIndexInBase( const unsigned& idata ) const override;
      58             : /// This gives an error as if we read in the matrix we dont have the coordinates
      59             :   DataCollectionObject& getStoredData( const unsigned& idata, const bool& calcdist ) override;
      60             : /// Tell everyone we have dissimilarities
      61          11 :   bool dissimilaritiesWereSet() const override {
      62          11 :     return true;
      63             :   }
      64             : /// Get the dissimilarity between two data points
      65             :   double getDissimilarity( const unsigned&, const unsigned& ) override;
      66             : /// Get the weight from the input file
      67             :   double getWeight( const unsigned& idata ) override;
      68             : /// Just tell plumed to stop
      69             :   void update() override;
      70             : /// Read in the dissimilarity matrix
      71             :   void runFinalJobs() override;
      72             : /// This does nothing
      73           0 :   void performAnalysis() override {};
      74             : /// Overwrite virtual function in base class
      75           0 :   void performTask( const unsigned&, const unsigned&, MultiValue& ) const override {
      76           0 :     plumed_error();
      77             :   }
      78             : };
      79             : 
      80       13789 : PLUMED_REGISTER_ACTION(ReadDissimilarityMatrix,"READ_DISSIMILARITY_MATRIX")
      81             : 
      82           6 : void ReadDissimilarityMatrix::registerKeywords( Keywords& keys ) {
      83           6 :   AnalysisBase::registerKeywords( keys );
      84          12 :   keys.add("compulsory","FILE","an input file containing the matrix of dissimilarities");
      85          12 :   keys.add("optional","WFILE","input file containing weights of points");
      86          12 :   keys.reset_style("USE_OUTPUT_DATA_FROM","optional");
      87           6 : }
      88             : 
      89           2 : ReadDissimilarityMatrix::ReadDissimilarityMatrix( const ActionOptions& ao ):
      90             :   Action(ao),
      91             :   AnalysisBase(ao),
      92           2 :   nnodes(1) {
      93           2 :   setStride(1); // Set the stride equal to one to ensure we don't get stuck in an infinite loop
      94           2 :   std::vector<ActionSetup*> setupActions=plumed.getActionSet().select<ActionSetup*>();
      95           2 :   if( my_input_data && (plumed.getActionSet().size()-setupActions.size())!=1 ) {
      96           0 :     error("should only be this action and the READ_ANALYSIS_FRAMES command in the input file");
      97             :   }
      98           2 :   if( !my_input_data && plumed.getActionSet().size()!=0 ) {
      99           0 :     error("read dissimilarity matrix command must be at top of input file");
     100             :   }
     101             : 
     102           2 :   parse("FILE",fname);
     103           2 :   log.printf("  reading dissimilarity matrix from file %s \n",fname.c_str() );
     104           4 :   parse("WFILE",wfile);
     105             : 
     106           2 :   if( wfile.length()>0 ) {
     107           0 :     log.printf("  reading weights of nodes from file named %s \n",wfile.c_str() );
     108             :   } else {
     109           2 :     log.printf("  setting weights of all nodes equal to one\n");
     110             :   }
     111           2 : }
     112             : 
     113           7 : void ReadDissimilarityMatrix::update() {
     114           7 :   if(!my_input_data) {
     115           1 :     plumed.stop();
     116             :   }
     117           7 : }
     118             : 
     119           2 : void ReadDissimilarityMatrix::runFinalJobs() {
     120           2 :   IFile mfile;
     121           2 :   mfile.open(fname);
     122             :   // Read in first line
     123             :   std::vector<std::string> words;
     124           2 :   nnodes=0;
     125           4 :   while( nnodes==0 ) {
     126           2 :     Tools::getParsedLine( mfile, words );
     127           2 :     nnodes=words.size();
     128             :   }
     129             : 
     130           2 :   std::vector<double> tmpdis( nnodes );
     131          20 :   for(unsigned j=0; j<nnodes; ++j) {
     132          18 :     Tools::convert( words[j], tmpdis[j] );
     133             :   }
     134           2 :   dissimilarities.push_back( tmpdis );
     135             : 
     136          18 :   while( Tools::getParsedLine( mfile, words ) ) {
     137          16 :     if( words.size()!=nnodes ) {
     138           0 :       error("bad formatting in matrix file");
     139             :     }
     140         192 :     for(unsigned j=0; j<nnodes; ++j) {
     141         176 :       Tools::convert( words[j], tmpdis[j] );
     142             :     }
     143          16 :     dissimilarities.push_back( tmpdis );
     144             :   }
     145           2 :   mfile.close();
     146           2 :   if( my_input_data && dissimilarities.size()!=getNumberOfDataPoints() ) {
     147           0 :     error("mismatch between number of data points in trajectory and the dimensions of the dissimilarity matrix");
     148             :   }
     149           2 :   if( !my_input_data ) {
     150           1 :     fake_data.resize( dissimilarities.size() );
     151             :   }
     152             : 
     153           2 :   weights.resize( dissimilarities.size() );
     154           2 :   if( wfile.length()>0 ) {
     155           0 :     IFile wfilef;
     156           0 :     wfilef.open(wfile);
     157           0 :     for(unsigned i=0; i<weights.size(); ++i) {
     158           0 :       Tools::getParsedLine( wfilef, words );
     159           0 :       Tools::convert( words[0], weights[i] );
     160             :     }
     161           0 :     wfilef.close();
     162           0 :   } else {
     163           2 :     weights.assign(weights.size(),1.0);
     164             :   }
     165           2 : }
     166             : 
     167         257 : unsigned ReadDissimilarityMatrix::getNumberOfDataPoints() const {
     168         257 :   if( my_input_data ) {
     169          45 :     return AnalysisBase::getNumberOfDataPoints();
     170             :   }
     171         212 :   return dissimilarities.size();
     172             : }
     173             : 
     174           0 : unsigned ReadDissimilarityMatrix::getDataPointIndexInBase( const unsigned& idata ) const {
     175           0 :   return idata;
     176             : }
     177             : 
     178         334 : double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ) {
     179         334 :   return dissimilarities[iframe][jframe]*dissimilarities[iframe][jframe];
     180             : }
     181             : 
     182           5 : DataCollectionObject& ReadDissimilarityMatrix::getStoredData( const unsigned& idata, const bool& calcdist ) {
     183           5 :   plumed_massert( !calcdist, "cannot calc dist as this data was read in from input");
     184           5 :   if( my_input_data ) {
     185           5 :     return AnalysisBase::getStoredData( idata, calcdist );
     186             :   }
     187           0 :   return fake_data[idata];
     188             : }
     189             : 
     190          18 : double ReadDissimilarityMatrix::getWeight( const unsigned& idata ) {
     191          18 :   plumed_assert( idata<dissimilarities.size() );
     192          18 :   return weights[idata];
     193             : }
     194             : 
     195             : }
     196             : }