Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "core/ActionWithMatrix.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVAR VORONOI
      26             : /*
      27             : Do a voronoi analysis
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace matrixtools {
      36             : 
      37             : class Voronoi : public ActionWithMatrix {
      38             : public:
      39             :   static void registerKeywords( Keywords& keys );
      40             :   explicit Voronoi(const ActionOptions&);
      41             :   void prepare() override ;
      42           0 :   unsigned getNumberOfDerivatives() override {
      43           0 :     return 0;
      44             :   }
      45          12 :   unsigned getNumberOfColumns() const override {
      46          12 :     return getConstPntrToComponent(0)->getShape()[1];
      47             :   }
      48        1036 :   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const override {}
      49           0 :   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override {}
      50        1036 :   void runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const override {}
      51             :   void gatherStoredValue( const unsigned& valindex, const unsigned& code, const MultiValue& myvals,
      52             :                           const unsigned& bufstart, std::vector<double>& buffer ) const override ;
      53             : };
      54             : 
      55             : PLUMED_REGISTER_ACTION(Voronoi,"VORONOI")
      56             : 
      57          11 : void Voronoi::registerKeywords( Keywords& keys ) {
      58          11 :   ActionWithMatrix::registerKeywords(keys);
      59          22 :   keys.addInputKeyword("compulsory","ARG","matrix","the distance/adjacency matrix that should be used to perform the voronoi analysis");
      60          22 :   keys.setValueDescription("matrix","a matrix in which element ij is equal to one if the ij component of the input matrix is lower than all the ik elements of the matrix where k is not j and zero otherwise");
      61          11 : }
      62             : 
      63           6 : Voronoi::Voronoi(const ActionOptions&ao):
      64             :   Action(ao),
      65           6 :   ActionWithMatrix(ao) {
      66           6 :   if( getNumberOfArguments()!=1 ) {
      67           0 :     error("should be one arguments to this action, a matrix");
      68             :   }
      69           6 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) {
      70           0 :     error("argument to this action should be a matrix");
      71             :   }
      72           6 :   if( getPntrToArgument(0)->getShape()[1]>getPntrToArgument(0)->getShape()[0] ) {
      73           0 :     warning("would expect number of columns in matrix to exceed number of rows");
      74             :   }
      75           6 :   getPntrToArgument(0)->buildDataStore();
      76           6 :   std::vector<unsigned> shape( getPntrToArgument(0)->getShape() );
      77           6 :   addValue( shape );
      78           6 :   setNotPeriodic();
      79           6 :   getPntrToComponent(0)->buildDataStore();
      80           6 : }
      81             : 
      82           6 : void Voronoi::prepare() {
      83           6 :   Value* myval = getPntrToComponent(0);
      84           6 :   if( myval->getShape()[0]==getPntrToArgument(0)->getShape()[0] && myval->getShape()[1]==getPntrToArgument(0)->getShape()[1] ) {
      85           0 :     return;
      86             :   }
      87           6 :   std::vector<unsigned> shape( getPntrToArgument(0)->getShape() );
      88           6 :   myval->setShape(shape);
      89             : }
      90             : 
      91        1036 : void Voronoi::gatherStoredValue( const unsigned& valindex, const unsigned& code, const MultiValue& myvals,
      92             :                                  const unsigned& bufstart, std::vector<double>& buffer ) const {
      93             :   Value* arg0 = getPntrToArgument(0);
      94             :   unsigned nv = 0;
      95        1036 :   std::size_t cc=code;
      96        1036 :   double minmax = arg0->get( cc*arg0->getShape()[1] );
      97      251175 :   for(unsigned i=0; i<arg0->getShape()[1]; ++i) {
      98      250139 :     double value = arg0->get( code*arg0->getShape()[1] + i );
      99      250139 :     if( value<minmax ) {
     100             :       minmax = value;
     101             :       nv = i;
     102             :     }
     103             :   }
     104        1036 :   buffer[bufstart + code*arg0->getShape()[1] + nv] = 1;
     105        1036 : }
     106             : 
     107             : }
     108             : }