Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2017 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/ActionWithValue.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : //+PLUMEDOC FUNCTION FLATTEN
      27             : /*
      28             : Convert a matrix into a vector
      29             : 
      30             : \par Examples
      31             : 
      32             : 
      33             : */
      34             : //+ENDPLUMEDOC
      35             : 
      36             : namespace PLMD {
      37             : namespace valtools {
      38             : 
      39             : class Flatten :
      40             :   public ActionWithValue,
      41             :   public ActionWithArguments {
      42             : public:
      43             :   static void registerKeywords( Keywords& keys );
      44             : /// Constructor
      45             :   explicit Flatten(const ActionOptions&);
      46             : /// Get the number of derivatives
      47          10 :   unsigned getNumberOfDerivatives() override { return 0; }
      48             : /// Do the calculation
      49             :   void calculate() override;
      50             : ///
      51             :   void apply() override;
      52             : };
      53             : 
      54             : PLUMED_REGISTER_ACTION(Flatten,"FLATTEN")
      55             : 
      56          20 : void Flatten::registerKeywords( Keywords& keys ) {
      57          20 :   Action::registerKeywords( keys ); ActionWithValue::registerKeywords( keys );
      58          20 :   ActionWithArguments::registerKeywords( keys );
      59          40 :   keys.addInputKeyword("compulsory","ARG","matrix","the label for the matrix that you would like to flatten to a vector");
      60          40 :   keys.setValueDescription("vector","a vector containing all the elements of the input matrix");
      61          20 : }
      62             : 
      63           9 : Flatten::Flatten(const ActionOptions& ao):
      64             :   Action(ao),
      65             :   ActionWithValue(ao),
      66           9 :   ActionWithArguments(ao)
      67             : {
      68           9 :   if( getNumberOfArguments()!=1 ) error("should only be one argument for this action");
      69           9 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) error("input to this action should be a matrix");
      70           9 :   getPntrToArgument(0)->buildDataStore(true);
      71           9 :   std::vector<unsigned> inshape( getPntrToArgument(0)->getShape() );
      72           9 :   std::vector<unsigned> shape( 1 ); shape[0]=inshape[0]*inshape[1];
      73           9 :   addValue( shape ); setNotPeriodic(); getPntrToComponent(0)->buildDataStore();
      74           9 : }
      75             : 
      76           9 : void Flatten::calculate() {
      77           9 :   Value* myval = getPntrToComponent(0); unsigned ss=getPntrToArgument(0)->getShape()[1];
      78             :   std::vector<double> vals; std::vector<std::pair<unsigned,unsigned> > pairs;
      79             :   bool symmetric=getPntrToArgument(0)->isSymmetric();
      80           9 :   unsigned nedge=0; getPntrToArgument(0)->retrieveEdgeList( nedge, pairs, vals );
      81        8139 :   for(unsigned l=0; l<nedge; ++l ) {
      82        8130 :     unsigned i=pairs[l].first, j=pairs[l].second;
      83        8130 :     myval->set( i*ss + j, vals[l] );
      84        8130 :     if( symmetric ) myval->set( j*ss + i, vals[l] );
      85             :   }
      86           9 : }
      87             : 
      88           7 : void Flatten::apply() {
      89           7 :   if( doNotCalculateDerivatives() || !getPntrToComponent(0)->forcesWereAdded() ) return;
      90             : 
      91           3 :   Value* myval=getPntrToComponent(0); Value* myarg=getPntrToArgument(0);
      92          22 :   unsigned nvals=myval->getNumberOfValues(); for(unsigned j=0; j<nvals; ++j) myarg->addForce( j, myval->getForce(j) );
      93             : }
      94             : 
      95             : }
      96             : }