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 {
      48          10 :     return 0;
      49             :   }
      50             : /// Do the calculation
      51             :   void calculate() override;
      52             : ///
      53             :   void apply() override;
      54             : };
      55             : 
      56             : PLUMED_REGISTER_ACTION(Flatten,"FLATTEN")
      57             : 
      58          20 : void Flatten::registerKeywords( Keywords& keys ) {
      59          20 :   Action::registerKeywords( keys );
      60          20 :   ActionWithValue::registerKeywords( keys );
      61          20 :   ActionWithArguments::registerKeywords( keys );
      62          20 :   keys.use("ARG");
      63          20 :   keys.setValueDescription("a vector containing all the elements of the input matrix");
      64          20 : }
      65             : 
      66           9 : Flatten::Flatten(const ActionOptions& ao):
      67             :   Action(ao),
      68             :   ActionWithValue(ao),
      69           9 :   ActionWithArguments(ao) {
      70           9 :   if( getNumberOfArguments()!=1 ) {
      71           0 :     error("should only be one argument for this action");
      72             :   }
      73           9 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) {
      74           0 :     error("input to this action should be a matrix");
      75             :   }
      76           9 :   getPntrToArgument(0)->buildDataStore(true);
      77           9 :   std::vector<unsigned> inshape( getPntrToArgument(0)->getShape() );
      78           9 :   std::vector<unsigned> shape( 1 );
      79           9 :   shape[0]=inshape[0]*inshape[1];
      80           9 :   addValue( shape );
      81           9 :   setNotPeriodic();
      82           9 :   getPntrToComponent(0)->buildDataStore();
      83           9 : }
      84             : 
      85           9 : void Flatten::calculate() {
      86           9 :   Value* myval = getPntrToComponent(0);
      87           9 :   unsigned ss=getPntrToArgument(0)->getShape()[1];
      88             :   std::vector<double> vals;
      89             :   std::vector<std::pair<unsigned,unsigned> > pairs;
      90             :   bool symmetric=getPntrToArgument(0)->isSymmetric();
      91           9 :   unsigned nedge=0;
      92           9 :   getPntrToArgument(0)->retrieveEdgeList( nedge, pairs, vals );
      93        8139 :   for(unsigned l=0; l<nedge; ++l ) {
      94        8130 :     unsigned i=pairs[l].first, j=pairs[l].second;
      95        8130 :     myval->set( i*ss + j, vals[l] );
      96        8130 :     if( symmetric ) {
      97           0 :       myval->set( j*ss + i, vals[l] );
      98             :     }
      99             :   }
     100           9 : }
     101             : 
     102           7 : void Flatten::apply() {
     103           7 :   if( doNotCalculateDerivatives() || !getPntrToComponent(0)->forcesWereAdded() ) {
     104           4 :     return;
     105             :   }
     106             : 
     107           3 :   Value* myval=getPntrToComponent(0);
     108             :   Value* myarg=getPntrToArgument(0);
     109           3 :   unsigned nvals=myval->getNumberOfValues();
     110          22 :   for(unsigned j=0; j<nvals; ++j) {
     111          19 :     myarg->addForce( j, myval->getForce(j) );
     112             :   }
     113             : }
     114             : 
     115             : }
     116             : }