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             : This action can be used to convert an input matrix to a vector. The input matrix is flattened
      31             : in row-major order so if the input matrix is $N \times $M$ the output vector has $N\times M$ elements.
      32             : The first $M$ of these elements contain the first row of the input matrix, the second $M$ contain the
      33             : second row of the input matrix and so on.
      34             : 
      35             : The following example illustrates how we can convert a $5\times 5$ contact matrix into a vector with
      36             : 25 elements:
      37             : 
      38             : ```plumed
      39             : c1: CONTACT_MATRIX GROUP=1,2,3,4,5 SWITCH={RATIONAL R_0=0.1}
      40             : f: FLATTEN ARG=c1
      41             : PRINT ARG=f FILE=colvar
      42             : ```
      43             : 
      44             : 
      45             : */
      46             : //+ENDPLUMEDOC
      47             : 
      48             : namespace PLMD {
      49             : namespace valtools {
      50             : 
      51             : class Flatten :
      52             :   public ActionWithValue,
      53             :   public ActionWithArguments {
      54             : public:
      55             :   static void registerKeywords( Keywords& keys );
      56             : /// Constructor
      57             :   explicit Flatten(const ActionOptions&);
      58             : /// Get the number of derivatives
      59          10 :   unsigned getNumberOfDerivatives() override {
      60          10 :     return 0;
      61             :   }
      62             : /// Do the calculation
      63             :   void calculate() override;
      64             : ///
      65             :   void apply() override;
      66             : };
      67             : 
      68             : PLUMED_REGISTER_ACTION(Flatten,"FLATTEN")
      69             : 
      70          20 : void Flatten::registerKeywords( Keywords& keys ) {
      71          20 :   Action::registerKeywords( keys );
      72          20 :   ActionWithValue::registerKeywords( keys );
      73          20 :   ActionWithArguments::registerKeywords( keys );
      74          40 :   keys.addInputKeyword("compulsory","ARG","matrix","the label for the matrix that you would like to flatten to a vector");
      75          40 :   keys.setValueDescription("vector","a vector containing all the elements of the input matrix");
      76          20 : }
      77             : 
      78           9 : Flatten::Flatten(const ActionOptions& ao):
      79             :   Action(ao),
      80             :   ActionWithValue(ao),
      81           9 :   ActionWithArguments(ao) {
      82           9 :   if( getNumberOfArguments()!=1 ) {
      83           0 :     error("should only be one argument for this action");
      84             :   }
      85           9 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) {
      86           0 :     error("input to this action should be a matrix");
      87             :   }
      88           9 :   getPntrToArgument(0)->buildDataStore(true);
      89           9 :   std::vector<unsigned> inshape( getPntrToArgument(0)->getShape() );
      90           9 :   std::vector<unsigned> shape( 1 );
      91           9 :   shape[0]=inshape[0]*inshape[1];
      92           9 :   addValue( shape );
      93           9 :   setNotPeriodic();
      94           9 :   getPntrToComponent(0)->buildDataStore();
      95           9 : }
      96             : 
      97           9 : void Flatten::calculate() {
      98           9 :   Value* myval = getPntrToComponent(0);
      99           9 :   unsigned ss=getPntrToArgument(0)->getShape()[1];
     100             :   std::vector<double> vals;
     101             :   std::vector<std::pair<unsigned,unsigned> > pairs;
     102             :   bool symmetric=getPntrToArgument(0)->isSymmetric();
     103           9 :   unsigned nedge=0;
     104           9 :   getPntrToArgument(0)->retrieveEdgeList( nedge, pairs, vals );
     105        8139 :   for(unsigned l=0; l<nedge; ++l ) {
     106        8130 :     unsigned i=pairs[l].first, j=pairs[l].second;
     107        8130 :     myval->set( i*ss + j, vals[l] );
     108        8130 :     if( symmetric ) {
     109           0 :       myval->set( j*ss + i, vals[l] );
     110             :     }
     111             :   }
     112           9 : }
     113             : 
     114           7 : void Flatten::apply() {
     115           7 :   if( doNotCalculateDerivatives() || !getPntrToComponent(0)->forcesWereAdded() ) {
     116           4 :     return;
     117             :   }
     118             : 
     119           3 :   Value* myval=getPntrToComponent(0);
     120             :   Value* myarg=getPntrToArgument(0);
     121           3 :   unsigned nvals=myval->getNumberOfValues();
     122          22 :   for(unsigned j=0; j<nvals; ++j) {
     123          19 :     myarg->addForce( j, myval->getForce(j) );
     124             :   }
     125             : }
     126             : 
     127             : }
     128             : }