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 "MatrixOperationBase.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVAR TRANSPOSE
      26             : /*
      27             : Calculate the transpose of a matrix
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace matrixtools {
      36             : 
      37             : class TransposeMatrix : public MatrixOperationBase {
      38             : public:
      39             :   static void registerKeywords( Keywords& keys );
      40             : /// Constructor
      41             :   explicit TransposeMatrix(const ActionOptions&);
      42             : ///
      43         256 :   unsigned getNumberOfDerivatives() override { return 0; }
      44             : ///
      45             :   void prepare() override ;
      46             : ///
      47             :   void calculate() override ;
      48             : ///
      49             :   void apply() override ;
      50             : ///
      51             :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override;
      52             : };
      53             : 
      54             : PLUMED_REGISTER_ACTION(TransposeMatrix,"TRANSPOSE")
      55             : 
      56         279 : void TransposeMatrix::registerKeywords( Keywords& keys ) {
      57         279 :   MatrixOperationBase::registerKeywords( keys );
      58         279 :   keys.setValueDescription("the transpose of the input matrix");
      59         279 : }
      60             : 
      61         162 : TransposeMatrix::TransposeMatrix(const ActionOptions& ao):
      62             :   Action(ao),
      63         162 :   MatrixOperationBase(ao)
      64             : {
      65         162 :   if( getPntrToArgument(0)->isSymmetric() ) error("input matrix is symmetric.  Transposing will achieve nothing!");
      66             :   std::vector<unsigned> shape;
      67         162 :   if( getPntrToArgument(0)->getRank()==0 ) error("transposing a scalar?");
      68         162 :   else if( getPntrToArgument(0)->getRank()==1 ) { shape.resize(2); shape[0]=1; shape[1]=getPntrToArgument(0)->getShape()[0]; }
      69         145 :   else if( getPntrToArgument(0)->getShape()[0]==1 ) { shape.resize(1); shape[0] = getPntrToArgument(0)->getShape()[1]; }
      70          84 :   else { shape.resize(2); shape[0]=getPntrToArgument(0)->getShape()[1]; shape[1]=getPntrToArgument(0)->getShape()[0]; }
      71         162 :   addValue( shape ); setNotPeriodic(); getPntrToComponent(0)->buildDataStore();
      72         162 :   if( shape.size()==2 ) getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
      73         162 : }
      74             : 
      75        4821 : void TransposeMatrix::prepare() {
      76        4821 :   Value* myval = getPntrToComponent(0); Value* myarg = getPntrToArgument(0);
      77        4821 :   if( myarg->getRank()==1 ) {
      78         586 :     if( myval->getShape()[0]!=1 || myval->getShape()[1]!=myarg->getShape()[0] ) {
      79           6 :       std::vector<unsigned> shape(2); shape[0] = 1; shape[1] = myarg->getShape()[0];
      80           6 :       myval->setShape( shape ); myval->reshapeMatrixStore( shape[1] );
      81             :     }
      82        4235 :   } else if( myarg->getShape()[0]==1 ) {
      83        2392 :     if( myval->getShape()[0]!=myarg->getShape()[1] ) { std::vector<unsigned> shape(1); shape[0] = myarg->getShape()[1]; myval->setShape( shape ); }
      84        1843 :   } else if( myarg->getShape()[0]!=myval->getShape()[1] || myarg->getShape()[1]!=myval->getShape()[0] ) {
      85          19 :     std::vector<unsigned> shape(2); shape[0] = myarg->getShape()[1]; shape[1] = myarg->getShape()[0];
      86          19 :     myval->setShape( shape ); myval->reshapeMatrixStore( shape[1] );
      87             :   }
      88        4821 : }
      89             : 
      90        4225 : void TransposeMatrix::calculate() {
      91             :   // Retrieve the non-zero pairs
      92        4225 :   Value* myarg=getPntrToArgument(0); Value* myval=getPntrToComponent(0);
      93        4225 :   if( myarg->getRank()<=1 || myval->getRank()==1 ) {
      94        2389 :     if( myarg->getRank()<=1 && myval->getShape()[1]!=myarg->getShape()[0] ) {
      95           0 :       std::vector<unsigned> shape( 2 ); shape[0] = 1; shape[1] = myarg->getShape()[0];
      96           0 :       myval->setShape( shape ); myval->reshapeMatrixStore( shape[1] );
      97        2389 :     } else if( myval->getRank()==1 && myval->getShape()[0]!=myarg->getShape()[1] ) {
      98           0 :       std::vector<unsigned> shape( 1 ); shape[0] = myarg->getShape()[1];
      99           0 :       myval->setShape( shape );
     100             :     }
     101        2389 :     unsigned nv=myarg->getNumberOfValues();
     102       49015 :     for(unsigned i=0; i<nv; ++i) myval->set( i, myarg->get(i) );
     103             :   } else {
     104        1836 :     if( myarg->getShape()[0]!=myval->getShape()[1] || myarg->getShape()[1]!=myval->getShape()[0] ) {
     105           0 :       std::vector<unsigned> shape( 2 ); shape[0] = myarg->getShape()[1]; shape[1] = myarg->getShape()[0];
     106           0 :       myval->setShape( shape ); myval->reshapeMatrixStore( shape[1] );
     107             :     }
     108             :     std::vector<double> vals; std::vector<std::pair<unsigned,unsigned> > pairs;
     109        1836 :     std::vector<unsigned> shape( myval->getShape() ); unsigned nedge=0; myarg->retrieveEdgeList( nedge, pairs, vals );
     110     2758860 :     for(unsigned i=0; i<nedge; ++i) myval->set( pairs[i].second*shape[1] + pairs[i].first, vals[i] );
     111             :   }
     112        4225 : }
     113             : 
     114        4144 : void TransposeMatrix::apply() {
     115        4144 :   if( doNotCalculateDerivatives() ) return;
     116             : 
     117             :   // Apply force on the matrix
     118        1930 :   if( getPntrToComponent(0)->forcesWereAdded() ) {
     119        1930 :     Value* myarg=getPntrToArgument(0); Value* myval=getPntrToComponent(0);
     120        1930 :     if( myarg->getRank()<=1 || myval->getRank()==1 ) {
     121         588 :       unsigned nv=myarg->getNumberOfValues();
     122        2408 :       for(unsigned i=0; i<nv; ++i) myarg->addForce( i, myval->getForce(i) );
     123        1342 :     } else MatrixOperationBase::apply();
     124             :   }
     125             : }
     126             : 
     127     4124572 : double TransposeMatrix::getForceOnMatrixElement( const unsigned& jrow, const unsigned& kcol ) const {
     128     4124572 :   return getConstPntrToComponent(0)->getForce(kcol*getConstPntrToComponent(0)->getShape()[1]+jrow);
     129             : }
     130             : 
     131             : 
     132             : }
     133             : }