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 {
      44         256 :     return 0;
      45             :   }
      46             : ///
      47             :   void prepare() override ;
      48             : ///
      49             :   void calculate() override ;
      50             : ///
      51             :   void apply() override ;
      52             : ///
      53             :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override;
      54             : };
      55             : 
      56             : PLUMED_REGISTER_ACTION(TransposeMatrix,"TRANSPOSE")
      57             : 
      58         279 : void TransposeMatrix::registerKeywords( Keywords& keys ) {
      59         279 :   MatrixOperationBase::registerKeywords( keys );
      60         279 :   keys.setValueDescription("the transpose of the input matrix");
      61         279 : }
      62             : 
      63         162 : TransposeMatrix::TransposeMatrix(const ActionOptions& ao):
      64             :   Action(ao),
      65         162 :   MatrixOperationBase(ao) {
      66         162 :   if( getPntrToArgument(0)->isSymmetric() ) {
      67           0 :     error("input matrix is symmetric.  Transposing will achieve nothing!");
      68             :   }
      69             :   std::vector<unsigned> shape;
      70         162 :   if( getPntrToArgument(0)->getRank()==0 ) {
      71           0 :     error("transposing a scalar?");
      72         162 :   } else if( getPntrToArgument(0)->getRank()==1 ) {
      73          17 :     shape.resize(2);
      74          17 :     shape[0]=1;
      75          17 :     shape[1]=getPntrToArgument(0)->getShape()[0];
      76         145 :   } else if( getPntrToArgument(0)->getShape()[0]==1 ) {
      77          61 :     shape.resize(1);
      78          61 :     shape[0] = getPntrToArgument(0)->getShape()[1];
      79             :   } else {
      80          84 :     shape.resize(2);
      81          84 :     shape[0]=getPntrToArgument(0)->getShape()[1];
      82          84 :     shape[1]=getPntrToArgument(0)->getShape()[0];
      83             :   }
      84         162 :   addValue( shape );
      85         162 :   setNotPeriodic();
      86         162 :   getPntrToComponent(0)->buildDataStore();
      87         162 :   if( shape.size()==2 ) {
      88         101 :     getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
      89             :   }
      90         162 : }
      91             : 
      92        4821 : void TransposeMatrix::prepare() {
      93        4821 :   Value* myval = getPntrToComponent(0);
      94             :   Value* myarg = getPntrToArgument(0);
      95        4821 :   if( myarg->getRank()==1 ) {
      96         586 :     if( myval->getShape()[0]!=1 || myval->getShape()[1]!=myarg->getShape()[0] ) {
      97           6 :       std::vector<unsigned> shape(2);
      98           6 :       shape[0] = 1;
      99           6 :       shape[1] = myarg->getShape()[0];
     100           6 :       myval->setShape( shape );
     101           6 :       myval->reshapeMatrixStore( shape[1] );
     102             :     }
     103        4235 :   } else if( myarg->getShape()[0]==1 ) {
     104        2392 :     if( myval->getShape()[0]!=myarg->getShape()[1] ) {
     105           6 :       std::vector<unsigned> shape(1);
     106           6 :       shape[0] = myarg->getShape()[1];
     107           6 :       myval->setShape( shape );
     108             :     }
     109        1843 :   } else if( myarg->getShape()[0]!=myval->getShape()[1] || myarg->getShape()[1]!=myval->getShape()[0] ) {
     110          19 :     std::vector<unsigned> shape(2);
     111          19 :     shape[0] = myarg->getShape()[1];
     112          19 :     shape[1] = myarg->getShape()[0];
     113          19 :     myval->setShape( shape );
     114          19 :     myval->reshapeMatrixStore( shape[1] );
     115             :   }
     116        4821 : }
     117             : 
     118        4225 : void TransposeMatrix::calculate() {
     119             :   // Retrieve the non-zero pairs
     120             :   Value* myarg=getPntrToArgument(0);
     121        4225 :   Value* myval=getPntrToComponent(0);
     122        4225 :   if( myarg->getRank()<=1 || myval->getRank()==1 ) {
     123        2389 :     if( myarg->getRank()<=1 && myval->getShape()[1]!=myarg->getShape()[0] ) {
     124           0 :       std::vector<unsigned> shape( 2 );
     125           0 :       shape[0] = 1;
     126           0 :       shape[1] = myarg->getShape()[0];
     127           0 :       myval->setShape( shape );
     128           0 :       myval->reshapeMatrixStore( shape[1] );
     129        2389 :     } else if( myval->getRank()==1 && myval->getShape()[0]!=myarg->getShape()[1] ) {
     130           0 :       std::vector<unsigned> shape( 1 );
     131           0 :       shape[0] = myarg->getShape()[1];
     132           0 :       myval->setShape( shape );
     133             :     }
     134        2389 :     unsigned nv=myarg->getNumberOfValues();
     135       49015 :     for(unsigned i=0; i<nv; ++i) {
     136       46626 :       myval->set( i, myarg->get(i) );
     137             :     }
     138             :   } else {
     139        1836 :     if( myarg->getShape()[0]!=myval->getShape()[1] || myarg->getShape()[1]!=myval->getShape()[0] ) {
     140           0 :       std::vector<unsigned> shape( 2 );
     141           0 :       shape[0] = myarg->getShape()[1];
     142           0 :       shape[1] = myarg->getShape()[0];
     143           0 :       myval->setShape( shape );
     144           0 :       myval->reshapeMatrixStore( shape[1] );
     145             :     }
     146             :     std::vector<double> vals;
     147             :     std::vector<std::pair<unsigned,unsigned> > pairs;
     148        1836 :     std::vector<unsigned> shape( myval->getShape() );
     149        1836 :     unsigned nedge=0;
     150        1836 :     myarg->retrieveEdgeList( nedge, pairs, vals );
     151     2758860 :     for(unsigned i=0; i<nedge; ++i) {
     152     2757024 :       myval->set( pairs[i].second*shape[1] + pairs[i].first, vals[i] );
     153             :     }
     154             :   }
     155        4225 : }
     156             : 
     157        4144 : void TransposeMatrix::apply() {
     158        4144 :   if( doNotCalculateDerivatives() ) {
     159             :     return;
     160             :   }
     161             : 
     162             :   // Apply force on the matrix
     163        1930 :   if( getPntrToComponent(0)->forcesWereAdded() ) {
     164             :     Value* myarg=getPntrToArgument(0);
     165        1930 :     Value* myval=getPntrToComponent(0);
     166        1930 :     if( myarg->getRank()<=1 || myval->getRank()==1 ) {
     167         588 :       unsigned nv=myarg->getNumberOfValues();
     168        2408 :       for(unsigned i=0; i<nv; ++i) {
     169        1820 :         myarg->addForce( i, myval->getForce(i) );
     170             :       }
     171             :     } else {
     172        1342 :       MatrixOperationBase::apply();
     173             :     }
     174             :   }
     175             : }
     176             : 
     177     4124572 : double TransposeMatrix::getForceOnMatrixElement( const unsigned& jrow, const unsigned& kcol ) const {
     178     4124572 :   return getConstPntrToComponent(0)->getForce(kcol*getConstPntrToComponent(0)->getShape()[1]+jrow);
     179             : }
     180             : 
     181             : 
     182             : }
     183             : }