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 ANALYSIS DIAGONALIZE
      26             : /*
      27             : Calculate the eigenvalues and eigenvectors of a square matrix
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace matrixtools {
      36             : 
      37             : class DiagonalizeMatrix : public MatrixOperationBase {
      38             : private:
      39             :   std::vector<unsigned> desired_vectors;
      40             :   Matrix<double> mymatrix;
      41             :   std::vector<double> eigvals;
      42             :   Matrix<double> eigvecs;
      43             : public:
      44             :   static void registerKeywords( Keywords& keys );
      45             : /// Constructor
      46             :   explicit DiagonalizeMatrix(const ActionOptions&);
      47             : /// This is required to set the number of derivatives for the eigenvalues
      48         276 :   unsigned getNumberOfDerivatives() override { return getPntrToArgument(0)->getNumberOfValues(); }
      49             : ///
      50             :   void prepare() override ;
      51             : ///
      52             :   void calculate() override ;
      53             : ///
      54             :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override;
      55             : };
      56             : 
      57             : PLUMED_REGISTER_ACTION(DiagonalizeMatrix,"DIAGONALIZE")
      58             : 
      59          41 : void DiagonalizeMatrix::registerKeywords( Keywords& keys ) {
      60          41 :   MatrixOperationBase::registerKeywords( keys );
      61          82 :   keys.add("compulsory","VECTORS","all","the eigenvalues and vectors that you would like to calculate.  1=largest, 2=second largest and so on");
      62          82 :   keys.addOutputComponent("vals","default","the eigevalues of the input matrix");
      63          82 :   keys.addOutputComponent("vecs","default","the eigenvectors of the input matrix");
      64          41 : }
      65             : 
      66          22 : DiagonalizeMatrix::DiagonalizeMatrix(const ActionOptions& ao):
      67             :   Action(ao),
      68          22 :   MatrixOperationBase(ao)
      69             : {
      70          22 :   if( getPntrToArgument(0)->getShape()[0]!=getPntrToArgument(0)->getShape()[1] ) error("input matrix should be square");
      71             : 
      72          44 :   std::vector<std::string> eigv; parseVector("VECTORS",eigv);
      73          22 :   if( eigv.size()>1 ) {
      74          10 :     Tools::interpretRanges(eigv); desired_vectors.resize( eigv.size() );
      75          30 :     for(unsigned i=0; i<eigv.size(); ++i) Tools::convert( eigv[i], desired_vectors[i] );
      76             :   } else  {
      77          12 :     if( eigv.size()==0 ) error("missing input to VECTORS keyword");
      78             :     unsigned ivec;
      79          12 :     if( eigv[0]=="all" ) {
      80           7 :       desired_vectors.resize( getPntrToArgument(0)->getShape()[0] );
      81          21 :       for(unsigned i=0; i<desired_vectors.size(); ++i) desired_vectors[i] = i + 1;
      82             :     } else {
      83           5 :       Tools::convert( eigv[0], ivec );
      84           5 :       desired_vectors.resize(1); desired_vectors[0]=ivec;
      85             :     }
      86             :   }
      87             : 
      88          22 :   std::string num; std::vector<unsigned> eval_shape(0);
      89          22 :   std::vector<unsigned> evec_shape(1); evec_shape[0] = getPntrToArgument(0)->getShape()[0];
      90          61 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
      91          39 :     Tools::convert( desired_vectors[i], num );
      92          78 :     addComponent( "vals-" + num, eval_shape ); componentIsNotPeriodic( "vals-" + num );
      93          78 :     addComponent( "vecs-" + num, evec_shape ); componentIsNotPeriodic( "vecs-" + num );
      94             :     // Make sure eigenvalues are always stored
      95          39 :     getPntrToComponent( 2*i+1 )->buildDataStore();
      96             :   }
      97             : 
      98          22 :   std::vector<unsigned> eigvecs_shape(2); eigvecs_shape[0]=eigvecs_shape[1]=getPntrToArgument(0)->getShape()[0];
      99          22 :   mymatrix.resize( eigvecs_shape[0], eigvecs_shape[1] ); eigvals.resize( eigvecs_shape[0] ); eigvecs.resize( eigvecs_shape[0], eigvecs_shape[1] );
     100          22 : }
     101             : 
     102         124 : void DiagonalizeMatrix::prepare() {
     103         124 :   std::vector<unsigned> shape(1); shape[0]=getPntrToArgument(0)->getShape()[0];
     104         303 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     105         179 :     if( getPntrToComponent( 2*i+1 )->getShape()[0]!=shape[0] ) getPntrToComponent( 2*i+1 )->setShape( shape );
     106             :   }
     107             : 
     108         124 : }
     109             : 
     110         122 : void DiagonalizeMatrix::calculate() {
     111         122 :   if( getPntrToArgument(0)->getShape()[0]==0 ) return ;
     112             :   // Resize stuff that might need resizing
     113             :   unsigned nvals=getPntrToArgument(0)->getShape()[0];
     114         127 :   if( eigvals.size()!=nvals ) { mymatrix.resize( nvals, nvals ); eigvals.resize( nvals ); eigvecs.resize( nvals, nvals ); }
     115             : 
     116             :   // Retrieve the matrix from input
     117         122 :   retrieveFullMatrix( mymatrix );
     118             :   // Now diagonalize the matrix
     119         122 :   diagMat( mymatrix, eigvals, eigvecs );
     120             :   // And set the eigenvalues and eigenvectors
     121         297 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     122         175 :     getPntrToComponent(2*i)->set( eigvals[ mymatrix.ncols()-desired_vectors[i]] );
     123         175 :     Value* evec_out = getPntrToComponent(2*i+1); unsigned vreq = mymatrix.ncols()-desired_vectors[i];
     124        4526 :     for(unsigned j=0; j<mymatrix.ncols(); ++j) evec_out->set( j, eigvecs( vreq, j ) );
     125             :   }
     126             : }
     127             : 
     128       12495 : double DiagonalizeMatrix::getForceOnMatrixElement( const unsigned& jrow, const unsigned& kcol ) const {
     129             :   double ff = 0;
     130       31654 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     131             :     // Deal with forces on eigenvalues
     132       19159 :     if( getConstPntrToComponent(2*i)->forcesWereAdded() ) {
     133        8330 :       unsigned ncol = mymatrix.ncols()-desired_vectors[i];
     134        8330 :       ff += getConstPntrToComponent(2*i)->getForce(0)*eigvecs(ncol,jrow)*eigvecs(ncol,kcol);
     135             :     }
     136             :     // And forces on eigenvectors
     137       19159 :     if( !getConstPntrToComponent(2*i+1)->forcesWereAdded() ) continue;
     138             : 
     139        7497 :     unsigned ncol = mymatrix.ncols()-desired_vectors[i];
     140      106624 :     for(unsigned n=0; n<mymatrix.nrows(); ++n) {
     141             :       double tmp2 = 0;
     142     1446088 :       for(unsigned m=0; m<mymatrix.nrows(); ++m) {
     143     1346961 :         if( m==ncol ) continue;
     144     1247834 :         tmp2 += eigvecs(m,n)*eigvecs(m,jrow)*eigvecs(ncol,kcol) / (eigvals[ncol]-eigvals[m]);
     145             :       }
     146       99127 :       ff += getConstPntrToComponent(2*i+1)->getForce(n) * tmp2;
     147             :     }
     148             :   }
     149       12495 :   return ff;
     150             : }
     151             : 
     152             : }
     153             : }