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 {
      49         276 :     return getPntrToArgument(0)->getNumberOfValues();
      50             :   }
      51             : ///
      52             :   void prepare() override ;
      53             : ///
      54             :   void calculate() override ;
      55             : ///
      56             :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override;
      57             : };
      58             : 
      59             : PLUMED_REGISTER_ACTION(DiagonalizeMatrix,"DIAGONALIZE")
      60             : 
      61          41 : void DiagonalizeMatrix::registerKeywords( Keywords& keys ) {
      62          41 :   MatrixOperationBase::registerKeywords( keys );
      63          82 :   keys.add("compulsory","VECTORS","all","the eigenvalues and vectors that you would like to calculate.  1=largest, 2=second largest and so on");
      64          82 :   keys.addOutputComponent("vals","default","the eigevalues of the input matrix");
      65          82 :   keys.addOutputComponent("vecs","default","the eigenvectors of the input matrix");
      66          41 : }
      67             : 
      68          22 : DiagonalizeMatrix::DiagonalizeMatrix(const ActionOptions& ao):
      69             :   Action(ao),
      70          22 :   MatrixOperationBase(ao) {
      71          22 :   if( getPntrToArgument(0)->getShape()[0]!=getPntrToArgument(0)->getShape()[1] ) {
      72           0 :     error("input matrix should be square");
      73             :   }
      74             : 
      75             :   std::vector<std::string> eigv;
      76          44 :   parseVector("VECTORS",eigv);
      77          22 :   if( eigv.size()>1 ) {
      78          10 :     Tools::interpretRanges(eigv);
      79          10 :     desired_vectors.resize( eigv.size() );
      80          30 :     for(unsigned i=0; i<eigv.size(); ++i) {
      81          20 :       Tools::convert( eigv[i], desired_vectors[i] );
      82             :     }
      83             :   } else  {
      84          12 :     if( eigv.size()==0 ) {
      85           0 :       error("missing input to VECTORS keyword");
      86             :     }
      87             :     unsigned ivec;
      88          12 :     if( eigv[0]=="all" ) {
      89           7 :       desired_vectors.resize( getPntrToArgument(0)->getShape()[0] );
      90          21 :       for(unsigned i=0; i<desired_vectors.size(); ++i) {
      91          14 :         desired_vectors[i] = i + 1;
      92             :       }
      93             :     } else {
      94           5 :       Tools::convert( eigv[0], ivec );
      95           5 :       desired_vectors.resize(1);
      96           5 :       desired_vectors[0]=ivec;
      97             :     }
      98             :   }
      99             : 
     100             :   std::string num;
     101          22 :   std::vector<unsigned> eval_shape(0);
     102          22 :   std::vector<unsigned> evec_shape(1);
     103          22 :   evec_shape[0] = getPntrToArgument(0)->getShape()[0];
     104          61 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     105          39 :     Tools::convert( desired_vectors[i], num );
     106          39 :     addComponent( "vals-" + num, eval_shape );
     107          39 :     componentIsNotPeriodic( "vals-" + num );
     108          39 :     addComponent( "vecs-" + num, evec_shape );
     109          39 :     componentIsNotPeriodic( "vecs-" + num );
     110             :     // Make sure eigenvalues are always stored
     111          39 :     getPntrToComponent( 2*i+1 )->buildDataStore();
     112             :   }
     113             : 
     114          22 :   std::vector<unsigned> eigvecs_shape(2);
     115          22 :   eigvecs_shape[0]=eigvecs_shape[1]=getPntrToArgument(0)->getShape()[0];
     116          22 :   mymatrix.resize( eigvecs_shape[0], eigvecs_shape[1] );
     117          22 :   eigvals.resize( eigvecs_shape[0] );
     118          22 :   eigvecs.resize( eigvecs_shape[0], eigvecs_shape[1] );
     119          22 : }
     120             : 
     121         124 : void DiagonalizeMatrix::prepare() {
     122         124 :   std::vector<unsigned> shape(1);
     123         124 :   shape[0]=getPntrToArgument(0)->getShape()[0];
     124         303 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     125         179 :     if( getPntrToComponent( 2*i+1 )->getShape()[0]!=shape[0] ) {
     126           9 :       getPntrToComponent( 2*i+1 )->setShape( shape );
     127             :     }
     128             :   }
     129             : 
     130         124 : }
     131             : 
     132         122 : void DiagonalizeMatrix::calculate() {
     133         122 :   if( getPntrToArgument(0)->getShape()[0]==0 ) {
     134             :     return ;
     135             :   }
     136             :   // Resize stuff that might need resizing
     137             :   unsigned nvals=getPntrToArgument(0)->getShape()[0];
     138         122 :   if( eigvals.size()!=nvals ) {
     139             :     mymatrix.resize( nvals, nvals );
     140           5 :     eigvals.resize( nvals );
     141             :     eigvecs.resize( nvals, nvals );
     142             :   }
     143             : 
     144             :   // Retrieve the matrix from input
     145         122 :   retrieveFullMatrix( mymatrix );
     146             :   // Now diagonalize the matrix
     147         122 :   diagMat( mymatrix, eigvals, eigvecs );
     148             :   // And set the eigenvalues and eigenvectors
     149         297 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     150         175 :     getPntrToComponent(2*i)->set( eigvals[ mymatrix.ncols()-desired_vectors[i]] );
     151         175 :     Value* evec_out = getPntrToComponent(2*i+1);
     152         175 :     unsigned vreq = mymatrix.ncols()-desired_vectors[i];
     153        4526 :     for(unsigned j=0; j<mymatrix.ncols(); ++j) {
     154        4351 :       evec_out->set( j, eigvecs( vreq, j ) );
     155             :     }
     156             :   }
     157             : }
     158             : 
     159       12495 : double DiagonalizeMatrix::getForceOnMatrixElement( const unsigned& jrow, const unsigned& kcol ) const {
     160             :   double ff = 0;
     161       31654 :   for(unsigned i=0; i<desired_vectors.size(); ++i) {
     162             :     // Deal with forces on eigenvalues
     163       19159 :     if( getConstPntrToComponent(2*i)->forcesWereAdded() ) {
     164        8330 :       unsigned ncol = mymatrix.ncols()-desired_vectors[i];
     165        8330 :       ff += getConstPntrToComponent(2*i)->getForce(0)*eigvecs(ncol,jrow)*eigvecs(ncol,kcol);
     166             :     }
     167             :     // And forces on eigenvectors
     168       19159 :     if( !getConstPntrToComponent(2*i+1)->forcesWereAdded() ) {
     169             :       continue;
     170             :     }
     171             : 
     172        7497 :     unsigned ncol = mymatrix.ncols()-desired_vectors[i];
     173      106624 :     for(unsigned n=0; n<mymatrix.nrows(); ++n) {
     174             :       double tmp2 = 0;
     175     1446088 :       for(unsigned m=0; m<mymatrix.nrows(); ++m) {
     176     1346961 :         if( m==ncol ) {
     177       99127 :           continue;
     178             :         }
     179     1247834 :         tmp2 += eigvecs(m,n)*eigvecs(m,jrow)*eigvecs(ncol,kcol) / (eigvals[ncol]-eigvals[m]);
     180             :       }
     181       99127 :       ff += getConstPntrToComponent(2*i+1)->getForce(n) * tmp2;
     182             :     }
     183             :   }
     184       12495 :   return ff;
     185             : }
     186             : 
     187             : }
     188             : }