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/ActionSetup.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : //+PLUMEDOC MCOLVAR INVERT_MATRIX
      27             : /*
      28             : Calculate the inverse of the input matrix
      29             : 
      30             : This action allows you to calculate the inverse of a real symmetric matrix.
      31             : If the matrix is not symmetric then the [dgetrf](https://www.netlib.org/lapack/explore-html-3.6.1/dd/d9a/group__double_g_ecomputational_ga0019443faea08275ca60a734d0593e60.html)
      32             : and [dgetri](https://www.netlib.org/lapack/explore-html-3.6.1/dd/d9a/group__double_g_ecomputational_ga56d9c860ce4ce42ded7f914fdb0683ff.html)
      33             : functions from the [LAPACK](https://www.netlib.org/lapack/explore-html/) library are used.
      34             : If the matrix is symmetric then we use [dsyevr](https://www.netlib.org/lapack/explore-html/d1/d56/group__heevr_gaa334ac0c11113576db0fc37b7565e8b5.html#gaa334ac0c11113576db0fc37b7565e8b5)
      35             : to find the eigenvalues. The inverse matrix of the input matrix $M$ with [eigendecomposition](https://en.wikipedia.org/wiki/Eigendecomposition_of_a_matrix).:
      36             : 
      37             : $$
      38             : M = Q \Lambda Q^{-1}
      39             : $$
      40             : 
      41             : is then found as:
      42             : 
      43             : $$
      44             : M^{-1} = Q \Lambda^{-1} Q^{-1}
      45             : $$
      46             : 
      47             : where $\Lambda^{-1}$ is the inverse of the (diagonal) matrix of eigenvalues $\Lambda$ and $Q$ is the matrix of eigenvectors.
      48             : 
      49             : The following example shows how this action is used in practise:
      50             : 
      51             : ```plumed
      52             : c: DISTANCE_MATRIX ATOMS=1-4
      53             : ci: INVERT_MATRIX ARG=c
      54             : PRINT ARG=ci FILE=colvar
      55             : ```
      56             : 
      57             : */
      58             : //+ENDPLUMEDOC
      59             : 
      60             : namespace PLMD {
      61             : namespace matrixtools {
      62             : 
      63             : class InvertMatrix : public MatrixOperationBase {
      64             : private:
      65             :   bool input_is_constant;
      66             :   Matrix<double> mymatrix;
      67             :   Matrix<double> inverse;
      68             : public:
      69             :   static void registerKeywords( Keywords& keys );
      70             : /// Constructor
      71             :   explicit InvertMatrix(const ActionOptions&);
      72             : ///
      73           6 :   unsigned getNumberOfDerivatives() override {
      74           6 :     return 0;
      75             :   }
      76             : /// Do the calculation
      77             :   void calculate() override;
      78             : ///
      79             :   void apply() override;
      80           0 :   double getForceOnMatrixElement( const unsigned& jrow, const unsigned& krow ) const override {
      81           0 :     plumed_error();
      82             :   }
      83             : };
      84             : 
      85             : PLUMED_REGISTER_ACTION(InvertMatrix,"INVERT_MATRIX")
      86             : 
      87          18 : void InvertMatrix::registerKeywords( Keywords& keys ) {
      88          18 :   MatrixOperationBase::registerKeywords( keys );
      89          36 :   keys.setValueDescription("matrix","the inverse of the input matrix");
      90          18 : }
      91             : 
      92           9 : InvertMatrix::InvertMatrix(const ActionOptions& ao):
      93             :   Action(ao),
      94             :   MatrixOperationBase(ao),
      95           9 :   input_is_constant(false) {
      96           9 :   if( getPntrToArgument(0)->getShape()[0]!=getPntrToArgument(0)->getShape()[1] ) {
      97           0 :     error("input matrix should be square");
      98             :   }
      99             : 
     100           9 :   ActionSetup* as = dynamic_cast<ActionSetup*>( getPntrToArgument(0)->getPntrToAction() );
     101           9 :   if(as) {
     102           0 :     input_is_constant=true;
     103             :   }
     104             : 
     105           9 :   std::vector<unsigned> shape(2);
     106           9 :   shape[0]=shape[1]=getPntrToArgument(0)->getShape()[0];
     107           9 :   addValue( shape );
     108           9 :   setNotPeriodic();
     109           9 :   getPntrToComponent(0)->buildDataStore();
     110           9 :   getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
     111           9 :   mymatrix.resize( shape[0], shape[1] );
     112           9 :   inverse.resize( shape[0], shape[1] );
     113           9 : }
     114             : 
     115           9 : void InvertMatrix::calculate() {
     116             :   // Retrieve the matrix from input
     117           9 :   retrieveFullMatrix( mymatrix );
     118             :   // Now invert the matrix
     119           9 :   Invert( mymatrix, inverse );
     120             :   // And set the inverse
     121             :   unsigned k = 0;
     122           9 :   Value* myval=getPntrToComponent(0);
     123          30 :   for(unsigned i=0; i<mymatrix.nrows(); ++i) {
     124          78 :     for(unsigned j=0; j<mymatrix.ncols(); ++j) {
     125          57 :       myval->set( k, inverse(i,j) );
     126          57 :       k++;
     127             :     }
     128             :   }
     129             : 
     130           9 :   if( !doNotCalculateDerivatives() && !input_is_constant ) {
     131           0 :     error("derivatives of inverse matrix have not been implemented");
     132             :   }
     133           9 : }
     134             : 
     135           0 : void InvertMatrix::apply() {
     136           0 :   if( doNotCalculateDerivatives() || input_is_constant ) {
     137           0 :     return;
     138             :   }
     139           0 :   error("derivatives of inverse matrix have not been implemented");
     140             : }
     141             : 
     142             : }
     143             : }