Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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             : 
      24             : namespace PLMD {
      25             : namespace matrixtools {
      26             : 
      27         363 : void MatrixOperationBase::registerKeywords( Keywords& keys ) {
      28         363 :   Action::registerKeywords( keys );
      29         363 :   ActionWithArguments::registerKeywords( keys );
      30         363 :   ActionWithValue::registerKeywords( keys );
      31         726 :   keys.addInputKeyword("compulsory","ARG","matrix","the input matrix");
      32         726 :   keys.remove("NUMERICAL_DERIVATIVES");
      33         363 :   keys.add("optional","MATRIX","the input matrix (can use ARG instead)");
      34         363 : }
      35             : 
      36         211 : MatrixOperationBase::MatrixOperationBase(const ActionOptions&ao):
      37             :   Action(ao),
      38             :   ActionWithArguments(ao),
      39         211 :   ActionWithValue(ao) {
      40         211 :   if( getNumberOfArguments()==0 ) {
      41             :     std::vector<Value*> args;
      42           0 :     parseArgumentList("MATRIX",args);
      43           0 :     requestArguments(args);
      44             :   }
      45         211 :   if( getNumberOfArguments()!=1 ) {
      46           0 :     error("should only be one argument to this action");
      47             :   }
      48         211 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) {
      49          17 :     if( getName()=="TRANSPOSE" ) {
      50          17 :       if (getPntrToArgument(0)->getRank()!=1 || getPntrToArgument(0)->hasDerivatives() ) {
      51           0 :         error("input to this argument should be a matrix or vector");
      52             :       }
      53             :     } else {
      54           0 :       error("input to this argument should be a matrix");
      55             :     }
      56             :   }
      57         211 :   getPntrToArgument(0)->buildDataStore();
      58         211 : }
      59             : 
      60         131 : void MatrixOperationBase::retrieveFullMatrix( Matrix<double>& mymatrix ) {
      61         131 :   if( mymatrix.nrows()!=getPntrToArgument(0)->getShape()[0] || mymatrix.nrows()!=getPntrToArgument(0)->getShape()[1] ) {
      62           0 :     mymatrix.resize( getPntrToArgument(0)->getShape()[0], getPntrToArgument(0)->getShape()[1] );
      63             :   }
      64             :   unsigned nedge;
      65         131 :   getPntrToArgument(0)->retrieveEdgeList( nedge, pairs, vals  );
      66             :   mymatrix=0;
      67             :   bool symmetric = getPntrToArgument(0)->isSymmetric();
      68      373270 :   for(unsigned i=0; i<nedge; ++i ) {
      69      373139 :     mymatrix( pairs[i].first, pairs[i].second ) = vals[i];
      70      373139 :     if( symmetric ) {
      71         714 :       mymatrix( pairs[i].second, pairs[i].first ) = vals[i];
      72             :     }
      73             :   }
      74         131 : }
      75             : 
      76             : 
      77        1448 : void MatrixOperationBase::apply() {
      78        1448 :   if( doNotCalculateDerivatives() ) {
      79             :     return;
      80             :   }
      81             : 
      82             :   bool forces=false;
      83        1546 :   for(int i=0; i<getNumberOfComponents(); ++i) {
      84        1546 :     if( getPntrToComponent(i)->forcesWereAdded() ) {
      85             :       forces=true;
      86             :       break;
      87             :     }
      88             :   }
      89        1444 :   if( !forces ) {
      90             :     return;
      91             :   }
      92             : 
      93             :   Value* mat = getPntrToArgument(0);
      94             :   unsigned ncols=mat->getNumberOfColumns();
      95      147286 :   for(unsigned i=0; i<mat->getShape()[0]; ++i) {
      96             :     unsigned ncol = mat->getRowLength(i);
      97     4282909 :     for(unsigned j=0; j<ncol; ++j) {
      98     4137067 :       mat->addForce( i*ncols+j, getForceOnMatrixElement( i, mat->getRowIndex(i,j) ), false );
      99             :     }
     100             :   }
     101             : }
     102             : 
     103             : 
     104             : }
     105             : }