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