Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2019 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             : #ifndef __PLUMED_adjmat_ActionWithInputMatrix_h
      23             : #define __PLUMED_adjmat_ActionWithInputMatrix_h
      24             : 
      25             : #include "core/ActionWithValue.h"
      26             : #include "core/ActionAtomistic.h"
      27             : #include "multicolvar/MultiColvarBase.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace adjmat {
      31             : 
      32             : class AdjacencyMatrixVessel;
      33             : 
      34          25 : class ActionWithInputMatrix : public multicolvar::MultiColvarBase {
      35             : protected:
      36             : /// The vessel that holds the adjacency matrix
      37             :   AdjacencyMatrixVessel* mymatrix;
      38             : /// Get number of base multicolvar types
      39             :   unsigned getNumberOfNodeTypes() const ;
      40             : /// Get number of atoms in each base multicolvar
      41             :   unsigned getNumberOfAtomsInGroup( const unsigned& igrp ) const ;
      42             : /// Get a pointer to the igrp th base multicolvar
      43             :   multicolvar::MultiColvarBase* getBaseMultiColvar( const unsigned& igrp ) const ;
      44             : public:
      45             :   static void registerKeywords( Keywords& keys );
      46             :   explicit ActionWithInputMatrix(const ActionOptions&);
      47             : /// Retrieve the vessel that holds the adjacency matrix
      48             :   AdjacencyMatrixVessel* getAdjacencyVessel() const ;
      49             : /// Retrieve the value of the connection
      50             :   double retrieveConnectionValue( const unsigned& i, const unsigned& j, std::vector<double>& vals ) const ;
      51             : /// Get the vector for task ind
      52             :   virtual void getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const ;
      53             : /// Add the derivatives on a connection
      54             :   void addConnectionDerivatives( const unsigned& i, const unsigned& j, MultiValue& myvals, MultiValue& myvout ) const ;
      55             : /// Get vector derivatives
      56             :   virtual MultiValue& getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const ;
      57             :   virtual unsigned getNumberOfDerivatives();
      58             : ///  Get the number of rows/cols in the adjacency matrix vessel
      59             :   virtual unsigned getNumberOfNodes() const ;
      60          78 :   bool isPeriodic() { return false; }
      61             :   virtual unsigned getNumberOfQuantities() const ;
      62             : ///
      63             :   virtual AtomNumber getAbsoluteIndexOfCentralAtom(const unsigned& i) const ;
      64             : /// No loop over tasks for ActionWithInputMatrix
      65           0 :   double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const { plumed_error(); }
      66             : ///
      67             :   virtual Vector getPositionOfAtomForLinkCells( const unsigned& iatom ) const ;
      68             : };
      69             : 
      70             : }
      71             : }
      72             : #endif