Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2015-2018 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 : #include "multicolvar/MultiColvarFunction.h"
29 :
30 : namespace PLMD {
31 : namespace adjmat {
32 :
33 : class AdjacencyMatrixVessel;
34 :
35 19 : class ActionWithInputMatrix : public multicolvar::MultiColvarFunction {
36 : protected:
37 : /// The vessel that holds the adjacency matrix
38 : AdjacencyMatrixVessel* mymatrix;
39 : /// Get number of base multicolvar types
40 : unsigned getNumberOfNodeTypes() const ;
41 : /// Get number of atoms in each base multicolvar
42 : unsigned getNumberOfAtomsInGroup( const unsigned& igrp ) const ;
43 : /// Get a pointer to the igrp th base multicolvar
44 : multicolvar::MultiColvarBase* getBaseMultiColvar( const unsigned& igrp ) const ;
45 : public:
46 : static void registerKeywords( Keywords& keys );
47 : explicit ActionWithInputMatrix(const ActionOptions&);
48 : /// Retrieve the vessel that holds the adjacency matrix
49 : AdjacencyMatrixVessel* getAdjacencyVessel() const ;
50 : /// Retrieve the value of the connection
51 : double retrieveConnectionValue( const unsigned& i, const unsigned& j, std::vector<double>& vals ) const ;
52 : /// Get the vector for task ind
53 : virtual void getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const ;
54 : /// Add the derivatives on a connection
55 : void addConnectionDerivatives( const unsigned& i, const unsigned& j, std::vector<double>& vals, MultiValue& myvals, MultiValue& myvout ) const ;
56 : /// Get vector derivatives
57 : virtual MultiValue& getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const ;
58 : virtual unsigned getNumberOfDerivatives();
59 : /// Get the number of rows/cols in the adjacency matrix vessel
60 : virtual unsigned getNumberOfNodes() const ;
61 52 : bool isPeriodic() { return false; }
62 : virtual unsigned getNumberOfQuantities() const ;
63 : ///
64 : virtual AtomNumber getAbsoluteIndexOfCentralAtom(const unsigned& i) const ;
65 : /// No loop over tasks for ActionWithInputMatrix
66 0 : double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const { plumed_error(); }
67 : ///
68 : virtual Vector getPositionOfAtomForLinkCells( const unsigned& iatom ) const ;
69 : };
70 :
71 : }
72 : }
73 : #endif
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