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_AdjacencyMatrixBase_h
23 : #define __PLUMED_adjmat_AdjacencyMatrixBase_h
24 :
25 : #include "multicolvar/MultiColvarBase.h"
26 : #include "AdjacencyMatrixVessel.h"
27 :
28 : namespace PLMD {
29 : namespace adjmat {
30 :
31 15 : class AdjacencyMatrixBase : public multicolvar::MultiColvarBase {
32 : friend class AdjacencyMatrixVessel;
33 : friend class ActionWithInputMatrix;
34 : friend class MatrixColumnSums;
35 : friend class MatrixRowSums;
36 : private:
37 : /// Used for read in of multiple connection descriptors
38 : unsigned connect_id;
39 : /// Do we need to separate out the tasks for the third atoms
40 : bool no_third_dim_accum;
41 : /// This is the vessel that stores the adjacency matrix
42 : AdjacencyMatrixVessel* mat;
43 : /// This is used within AdjacencyMatrixVessel to recalculate matrix elements
44 : /// whcih is useful when we are operating with lowmem
45 : void recalculateMatrixElement( const unsigned& myelem, MultiValue& myvals );
46 : /// Finish the setup of the matrix
47 : void finishMatrixSetup( const bool& symmetric, const std::vector<AtomNumber>& all_atoms );
48 : protected:
49 : /// Read in a matrix involving a maximum of two species
50 : void readMaxTwoSpeciesMatrix( const std::string& key0, const std::string& key1, const std::string& key2, const bool& symmetric );
51 : /// Read in a matrix involving a maximum of three species
52 : void readMaxThreeSpeciesMatrix( const std::string& key0, const std::string& key1, const std::string& key2, const std::string& keym, const bool& symmetric );
53 : /// Get the dimensions of the matrix of types
54 : void retrieveTypeDimensions( unsigned& nrows, unsigned& ncols, unsigned& ntype ) const ;
55 : /// Retrieve the vessel that holds the adjacency matrix
56 : AdjacencyMatrixVessel* getAdjacencyVessel();
57 : /// Put the indices of the matrix elements in current atoms
58 : void setMatrixIndexesForTask( const unsigned& ii );
59 : /// Add derivatives to a matrix element
60 : void addDerivativesOnMatrixElement( const unsigned& ielem, const unsigned& jrow, const double& df, Matrix<double>& der );
61 : /// Read in the information on the connectors
62 : void parseConnectionDescriptions( const std::string& key, const bool& multiple, const unsigned& nrow_t );
63 : protected:
64 : /// Get the number of nodes of different types
65 : unsigned getNumberOfNodeTypes() const ;
66 : /// Get the size of the vectors that were stored in the base colvars
67 : unsigned getSizeOfInputVectors() const ;
68 : /// Return the group this atom is a part of
69 : unsigned getBaseColvarNumber( const unsigned& ) const ;
70 : public:
71 : static void registerKeywords( Keywords& keys );
72 : explicit AdjacencyMatrixBase(const ActionOptions&);
73 : /// Create the connection object
74 : virtual void setupConnector( const unsigned& id, const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) = 0;
75 : /// None of these things are allowed
76 17 : bool isPeriodic() { return false; }
77 : Vector getCentralAtom() { plumed_merror("cannot find central atoms for adjacency matrix actions"); Vector dum; return dum; }
78 : /// Transforms the stored values in whatever way is required
79 : virtual double transformStoredValues( const std::vector<double>& myvals, unsigned& vout, double& df ) const ;
80 : /// Used to check for connections between atoms
81 : virtual bool checkForConnection( const std::vector<double>& myvals ) const;
82 : /// Get the atom number
83 : AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned& i ) const ;
84 : };
85 :
86 : inline
87 : AdjacencyMatrixVessel* AdjacencyMatrixBase::getAdjacencyVessel() {
88 : return mat;
89 : }
90 :
91 : inline
92 2451101 : unsigned AdjacencyMatrixBase::getBaseColvarNumber( const unsigned& inum ) const {
93 2451101 : if( atom_lab[inum].first>0 ) return atom_lab[inum].first-1;
94 2091063 : return 0;
95 : }
96 :
97 : inline
98 156 : AtomNumber AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom( const unsigned& iatom ) const {
99 156 : if( atom_lab[iatom].first>0 ) {
100 156 : unsigned mmc=atom_lab[ iatom ].first - 1;
101 156 : return mybasemulticolvars[mmc]->getAbsoluteIndexOfCentralAtom( atom_lab[iatom].second );
102 : }
103 0 : return ActionAtomistic::getAbsoluteIndex( atom_lab[iatom].second );
104 : }
105 :
106 : inline
107 12411 : double AdjacencyMatrixBase::transformStoredValues( const std::vector<double>& myvals, unsigned& vout, double& df ) const {
108 12411 : plumed_dbg_assert( myvals.size()==2 ); vout=1; df=1; return myvals[1];
109 : }
110 :
111 : inline
112 11169 : bool AdjacencyMatrixBase::checkForConnection( const std::vector<double>& myvals ) const {
113 11169 : return (myvals[0]*myvals[1]>epsilon);
114 : }
115 :
116 : }
117 : }
118 :
119 : #endif
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