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 : #include "ActionWithInputMatrix.h"
23 : #include "multicolvar/AtomValuePack.h"
24 : #include "AdjacencyMatrixVessel.h"
25 : #include "AdjacencyMatrixBase.h"
26 : #include "core/ActionRegister.h"
27 : #include "core/PlumedMain.h"
28 : #include "core/ActionSet.h"
29 :
30 : //+PLUMEDOC MATRIXF COLUMNSUMS
31 : /*
32 : Sum the columns of a contact matrix
33 :
34 : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the
35 : so called adjacency matrix. An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether
36 : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not. This action allows you to calculate
37 : the sum of the columns in this adjacency matrix and to then calculate further functions of these quantities.
38 :
39 : \par Examples
40 :
41 : The first instruction in the following input file tells PLUMED to compute a \f$10 \times 10\f$ matrix in which the \f$ij\f$-element
42 : tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other. The numbers in each of this rows are then added together
43 : and the average value is computed. As such the following input provides an alternative method for calculating the coordination numbers
44 : of atoms 1 to 10.
45 :
46 : \verbatim
47 : mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}
48 : rsums: COLUMNSUMS MATRIX=mat MEAN
49 : PRINT ARG=rsums.* FILE=colvar
50 : \endverbatim
51 :
52 : The following input demonstrates another way that an average coordination number can be computed. This input calculates the number of atoms
53 : with indices between 1 and 5 that are within the first coordination spheres of each of the atoms within indices between 6 and 15. The average
54 : coordination number is then calculated from these fifteen coordination numbers and this quantity is output to a file.
55 :
56 : \verbatim
57 : mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}
58 : rsums: COLUMNSUMS MATRIX=mat2 MEAN
59 : PRINT ARG=rsums.* FILE=colvar
60 : \endverbatim
61 :
62 : */
63 : //+ENDPLUMEDOC
64 :
65 : namespace PLMD {
66 : namespace adjmat {
67 :
68 6 : class MatrixColumnSums : public ActionWithInputMatrix {
69 : public:
70 : static void registerKeywords( Keywords& keys );
71 : explicit MatrixColumnSums(const ActionOptions&);
72 : double compute( const unsigned& tinded, multicolvar::AtomValuePack& myatoms ) const ;
73 : };
74 :
75 2526 : PLUMED_REGISTER_ACTION(MatrixColumnSums,"COLUMNSUMS")
76 :
77 4 : void MatrixColumnSums::registerKeywords( Keywords& keys ) {
78 4 : ActionWithInputMatrix::registerKeywords( keys );
79 4 : keys.use("ALT_MIN"); keys.use("LOWEST"); keys.use("HIGHEST"); keys.use("MEAN");
80 4 : keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN");
81 4 : keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
82 4 : }
83 :
84 3 : MatrixColumnSums::MatrixColumnSums(const ActionOptions& ao):
85 : Action(ao),
86 3 : ActionWithInputMatrix(ao)
87 : {
88 3 : if( (mymatrix->getMatrixAction())->mybasemulticolvars.size()>0 ) error("matrix row sums should only be calculated when inputs are atoms");
89 : // Setup the tasks
90 3 : unsigned ncols = mymatrix->getNumberOfColumns();
91 3 : ablocks.resize(1); ablocks[0].resize( ncols );
92 3 : for(unsigned i=0; i<ncols; ++i) addTaskToList( i );
93 : // Set the positions - this is only used when getting positions for central atoms
94 3 : if( mymatrix->undirectedGraph() ) {
95 2 : for(unsigned i=0; i<ncols; ++i) ablocks[0][i]=i;
96 : } else {
97 1 : for(unsigned i=0; i<ncols; ++i) ablocks[0][i]=mymatrix->getNumberOfRows() + i;
98 : }
99 3 : std::vector<AtomNumber> fake_atoms; setupMultiColvarBase( fake_atoms );
100 3 : }
101 :
102 164 : double MatrixColumnSums::compute( const unsigned& tinded, multicolvar::AtomValuePack& myatoms ) const {
103 164 : double sum=0.0; std::vector<double> tvals( mymatrix->getNumberOfComponents() );
104 164 : unsigned nrows = mymatrix->getNumberOfRows();
105 5010 : for(unsigned i=0; i<nrows; ++i) {
106 4846 : if( mymatrix->undirectedGraph() && tinded==i ) continue;
107 4732 : sum+=retrieveConnectionValue( i, tinded, tvals );
108 : }
109 :
110 164 : if( !doNotCalculateDerivatives() ) {
111 100 : MultiValue myvals( mymatrix->getNumberOfComponents(), myatoms.getNumberOfDerivatives() );
112 100 : MultiValue& myvout=myatoms.getUnderlyingMultiValue();
113 850 : for(unsigned i=0; i<nrows; ++i) {
114 750 : if( mymatrix->isSymmetric() && tinded==i ) continue ;
115 700 : addConnectionDerivatives( i, tinded, tvals, myvals, myvout );
116 100 : }
117 : }
118 164 : return sum;
119 : }
120 :
121 : }
122 2523 : }
|
