Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "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             : \plumedfile
      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             : \endplumedfile
      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             : \plumedfile
      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             : \endplumedfile
      61             : 
      62             : */
      63             : //+ENDPLUMEDOC
      64             : 
      65             : namespace PLMD {
      66             : namespace adjmat {
      67             : 
      68             : 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 override;
      73             : };
      74             : 
      75       13795 : PLUMED_REGISTER_ACTION(MatrixColumnSums,"COLUMNSUMS")
      76             : 
      77           9 : void MatrixColumnSums::registerKeywords( Keywords& keys ) {
      78           9 :   ActionWithInputMatrix::registerKeywords( keys );
      79           9 :   keys.use("ALT_MIN");
      80           9 :   keys.use("LOWEST");
      81           9 :   keys.use("HIGHEST");
      82           9 :   keys.use("MEAN");
      83           9 :   keys.use("MIN");
      84           9 :   keys.use("MAX");
      85           9 :   keys.use("LESS_THAN");
      86           9 :   keys.use("MORE_THAN");
      87           9 :   keys.use("BETWEEN");
      88           9 :   keys.use("HISTOGRAM");
      89           9 :   keys.use("MOMENTS");
      90           9 : }
      91             : 
      92           5 : MatrixColumnSums::MatrixColumnSums(const ActionOptions& ao):
      93             :   Action(ao),
      94           5 :   ActionWithInputMatrix(ao) {
      95           5 :   if( (mymatrix->getMatrixAction())->mybasemulticolvars.size()>0 ) {
      96           0 :     error("matrix row sums should only be calculated when inputs are atoms");
      97             :   }
      98             :   // Setup the tasks
      99           5 :   unsigned ncols = mymatrix->getNumberOfColumns();
     100           5 :   ablocks.resize(1);
     101           5 :   ablocks[0].resize( ncols );
     102         155 :   for(unsigned i=0; i<ncols; ++i) {
     103         150 :     addTaskToList( i );
     104             :   }
     105             :   // Set the positions - this is only used when getting positions for central atoms
     106           5 :   if( mymatrix->undirectedGraph() ) {
     107         144 :     for(unsigned i=0; i<ncols; ++i) {
     108         140 :       ablocks[0][i]=i;
     109             :     }
     110             :   } else {
     111          11 :     for(unsigned i=0; i<ncols; ++i) {
     112          10 :       ablocks[0][i]=mymatrix->getNumberOfRows() + i;
     113             :     }
     114             :   }
     115             :   std::vector<AtomNumber> fake_atoms;
     116           5 :   setupMultiColvarBase( fake_atoms );
     117           5 : }
     118             : 
     119         238 : double MatrixColumnSums::compute( const unsigned& tinded, multicolvar::AtomValuePack& myatoms ) const {
     120             :   double sum=0.0;
     121         238 :   std::vector<double> tvals( mymatrix->getNumberOfComponents() );
     122         238 :   unsigned nrows = mymatrix->getNumberOfRows();
     123        9200 :   for(unsigned i=0; i<nrows; ++i) {
     124        8962 :     if( mymatrix->undirectedGraph() && tinded==i ) {
     125         188 :       continue;
     126             :     }
     127        8774 :     sum+=retrieveConnectionValue( i, tinded, tvals );
     128             :   }
     129             : 
     130         238 :   if( !doNotCalculateDerivatives() ) {
     131         110 :     MultiValue myvals( mymatrix->getNumberOfComponents(), myatoms.getNumberOfDerivatives() );
     132             :     MultiValue& myvout=myatoms.getUnderlyingMultiValue();
     133         880 :     for(unsigned i=0; i<nrows; ++i) {
     134         770 :       if( mymatrix->isSymmetric() && tinded==i ) {
     135          60 :         continue ;
     136             :       }
     137         710 :       addConnectionDerivatives( i, tinded, myvals, myvout );
     138             :     }
     139         110 :   }
     140         238 :   return sum;
     141             : }
     142             : 
     143             : }
     144             : }