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 "AdjacencyMatrixBase.h"
      23             : #include "multicolvar/AtomValuePack.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "tools/SwitchingFunction.h"
      26             : #include "tools/Matrix.h"
      27             : 
      28             : //+PLUMEDOC MATRIX CONTACT_MATRIX
      29             : /*
      30             : Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.
      31             : 
      32             : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the
      33             : 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
      34             : 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.  These matrices can then be further
      35             : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.
      36             : 
      37             : For this action the elements of the contact matrix are calculated using:
      38             : 
      39             : \f[
      40             :  a_{ij} = \sigma( |\mathbf{r}_{ij}| )
      41             : \f]
      42             : 
      43             : where \f$|\mathbf{r}_{ij}|\f$ is the magnitude of the vector connecting atoms \f$i\f$ and \f$j\f$ and where \f$\sigma\f$ is a \ref switchingfunction.
      44             : 
      45             : \par Examples
      46             : 
      47             : The input shown below calculates a \f$6 \times 6\f$ matrix whose elements are equal to one if atom \f$i\f$ and atom \f$j\f$ are within 0.3 nm
      48             : of each other and which is zero otherwise.  The columns in this matrix are then summed so as to give the coordination number for each atom.
      49             : The final quantity output in the colvar file is thus the average coordination number.
      50             : 
      51             : \plumedfile
      52             : mat: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}
      53             : COLUMNSUMS MATRIX=mat MEAN LABEL=csums
      54             : PRINT ARG=csums.* FILE=colvar
      55             : \endplumedfile
      56             : 
      57             : */
      58             : //+ENDPLUMEDOC
      59             : 
      60             : 
      61             : namespace PLMD {
      62             : namespace adjmat {
      63             : 
      64             : class ContactMatrix : public AdjacencyMatrixBase {
      65             : private:
      66             : /// Number of types that are in rows
      67             :   unsigned ncol_t;
      68             : /// switching function
      69             :   Matrix<SwitchingFunction> switchingFunction;
      70             : public:
      71             : /// Create manual
      72             :   static void registerKeywords( Keywords& keys );
      73             : /// Constructor
      74             :   explicit ContactMatrix(const ActionOptions&);
      75             : /// Create the ith, ith switching function
      76             :   void setupConnector( const unsigned& id, const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) override;
      77             : /// This actually calculates the value of the contact function
      78             :   double calculateWeight( const unsigned& taskCode, const double& weight, multicolvar::AtomValuePack& myatoms ) const override;
      79             : /// This does nothing
      80             :   double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const override;
      81             : };
      82             : 
      83       10443 : PLUMED_REGISTER_ACTION(ContactMatrix,"CONTACT_MATRIX")
      84             : 
      85          13 : void ContactMatrix::registerKeywords( Keywords& keys ) {
      86          13 :   AdjacencyMatrixBase::registerKeywords( keys );
      87          26 :   keys.add("atoms","ATOMS","The list of atoms for which you would like to calculate the contact matrix.  The atoms involved must be specified "
      88             :            "as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use "
      89             :            "the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of "
      90             :            "other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider "
      91             :            "variety of functions of the contact matrix as described in \\ref contactmatrix");
      92          26 :   keys.add("numbered","SWITCH","This keyword is used if you want to employ an alternative to the continuous switching function defined above. "
      93             :            "The following provides information on the \\ref switchingfunction that are available. ");
      94             : // I added these keywords so I can test the results I get for column and row sums against output from COORDINATIONNUMBERS
      95             : /// These  should never be used in production as I think they will be much slower than COORDINATIONNUMBERS
      96          39 :   keys.add("hidden","ATOMSA",""); keys.add("hidden","ATOMSB","");
      97          13 : }
      98             : 
      99          12 : ContactMatrix::ContactMatrix( const ActionOptions& ao ):
     100             :   Action(ao),
     101          12 :   AdjacencyMatrixBase(ao)
     102             : {
     103             :   // Read in the atoms and setup the matrix
     104          24 :   readMaxTwoSpeciesMatrix( "ATOMS", "ATOMSA", "ATOMSB", true );
     105          12 :   unsigned nrows, ncols; retrieveTypeDimensions( nrows, ncols, ncol_t );
     106          12 :   switchingFunction.resize( nrows, ncols );
     107             :   // Read in the switching functions
     108          24 :   parseConnectionDescriptions("SWITCH",false,ncol_t);
     109             : 
     110             :   // Find the largest sf cutoff
     111          12 :   double sfmax=switchingFunction(0,0).get_dmax();
     112          25 :   for(unsigned i=0; i<switchingFunction.nrows(); ++i) {
     113          28 :     for(unsigned j=0; j<switchingFunction.ncols(); ++j) {
     114          15 :       double tsf=switchingFunction(i,j).get_dmax();
     115          15 :       if( tsf>sfmax ) sfmax=tsf;
     116             :     }
     117             :   }
     118             :   // And set the link cell cutoff
     119          12 :   setLinkCellCutoff( sfmax );
     120          12 : }
     121             : 
     122          14 : void ContactMatrix::setupConnector( const unsigned& id, const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) {
     123          14 :   plumed_assert( id==0 && desc.size()==1 ); std::string errors; switchingFunction(j,i).set(desc[0],errors);
     124          14 :   if( errors.length()!=0 ) error("problem reading switching function description " + errors);
     125          14 :   if( j!=i) switchingFunction(i,j).set(desc[0],errors);
     126          28 :   log.printf("  %u th and %u th multicolvar groups must be within %s\n",i+1,j+1,(switchingFunction(i,j).description()).c_str() );
     127          14 : }
     128             : 
     129       55746 : double ContactMatrix::calculateWeight( const unsigned& taskCode, const double& weight, multicolvar::AtomValuePack& myatoms ) const {
     130       55746 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
     131      166288 :   if( distance.modulo2()<switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).get_dmax2() ) return 1.0;
     132             :   return 0.0;
     133             : }
     134             : 
     135       28888 : double ContactMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
     136       28888 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
     137             :   double dfunc;
     138       57301 :   double sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );
     139             : 
     140       28888 :   if( !doNotCalculateDerivatives() ) {
     141       28654 :     addAtomDerivatives( 1, 0, (-dfunc)*distance, myatoms );
     142       28654 :     addAtomDerivatives( 1, 1, (+dfunc)*distance, myatoms );
     143       28654 :     myatoms.addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) );
     144             :   }
     145       28888 :   return sw;
     146             : }
     147             : 
     148             : }
     149             : }
     150             :