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 "core/ActionRegister.h"
      24             : #include "tools/SwitchingFunction.h"
      25             : #include "tools/Matrix.h"
      26             : 
      27             : //+PLUMEDOC MATRIX CONTACT_MATRIX_PROPER
      28             : /*
      29             : Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.
      30             : 
      31             : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the
      32             : 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
      33             : 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
      34             : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.
      35             : 
      36             : For this action the elements of the contact matrix are calculated using:
      37             : 
      38             : \f[
      39             :  a_{ij} = \sigma( |\mathbf{r}_{ij}| )
      40             : \f]
      41             : 
      42             : 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.
      43             : 
      44             : \par Examples
      45             : 
      46             : 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
      47             : 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.
      48             : The final quantity output in the colvar file is thus the average coordination number.
      49             : 
      50             : \plumedfile
      51             : mat: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}
      52             : COLUMNSUMS MATRIX=mat MEAN LABEL=csums
      53             : PRINT ARG=csums.* FILE=colvar
      54             : \endplumedfile
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : 
      60             : namespace PLMD {
      61             : namespace adjmat {
      62             : 
      63             : class ContactMatrix : public AdjacencyMatrixBase {
      64             : private:
      65             : /// switching function
      66             :   SwitchingFunction switchingFunction;
      67             : public:
      68             : /// Create manual
      69             :   static void registerKeywords( Keywords& keys );
      70             : /// Constructor
      71             :   explicit ContactMatrix(const ActionOptions&);
      72             : /// This does nothing
      73             :   double calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const override;
      74             : /// Override this so we write the graph properly
      75           8 :   std::string writeInGraph() const override { return "CONTACT_MATRIX"; }
      76             : };
      77             : 
      78             : PLUMED_REGISTER_ACTION(ContactMatrix,"CONTACT_MATRIX_PROPER")
      79             : 
      80         424 : void ContactMatrix::registerKeywords( Keywords& keys ) {
      81         424 :   AdjacencyMatrixBase::registerKeywords( keys ); keys.setDisplayName("CONTACT_MATRIX");
      82         848 :   keys.add("compulsory","NN","6","The n parameter of the switching function ");
      83         848 :   keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN");
      84         848 :   keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
      85         848 :   keys.add("compulsory","R_0","The r_0 parameter of the switching function");
      86         848 :   keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
      87             :            "The following provides information on the \\ref switchingfunction that are available. "
      88             :            "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
      89         424 : }
      90             : 
      91         210 : ContactMatrix::ContactMatrix( const ActionOptions& ao ):
      92             :   Action(ao),
      93         210 :   AdjacencyMatrixBase(ao)
      94             : {
      95         420 :   std::string errors, input; parse("SWITCH",input);
      96         210 :   if( input.length()>0 ) {
      97         183 :     switchingFunction.set( input, errors );
      98         183 :     if( errors.length()!=0 ) error("problem reading switching function description " + errors);
      99             :   } else {
     100          27 :     double r_0=-1.0, d_0; int nn, mm;
     101          54 :     parse("NN",nn); parse("MM",mm);
     102          54 :     parse("R_0",r_0); parse("D_0",d_0);
     103          27 :     if( r_0<0.0 ) error("you must set a value for R_0");
     104          27 :     switchingFunction.set(nn,mm,r_0,d_0);
     105             :   }
     106             :   // And set the link cell cutoff
     107         210 :   log.printf("  switching function cutoff is %s \n",switchingFunction.description().c_str() );
     108         210 :   setLinkCellCutoff( true, switchingFunction.get_dmax() );
     109         210 : }
     110             : 
     111    15298242 : double ContactMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
     112    15298242 :   Vector distance = pos2; double mod2 = distance.modulo2();
     113    15298242 :   if( mod2<epsilon ) return 0.0;  // Atoms can't be bonded to themselves
     114    15296728 :   double dfunc, val = switchingFunction.calculateSqr( mod2, dfunc );
     115    15296728 :   if( val<epsilon ) return 0.0;
     116     8264002 :   if( doNotCalculateDerivatives() ) return val;
     117     5500819 :   addAtomDerivatives( 0, (-dfunc)*distance, myvals );
     118     5500819 :   addAtomDerivatives( 1, (+dfunc)*distance, myvals );
     119     5500819 :   addBoxDerivatives( (-dfunc)*Tensor(distance,distance), myvals );
     120     5500819 :   return val;
     121             : }
     122             : 
     123             : }
     124             : }
     125             :