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 "AlignedMatrixBase.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "tools/Matrix.h"
      25             : 
      26             : //+PLUMEDOC MATRIX ALIGNED_MATRIX
      27             : /*
      28             : Adjacency matrix in which two molecule are adjacent if they are within a certain cutoff and if they have the same orientation.
      29             : 
      30             : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the
      31             : 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
      32             : 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
      33             : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.
      34             : 
      35             : For this action the elements of the adjacency matrix are calculated using:
      36             : 
      37             : \f[
      38             : a_{ij} = \sigma_1( |\mathbf{r}_{ij}| ) \sigma_2( \mathbf{v}_i . \mathbf{v}_j )
      39             : \f]
      40             : 
      41             : This form of adjacency matrix can only be used if the input species are objects that lie at a point in space and that have an orientation, \f$\mathbf{v}\f$.
      42             : These orientations might represent the
      43             : orientation of a molecule, which could be calculated using \ref MOLECULES or \ref PLANES, or it might be the complex vectors calculated using the
      44             : Steinhardt parameters \ref Q3, \ref Q4 or \ref Q6.  In the expression above \f$\mathbf{r}_{ij}\f$ is the vector connecting the points in space
      45             : where objects \f$i\f$ and \f$j\f$ find themselves and \f$\sigma_1\f$ is a \ref switchingfunction that acts upon the magnitude of this vector.
      46             : \f$\sigma_2\f$ is a second \ref switchingfunction that acts on the dot product of the directors of the vectors that define the orientations of
      47             : objects \f$i\f$ and \f$j\f$.
      48             : 
      49             : \par Examples
      50             : 
      51             : The example input below is necessarily but gives you an idea of what can be achieved using this action.
      52             : The orientations and positions of four molecules are defined using the \ref MOLECULES action as the position of the
      53             : centers of mass of the two atoms specified and the direction of the vector connecting the two atoms that were specified.
      54             : A \f$4 \times 4\f$ matrix is then computed using the formula above.  The \f$ij\f$-element of this matrix tells us whether
      55             : or not atoms \f$i\f$ and \f$j\f$ are within 0.1 nm of each other and whether or not the dot-product of their orientation vectors
      56             : is greater than 0.5.  The sum of the rows of this matrix are then computed.  The sums of the \f$i\f$th row of this matrix tells us how
      57             : many of the molecules that are within the first coordination sphere of molecule \f$i\f$ have an orientation that is similar to that of
      58             : molecule \f$i\f$.  We thus calculate the number of these "coordination numbers" that are greater than 1.0 and output this quantity to a file.
      59             : 
      60             : \plumedfile
      61             : m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8
      62             : mat: ALIGNED_MATRIX ATOMS=m1 SWITCH={RATIONAL R_0=0.1} ORIENTATION_SWITCH={RATIONAL R_0=0.1 D_MAX=0.5}
      63             : row: ROWSUMS MATRIX=mat MORE_THAN={RATIONAL D_0=1.0 R_0=0.1}
      64             : PRINT ARG=row.* FILE=colvar
      65             : \endplumedfile
      66             : 
      67             : */
      68             : //+ENDPLUMEDOC
      69             : 
      70             : namespace PLMD {
      71             : namespace adjmat {
      72             : 
      73             : class ContactAlignedMatrix : public AlignedMatrixBase {
      74             : private:
      75             :   Matrix<SwitchingFunction> sf;
      76             : public:
      77             :   ///
      78             :   static void registerKeywords( Keywords& keys );
      79             :   ///
      80             :   explicit ContactAlignedMatrix(const ActionOptions&);
      81             :   void readOrientationConnector( const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) override;
      82             :   double computeVectorFunction( const unsigned& iv, const unsigned& jv,
      83             :                                 const Vector& conn, const std::vector<double>& vec1, const std::vector<double>& vec2,
      84             :                                 Vector& dconn, std::vector<double>& dvec1, std::vector<double>& dvec2 ) const override;
      85             : };
      86             : 
      87       10419 : PLUMED_REGISTER_ACTION(ContactAlignedMatrix,"ALIGNED_MATRIX")
      88             : 
      89           1 : void ContactAlignedMatrix::registerKeywords( Keywords& keys ) {
      90           1 :   AlignedMatrixBase::registerKeywords( keys );
      91           3 :   keys.add("numbered","ORIENTATION_SWITCH","A switching function that transforms the dot product of the input vectors.");
      92           1 : }
      93             : 
      94           0 : ContactAlignedMatrix::ContactAlignedMatrix( const ActionOptions& ao ):
      95             :   Action(ao),
      96           0 :   AlignedMatrixBase(ao)
      97             : {
      98           0 :   unsigned nrows, ncols, ig; retrieveTypeDimensions( nrows, ncols, ig );
      99           0 :   sf.resize( nrows, ncols );
     100           0 :   parseConnectionDescriptions("ORIENTATION_SWITCH",false,0);
     101           0 : }
     102             : 
     103           0 : void ContactAlignedMatrix::readOrientationConnector( const unsigned& i, const unsigned& j, const std::vector<std::string>& desc ) {
     104           0 :   plumed_assert( desc.size()==1 ); std::string errors; sf(j,i).set(desc[0],errors);
     105           0 :   if( j!=i ) sf(i,j).set(desc[0],errors);
     106           0 :   log.printf("  vectors in %u th and %u th groups must have a dot product that is greater than %s \n",i+1,j+1,(sf(i,j).description()).c_str() );
     107           0 : }
     108             : 
     109           0 : double ContactAlignedMatrix::computeVectorFunction( const unsigned& iv, const unsigned& jv,
     110             :     const Vector& conn, const std::vector<double>& vec1, const std::vector<double>& vec2,
     111             :     Vector& dconn, std::vector<double>& dvec1, std::vector<double>& dvec2 ) const {
     112           0 :   double dot_df, dot=0; dconn.zero();
     113           0 :   for(unsigned k=2; k<vec1.size(); ++k) dot+=vec1[k]*vec2[k];
     114           0 :   double f_dot = sf(iv,jv).calculate( dot, dot_df );
     115           0 :   for(unsigned k=2; k<vec1.size(); ++k) { dvec1[k]=dot_df*vec2[k]; dvec2[k]=dot_df*vec1[k]; }
     116           0 :   return f_dot;
     117             : }
     118             : 
     119             : }
     120             : }
     121             : 
     122             : 
     123             :