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 "ClusterAnalysisBase.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC CONCOMP CLUSTER_NATOMS
      26             : /*
      27             : Gives the number of atoms in the connected component
      28             : 
      29             : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the
      30             : 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
      31             : 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.  When analyzing these matrix
      32             : we can treat them as a graph and find connected components using some clustering algorithm.  This action is used in tandem with this form of analysis
      33             : to output the number of atoms that are connected together in a particular connected component.  It is important to note that the quantity that is
      34             : output by this action cannot be differentiated.  As such it cannot be used as a collective variable in a biased simulation.
      35             : 
      36             : \par Examples
      37             : 
      38             : The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater
      39             : than 2.0 and if they are within 6.0 nm of each other.  Depth first search clustering is used to find the connected components in this matrix and then
      40             : the number of atoms in the largest cluster is found.  This quantity is then output to a file called colvar
      41             : 
      42             : \plumedfile
      43             : # Calculate coordination numbers
      44             : c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
      45             : # Select coordination numbers that are more than 2.0
      46             : cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
      47             : # Build a contact matrix
      48             : mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
      49             : # Find largest cluster
      50             : dfs: DFSCLUSTERING MATRIX=mat
      51             : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
      52             : nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
      53             : PRINT ARG=nat FILE=COLVAR
      54             : \endplumedfile
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : namespace PLMD {
      60             : namespace adjmat {
      61             : 
      62             : class ClusterSize : public ClusterAnalysisBase {
      63             : private:
      64             : /// The cluster we are looking for
      65             :   unsigned clustr;
      66             : public:
      67             : /// Create manual
      68             :   static void registerKeywords( Keywords& keys );
      69             : /// Constructor
      70             :   explicit ClusterSize(const ActionOptions&);
      71             : ///
      72             :   void calculate() override;
      73             : ///
      74           0 :   void performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const override {
      75           0 :     plumed_error();
      76             :   }
      77             : ///
      78             :   void turnOnDerivatives() override;
      79             : };
      80             : 
      81       13833 : PLUMED_REGISTER_ACTION(ClusterSize,"CLUSTER_NATOMS")
      82             : 
      83          28 : void ClusterSize::registerKeywords( Keywords& keys ) {
      84          28 :   ClusterAnalysisBase::registerKeywords( keys );
      85          56 :   keys.add("compulsory","CLUSTER","1","which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.");
      86          28 : }
      87             : 
      88          24 : ClusterSize::ClusterSize(const ActionOptions&ao):
      89             :   Action(ao),
      90          24 :   ClusterAnalysisBase(ao) {
      91             :   // Find out which cluster we want
      92          24 :   parse("CLUSTER",clustr);
      93             : 
      94          24 :   if( clustr<1 ) {
      95           0 :     error("cannot look for a cluster larger than the largest cluster");
      96             :   }
      97          24 :   if( clustr>getNumberOfNodes() ) {
      98           0 :     error("cluster selected is invalid - too few atoms in system");
      99             :   }
     100             : 
     101             :   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
     102       11488 :   for(unsigned i=0; i<getNumberOfNodes(); ++i) {
     103       11464 :     addTaskToList(i);
     104             :   }
     105             :   // And now finish the setup of everything in the base
     106             :   std::vector<AtomNumber> fake_atoms;
     107          24 :   setupMultiColvarBase( fake_atoms );
     108          24 :   addValue();
     109          24 :   setNotPeriodic();
     110          24 : }
     111             : 
     112           0 : void ClusterSize::turnOnDerivatives() {
     113           0 :   error("cannot calculate derivatives of number of atoms in cluster.  This quantity is not differentiable");
     114             : }
     115             : 
     116          27 : void ClusterSize::calculate() {
     117             :   // Retrieve the atoms in the largest cluster
     118             :   std::vector<unsigned> myatoms;
     119          27 :   retrieveAtomsInCluster( clustr, myatoms );
     120          27 :   setValue( myatoms.size() );
     121          27 : }
     122             : 
     123             : }
     124             : }