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 "ClusteringBase.h"
      23             : #include "AdjacencyMatrixVessel.h"
      24             : #include "AdjacencyMatrixBase.h"
      25             : #include "core/ActionRegister.h"
      26             : 
      27             : //+PLUMEDOC MATRIXF CLUSTER_WITHSURFACE
      28             : /*
      29             : Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster.
      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.  When analyzing these matrix
      34             : 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
      35             : and takes one of the connected components that was found during this analysis and creates a new cluster that includes all the atoms within the
      36             : connected component that was found together that were within a certain cutoff distance of the atoms in the connected component.  This form of analysis
      37             : has been used successfully in the forward flux sampling simulations described in this paper \cite gab-ice-kaolinite
      38             : 
      39             : \par Examples
      40             : 
      41             : 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 less
      42             : than 13.5 and if they are within 0.38 nm of each other.  Depth first search clustering is used to find the connected components in this matrix.  The
      43             : number of atoms with indices that are between 1 and 1996 and that are either in the second largest cluster or that are within within 0.3 nm of one of the
      44             : atoms within the the second largest cluster are then counted and this number of atoms is output to a file called size.  In addition the indices of the atoms
      45             : that were counted are output to a file called dfs2.dat.
      46             : 
      47             : \plumedfile
      48             : c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
      49             : cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
      50             : mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
      51             : dfs: DFSCLUSTERING MATRIX=mat
      52             : clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3
      53             : size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2
      54             : PRINT ARG=size2a FILE=size FMT=%8.4f
      55             : OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat
      56             : \endplumedfile
      57             : 
      58             : 
      59             : */
      60             : //+ENDPLUMEDOC
      61             : 
      62             : namespace PLMD {
      63             : namespace adjmat {
      64             : 
      65             : class ClusterWithSurface : public ClusteringBase {
      66             : private:
      67             : /// The clusters that we are adding surface atoms to
      68             :   ClusteringBase* myclusters;
      69             : /// The cutoff for surface atoms
      70             :   double rcut_surf2;
      71             : public:
      72             : /// Create manual
      73             :   static void registerKeywords( Keywords& keys );
      74             : /// Constructor
      75             :   explicit ClusterWithSurface(const ActionOptions&);
      76             : ///
      77             :   unsigned getNumberOfDerivatives() override;
      78             : ///
      79             :   unsigned getNumberOfNodes() const override;
      80             : ///
      81             :   AtomNumber getAbsoluteIndexOfCentralAtom(const unsigned& i) const override;
      82             : ///
      83             :   void retrieveAtomsInCluster( const unsigned& clust, std::vector<unsigned>& myatoms ) const override;
      84             : ///
      85             :   void getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const override;
      86             : ///
      87             :   MultiValue& getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const override;
      88             : ///
      89             :   unsigned getNumberOfQuantities() const override;
      90             : /// Do the calculation
      91           2 :   void performClustering() override {};
      92             : ///
      93             :   double  getCutoffForConnection() const override;
      94             : ///
      95             :   Vector getPositionOfAtomForLinkCells( const unsigned& taskIndex ) const override;
      96             : };
      97             : 
      98       13789 : PLUMED_REGISTER_ACTION(ClusterWithSurface,"CLUSTER_WITHSURFACE")
      99             : 
     100           6 : void ClusterWithSurface::registerKeywords( Keywords& keys ) {
     101           6 :   ClusteringBase::registerKeywords( keys );
     102           6 :   keys.remove("MATRIX");
     103          12 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
     104          12 :   keys.add("compulsory","RCUT_SURF","you also have the option to find the atoms on the surface of the cluster.  An atom must be within this distance of one of the atoms "
     105             :            "of the cluster in order to be considered a surface atom");
     106           6 : }
     107             : 
     108           2 : ClusterWithSurface::ClusterWithSurface(const ActionOptions&ao):
     109             :   Action(ao),
     110           2 :   ClusteringBase(ao) {
     111             :   std::vector<AtomNumber> fake_atoms;
     112           4 :   if( !parseMultiColvarAtomList("CLUSTERS",-1,fake_atoms ) ) {
     113           0 :     error("unable to find CLUSTERS input");
     114             :   }
     115           2 :   if( mybasemulticolvars.size()!=1 ) {
     116           0 :     error("should be exactly one multicolvar input");
     117             :   }
     118             : 
     119             :   // Retrieve the adjacency matrix of interest
     120           2 :   atom_lab.resize(0);
     121           2 :   myclusters = dynamic_cast<ClusteringBase*>( mybasemulticolvars[0] );
     122           2 :   if( !myclusters ) {
     123           0 :     error( mybasemulticolvars[0]->getLabel() + " does not calculate clusters");
     124             :   }
     125             : 
     126             :   // Setup switching function for surface atoms
     127             :   double rcut_surf;
     128           2 :   parse("RCUT_SURF",rcut_surf);
     129           2 :   if( rcut_surf>0 ) {
     130           2 :     log.printf("  counting surface atoms that are within %f of the cluster atoms \n",rcut_surf);
     131             :   }
     132           2 :   rcut_surf2=rcut_surf*rcut_surf;
     133             : 
     134             :   // And now finish the setup of everything in the base
     135           2 :   setupMultiColvarBase( fake_atoms );
     136           2 : }
     137             : 
     138           4 : unsigned ClusterWithSurface::getNumberOfDerivatives() {
     139           4 :   return myclusters->getNumberOfDerivatives();
     140             : }
     141             : 
     142    16155834 : unsigned ClusterWithSurface::getNumberOfNodes() const {
     143    16155834 :   return myclusters->getNumberOfNodes();
     144             : }
     145             : 
     146         128 : AtomNumber ClusterWithSurface::getAbsoluteIndexOfCentralAtom(const unsigned& i) const {
     147         128 :   return myclusters->getAbsoluteIndexOfCentralAtom(i);
     148             : }
     149             : 
     150           0 : void ClusterWithSurface::getInputData( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms, std::vector<double>& orient0 ) const {
     151           0 :   myclusters->getInputData( ind, normed, myatoms, orient0 );
     152           0 : }
     153             : 
     154           0 : MultiValue& ClusterWithSurface::getInputDerivatives( const unsigned& ind, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const {
     155           0 :   return myclusters->getInputDerivatives( ind, normed, myatoms );
     156             : }
     157             : 
     158          14 : unsigned ClusterWithSurface::getNumberOfQuantities() const {
     159          14 :   return myclusters->getNumberOfQuantities();
     160             : }
     161             : 
     162           2 : double  ClusterWithSurface::getCutoffForConnection() const {
     163           2 :   double tcut = myclusters->getCutoffForConnection();
     164           2 :   if( tcut>std::sqrt(rcut_surf2) ) {
     165             :     return tcut;
     166             :   }
     167           0 :   return std::sqrt(rcut_surf2);
     168             : }
     169             : 
     170           6 : void ClusterWithSurface::retrieveAtomsInCluster( const unsigned& clust, std::vector<unsigned>& myatoms ) const {
     171             :   std::vector<unsigned> tmpat;
     172           6 :   myclusters->retrieveAtomsInCluster( clust, tmpat );
     173             : 
     174             :   // Prevent double counting
     175           6 :   std::vector<bool> incluster( getNumberOfNodes(), false );
     176          90 :   for(unsigned i=0; i<tmpat.size(); ++i) {
     177          84 :     incluster[tmpat[i]]=true;
     178             :   }
     179             : 
     180             :   // Find the atoms in the the clusters
     181           6 :   std::vector<bool> surface_atom( getNumberOfNodes(), false );
     182          90 :   for(unsigned i=0; i<tmpat.size(); ++i) {
     183      167748 :     for(unsigned j=0; j<getNumberOfNodes(); ++j) {
     184      167664 :       if( incluster[j] ) {
     185        1176 :         continue;
     186             :       }
     187      166488 :       double dist2=getSeparation( getPosition(tmpat[i]), getPosition(j) ).modulo2();
     188      166488 :       if( dist2<rcut_surf2 ) {
     189             :         surface_atom[j]=true;
     190             :       }
     191             :     }
     192             :   }
     193             :   unsigned nsurf_at=0;
     194       11982 :   for(unsigned j=0; j<getNumberOfNodes(); ++j) {
     195       11976 :     if( surface_atom[j] ) {
     196         300 :       nsurf_at++;
     197             :     }
     198             :   }
     199           6 :   myatoms.resize( nsurf_at + tmpat.size() );
     200          90 :   for(unsigned i=0; i<tmpat.size(); ++i) {
     201          84 :     myatoms[i]=tmpat[i];
     202             :   }
     203           6 :   unsigned nn=tmpat.size();
     204       11982 :   for(unsigned j=0; j<getNumberOfNodes(); ++j) {
     205       11976 :     if( surface_atom[j] ) {
     206         300 :       myatoms[nn]=j;
     207         300 :       nn++;
     208             :     }
     209             :   }
     210           6 :   plumed_assert( nn==myatoms.size() );
     211           6 : }
     212             : 
     213           0 : Vector ClusterWithSurface::getPositionOfAtomForLinkCells( const unsigned& iatom ) const {
     214           0 :   return myclusters->getPositionOfAtomForLinkCells( iatom );
     215             : }
     216             : 
     217             : }
     218             : }