Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2020 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 "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "multicolvar/MultiColvarShortcuts.h"
      25             : 
      26             : //+PLUMEDOC CONCOMP CLUSTER_PROPERTIES
      27             : /*
      28             : Calculate properties of the distribution of some quantities that are part of a connected component
      29             : 
      30             : This collective variable was developed for looking at nucleation phenomena, where you are
      31             : interested in using studying the behavior of atoms in small aggregates or nuclei.  In these sorts of
      32             : problems you might be interested in the degree the atoms in a nucleus have adopted their crystalline
      33             : structure or (in the case of heterogeneous nucleation of a solute from a solvent) you might be
      34             : interested in how many atoms are present in the largest cluster \cite tribello-clustering.
      35             : 
      36             : \par Examples
      37             : 
      38             : The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency
      39             : matrix whose elements measures whether atoms \f$i\f$ and \f$j\f$ are within 0.55 nm of each other.  The action
      40             : labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining
      41             : a graph.  This dfs action then finds the largest connected component in this graph.  The sum of the coordination
      42             : numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
      43             : file.  The way this input can be used is described in detail in \cite tribello-clustering.
      44             : 
      45             : \plumedfile
      46             : lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55} LOWMEM
      47             : cm: CONTACT_MATRIX ATOMS=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
      48             : dfs: DFSCLUSTERING MATRIX=cm
      49             : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
      50             : PRINT ARG=clust1.* FILE=colvar
      51             : \endplumedfile
      52             : 
      53             : */
      54             : //+ENDPLUMEDOC
      55             : 
      56             : namespace PLMD {
      57             : namespace clusters {
      58             : 
      59             : class ClusterProperties : public ActionShortcut {
      60             : public:
      61             :   static void registerKeywords(Keywords& keys);
      62             :   explicit ClusterProperties(const ActionOptions&);
      63             : };
      64             : 
      65             : PLUMED_REGISTER_ACTION(ClusterProperties,"CLUSTER_PROPERTIES")
      66             : 
      67          54 : void ClusterProperties::registerKeywords(Keywords& keys) {
      68          54 :   ActionShortcut::registerKeywords( keys );
      69         108 :   keys.add("compulsory","ARG","calculate the sum of the arguments calculated by this action for the cluster");
      70         108 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      71         108 :   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.");
      72         108 :   keys.setValueDescription("vector","a vector that is one if the atom is part of the cluster or interest and zero otherwise");
      73          54 :   multicolvar::MultiColvarShortcuts::shortcutKeywords( keys );
      74          54 :   keys.needsAction("CLUSTER_WEIGHTS");
      75          54 : }
      76             : 
      77          20 : ClusterProperties::ClusterProperties(const ActionOptions& ao):
      78             :   Action(ao),
      79          20 :   ActionShortcut(ao)
      80             : {
      81             :   // Read the property we are interested in
      82          40 :   std::string argstr; parse("ARG",argstr);
      83             :   // Read in the shortcut keywords
      84          20 :   std::map<std::string,std::string> keymap; multicolvar::MultiColvarShortcuts::readShortcutKeywords( keymap, this );
      85             :   // Create a cluster weights object
      86          40 :   readInputLine( getShortcutLabel() + ": CLUSTER_WEIGHTS " + convertInputLineToString() );
      87             :   // Now do the multicolvar bit
      88          20 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), argstr, getShortcutLabel(), keymap, this );
      89          20 : }
      90             : 
      91             : }
      92             : }