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 shortcut action is present to ensure that inputs for older PLUMED versions remain compatible.  We STRONGLY
      31             : encourage you to use the newer (and simpler) syntax for clustering calculations__  Look at the documentation for
      32             : CLUSTER_WEIGHTS and the expanded version of the input below to see how this new input syntax operates.
      33             : 
      34             : This collective variable was developed for looking at nucleation phenomena, where you are
      35             : interested in using studying the behavior of atoms in small aggregates or nuclei.  In these sorts of
      36             : problems you might be interested in the degree the atoms in a nucleus have adopted their crystalline
      37             : structure or (in the case of heterogeneous nucleation of a solute from a solvent) you might be
      38             : interested in how many atoms are present in the largest cluster.
      39             : 
      40             : The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency
      41             : matrix whose elements measures whether atoms $i$ and $j$ are within 0.55 nm of each other.  The action
      42             : labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining
      43             : a graph.  This dfs action then finds the largest connected component in this graph.  The sum of the coordination
      44             : numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
      45             : file.
      46             : 
      47             : ```plumed
      48             : lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
      49             : cm: CONTACT_MATRIX GROUP=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
      50             : dfs: DFSCLUSTERING ARG=cm
      51             : clust1: CLUSTER_PROPERTIES ARG=lq CLUSTERS=dfs CLUSTER=1 SUM
      52             : PRINT ARG=clust1.sum FILE=colvar
      53             : ```
      54             : 
      55             : */
      56             : //+ENDPLUMEDOC
      57             : 
      58             : namespace PLMD {
      59             : namespace clusters {
      60             : 
      61             : class ClusterProperties : public ActionShortcut {
      62             : public:
      63             :   static void registerKeywords(Keywords& keys);
      64             :   explicit ClusterProperties(const ActionOptions&);
      65             : };
      66             : 
      67             : PLUMED_REGISTER_ACTION(ClusterProperties,"CLUSTER_PROPERTIES")
      68             : 
      69          54 : void ClusterProperties::registerKeywords(Keywords& keys) {
      70          54 :   ActionShortcut::registerKeywords( keys );
      71          54 :   keys.add("compulsory","ARG","calculate the sum of the arguments calculated by this action for the cluster");
      72          54 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      73          54 :   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.");
      74         108 :   keys.setValueDescription("vector","a vector that is one if the atom is part of the cluster or interest and zero otherwise");
      75          54 :   multicolvar::MultiColvarShortcuts::shortcutKeywords( keys );
      76          54 :   keys.needsAction("CLUSTER_WEIGHTS");
      77          54 : }
      78             : 
      79          20 : ClusterProperties::ClusterProperties(const ActionOptions& ao):
      80             :   Action(ao),
      81          20 :   ActionShortcut(ao) {
      82             :   // Read the property we are interested in
      83             :   std::string argstr;
      84          40 :   parse("ARG",argstr);
      85             :   // Read in the shortcut keywords
      86             :   std::map<std::string,std::string> keymap;
      87          20 :   multicolvar::MultiColvarShortcuts::readShortcutKeywords( keymap, this );
      88             :   // Create a cluster weights object
      89          40 :   readInputLine( getShortcutLabel() + ": CLUSTER_WEIGHTS " + convertInputLineToString() );
      90             :   // Now do the multicolvar bit
      91          20 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), argstr, getShortcutLabel(), keymap, this );
      92          20 : }
      93             : 
      94             : }
      95             : }