Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 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             : 
      25             : //+PLUMEDOC CONCOMP CLUSTER_NATOMS
      26             : /*
      27             : Calculate the number of atoms in the cluster of interest
      28             : 
      29             : An example input that determines the number of atoms in the second largest cluster that is identified by
      30             : analysing the connected components of a [CONTACT_MATRIX](CONTACT_MATRIX.md) using [DFSCLUSTERING](DFSCLUSTERING.md) is shown below:
      31             : 
      32             : ```plumed
      33             : # Calculate a contact matrix between the first 100 atoms in the configuration
      34             : cm: CONTACT_MATRIX GROUP=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
      35             : # Find the connected components from the contact matrix
      36             : dfs: DFSCLUSTERING ARG=cm
      37             : # And determine the size of the second largest cluster that was identified
      38             : c1: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=2
      39             : PRINT ARG=c1 FILE=colvar
      40             : ```
      41             : 
      42             : __The output from this action is NOT differentiable__
      43             : 
      44             : */
      45             : //+ENDPLUMEDOC
      46             : 
      47             : namespace PLMD {
      48             : namespace clusters {
      49             : 
      50             : class ClusterNatoms : public ActionShortcut {
      51             : public:
      52             :   static void registerKeywords(Keywords& keys);
      53             :   explicit ClusterNatoms(const ActionOptions&);
      54             : };
      55             : 
      56             : PLUMED_REGISTER_ACTION(ClusterNatoms,"CLUSTER_NATOMS")
      57             : 
      58           4 : void ClusterNatoms::registerKeywords(Keywords& keys) {
      59           4 :   ActionShortcut::registerKeywords( keys );
      60           4 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      61           4 :   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.");
      62           8 :   keys.setValueDescription("scalar","the number of atoms in the cluster");
      63           4 :   keys.needsAction("CLUSTER_WEIGHTS");
      64           4 :   keys.needsAction("SUM");
      65           4 : }
      66             : 
      67           2 : ClusterNatoms::ClusterNatoms(const ActionOptions& ao):
      68             :   Action(ao),
      69           2 :   ActionShortcut(ao) {
      70             :   // Create a cluster weights object
      71           4 :   readInputLine( getShortcutLabel() + "_weights: CLUSTER_WEIGHTS " + convertInputLineToString() );
      72             :   // Add all the weights together (weights are 1 or 0)
      73           4 :   readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_weights PERIODIC=NO");
      74           2 : }
      75             : 
      76             : }
      77             : }