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             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace clusters {
      36             : 
      37             : class ClusterNatoms : public ActionShortcut {
      38             : public:
      39             :   static void registerKeywords(Keywords& keys);
      40             :   explicit ClusterNatoms(const ActionOptions&);
      41             : };
      42             : 
      43             : PLUMED_REGISTER_ACTION(ClusterNatoms,"CLUSTER_NATOMS")
      44             : 
      45           4 : void ClusterNatoms::registerKeywords(Keywords& keys) {
      46           4 :   ActionShortcut::registerKeywords( keys );
      47           8 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      48           8 :   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.");
      49           8 :   keys.setValueDescription("scalar","the number of atoms in the cluster");
      50           8 :   keys.needsAction("CLUSTER_WEIGHTS"); keys.needsAction("SUM");
      51           4 : }
      52             : 
      53           2 : ClusterNatoms::ClusterNatoms(const ActionOptions& ao):
      54             :   Action(ao),
      55           2 :   ActionShortcut(ao)
      56             : {
      57             :   // Create a cluster weights object
      58           4 :   readInputLine( getShortcutLabel() + "_weights: CLUSTER_WEIGHTS " + convertInputLineToString() );
      59             :   // Add all the weights together (weights are 1 or 0)
      60           4 :   readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_weights PERIODIC=NO");
      61           2 : }
      62             : 
      63             : }
      64             : }