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_DIAMETER
      26             : /*
      27             : Print out the diameter of one of the connected components.
      28             : 
      29             : An example input that determines the diameter of 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             : # Returns a 100-dimensional vector that is 1 if the correpsonding atom index is in the largest cluster and is zero otherwise
      38             : clust: CLUSTER_WEIGHTS CLUSTERS=dfs CLUSTER=1
      39             : # And determine the size of the largest cluster that was identified
      40             : c1: CLUSTER_DIAMETER ARG=clust ATOMS=1-100
      41             : PRINT ARG=c1 FILE=colvar
      42             : ```
      43             : 
      44             : The diameter here is defined as the largest of all the distances between the pairs of atom in the cluster
      45             : 
      46             : __The output from this action is NOT differentiable__
      47             : 
      48             : */
      49             : //+ENDPLUMEDOC
      50             : 
      51             : namespace PLMD {
      52             : namespace clusters {
      53             : 
      54             : class ClusterDiameter : public ActionShortcut {
      55             : public:
      56             :   static void registerKeywords(Keywords& keys);
      57             :   explicit ClusterDiameter(const ActionOptions&);
      58             : };
      59             : 
      60             : PLUMED_REGISTER_ACTION(ClusterDiameter,"CLUSTER_DIAMETER")
      61             : 
      62           4 : void ClusterDiameter::registerKeywords( Keywords& keys ) {
      63           4 :   ActionShortcut::registerKeywords( keys );
      64           4 :   keys.add("optional","ARG","calculate ths radius of the cluster that are in this particular cluster");
      65           4 :   keys.add("compulsory","ATOMS","the atoms that were used to calculate the matrix that was clustered");
      66           8 :   keys.setValueDescription("scalar","the largest of all the distances between the pairs of atom in the cluster");
      67           4 :   keys.needsAction("DISTANCE_MATRIX");
      68           4 :   keys.needsAction("OUTER_PRODUCT");
      69           4 :   keys.needsAction("CUSTOM");
      70           4 :   keys.needsAction("FLATTEN");
      71           4 :   keys.needsAction("HIGHEST");
      72           4 :   keys.addDOI("https://doi.org/10.1021/acs.jctc.6b01073");
      73           4 : }
      74             : 
      75           2 : ClusterDiameter::ClusterDiameter(const ActionOptions& ao):
      76             :   Action(ao),
      77           2 :   ActionShortcut(ao) {
      78             :   // Read in the argument
      79             :   std::string arg_str, atdata;
      80           2 :   parse("ARG",arg_str);
      81           2 :   parse("ATOMS",atdata);
      82             :   // Distance matrix
      83           4 :   readInputLine( getShortcutLabel() + "_dmat: DISTANCE_MATRIX GROUP=" + atdata );
      84             :   // Matrix of bonds in cluster
      85           4 :   readInputLine( getShortcutLabel() + "_bmat: OUTER_PRODUCT FUNC=x*y ARG=" + arg_str + "," + arg_str );
      86             :   // Product of matrices
      87           4 :   readInputLine( getShortcutLabel() + "_dcls: CUSTOM ARG=" + getShortcutLabel() + "_dmat," + getShortcutLabel() + "_bmat FUNC=x*y PERIODIC=NO");
      88             :   // Convert matrix to a vector to get highest
      89           4 :   readInputLine( getShortcutLabel() + "_vdcls: FLATTEN ARG=" + getShortcutLabel() + "_dcls" );
      90             :   // And take the highest value
      91           4 :   readInputLine( getShortcutLabel() + ": HIGHEST ARG=" + getShortcutLabel() + "_vdcls");
      92           2 : }
      93             : 
      94             : }
      95             : }