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_WITHSURFACE
      26             : /*
      27             : Determine the atoms that are within a certain cutoff of the atoms in a cluster.
      28             : 
      29             : This shortcut action can be used to identify the atoms within the largest connected cluster in a system as well
      30             : as the atoms around the cluster as shown in the example input below:
      31             : 
      32             : ```plumed
      33             : # Calculate a matrix with elements that are non zero if the corresponding atoms are within 0.38 of each other
      34             : cmat: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
      35             : # Calculate the coordination numbers of all the atoms
      36             : ones: ONES SIZE=1996
      37             : c1: MATRIX_VECTOR_PRODUCT ARG=cmat,ones
      38             : # Now identify those atoms that have a coordination number that is less than 13.5
      39             : cf: LESS_THAN ARG=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
      40             : 
      41             : # Now construct an adjacency matrix with elements that are equal to one if atoms are within 0.38 of each other
      42             : # and if they both have a coordination number that is less than 13.5
      43             : cmat2: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
      44             : dmat: OUTER_PRODUCT ARG=cf,cf
      45             : mat: CUSTOM ARG=cmat2,dmat FUNC=x*y PERIODIC=NO
      46             : # Find the connected componets of this matrix
      47             : dfs: DFSCLUSTERING ARG=mat
      48             : 
      49             : # Now identify the atoms that are within the largest cluster and the atoms that are within 0.38 nm of the
      50             : # atoms that are within this cluster.  Determine how many atoms in total satisfy this condition and the
      51             : # distance betwen the two atoms in this set that are farthest appart.
      52             : clust2a: CLUSTER_WITHSURFACE ATOMS=1-1996 CLUSTERS=dfs CLUSTER=1 RCUT_SURF={CUBIC D_0=0.34 D_MAX=0.38}
      53             : size2a: SUM ARG=clust2a PERIODIC=NO
      54             : dia2a: CLUSTER_DIAMETER ATOMS=1-1996 ARG=clust2a
      55             : PRINT ARG=size2a,dia2a
      56             : ```
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : namespace PLMD {
      62             : namespace clusters {
      63             : 
      64             : class ClusterWithSurface : public ActionShortcut {
      65             : public:
      66             :   static void registerKeywords(Keywords& keys);
      67             :   explicit ClusterWithSurface(const ActionOptions&);
      68             : };
      69             : 
      70             : PLUMED_REGISTER_ACTION(ClusterWithSurface,"CLUSTER_WITHSURFACE")
      71             : 
      72           4 : void ClusterWithSurface::registerKeywords(Keywords& keys) {
      73           4 :   ActionShortcut::registerKeywords(keys);
      74           4 :   keys.add("optional","RCUT_SURF","the cutoff to use for determining which atoms are connected to the surface of the cluster");
      75           4 :   keys.add("compulsory","ATOMS","the atoms that were used to calculate the matrix that was clustered");
      76           4 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      77           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.");
      78           8 :   keys.setValueDescription("vector","a vector that is one for those atoms that are within the cluster or that are within a cetain cutoff of one of the atoms in the cluster and zero otherwise");
      79           4 :   keys.needsAction("CLUSTER_WEIGHTS");
      80           4 :   keys.needsAction("CONTACT_MATRIX");
      81           4 :   keys.needsAction("OUTER_PRODUCT");
      82           4 :   keys.needsAction("CUSTOM");
      83           4 :   keys.needsAction("DFSCLUSTERING");
      84           4 :   keys.addDOI("https://doi.org/10.1021/acs.jctc.6b01073");
      85           4 : }
      86             : 
      87           2 : ClusterWithSurface::ClusterWithSurface(const ActionOptions& ao):
      88             :   Action(ao),
      89           2 :   ActionShortcut(ao) {
      90             :   // Read atoms for contact matrix
      91             :   std::string atdata;
      92           4 :   parse("ATOMS",atdata);
      93             :   // Read rcut input
      94             :   std::string rcut_surf_str;
      95           2 :   parse("RCUT_SURF",rcut_surf_str);
      96             :   // Create a cluster weights object
      97           4 :   readInputLine( getShortcutLabel() + "_wnosurf: CLUSTER_WEIGHTS " + convertInputLineToString() );
      98             :   // Now create a contact matrix
      99           4 :   readInputLine( getShortcutLabel() + "_cmat: CONTACT_MATRIX GROUP=" + atdata + " SWITCH={" + rcut_surf_str +"}" );
     100             :   // Now create a custom matrix
     101           4 :   readInputLine( getShortcutLabel() + "_cwmat: OUTER_PRODUCT ARG=" + getShortcutLabel() + "_wnosurf," + getShortcutLabel() + "_wnosurf FUNC=max");
     102             :   // Product of matrices
     103           4 :   readInputLine( getShortcutLabel() + "_pmat: CUSTOM ARG=" + getShortcutLabel() + "_cmat," + getShortcutLabel() + "_cwmat FUNC=x*y PERIODIC=NO");
     104             :   // DFS clustering
     105           4 :   readInputLine( getShortcutLabel() + "_clust: DFSCLUSTERING ARG=" + getShortcutLabel() + "_pmat");
     106             :   // And final cluster weights
     107           4 :   readInputLine( getShortcutLabel() + ": CLUSTER_WEIGHTS CLUSTERS=" + getShortcutLabel() + "_clust CLUSTER=1");
     108           2 : }
     109             : 
     110             : }
     111             : }