Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2017 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/ActionWithValue.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : #include "ClusteringBase.h"
      28             : 
      29             : //+PLUMEDOC CONCOMP CLUSTER_WEIGHTS
      30             : /*
      31             : Setup a vector that has one for all the atoms that form part of the cluster of interest and that has zero for all other atoms.
      32             : 
      33             : This method is designed to be used in tandem with the [DFSCLUSTERING](DFSCLUSTERING.md) action.  An example input that uses this action and
      34             : that calculates the average coordination number for the atoms in the largest cluster in the system is shown below.
      35             : 
      36             : ```plumed
      37             : # Calculate a contact matrix between the first 100 atoms in the configuration
      38             : cm: CONTACT_MATRIX GROUP=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
      39             : # Evaluate the coordination numbers of the 100 atoms with themselves
      40             : ones: ONES SIZE=100
      41             : coord: MATRIX_VECTOR_PRODUCT ARG=cm,ones
      42             : # Find the connected components from the contact matrix
      43             : dfs: DFSCLUSTERING ARG=cm
      44             : # Returns a 100-dimensional vector that is 1 if the corresponding atom index is in the largest cluster and is zero otherwise
      45             : c1: CLUSTER_WEIGHTS CLUSTERS=dfs CLUSTER=1
      46             : # Now evaluate the sum of the coordination numbers of the atoms in the larget cluster
      47             : numerv: CUSTOM ARG=c1,coord FUNC=x*y PERIODIC=NO
      48             : numer: SUM ARG=numerv PERIODIC=NO
      49             : # Evaluate the total number of atoms in the largest cluster
      50             : denom: SUM ARG=c1 PERIODIC=NO
      51             : # And finally calculate the average coordination number for the atoms in the largest cluster
      52             : f: CUSTOM ARG=numer,denom FUNC=x/y PERIODIC=NO
      53             : PRINT ARG=f FILE=colvar
      54             : ```
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : namespace PLMD {
      60             : namespace clusters {
      61             : 
      62             : class ClusterWeights :
      63             :   public ActionWithArguments,
      64             :   public ActionWithValue {
      65             : private:
      66             : /// The cluster we are looking for
      67             :   unsigned clustr;
      68             : /// The forces
      69             :   std::vector<double> forcesToApply;
      70             : public:
      71             : /// Create manual
      72             :   static void registerKeywords( Keywords& keys );
      73             : /// Constructor
      74             :   explicit ClusterWeights(const ActionOptions&);
      75             : /// The number of derivatives
      76             :   unsigned getNumberOfDerivatives() override ;
      77             : /// Do the calculation
      78             :   void calculate() override ;
      79             : ///
      80          62 :   void apply() override {}
      81             : };
      82             : 
      83             : PLUMED_REGISTER_ACTION(ClusterWeights,"CLUSTER_WEIGHTS")
      84             : 
      85          69 : void ClusterWeights::registerKeywords( Keywords& keys ) {
      86          69 :   Action::registerKeywords( keys );
      87          69 :   ActionWithArguments::registerKeywords( keys );
      88          69 :   ActionWithValue::registerKeywords( keys );
      89          69 :   keys.remove("NUMERICAL_DERIVATIVES");
      90         138 :   keys.addInputKeyword("compulsory","CLUSTERS","vector","the label of the action that does the clustering");
      91          69 :   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 third largest and so on.");
      92         138 :   keys.addDeprecatedFlag("LOWMEM","");
      93         138 :   keys.setValueDescription("vector","vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise");
      94          69 :   keys.addDOI("https://doi.org/10.1021/acs.jctc.6b01073");
      95          69 : }
      96             : 
      97          34 : ClusterWeights::ClusterWeights(const ActionOptions&ao):
      98             :   Action(ao),
      99             :   ActionWithArguments(ao),
     100          34 :   ActionWithValue(ao) {
     101             :   bool lowmem;
     102          34 :   parseFlag("LOWMEM",lowmem);
     103          34 :   if( lowmem ) {
     104           0 :     warning("LOWMEM flag is deprecated and is no longer required for this action");
     105             :   }
     106             :   // Read in the clustering object
     107          34 :   std::vector<Value*> clusters;
     108          68 :   parseArgumentList("CLUSTERS",clusters);
     109          34 :   if( clusters.size()!=1 ) {
     110           0 :     error("should pass only one matrix to clustering base");
     111             :   }
     112          34 :   ClusteringBase* cc = dynamic_cast<ClusteringBase*>( clusters[0]->getPntrToAction() );
     113          34 :   if( !cc ) {
     114           0 :     error("input to CLUSTERS keyword should be a clustering action");
     115             :   }
     116             :   // Request the arguments
     117          34 :   requestArguments( clusters );
     118             :   // Now create the value
     119          34 :   std::vector<std::size_t> shape(1);
     120          34 :   shape[0]=clusters[0]->getShape()[0];
     121          34 :   addValue( shape );
     122          34 :   setNotPeriodic();
     123             :   // Find out which cluster we want
     124          34 :   parse("CLUSTER",clustr);
     125          34 :   if( clustr<1 ) {
     126           0 :     error("cannot look for a cluster larger than the largest cluster");
     127             :   }
     128          34 :   if( clustr>clusters[0]->getShape()[0] ) {
     129           0 :     error("cluster selected is invalid - too few atoms in system");
     130             :   }
     131          34 :   log.printf("  atoms in %dth largest cluster calculated by %s are equal to one \n",clustr, cc->getLabel().c_str() );
     132          68 : }
     133             : 
     134          24 : unsigned ClusterWeights::getNumberOfDerivatives() {
     135          24 :   return 0;
     136             : }
     137             : 
     138          62 : void ClusterWeights::calculate() {
     139          62 :   plumed_assert( getPntrToArgument(0)->valueHasBeenSet() );
     140       37136 :   for(unsigned i=0; i<getPntrToArgument(0)->getShape()[0]; ++i) {
     141       37074 :     if( fabs(getPntrToArgument(0)->get(i)-clustr)<epsilon ) {
     142       10039 :       getPntrToComponent(0)->set( i, 1.0 );
     143             :     }
     144             :   }
     145          62 : }
     146             : 
     147             : }
     148             : }