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             : \par Examples
      34             : 
      35             : 
      36             : */
      37             : //+ENDPLUMEDOC
      38             : 
      39             : namespace PLMD {
      40             : namespace clusters {
      41             : 
      42             : class ClusterWeights :
      43             :   public ActionWithArguments,
      44             :   public ActionWithValue {
      45             : private:
      46             : /// The cluster we are looking for
      47             :   unsigned clustr;
      48             : /// The forces
      49             :   std::vector<double> forcesToApply;
      50             : public:
      51             : /// Create manual
      52             :   static void registerKeywords( Keywords& keys );
      53             : /// Constructor
      54             :   explicit ClusterWeights(const ActionOptions&);
      55             : /// The number of derivatives
      56             :   unsigned getNumberOfDerivatives() override ;
      57             : /// Do the calculation
      58             :   void calculate() override ;
      59             : ///
      60          51 :   void apply() override {}
      61             : };
      62             : 
      63             : PLUMED_REGISTER_ACTION(ClusterWeights,"CLUSTER_WEIGHTS")
      64             : 
      65          57 : void ClusterWeights::registerKeywords( Keywords& keys ) {
      66          57 :   Action::registerKeywords( keys );
      67          57 :   ActionWithArguments::registerKeywords( keys ); keys.remove("ARG");
      68          57 :   ActionWithValue::registerKeywords( keys ); keys.remove("NUMERICAL_DERIVATIVES");
      69         114 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
      70         114 :   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.");
      71         114 :   keys.addFlag("LOWMEM",false,"this flag does nothing and is present only to ensure back-compatibility");
      72             :   // keys.add("hidden","FROM_PROPERTIES","indicates that this is created from CLUSTER_PROPERTIES shortcut");
      73          57 :   keys.setValueDescription("vector with elements that are one if the atom of interest is part of the required cluster and zero otherwise");
      74          57 : }
      75             : 
      76          29 : ClusterWeights::ClusterWeights(const ActionOptions&ao):
      77             :   Action(ao),
      78             :   ActionWithArguments(ao),
      79          29 :   ActionWithValue(ao)
      80             : {
      81          29 :   bool lowmem; parseFlag("LOWMEM",lowmem);
      82          29 :   if( lowmem ) warning("LOWMEM flag is deprecated and is no longer required for this action");
      83             :   // Read in the clustering object
      84          58 :   std::vector<Value*> clusters; parseArgumentList("CLUSTERS",clusters);
      85          29 :   if( clusters.size()!=1 ) error("should pass only one matrix to clustering base");
      86          29 :   ClusteringBase* cc = dynamic_cast<ClusteringBase*>( clusters[0]->getPntrToAction() );
      87          29 :   if( !cc ) error("input to CLUSTERS keyword should be a clustering action");
      88             :   // Request the arguments
      89          29 :   requestArguments( clusters );
      90             :   // Now create the value
      91          29 :   std::vector<unsigned> shape(1); shape[0]=clusters[0]->getShape()[0];
      92          29 :   addValue( shape ); setNotPeriodic(); getPntrToComponent(0)->buildDataStore();
      93             :   // Find out which cluster we want
      94          29 :   parse("CLUSTER",clustr);
      95          29 :   if( clustr<1 ) error("cannot look for a cluster larger than the largest cluster");
      96          29 :   if( clustr>clusters[0]->getShape()[0] ) error("cluster selected is invalid - too few atoms in system");
      97          29 :   log.printf("  atoms in %dth largest cluster calculated by %s are equal to one \n",clustr, cc->getLabel().c_str() );
      98          29 : }
      99             : 
     100          24 : unsigned ClusterWeights::getNumberOfDerivatives() {
     101          24 :   return 0;
     102             : }
     103             : 
     104          51 : void ClusterWeights::calculate() {
     105          51 :   plumed_assert( getPntrToArgument(0)->valueHasBeenSet() );
     106       36627 :   for(unsigned i=0; i<getPntrToArgument(0)->getShape()[0]; ++i) {
     107       36576 :     if( fabs(getPntrToArgument(0)->get(i)-clustr)<epsilon ) getPntrToComponent(0)->set( i, 1.0 );
     108             :   }
     109          51 : }
     110             : 
     111             : }
     112             : }