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/ActionWithValue.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "core/ActionShortcut.h"
      26             : #include "core/PlumedMain.h"
      27             : #include "multicolvar/MultiColvarShortcuts.h"
      28             : #include "ClusteringBase.h"
      29             : 
      30             : //+PLUMEDOC CONCOMP CLUSTER_DISTRIBUTION
      31             : /*
      32             : Calculate functions of the distribution of properties in your connected components.
      33             : 
      34             : __This shortcut action is present to ensure that inputs for older PLUMED versions remain compatible.  We STRONGLY
      35             : encourage you to use the newer (and simpler) syntax for clustering calculations__  Look at the documentation for
      36             : [CLUSTER_WEIGHTS](CLUSTER_WEIGHTS.md) and the expanded version of the input below to see how this new input syntax operates.
      37             : 
      38             : The input provided below calculates the local q6 Steinhardt parameter on each atom.  The coordination number
      39             : that atoms with a high value for the local q6 Steinhardt parameter have with other atoms that have a high
      40             : value for the local q6 Steinhardt parameter is then computed.  A contact matrix is then computed that measures
      41             : whether atoms atoms $i$ and $j$ have a high value for this coordination number and if they are within
      42             : 3.6 nm of each other.  The connected components of this matrix are then found using a depth first clustering
      43             : algorithm on the corresponding graph. The number of components in this graph that contain more than 27 atoms is then computed.
      44             : An input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous GeTe in the paper cited below
      45             : 
      46             : ```plumed
      47             : q6: Q6 SPECIES=1-300 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
      48             : lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
      49             : flq6: MORE_THAN ARG=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
      50             : cc: COORDINATIONNUMBER SPECIES=1-300 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
      51             : fcc: MORE_THAN ARG=cc SWITCH={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}
      52             : mat: CONTACT_MATRIX GROUP=1-300 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
      53             : dfs: DFSCLUSTERING ARG=mat
      54             : nclust: CLUSTER_DISTRIBUTION ...
      55             :    CLUSTERS=dfs WEIGHTS=fcc
      56             :    MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
      57             : ...
      58             : PRINT ARG=nclust.* FILE=colvar
      59             : ```
      60             : 
      61             : */
      62             : //+ENDPLUMEDOC
      63             : 
      64             : //+PLUMEDOC CONCOMP CLUSTER_DISTRIBUTION_CALC
      65             : /*
      66             : Calculate functions of the distribution of properties in your connected components.
      67             : 
      68             : See \ref CLUSTER_DISTRIBUTION
      69             : 
      70             : \par Examples
      71             : 
      72             : */
      73             : //+ENDPLUMEDOC
      74             : 
      75             : 
      76             : namespace PLMD {
      77             : namespace clusters {
      78             : 
      79             : class ClusterDistribution :
      80             :   public ActionWithArguments,
      81             :   public ActionWithValue {
      82             : public:
      83             : /// Create manual
      84             :   static void registerKeywords( Keywords& keys );
      85             : /// Constructor
      86             :   explicit ClusterDistribution(const ActionOptions&);
      87             : /// The number of derivatives
      88             :   unsigned getNumberOfDerivatives() override ;
      89             : /// Do the calculation
      90             :   void calculate() override;
      91             : /// We can use ActionWithVessel to run all the calculation
      92           2 :   void apply() override {}
      93             : };
      94             : 
      95             : PLUMED_REGISTER_ACTION(ClusterDistribution,"CLUSTER_DISTRIBUTION_CALC")
      96             : 
      97           6 : void ClusterDistribution::registerKeywords( Keywords& keys ) {
      98           6 :   Action::registerKeywords( keys );
      99           6 :   ActionWithArguments::registerKeywords( keys );
     100           6 :   ActionWithValue::registerKeywords( keys );
     101           6 :   keys.remove("NUMERICAL_DERIVATIVES");
     102          12 :   keys.addInputKeyword("compulsory","CLUSTERS","vector","the label of the action that does the clustering");
     103           6 :   keys.setDisplayName("CLUSTER_DISTRIBUTION");
     104          12 :   keys.addInputKeyword("optional","WEIGHTS","vector","use the vector of values calculated by this action as weights rather than giving each atom a unit weight");
     105          12 :   keys.setValueDescription("vector","a vector containing the sum of a atomic-cv that is calculated for each of the identified clusters");
     106           6 :   keys.addDOI("https://doi.org/10.1021/acs.jctc.6b01073");
     107           6 : }
     108             : 
     109           2 : ClusterDistribution::ClusterDistribution(const ActionOptions&ao):
     110             :   Action(ao),
     111             :   ActionWithArguments(ao),
     112           2 :   ActionWithValue(ao) {
     113             :   // Read in the clustering object
     114             :   std::vector<Value*> clusters;
     115           4 :   parseArgumentList("CLUSTERS",clusters);
     116           2 :   if( clusters.size()!=1 ) {
     117           0 :     error("should pass only one matrix to clustering base");
     118             :   }
     119           2 :   ClusteringBase* cc = dynamic_cast<ClusteringBase*>( clusters[0]->getPntrToAction() );
     120           2 :   if( !cc ) {
     121           0 :     error("input to CLUSTERS keyword should be a clustering action");
     122             :   }
     123             :   std::vector<Value*> weights;
     124           4 :   parseArgumentList("WEIGHTS",weights);
     125           2 :   if( weights.size()==0 ) {
     126           1 :     log.printf("  using unit weights in cluster distribution \n");
     127           1 :   } else if( weights.size()==1 ) {
     128           1 :     if( weights[0]->getRank()!=1 ) {
     129           0 :       error("input weights has wrong shape");
     130             :     }
     131           1 :     if( weights[0]->getShape()[0]!=clusters[0]->getShape()[0] ) {
     132           0 :       error("mismatch between number of weights and number of atoms");
     133             :     }
     134           1 :     log.printf("  using weights from action with label %s in cluster distribution \n", weights[0]->getName().c_str() );
     135           1 :     clusters.push_back( weights[0] );
     136             :   } else {
     137           0 :     error("should have only one argument for weights \n");
     138             :   }
     139             :   // Request the arguments
     140           2 :   requestArguments( clusters );
     141           2 :   getPntrToArgument(0)->buildDataStore();
     142           2 :   if( getNumberOfArguments()>1 ) {
     143           1 :     getPntrToArgument(1)->buildDataStore();
     144             :   }
     145             :   // Now create the value
     146           2 :   std::vector<unsigned> shape(1);
     147           2 :   shape[0]=clusters[0]->getShape()[0];
     148           2 :   addValue( shape );
     149           2 :   setNotPeriodic();
     150           2 :   getPntrToValue()->buildDataStore();
     151           2 : }
     152             : 
     153           0 : unsigned ClusterDistribution::getNumberOfDerivatives() {
     154           0 :   return 0;
     155             : }
     156             : 
     157           2 : void ClusterDistribution::calculate() {
     158           2 :   plumed_assert( getPntrToArgument(0)->valueHasBeenSet() );
     159           2 :   if( getNumberOfArguments()>1 ) {
     160           1 :     plumed_assert( getPntrToArgument(1)->valueHasBeenSet() );
     161             :   }
     162           2 :   double csize = getPntrToArgument(0)->get(0);
     163          12 :   for(unsigned i=1; i<getPntrToArgument(0)->getShape()[0]; ++i) {
     164          10 :     if( getPntrToArgument(0)->get(i)>csize ) {
     165           4 :       csize = getPntrToArgument(0)->get(i);
     166             :     }
     167             :   }
     168           2 :   unsigned ntasks = static_cast<unsigned>( csize );
     169           8 :   for(unsigned i=0; i<ntasks; ++i) {
     170          42 :     for(unsigned j=0; j<getPntrToArgument(0)->getShape()[0]; ++j) {
     171          36 :       if( fabs(getPntrToArgument(0)->get(j)-i)<epsilon ) {
     172          10 :         if( getNumberOfArguments()==2 ) {
     173           5 :           getPntrToValue()->add( i, getPntrToArgument(1)->get(j) );
     174             :         } else {
     175           5 :           getPntrToValue()->add( i, 1.0 );
     176             :         }
     177             :       }
     178             :     }
     179             :   }
     180           2 : }
     181             : 
     182             : class ClusterDistributionShortcut : public ActionShortcut {
     183             : public:
     184             :   static void registerKeywords( Keywords& keys );
     185             :   ClusterDistributionShortcut(const ActionOptions&);
     186             : };
     187             : 
     188             : PLUMED_REGISTER_ACTION(ClusterDistributionShortcut,"CLUSTER_DISTRIBUTION")
     189             : 
     190           6 : void ClusterDistributionShortcut::registerKeywords( Keywords& keys ) {
     191           6 :   ActionShortcut::registerKeywords( keys );
     192           6 :   keys.add("compulsory","CLUSTERS","the label of the action that does the clustering");
     193           6 :   keys.add("optional","WEIGHTS","use the vector of values calculated by this action as weights rather than giving each atom a unit weight");
     194           6 :   multicolvar::MultiColvarShortcuts::shortcutKeywords( keys );
     195           6 :   keys.addActionNameSuffix("_CALC");
     196           6 : }
     197             : 
     198           2 : ClusterDistributionShortcut::ClusterDistributionShortcut(const ActionOptions&ao):
     199             :   Action(ao),
     200           2 :   ActionShortcut(ao) {
     201             :   std::map<std::string,std::string> keymap;
     202           2 :   multicolvar::MultiColvarShortcuts::readShortcutKeywords( keymap, this );
     203           4 :   readInputLine( getShortcutLabel() + ": CLUSTER_DISTRIBUTION_CALC " + convertInputLineToString() );
     204           4 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(),  getShortcutLabel(),  "", keymap, this );
     205           2 : }
     206             : 
     207             : }
     208             : }