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 "ClusteringBase.h"
      23             : #include "core/PlumedMain.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace clusters {
      27             : 
      28          21 : void ClusteringBase::registerKeywords( Keywords& keys ) {
      29          21 :   matrixtools::MatrixOperationBase::registerKeywords( keys ); keys.use("ARG");
      30          21 :   keys.setValueDescription("vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of");
      31          21 : }
      32             : 
      33          17 : ClusteringBase::ClusteringBase(const ActionOptions&ao):
      34             :   Action(ao),
      35             :   matrixtools::MatrixOperationBase(ao),
      36          17 :   number_of_cluster(-1)
      37             : {
      38             :   // Do some checks on the input
      39          17 :   if( getPntrToArgument(0)->getShape()[0]!=getPntrToArgument(0)->getShape()[1] ) error("input matrix should be square");
      40             : 
      41             :   // Now create a value - this holds the data on which cluster each guy is in
      42          17 :   std::vector<unsigned> shape(1); shape[0]=getPntrToArgument(0)->getShape()[0];
      43             :   // Build the store here to make sure that next action has all data
      44          17 :   addValue( shape ); setNotPeriodic(); getPntrToValue()->buildDataStore();
      45             :   // Resize local variables
      46          17 :   which_cluster.resize( getPntrToArgument(0)->getShape()[0] ); cluster_sizes.resize( getPntrToArgument(0)->getShape()[0] );
      47          17 : }
      48             : 
      49          38 : void ClusteringBase::retrieveAdjacencyLists( std::vector<unsigned>& nneigh, Matrix<unsigned>& adj_list ) {
      50             :   // Make sure we have the edges stored
      51             :   std::vector<std::pair<unsigned,unsigned> > pairs; std::vector<double> vals;
      52          38 :   unsigned nedge; getPntrToArgument(0)->retrieveEdgeList( nedge, pairs, vals );
      53             :   // Currently everything has zero neighbors
      54       20912 :   for(unsigned i=0; i<nneigh.size(); ++i) nneigh[i]=0;
      55             :   // Resize the adjacency list if it is needed
      56          38 :   if( adj_list.ncols()!=getPntrToArgument(0)->getNumberOfColumns() ) {
      57          21 :     unsigned nrows = getPntrToArgument(0)->getShape()[0];
      58             :     adj_list.resize( nrows, getPntrToArgument(0)->getNumberOfColumns() );
      59             :   }
      60             : 
      61             :   // And set up the adjacency list
      62       66502 :   for(unsigned i=0; i<nedge; ++i) {
      63             :     // Store if atoms are connected
      64       66464 :     unsigned j=pairs[i].first, k=pairs[i].second;
      65       66464 :     if( j==k ) continue;
      66       66464 :     adj_list(j,nneigh[j])=k; nneigh[j]++;
      67       66464 :     adj_list(k,nneigh[k])=j; nneigh[k]++;
      68             :   }
      69          38 : }
      70             : 
      71          38 : void ClusteringBase::calculate() {
      72             :   // All the clusters have zero size initially
      73       20912 :   for(unsigned i=0; i<cluster_sizes.size(); ++i) { cluster_sizes[i].first=0; cluster_sizes[i].second=i; }
      74             :   // Do the clustering bit
      75          38 :   performClustering();
      76             :   // Order the clusters in the system by size (this returns ascending order )
      77          38 :   std::sort( cluster_sizes.begin(), cluster_sizes.end() );
      78             :   // Set the elements of the value to the cluster identies
      79       20912 :   for(unsigned i=0; i<cluster_sizes.size(); ++i) {
      80       20874 :     double this_size = static_cast<double>(cluster_sizes.size()-i);
      81    21921410 :     for(unsigned j=0; j<cluster_sizes.size(); ++j) {
      82    21900536 :       if( which_cluster[j]==cluster_sizes[i].second ) getPntrToValue()->set( j, this_size );
      83             :     }
      84             :   }
      85          38 : }
      86             : 
      87          38 : void ClusteringBase::apply() {
      88          38 :   if( getPntrToComponent(0)->forcesWereAdded() ) error("forces on clustering actions cannot work as clustering is not differentiable");
      89          38 : }
      90             : 
      91             : }
      92             : }