Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2019 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 "LandmarkSelectionBase.h"
      23             : #include "reference/MultiReferenceBase.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace analysis {
      27             : 
      28           1 : LandmarkSelectionOptions::LandmarkSelectionOptions( const std::vector<std::string>& input, AnalysisWithLandmarks* myanalysis ):
      29             :   words(input),
      30           1 :   action(myanalysis)
      31             : {
      32           1 : }
      33             : 
      34           1 : LandmarkSelectionBase::LandmarkSelectionBase( const LandmarkSelectionOptions& lo ):
      35             :   style(lo.words[0]),
      36             :   input(lo.words),
      37           2 :   action(lo.action)
      38             : {
      39             :   input.erase( input.begin() );
      40           1 :   if( style=="ALL" ) {
      41           1 :     novoronoi=true;
      42             :   } else {
      43           0 :     parse("N",nlandmarks);
      44           0 :     parseFlag("NOVORONOI",novoronoi);
      45             :   }
      46           2 :   parseFlag("IGNORE_WEIGHTS",noweights);
      47           1 : }
      48             : 
      49           2 : LandmarkSelectionBase::~LandmarkSelectionBase() {
      50           1 : }
      51             : 
      52           1 : void LandmarkSelectionBase::parseFlag(const std::string& key, bool& t) {
      53           1 :   Tools::parseFlag(input,key,t);
      54           1 : }
      55             : 
      56           1 : void LandmarkSelectionBase::checkRead() const {
      57           1 :   if(!input.empty()) {
      58           0 :     std::string msg="cannot understand the following words from landmark selection input : ";
      59           0 :     for(unsigned i=0; i<input.size(); ++i) msg = msg + input[i] + ", ";
      60           0 :     plumed_merror(msg);
      61             :   }
      62           1 : }
      63             : 
      64           1 : std::string LandmarkSelectionBase::description() {
      65           2 :   std::ostringstream ostr;
      66           2 :   if( style=="ALL") {
      67           1 :     ostr<<"using all data";
      68             :   } else {
      69           0 :     ostr<<"selecting "<<nlandmarks<<" using "<<style<<" algorithm to analyze\n";
      70           0 :     ostr<<"  "<<rest_of_description()<<"\n";
      71           0 :     if(noweights) ostr<<"  ignoring all reweighting of data during landmark selection\n";
      72           0 :     if(novoronoi) ostr<<"  voronoi weights will not be ascribed to points\n";
      73             :   }
      74           1 :   return ostr.str();
      75             : }
      76             : 
      77           0 : double LandmarkSelectionBase::getWeightOfFrame( const unsigned& iframe ) {
      78           0 :   if(noweights) return 1.0;
      79           0 :   return action->getWeight(iframe);
      80             : }
      81           0 : double LandmarkSelectionBase::getDistanceBetweenFrames( const unsigned& iframe, const unsigned& jframe  ) {
      82           0 :   return distance( action->getPbc(), action->getArguments(), action->data[iframe], action->data[jframe], false );
      83             : }
      84             : 
      85         200 : void LandmarkSelectionBase::selectFrame( const unsigned& iframe, MultiReferenceBase* myframes) {
      86         200 :   plumed_assert( myframes->getNumberOfReferenceFrames()<nlandmarks );
      87         400 :   myframes->copyFrame( action->data[iframe] );
      88         200 : }
      89             : 
      90           2 : void LandmarkSelectionBase::selectLandmarks( MultiReferenceBase* myframes ) {
      91             :   // Select landmarks
      92           2 :   myframes->clearFrames(); select( myframes );
      93           0 :   plumed_assert( myframes->getNumberOfReferenceFrames()==nlandmarks );
      94             : 
      95             :   // Now calculate voronoi weights
      96           2 :   if( !novoronoi ) {
      97           0 :     unsigned rank=action->comm.Get_rank();
      98           0 :     unsigned size=action->comm.Get_size();
      99           0 :     std::vector<double> weights( nlandmarks, 0.0 );
     100           0 :     for(unsigned i=rank; i<action->data.size(); i+=size) {
     101             :       unsigned closest=0;
     102           0 :       double mindist=distance( action->getPbc(), action->getArguments(), action->data[i], myframes->getFrame(0), false );
     103           0 :       for(unsigned j=1; j<nlandmarks; ++j) {
     104           0 :         double dist=distance( action->getPbc(), action->getArguments(), action->data[i], myframes->getFrame(j), false );
     105           0 :         if( dist<mindist ) { mindist=dist; closest=j; }
     106             :       }
     107           0 :       weights[closest] += getWeightOfFrame(i);
     108             :     }
     109           0 :     action->comm.Sum( &weights[0], weights.size() );
     110           0 :     myframes->setWeights( weights );
     111             :   }
     112           2 : }
     113             : 
     114             : }
     115        4839 : }
     116             :