Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "ReadAnalysisFrames.h"
      23             : #include "core/PlumedMain.h"
      24             : #include "core/ActionSet.h"
      25             : #include "core/ActionRegister.h"
      26             : 
      27             : //+PLUMEDOC ANALYSIS COLLECT_FRAMES
      28             : /*
      29             : This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object
      30             : 
      31             : \par Examples
      32             : 
      33             : */
      34             : //+ENDPLUMEDOC
      35             : 
      36             : namespace PLMD {
      37             : namespace analysis {
      38             : 
      39       13845 : PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"COLLECT_FRAMES")
      40             : 
      41          34 : void ReadAnalysisFrames::registerKeywords( Keywords& keys ) {
      42          34 :   AnalysisBase::registerKeywords( keys );
      43          34 :   keys.remove("SERIAL");
      44          34 :   keys.remove("USE_OUTPUT_DATA_FROM");
      45          34 :   keys.use("ARG");
      46          68 :   keys.add("atoms-1","ATOMS","the atoms whose positions we are tracking for the purpose of analyzing the data");
      47          68 :   keys.add("atoms-1","STRIDE","the frequency with which data should be stored for analysis.  By default data is collected on every step");
      48          68 :   keys.add("compulsory","CLEAR","0","the frequency with which data should all be deleted and restarted");
      49          68 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      50          34 :   ActionWithValue::useCustomisableComponents( keys );
      51          34 : }
      52             : 
      53          30 : ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
      54             :   Action(ao),
      55             :   AnalysisBase(ao),
      56          30 :   clearonnextstep(false),
      57          30 :   wham_pointer(NULL),
      58          30 :   weights_calculated(false) {
      59          30 :   parse("CLEAR",clearstride);
      60          30 :   if( clearstride!=0 ) {
      61           5 :     log.printf("  clearing stored data every %u steps\n",clearstride);
      62             :   }
      63             :   // Get the names of the argumes
      64          30 :   argument_names.resize( getNumberOfArguments() );
      65          64 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
      66             :     argument_names[i]=getPntrToArgument(i)->getName();
      67             :   }
      68             :   // Find the atom numbers to read in
      69          60 :   parseAtomList("ATOMS",atom_numbers);
      70          30 :   if( atom_numbers.size()>0 ) {
      71           5 :     log.printf("  monitoring positions of atoms ");
      72          79 :     for(unsigned i=0; i<atom_numbers.size(); ++i) {
      73          74 :       log.printf("%d ",atom_numbers[i].serial() );
      74             :     }
      75           5 :     log.printf("\n");
      76           5 :     requestAtoms(atom_numbers);
      77             :   }
      78             : 
      79             :   // Get stuff for any reweighting that should go on
      80             :   std::vector<std::string> wwstr;
      81          60 :   parseVector("LOGWEIGHTS",wwstr);
      82          30 :   if( wwstr.size()>0 ) {
      83          12 :     log.printf("  reweighting using weights from ");
      84             :   }
      85          30 :   std::vector<Value*> arg( ActionWithArguments::getArguments() );
      86          42 :   for(unsigned i=0; i<wwstr.size(); ++i) {
      87          12 :     ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      88          12 :     if( !val ) {
      89           0 :       error("could not find value named");
      90             :     }
      91          12 :     weight_vals.push_back( val->copyOutput(val->getLabel()) );
      92          12 :     arg.push_back( val->copyOutput(val->getLabel()) );
      93          12 :     log.printf("%s ",wwstr[i].c_str() );
      94             :   }
      95          30 :   if( wwstr.size()>0 ) {
      96          12 :     log.printf("\n");
      97          12 :     wham_pointer = dynamic_cast<bias::ReweightBase*>( weight_vals[0]->getPntrToAction() );
      98          12 :     if( !wham_pointer ) {
      99           0 :       wham_pointer = NULL;
     100          12 :     } else if( !wham_pointer->buildsWeightStore() ) {
     101           0 :       wham_pointer = NULL;
     102             :     }
     103          12 :     if( wham_pointer && weight_vals.size()!=1 ) {
     104           0 :       error("can only extract weights from one wham object");
     105             :     }
     106             :   } else {
     107          18 :     log.printf("  weights are all equal to one\n");
     108             :   }
     109          30 :   requestArguments( arg );
     110             : 
     111             :   // Now add fake components to the underlying ActionWithValue for the arguments
     112          64 :   for(unsigned i=0; i<argument_names.size(); ++i) {
     113          34 :     addComponent( argument_names[i] );
     114          34 :     componentIsNotPeriodic( argument_names[i] );
     115             :   }
     116          30 : }
     117             : 
     118          62 : std::vector<Value*> ReadAnalysisFrames::getArgumentList() {
     119          62 :   std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
     120          68 :   for(unsigned i=0; i<weight_vals.size(); ++i) {
     121             :     arg_vals.erase(arg_vals.end()-1);
     122             :   }
     123          62 :   return arg_vals;
     124             : }
     125             : 
     126           5 : std::string ReadAnalysisFrames::getDissimilarityInstruction() const {
     127           5 :   return "TYPE=UNKNOWN";
     128             : }
     129             : 
     130          12 : const std::vector<AtomNumber>& ReadAnalysisFrames::getAtomIndexes() const {
     131          12 :   return getAbsoluteIndexes();
     132             : }
     133             : 
     134          26 : void ReadAnalysisFrames::calculateWeights() {
     135          26 :   weights_calculated=true;
     136          26 :   weights.resize( logweights.size() );
     137          26 :   if( weight_vals.empty() ) {
     138        3261 :     for(unsigned i=0; i<logweights.size(); ++i) {
     139        3242 :       weights[i]=1.0;
     140             :     }
     141             :   } else {
     142           7 :     if( wham_pointer ) {
     143           7 :       wham_pointer->calculateWeights( logweights.size() );
     144        2464 :       for(unsigned i=0; i<logweights.size(); ++i) {
     145        2457 :         weights[i]=wham_pointer->getWeight(i);
     146             :       }
     147             :     } else {
     148             :       // Find the maximum weight
     149           0 :       double maxweight=logweights[0];
     150           0 :       for(unsigned i=1; i<getNumberOfDataPoints(); ++i) {
     151           0 :         if(logweights[i]>maxweight) {
     152             :           maxweight=logweights[i];
     153             :         }
     154             :       }
     155             :       // Calculate weights (no memory) -- business here with maxweight is to prevent overflows
     156           0 :       for(unsigned i=0; i<logweights.size(); ++i) {
     157           0 :         weights[i]=std::exp( logweights[i]-maxweight );
     158             :       }
     159             :     }
     160             :   }
     161          26 : }
     162             : 
     163        7500 : void ReadAnalysisFrames::update() {
     164        7500 :   if( getStep()==0 ) {
     165          28 :     return;
     166             :   }
     167             :   // Delete everything we stored now that it has been analyzed
     168        7472 :   if( clearonnextstep ) {
     169           5 :     my_data_stash.clear();
     170           5 :     my_data_stash.resize(0);
     171           5 :     logweights.clear();
     172           5 :     logweights.resize(0);
     173           5 :     if( wham_pointer ) {
     174           0 :       wham_pointer->clearData();
     175             :     }
     176           5 :     clearonnextstep=false;
     177             :   }
     178             : 
     179             :   // Get the weight and store it in the weights array
     180        7472 :   double ww=0;
     181       11684 :   for(unsigned i=0; i<weight_vals.size(); ++i) {
     182        4212 :     ww+=weight_vals[i]->get();
     183             :   }
     184        7472 :   weights_calculated=false;
     185        7472 :   logweights.push_back(ww);
     186             : 
     187             :   // Now create the data collection object and push it back to be stored
     188             :   unsigned index = my_data_stash.size();
     189        7472 :   my_data_stash.push_back( DataCollectionObject() );
     190        7472 :   my_data_stash[index].setAtomNumbersAndArgumentNames( getLabel(), atom_numbers, argument_names );
     191        7472 :   my_data_stash[index].setAtomPositions( getPositions() );
     192       16079 :   for(unsigned i=0; i<argument_names.size(); ++i) {
     193        8607 :     my_data_stash[index].setArgument( argument_names[i], getArgument(i) );
     194             :   }
     195             : 
     196        7472 :   if( clearstride>0 ) {
     197         475 :     if( getStep()%clearstride==0 ) {
     198           9 :       clearonnextstep=true;
     199             :     }
     200             :   }
     201             : }
     202             : 
     203             : }
     204             : }