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       10479 : PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"COLLECT_FRAMES")
      40             : 
      41          31 : void ReadAnalysisFrames::registerKeywords( Keywords& keys ) {
      42          31 :   AnalysisBase::registerKeywords( keys );
      43          93 :   keys.remove("SERIAL"); keys.remove("USE_OUTPUT_DATA_FROM"); keys.use("ARG");
      44          62 :   keys.add("atoms-1","ATOMS","the atoms whose positions we are tracking for the purpose of analyzing the data");
      45          62 :   keys.add("atoms-1","STRIDE","the frequency with which data should be stored for analysis.  By default data is collected on every step");
      46          62 :   keys.add("compulsory","CLEAR","0","the frequency with which data should all be deleted and restarted");
      47          62 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      48          31 :   ActionWithValue::useCustomisableComponents( keys );
      49          31 : }
      50             : 
      51          30 : ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
      52             :   Action(ao),
      53             :   AnalysisBase(ao),
      54          30 :   clearonnextstep(false),
      55          30 :   wham_pointer(NULL),
      56          30 :   weights_calculated(false)
      57             : {
      58          30 :   parse("CLEAR",clearstride);
      59          30 :   if( clearstride!=0 ) log.printf("  clearing stored data every %u steps\n",clearstride);
      60             :   // Get the names of the argumes
      61          30 :   argument_names.resize( getNumberOfArguments() );
      62          64 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) argument_names[i]=getPntrToArgument(i)->getName();
      63             :   // Find the atom numbers to read in
      64          60 :   parseAtomList("ATOMS",atom_numbers);
      65          30 :   if( atom_numbers.size()>0 ) {
      66           5 :     log.printf("  monitoring positions of atoms ");
      67          79 :     for(unsigned i=0; i<atom_numbers.size(); ++i) log.printf("%d ",atom_numbers[i].serial() );
      68           5 :     log.printf("\n"); requestAtoms(atom_numbers);
      69             :   }
      70             : 
      71             :   // Get stuff for any reweighting that should go on
      72          60 :   std::vector<std::string> wwstr; parseVector("LOGWEIGHTS",wwstr);
      73          30 :   if( wwstr.size()>0 ) log.printf("  reweighting using weights from ");
      74          30 :   std::vector<Value*> arg( ActionWithArguments::getArguments() );
      75          42 :   for(unsigned i=0; i<wwstr.size(); ++i) {
      76          12 :     ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      77          12 :     if( !val ) error("could not find value named");
      78          12 :     weight_vals.push_back( val->copyOutput(val->getLabel()) );
      79          12 :     arg.push_back( val->copyOutput(val->getLabel()) );
      80          12 :     log.printf("%s ",wwstr[i].c_str() );
      81             :   }
      82          30 :   if( wwstr.size()>0 ) {
      83          12 :     log.printf("\n");
      84          12 :     wham_pointer = dynamic_cast<bias::ReweightBase*>( weight_vals[0]->getPntrToAction() );
      85          12 :     if( !wham_pointer ) wham_pointer = NULL;
      86          12 :     else if( !wham_pointer->buildsWeightStore() ) wham_pointer = NULL;
      87          12 :     if( wham_pointer && weight_vals.size()!=1 ) error("can only extract weights from one wham object");
      88          18 :   } else log.printf("  weights are all equal to one\n");
      89          30 :   requestArguments( arg );
      90             : 
      91             :   // Now add fake components to the underlying ActionWithValue for the arguments
      92          64 :   for(unsigned i=0; i<argument_names.size(); ++i) { addComponent( argument_names[i] ); componentIsNotPeriodic( argument_names[i] ); }
      93          30 : }
      94             : 
      95          62 : std::vector<Value*> ReadAnalysisFrames::getArgumentList() {
      96          62 :   std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
      97          68 :   for(unsigned i=0; i<weight_vals.size(); ++i) arg_vals.erase(arg_vals.end()-1);
      98          62 :   return arg_vals;
      99             : }
     100             : 
     101           5 : std::string ReadAnalysisFrames::getDissimilarityInstruction() const {
     102           5 :   return "TYPE=UNKNOWN";
     103             : }
     104             : 
     105          12 : const std::vector<AtomNumber>& ReadAnalysisFrames::getAtomIndexes() const {
     106          12 :   return getAbsoluteIndexes();
     107             : }
     108             : 
     109          26 : void ReadAnalysisFrames::calculateWeights() {
     110          26 :   weights_calculated=true;
     111          26 :   weights.resize( logweights.size() );
     112          26 :   if( weight_vals.empty() ) {
     113        3261 :     for(unsigned i=0; i<logweights.size(); ++i) weights[i]=1.0;
     114             :   } else {
     115           7 :     if( wham_pointer ) {
     116           7 :       wham_pointer->calculateWeights( logweights.size() );
     117        2464 :       for(unsigned i=0; i<logweights.size(); ++i) weights[i]=wham_pointer->getWeight(i);
     118             :     } else {
     119             :       // Find the maximum weight
     120           0 :       double maxweight=logweights[0];
     121           0 :       for(unsigned i=1; i<getNumberOfDataPoints(); ++i) {
     122           0 :         if(logweights[i]>maxweight) maxweight=logweights[i];
     123             :       }
     124             :       // Calculate weights (no memory) -- business here with maxweight is to prevent overflows
     125           0 :       for(unsigned i=0; i<logweights.size(); ++i) weights[i]=std::exp( logweights[i]-maxweight );
     126             :     }
     127             :   }
     128          26 : }
     129             : 
     130        7500 : void ReadAnalysisFrames::update() {
     131        7500 :   if( getStep()==0 ) return;
     132             :   // Delete everything we stored now that it has been analyzed
     133        7472 :   if( clearonnextstep ) {
     134           5 :     my_data_stash.clear(); my_data_stash.resize(0);
     135          10 :     logweights.clear(); logweights.resize(0);
     136           5 :     if( wham_pointer ) wham_pointer->clearData();
     137           5 :     clearonnextstep=false;
     138             :   }
     139             : 
     140             :   // Get the weight and store it in the weights array
     141       11684 :   double ww=0; for(unsigned i=0; i<weight_vals.size(); ++i) ww+=weight_vals[i]->get();
     142        7472 :   weights_calculated=false; logweights.push_back(ww);
     143             : 
     144             :   // Now create the data collection object and push it back to be stored
     145        7472 :   unsigned index = my_data_stash.size(); my_data_stash.push_back( DataCollectionObject() );
     146        7472 :   my_data_stash[index].setAtomNumbersAndArgumentNames( getLabel(), atom_numbers, argument_names );
     147        7472 :   my_data_stash[index].setAtomPositions( getPositions() );
     148       16079 :   for(unsigned i=0; i<argument_names.size(); ++i) my_data_stash[index].setArgument( argument_names[i], getArgument(i) );
     149             : 
     150        7472 :   if( clearstride>0 ) {
     151         475 :     if( getStep()%clearstride==0 ) clearonnextstep=true;
     152             :   }
     153             : }
     154             : 
     155             : }
     156             : }