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 "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        7416 : PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"COLLECT_FRAMES")
      40             : 
      41          31 : void ReadAnalysisFrames::registerKeywords( Keywords& keys ) {
      42          31 :   AnalysisBase::registerKeywords( keys );
      43         124 :   keys.remove("SERIAL"); keys.remove("USE_OUTPUT_DATA_FROM"); keys.use("ARG");
      44         124 :   keys.add("atoms-1","ATOMS","the atoms whose positions we are tracking for the purpose of analyzing the data");
      45         124 :   keys.add("atoms-1","STRIDE","the frequency with which data should be stored for analysis.  By default data is collected on every step");
      46         155 :   keys.add("compulsory","CLEAR","0","the frequency with which data should all be deleted and restarted");
      47         124 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      48          31 : }
      49             : 
      50          30 : ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
      51             :   Action(ao),
      52             :   AnalysisBase(ao),
      53             :   clearonnextstep(false),
      54             :   wham_pointer(NULL),
      55         150 :   weights_calculated(false)
      56             : {
      57          60 :   parse("CLEAR",clearstride);
      58          30 :   if( clearstride!=0 ) log.printf("  clearing stored data every %u steps\n",clearstride);
      59             :   // Get the names of the argumes
      60          30 :   argument_names.resize( getNumberOfArguments() );
      61          98 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) argument_names[i]=getPntrToArgument(i)->getName();
      62             :   // Find the atom numbers to read in
      63          60 :   parseAtomList("ATOMS",atom_numbers);
      64          30 :   if( atom_numbers.size()>0 ) {
      65           5 :     log.printf("  monitoring positions of atoms ");
      66         232 :     for(unsigned i=0; i<atom_numbers.size(); ++i) log.printf("%d ",atom_numbers[i].serial() );
      67           5 :     log.printf("\n"); requestAtoms(atom_numbers);
      68             :   }
      69             : 
      70             :   // Get stuff for any reweighting that should go on
      71          90 :   std::vector<std::string> wwstr; parseVector("LOGWEIGHTS",wwstr);
      72          30 :   if( wwstr.size()>0 ) log.printf("  reweighting using weights from ");
      73          30 :   std::vector<Value*> arg( ActionWithArguments::getArguments() );
      74          96 :   for(unsigned i=0; i<wwstr.size(); ++i) {
      75          24 :     ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      76          12 :     if( !val ) error("could not find value named");
      77          36 :     weight_vals.push_back( val->copyOutput(val->getLabel()) );
      78          36 :     arg.push_back( val->copyOutput(val->getLabel()) );
      79          24 :     log.printf("%s ",wwstr[i].c_str() );
      80             :   }
      81          30 :   if( wwstr.size()>0 ) {
      82          12 :     log.printf("\n");
      83          12 :     wham_pointer = dynamic_cast<bias::ReweightBase*>( weight_vals[0]->getPntrToAction() );
      84          12 :     if( !wham_pointer ) wham_pointer = NULL;
      85          12 :     else if( !wham_pointer->buildsWeightStore() ) wham_pointer = NULL;
      86          24 :     if( wham_pointer && weight_vals.size()!=1 ) error("can only extract weights from one wham object");
      87          18 :   } else log.printf("  weights are all equal to one\n");
      88          30 :   requestArguments( arg );
      89             : 
      90             :   // Now add fake components to the underlying ActionWithValue for the arguments
      91         196 :   for(unsigned i=0; i<argument_names.size(); ++i) { addComponent( argument_names[i] ); componentIsNotPeriodic( argument_names[i] ); }
      92          30 : }
      93             : 
      94          62 : std::vector<Value*> ReadAnalysisFrames::getArgumentList() {
      95          62 :   std::vector<Value*> arg_vals( ActionWithArguments::getArguments() );
      96         142 :   for(unsigned i=0; i<weight_vals.size(); ++i) arg_vals.erase(arg_vals.end()-1);
      97          62 :   return arg_vals;
      98             : }
      99             : 
     100           5 : std::string ReadAnalysisFrames::getDissimilarityInstruction() const {
     101           5 :   return "TYPE=UNKNOWN";
     102             : }
     103             : 
     104          12 : const std::vector<AtomNumber>& ReadAnalysisFrames::getAtomIndexes() const {
     105          12 :   return getAbsoluteIndexes();
     106             : }
     107             : 
     108          26 : void ReadAnalysisFrames::calculateWeights() {
     109          26 :   weights_calculated=true;
     110          52 :   weights.resize( logweights.size() );
     111          26 :   if( weight_vals.empty() ) {
     112        9764 :     for(unsigned i=0; i<logweights.size(); ++i) weights[i]=1.0;
     113             :   } else {
     114           7 :     if( wham_pointer ) {
     115          14 :       wham_pointer->calculateWeights( logweights.size() );
     116        4928 :       for(unsigned i=0; i<logweights.size(); ++i) weights[i]=wham_pointer->getWeight(i);
     117             :     } else {
     118             :       // Find the maximum weight
     119           0 :       double maxweight=logweights[0];
     120           0 :       for(unsigned i=1; i<getNumberOfDataPoints(); ++i) {
     121           0 :         if(logweights[i]>maxweight) maxweight=logweights[i];
     122             :       }
     123             :       // Calculate weights (no memory) -- business here with maxweight is to prevent overflows
     124           0 :       for(unsigned i=0; i<logweights.size(); ++i) weights[i]=exp( logweights[i]-maxweight );
     125             :     }
     126             :   }
     127          26 : }
     128             : 
     129        7500 : void ReadAnalysisFrames::update() {
     130        7528 :   if( getStep()==0 ) return;
     131             :   // Delete everything we stored now that it has been analyzed
     132        7472 :   if( clearonnextstep ) {
     133          10 :     my_data_stash.clear(); my_data_stash.resize(0);
     134          10 :     logweights.clear(); logweights.resize(0);
     135           5 :     if( wham_pointer ) wham_pointer->clearData();
     136           5 :     clearonnextstep=false;
     137             :   }
     138             : 
     139             :   // Get the weight and store it in the weights array
     140       27580 :   double ww=0; for(unsigned i=0; i<weight_vals.size(); ++i) ww+=weight_vals[i]->get();
     141        7472 :   weights_calculated=false; logweights.push_back(ww);
     142             : 
     143             :   // Now create the data collection object and push it back to be stored
     144       14944 :   unsigned index = my_data_stash.size(); my_data_stash.push_back( DataCollectionObject() );
     145       22416 :   my_data_stash[index].setAtomNumbersAndArgumentNames( getLabel(), atom_numbers, argument_names );
     146        7472 :   my_data_stash[index].setAtomPositions( getPositions() );
     147       49372 :   for(unsigned i=0; i<argument_names.size(); ++i) my_data_stash[index].setArgument( argument_names[i], getArgument(i) );
     148             : 
     149        7472 :   if( clearstride>0 ) {
     150         475 :     if( getStep()%clearstride==0 ) clearonnextstep=true;
     151             :   }
     152             : }
     153             : 
     154             : }
     155        5517 : }