Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2019 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 "ActionWithAveraging.h"
      23             : #include "analysis/DataCollectionObject.h"
      24             : #include "analysis/ReadAnalysisFrames.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : #include "bias/ReweightBase.h"
      28             : 
      29             : namespace PLMD {
      30             : namespace vesselbase {
      31             : 
      32          74 : void ActionWithAveraging::registerKeywords( Keywords& keys ) {
      33          74 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );
      34          74 :   ActionWithArguments::registerKeywords( keys ); ActionWithValue::registerKeywords( keys ); ActionWithVessel::registerKeywords( keys );
      35         370 :   keys.add("compulsory","STRIDE","1","the frequency with which the data should be collected and added to the quantity being averaged");
      36             :   keys.add("compulsory","CLEAR","0","the frequency with which to clear all the accumulated data.  The default value "
      37         370 :            "of 0 implies that all the data will be used and that the grid will never be cleared");
      38         296 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      39         370 :   keys.add("compulsory","NORMALIZATION","true","This controls how the data is normalized it can be set equal to true, false or ndata.  The differences between these options are explained in the manual page for \\ref HISTOGRAM");
      40         148 :   keys.remove("NUMERICAL_DERIVATIVES");
      41          74 : }
      42             : 
      43          64 : ActionWithAveraging::ActionWithAveraging( const ActionOptions& ao ):
      44             :   Action(ao),
      45             :   ActionPilot(ao),
      46             :   ActionAtomistic(ao),
      47             :   ActionWithArguments(ao),
      48             :   ActionWithValue(ao),
      49             :   ActionWithVessel(ao),
      50             :   myaverage(NULL),
      51             :   activated(false),
      52             :   my_analysis_object(NULL),
      53             :   normalization(t),
      54             :   useRunAllTasks(false),
      55             :   clearstride(0),
      56         128 :   lweight(0),cweight(0)
      57             : {
      58         128 :   if( keywords.exists("CLEAR") ) {
      59         106 :     parse("CLEAR",clearstride);
      60          53 :     if( clearstride>0 ) {
      61          12 :       if( clearstride%getStride()!=0 ) error("CLEAR parameter must be a multiple of STRIDE");
      62          12 :       log.printf("  clearing grid every %u steps \n",clearstride);
      63             :     }
      64             :   }
      65          64 :   if( getNumberOfArguments()>0 ) {
      66          26 :     my_analysis_object=dynamic_cast<analysis::AnalysisBase*>( getPntrToArgument(0)->getPntrToAction() );
      67          68 :     for(unsigned i=1; i<getNumberOfArguments(); i++) {
      68           8 :       if( my_analysis_object && my_analysis_object->getLabel()!=(getPntrToArgument(i)->getPntrToAction())->getLabel() ) {
      69           0 :         error("all arguments should be from one single analysis object");
      70             :       }
      71             :     }
      72          26 :     if( my_analysis_object ) {
      73           7 :       if( getStride()!=1 ) error("stride should not have been set when calculating average from analysis data");
      74           7 :       setStride(0); addDependency( my_analysis_object );
      75             :     }
      76             :   }
      77         128 :   if( keywords.exists("LOGWEIGHTS") ) {
      78         106 :     std::vector<std::string> wwstr; parseVector("LOGWEIGHTS",wwstr);
      79          53 :     if( wwstr.size()>0 ) log.printf("  reweighting using weights from ");
      80          53 :     std::vector<Value*> arg( getArguments() );
      81          67 :     for(unsigned i=0; i<wwstr.size(); ++i) {
      82          14 :       ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      83           7 :       if( !val ) error("could not find value named");
      84           7 :       bias::ReweightBase* iswham=dynamic_cast<bias::ReweightBase*>( val );
      85           7 :       if( iswham->buildsWeightStore() ) error("to use wham you must gather data using COLLECT_FRAMES");
      86          14 :       weights.push_back( val->copyOutput(val->getLabel()) );
      87          14 :       arg.push_back( val->copyOutput(val->getLabel()) );
      88           7 :       log.printf("%s ",wwstr[i].c_str() );
      89             :     }
      90          53 :     if( wwstr.size()>0 ) log.printf("\n");
      91          47 :     else log.printf("  weights are all equal to one\n");
      92         106 :     requestArguments( arg );
      93             :   }
      94         128 :   if( keywords.exists("NORMALIZATION") ) {
      95         106 :     std::string normstr; parse("NORMALIZATION",normstr);
      96          53 :     if( normstr=="true" ) normalization=t;
      97          31 :     else if( normstr=="false" ) normalization=f;
      98          22 :     else if( normstr=="ndata" ) normalization=ndata;
      99           0 :     else error("invalid instruction for NORMALIZATION flag should be true, false, or ndata");
     100             :   }
     101          64 : }
     102             : 
     103          59 : bool ActionWithAveraging::ignoreNormalization() const {
     104          59 :   if( normalization==f ) return true;
     105          50 :   return false;
     106             : }
     107             : 
     108          59 : void ActionWithAveraging::setAveragingAction( std::unique_ptr<AveragingVessel> av_vessel, const bool& usetasks ) {
     109          59 :   myaverage=av_vessel.get();
     110         118 :   addVessel( std::move(av_vessel) );
     111          59 :   useRunAllTasks=usetasks; resizeFunctions();
     112          59 : }
     113             : 
     114        1185 : void ActionWithAveraging::lockRequests() {
     115             :   ActionAtomistic::lockRequests();
     116             :   ActionWithArguments::lockRequests();
     117        1185 : }
     118             : 
     119        1185 : void ActionWithAveraging::unlockRequests() {
     120             :   ActionAtomistic::unlockRequests();
     121             :   ActionWithArguments::unlockRequests();
     122        1185 : }
     123             : 
     124         206 : unsigned ActionWithAveraging::getNumberOfQuantities() const {
     125         206 :   if( my_analysis_object ) return getNumberOfArguments()+2;
     126             :   return 2;
     127             : }
     128             : 
     129           0 : void ActionWithAveraging::calculateNumericalDerivatives(PLMD::ActionWithValue*) {
     130           0 :   error("not possible to compute numerical derivatives for this action");
     131           0 : }
     132             : 
     133        1199 : void ActionWithAveraging::update() {
     134        1199 :   if( (clearstride!=1 && getStep()==0) || (!onStep() && !my_analysis_object) ) return;
     135        1123 :   if( my_analysis_object ) {
     136           7 :     analysis::ReadAnalysisFrames* myfram = dynamic_cast<analysis::ReadAnalysisFrames*>( my_analysis_object );
     137           7 :     if( !activated && !myfram && !onStep() ) return ;
     138           7 :     else if( !activated && !my_analysis_object->onStep() ) return ;
     139             :   }
     140             : 
     141             :   // Clear if it is time to reset
     142        1123 :   if( myaverage ) {
     143        1122 :     if( myaverage->wasreset() ) clearAverage();
     144             :   }
     145             :   // Calculate the weight for all reweighting
     146        1123 :   if ( weights.size()>0 && !my_analysis_object ) {
     147        7028 :     double sum=0; for(unsigned i=0; i<weights.size(); ++i) sum+=weights[i]->get();
     148        1007 :     lweight=sum; cweight = exp( sum );
     149             :   } else {
     150         116 :     lweight=0; cweight=1.0;
     151             :   }
     152             :   // Prepare the task list for averaging
     153        1123 :   if( my_analysis_object ) {
     154           7 :     for(unsigned i=getFullNumberOfTasks(); i<my_analysis_object->getNumberOfDataPoints(); ++i) addTaskToList(i);
     155           7 :     deactivateAllTasks(); cweight=0;
     156        2115 :     for(unsigned i=0; i<my_analysis_object->getNumberOfDataPoints(); ++i) {
     157        4216 :       taskFlags[i]=1; cweight += my_analysis_object->getWeight(i);
     158             :     }
     159           7 :     lockContributors();
     160             :   }
     161             :   // Prepare to do the averaging
     162        1123 :   prepareForAveraging();
     163             :   // Run all the tasks (if required
     164        1123 :   if( my_analysis_object || useRunAllTasks ) runAllTasks();
     165             :   // This the averaging if it is not done using task list
     166        1028 :   else performOperations( true );
     167             :   // Update the norm
     168        1123 :   double normt = cweight; if( !my_analysis_object && normalization==ndata ) normt = 1;
     169        1123 :   if( myaverage && my_analysis_object ) myaverage->setNorm( normt );
     170        2231 :   else if( myaverage ) myaverage->setNorm( normt + myaverage->getNorm() );
     171             :   // Finish the averaging
     172        1123 :   finishAveraging();
     173             :   // By resetting here we are ensuring that the grid will be cleared at the start of the next step
     174        1123 :   if( myaverage ) {
     175        1122 :     if( getStride()==0 || (clearstride>0 && getStep()%clearstride==0) ) myaverage->reset();
     176             :   }
     177             : }
     178             : 
     179       50918 : void ActionWithAveraging::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
     180       50918 :   if( my_analysis_object ) {
     181        2108 :     analysis::DataCollectionObject& mystore=my_analysis_object->getStoredData( current, false );
     182        8432 :     for(unsigned i=0; i<getNumberOfArguments(); ++i) myvals.setValue( 1+i, mystore.getArgumentValue( ActionWithArguments::getArguments()[i]->getName() ) );
     183        2108 :     myvals.setValue( 0, my_analysis_object->getWeight(current) );
     184        4216 :     if( normalization==f ) myvals.setValue( 1+getNumberOfArguments(), 1.0 ); else myvals.setValue( 1+getNumberOfArguments(), 1.0 / cweight );
     185        2108 :     accumulateAverage( myvals );
     186             :   } else {
     187       48810 :     runTask( current, myvals );
     188             :   }
     189       50909 : }
     190             : 
     191          93 : void ActionWithAveraging::clearAverage() { plumed_assert( myaverage->wasreset() ); myaverage->clear(); }
     192             : 
     193           0 : void ActionWithAveraging::performOperations( const bool& from_update ) { plumed_error(); }
     194             : 
     195          53 : void ActionWithAveraging::runFinalJobs() {
     196          53 :   if( my_analysis_object && getStride()==0 ) { activated=true; update(); }
     197          53 : }
     198             : 
     199             : }
     200        5874 : }