Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2020 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 "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          80 : void ActionWithAveraging::registerKeywords( Keywords& keys ) {
      33          80 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );
      34          80 :   ActionWithArguments::registerKeywords( keys ); ActionWithValue::registerKeywords( keys ); ActionWithVessel::registerKeywords( keys );
      35         400 :   keys.add("compulsory","STRIDE","1","the frequency with which the data should be collected and added to the quantity being averaged");
      36         400 :   keys.add("compulsory","CLEAR","0","the frequency with which to clear all the accumulated data.  The default value "
      37             :            "of 0 implies that all the data will be used and that the grid will never be cleared");
      38         320 :   keys.add("optional","LOGWEIGHTS","list of actions that calculates log weights that should be used to weight configurations when calculating averages");
      39         400 :   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         160 :   keys.remove("NUMERICAL_DERIVATIVES");
      41          80 : }
      42             : 
      43          70 : 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         140 :   lweight(0),cweight(0)
      57             : {
      58         140 :   if( keywords.exists("CLEAR") ) {
      59         114 :     parse("CLEAR",clearstride);
      60          57 :     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          70 :   if( getNumberOfArguments()>0 ) {
      66          28 :     my_analysis_object=dynamic_cast<analysis::AnalysisBase*>( getPntrToArgument(0)->getPntrToAction() );
      67          46 :     for(unsigned i=1; i<getNumberOfArguments(); i++) {
      68           9 :       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          28 :     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         140 :   if( keywords.exists("LOGWEIGHTS") ) {
      78         171 :     std::vector<std::string> wwstr; parseVector("LOGWEIGHTS",wwstr);
      79          57 :     if( wwstr.size()>0 ) log.printf("  reweighting using weights from ");
      80          57 :     std::vector<Value*> arg( getArguments() );
      81         132 :     for(unsigned i=0; i<wwstr.size(); ++i) {
      82          12 :       ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      83           6 :       if( !val ) error("could not find value named");
      84           6 :       bias::ReweightBase* iswham=dynamic_cast<bias::ReweightBase*>( val );
      85           6 :       if( iswham && iswham->buildsWeightStore() ) error("to use wham you must gather data using COLLECT_FRAMES");
      86          18 :       weights.push_back( val->copyOutput(val->getLabel()) );
      87          18 :       arg.push_back( val->copyOutput(val->getLabel()) );
      88          12 :       log.printf("%s ",wwstr[i].c_str() );
      89             :     }
      90          57 :     if( wwstr.size()>0 ) log.printf("\n");
      91          51 :     else log.printf("  weights are all equal to one\n");
      92          57 :     requestArguments( arg );
      93             :   }
      94         140 :   if( keywords.exists("NORMALIZATION") ) {
      95         114 :     std::string normstr; parse("NORMALIZATION",normstr);
      96          57 :     if( normstr=="true" ) normalization=t;
      97          35 :     else if( normstr=="false" ) normalization=f;
      98          26 :     else if( normstr=="ndata" ) normalization=ndata;
      99           0 :     else error("invalid instruction for NORMALIZATION flag should be true, false, or ndata");
     100             :   }
     101          70 : }
     102             : 
     103          65 : bool ActionWithAveraging::ignoreNormalization() const {
     104          65 :   if( normalization==f ) return true;
     105          56 :   return false;
     106             : }
     107             : 
     108          65 : void ActionWithAveraging::setAveragingAction( std::unique_ptr<AveragingVessel> av_vessel, const bool& usetasks ) {
     109          65 :   myaverage=av_vessel.get();
     110         195 :   addVessel( std::move(av_vessel) );
     111          65 :   useRunAllTasks=usetasks; resizeFunctions();
     112          65 : }
     113             : 
     114         239 : void ActionWithAveraging::lockRequests() {
     115             :   ActionAtomistic::lockRequests();
     116             :   ActionWithArguments::lockRequests();
     117         239 : }
     118             : 
     119         239 : void ActionWithAveraging::unlockRequests() {
     120             :   ActionAtomistic::unlockRequests();
     121             :   ActionWithArguments::unlockRequests();
     122         239 : }
     123             : 
     124         374 : unsigned ActionWithAveraging::getNumberOfQuantities() const {
     125         374 :   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         255 : void ActionWithAveraging::update() {
     134         255 :   if( (clearstride!=1 && getStep()==0) || (!onStep() && !my_analysis_object) ) return;
     135         175 :   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         175 :   if( myaverage ) {
     143         174 :     if( myaverage->wasreset() ) clearAverage();
     144             :   }
     145             :   // Calculate the weight for all reweighting
     146         175 :   if ( weights.size()>0 && !my_analysis_object ) {
     147          36 :     double sum=0; for(unsigned i=0; i<weights.size(); ++i) sum+=weights[i]->get();
     148           9 :     lweight=sum; cweight = exp( sum );
     149             :   } else {
     150         166 :     lweight=0; cweight=1.0;
     151             :   }
     152             :   // Prepare the task list for averaging
     153         175 :   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         175 :   prepareForAveraging();
     163             :   // Run all the tasks (if required
     164         175 :   if( my_analysis_object || useRunAllTasks ) runAllTasks();
     165             :   // This the averaging if it is not done using task list
     166          32 :   else performOperations( true );
     167             :   // Update the norm
     168         175 :   double normt = cweight; if( !my_analysis_object && normalization==ndata ) normt = 1;
     169         175 :   if( myaverage && my_analysis_object ) myaverage->setNorm( normt );
     170         335 :   else if( myaverage ) myaverage->setNorm( normt + myaverage->getNorm() );
     171             :   // Finish the averaging
     172         175 :   finishAveraging();
     173             :   // By resetting here we are ensuring that the grid will be cleared at the start of the next step
     174         175 :   if( myaverage ) {
     175         174 :     if( getStride()==0 || (clearstride>0 && getStep()%clearstride==0) ) myaverage->reset();
     176             :   }
     177             : }
     178             : 
     179       57410 : void ActionWithAveraging::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
     180       57410 :   if( my_analysis_object ) {
     181        2108 :     analysis::DataCollectionObject& mystore=my_analysis_object->getStoredData( current, false );
     182       10540 :     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       55302 :     runTask( current, myvals );
     188             :   }
     189       57410 : }
     190             : 
     191          99 : void ActionWithAveraging::clearAverage() { plumed_assert( myaverage->wasreset() ); myaverage->clear(); }
     192             : 
     193           0 : void ActionWithAveraging::performOperations( const bool& from_update ) { plumed_error(); }
     194             : 
     195          57 : void ActionWithAveraging::runFinalJobs() {
     196          57 :   if( my_analysis_object && getStride()==0 ) { activated=true; update(); }
     197          57 : }
     198             : 
     199             : }
     200        5517 : }