C++ (Cpp) requestArguments Examples

Example #1

File: Mapping.cpp Project: psolsson/plumed2

void Mapping::prepare(){
  if( mymap->mappingNeedsSetup() ){
      // Get the arguments and atoms that are required
      std::vector<AtomNumber> atoms; std::vector<std::string> args;
      mymap->getAtomAndArgumentRequirements( atoms, args );
      requestAtoms( atoms ); std::vector<Value*> req_args; 
      interpretArgumentList( args, req_args ); requestArguments( req_args );
      // Duplicate all frames (duplicates are used by sketch-map)
      mymap->duplicateFrameList();
      // Get the number of frames in the path
      unsigned nfram=getNumberOfReferencePoints();
      fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 ); 
      plumed_assert( !mymap->mappingNeedsSetup() );
      // Resize all derivative arrays
      mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
      // Resize forces array
      forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
  }
}

Example #2

File: ActionWithAveraging.cpp Project: JFDama/plumed2

ActionWithAveraging::ActionWithAveraging( const ActionOptions& ao ):
  Action(ao),
  ActionPilot(ao),
  ActionAtomistic(ao),
  ActionWithArguments(ao),
  ActionWithValue(ao),
  ActionWithVessel(ao),
  myaverage(NULL),
  useRunAllTasks(false),
  clearstride(0),
  lweight(0),cweight(0)
{
  if( keywords.exists("CLEAR") ) {
    parse("CLEAR",clearstride);
    if( clearstride>0 ) {
      if( clearstride%getStride()!=0 ) error("CLEAR parameter must be a multiple of STRIDE");
      log.printf("  clearing grid every %u steps \n",clearstride);
    }
  }
  if( keywords.exists("LOGWEIGHTS") ) {
    std::vector<std::string> wwstr; parseVector("LOGWEIGHTS",wwstr);
    if( wwstr.size()>0 ) log.printf("  reweighting using weights from ");
    std::vector<Value*> arg( getArguments() );
    for(unsigned i=0; i<wwstr.size(); ++i) {
      ActionWithValue* val = plumed.getActionSet().selectWithLabel<ActionWithValue*>(wwstr[i]);
      if( !val ) error("could not find value named");
      weights.push_back( val->copyOutput(val->getLabel()) );
      arg.push_back( val->copyOutput(val->getLabel()) );
      log.printf("%s ",wwstr[i].c_str() );
    }
    if( wwstr.size()>0 ) log.printf("\n");
    else log.printf("  weights are all equal to one\n");
    requestArguments( arg );
  }
  if( keywords.exists("UNORMALIZED") ) parseFlag("UNORMALIZED",unormalised);
}

Example #3

File: Mapping.cpp Project: psolsson/plumed2

Mapping::Mapping(const ActionOptions&ao):
Action(ao),
ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithValue(ao),
ActionWithVessel(ao)
{
  // Read the input
  std::string mtype; parse("TYPE",mtype);
  bool skipchecks; parseFlag("DISABLE_CHECKS",skipchecks);
  // Setup the object that does the mapping
  mymap = new PointWiseMapping( mtype, skipchecks ); 
 
  // Read the properties we require
  if( keywords.exists("PROPERTY") ){
     std::vector<std::string> property;
     parseVector("PROPERTY",property);
     if(property.size()==0) error("no properties were specified");
     mymap->setPropertyNames( property, false );
  } else {
     std::vector<std::string> property(1); 
     property[0]="sss";
     mymap->setPropertyNames( property, true );
  }

  // Open reference file
  std::string reference; parse("REFERENCE",reference); 
  FILE* fp=fopen(reference.c_str(),"r"); 
  if(!fp) error("could not open reference file " + reference );

  // Read all reference configurations 
  bool do_read=true; std::vector<double> weights; 
  unsigned nfram=0, wnorm=0., ww;
  while (do_read){
     PDB mypdb; 
     // Read the pdb file
     do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
     // Fix argument names
     expandArgKeywordInPDB( mypdb );
     if(do_read){
        mymap->readFrame( mypdb ); ww=mymap->getWeight( nfram ); 
        weights.push_back( ww );
        wnorm+=ww; nfram++;
     } else {
        break;
     }
  }
  fclose(fp); 

  if(nfram==0 ) error("no reference configurations were specified");
  log.printf("  found %d configurations in file %s\n",nfram,reference.c_str() );
  for(unsigned i=0;i<weights.size();++i) weights[i] /= wnorm;
  mymap->setWeights( weights );

  // Finish the setup of the mapping object
  // Get the arguments and atoms that are required
  std::vector<AtomNumber> atoms; std::vector<std::string> args;
  mymap->getAtomAndArgumentRequirements( atoms, args );
  requestAtoms( atoms ); std::vector<Value*> req_args;
  interpretArgumentList( args, req_args ); requestArguments( req_args );
  // Duplicate all frames (duplicates are used by sketch-map)
  mymap->duplicateFrameList(); 
  fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
  plumed_assert( !mymap->mappingNeedsSetup() );
  // Resize all derivative arrays
  mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
  // Resize forces array
  if( getNumberOfAtoms()>0 ){ 
     forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
  } else {
     forcesToApply.resize( getNumberOfArguments() );
  }
}