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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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*/ |
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#include "UseTheForce/EAM_FF.hpp" |
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#include "UseTheForce/DarkSide/eam_interface.h" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/charge_interface.h" |
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#include "UseTheForce/DarkSide/dipole_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/BaseAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
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#include "io/EAMAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "io/OptionSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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EAM_FF::EAM_FF(){ |
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EAM_FF::EAM_FF(){ |
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//set default force field filename |
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setForceFieldFileName("EAM.frc"); |
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//the order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
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//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
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//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
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//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
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//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom type section parsers. |
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//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
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//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
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//not important. |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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//OptionSectionParser must come first to set options for other parsers |
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spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BaseAtomTypesSectionParser()); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
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spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
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spMan_.push_back(new EAMAtomTypesSectionParser()); |
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spMan_.push_back(new StickyAtomTypesSectionParser()); |
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spMan_.push_back(new BondTypesSectionParser()); |
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spMan_.push_back(new BendTypesSectionParser()); |
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spMan_.push_back(new TorsionTypesSectionParser()); |
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} |
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spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
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} |
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void EAM_FF::parse(const std::string& filename) { |
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void EAM_FF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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ffStream = openForceFieldFile(filename); |
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AtomType* at; |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->makeFortranAtomType(); |
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// useBase sets the responsibilities, and these have to be done |
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// after the atomTypes and Base types have all been scanned: |
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std::vector<AtomType*> ayb = at->allYourBase(); |
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if (ayb.size() > 1) { |
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for (int j = ayb.size()-1; j > 0; j--) { |
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ayb[j-1]->useBase(ayb[j]); |
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} |
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} |
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at->makeFortranAtomType(); |
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} |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->complete(); |
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at->complete(); |
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} |
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} |
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delete ffStream; |
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} |
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double EAM_FF::getRcutFromAtomType(AtomType* at){ |
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double rcut = 0.0; |
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RealType EAM_FF::getRcutFromAtomType(AtomType* at){ |
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RealType rcut = 0.0; |
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if (at->isEAM()) { |
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GenericData* data = at->getPropertyByName("EAM"); |
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if (data != NULL) { |
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EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
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GenericData* data = at->getPropertyByName("EAM"); |
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if (data != NULL) { |
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EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
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if (eamData != NULL) { |
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if (eamData != NULL) { |
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EAMParam& eamParam = eamData->getData(); |
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rcut = eamParam.rcut; |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to EAMParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find EAM Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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EAMParam& eamParam = eamData->getData(); |
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rcut = eamParam.rcut; |
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} else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to EAMParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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sprintf( painCave.errMsg, "Can not find EAM Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} else { |
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rcut = ForceField::getRcutFromAtomType(at); |
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rcut = ForceField::getRcutFromAtomType(at); |
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} |
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return rcut; |
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} |
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} |
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EAM_FF::~EAM_FF(){ |
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// We need to clean up the fortran side so we don't have bad things happen if |
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// we try to create a second EAM force field. |
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destroyEAMTypes(); |
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} |
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} //end namespace oopse |
