--- branches/development/src/UseTheForce/ForceField.cpp 2011/09/14 21:15:17 1629 +++ branches/development/src/brains/ForceField.cpp 2012/05/26 18:13:43 1725 @@ -36,7 +36,8 @@ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ /** @@ -48,12 +49,39 @@ */ #include -#include "UseTheForce/ForceField.hpp" +#include "brains/ForceField.hpp" #include "utils/simError.h" -#include "utils/Tuple.hpp" + +#include "io/OptionSectionParser.hpp" +#include "io/BaseAtomTypesSectionParser.hpp" +#include "io/DirectionalAtomTypesSectionParser.hpp" +#include "io/AtomTypesSectionParser.hpp" +#include "io/BendTypesSectionParser.hpp" +#include "io/BondTypesSectionParser.hpp" +#include "io/ChargeAtomTypesSectionParser.hpp" +#include "io/EAMAtomTypesSectionParser.hpp" +#include "io/FluctuatingChargeAtomTypesSectionParser.hpp" +#include "io/GayBerneAtomTypesSectionParser.hpp" +#include "io/InversionTypesSectionParser.hpp" +#include "io/LennardJonesAtomTypesSectionParser.hpp" +#include "io/MultipoleAtomTypesSectionParser.hpp" +#include "io/NonBondedInteractionsSectionParser.hpp" +#include "io/PolarizableAtomTypesSectionParser.hpp" +#include "io/SCAtomTypesSectionParser.hpp" +#include "io/ShapeAtomTypesSectionParser.hpp" +#include "io/StickyAtomTypesSectionParser.hpp" +#include "io/StickyPowerAtomTypesSectionParser.hpp" +#include "io/TorsionTypesSectionParser.hpp" + +#include "types/LennardJonesAdapter.hpp" +#include "types/EAMAdapter.hpp" +#include "types/SuttonChenAdapter.hpp" +#include "types/GayBerneAdapter.hpp" +#include "types/StickyAdapter.hpp" + namespace OpenMD { - ForceField::ForceField() { + ForceField::ForceField(std::string ffName) { char* tempPath; tempPath = getenv("FORCE_PARAM_PATH"); @@ -64,6 +92,83 @@ namespace OpenMD { } else { ffPath_ = tempPath; } + + setForceFieldFileName(ffName + ".frc"); + + /** + * The order of adding section parsers is important. + * + * OptionSectionParser must come first to set options for other + * parsers + * + * DirectionalAtomTypesSectionParser should be added before + * AtomTypesSectionParser, and these two section parsers will + * actually create "real" AtomTypes (AtomTypesSectionParser will + * create AtomType and DirectionalAtomTypesSectionParser will + * create DirectionalAtomType, which is a subclass of AtomType and + * should come first). + * + * Other AtomTypes Section Parsers will not create the "real" + * AtomType, they only add and set some attributes of the AtomType + * (via the Adapters). Thus ordering of these is not important. + * AtomTypesSectionParser should be added before other atom type + * + * The order of BondTypesSectionParser, BendTypesSectionParser and + * TorsionTypesSectionParser, etc. are not important. + */ + + spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); + spMan_.push_back(new BaseAtomTypesSectionParser()); + spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new AtomTypesSectionParser()); + + spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); + + spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); + spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); + + spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_)); + } + + void ForceField::parse(const std::string& filename) { + ifstrstream* ffStream; + + ffStream = openForceFieldFile(filename); + + spMan_.parse(*ffStream, *this); + + ForceField::AtomTypeContainer::MapTypeIterator i; + AtomType* at; + + for (at = atomTypeCont_.beginType(i); at != NULL; + at = atomTypeCont_.nextType(i)) { + + // useBase sets the responsibilities, and these have to be done + // after the atomTypes and Base types have all been scanned: + + std::vector ayb = at->allYourBase(); + if (ayb.size() > 1) { + for (int j = ayb.size()-1; j > 0; j--) { + + ayb[j-1]->useBase(ayb[j]); + + } + } + } + + delete ffStream; } /** @@ -634,35 +739,29 @@ namespace OpenMD { } RealType ForceField::getRcutFromAtomType(AtomType* at) { - /**@todo */ - GenericData* data; - RealType rcut = 0.0; + RealType rcut(0.0); - if (at->isLennardJones()) { - data = at->getPropertyByName("LennardJones"); - if (data != NULL) { - LJParamGenericData* ljData = dynamic_cast(data); - - if (ljData != NULL) { - LJParam ljParam = ljData->getData(); - - //by default use 2.5*sigma as cutoff radius - rcut = 2.5 * ljParam.sigma; - - } else { - sprintf( painCave.errMsg, - "Can not cast GenericData to LJParam\n"); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } - } else { - sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); - painCave.severity = OPENMD_ERROR; - painCave.isFatal = 1; - simError(); - } + LennardJonesAdapter lja = LennardJonesAdapter(at); + if (lja.isLennardJones()) { + rcut = 2.5 * lja.getSigma(); } + EAMAdapter ea = EAMAdapter(at); + if (ea.isEAM()) { + rcut = max(rcut, ea.getRcut()); + } + SuttonChenAdapter sca = SuttonChenAdapter(at); + if (sca.isSuttonChen()) { + rcut = max(rcut, 2.0 * sca.getAlpha()); + } + GayBerneAdapter gba = GayBerneAdapter(at); + if (gba.isGayBerne()) { + rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL())); + } + StickyAdapter sa = StickyAdapter(at); + if (sa.isSticky()) { + rcut = max(rcut, max(sa.getRu(), sa.getRup())); + } + return rcut; }