--- trunk/src/UseTheForce/ForceField.cpp 2010/07/07 15:04:32 1460 +++ 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). */ /** @@ -48,15 +49,39 @@ */ #include -#include "UseTheForce/ForceField.hpp" +#include "brains/ForceField.hpp" #include "utils/simError.h" -#include "utils/Tuple.hpp" -#include "UseTheForce/DarkSide/atype_interface.h" -#include "UseTheForce/DarkSide/fForceOptions_interface.h" -#include "UseTheForce/DarkSide/switcheroo_interface.h" + +#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"); @@ -67,20 +92,108 @@ 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; - ForceField::~ForceField() { - deleteAtypes(); - deleteSwitch(); + 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; } + /** + * getAtomType by string + * + * finds the requested atom type in this force field using the string + * name of the atom type. + */ AtomType* ForceField::getAtomType(const std::string &at) { std::vector keys; keys.push_back(at); return atomTypeCont_.find(keys); } + /** + * getAtomType by ident + * + * finds the requested atom type in this force field using the + * integer ident instead of the string name of the atom type. + */ + AtomType* ForceField::getAtomType(int ident) { + std::string at = atypeIdentToName.find(ident)->second; + return getAtomType(at); + } + BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) { std::vector keys; @@ -440,6 +553,7 @@ namespace OpenMD { } NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { + std::vector keys; keys.push_back(at1); keys.push_back(at2); @@ -449,9 +563,63 @@ namespace OpenMD { if (nbiType) { return nbiType; } else { - //if no exact match found, try wild card match - return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); - } + AtomType* atype1; + AtomType* atype2; + std::vector at1key; + at1key.push_back(at1); + atype1 = atomTypeCont_.find(at1key); + + std::vector at2key; + at2key.push_back(at2); + atype2 = atomTypeCont_.find(at2key); + + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); + + std::vector::iterator i; + std::vector::iterator j; + + int ii = 0; + int jj = 0; + int nbiTypeScore; + + std::vector > > foundNBI; + + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + jj = 0; + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + + nbiTypeScore = ii + jj; + + std::vector myKeys; + myKeys.push_back((*i)->getName()); + myKeys.push_back((*j)->getName()); + + NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); + if (nbiType) { + foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); + } + jj++; + } + ii++; + } + + + if (foundNBI.size() > 0) { + // sort the foundNBI by the score: + std::sort(foundNBI.begin(), foundNBI.end()); + + int bestScore = foundNBI[0].first; + std::vector theKeys = foundNBI[0].second; + + NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); + return bestType; + } else { + //if no exact match found, try wild card match + return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); + } + } } BondType* ForceField::getExactBondType(const std::string &at1, @@ -507,12 +675,14 @@ namespace OpenMD { bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { std::vector keys; keys.push_back(at); + atypeIdentToName[atomType->getIdent()] = at; return atomTypeCont_.add(keys, atomType); } bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { std::vector keys; keys.push_back(at); + atypeIdentToName[atomType->getIdent()] = at; return atomTypeCont_.replace(keys, atomType); } @@ -569,35 +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; } @@ -631,9 +795,4 @@ namespace OpenMD { return ffStream; } - void ForceField::setFortranForceOptions(){ - ForceOptions theseFortranOptions; - forceFieldOptions_.makeFortranOptions(theseFortranOptions); - setfForceOptions(&theseFortranOptions); - } } //end namespace OpenMD