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#include <cmath> |
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#include "nonbonded/Morse.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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#include "types/MorseInteractionType.hpp" |
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using namespace std; |
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void Morse::initialize() { |
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stringToEnumMap_["shiftedMorse"] = shiftedMorse; |
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stringToEnumMap_["repulsiveMorse"] = repulsiveMorse; |
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ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes(); |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j; |
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NonBondedInteractionType* nbt; |
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ForceField::NonBondedInteractionTypeContainer::KeyType keys; |
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for (nbt = nbiTypes->beginType(j); nbt != NULL; |
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nbt = nbiTypes->nextType(j)) { |
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if (nbt->isMorse()) { |
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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GenericData* data = nbt->getPropertyByName("Morse"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Morse::initialize could not find\n" |
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"\tMorse parameters for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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MorseData* morseData = dynamic_cast<MorseData*>(data); |
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if (morseData == NULL) { |
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sprintf( painCave.errMsg, |
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"Morse::initialize could not convert GenericData to\n" |
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"\tMorseData for %s - %s interaction.\n", |
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atypes.first->getName().c_str(), |
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atypes.second->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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MorseParam morseParam = morseData->getData(); |
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keys = nbiTypes->getKeys(j); |
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AtomType* at1 = forceField_->getAtomType(keys[0]); |
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AtomType* at2 = forceField_->getAtomType(keys[1]); |
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RealType De = morseParam.De; |
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RealType Re = morseParam.Re; |
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RealType beta = morseParam.beta; |
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string interactionType = morseParam.interactionType; |
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MorseInteractionType* mit = dynamic_cast<MorseInteractionType*>(nbt); |
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toUpper(interactionType); |
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map<string, MorseInteractionType>::iterator i; |
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i = stringToEnumMap_.find(interactionType); |
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if (i != stringToEnumMap_.end()) { |
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addExplicitInteraction(atypes.first, atypes.second, |
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De, Re, beta, i->second ); |
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} else { |
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if (mit == NULL) { |
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sprintf( painCave.errMsg, |
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"Morse::initialize found unknown Morse interaction type\n" |
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"\t(%s) for %s - %s interaction.\n", |
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morseParam.interactionType.c_str(), |
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atypes.first->getName().c_str(), |
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atypes.second->getName().c_str()); |
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"Morse::initialize could not convert NonBondedInteractionType\n" |
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"\tto MorseInteractionType for %s - %s interaction.\n", |
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at1->getName().c_str(), |
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at2->getName().c_str()); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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RealType De = mit->getD(); |
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RealType Re = mit->getR(); |
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RealType beta = mit->getBeta(); |
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MorseType variant = mit->getInteractionType(); |
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addExplicitInteraction(at1, at2, De, Re, beta, variant ); |
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} |
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} |
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initialized_ = true; |
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void Morse::addExplicitInteraction(AtomType* atype1, AtomType* atype2, |
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RealType De, RealType Re, RealType beta, |
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MorseInteractionType mit) { |
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MorseType mt) { |
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MorseInteractionData mixer; |
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mixer.De = De; |
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mixer.Re = Re; |
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mixer.beta = beta; |
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mixer.interactionType = mit; |
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mixer.variant = mt; |
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atype1, atype2); |
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RealType De = mixer.De; |
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RealType Re = mixer.Re; |
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RealType beta = mixer.beta; |
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MorseInteractionType interactionType = mixer.interactionType; |
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MorseType variant = mixer.variant; |
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// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2) |
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} |
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switch(interactionType) { |
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case shiftedMorse : { |
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switch(variant) { |
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case mtShifted : { |
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myPot = De * (expfnc2 - 2.0 * expfnc); |
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myDeriv = 2.0 * De * beta * (expfnc - expfnc2); |
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break; |
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} |
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case repulsiveMorse : { |
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case mtRepulsive : { |
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myPot = De * expfnc2; |
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myDeriv = -2.0 * De * beta * expfnc2; |
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break; |
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} |
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case mtUnknown: { |
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// don't know what to do so don't do anything |
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break; |
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} |
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} |
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RealType pot_temp = *(idat.vdwMult) * (myPot - myPotC); |
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*(idat.vpair) += pot_temp; |
