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#include <cmath> |
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#include "nonbonded/LJ.hpp" |
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#include "utils/simError.h" |
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#include "types/LennardJonesInteractionType.hpp" |
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namespace OpenMD { |
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for (at = atomTypes->beginType(i); at != NULL; |
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at = atomTypes->nextType(i)) { |
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if (at->isLennardJones()) |
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addType(at); |
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if (at->isLennardJones()){ |
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addType(at); |
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} |
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} |
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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->isLennardJones()) { |
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pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes(); |
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GenericData* data = nbt->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n" |
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"\tLennard-Jones 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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LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
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if (ljData == NULL) { |
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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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LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt); |
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if (ljit == NULL) { |
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sprintf( painCave.errMsg, |
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"LJ::rebuildMixingMap could not convert GenericData to\n" |
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"\tLJParam 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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"LJ::initialize could not convert NonBondedInteractionType\n" |
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"\tto LennardJonesInteractionType 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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LJParam ljParam = ljData->getData(); |
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RealType sigma = ljParam.sigma; |
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RealType epsilon = ljParam.epsilon; |
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addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon); |
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RealType sigma = ljit->getSigma(); |
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RealType epsilon = ljit->getEpsilon(); |
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addExplicitInteraction(at1, at2, sigma, epsilon); |
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} |
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} |
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initialized_ = true; |
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void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){ |
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// in case these weren't already in the map |
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addType(atype1); |
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addType(atype2); |
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LJInteractionData mixer; |
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mixer.sigma = sigma; |
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mixer.epsilon = epsilon; |
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} |
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void LJ::calcForce(InteractionData &idat) { |
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if (!initialized_) initialize(); |
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map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it; |
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it = MixingMap.find( idat.atypes ); |
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