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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/LennardJonesAdapter.hpp" |
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#include "types/LennardJonesInteractionType.hpp" |
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namespace OpenMD { |
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LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {} |
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LJParam LJ::getLJParam(AtomType* atomType) { |
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// Do sanity checking on the AtomType we were passed before |
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// building any data structures: |
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if (!atomType->isLennardJones()) { |
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sprintf( painCave.errMsg, |
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"LJ::getLJParam was passed an atomType (%s) that does not\n" |
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"\tappear to be a Lennard-Jones atom.\n", |
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atomType->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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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n" |
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"\tparameters for atomType %s.\n", atomType->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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sprintf( painCave.errMsg, |
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"LJ::getLJParam could not convert GenericData to LJParam for\n" |
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"\tatom type %s\n", atomType->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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return ljData->getData(); |
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} |
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RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
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RealType LJ::getSigma(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.sigma; |
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} |
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RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) { |
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RealType sigma1 = getSigma(atomType1); |
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RealType sigma2 = getSigma(atomType2); |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
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RealType sigma1 = lja1.getSigma(); |
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RealType sigma2 = lja2.getSigma(); |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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string DistanceMix = fopts.getDistanceMixingRule(); |
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return 0.5 * (sigma1 + sigma2); |
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} |
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RealType LJ::getEpsilon(AtomType* atomType) { |
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LJParam ljParam = getLJParam(atomType); |
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return ljParam.epsilon; |
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} |
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RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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RealType epsilon1 = getEpsilon(atomType1); |
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RealType epsilon2 = getEpsilon(atomType2); |
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RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) { |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1); |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2); |
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RealType epsilon1 = lja1.getEpsilon(); |
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RealType epsilon2 = lja2.getEpsilon(); |
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return sqrt(epsilon1 * epsilon2); |
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} |
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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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LennardJonesAdapter lja = LennardJonesAdapter(at); |
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if (lja.isLennardJones()){ |
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addType(at); |
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} |
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} |
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void LJ::addType(AtomType* atomType){ |
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RealType sigma1 = getSigma(atomType); |
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RealType epsilon1 = getEpsilon(atomType); |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
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RealType sigma1 = lja1.getSigma(); |
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RealType epsilon1 = lja1.getEpsilon(); |
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// add it to the map: |
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AtomTypeProperties atp = atomType->getATP(); |
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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ret = LJMap.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"LJ already had a previous entry with ident %d\n", |
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atp.ident); |
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atomType->getIdent()); |
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painCave.severity = OPENMD_INFO; |
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painCave.isFatal = 0; |
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simError(); |
