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#include <cmath> |
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#include "nonbonded/GB.hpp" |
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#include "utils/simError.h" |
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#include "types/LennardJonesAdapter.hpp" |
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#include "types/GayBerneAdapter.hpp" |
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using namespace std; |
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namespace OpenMD { |
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GB::GB() : name_("GB"), initialized_(false), mu_(2.0), nu_(1.0), forceField_(NULL) {} |
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GayBerneParam GB::getGayBerneParam(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->isGayBerne()) { |
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sprintf( painCave.errMsg, |
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"GB::getGayBerneParam was passed an atomType (%s) that does\n" |
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"\tnot appear to be a Gay-Berne 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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|
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
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GenericData* data = daType->getPropertyByName("GayBerne"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "GB::getGayBerneParam could not find\n" |
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"\tGay-Berne parameters for atomType %s.\n", |
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daType->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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GayBerneParamGenericData* gbData = dynamic_cast<GayBerneParamGenericData*>(data); |
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if (gbData == NULL) { |
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sprintf( painCave.errMsg, |
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"GB::getGayBerneParam could not convert GenericData to\n" |
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"\tGayBerneParamGenericData for atom type %s\n", |
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daType->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 gbData->getData(); |
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} |
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LJParam GB::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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"GB::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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|
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GenericData* data = atomType->getPropertyByName("LennardJones"); |
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if (data == NULL) { |
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sprintf( painCave.errMsg, "GB::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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"GB::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 GB::getLJEpsilon(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 GB::getLJSigma(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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void GB::initialize() { |
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ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
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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->isGayBerne() || at->isLennardJones()) |
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LennardJonesAdapter lja = LennardJonesAdapter(at); |
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GayBerneAdapter gba = GayBerneAdapter(at); |
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if (gba.isGayBerne() || lja.isLennardJones()) |
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addType(at); |
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} |
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void GB::addType(AtomType* atomType){ |
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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 = GBMap.insert( pair<int, AtomType*>(atp.ident, atomType) ); |
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ret = GBMap.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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"GB 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(); |
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} |
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RealType d1, l1, eX1, eS1, eE1, dw1; |
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if (atomType->isGayBerne()) { |
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GayBerneParam gb1 = getGayBerneParam(atomType); |
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d1 = gb1.GB_d; |
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l1 = gb1.GB_l; |
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eX1 = gb1.GB_eps_X; |
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eS1 = gb1.GB_eps_S; |
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eE1 = gb1.GB_eps_E; |
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dw1 = gb1.GB_dw; |
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} else if (atomType->isLennardJones()) { |
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d1 = getLJSigma(atomType) / sqrt(2.0); |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atomType); |
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GayBerneAdapter gba1 = GayBerneAdapter(atomType); |
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if (gba1.isGayBerne()) { |
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d1 = gba1.getD(); |
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l1 = gba1.getL(); |
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eX1 = gba1.getEpsX(); |
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eS1 = gba1.getEpsS(); |
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eE1 = gba1.getEpsE(); |
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dw1 = gba1.getDw(); |
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} else if (lja1.isLennardJones()) { |
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d1 = lja1.getSigma() / sqrt(2.0); |
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l1 = d1; |
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eX1 = getLJEpsilon(atomType); |
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eX1 = lja1.getEpsilon(); |
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eS1 = eX1; |
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eE1 = eX1; |
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dw1 = 1.0; |
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for( it = GBMap.begin(); it != GBMap.end(); ++it) { |
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AtomType* atype2 = (*it).second; |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atype2); |
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GayBerneAdapter gba2 = GayBerneAdapter(atype2); |
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RealType d2, l2, eX2, eS2, eE2, dw2; |
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if (atype2->isGayBerne()) { |
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GayBerneParam gb2 = getGayBerneParam(atype2); |
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d2 = gb2.GB_d; |
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l2 = gb2.GB_l; |
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eX2 = gb2.GB_eps_X; |
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eS2 = gb2.GB_eps_S; |
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eE2 = gb2.GB_eps_E; |
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dw2 = gb2.GB_dw; |
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} else if (atype2->isLennardJones()) { |
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d2 = getLJSigma(atype2) / sqrt(2.0); |
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if (gba2.isGayBerne()) { |
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d2 = gba2.getD(); |
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l2 = gba2.getL(); |
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eX2 = gba2.getEpsX(); |
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eS2 = gba2.getEpsS(); |
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eE2 = gba2.getEpsE(); |
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dw2 = gba2.getDw(); |
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} else if (lja2.isLennardJones()) { |
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d2 = lja2.getSigma() / sqrt(2.0); |
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l2 = d2; |
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eX2 = getLJEpsilon(atype2); |
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eX2 = lja2.getEpsilon(); |
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eS2 = eX2; |
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eE2 = eX2; |
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dw2 = 1.0; |
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// only add this pairing if at least one of the atoms is a Gay-Berne atom |
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if (atomType->isGayBerne() || atype2->isGayBerne()) { |
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if (gba1.isGayBerne() || gba2.isGayBerne()) { |
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pair<AtomType*, AtomType*> key1, key2; |
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key1 = make_pair(atomType, atype2); |
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RealType a, b, g; |
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// This is not good. We should store this in the mixing map, and not |
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// query atom types in calc force. |
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bool i_is_LJ = idat.atypes.first->isLennardJones(); |
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bool j_is_LJ = idat.atypes.second->isLennardJones(); |
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RealType cut = 0.0; |
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if (atypes.first->isGayBerne()) { |
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GayBerneParam gb1 = getGayBerneParam(atypes.first); |
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RealType d1 = gb1.GB_d; |
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RealType l1 = gb1.GB_l; |
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LennardJonesAdapter lja1 = LennardJonesAdapter(atypes.first); |
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GayBerneAdapter gba1 = GayBerneAdapter(atypes.first); |
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LennardJonesAdapter lja2 = LennardJonesAdapter(atypes.second); |
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GayBerneAdapter gba2 = GayBerneAdapter(atypes.second); |
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if (gba1.isGayBerne()) { |
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RealType d1 = gba1.getD(); |
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RealType l1 = gba1.getL(); |
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// sigma is actually sqrt(2)*l for prolate ellipsoids |
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cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d1, l1)); |
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} else if (atypes.first->isLennardJones()) { |
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cut = max(cut, RealType(2.5) * getLJSigma(atypes.first)); |
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} else if (lja1.isLennardJones()) { |
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cut = max(cut, RealType(2.5) * lja1.getSigma()); |
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} |
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if (atypes.second->isGayBerne()) { |
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GayBerneParam gb2 = getGayBerneParam(atypes.second); |
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RealType d2 = gb2.GB_d; |
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RealType l2 = gb2.GB_l; |
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if (gba2.isGayBerne()) { |
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RealType d2 = gba2.getD(); |
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RealType l2 = gba2.getL(); |
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cut = max(cut, RealType(2.5) * sqrt(RealType(2.0)) * max(d2, l2)); |
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} else if (atypes.second->isLennardJones()) { |
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cut = max(cut, RealType(2.5) * getLJSigma(atypes.second)); |
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} else if (lja2.isLennardJones()) { |
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cut = max(cut, RealType(2.5) * lja2.getSigma()); |
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} |
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return cut; |
