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#include "nonbonded/Electrostatic.hpp" |
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#include "utils/simError.h" |
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#include "types/NonBondedInteractionType.hpp" |
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#include "types/DirectionalAtomType.hpp" |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/MultipoleAdapter.hpp" |
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#include "io/Globals.hpp" |
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#include "nonbonded/SlaterIntegrals.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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|
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|
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namespace OpenMD { |
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|
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electrostaticAtomData.is_SplitDipole = false; |
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electrostaticAtomData.is_Quadrupole = false; |
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|
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if (atomType->isCharge()) { |
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GenericData* data = atomType->getPropertyByName("Charge"); |
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FixedChargeAdapter fca = FixedChargeAdapter(atomType); |
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|
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if (data == NULL) { |
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sprintf( painCave.errMsg, "Electrostatic::addType could not find " |
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"Charge\n" |
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"\tparameters for atomType %s.\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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DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (doubleData == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not convert GenericData to " |
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"Charge 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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if (fca.isFixedCharge()) { |
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electrostaticAtomData.is_Charge = true; |
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electrostaticAtomData.charge = doubleData->getData(); |
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electrostaticAtomData.charge = fca.getCharge(); |
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} |
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|
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if (atomType->isDirectional()) { |
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DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType); |
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|
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if (daType->isDipole()) { |
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GenericData* data = daType->getPropertyByName("Dipole"); |
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|
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if (data == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not find Dipole\n" |
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"\tparameters 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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|
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DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (doubleData == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not convert GenericData to " |
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"Dipole Moment\n" |
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"\tfor atom type %s\n", 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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MultipoleAdapter ma = MultipoleAdapter(atomType); |
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if (ma.isMultipole()) { |
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if (ma.isDipole()) { |
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electrostaticAtomData.is_Dipole = true; |
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electrostaticAtomData.dipole_moment = doubleData->getData(); |
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electrostaticAtomData.dipole_moment = ma.getDipoleMoment(); |
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} |
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|
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if (daType->isSplitDipole()) { |
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GenericData* data = daType->getPropertyByName("SplitDipoleDistance"); |
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|
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if (data == NULL) { |
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sprintf(painCave.errMsg, |
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"Electrostatic::addType could not find SplitDipoleDistance\n" |
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"\tparameter 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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|
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DoubleGenericData* doubleData = dynamic_cast<DoubleGenericData*>(data); |
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if (doubleData == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not convert GenericData to " |
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"SplitDipoleDistance for\n" |
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"\tatom type %s\n", 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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if (ma.isSplitDipole()) { |
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electrostaticAtomData.is_SplitDipole = true; |
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electrostaticAtomData.split_dipole_distance = doubleData->getData(); |
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electrostaticAtomData.split_dipole_distance = ma.getSplitDipoleDistance(); |
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} |
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|
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if (daType->isQuadrupole()) { |
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GenericData* data = daType->getPropertyByName("QuadrupoleMoments"); |
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|
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if (data == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not find QuadrupoleMoments\n" |
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"\tparameter 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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|
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if (ma.isQuadrupole()) { |
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// Quadrupoles in OpenMD are set as the diagonal elements |
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// of the diagonalized traceless quadrupole moment tensor. |
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// The column vectors of the unitary matrix that diagonalizes |
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// the quadrupole moment tensor become the eFrame (or the |
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// electrostatic version of the body-fixed frame. |
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|
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Vector3dGenericData* v3dData = dynamic_cast<Vector3dGenericData*>(data); |
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if (v3dData == NULL) { |
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sprintf( painCave.errMsg, |
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"Electrostatic::addType could not convert GenericData to " |
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"Quadrupole Moments for\n" |
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"\tatom type %s\n", 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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electrostaticAtomData.is_Quadrupole = true; |
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electrostaticAtomData.quadrupole_moments = v3dData->getData(); |
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electrostaticAtomData.quadrupole_moments = ma.getQuadrupoleMoments(); |
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} |
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} |
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|
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AtomTypeProperties atp = atomType->getATP(); |
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> |
FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType); |
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|
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if (fqa.isFluctuatingCharge()) { |
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electrostaticAtomData.is_FluctuatingCharge = true; |
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electrostaticAtomData.electronegativity = fca.getElectronegativity(); |
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electrostaticAtomData.hardness = fca.getHardness(); |
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electrostaticAtomData.slaterN = fca.getSlaterN(); |
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electrostaticAtomData.slaterZeta = fca.getSlaterZeta(); |
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} |
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|
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pair<map<int,AtomType*>::iterator,bool> ret; |
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ret = ElectrostaticList.insert( pair<int,AtomType*>(atp.ident, atomType) ); |
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> |
ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(), |
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> |
atomType) ); |
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if (ret.second == false) { |
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sprintf( painCave.errMsg, |
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"Electrostatic 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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|
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< |
ElectrostaticMap[atomType] = electrostaticAtomData; |
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> |
ElectrostaticMap[atomType] = electrostaticAtomData; |
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> |
|
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> |
// Now, iterate over all known types and add to the mixing map: |
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> |
|
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> |
map<AtomType*, ElectrostaticAtomData>::iterator it; |
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> |
for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) { |
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> |
AtomType* atype2 = (*it).first; |
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> |
|
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> |
if ((*it).is_FluctuatingCharge && electrostaticAtomData.is_FluctuatingCharge) { |
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> |
|
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> |
RealType a = electrostaticAtomData.slaterZeta; |
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> |
RealType b = (*it).slaterZeta; |
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> |
int m = electrostaticAtomData.slaterN; |
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> |
int n = (*it).slaterN; |
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> |
|
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> |
// Create the spline of the coulombic integral for s-type |
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> |
// Slater orbitals. Add a 2 angstrom safety window to deal |
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> |
// with cutoffGroups that have charged atoms longer than the |
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> |
// cutoffRadius away from each other. |
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> |
|
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> |
RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1); |
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> |
vector<RealType> rvals; |
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> |
vector<RealType> J1vals; |
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> |
vector<RealType> J2vals; |
| 361 |
> |
for (int i = 0; i < np_; i++) { |
| 362 |
> |
rval = RealType(i) * dr; |
| 363 |
> |
rvals.push_back(rval); |
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> |
J1vals.push_back( sSTOCoulInt( a, b, m, n, rval * PhysicalConstants::angstromsToBohr ) ); |
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> |
J2vals.push_back( sSTOCoulInt( b, a, n, m, rval * PhysicalConstants::angstromsToBohr ) ); |
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> |
} |
| 367 |
> |
|
| 368 |
> |
CubicSpline J1 = new CubicSpline(); |
| 369 |
> |
J1->addPoints(rvals, J1vals); |
| 370 |
> |
CubicSpline J2 = new CubicSpline(); |
| 371 |
> |
J2->addPoints(rvals, J2vals); |
| 372 |
> |
|
| 373 |
> |
pair<AtomType*, AtomType*> key1, key2; |
| 374 |
> |
key1 = make_pair(atomType, atype2); |
| 375 |
> |
key2 = make_pair(atype2, atomType); |
| 376 |
> |
|
| 377 |
> |
Jij[key1] = J1; |
| 378 |
> |
Jij[key2] = J2; |
| 379 |
> |
} |
| 380 |
> |
} |
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> |
|
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|
return; |
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|
} |
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|
