Interference2DLattice Class Reference

Description

Interference function of a 2D lattice.

Definition at line 25 of file Interference2DLattice.h.

Inheritance diagram for Interference2DLattice:

Collaboration diagram for Interference2DLattice:

Public Member Functions
	Interference2DLattice (const Lattice2D &lattice)
	~Interference2DLattice () override
void	checkNodeArgs () const
	Raises exception if a parameter value is invalid. More...
std::string	className () const final
	Returns the class name, to be hard-coded in each leaf class that inherits from INode. More...
Interference2DLattice *	clone () const override
double	DWfactor (R3 q) const
	structureFactors the Debye-Waller factor for a given wavevector transfer More...
bool	integrationOverXi () const
const Lattice2D &	lattice () const
std::vector< const INode * >	nodeChildren () const override
	Returns all children. More...
std::vector< const INode * >	nodeOffspring () const
	Returns all descendants. More...
virtual std::vector< ParaMeta >	parDefs () const
	Returns the parameter definitions, to be hard-coded in each leaf class. More...
double	particleDensity () const override
	Returns the particle density associated with this 2d lattice. More...
double	positionVariance () const
	Returns the position variance. More...
void	setDecayFunction (const IProfile2D &decay)
	Sets two-dimensional decay function. More...
void	setIntegrationOverXi (bool integrate_xi)
void	setPositionVariance (double var)
	Sets the variance of the position for the calculation of the DW factor It is defined as the variance in each relevant dimension. More...
virtual double	structureFactor (R3 q, double outer_iff=1.0) const
	The interference function for a given wavevector transfer. More...
virtual bool	supportsMultilayer () const
	Indicates if this interference function can be used with a sample (DWBA mode) More...
virtual void	transferToCPP ()
	Used for Python overriding of clone (see swig/tweaks.py) More...

Protected Member Functions
double	iff_no_inner (R3 q, double outer_iff) const
	Calculates the structure factor in the absence of extra inner structure. More...

Protected Attributes
std::vector< double >	m_P
double	m_position_var

Private Member Functions
std::pair< double, double >	calculateReciprocalVectorFraction (double qx, double qy, double xi) const
	Returns qx,qy coordinates of q - qint, where qint is a reciprocal lattice vector bounding the reciprocal unit cell to which q belongs. More...
double	iff_without_dw (R3 q) const override
	Calculates the structure factor without Debye-Waller factor. More...
double	interferenceAtOneRecLatticePoint (double qx, double qy) const
	Returns interference from a single reciprocal lattice vector. More...
double	interferenceForXi (double xi, double qx, double qy) const
std::pair< double, double >	rotateOrthonormal (double qx, double qy, double gamma) const
	Returns reciprocal coordinates in the coordinate system rotated by the angle gamma. More...

Private Attributes
std::unique_ptr< IProfile2D >	m_decay
bool	m_integrate_xi
	Integrate over the orientation xi. More...
std::unique_ptr< Lattice2D >	m_lattice
int	m_na
int	m_nb
	determines the number of reciprocal lattice points to use More...
Lattice2D::ReciprocalBases	m_sbase
	reciprocal lattice is stored without xi More...

Constructor & Destructor Documentation

Interference2DLattice()

Interference2DLattice::Interference2DLattice

(

const Lattice2D &

lattice

)

Definition at line 50 of file Interference2DLattice.cpp.

    : IInterference(0)
    , m_integrate_xi(false)
{
    m_lattice.reset(lattice.clone());
    if (!m_lattice)
        throw std::runtime_error("Interference2DLattice::initialize_rec_vectors() -> "
                                 "Error. No lattice defined yet");
 
    BasicLattice2D base_lattice(m_lattice->length1(), m_lattice->length2(),
                                m_lattice->latticeAngle(), 0.);
    m_sbase = base_lattice.reciprocalBases();
}

References Lattice2D::clone(), lattice(), m_lattice, m_sbase, and Lattice2D::reciprocalBases().

Referenced by clone().

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~Interference2DLattice()

Interference2DLattice::~Interference2DLattice ( )

overridedefault

Member Function Documentation

calculateReciprocalVectorFraction()

std::pair< double, double > Interference2DLattice::calculateReciprocalVectorFraction ( double  qx, double  qy, double  xi  ) const

private

Returns qx,qy coordinates of q - qint, where qint is a reciprocal lattice vector bounding the reciprocal unit cell to which q belongs.

Definition at line 171 of file Interference2DLattice.cpp.

{
    double a = m_lattice->length1();
    double b = m_lattice->length2();
    double alpha = m_lattice->latticeAngle();
    // first rotate the input to the system of m_sbase:
    double qx_rot = qx * std::cos(xi) + qy * std::sin(xi);
    double qy_rot = -qx * std::sin(xi) + qy * std::cos(xi);
 
    // find the reciprocal lattice coordinates of (qx_rot, qy_rot):
    int qa_int = static_cast<int>(std::lround(a * qx_rot / M_TWOPI));
    int qb_int = static_cast<int>(
        std::lround(b * (qx_rot * std::cos(alpha) + qy_rot * std::sin(alpha)) / M_TWOPI));
    // take the fractional part only (in m_sbase coordinates)
    double qx_frac = qx_rot - qa_int * m_sbase.m_asx - qb_int * m_sbase.m_bsx;
    double qy_frac = qy_rot - qa_int * m_sbase.m_asy - qb_int * m_sbase.m_bsy;
    return {qx_frac, qy_frac};
}

References Lattice2D::ReciprocalBases::m_asx, Lattice2D::ReciprocalBases::m_asy, Lattice2D::ReciprocalBases::m_bsx, Lattice2D::ReciprocalBases::m_bsy, m_lattice, m_sbase, and M_TWOPI.

Referenced by interferenceForXi().

checkNodeArgs()

void INode::checkNodeArgs ( ) const

inherited

Raises exception if a parameter value is invalid.

Definition at line 27 of file INode.cpp.

{
    size_t nP = m_P.size();
    if (parDefs().size() != nP) {
        std::cerr << "BUG in class " << className() << std::endl;
        std::cerr << "#m_P = " << nP << std::endl;
        std::cerr << "#PDf = " << parDefs().size() << std::endl;
        for (const ParaMeta& pm : parDefs())
            std::cerr << "  PDf: " << pm.name << std::endl;
        ASSERT(0);
    }
    ASSERT(parDefs().size() == nP);
    for (size_t i = 0; i < nP; ++i) {
        const ParaMeta pm = parDefs()[i];
 
        RealLimits limits = RealLimits::limitless();
        if (pm.vMin == -INF) {
            ASSERT(pm.vMax == +INF);
            // nothing to do
        } else if (pm.vMax == +INF) {
            ASSERT(pm.vMin == 0);
            limits = RealLimits::nonnegative();
        } else {
            limits = RealLimits::limited(pm.vMin, pm.vMax);
        }
        limits.check(pm.name, m_P[i]);
    }
}

References ASSERT, RealLimits::check(), INode::className(), INF, RealLimits::limited(), RealLimits::limitless(), INode::m_P, ParaMeta::name, RealLimits::nonnegative(), INode::parDefs(), ParaMeta::vMax, and ParaMeta::vMin.

Referenced by BarGauss::BarGauss(), BarLorentz::BarLorentz(), Bipyramid4::Bipyramid4(), Box::Box(), CantellatedCube::CantellatedCube(), Cone::Cone(), ConstantBackground::ConstantBackground(), CosineRippleBox::CosineRippleBox(), CosineRippleGauss::CosineRippleGauss(), CosineRippleLorentz::CosineRippleLorentz(), Cylinder::Cylinder(), DistributionCosine::DistributionCosine(), DistributionGate::DistributionGate(), DistributionGaussian::DistributionGaussian(), DistributionLogNormal::DistributionLogNormal(), DistributionLorentz::DistributionLorentz(), DistributionTrapezoid::DistributionTrapezoid(), Dodecahedron::Dodecahedron(), EllipsoidalCylinder::EllipsoidalCylinder(), FootprintGauss::FootprintGauss(), FootprintSquare::FootprintSquare(), FuzzySphere::FuzzySphere(), GaussSphere::GaussSphere(), HemiEllipsoid::HemiEllipsoid(), HollowSphere::HollowSphere(), HorizontalCylinder::HorizontalCylinder(), Icosahedron::Icosahedron(), LongBoxGauss::LongBoxGauss(), LongBoxLorentz::LongBoxLorentz(), PlatonicOctahedron::PlatonicOctahedron(), PlatonicTetrahedron::PlatonicTetrahedron(), Prism3::Prism3(), Prism6::Prism6(), Profile1DCauchy::Profile1DCauchy(), Profile1DCosine::Profile1DCosine(), Profile1DGate::Profile1DGate(), Profile1DGauss::Profile1DGauss(), Profile1DTriangle::Profile1DTriangle(), Profile1DVoigt::Profile1DVoigt(), Profile2DCauchy::Profile2DCauchy(), Profile2DCone::Profile2DCone(), Profile2DGate::Profile2DGate(), Profile2DGauss::Profile2DGauss(), Profile2DVoigt::Profile2DVoigt(), Pyramid2::Pyramid2(), Pyramid3::Pyramid3(), Pyramid4::Pyramid4(), Pyramid6::Pyramid6(), RotationEuler::RotationEuler(), RotationX::RotationX(), RotationY::RotationY(), RotationZ::RotationZ(), SawtoothRippleBox::SawtoothRippleBox(), SawtoothRippleGauss::SawtoothRippleGauss(), SawtoothRippleLorentz::SawtoothRippleLorentz(), Sphere::Sphere(), Spheroid::Spheroid(), TruncatedCube::TruncatedCube(), TruncatedSphere::TruncatedSphere(), and TruncatedSpheroid::TruncatedSpheroid().

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className()

std::string Interference2DLattice::className ( ) const

inlinefinalvirtual

Returns the class name, to be hard-coded in each leaf class that inherits from INode.

Implements INode.

Definition at line 31 of file Interference2DLattice.h.

{ return "Interference2DLattice"; }

clone()

Interference2DLattice * Interference2DLattice::clone ( ) const

overridevirtual

Implements IInterference.

Definition at line 66 of file Interference2DLattice.cpp.

{
    auto* result = new Interference2DLattice(*m_lattice);
    result->setPositionVariance(m_position_var);
    result->setIntegrationOverXi(integrationOverXi());
    if (m_decay)
        result->setDecayFunction(*m_decay);
    return result;
}

References Interference2DLattice(), integrationOverXi(), m_decay, m_lattice, and IInterference::m_position_var.

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DWfactor()

double IInterference::DWfactor ( R3  q ) const

inherited

structureFactors the Debye-Waller factor for a given wavevector transfer

Definition at line 48 of file IInterference.cpp.

{
    // remove z component for two-dimensional interference functions:
    if (supportsMultilayer())
        q.setZ(0.0);
    return std::exp(-q.mag2() * m_position_var);
}

References IInterference::m_position_var, and IInterference::supportsMultilayer().

Referenced by IInterference::iff_no_inner(), and Interference2DSuperLattice::interferenceForXi().

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iff_no_inner()

double IInterference::iff_no_inner ( R3  q, double  outer_iff  ) const

protectedinherited

Calculates the structure factor in the absence of extra inner structure.

Definition at line 56 of file IInterference.cpp.

{
    return DWfactor(q) * (iff_without_dw(q) * outer_iff - 1.0) + 1.0;
}

References IInterference::DWfactor(), and IInterference::iff_without_dw().

Referenced by IInterference::structureFactor().

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iff_without_dw()

double Interference2DLattice::iff_without_dw ( R3  q ) const

overrideprivatevirtual

Calculates the structure factor without Debye-Waller factor.

Implements IInterference.

Definition at line 120 of file Interference2DLattice.cpp.

{
    if (!m_decay)
        throw std::runtime_error("Interference2DLattice::evaluate"
                                 " -> Error! No decay function defined.");
    if (!m_integrate_xi)
        return interferenceForXi(m_lattice->rotationAngle(), q.x(), q.y());
    return RealIntegrator().integrate(
               [&](double xi) -> double { return interferenceForXi(xi, q.x(), q.y()); }, 0.0,
               M_TWOPI)
           / M_TWOPI;
}

References RealIntegrator::integrate(), interferenceForXi(), m_decay, m_integrate_xi, m_lattice, and M_TWOPI.

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integrationOverXi()

bool Interference2DLattice::integrationOverXi ( ) const

inline

Definition at line 36 of file Interference2DLattice.h.

{ return m_integrate_xi; }

References m_integrate_xi.

Referenced by clone().

interferenceAtOneRecLatticePoint()

double Interference2DLattice::interferenceAtOneRecLatticePoint ( double  qx, double  qy  ) const

private

Returns interference from a single reciprocal lattice vector.

Definition at line 148 of file Interference2DLattice.cpp.

{
    if (!m_decay)
        throw std::runtime_error("Interference2DLattice::interferenceAtOneRecLatticePoint"
                                 " -> Error! No decay function defined.");
    double gamma = m_decay->gamma();
    auto qXY = rotateOrthonormal(qx, qy, gamma);
    return m_decay->decayFT2D(qXY.first, qXY.second);
}

References ROOT::Math::Cephes::gamma(), m_decay, and rotateOrthonormal().

Referenced by interferenceForXi().

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interferenceForXi()

double Interference2DLattice::interferenceForXi ( double  xi, double  qx, double  qy  ) const

private

Definition at line 133 of file Interference2DLattice.cpp.

{
    double result = 0.0;
    auto q_frac = calculateReciprocalVectorFraction(qx, qy, xi);
 
    for (int i = -m_na - 1; i < m_na + 2; ++i) {
        for (int j = -m_nb - 1; j < m_nb + 2; ++j) {
            const double px = q_frac.first + i * m_sbase.m_asx + j * m_sbase.m_bsx;
            const double py = q_frac.second + i * m_sbase.m_asy + j * m_sbase.m_bsy;
            result += interferenceAtOneRecLatticePoint(px, py);
        }
    }
    return particleDensity() * result;
}

References calculateReciprocalVectorFraction(), interferenceAtOneRecLatticePoint(), Lattice2D::ReciprocalBases::m_asx, Lattice2D::ReciprocalBases::m_asy, Lattice2D::ReciprocalBases::m_bsx, Lattice2D::ReciprocalBases::m_bsy, m_na, m_nb, m_sbase, and particleDensity().

Referenced by iff_without_dw().

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lattice()

const Lattice2D & Interference2DLattice::lattice

(

)

const

Definition at line 101 of file Interference2DLattice.cpp.

{
    if (!m_lattice)
        throw std::runtime_error("Interference2DLattice::lattice() -> Error. "
                                 "No lattice defined.");
    return *m_lattice;
}

References m_lattice.

Referenced by Interference2DLattice().

nodeChildren()

std::vector< const INode * > Interference2DLattice::nodeChildren ( ) const

overridevirtual

Returns all children.

Reimplemented from INode.

Definition at line 115 of file Interference2DLattice.cpp.

{
    return std::vector<const INode*>() << m_decay << m_lattice;
}

References m_decay, and m_lattice.

nodeOffspring()

std::vector< const INode * > INode::nodeOffspring ( ) const

inherited

Returns all descendants.

Definition at line 61 of file INode.cpp.

{
    std::vector<const INode*> result;
    result.push_back(this);
    for (const auto* child : nodeChildren()) {
        for (const auto* p : child->nodeOffspring())
            result.push_back(p);
    }
    return result;
}

References INode::nodeChildren().

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parDefs()

virtual std::vector<ParaMeta> INode::parDefs ( ) const

inlinevirtualinherited

Returns the parameter definitions, to be hard-coded in each leaf class.

Reimplemented in ConstantBackground, GaussSphere, FuzzySphere, RotationEuler, RotationZ, RotationY, RotationX, Crystal, Layer, HexagonalLattice2D, SquareLattice2D, BasicLattice2D, LayerRoughness, TruncatedSpheroid, TruncatedSphere, TruncatedCube, Spheroid, Sphere, SawtoothRippleLorentz, SawtoothRippleGauss, SawtoothRippleBox, Pyramid6, Pyramid4, Pyramid3, Pyramid2, Prism6, Prism3, PlatonicTetrahedron, PlatonicOctahedron, LongBoxLorentz, LongBoxGauss, Icosahedron, HorizontalCylinder, HollowSphere, HemiEllipsoid, EllipsoidalCylinder, Dodecahedron, Cylinder, CosineRippleLorentz, CosineRippleGauss, CosineRippleBox, Cone, CantellatedCube, Box, Bipyramid4, BarLorentz, BarGauss, Profile2DVoigt, Profile2DCone, Profile2DGate, Profile2DGauss, Profile2DCauchy, Profile1DVoigt, Profile1DCosine, Profile1DTriangle, Profile1DGate, Profile1DGauss, Profile1DCauchy, MisesGaussPeakShape, MisesFisherGaussPeakShape, LorentzFisherPeakShape, GaussFisherPeakShape, IsotropicLorentzPeakShape, IsotropicGaussPeakShape, ParticleLayout, InterferenceTwin, InterferenceRadialParaCrystal, InterferenceHardDisk, Interference2DSuperLattice, Interference2DParaCrystal, Interference1DLattice, DistributionTrapezoid, DistributionCosine, DistributionLogNormal, DistributionGaussian, DistributionLorentz, DistributionGate, ResolutionFunction2DGaussian, PolFilter, FootprintSquare, and FootprintGauss.

Definition at line 51 of file INode.h.

{ return {}; }

Referenced by INode::checkNodeArgs(), and IFormFactor::pythonConstructor().

particleDensity()

double Interference2DLattice::particleDensity ( ) const

overridevirtual

Returns the particle density associated with this 2d lattice.

Reimplemented from IInterference.

Definition at line 109 of file Interference2DLattice.cpp.

{
    double area = m_lattice->unitCellArea();
    return area == 0.0 ? 0.0 : 1.0 / area;
}

References m_lattice.

Referenced by interferenceForXi().

positionVariance()

double IInterference::positionVariance ( ) const

inlineinherited

Returns the position variance.

Definition at line 40 of file IInterference.h.

{ return m_position_var; }

References IInterference::m_position_var.

rotateOrthonormal()

std::pair< double, double > Interference2DLattice::rotateOrthonormal ( double  qx, double  qy, double  gamma  ) const

private

Returns reciprocal coordinates in the coordinate system rotated by the angle gamma.

Definition at line 159 of file Interference2DLattice.cpp.

{
    double q_X = qx * std::cos(gamma) + qy * std::sin(gamma);
    double q_Y = -qx * std::sin(gamma) + qy * std::cos(gamma);
    return {q_X, q_Y};
}

References ROOT::Math::Cephes::gamma().

Referenced by interferenceAtOneRecLatticePoint().

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setDecayFunction()

void Interference2DLattice::setDecayFunction

(

const IProfile2D &

decay

)

Sets two-dimensional decay function.

Parameters

decay

two-dimensional decay function in reciprocal space

Definition at line 78 of file Interference2DLattice.cpp.

{
    m_decay.reset(decay.clone());
    if (!m_decay)
        throw std::runtime_error("Interference2DLattice::initialize_calc_factors"
                                 " -> Error! No decay function defined.");
 
    // number of reciprocal lattice points to use
    auto q_bounds = boundingReciprocalLatticeCoordinates(
        nmax / m_decay->decayLengthX(), nmax / m_decay->decayLengthY(), m_lattice->length1(),
        m_lattice->length2(), m_lattice->latticeAngle(), m_decay->gamma());
    m_na = static_cast<int>(std::lround(q_bounds.first + 0.5));
    m_nb = static_cast<int>(std::lround(q_bounds.second + 0.5));
    m_na = std::max(m_na, min_points);
    m_nb = std::max(m_nb, min_points);
}

References IProfile2D::clone(), m_decay, m_lattice, m_na, and m_nb.

Referenced by ExemplarySamples::createBasic2DLattice(), ExemplarySamples::createBoxesSquareLattice2D(), ExemplarySamples::createCenteredSquareLattice2D(), ExemplarySamples::createParticleComposition(), ExemplarySamples::createRotatedSquareLattice2D(), and ExemplarySamples::createSquareLattice2D().

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setIntegrationOverXi()

void Interference2DLattice::setIntegrationOverXi

(

bool

integrate_xi

)

Definition at line 95 of file Interference2DLattice.cpp.

{
    m_integrate_xi = integrate_xi;
    m_lattice->setRotationEnabled(!m_integrate_xi); // deregister Xi in the case of integration
}

References m_integrate_xi, and m_lattice.

setPositionVariance()

void IInterference::setPositionVariance ( double  var )

inherited

Sets the variance of the position for the calculation of the DW factor It is defined as the variance in each relevant dimension.

Definition at line 40 of file IInterference.cpp.

{
    if (var < 0.0)
        throw std::runtime_error("IInterference::setPositionVariance: "
                                 "variance should be positive.");
    m_position_var = var;
}

References IInterference::m_position_var.

Referenced by ExemplarySamples::createFiniteSquareLattice2D(), and ExemplarySamples::createSuperLattice().

structureFactor()

double IInterference::structureFactor ( R3  q, double  outer_iff = 1.0  ) const

virtualinherited

The interference function for a given wavevector transfer.

Reimplemented in Interference2DSuperLattice.

Definition at line 35 of file IInterference.cpp.

{
    return iff_no_inner(q, outer_iff);
}

References IInterference::iff_no_inner().

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supportsMultilayer()

virtual bool IInterference::supportsMultilayer ( ) const

inlinevirtualinherited

Indicates if this interference function can be used with a sample (DWBA mode)

Reimplemented in InterferenceFinite3DLattice, and Interference3DLattice.

Definition at line 47 of file IInterference.h.

{ return true; }

Referenced by IInterference::DWfactor().

transferToCPP()

virtual void ICloneable::transferToCPP ( )

inlinevirtualinherited

Used for Python overriding of clone (see swig/tweaks.py)

Definition at line 32 of file ICloneable.h.

Member Data Documentation

m_decay

std::unique_ptr<IProfile2D> Interference2DLattice::m_decay

private

Definition at line 62 of file Interference2DLattice.h.

Referenced by clone(), iff_without_dw(), interferenceAtOneRecLatticePoint(), nodeChildren(), and setDecayFunction().

m_integrate_xi

bool Interference2DLattice::m_integrate_xi

private

Integrate over the orientation xi.

Definition at line 61 of file Interference2DLattice.h.

Referenced by iff_without_dw(), integrationOverXi(), and setIntegrationOverXi().

m_lattice

std::unique_ptr<Lattice2D> Interference2DLattice::m_lattice

private

Definition at line 63 of file Interference2DLattice.h.

Referenced by Interference2DLattice(), calculateReciprocalVectorFraction(), clone(), iff_without_dw(), lattice(), nodeChildren(), particleDensity(), setDecayFunction(), and setIntegrationOverXi().

m_na

int Interference2DLattice::m_na

private

Definition at line 65 of file Interference2DLattice.h.

Referenced by interferenceForXi(), and setDecayFunction().

m_nb

int Interference2DLattice::m_nb

private

determines the number of reciprocal lattice points to use

Definition at line 65 of file Interference2DLattice.h.

Referenced by interferenceForXi(), and setDecayFunction().

m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 63 of file INode.h.

Referenced by IFootprintFactor::IFootprintFactor(), INode::checkNodeArgs(), IProfile1D::pythonConstructor(), IProfile2D::pythonConstructor(), IFormFactor::pythonConstructor(), Profile1DVoigt::pythonConstructor(), and Profile2DVoigt::pythonConstructor().

m_position_var

double IInterference::m_position_var

protectedinherited

Definition at line 53 of file IInterference.h.

Referenced by IInterference::IInterference(), Interference1DLattice::clone(), clone(), Interference2DParaCrystal::clone(), Interference2DSuperLattice::clone(), Interference3DLattice::clone(), InterferenceFinite2DLattice::clone(), InterferenceFinite3DLattice::clone(), InterferenceHardDisk::clone(), InterferenceNone::clone(), InterferenceRadialParaCrystal::clone(), InterferenceTwin::clone(), IInterference::DWfactor(), IInterference::positionVariance(), and IInterference::setPositionVariance().

m_sbase

Lattice2D::ReciprocalBases Interference2DLattice::m_sbase

private

reciprocal lattice is stored without xi

Definition at line 64 of file Interference2DLattice.h.

Referenced by Interference2DLattice(), calculateReciprocalVectorFraction(), and interferenceForXi().

---

The documentation for this class was generated from the following files:

• /home/build/builds/o5h8MZZm/0/mlz/bornagain/Sample/Aggregate/Interference2DLattice.h
• /home/build/builds/o5h8MZZm/0/mlz/bornagain/Sample/Aggregate/Interference2DLattice.cpp