MisesFisherGaussPeakShape Class Reference

Description

A peak shape that is Gaussian in the radial direction and a convolution of a Mises-Fisher distribution with a Mises distribution on the two-sphere.

Definition at line 145 of file IPeakShape.h.

Inheritance diagram for MisesFisherGaussPeakShape:

Collaboration diagram for MisesFisherGaussPeakShape:

Public Member Functions
	MisesFisherGaussPeakShape (double max_intensity, double radial_size, R3 zenith, double kappa_1, double kappa_2)
	~MisesFisherGaussPeakShape () override
bool	angularDisorder () const override
	Indicates if the peak shape encodes angular disorder, in which case all peaks in a spherical shell are needed. More...
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...
MisesFisherGaussPeakShape *	clone () const override
virtual std::vector< const INode * >	nodeChildren () const
	Returns all children. More...
std::vector< const INode * >	nodeOffspring () const
	Returns all descendants. More...
std::vector< ParaMeta >	parDefs () const final
	Returns the parameter definitions, to be hard-coded in each leaf class. More...
double	peakDistribution (R3 q, R3 q_lattice_point) const override
	Peak shape at q from a reciprocal lattice point at q_lattice_point. More...
virtual void	transferToCPP ()
	Used for Python overriding of clone (see swig/tweaks.py) More...

Protected Attributes
std::vector< double >	m_P

Private Attributes
double	m_kappa_1
double	m_kappa_2
double	m_max_intensity
double	m_radial_size
R3	m_zenith

Constructor & Destructor Documentation

MisesFisherGaussPeakShape()

MisesFisherGaussPeakShape::MisesFisherGaussPeakShape	(	double	max_intensity,
		double	radial_size,
		R3	zenith,
		double	kappa_1,
		double	kappa_2
	)

Definition at line 210 of file IPeakShape.cpp.

    : m_max_intensity(max_intensity)
    , m_radial_size(radial_size)
    , m_zenith(zenith.unit())
    , m_kappa_1(kappa_1)
    , m_kappa_2(kappa_2)
{
}

Referenced by clone().

~MisesFisherGaussPeakShape()

MisesFisherGaussPeakShape::~MisesFisherGaussPeakShape ( )

overridedefault

Member Function Documentation

angularDisorder()

bool MisesFisherGaussPeakShape::angularDisorder ( ) const

inlineoverridevirtual

Indicates if the peak shape encodes angular disorder, in which case all peaks in a spherical shell are needed.

Reimplemented from IPeakShape.

Definition at line 163 of file IPeakShape.h.

{ return true; }

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 MisesFisherGaussPeakShape::className ( ) const

inlinefinalvirtual

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

Implements INode.

Definition at line 152 of file IPeakShape.h.

{ return "MisesFisherGaussPeakShape"; }

clone()

MisesFisherGaussPeakShape * MisesFisherGaussPeakShape::clone ( ) const

overridevirtual

Implements IPeakShape.

Definition at line 222 of file IPeakShape.cpp.

{
    return new MisesFisherGaussPeakShape(m_max_intensity, m_radial_size, m_zenith, m_kappa_1,
                                         m_kappa_2);
}

References MisesFisherGaussPeakShape(), m_kappa_1, m_kappa_2, m_max_intensity, m_radial_size, and m_zenith.

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nodeChildren()

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

virtualinherited

Returns all children.

Reimplemented in ISimulation2D, ISimulation, ParticleCoreShell, ParticleComposition, Particle, MesoCrystal, IParticle, Crystal, MultiLayer, Layer, LayerInterface, ParticleLayout, InterferenceRadialParaCrystal, InterferenceFinite3DLattice, InterferenceFinite2DLattice, Interference3DLattice, Interference2DSuperLattice, Interference2DParaCrystal, Interference2DLattice, Interference1DLattice, ConvolutionDetectorResolution, IDetector, and Beam.

Definition at line 56 of file INode.cpp.

{
    return {};
}

Referenced by NodeUtils::AllDescendantsOfType(), NodeUtils::ChildNodesOfType(), ISampleNode::containedMaterials(), and INode::nodeOffspring().

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()

std::vector<ParaMeta> MisesFisherGaussPeakShape::parDefs ( ) const

inlinefinalvirtual

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

Reimplemented from INode.

Definition at line 153 of file IPeakShape.h.

    {
        return {{"MaxIntensity", "", "maximum intensity", 0, +INF, -1},
                {"Radial Size", "nm", "radial size", 0, +INF, -1},
                {"Kappa1", "", "?", 0, +INF, -1},
                {"Kappa2", "", "?", 0, +INF, -1}};
    }

References INF.

peakDistribution()

double MisesFisherGaussPeakShape::peakDistribution ( R3  q, R3  q_lattice_point  ) const

overridevirtual

Peak shape at q from a reciprocal lattice point at q_lattice_point.

Implements IPeakShape.

Definition at line 228 of file IPeakShape.cpp.

{
    // radial part
    const double q_r = q.mag();
    const double q_lat_r = q_lattice_point.mag();
    const double dq2 = (q_r - q_lat_r) * (q_r - q_lat_r);
    if (q_lat_r == 0.0 || q_r == 0.0)
        return m_max_intensity * Gauss3D(dq2, m_radial_size);
    const double norm_factor = m_radial_size / std::sqrt(M_TWOPI);
    const double radial_part = norm_factor * std::exp(-dq2 * m_radial_size * m_radial_size / 2.0);
    // angular part
    const R3 vy = m_zenith.cross(q_lattice_point);
    const R3 zxq = m_zenith.cross(q);
    const R3 up = q_lattice_point.unit();
    if (vy.mag2() <= 0.0 || zxq.mag2() <= 0.0) {
        const double x = q.unit().dot(up);
        const double angular_part = FisherDistribution(x, m_kappa_1);
        return m_max_intensity * radial_part * angular_part;
    }
    const R3 uy = vy.unit();
    const R3 ux = uy.cross(m_zenith);
    const R3 q_ortho = q - q.dot(m_zenith) * m_zenith;
    const double phi0 = std::acos(q_ortho.unit().dot(ux));
    const double theta = std::acos(q.unit().dot(m_zenith));
    const double pre_1 = FisherPrefactor(m_kappa_1);
    const double pre_2 = MisesPrefactor(m_kappa_2);
    const double integral = RealIntegrator().integrate(
        [=](double phi) -> double {
            const R3 u_q = std::sin(theta) * std::cos(phi) * ux
                           + std::sin(theta) * std::sin(phi) * uy + std::cos(theta) * m_zenith;
            const double fisher = std::exp(m_kappa_1 * (u_q.dot(up) - 1.0));
            const double mises = std::exp(m_kappa_2 * (std::cos(phi0 - phi) - 1.0));
            return fisher * mises;
        },
        0.0, M_TWOPI);
    return m_max_intensity * radial_part * pre_1 * pre_2 * integral;
}

References RealIntegrator::integrate(), m_kappa_1, m_kappa_2, m_max_intensity, m_radial_size, M_TWOPI, and m_zenith.

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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_kappa_1

double MisesFisherGaussPeakShape::m_kappa_1

private

Definition at line 169 of file IPeakShape.h.

Referenced by clone(), and peakDistribution().

m_kappa_2

double MisesFisherGaussPeakShape::m_kappa_2

private

Definition at line 169 of file IPeakShape.h.

Referenced by clone(), and peakDistribution().

m_max_intensity

double MisesFisherGaussPeakShape::m_max_intensity

private

Definition at line 166 of file IPeakShape.h.

Referenced by clone(), and peakDistribution().

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_radial_size

double MisesFisherGaussPeakShape::m_radial_size

private

Definition at line 167 of file IPeakShape.h.

Referenced by clone(), and peakDistribution().

m_zenith

R3 MisesFisherGaussPeakShape::m_zenith

private

Definition at line 168 of file IPeakShape.h.

Referenced by clone(), and peakDistribution().

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

• /home/build/builds/o5h8MZZm/0/mlz/bornagain/Sample/Correlations/IPeakShape.h
• /home/build/builds/o5h8MZZm/0/mlz/bornagain/Sample/Correlations/IPeakShape.cpp