InterferenceFunction2DParaCrystal Class Reference

Interference function of a 2D paracrystal. More...

Inheritance diagram for InterferenceFunction2DParaCrystal:

Collaboration diagram for InterferenceFunction2DParaCrystal:

Public Member Functions
	InterferenceFunction2DParaCrystal (const Lattice2D &lattice, double damping_length, double domain_size_1, double domain_size_2)
	~InterferenceFunction2DParaCrystal () override
void	accept (INodeVisitor *visitor) const override
	Calls the INodeVisitor's visit method. More...
InterferenceFunction2DParaCrystal *	clone () const override
	Returns a clone of this ISampleNode object. More...
std::vector< const Material * >	containedMaterials () const
	Returns set of unique materials contained in this ISampleNode. More...
int	copyNumber (const INode *node) const
	Returns copyNumber of child, which takes into account existence of children with same name. More...
ParameterPool *	createParameterTree () const
	Creates new parameter pool, with all local parameters and those of its children. More...
double	dampingLength () const
std::string	displayName () const
	Returns display name, composed from the name of node and it's copy number. More...
std::vector< double >	domainSizes () const
double	DWfactor (kvector_t q) const
	Evaluates the Debye-Waller factor for a given wavevector transfer. More...
virtual double	evaluate (const kvector_t q, double outer_iff=1.0) const
	Evaluates the interference function for a given wavevector transfer. More...
std::vector< const INode * >	getChildren () const override
	Returns a vector of children. More...
const std::string &	getName () const
double	getParticleDensity () const override
	If defined by this interference function's parameters, returns the particle density (per area). More...
bool	integrationOverXi () const
bool	isMagnetic () const
	Returns true if there is any magnetic material in this ISampleNode. More...
const Lattice2D &	lattice () const
virtual const Material *	material () const
	Returns nullptr, unless overwritten to return a specific material. More...
virtual void	onChange ()
	Action to be taken in inherited class when a parameter has changed. More...
RealParameter *	parameter (const std::string &name) const
	Returns parameter with given 'name'. More...
ParameterPool *	parameterPool () const
	Returns pointer to the parameter pool. More...
std::string	parametersToString () const
	Returns multiline string representing available parameters. More...
INode *	parent ()
const INode *	parent () const
const IFTDistribution2D *	pdf1 () const
const IFTDistribution2D *	pdf2 () const
double	positionVariance () const
	Returns the position variance. More...
std::vector< const INode * >	progeny () const
	Returns a vector of all descendants. More...
void	registerChild (INode *node)
RealParameter &	registerParameter (const std::string &name, double *parpointer)
void	registerVector (const std::string &base_name, kvector_t *p_vec, const std::string &units="nm")
void	removeParameter (const std::string &name)
void	removeVector (const std::string &base_name)
void	setDampingLength (double damping_length)
	Sets the damping length. More...
void	setDomainSizes (double size_1, double size_2)
	Sets the sizes of coherence domains. More...
void	setIntegrationOverXi (bool integrate_xi)
	Enables/disables averaging over the lattice rotation angle. More...
void	setName (const std::string &name)
void	setParameterValue (const std::string &name, double value)
virtual void	setParent (const INode *newParent)
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...
void	setProbabilityDistributions (const IFTDistribution2D &pdf_1, const IFTDistribution2D &pdf_2)
	Sets the probability distributions (Fourier transformed) for the two lattice directions. More...
void	setVectorValue (const std::string &base_name, kvector_t value)
virtual bool	supportsMultilayer () const
	Indicates if this interference function can be used with a multilayer (DWBA mode) More...
virtual void	transferToCPP ()
	Used for Python overriding of clone (see swig/tweaks.py) More...
virtual std::string	treeToString () const
	Returns multiline string representing tree structure below the node. More...

Static Public Member Functions
static std::string	XComponentName (const std::string &base_name)
static std::string	YComponentName (const std::string &base_name)
static std::string	ZComponentName (const std::string &base_name)

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

Protected Attributes
const size_t	m_NP
std::vector< double >	m_P
double	m_position_var

Private Member Functions
complex_t	FTPDF (double qx, double qy, double xi, size_t index) const
double	iff_without_dw (const kvector_t q) const override
	Calculates the structure factor without Debye-Waller factor. More...
double	interference1D (double qx, double qy, double xi, size_t index) const
	Returns interference function for fixed xi in the dimension determined by the given index. More...
double	interferenceForXi (double xi) const
	Returns interference function for fixed angle xi. More...
void	transformToPrincipalAxes (double qx, double qy, double gamma, double delta, double &q_pa_1, double &q_pa_2) const

Private Attributes
double	m_damping_length
	Damping length for removing delta function singularity at q=0. More...
double	m_domain_sizes [2]
	Coherence domain sizes. More...
bool	m_integrate_xi
	Integrate over the orientation xi. More...
std::unique_ptr< Lattice2D >	m_lattice
std::string	m_name
const INode *	m_parent {nullptr}
std::unique_ptr< IFTDistribution2D >	m_pdf1
std::unique_ptr< IFTDistribution2D >	m_pdf2
std::unique_ptr< ParameterPool >	m_pool
	parameter pool (kind of pointer-to-implementation) More...
double	m_qx
double	m_qy

Detailed Description

Interference function of a 2D paracrystal.

Definition at line 28 of file InterferenceFunction2DParaCrystal.h.

Constructor & Destructor Documentation

InterferenceFunction2DParaCrystal()

InterferenceFunction2DParaCrystal::InterferenceFunction2DParaCrystal	(	const Lattice2D &	lattice,
		double	damping_length,
		double	domain_size_1,
		double	domain_size_2
	)

Definition at line 21 of file InterferenceFunction2DParaCrystal.cpp.

    : IInterferenceFunction(0), m_integrate_xi(false), m_damping_length(damping_length)
{
    setName("Interference2DParaCrystal");
    m_lattice.reset(lattice.clone());
    registerChild(m_lattice.get());
    setDomainSizes(domain_size_1, domain_size_2);
    registerParameter("DampingLength", &m_damping_length).setUnit("nm").setNonnegative();
    registerParameter("DomainSize1", &m_domain_sizes[0]).setUnit("nm").setNonnegative();
    registerParameter("DomainSize2", &m_domain_sizes[1]).setUnit("nm").setNonnegative();
}

References Lattice2D::clone(), lattice(), m_damping_length, m_domain_sizes, m_lattice, INode::registerChild(), IParametricComponent::registerParameter(), setDomainSizes(), IParametricComponent::setName(), RealParameter::setNonnegative(), and RealParameter::setUnit().

Referenced by clone().

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~InterferenceFunction2DParaCrystal()

InterferenceFunction2DParaCrystal::~InterferenceFunction2DParaCrystal ( )

overridedefault

Member Function Documentation

accept()

void InterferenceFunction2DParaCrystal::accept ( INodeVisitor *  visitor ) const

inlineoverridevirtual

Calls the INodeVisitor's visit method.

Implements INode.

Definition at line 37 of file InterferenceFunction2DParaCrystal.h.

{ visitor->visit(this); }

References INodeVisitor::visit().

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clone()

InterferenceFunction2DParaCrystal * InterferenceFunction2DParaCrystal::clone ( ) const

overridevirtual

Returns a clone of this ISampleNode object.

Implements IInterferenceFunction.

Definition at line 38 of file InterferenceFunction2DParaCrystal.cpp.

{
    auto* ret = new InterferenceFunction2DParaCrystal(*m_lattice, m_damping_length,
                                                      m_domain_sizes[0], m_domain_sizes[1]);
    ret->setPositionVariance(m_position_var);
    if (m_pdf1 && m_pdf2)
        ret->setProbabilityDistributions(*m_pdf1, *m_pdf2);
    ret->setIntegrationOverXi(m_integrate_xi);
    return ret;
}

References InterferenceFunction2DParaCrystal(), m_damping_length, m_domain_sizes, m_integrate_xi, m_lattice, m_pdf1, m_pdf2, and IInterferenceFunction::m_position_var.

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containedMaterials()

std::vector< const Material * > ISampleNode::containedMaterials ( ) const

inherited

Returns set of unique materials contained in this ISampleNode.

Definition at line 26 of file ISampleNode.cpp.

{
    std::vector<const Material*> result;
    if (const Material* p_material = material())
        result.push_back(p_material);
    for (const auto* child : getChildren()) {
        if (const ISampleNode* sample = dynamic_cast<const ISampleNode*>(child)) {
            for (const Material* p_material : sample->containedMaterials())
                result.push_back(p_material);
        }
    }
    return result;
}

References INode::getChildren(), and ISampleNode::material().

Referenced by MultiLayerUtils::ContainsCompatibleMaterials(), SampleToPython::initLabels(), and ISampleNode::isMagnetic().

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copyNumber()

int INode::copyNumber ( const INode *  node ) const

inherited

Returns copyNumber of child, which takes into account existence of children with same name.

Definition at line 94 of file INode.cpp.

{
    if (node->parent() != this)
        return -1;
 
    int result(-1), count(0);
    for (auto child : getChildren()) {
 
        if (child == nullptr)
            throw std::runtime_error("INode::copyNumber() -> Error. Nullptr as child.");
 
        if (child == node)
            result = count;
 
        if (child->getName() == node->getName())
            ++count;
    }
 
    return count > 1 ? result : -1;
}

References INode::getChildren(), IParametricComponent::getName(), and INode::parent().

Referenced by INode::displayName().

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createParameterTree()

ParameterPool * INode::createParameterTree ( ) const

virtualinherited

Creates new parameter pool, with all local parameters and those of its children.

Reimplemented from IParametricComponent.

Definition at line 126 of file INode.cpp.

{
    std::unique_ptr<ParameterPool> result(new ParameterPool);
 
    for (const INode* child : progeny()) {
        const std::string path = NodeUtils::nodePath(child, parent()) + "/";
        child->parameterPool()->copyToExternalPool(path, result.get());
    }
 
    return result.release();
}

References NodeUtils::nodePath(), INode::parent(), and INode::progeny().

Referenced by ISimulation::runSimulation(), DepthProbeSimulation::validateParametrization(), OffSpecularSimulation::validateParametrization(), and SpecularSimulation::validateParametrization().

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dampingLength()

double InterferenceFunction2DParaCrystal::dampingLength ( ) const

inline

Definition at line 50 of file InterferenceFunction2DParaCrystal.h.

{ return m_damping_length; }

References m_damping_length.

Referenced by TransformFromDomain::set2DParaCrystalItem().

displayName()

std::string INode::displayName ( ) const

inherited

Returns display name, composed from the name of node and it's copy number.

Definition at line 115 of file INode.cpp.

{
    std::string result = getName();
    if (m_parent) {
        int index = m_parent->copyNumber(this);
        if (index >= 0)
            result = result + std::to_string(index);
    }
    return result;
}

References INode::copyNumber(), IParametricComponent::getName(), and INode::m_parent.

Referenced by NodeUtils::nodePath().

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domainSizes()

std::vector< double > InterferenceFunction2DParaCrystal::domainSizes

(

)

const

Definition at line 177 of file InterferenceFunction2DParaCrystal.cpp.

{
    return {m_domain_sizes[0], m_domain_sizes[1]};
}

References m_domain_sizes.

Referenced by TransformFromDomain::set2DParaCrystalItem().

DWfactor()

double IInterferenceFunction::DWfactor ( kvector_t  q ) const

inherited

Evaluates the Debye-Waller factor for a given wavevector transfer.

Definition at line 48 of file IInterferenceFunction.cpp.

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

References IInterferenceFunction::m_position_var, BasicVector3D< T >::mag2(), BasicVector3D< T >::setZ(), and IInterferenceFunction::supportsMultilayer().

Referenced by IInterferenceFunction::iff_no_inner().

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evaluate()

double IInterferenceFunction::evaluate ( const kvector_t  q, double  outer_iff = 1.0  ) const

virtualinherited

Evaluates the interference function for a given wavevector transfer.

Reimplemented in InterferenceFunction2DSuperLattice.

Definition at line 35 of file IInterferenceFunction.cpp.

{
    return iff_no_inner(q, outer_iff);
}

References IInterferenceFunction::iff_no_inner().

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FTPDF()

complex_t InterferenceFunction2DParaCrystal::FTPDF ( double  qx, double  qy, double  xi, size_t  index  ) const

private

Definition at line 157 of file InterferenceFunction2DParaCrystal.cpp.

{
    double length = (index ? m_lattice->length2() : m_lattice->length1());
 
    const IFTDistribution2D* pdf = (index ? m_pdf2.get() : m_pdf1.get());
    double qa = qx * length * std::cos(xi) + qy * length * std::sin(xi);
    complex_t phase = exp_I(qa);
    // transform q to principal axes:
    double qp1, qp2;
    double gamma = xi + pdf->gamma();
    double delta = pdf->delta();
    transformToPrincipalAxes(qx, qy, gamma, delta, qp1, qp2);
    double amplitude = pdf->evaluate(qp1, qp2);
    complex_t result = phase * amplitude;
    if (m_damping_length != 0.0)
        result *= std::exp(-length / m_damping_length);
    return result;
}

References IFTDistribution2D::delta(), IFTDistribution2D::evaluate(), exp_I(), IFTDistribution2D::gamma(), m_damping_length, m_lattice, m_pdf1, m_pdf2, and transformToPrincipalAxes().

Referenced by interference1D().

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getChildren()

std::vector< const INode * > InterferenceFunction2DParaCrystal::getChildren ( ) const

overridevirtual

Returns a vector of children.

Reimplemented from INode.

Definition at line 76 of file InterferenceFunction2DParaCrystal.cpp.

{
    return std::vector<const INode*>() << m_pdf1 << m_pdf2 << m_lattice;
}

References m_lattice, m_pdf1, and m_pdf2.

getName()

const std::string& IParametricComponent::getName ( ) const

inlineinherited

Definition at line 70 of file IParametricComponent.h.

{ return m_name; }

References IParametricComponent::m_name.

Referenced by Beam::Beam(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), IDetector::IDetector(), Instrument::Instrument(), IParametricComponent::IParametricComponent(), SampleBuilderNode::SampleBuilderNode(), Layer::clone(), INode::copyNumber(), IParametricComponent::createParameterTree(), IFormFactor::createSlicedFormFactor(), SampleToPython::defineInterferenceFunctions(), INode::displayName(), Beam::operator=(), SampleBuilderNode::operator=(), GUIObjectBuilder::populateInstrumentModel(), PyImportAssistant::populateModels(), GUIDomainSampleVisitor::populateSampleModel(), IParametricComponent::registerParameter(), IFormFactor::sliceFormFactor(), and GUIDomainSampleVisitor::visit().

getParticleDensity()

double InterferenceFunction2DParaCrystal::getParticleDensity ( ) const

overridevirtual

If defined by this interference function's parameters, returns the particle density (per area).

Otherwise, returns zero or a user-defined value

Reimplemented from IInterferenceFunction.

Definition at line 70 of file InterferenceFunction2DParaCrystal.cpp.

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

References m_lattice.

iff_no_inner()

double IInterferenceFunction::iff_no_inner ( const kvector_t  q, double  outer_iff  ) const

protectedinherited

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

Definition at line 56 of file IInterferenceFunction.cpp.

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

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

Referenced by IInterferenceFunction::evaluate(), and InterferenceFunction2DSuperLattice::interferenceForXi().

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iff_without_dw()

double InterferenceFunction2DParaCrystal::iff_without_dw ( const kvector_t  q ) const

overrideprivatevirtual

Calculates the structure factor without Debye-Waller factor.

Implements IInterferenceFunction.

Definition at line 81 of file InterferenceFunction2DParaCrystal.cpp.

{
    m_qx = q.x();
    m_qy = q.y();
    if (!m_integrate_xi)
        return interferenceForXi(m_lattice->rotationAngle());
    return RealIntegrator().integrate([&](double xi) -> double { return interferenceForXi(xi); },
                                      0.0, M_TWOPI)
           / M_TWOPI;
}

References RealIntegrator::integrate(), interferenceForXi(), m_integrate_xi, m_lattice, m_qx, m_qy, M_TWOPI, BasicVector3D< T >::x(), and BasicVector3D< T >::y().

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integrationOverXi()

bool InterferenceFunction2DParaCrystal::integrationOverXi ( ) const

inline

Definition at line 49 of file InterferenceFunction2DParaCrystal.h.

{ return m_integrate_xi; }

References m_integrate_xi.

Referenced by TransformFromDomain::set2DParaCrystalItem().

interference1D()

double InterferenceFunction2DParaCrystal::interference1D ( double  qx, double  qy, double  xi, size_t  index  ) const

private

Returns interference function for fixed xi in the dimension determined by the given index.

Definition at line 120 of file InterferenceFunction2DParaCrystal.cpp.

{
    if (index > 1)
        throw std::runtime_error("InterferenceFunction2DParaCrystal::"
                                 "interference1D() -> Error! Index of interference function "
                                 "probability must be < 2");
    if (!m_pdf1 || !m_pdf2)
        throw std::runtime_error("InterferenceFunction2DParaCrystal::"
                                 "interference1D() -> Error! Probability distributions for "
                                 "interference function not properly initialized");
 
    double length = index ? m_lattice->length2() : m_lattice->length1();
    int n = static_cast<int>(std::abs(m_domain_sizes[index] / length));
    double nd = static_cast<double>(n);
    complex_t fp = FTPDF(qx, qy, xi, index);
    if (n < 1)
        return ((1.0 + fp) / (1.0 - fp)).real();
    if (std::norm(1.0 - fp) < std::numeric_limits<double>::epsilon())
        return nd;
    // for (1-fp)*nd small, take the series expansion to second order in nd*(1-fp)
    if (std::abs(1.0 - fp) * nd < 2e-4) {
        complex_t intermediate =
            (nd - 1.0) / 2.0 + (nd * nd - 1.0) * (fp - 1.0) / 6.0
            + (nd * nd * nd - 2.0 * nd * nd - nd + 2.0) * (fp - 1.0) * (fp - 1.0) / 24.0;
        return 1.0 + 2.0 * intermediate.real();
    }
    complex_t tmp;
    if (std::abs(fp) == 0.0
        || std::log(std::abs(fp)) * nd < std::log(std::numeric_limits<double>::min()))
        tmp = 0.0;
    else
        tmp = std::pow(fp, n);
    complex_t intermediate = fp / (1.0 - fp) - fp * (1.0 - tmp) / nd / (1.0 - fp) / (1.0 - fp);
    return 1.0 + 2.0 * intermediate.real();
}

References FTPDF(), m_domain_sizes, m_lattice, m_pdf1, and m_pdf2.

Referenced by interferenceForXi().

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interferenceForXi()

double InterferenceFunction2DParaCrystal::interferenceForXi ( double  xi ) const

private

Returns interference function for fixed angle xi.

Definition at line 111 of file InterferenceFunction2DParaCrystal.cpp.

{
    // don't touch order of computation; problems under Windows
    double rx = interference1D(m_qx, m_qy, xi, 0);
    double ry = interference1D(m_qx, m_qy, xi + m_lattice->latticeAngle(), 1);
    return rx * ry;
}

References interference1D(), m_lattice, m_qx, and m_qy.

Referenced by iff_without_dw().

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isMagnetic()

bool ISampleNode::isMagnetic ( ) const

inherited

Returns true if there is any magnetic material in this ISampleNode.

Definition at line 40 of file ISampleNode.cpp.

{
    const auto materials = containedMaterials();
    return std::any_of(materials.cbegin(), materials.cend(),
                       [](const Material* mat) { return mat->isMagneticMaterial(); });
}

References ISampleNode::containedMaterials().

Referenced by ProcessedSample::initLayouts().

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lattice()

const Lattice2D & InterferenceFunction2DParaCrystal::lattice

(

)

const

Definition at line 191 of file InterferenceFunction2DParaCrystal.cpp.

{
    if (!m_lattice)
        throw std::runtime_error("InterferenceFunction2DParaCrystal::lattice() -> Error. "
                                 "No lattice defined.");
    return *m_lattice;
}

References m_lattice.

Referenced by InterferenceFunction2DParaCrystal(), RealSpace2DParacrystalUtils::Compute2DParacrystalLatticePositions(), and TransformFromDomain::set2DParaCrystalItem().

material()

virtual const Material* ISampleNode::material ( ) const

inlinevirtualinherited

Returns nullptr, unless overwritten to return a specific material.

Reimplemented in Particle, and Layer.

Definition at line 37 of file ISampleNode.h.

{ return nullptr; }

Referenced by ISampleNode::containedMaterials(), FormFactorCoreShell::setAmbientMaterial(), FormFactorCrystal::setAmbientMaterial(), FormFactorWeighted::setAmbientMaterial(), FormFactorDecoratorMaterial::setAmbientMaterial(), IFormFactorDecorator::setAmbientMaterial(), and FormFactorDecoratorMaterial::setMaterial().

onChange()

virtual void IParametricComponent::onChange ( )

inlinevirtualinherited

Action to be taken in inherited class when a parameter has changed.

Reimplemented in IProfileRipple, Lattice3D, InterferenceFunction3DLattice, InterferenceFunction2DLattice, FormFactorSphereLogNormalRadius, FormFactorSphereGaussianRadius, FormFactorGaussSphere, ISawtoothRipple, ICosineRipple, IProfileRectangularRipple, FormFactorTruncatedSpheroid, FormFactorTruncatedSphere, FormFactorTruncatedCube, FormFactorTetrahedron, FormFactorPyramid, FormFactorPrism6, FormFactorPrism3, FormFactorLongBoxLorentz, FormFactorLongBoxGauss, FormFactorIcosahedron, FormFactorHollowSphere, FormFactorHemiEllipsoid, FormFactorFullSpheroid, FormFactorFullSphere, FormFactorEllipsoidalCylinder, FormFactorDodecahedron, FormFactorCylinder, FormFactorCuboctahedron, FormFactorCone6, FormFactorCone, FormFactorCantellatedCube, FormFactorBox, FormFactorAnisoPyramid, and Lattice2D.

Definition at line 59 of file IParametricComponent.h.

{}

Referenced by Lattice2D::onChange(), and IParametricComponent::registerParameter().

parameter()

RealParameter * IParametricComponent::parameter ( const std::string &  name ) const

inherited

Returns parameter with given 'name'.

Definition at line 86 of file IParametricComponent.cpp.

{
    return m_pool->parameter(name);
}

References IParametricComponent::m_pool, and RealSpace::Particles::name().

Referenced by DepthProbeSimulation::initialize(), SpecularSimulation::initialize(), Lattice3D::initialize(), IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), IParticle::registerPosition(), Layer::registerThickness(), Lattice2D::setRotationEnabled(), and DistributionLogNormal::setUnits().

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parameterPool()

ParameterPool* IParametricComponent::parameterPool ( ) const

inlineinherited

Returns pointer to the parameter pool.

Definition at line 39 of file IParametricComponent.h.

{ return m_pool.get(); } // has non-const usages!

References IParametricComponent::m_pool.

Referenced by INode::INode(), IParametricComponent::IParametricComponent(), pyfmt2::argumentList(), SampleBuilderNode::borrow_builder_parameters(), SampleBuilderNode::reset(), and IDistribution1D::setUnits().

parametersToString()

std::string IParametricComponent::parametersToString ( ) const

inherited

Returns multiline string representing available parameters.

Definition at line 43 of file IParametricComponent.cpp.

{
    std::ostringstream result;
    std::unique_ptr<ParameterPool> P_pool(createParameterTree());
    result << *P_pool << "\n";
    return result.str();
}

References IParametricComponent::createParameterTree().

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parent() [1/2]

INode * INode::parent ( )

inherited

Definition at line 89 of file INode.cpp.

{
    return const_cast<INode*>(m_parent);
}

References INode::m_parent.

parent() [2/2]

const INode * INode::parent ( ) const

inherited

Definition at line 84 of file INode.cpp.

{
    return m_parent;
}

References INode::m_parent.

Referenced by INode::copyNumber(), INode::createParameterTree(), ParticleDistribution::generateParticles(), NodeUtils::nodePath(), Lattice2D::onChange(), SampleProvider::setBuilder(), SampleProvider::setParent(), and SampleProvider::setSample().

pdf1()

const IFTDistribution2D* InterferenceFunction2DParaCrystal::pdf1 ( ) const

inline

Definition at line 58 of file InterferenceFunction2DParaCrystal.h.

{ return m_pdf1.get(); }

References m_pdf1.

Referenced by RealSpace2DParacrystalUtils::Compute2DParacrystalLatticePositions().

pdf2()

const IFTDistribution2D* InterferenceFunction2DParaCrystal::pdf2 ( ) const

inline

Definition at line 60 of file InterferenceFunction2DParaCrystal.h.

{ return m_pdf2.get(); }

References m_pdf2.

Referenced by RealSpace2DParacrystalUtils::Compute2DParacrystalLatticePositions().

positionVariance()

double IInterferenceFunction::positionVariance ( ) const

inlineinherited

Returns the position variance.

Definition at line 39 of file IInterferenceFunction.h.

{ return m_position_var; }

References IInterferenceFunction::m_position_var.

Referenced by TransformFromDomain::setFinite2DLatticeItem().

progeny()

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

inherited

Returns a vector of all descendants.

Definition at line 68 of file INode.cpp.

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

References INode::getChildren().

Referenced by INode::createParameterTree(), and ParticleDistribution::generateParticles().

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registerChild()

void INode::registerChild ( INode *  node )

inherited

Definition at line 57 of file INode.cpp.

{
    ASSERT(node);
    node->setParent(this);
}

References ASSERT, and INode::setParent().

Referenced by Beam::Beam(), Crystal::Crystal(), IDetector::IDetector(), Instrument::Instrument(), InterferenceFunction2DLattice::InterferenceFunction2DLattice(), InterferenceFunction2DParaCrystal(), InterferenceFunction2DSuperLattice::InterferenceFunction2DSuperLattice(), InterferenceFunctionFinite2DLattice::InterferenceFunctionFinite2DLattice(), Particle::Particle(), ParticleDistribution::ParticleDistribution(), ParticleLayout::addAndRegisterAbstractParticle(), ParticleCoreShell::addAndRegisterCore(), MultiLayer::addAndRegisterInterface(), MultiLayer::addAndRegisterLayer(), ParticleCoreShell::addAndRegisterShell(), Layer::addLayout(), ParticleComposition::addParticlePointer(), ISimulation::initialize(), MesoCrystal::initialize(), Beam::operator=(), Instrument::operator=(), IParticle::rotate(), ParticleLayout::setAndRegisterInterferenceFunction(), ISimulation::setBackground(), InterferenceFunction1DLattice::setDecayFunction(), InterferenceFunction2DLattice::setDecayFunction(), Instrument::setDetector(), IDetector::setDetectorResolution(), Beam::setFootprintFactor(), Particle::setFormFactor(), InterferenceFunctionFinite3DLattice::setLattice(), InterferenceFunctionRadialParaCrystal::setProbabilityDistribution(), setProbabilityDistributions(), ConvolutionDetectorResolution::setResolutionFunction(), IParticle::setRotation(), LayerInterface::setRoughness(), and InterferenceFunction2DSuperLattice::setSubstructureIFF().

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registerParameter()

RealParameter & IParametricComponent::registerParameter ( const std::string &  name, double *  parpointer  )

inherited

Definition at line 51 of file IParametricComponent.cpp.

{
    return m_pool->addParameter(
        new RealParameter(name, data, getName(), [&]() -> void { onChange(); }));
}

References IParametricComponent::getName(), IParametricComponent::m_pool, RealSpace::Particles::name(), and IParametricComponent::onChange().

Referenced by BasicLattice2D::BasicLattice2D(), Beam::Beam(), CylindersInBABuilder::CylindersInBABuilder(), DetectionProperties::DetectionProperties(), HexagonalLattice2D::HexagonalLattice2D(), IInterferenceFunction::IInterferenceFunction(), INode::INode(), InterferenceFunction1DLattice::InterferenceFunction1DLattice(), InterferenceFunction2DParaCrystal(), InterferenceFunctionHardDisk::InterferenceFunctionHardDisk(), InterferenceFunctionRadialParaCrystal::InterferenceFunctionRadialParaCrystal(), InterferenceFunctionTwin::InterferenceFunctionTwin(), Lattice2D::Lattice2D(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), ParticleDistribution::ParticleDistribution(), PlainMultiLayerBySLDBuilder::PlainMultiLayerBySLDBuilder(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), ResonatorBuilder::ResonatorBuilder(), SquareLattice2D::SquareLattice2D(), TriangularRippleBuilder::TriangularRippleBuilder(), IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), Layer::registerThickness(), IParametricComponent::registerVector(), ParticleLayout::registerWeight(), and Lattice2D::setRotationEnabled().

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registerVector()

void IParametricComponent::registerVector ( const std::string &  base_name, kvector_t *  p_vec, const std::string &  units = "nm"  )

inherited

Definition at line 57 of file IParametricComponent.cpp.

{
    registerParameter(XComponentName(base_name), &((*p_vec)[0])).setUnit(units);
    registerParameter(YComponentName(base_name), &((*p_vec)[1])).setUnit(units);
    registerParameter(ZComponentName(base_name), &((*p_vec)[2])).setUnit(units);
}

References ModelView::Utils::base_name(), IParametricComponent::registerParameter(), RealParameter::setUnit(), IParametricComponent::XComponentName(), IParametricComponent::YComponentName(), and IParametricComponent::ZComponentName().

Referenced by Beam::Beam(), DetectionProperties::DetectionProperties(), InterferenceFunctionTwin::InterferenceFunctionTwin(), MultiLayer::MultiLayer(), Lattice3D::initialize(), and IParticle::registerPosition().

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removeParameter()

void IParametricComponent::removeParameter ( const std::string &  name )

inherited

Definition at line 91 of file IParametricComponent.cpp.

{
    m_pool->removeParameter(name);
}

References IParametricComponent::m_pool, and RealSpace::Particles::name().

Referenced by IParticle::registerAbundance(), ParticleLayout::registerParticleDensity(), Layer::registerThickness(), IParametricComponent::removeVector(), and Lattice2D::setRotationEnabled().

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removeVector()

void IParametricComponent::removeVector ( const std::string &  base_name )

inherited

Definition at line 96 of file IParametricComponent.cpp.

{
    removeParameter(XComponentName(base_name));
    removeParameter(YComponentName(base_name));
    removeParameter(ZComponentName(base_name));
}

References ModelView::Utils::base_name(), IParametricComponent::removeParameter(), IParametricComponent::XComponentName(), IParametricComponent::YComponentName(), and IParametricComponent::ZComponentName().

Referenced by IParticle::registerPosition().

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setDampingLength()

void InterferenceFunction2DParaCrystal::setDampingLength

(

double

damping_length

)

Sets the damping length.

Parameters

damping_length

the damping (coherence) length of the paracrystal in nanometers

Definition at line 65 of file InterferenceFunction2DParaCrystal.cpp.

{
    m_damping_length = damping_length;
}

References m_damping_length.

setDomainSizes()

void InterferenceFunction2DParaCrystal::setDomainSizes	(	double	size_1,
		double	size_2
	)

Sets the sizes of coherence domains.

Parameters

size_1	coherence domain size along the first basis vector in nanometers
size_2	coherence domain size along the second basis vector in nanometers

Definition at line 96 of file InterferenceFunction2DParaCrystal.cpp.

{
    m_domain_sizes[0] = size_1;
    m_domain_sizes[1] = size_2;
}

References m_domain_sizes.

Referenced by InterferenceFunction2DParaCrystal(), and RectParaCrystalBuilder::buildSample().

setIntegrationOverXi()

void InterferenceFunction2DParaCrystal::setIntegrationOverXi

(

bool

integrate_xi

)

Enables/disables averaging over the lattice rotation angle.

Parameters

integrate_xi

integration flag

Definition at line 185 of file InterferenceFunction2DParaCrystal.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.

Referenced by HexParaCrystalBuilder::buildSample(), and RectParaCrystalBuilder::buildSample().

setName()

void IParametricComponent::setName ( const std::string &  name )

inlineinherited

Definition at line 69 of file IParametricComponent.h.

{ m_name = name; }

References IParametricComponent::m_name, and RealSpace::Particles::name().

Referenced by BasicLattice2D::BasicLattice2D(), Beam::Beam(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), Crystal::Crystal(), DetectionProperties::DetectionProperties(), DistributionHandler::DistributionHandler(), FormFactorCoreShell::FormFactorCoreShell(), FormFactorCrystal::FormFactorCrystal(), FormFactorDecoratorMaterial::FormFactorDecoratorMaterial(), FormFactorDecoratorPositionFactor::FormFactorDecoratorPositionFactor(), FormFactorDecoratorRotation::FormFactorDecoratorRotation(), FormFactorWeighted::FormFactorWeighted(), HexagonalLattice2D::HexagonalLattice2D(), IDetector::IDetector(), INode::INode(), Instrument::Instrument(), InterferenceFunction1DLattice::InterferenceFunction1DLattice(), InterferenceFunction2DLattice::InterferenceFunction2DLattice(), InterferenceFunction2DParaCrystal(), InterferenceFunction2DSuperLattice::InterferenceFunction2DSuperLattice(), InterferenceFunction3DLattice::InterferenceFunction3DLattice(), InterferenceFunctionFinite2DLattice::InterferenceFunctionFinite2DLattice(), InterferenceFunctionFinite3DLattice::InterferenceFunctionFinite3DLattice(), InterferenceFunctionHardDisk::InterferenceFunctionHardDisk(), InterferenceFunctionNone::InterferenceFunctionNone(), InterferenceFunctionRadialParaCrystal::InterferenceFunctionRadialParaCrystal(), InterferenceFunctionTwin::InterferenceFunctionTwin(), ISampleBuilder::ISampleBuilder(), IsGISAXSDetector::IsGISAXSDetector(), Lattice3D::Lattice3D(), Layer::Layer(), LayerInterface::LayerInterface(), LayerRoughness::LayerRoughness(), MultiLayer::MultiLayer(), ParticleCoreShell::ParticleCoreShell(), ParticleDistribution::ParticleDistribution(), ParticleLayout::ParticleLayout(), RectangularDetector::RectangularDetector(), ResolutionFunction2DGaussian::ResolutionFunction2DGaussian(), SampleBuilderNode::SampleBuilderNode(), SphericalDetector::SphericalDetector(), SquareLattice2D::SquareLattice2D(), Layer::clone(), LayersWithAbsorptionBuilder::createSampleByIndex(), Basic2DParaCrystalBuilder::createSampleByIndex(), ParticleInVacuumBuilder::createSampleByIndex(), SimpleMagneticRotationBuilder::createSampleByIndex(), DepthProbeSimulation::initialize(), GISASSimulation::initialize(), OffSpecularSimulation::initialize(), SpecularSimulation::initialize(), SpecularDetector1D::initialize(), MesoCrystal::initialize(), Particle::initialize(), ParticleComposition::initialize(), Beam::operator=(), SampleBuilderNode::operator=(), SampleBuilderNode::reset(), and SampleBuilderNode::setSBN().

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setParameterValue()

void IParametricComponent::setParameterValue ( const std::string &  name, double  value  )

inherited

Definition at line 65 of file IParametricComponent.cpp.

{
    if (name.find('*') == std::string::npos && name.find('/') == std::string::npos) {
        m_pool->setParameterValue(name, value);
    } else {
        std::unique_ptr<ParameterPool> P_pool{createParameterTree()};
        if (name.find('*') != std::string::npos)
            P_pool->setMatchedParametersValue(name, value);
        else
            P_pool->setParameterValue(name, value);
    }
}

References IParametricComponent::createParameterTree(), IParametricComponent::m_pool, RealSpace::Particles::name(), and ParameterPool::setMatchedParametersValue().

Referenced by AsymRippleBuilder::buildSample(), and IParametricComponent::setVectorValue().

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setParent()

void INode::setParent ( const INode *  newParent )

virtualinherited

Reimplemented in SampleProvider.

Definition at line 79 of file INode.cpp.

{
    m_parent = newParent;
}

References INode::m_parent.

Referenced by INode::registerChild(), SampleProvider::setBuilder(), and SampleProvider::setParent().

setPositionVariance()

void IInterferenceFunction::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 IInterferenceFunction.cpp.

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

References IInterferenceFunction::m_position_var.

Referenced by FiniteSquareLattice2DBuilder::buildSample(), SuperLatticeBuilder::buildSample(), and InterferenceFunctionItem::setPositionVariance().

setProbabilityDistributions()

void InterferenceFunction2DParaCrystal::setProbabilityDistributions	(	const IFTDistribution2D &	pdf_1,
		const IFTDistribution2D &	pdf_2
	)

Sets the probability distributions (Fourier transformed) for the two lattice directions.

Parameters

pdf_1	probability distribution in first lattice direction
pdf_2	probability distribution in second lattice direction

Definition at line 53 of file InterferenceFunction2DParaCrystal.cpp.

{
    m_pdf1.reset(pdf_1.clone());
    registerChild(m_pdf1.get());
    m_pdf2.reset(pdf_2.clone());
    registerChild(m_pdf2.get());
}

References IFTDistribution2D::clone(), m_pdf1, m_pdf2, and INode::registerChild().

Referenced by Basic2DParaCrystalBuilder::buildSample(), HexParaCrystalBuilder::buildSample(), and RectParaCrystalBuilder::buildSample().

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setVectorValue()

void IParametricComponent::setVectorValue ( const std::string &  base_name, kvector_t  value  )

inherited

Definition at line 78 of file IParametricComponent.cpp.

{
    setParameterValue(XComponentName(base_name), value.x());
    setParameterValue(YComponentName(base_name), value.y());
    setParameterValue(ZComponentName(base_name), value.z());
}

References ModelView::Utils::base_name(), IParametricComponent::setParameterValue(), BasicVector3D< T >::x(), IParametricComponent::XComponentName(), BasicVector3D< T >::y(), IParametricComponent::YComponentName(), BasicVector3D< T >::z(), and IParametricComponent::ZComponentName().

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supportsMultilayer()

virtual bool IInterferenceFunction::supportsMultilayer ( ) const

inlinevirtualinherited

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

Reimplemented in InterferenceFunctionFinite3DLattice, and InterferenceFunction3DLattice.

Definition at line 46 of file IInterferenceFunction.h.

{ return true; }

Referenced by IInterferenceFunction::DWfactor().

transferToCPP()

virtual void ICloneable::transferToCPP ( )

inlinevirtualinherited

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

Definition at line 34 of file ICloneable.h.

transformToPrincipalAxes()

void InterferenceFunction2DParaCrystal::transformToPrincipalAxes ( double  qx, double  qy, double  gamma, double  delta, double &  q_pa_1, double &  q_pa_2  ) const

private

Definition at line 102 of file InterferenceFunction2DParaCrystal.cpp.

{
    q_pa_1 = qx * std::cos(gamma) + qy * std::sin(gamma);
    q_pa_2 = qx * std::cos(gamma + delta) + qy * std::sin(gamma + delta);
}

Referenced by FTPDF().

treeToString()

std::string INode::treeToString ( ) const

virtualinherited

Returns multiline string representing tree structure below the node.

Definition at line 52 of file INode.cpp.

{
    return NodeUtils::nodeToString(this);
}

References NodeUtils::nodeToString().

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XComponentName()

std::string IParametricComponent::XComponentName ( const std::string &  base_name )

staticinherited

Definition at line 103 of file IParametricComponent.cpp.

{
    return base_name + "X";
}

References ModelView::Utils::base_name().

Referenced by Lattice3D::initialize(), IParticle::registerPosition(), IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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YComponentName()

std::string IParametricComponent::YComponentName ( const std::string &  base_name )

staticinherited

Definition at line 108 of file IParametricComponent.cpp.

{
    return base_name + "Y";
}

References ModelView::Utils::base_name().

Referenced by IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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ZComponentName()

std::string IParametricComponent::ZComponentName ( const std::string &  base_name )

staticinherited

Definition at line 113 of file IParametricComponent.cpp.

{
    return base_name + "Z";
}

References ModelView::Utils::base_name().

Referenced by IParametricComponent::registerVector(), IParametricComponent::removeVector(), IParametricComponent::setVectorValue(), and VectorParameterTranslator::translate().

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Member Data Documentation

m_damping_length

double InterferenceFunction2DParaCrystal::m_damping_length

private

Damping length for removing delta function singularity at q=0.

Definition at line 74 of file InterferenceFunction2DParaCrystal.h.

Referenced by InterferenceFunction2DParaCrystal(), clone(), dampingLength(), FTPDF(), and setDampingLength().

m_domain_sizes

double InterferenceFunction2DParaCrystal::m_domain_sizes[2]

private

Coherence domain sizes.

Definition at line 75 of file InterferenceFunction2DParaCrystal.h.

Referenced by InterferenceFunction2DParaCrystal(), clone(), domainSizes(), interference1D(), and setDomainSizes().

m_integrate_xi

bool InterferenceFunction2DParaCrystal::m_integrate_xi

private

Integrate over the orientation xi.

Definition at line 71 of file InterferenceFunction2DParaCrystal.h.

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

m_lattice

std::unique_ptr<Lattice2D> InterferenceFunction2DParaCrystal::m_lattice

private

Definition at line 73 of file InterferenceFunction2DParaCrystal.h.

Referenced by InterferenceFunction2DParaCrystal(), clone(), FTPDF(), getChildren(), getParticleDensity(), iff_without_dw(), interference1D(), interferenceForXi(), lattice(), and setIntegrationOverXi().

m_name

std::string IParametricComponent::m_name

privateinherited

Definition at line 73 of file IParametricComponent.h.

Referenced by IParametricComponent::getName(), and IParametricComponent::setName().

m_NP

const size_t INode::m_NP

protectedinherited

Definition at line 88 of file INode.h.

Referenced by INode::INode().

m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 89 of file INode.h.

Referenced by INode::INode(), and IFootprintFactor::setWidthRatio().

m_parent

const INode* INode::m_parent {nullptr}

privateinherited

Definition at line 83 of file INode.h.

Referenced by INode::displayName(), INode::parent(), and INode::setParent().

m_pdf1

std::unique_ptr<IFTDistribution2D> InterferenceFunction2DParaCrystal::m_pdf1

private

Definition at line 72 of file InterferenceFunction2DParaCrystal.h.

Referenced by clone(), FTPDF(), getChildren(), interference1D(), pdf1(), and setProbabilityDistributions().

m_pdf2

std::unique_ptr<IFTDistribution2D> InterferenceFunction2DParaCrystal::m_pdf2

private

Definition at line 72 of file InterferenceFunction2DParaCrystal.h.

Referenced by clone(), FTPDF(), getChildren(), interference1D(), pdf2(), and setProbabilityDistributions().

m_pool

std::unique_ptr<ParameterPool> IParametricComponent::m_pool

privateinherited

parameter pool (kind of pointer-to-implementation)

Definition at line 74 of file IParametricComponent.h.

Referenced by IParametricComponent::createParameterTree(), IParametricComponent::parameter(), IParametricComponent::parameterPool(), IParametricComponent::registerParameter(), IParametricComponent::removeParameter(), and IParametricComponent::setParameterValue().

m_position_var

double IInterferenceFunction::m_position_var

protectedinherited

Definition at line 52 of file IInterferenceFunction.h.

Referenced by IInterferenceFunction::IInterferenceFunction(), InterferenceFunctionNone::clone(), InterferenceFunctionRadialParaCrystal::clone(), InterferenceFunctionTwin::clone(), InterferenceFunction1DLattice::clone(), InterferenceFunction2DLattice::clone(), clone(), InterferenceFunction2DSuperLattice::clone(), InterferenceFunction3DLattice::clone(), InterferenceFunctionFinite2DLattice::clone(), InterferenceFunctionFinite3DLattice::clone(), InterferenceFunctionHardDisk::clone(), IInterferenceFunction::DWfactor(), IInterferenceFunction::positionVariance(), and IInterferenceFunction::setPositionVariance().

m_qx

double InterferenceFunction2DParaCrystal::m_qx

mutableprivate

Definition at line 76 of file InterferenceFunction2DParaCrystal.h.

Referenced by iff_without_dw(), and interferenceForXi().

m_qy

double InterferenceFunction2DParaCrystal::m_qy

mutableprivate

Definition at line 77 of file InterferenceFunction2DParaCrystal.h.

Referenced by iff_without_dw(), and interferenceForXi().

---

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

• /home/www/ba/Sample/Aggregate/InterferenceFunction2DParaCrystal.h
• /home/www/ba/Sample/Aggregate/InterferenceFunction2DParaCrystal.cpp