Lattice Class Reference

Inheritance diagram for Lattice:

Collaboration diagram for Lattice:

Public Member Functions
	Lattice ()
	Lattice (const kvector_t a1, const kvector_t a2, const kvector_t a3)
	Lattice (const Lattice &lattice)
	~Lattice () override
void	accept (INodeVisitor *visitor) const override
Lattice	createTransformedLattice (const Transform3D &transform) const
void	initialize () const
kvector_t	getBasisVectorA () const
kvector_t	getBasisVectorB () const
kvector_t	getBasisVectorC () const
void	resetBasis (const kvector_t a1, const kvector_t a2, const kvector_t a3)
kvector_t	getMillerDirection (double h, double k, double l) const
double	volume () const
void	getReciprocalLatticeBasis (kvector_t &b1, kvector_t &b2, kvector_t &b3) const
ivector_t	getNearestLatticeVectorCoordinates (const kvector_t vector_in) const
ivector_t	getNearestReciprocalLatticeVectorCoordinates (const kvector_t vector_in) const
std::vector< kvector_t >	reciprocalLatticeVectorsWithinRadius (const kvector_t input_vector, double radius) const
void	setSelectionRule (const ISelectionRule &p_selection_rule)
void	onChange () override
virtual std::string	treeToString () const
void	registerChild (INode *node)
virtual std::vector< const INode * >	getChildren () const
virtual void	setParent (const INode *newParent)
const INode *	parent () const
INode *	parent ()
int	copyNumber (const INode *node) const
std::string	displayName () const
ParameterPool *	createParameterTree () const
ParameterPool *	parameterPool () const
std::string	parametersToString () const
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	setParameterValue (const std::string &name, double value)
void	setVectorValue (const std::string &base_name, kvector_t value)
RealParameter *	parameter (const std::string &name) const
void	removeParameter (const std::string &name)
void	removeVector (const std::string &base_name)
void	setName (const std::string &name)
const std::string &	getName () const

Static Public Member Functions
static Lattice	createCubicLattice (double a)
static Lattice	createFCCLattice (double a)
static Lattice	createHexagonalLattice (double a, double c)
static Lattice	createHCPLattice (double a, double c)
static Lattice	createTetragonalLattice (double a, double c)
static Lattice	createBCTLattice (double a, double c)
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 Attributes
const size_t	m_NP
std::vector< double >	m_P

Private Member Functions
Lattice &	operator= (const Lattice &lattice)
void	registerBasisVectors ()
std::vector< kvector_t >	vectorsWithinRadius (const kvector_t input_vector, const ivector_t &nearest_coords, double radius, const kvector_t v1, const kvector_t v2, const kvector_t v3, const kvector_t rec1, const kvector_t rec2, const kvector_t rec3) const
void	computeReciprocalVectors () const

Static Private Member Functions
static void	computeInverseVectors (const kvector_t v1, const kvector_t v2, const kvector_t v3, kvector_t o1, kvector_t o2, kvector_t o3)

Private Attributes
ISelectionRule *	mp_selection_rule
kvector_t	m_a
kvector_t	m_b
kvector_t	m_c
kvector_t	m_ra
kvector_t	m_rb
kvector_t	m_rc
bool	m_cache_ok
const INode *	m_parent {nullptr}
std::string	m_name
std::unique_ptr< ParameterPool >	m_pool

Detailed Description

A lattice with three basis vectors.

Definition at line 27 of file Lattice.h.

Constructor & Destructor Documentation

Lattice() [1/3]

Lattice::Lattice

(

)

Definition at line 22 of file Lattice.cpp.

    : mp_selection_rule(nullptr), m_a({1.0, 0.0, 0.0}), m_b({0.0, 1.0, 0.0}), m_c({0.0, 0.0, 1.0}),
      m_cache_ok(false)
{
    setName("Lattice");
    initialize();
    registerBasisVectors();
}

Referenced by createBCTLattice(), createCubicLattice(), createFCCLattice(), createHCPLattice(), createHexagonalLattice(), and createTetragonalLattice().

Lattice() [2/3]

Lattice::Lattice	(	const kvector_t	a1,
		const kvector_t	a2,
		const kvector_t	a3
	)

Definition at line 31 of file Lattice.cpp.

    : mp_selection_rule(nullptr), m_a(a1), m_b(a2), m_c(a3), m_cache_ok(false)
{
    setName("Lattice");
    initialize();
    registerBasisVectors();
}

References initialize(), registerBasisVectors(), and IParameterized::setName().

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Lattice() [3/3]

Lattice::Lattice

(

const Lattice &

lattice

)

Definition at line 39 of file Lattice.cpp.

    : INode(), mp_selection_rule(nullptr), m_a(lattice.m_a), m_b(lattice.m_b), m_c(lattice.m_c),
      m_cache_ok(false)
{
    setName("Lattice");
    initialize();
    if (lattice.mp_selection_rule)
        setSelectionRule(*lattice.mp_selection_rule);
    registerBasisVectors();
}

References initialize(), mp_selection_rule, registerBasisVectors(), IParameterized::setName(), and setSelectionRule().

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~Lattice()

Lattice::~Lattice ( )

override

Definition at line 50 of file Lattice.cpp.

{
    delete mp_selection_rule;
}

References mp_selection_rule.

Member Function Documentation

accept()

void Lattice::accept ( INodeVisitor *  visitor ) const

inlineoverridevirtual

Calls the INodeVisitor's visit method.

Implements INode.

Definition at line 35 of file Lattice.h.

{ visitor->visit(this); }

References INodeVisitor::visit().

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createTransformedLattice()

Lattice Lattice::createTransformedLattice

(

const Transform3D &

transform

)

const

Creates transformed lattice.

Definition at line 55 of file Lattice.cpp.

{
    kvector_t a1 = transform.transformed(m_a);
    kvector_t a2 = transform.transformed(m_b);
    kvector_t a3 = transform.transformed(m_c);
    Lattice result = {a1, a2, a3};
    if (mp_selection_rule)
        result.setSelectionRule(*mp_selection_rule);
    return result;
}

References m_a, m_b, m_c, mp_selection_rule, setSelectionRule(), and Transform3D::transformed().

Referenced by LatticeUtils::createBCTLattice(), LatticeUtils::createFCCLattice(), LatticeUtils::createHCPLattice(), and Crystal::transformedLattice().

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initialize()

void Lattice::initialize

(

)

const

Initializes cached data.

Definition at line 66 of file Lattice.cpp.

{
    computeReciprocalVectors();
    m_cache_ok = true;
}

References computeReciprocalVectors(), and m_cache_ok.

Referenced by getReciprocalLatticeBasis(), Lattice(), and reciprocalLatticeVectorsWithinRadius().

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getBasisVectorA()

kvector_t Lattice::getBasisVectorA ( ) const

inline

Returns basis vector a.

Definition at line 44 of file Lattice.h.

{ return m_a; }

References m_a.

Referenced by FormFactorCrystal::calculateLargestReciprocalDistance(), SampleToPython::defineLattices(), InterferenceFunction3DLattice::initRecRadius(), and MillerIndexOrientation::usePrimitiveLattice().

getBasisVectorB()

kvector_t Lattice::getBasisVectorB ( ) const

inline

Returns basis vector b.

Definition at line 47 of file Lattice.h.

{ return m_b; }

References m_b.

Referenced by FormFactorCrystal::calculateLargestReciprocalDistance(), SampleToPython::defineLattices(), InterferenceFunction3DLattice::initRecRadius(), and MillerIndexOrientation::usePrimitiveLattice().

getBasisVectorC()

kvector_t Lattice::getBasisVectorC ( ) const

inline

Returns basis vector c.

Definition at line 50 of file Lattice.h.

{ return m_c; }

References m_c.

Referenced by FormFactorCrystal::calculateLargestReciprocalDistance(), SampleToPython::defineLattices(), InterferenceFunction3DLattice::initRecRadius(), and MillerIndexOrientation::usePrimitiveLattice().

resetBasis()

void Lattice::resetBasis	(	const kvector_t	a1,
		const kvector_t	a2,
		const kvector_t	a3
	)

Resets the basis vectors.

Definition at line 72 of file Lattice.cpp.

{
    m_a = a1;
    m_b = a2;
    m_c = a3;
    onChange();
}

References m_a, m_b, m_c, and onChange().

Referenced by MillerIndexOrientation::usePrimitiveLattice().

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getMillerDirection()

kvector_t Lattice::getMillerDirection	(	double	h,
		double	k,
		double	l
	)		const

Returns normalized direction corresponding to the given Miller indices.

Definition at line 80 of file Lattice.cpp.

{
    kvector_t b1, b2, b3;
    getReciprocalLatticeBasis(b1, b2, b3);
    kvector_t direction = h * b1 + k * b2 + l * b3;
    return direction.unit();
}

References getReciprocalLatticeBasis(), and BasicVector3D< T >::unit().

Referenced by MillerIndexOrientation::transformationMatrix().

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volume()

double Lattice::volume

(

)

const

Returns the volume of the unit cell.

Definition at line 88 of file Lattice.cpp.

{
    return std::abs(m_a.dot(m_b.cross(m_c)));
}

References BasicVector3D< T >::cross(), BasicVector3D< T >::dot(), m_a, m_b, and m_c.

Referenced by FormFactorCrystal::evaluate(), FormFactorCrystal::evaluatePol(), and Crystal::homogeneousRegions().

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getReciprocalLatticeBasis()

void Lattice::getReciprocalLatticeBasis	(	kvector_t &	b1,
		kvector_t &	b2,
		kvector_t &	b3
	)		const

Returns the reciprocal basis vectors.

Definition at line 93 of file Lattice.cpp.

{
    if (!m_cache_ok) {
        initialize();
    }
    b1 = m_ra;
    b2 = m_rb;
    b3 = m_rc;
    return;
}

References initialize(), m_cache_ok, m_ra, m_rb, and m_rc.

Referenced by getMillerDirection().

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getNearestLatticeVectorCoordinates()

ivector_t Lattice::getNearestLatticeVectorCoordinates

(

const kvector_t

vector_in

)

const

Returns the nearest lattice point from a given vector.

Definition at line 104 of file Lattice.cpp.

{
    double a1_coord = vector_in.dot(m_ra) / M_TWOPI;
    double a2_coord = vector_in.dot(m_rb) / M_TWOPI;
    double a3_coord = vector_in.dot(m_rc) / M_TWOPI;
    int c1 = static_cast<int>(std::floor(a1_coord + 0.5));
    int c2 = static_cast<int>(std::floor(a2_coord + 0.5));
    int c3 = static_cast<int>(std::floor(a3_coord + 0.5));
    return ivector_t(c1, c2, c3);
}

References BasicVector3D< T >::dot(), m_ra, m_rb, m_rc, and M_TWOPI.

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getNearestReciprocalLatticeVectorCoordinates()

ivector_t Lattice::getNearestReciprocalLatticeVectorCoordinates

(

const kvector_t

vector_in

)

const

Returns the nearest reciprocal lattice point from a given vector.

Definition at line 115 of file Lattice.cpp.

{
    double b1_coord = vector_in.dot(m_a) / M_TWOPI;
    double b2_coord = vector_in.dot(m_b) / M_TWOPI;
    double b3_coord = vector_in.dot(m_c) / M_TWOPI;
    int c1 = static_cast<int>(std::floor(b1_coord + 0.5));
    int c2 = static_cast<int>(std::floor(b2_coord + 0.5));
    int c3 = static_cast<int>(std::floor(b3_coord + 0.5));
    return ivector_t(c1, c2, c3);
}

References BasicVector3D< T >::dot(), m_a, m_b, m_c, and M_TWOPI.

Referenced by reciprocalLatticeVectorsWithinRadius().

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reciprocalLatticeVectorsWithinRadius()

std::vector< kvector_t > Lattice::reciprocalLatticeVectorsWithinRadius	(	const kvector_t	input_vector,
		double	radius
	)		const

Computes a list of reciprocal lattice vectors within a specified distance of a given vector.

Definition at line 126 of file Lattice.cpp.

{
    if (!m_cache_ok)
        initialize();
    ivector_t nearest_coords = getNearestReciprocalLatticeVectorCoordinates(input_vector);
    return vectorsWithinRadius(input_vector, nearest_coords, radius, m_ra, m_rb, m_rc, m_a, m_b,
                               m_c);
}

References getNearestReciprocalLatticeVectorCoordinates(), initialize(), m_a, m_b, m_c, m_cache_ok, m_ra, m_rb, m_rc, anonymous_namespace{SlicedCylindersBuilder.cpp}::radius(), and vectorsWithinRadius().

Referenced by FormFactorCrystal::evaluate(), FormFactorCrystal::evaluatePol(), and InterferenceFunction3DLattice::iff_without_dw().

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setSelectionRule()

void Lattice::setSelectionRule

(

const ISelectionRule &

p_selection_rule

)

Sets a selection rule for the reciprocal vectors.

Definition at line 277 of file Lattice.cpp.

{
    delete mp_selection_rule;
    mp_selection_rule = p_selection_rule.clone();
}

References ISelectionRule::clone(), and mp_selection_rule.

Referenced by createTransformedLattice(), and Lattice().

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createCubicLattice()

Lattice Lattice::createCubicLattice ( double  a )

static

Returns a primitive cubic (cP) lattice with edge length a.

Definition at line 136 of file Lattice.cpp.

{
    kvector_t a1(a, 0.0, 0.0);
    kvector_t a2(0.0, a, 0.0);
    kvector_t a3(0.0, 0.0, a);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createFCCLattice().

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createFCCLattice()

Lattice Lattice::createFCCLattice ( double  a )

static

Returns a face-centered cubic (cF) lattice with edge length a.

Definition at line 144 of file Lattice.cpp.

{
    double b = a / 2.0;
    kvector_t a1(0.0, b, b);
    kvector_t a2(b, 0.0, b);
    kvector_t a3(b, b, 0.0);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createFCCLattice().

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createHexagonalLattice()

Lattice Lattice::createHexagonalLattice ( double  a, double  c  )

static

Returns a primitive hexagonal (hP) lattice with hexagonal edge a and height c.

Definition at line 153 of file Lattice.cpp.

{
    kvector_t a1(a, 0.0, 0.0);
    kvector_t a2(-a / 2.0, std::sqrt(3.0) * a / 2.0, 0.0);
    kvector_t a3(0.0, 0.0, c);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createHCPLattice().

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createHCPLattice()

Lattice Lattice::createHCPLattice ( double  a, double  c  )

static

TODO: Clarify how this is meant: HCP is not a Bravais lattice.

Definition at line 161 of file Lattice.cpp.

{
    kvector_t a1(a, 0.0, 0.0);
    kvector_t a2(-a / 2.0, std::sqrt(3.0) * a / 2.0, 0);
    kvector_t a3(a / 2.0, a / std::sqrt(3.0) / 2.0, c / 2.0);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createHCPLattice().

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createTetragonalLattice()

Lattice Lattice::createTetragonalLattice ( double  a, double  c  )

static

Returns a primitive tetragonal (tP) lattice with square base edge a and height c.

Definition at line 169 of file Lattice.cpp.

{
    kvector_t a1(a, 0.0, 0.0);
    kvector_t a2(0.0, a, 0.0);
    kvector_t a3(0.0, 0.0, c);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createBCTLattice().

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createBCTLattice()

Lattice Lattice::createBCTLattice ( double  a, double  c  )

static

Returns a body-centered cubic (cI) lattice with edge length a.

TODO: Clarify meaning of c

Definition at line 177 of file Lattice.cpp.

{
    kvector_t a1(a, 0.0, 0.0);
    kvector_t a2(0.0, a, 0.0);
    kvector_t a3(a / 2.0, a / 2.0, c / 2.0);
    return Lattice(a1, a2, a3);
}

References Lattice().

Referenced by LatticeUtils::createBCTLattice().

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onChange()

void Lattice::onChange ( )

overridevirtual

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

Reimplemented from IParameterized.

Definition at line 185 of file Lattice.cpp.

{
    m_cache_ok = false;
}

References m_cache_ok.

Referenced by resetBasis().

operator=()

Lattice& Lattice::operator= ( const Lattice &  lattice )

private

registerBasisVectors()

void Lattice::registerBasisVectors ( )

private

Definition at line 190 of file Lattice.cpp.

{
    if (!parameter(XComponentName("BasisA"))) {
        registerVector("BasisA", &m_a, "nm");
        registerVector("BasisB", &m_b, "nm");
        registerVector("BasisC", &m_c, "nm");
    }
}

References m_a, m_b, m_c, IParameterized::parameter(), IParameterized::registerVector(), and IParameterized::XComponentName().

Referenced by Lattice().

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vectorsWithinRadius()

std::vector< kvector_t > Lattice::vectorsWithinRadius ( const kvector_t  input_vector, const ivector_t &  nearest_coords, double  radius, const kvector_t  v1, const kvector_t  v2, const kvector_t  v3, const kvector_t  rec1, const kvector_t  rec2, const kvector_t  rec3  ) const

private

Definition at line 209 of file Lattice.cpp.

{
    int max_X = static_cast<int>(std::floor(rec1.mag() * radius / M_TWOPI + 0.5));
    int max_Y = static_cast<int>(std::floor(rec2.mag() * radius / M_TWOPI + 0.5));
    int max_Z = static_cast<int>(std::floor(rec3.mag() * radius / M_TWOPI + 0.5));
 
    std::vector<kvector_t> ret;
    for (int index_X = -max_X; index_X <= max_X; ++index_X) {
        for (int index_Y = -max_Y; index_Y <= max_Y; ++index_Y) {
            for (int index_Z = -max_Z; index_Z <= max_Z; ++index_Z) {
                ivector_t coords(index_X + nearest_coords[0], index_Y + nearest_coords[1],
                                 index_Z + nearest_coords[2]);
                if (mp_selection_rule && !mp_selection_rule->coordinateSelected(coords))
                    continue;
                kvector_t latticePoint = coords[0] * v1 + coords[1] * v2 + coords[2] * v3;
                if ((latticePoint - input_vector).mag() <= radius)
                    ret.push_back(latticePoint);
            }
        }
    }
    return ret;
}

References ISelectionRule::coordinateSelected(), M_TWOPI, BasicVector3D< T >::mag(), mp_selection_rule, and anonymous_namespace{SlicedCylindersBuilder.cpp}::radius().

Referenced by reciprocalLatticeVectorsWithinRadius().

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computeReciprocalVectors()

void Lattice::computeReciprocalVectors ( ) const

private

Definition at line 199 of file Lattice.cpp.

{
    kvector_t a23 = m_b.cross(m_c);
    kvector_t a31 = m_c.cross(m_a);
    kvector_t a12 = m_a.cross(m_b);
    m_ra = M_TWOPI / m_a.dot(a23) * a23;
    m_rb = M_TWOPI / m_b.dot(a31) * a31;
    m_rc = M_TWOPI / m_c.dot(a12) * a12;
}

References BasicVector3D< T >::cross(), BasicVector3D< T >::dot(), m_a, m_b, m_c, m_ra, m_rb, m_rc, and M_TWOPI.

Referenced by initialize().

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computeInverseVectors()

void Lattice::computeInverseVectors ( const kvector_t  v1, const kvector_t  v2, const kvector_t  v3, kvector_t  o1, kvector_t  o2, kvector_t  o3  )

staticprivate

Definition at line 237 of file Lattice.cpp.

{
    gsl_matrix* p_basisMatrix = gsl_matrix_alloc(3, 3);
    gsl_matrix* p_inverseMatrix = gsl_matrix_alloc(3, 3);
    gsl_permutation* p_perm = gsl_permutation_alloc(3);
    int s;
 
    gsl_matrix_set(p_basisMatrix, 0, 0, v1.x());
    gsl_matrix_set(p_basisMatrix, 0, 1, v2.x());
    gsl_matrix_set(p_basisMatrix, 0, 2, v3.x());
 
    gsl_matrix_set(p_basisMatrix, 1, 0, v1.y());
    gsl_matrix_set(p_basisMatrix, 1, 1, v2.y());
    gsl_matrix_set(p_basisMatrix, 1, 2, v3.y());
 
    gsl_matrix_set(p_basisMatrix, 2, 0, v1.z());
    gsl_matrix_set(p_basisMatrix, 2, 1, v2.z());
    gsl_matrix_set(p_basisMatrix, 2, 2, v3.z());
 
    gsl_linalg_LU_decomp(p_basisMatrix, p_perm, &s);
    gsl_linalg_LU_invert(p_basisMatrix, p_perm, p_inverseMatrix);
 
    o1.setX(gsl_matrix_get(p_inverseMatrix, 0, 0));
    o1.setY(gsl_matrix_get(p_inverseMatrix, 1, 0));
    o1.setZ(gsl_matrix_get(p_inverseMatrix, 2, 0));
 
    o2.setX(gsl_matrix_get(p_inverseMatrix, 0, 1));
    o2.setY(gsl_matrix_get(p_inverseMatrix, 1, 1));
    o2.setZ(gsl_matrix_get(p_inverseMatrix, 2, 1));
 
    o3.setX(gsl_matrix_get(p_inverseMatrix, 0, 2));
    o3.setY(gsl_matrix_get(p_inverseMatrix, 1, 2));
    o3.setZ(gsl_matrix_get(p_inverseMatrix, 2, 2));
 
    gsl_permutation_free(p_perm);
    gsl_matrix_free(p_basisMatrix);
    gsl_matrix_free(p_inverseMatrix);
}

References BasicVector3D< T >::setX(), BasicVector3D< T >::setY(), BasicVector3D< T >::setZ(), BasicVector3D< T >::x(), BasicVector3D< T >::y(), and BasicVector3D< T >::z().

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treeToString()

std::string INode::treeToString ( ) const

virtualinherited

Returns multiline string representing tree structure below the node.

Definition at line 53 of file INode.cpp.

{
    return NodeUtils::nodeToString(*this);
}

References NodeUtils::nodeToString().

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registerChild()

void INode::registerChild ( INode *  node )

inherited

Definition at line 58 of file INode.cpp.

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

References ASSERT, and INode::setParent().

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

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getChildren()

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

virtualinherited

Returns a vector of children (const).

Reimplemented in ParticleDistribution, ParticleCoreShell, ParticleComposition, Particle, MesoCrystal, Crystal, Layer, InterferenceFunctionRadialParaCrystal, InterferenceFunctionFinite3DLattice, InterferenceFunctionFinite2DLattice, InterferenceFunction3DLattice, InterferenceFunction2DSuperLattice, InterferenceFunction2DParaCrystal, InterferenceFunction2DLattice, InterferenceFunction1DLattice, SampleProvider, IParticle, IDetector, Beam, MultiLayer, ParticleLayout, LayerInterface, ConvolutionDetectorResolution, Instrument, and Simulation.

Definition at line 64 of file INode.cpp.

{
    return {};
}

Referenced by INodeUtils::AllDescendantsOfType(), INodeUtils::ChildNodesOfType(), ISample::containedMaterials(), INode::copyNumber(), PostorderStrategy::first(), PreorderStrategy::next(), and PostorderStrategy::next().

setParent()

void INode::setParent ( const INode *  newParent )

virtualinherited

Reimplemented in SampleProvider.

Definition at line 69 of file INode.cpp.

{
    m_parent = newParent;
}

References INode::m_parent.

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

parent() [1/2]

const INode * INode::parent ( ) const

inherited

Definition at line 74 of file INode.cpp.

{
    return m_parent;
}

References INode::m_parent.

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

parent() [2/2]

INode * INode::parent ( )

inherited

Definition at line 79 of file INode.cpp.

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

References INode::m_parent.

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 84 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(), IParameterized::getName(), and INode::parent().

Referenced by INode::displayName().

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displayName()

std::string INode::displayName ( ) const

inherited

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

Definition at line 105 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(), IParameterized::getName(), and INode::m_parent.

Referenced by NodeUtils::nodePath(), and anonymous_namespace{NodeUtils.cpp}::nodeString().

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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 IParameterized.

Definition at line 116 of file INode.cpp.

{
    std::unique_ptr<ParameterPool> result(new ParameterPool);
 
    NodeIterator<PreorderStrategy> it(this);
    it.first();
    while (!it.isDone()) {
        const INode* child = it.getCurrent();
        const std::string path = NodeUtils::nodePath(*child, this->parent()) + "/";
        child->parameterPool()->copyToExternalPool(path, result.get());
        it.next();
    }
 
    return result.release();
}

References ParameterPool::copyToExternalPool(), NodeIterator< Strategy >::first(), NodeIterator< Strategy >::getCurrent(), NodeIterator< Strategy >::isDone(), NodeIterator< Strategy >::next(), NodeUtils::nodePath(), IParameterized::parameterPool(), and INode::parent().

Referenced by ParticleDistribution::generateParticles(), Simulation::runSimulation(), DepthProbeSimulation::validateParametrization(), OffSpecSimulation::validateParametrization(), and SpecularSimulation::validateParametrization().

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parameterPool()

ParameterPool* IParameterized::parameterPool ( ) const

inlineinherited

Returns pointer to the parameter pool.

Definition at line 38 of file IParameterized.h.

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

References IParameterized::m_pool.

Referenced by pyfmt2::argumentList(), SampleBuilderNode::borrow_builder_parameters(), INode::createParameterTree(), INode::INode(), IParameterized::IParameterized(), anonymous_namespace{NodeUtils.cpp}::poolToString(), SampleBuilderNode::reset(), and IDistribution1D::setUnits().

parametersToString()

std::string IParameterized::parametersToString ( ) const

inherited

Returns multiline string representing available parameters.

Definition at line 40 of file IParameterized.cpp.

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

References IParameterized::createParameterTree().

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registerParameter()

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

inherited

Definition at line 48 of file IParameterized.cpp.

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

References IParameterized::getName(), IParameterized::m_pool, and IParameterized::onChange().

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

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registerVector()

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

inherited

Definition at line 54 of file IParameterized.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 IParameterized::registerParameter(), RealParameter::setUnit(), IParameterized::XComponentName(), IParameterized::YComponentName(), and IParameterized::ZComponentName().

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

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setParameterValue()

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

inherited

Definition at line 62 of file IParameterized.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 IParameterized::createParameterTree(), IParameterized::m_pool, and ParameterPool::setMatchedParametersValue().

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

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setVectorValue()

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

inherited

Definition at line 75 of file IParameterized.cpp.

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

References IParameterized::setParameterValue(), BasicVector3D< T >::x(), IParameterized::XComponentName(), BasicVector3D< T >::y(), IParameterized::YComponentName(), BasicVector3D< T >::z(), and IParameterized::ZComponentName().

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parameter()

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

inherited

Returns parameter with given 'name'.

Definition at line 83 of file IParameterized.cpp.

{
    return m_pool->parameter(name);
}

References IParameterized::m_pool.

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

removeParameter()

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

inherited

Definition at line 88 of file IParameterized.cpp.

{
    m_pool->removeParameter(name);
}

References IParameterized::m_pool.

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

removeVector()

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

inherited

Definition at line 93 of file IParameterized.cpp.

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

References IParameterized::removeParameter(), IParameterized::XComponentName(), IParameterized::YComponentName(), and IParameterized::ZComponentName().

Referenced by IParticle::registerPosition().

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XComponentName()

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

staticinherited

Definition at line 100 of file IParameterized.cpp.

{
    return base_name + "X";
}

Referenced by registerBasisVectors(), IParticle::registerPosition(), IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

YComponentName()

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

staticinherited

Definition at line 105 of file IParameterized.cpp.

{
    return base_name + "Y";
}

Referenced by IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

ZComponentName()

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

staticinherited

Definition at line 110 of file IParameterized.cpp.

{
    return base_name + "Z";
}

Referenced by IParameterized::registerVector(), IParameterized::removeVector(), and IParameterized::setVectorValue().

setName()

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

inlineinherited

Definition at line 68 of file IParameterized.h.

{ m_name = name; }

References IParameterized::m_name.

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

getName()

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

inlineinherited

Definition at line 69 of file IParameterized.h.

{ return m_name; }

References IParameterized::m_name.

Referenced by Beam::Beam(), Layer::clone(), IFormFactorBorn::computeSlicingEffects(), ConvolutionDetectorResolution::ConvolutionDetectorResolution(), INode::copyNumber(), IParameterized::createParameterTree(), IFormFactor::createSlicedFormFactor(), SampleToPython::defineFormFactors(), SampleToPython::defineInterferenceFunctions(), INode::displayName(), IDetector::IDetector(), Instrument::Instrument(), IParameterized::IParameterized(), Beam::operator=(), SampleBuilderNode::operator=(), anonymous_namespace{ParticleLayout.cpp}::particleDensityIsProvidedByInterference(), IParameterized::registerParameter(), SampleBuilderNode::SampleBuilderNode(), and IFormFactor::sliceFormFactor().

Member Data Documentation

mp_selection_rule

ISelectionRule* Lattice::mp_selection_rule

private

Definition at line 112 of file Lattice.h.

Referenced by createTransformedLattice(), Lattice(), setSelectionRule(), vectorsWithinRadius(), and ~Lattice().

m_a

kvector_t Lattice::m_a

private

Definition at line 113 of file Lattice.h.

Referenced by computeReciprocalVectors(), createTransformedLattice(), getBasisVectorA(), getNearestReciprocalLatticeVectorCoordinates(), reciprocalLatticeVectorsWithinRadius(), registerBasisVectors(), resetBasis(), and volume().

m_b

kvector_t Lattice::m_b

private

Definition at line 113 of file Lattice.h.

Referenced by computeReciprocalVectors(), createTransformedLattice(), getBasisVectorB(), getNearestReciprocalLatticeVectorCoordinates(), reciprocalLatticeVectorsWithinRadius(), registerBasisVectors(), resetBasis(), and volume().

m_c

kvector_t Lattice::m_c

private

Basis vectors in real space.

Definition at line 113 of file Lattice.h.

Referenced by computeReciprocalVectors(), createTransformedLattice(), getBasisVectorC(), getNearestReciprocalLatticeVectorCoordinates(), reciprocalLatticeVectorsWithinRadius(), registerBasisVectors(), resetBasis(), and volume().

m_ra

kvector_t Lattice::m_ra

mutableprivate

Definition at line 114 of file Lattice.h.

Referenced by computeReciprocalVectors(), getNearestLatticeVectorCoordinates(), getReciprocalLatticeBasis(), and reciprocalLatticeVectorsWithinRadius().

m_rb

kvector_t Lattice::m_rb

private

Definition at line 114 of file Lattice.h.

Referenced by computeReciprocalVectors(), getNearestLatticeVectorCoordinates(), getReciprocalLatticeBasis(), and reciprocalLatticeVectorsWithinRadius().

m_rc

kvector_t Lattice::m_rc

private

Cache of basis vectors in reciprocal space.

Definition at line 114 of file Lattice.h.

Referenced by computeReciprocalVectors(), getNearestLatticeVectorCoordinates(), getReciprocalLatticeBasis(), and reciprocalLatticeVectorsWithinRadius().

m_cache_ok

bool Lattice::m_cache_ok

mutableprivate

Boolean indicating if the reciprocal vectors are already initialized in the cache.

Definition at line 116 of file Lattice.h.

Referenced by getReciprocalLatticeBasis(), initialize(), onChange(), and reciprocalLatticeVectorsWithinRadius().

m_parent

const INode* INode::m_parent {nullptr}

privateinherited

Definition at line 81 of file INode.h.

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

m_NP

const size_t INode::m_NP

protectedinherited

Definition at line 86 of file INode.h.

Referenced by INode::INode().

m_P

std::vector<double> INode::m_P

protectedinherited

Definition at line 87 of file INode.h.

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

m_name

std::string IParameterized::m_name

privateinherited

Definition at line 72 of file IParameterized.h.

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

m_pool

std::unique_ptr<ParameterPool> IParameterized::m_pool

privateinherited

parameter pool (kind of pointer-to-implementation)

Definition at line 73 of file IParameterized.h.

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

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

• /home/www/ba/Sample/Lattice/Lattice.h
• /home/www/ba/Sample/Lattice/Lattice.cpp