IsotropicAtomBraggScatterer calculates the structure factor for a given HKL using the following equation, which gives the structure factor for the j-th atom in the unit cell: More...

#include <IsotropicAtomBraggScatterer.h>

Inheritance diagram for Mantid::Geometry::IsotropicAtomBraggScatterer:

Public Member Functions
StructureFactor	calculateStructureFactor (const Kernel::V3D &hkl) const override
	Calculates the structure factor.

BraggScatterer_sptr	clone () const override
	Clones the instance.

const std::string &	getElement () const
	Returns the string representation of the contained element.

const PhysicalConstants::NeutronAtom &	getNeutronAtom () const
	Returns the internally stored NeutronAtom that holds element specific data.

double	getOccupancy () const
	Returns the occupancy.

double	getU () const
	Returns the isotropic atomic displacement parameter.

	IsotropicAtomBraggScatterer ()
	Constructor which takes an element symbol, fractional coordinates, isotropic atomic displacement parameter and occupancy.

std::string	name () const override

Public Member Functions inherited from Mantid::Geometry::BraggScattererInCrystalStructure
	BraggScattererInCrystalStructure ()
	Default constructor.

UnitCell	getCell () const
	Returns the cell which is currently set.

Kernel::V3D	getPosition () const
	Returns the position of the scatterer.

Public Member Functions inherited from Mantid::Geometry::BraggScatterer
	BraggScatterer ()
	Default constructor.

double	calculateFSquared (const Kernel::V3D &hkl) const
	Returns \|F(hkl)\|^2.

void	initialize ()
	Initialization method that calls declareProperties() and sets initialized state to true.

bool	isInitialized ()
	Returns whether the instance has been initialized.

bool	isPropertyExposedToComposite (const std::string &propertyName) const
	Checks whether a property with the given name is exposed to BraggScattererComposite.

bool	isPropertyExposedToComposite (Kernel::Property *property) const
	Checks if a property is exposed to BraggScattererComposite or throws std::invalid_argument if a null-pointer is supplied.

Public Member Functions inherited from Mantid::Kernel::PropertyManager
::Json::Value	asJson (bool withDefaultValues=false) const override
	Return the property manager serialized as a json object.

std::string	asString (bool withDefaultValues=false) const override
	Return the property manager serialized as a string.

void	clear () override final
	Clears the whole property map.

PropertyManager *	cloneInTimeROI (const Kernel::TimeROI &timeROI)
	Create a partial copy of this object such that every time series property is cloned according to the input TimeROI.

void	declareOrReplaceProperty (std::unique_ptr< Property > p, const std::string &doc="") override
	Add or replace a property in the list of managed properties.

void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string).

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties.

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string).

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator.

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties.

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties.

void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="") override
	Add a property to the list of managed properties.

virtual void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them)

bool	existsProperty (const std::string &name) const override
	Checks whether the named property is already in the list of managed property.

void	filterByProperty (Mantid::Kernel::LogFilter *logFilter, const std::vector< std::string > &excludedFromFiltering=std::vector< std::string >()) override
	Filter the managed properties by the given boolean property mask.

std::vector< std::string >	getDeclaredPropertyNames () const noexcept override
	Return the list of declared property names.

Property *	getPointerToProperty (const std::string &name) const override
	Get a property by name.

const std::vector< Property * > &	getProperties () const override
	Get the list of managed properties.

TypedValue	getProperty (const std::string &name) const override
	Get the value of a property.

std::string	getPropertyValue (const std::string &name) const override
	Get the value of a property as a string.

bool	operator!= (const PropertyManager &other) const

PropertyManager &	operator+= (const PropertyManager &rhs)
	Addition operator.

PropertyManager &	operator= (const PropertyManager &)
	Assignment operator - performs a deep copy.

bool	operator== (const PropertyManager &other) const

size_t	propertyCount () const override
	Count the number of properties under management.

	PropertyManager ()
	Default constructor.

	PropertyManager (const PropertyManager &)
	copy constructor

void	removeDataOutsideTimeROI (const Kernel::TimeROI &timeROI)
	For time series properties, remove time values outside of TimeROI regions, each defined as [roi_begin,roi_end].

void	removeProperty (const std::string &name, const bool delproperty=true) override
	removes the property from properties map

void	resetProperties () override
	Reset property values back to initial values (blank or default values)

void	setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Set the ordered list of properties by a json value collection.

void	setProperties (const ::Json::Value &jsonValue, IPropertyManager *targetPropertyManager, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)
	Set the ordered list of properties by a json value collection.

void	setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Set the ordered list of properties by one string of values, separated by semicolons.

void	setProperties (const std::string &propertiesJson, IPropertyManager *targetPropertyManager, const std::unordered_set< std::string > &ignoreProperties, bool createMissing=false)
	Set the ordered list of properties by one string of values, separated by semicolons.

void	setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >()) override
	Sets all the declared properties from a string.

void	setPropertyOrdinal (const int &index, const std::string &value) override
	Set the value of a property by an index N.B.

void	setPropertyValue (const std::string &name, const std::string &value) override
	Set the value of a property by string N.B.

void	setPropertyValueFromJson (const std::string &name, const Json::Value &value) override
	Set the value of a property by Json::Value.

std::unique_ptr< Property >	takeProperty (const size_t index) override
	removes the property from the properties map and returns a pointer to it

bool	validateProperties () const override
	Validates all the properties in the collection.

virtual	~PropertyManager () override
	Virtual destructor.

Public Member Functions inherited from Mantid::Kernel::IPropertyManager
void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string).

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties.

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string).

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator.

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties.

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties.

std::vector< Property * >	getPropertiesInGroup (const std::string &group) const
	Get the list of managed properties in a given group.

IPropertyManager *	setProperty (const std::string &name, const char *value)
	Specialised version of setProperty template method to handle const char *.

IPropertyManager *	setProperty (const std::string &name, const std::string &value)
	Specialised version of setProperty template method to handle std::string.

template<typename T >
IPropertyManager *	setProperty (const std::string &name, const T &value)
	Templated method to set the value of a PropertyWithValue.

template<typename T >
IPropertyManager *	setProperty (const std::string &name, std::unique_ptr< T > value)
	Templated method to set the value of a PropertyWithValue from a std::unique_ptr.

void	setPropertyGroup (const std::string &name, const std::string &group)
	Set the group for a given property.

void	setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings > settings)

void	updatePropertyValues (const IPropertyManager &other)
	Update values of the existing properties.

virtual	~IPropertyManager ()=default

Protected Member Functions
void	afterScattererPropertySet (const std::string &propertyName) override
	After setting the element as a string, the corresponding.

void	declareScattererProperties () override
	Declares properties of this scatterer model.

double	getDebyeWallerFactor (const Kernel::V3D &hkl) const
	Returns the Debye-Waller factor, using an isotropic atomic displacement and the stored unit cell.

double	getScatteringLength () const
	Returns the scattering length of the stored element.

void	setElement (const std::string &element)
	Tries to obtain element specific data for the given symbol using PhysicalConstants::getAtom.

Protected Member Functions inherited from Mantid::Geometry::BraggScattererInCrystalStructure
void	afterPropertySet (const std::string &propertyName) override
	Additional property processing.

void	declareProperties () override
	Declares basic properties, should not be overridden by subclasses, use declareScattererProperties instead.

Kernel::V3D	getPositionFromString (const std::string &positionString) const

virtual void	setCell (const UnitCell &cell)
	Assigns a unit cell, which may be required for certain calculations.

virtual void	setPosition (const Kernel::V3D &position)
	Sets the position of the scatterer to the supplied coordinates - vector is wrapped to [0, 1).

Protected Member Functions inherited from Mantid::Geometry::BraggScatterer
void	exposePropertyToComposite (const std::string &propertyName)
	Exposes the property with the supplied name to BraggScattererComposite.

const std::string &	getPropagatingGroupName () const
	Returns the group name that is used to mark properties that are propagated.

void	unexposePropertyFromComposite (const std::string &propertyName)
	Removes exposure to composite for specified property.

Protected Member Functions inherited from Mantid::Kernel::PropertyManager
Property *	getPointerToPropertyOrdinal (const int &index) const override
	Get a property by an index.

Property *	getPointerToPropertyOrNull (const std::string &name) const
	Get a property by name.

Protected Member Functions inherited from Mantid::Kernel::IPropertyManager
template<typename T >
T	getValue (const std::string &name) const
	Templated method to get the value of a property.

template<>
MANTID_KERNEL_DLL PropertyManager_sptr	getValue (const std::string &name) const

template<>
MANTID_KERNEL_DLL PropertyManager_const_sptr	getValue (const std::string &name) const

Protected Attributes
PhysicalConstants::NeutronAtom	m_atom

std::string	m_label

Protected Attributes inherited from Mantid::Geometry::BraggScattererInCrystalStructure
UnitCell	m_cell

Kernel::V3D	m_position

Additional Inherited Members
Static Public Member Functions inherited from Mantid::Kernel::PropertyManager
static std::string	getInvalidValuesFilterLogName (const std::string &logName)
	Gets the correct log name for the matching invalid values log for a given log name.

static std::string	getLogNameFromInvalidValuesFilter (const std::string &logName)

static bool	isAnInvalidValuesFilterLog (const std::string &logName)
	Determine if the log's name has a substring indicating it should not be filtered.

Static Public Attributes inherited from Mantid::Kernel::PropertyManager
static const std::string	INVALID_VALUES_SUFFIX = "_invalid_values"

Detailed Description

IsotropicAtomBraggScatterer calculates the structure factor for a given HKL using the following equation, which gives the structure factor for the j-th atom in the unit cell:

\[ F(hkl)_j = b_j \cdot o_j \cdot DWF_j(hkl) \cdot \exp\left[2\pi i \cdot \left(h\cdot x_j + k\cdot y_j + l\cdot z_j\right)\right] \]

Since there are many terms in that equation, further explanation is required. The j-th atom in a unit cell occupies a certain position, here denoted by the fractional coordinates (x, y, z). With this information, an important calculation can be already carried out, calculation of the so called "phase". This term is easier seen when the complex part is written using trigonometric functions:

\begin{eqnarray*} \phi &=& 2\pi\left(h\cdot x_j + k\cdot y_j + l\cdot z_j\right) \\ \exp i\phi &=& \cos\phi + i\sin\phi \end{eqnarray*}

The magnitude of the complex number is determined first of all by the scattering length, \(b_j\) (which is element specific and tabulated, in Mantid this is in PhysicalConstants::NeutronAtom). It is multiplied by the occupancy \(o_j\), which is a number on the interval [0, 1], where 0 is a bit meaningless, since it means "no atoms on this position" and 1 represents a fully occupied position in the crystal lattice. This number can be used to model statistically distributed defects.

\(DWF_j\) denotes the Debye-Waller-factor, which models the diminishing scattering power of atoms that are displaced from their position (either due to temperature or other effects). It is defined like this:

\[ DWF_j(hkl) = \exp\left[-2\pi^2\cdot U \cdot 1/d_{hkl}^2\right] \]

Here, \(U\) is given in \(\mathrm{\AA{}^2}\) (for a discussion of terms regarding atomic displacement parameters, please see [1]), it is often of the order 0.05. \(d_{hkl}\) is alculated using the unit cell. The model used in this class is isotropic (hence the class name), which may be insufficient depending on the crystal structure, but as a first approximation it is often enough.

This class is designed to handle atoms in the asymmetric unit of the cell, creation of symmetrically equivalent atoms in the entire unit cell has to be handled elsewhere.

One example where this is done can be found in CrystalStructure.

[1] http://ww1.iucr.org/comm/cnom/adp/finrep/finrep.html

Author: Michael Wedel, Paul Scherrer Institut - SINQ

Date: 21/10/2014

Definition at line 78 of file IsotropicAtomBraggScatterer.h.

Constructor & Destructor Documentation

◆ IsotropicAtomBraggScatterer()

Mantid::Geometry::IsotropicAtomBraggScatterer::IsotropicAtomBraggScatterer ( )

Constructor which takes an element symbol, fractional coordinates, isotropic atomic displacement parameter and occupancy.

Definition at line 27 of file IsotropicAtomBraggScatterer.cpp.

Member Function Documentation

◆ afterScattererPropertySet()

void Mantid::Geometry::IsotropicAtomBraggScatterer::afterScattererPropertySet ( const std::string & propertyName )

overrideprotectedvirtual

After setting the element as a string, the corresponding.

Reimplemented from Mantid::Geometry::BraggScattererInCrystalStructure.

Definition at line 101 of file IsotropicAtomBraggScatterer.cpp.

References Mantid::Kernel::PropertyManager::getPropertyValue(), and setElement().

◆ calculateStructureFactor()

StructureFactor Mantid::Geometry::IsotropicAtomBraggScatterer::calculateStructureFactor ( const Kernel::V3D & hkl ) const

overridevirtual

Calculates the structure factor.

This method calculates the structure factor. For details, please refer to the class documentation in the header file.

Parameters

hkl	:: HKL for which the structure factor should be calculated

Returns: Structure factor (complex).

Implements Mantid::Geometry::BraggScatterer.

Definition at line 62 of file IsotropicAtomBraggScatterer.cpp.

References getDebyeWallerFactor(), getOccupancy(), getScatteringLength(), Mantid::Geometry::BraggScattererInCrystalStructure::m_position, and Mantid::Kernel::V3D::scalar_prod().

◆ clone()

BraggScatterer_sptr Mantid::Geometry::IsotropicAtomBraggScatterer::clone ( ) const

overridevirtual

Clones the instance.

Implements Mantid::Geometry::BraggScatterer.

Definition at line 30 of file IsotropicAtomBraggScatterer.cpp.

References Mantid::Kernel::PropertyManager::asString(), and clone().

Referenced by clone().

◆ declareScattererProperties()

void Mantid::Geometry::IsotropicAtomBraggScatterer::declareScattererProperties ( )

overrideprotectedvirtual

Declares properties of this scatterer model.

In addition to the properties of BraggScatterer, this class implements three more properties, as described in the general class documentation, with some restrictions on allowed values: