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layer_area_per_molecule

MATERIAL_SOLVATED_DEFAULTS = {'solvent_fraction': {'description': 'Fraction of solvent in layer.', 'value': 0.2, 'unit': 'dimensionless', 'min': 0, 'max': 1, 'fixed': True}} module-attribute

LAYER_DEFAULTS = {'thickness': {'description': 'The thickness of the layer in angstroms', 'url': 'https://github.com/reflectivity/edu_outreach/blob/master/refl_maths/paper.tex', 'value': 10.0, 'unit': 'angstrom', 'min': 0.0, 'max': np.inf, 'fixed': True}, 'roughness': {'description': 'The interfacial roughness, Nevot-Croce, for the layer in angstroms.', 'url': 'https://doi.org/10.1051/rphysap:01980001503076100', 'value': 3.3, 'unit': 'angstrom', 'min': 0.0, 'max': np.inf, 'fixed': True}} module-attribute

DEFAULTS = {'molecular_formula': 'C10H18NO8P', 'area_per_molecule': {'description': 'Surface coverage', 'value': 48.2, 'unit': 'angstrom^2', 'min': 0, 'max': np.inf, 'fixed': True}, 'sl': {'description': 'The real scattering length for a molecule formula in angstrom.', 'url': 'https://www.ncnr.nist.gov/resources/activation/', 'value': 4.186, 'unit': 'angstrom', 'min': -np.inf, 'max': np.inf, 'fixed': True}, 'isl': {'description': 'The real scattering length for a molecule formula in angstrom.', 'url': 'https://www.ncnr.nist.gov/resources/activation/', 'value': 0.0, 'unit': 'angstrom', 'min': -np.inf, 'max': np.inf, 'fixed': True}} module-attribute

Material

Bases: BaseCore

Source code in src/easyreflectometry/sample/elements/materials/material.py 
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class Material(BaseCore):
    def __init__(
        self,
        sld: Union[Parameter, float, None] = None,
        isld: Union[Parameter, float, None] = None,
        name: str = 'EasyMaterial',
        unique_name: Optional[str] = None,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        sld : Union[Parameter, float, None], optional
            Real scattering length density. By default, None.
        isld : Union[Parameter, float, None], optional
            Imaginary scattering length density. By default, None.
        name : str, optional
            Name of the material. By default, 'EasyMaterial'.
        interface :
            Calculator interface. By default, None.
        """
        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        sld = get_as_parameter(
            name='sld',
            value=sld,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Sld',
        )
        apply_default_limits(sld, 'sld')

        isld = get_as_parameter(
            name='isld',
            value=isld,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Isld',
        )
        apply_default_limits(isld, 'isld')

        super().__init__(name=name, unique_name=unique_name)
        self._sld = sld
        self._isld = isld

        if interface is not None:
            self.interface = interface

    @property
    def sld(self) -> Parameter:
        return self._sld

    @sld.setter
    def sld(self, value: float) -> None:
        self._sld.value = value

    @property
    def isld(self) -> Parameter:
        return self._isld

    @isld.setter
    def isld(self, value: float) -> None:
        self._isld.value = value

    # Representation
    @property
    def _dict_repr(self) -> dict[str, str]:
        """A simplified dict representation."""
        return {
            self.name: {
                'sld': f'{self._sld.value:.3f}e-6 {self._sld.unit}',
                'isld': f'{self._isld.value:.3f}e-6 {self._isld.unit}',
            }
        }

__init__(sld=None, isld=None, name='EasyMaterial', unique_name=None, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
sld Union[Parameter, float, None]

Real scattering length density. By default, None.

 None
isld Union[Parameter, float, None]

Imaginary scattering length density. By default, None.

 None
name str

Name of the material. By default, 'EasyMaterial'.

 'EasyMaterial'
interface

Calculator interface. By default, None.

 None
Source code in src/easyreflectometry/sample/elements/materials/material.py 
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def __init__(
    self,
    sld: Union[Parameter, float, None] = None,
    isld: Union[Parameter, float, None] = None,
    name: str = 'EasyMaterial',
    unique_name: Optional[str] = None,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    sld : Union[Parameter, float, None], optional
        Real scattering length density. By default, None.
    isld : Union[Parameter, float, None], optional
        Imaginary scattering length density. By default, None.
    name : str, optional
        Name of the material. By default, 'EasyMaterial'.
    interface :
        Calculator interface. By default, None.
    """
    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    sld = get_as_parameter(
        name='sld',
        value=sld,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Sld',
    )
    apply_default_limits(sld, 'sld')

    isld = get_as_parameter(
        name='isld',
        value=isld,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Isld',
    )
    apply_default_limits(isld, 'isld')

    super().__init__(name=name, unique_name=unique_name)
    self._sld = sld
    self._isld = isld

    if interface is not None:
        self.interface = interface

MaterialSolvated

Bases: MaterialMixture

Source code in src/easyreflectometry/sample/elements/materials/material_solvated.py 
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class MaterialSolvated(MaterialMixture):
    def __init__(
        self,
        material: Union[Material, None] = None,
        solvent: Union[Material, None] = None,
        solvent_fraction: Union[Parameter, float, None] = None,
        name=None,
        unique_name: Optional[str] = None,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        material : Union[Material, None], optional
            The material being solvated. By default, None.
        solvent : Union[Material, None], optional
            The solvent material. By default, None.
        solvent_fraction : Union[Parameter, float, None], optional
            Fraction of solvent in layer. E.g. solvation or surface coverage. By default, None.
        name :
            Name of the material. By default, None.
        interface :
            Calculator interface. By default, None.
        """
        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        if material is None:
            material = Material(sld=6.36, isld=0, name='D2O', interface=interface)
        if solvent is None:
            solvent = Material(sld=-0.561, isld=0, name='H2O', interface=interface)

        solvent_fraction = get_as_parameter(
            name='solvent_fraction',
            value=solvent_fraction,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Fraction',
        )

        # In super class, the fraction is the fraction of material b in material a
        super().__init__(
            material_a=material,
            material_b=solvent,
            fraction=solvent_fraction,
            name=name,
            unique_name=unique_name,
            interface=interface,
        )
        if name is None:
            self._update_name()

    @property
    def material(self) -> Material:
        """Get material."""
        return self._material_a

    @material.setter
    def material(self, new_material: Material) -> None:
        """Set the material."""
        self.material_a = new_material

    @property
    def solvent(self) -> Material:
        """Get solvent."""
        return self._material_b

    @solvent.setter
    def solvent(self, new_solvent: Material) -> None:
        """Set the solvent."""
        self.material_b = new_solvent

    @property
    def solvent_fraction_parameter(self) -> Parameter:
        """Get the parameter for the fraction of layer described by the solvent."""
        return self._fraction

    @property
    def solvent_fraction(self) -> Parameter:
        """The Parameter for the fraction of the layer described by the solvent.

        This might be the fraction of:
        - solvation where solvent is within the layer, or
        - patches of solvent in the layer where no material is present.
        """
        return self._fraction

    @solvent_fraction.setter
    def solvent_fraction(self, solvent_fraction: float) -> None:
        """Set the fraction of layer covered by the material."""
        if not isinstance(solvent_fraction, (int, float)):
            raise ValueError('solvent_fraction must be a float between 0 and 1')
        if solvent_fraction < 0 or solvent_fraction > 1:
            raise ValueError('solvent_fraction must be between 0 and 1')
        self._fraction.value = solvent_fraction

    def _update_name(self) -> None:
        """Update name."""
        self.name = self._material_a.name + ' in ' + self._material_b.name

    # ----- deserialization -----

    @classmethod
    def from_dict(cls, obj_dict: dict) -> 'MaterialSolvated':
        """Re-route the saved ``solvent_fraction`` Parameter onto ``_fraction``.

        :class:`ModelBase.from_dict` writes the saved Parameter to
        ``_solvent_fraction`` because that's the constructor-arg name, but
        the live `solvent_fraction` property returns ``self._fraction``
        (the field MaterialMixture maintains). Without this override the
        saved fit metadata (fixed/bounds/etc.) is stranded on the unused
        ``_solvent_fraction`` attribute and the active parameter keeps the
        defaults from `__init__`.

        Also re-runs `_materials_constraints` so the parent MaterialMixture's
        mixed `_sld` / `_isld` depend on the live `_fraction`, not the
        temporary Parameter created from the float kwarg.
        """
        instance = super().from_dict(obj_dict)
        saved = instance.__dict__.pop('_solvent_fraction', None)
        if saved is not None:
            old = instance._fraction
            instance._fraction = saved
            try:
                instance._global_object.map.prune(old.unique_name)
            except (AttributeError, KeyError):
                pass
            instance._materials_constraints()
        return instance

    # Representation
    @property
    def _dict_repr(self) -> dict[str, str]:
        """A simplified dict representation."""
        return {
            self.name: {
                'solvent_fraction': f'{self._fraction.value:.3f} {self._fraction.unit}',
                'sld': f'{self._sld.value:.3f}e-6 {self._sld.unit}',
                'isld': f'{self._isld.value:.3f}e-6 {self._isld.unit}',
                'material': self.material._dict_repr,
                'solvent': self.solvent._dict_repr,
            }
        }

material property writable

Get material.

solvent property writable

Get solvent.

solvent_fraction_parameter property

Get the parameter for the fraction of layer described by the solvent.

solvent_fraction property writable

The Parameter for the fraction of the layer described by the solvent.

This might be the fraction of: - solvation where solvent is within the layer, or - patches of solvent in the layer where no material is present.

__init__(material=None, solvent=None, solvent_fraction=None, name=None, unique_name=None, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
material Union[Material, None]

The material being solvated. By default, None.

 None
solvent Union[Material, None]

The solvent material. By default, None.

 None
solvent_fraction Union[Parameter, float, None]

Fraction of solvent in layer. E.g. solvation or surface coverage. By default, None.

 None
name

Name of the material. By default, None.

 None
interface

Calculator interface. By default, None.

 None
Source code in src/easyreflectometry/sample/elements/materials/material_solvated.py 
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def __init__(
    self,
    material: Union[Material, None] = None,
    solvent: Union[Material, None] = None,
    solvent_fraction: Union[Parameter, float, None] = None,
    name=None,
    unique_name: Optional[str] = None,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    material : Union[Material, None], optional
        The material being solvated. By default, None.
    solvent : Union[Material, None], optional
        The solvent material. By default, None.
    solvent_fraction : Union[Parameter, float, None], optional
        Fraction of solvent in layer. E.g. solvation or surface coverage. By default, None.
    name :
        Name of the material. By default, None.
    interface :
        Calculator interface. By default, None.
    """
    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    if material is None:
        material = Material(sld=6.36, isld=0, name='D2O', interface=interface)
    if solvent is None:
        solvent = Material(sld=-0.561, isld=0, name='H2O', interface=interface)

    solvent_fraction = get_as_parameter(
        name='solvent_fraction',
        value=solvent_fraction,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Fraction',
    )

    # In super class, the fraction is the fraction of material b in material a
    super().__init__(
        material_a=material,
        material_b=solvent,
        fraction=solvent_fraction,
        name=name,
        unique_name=unique_name,
        interface=interface,
    )
    if name is None:
        self._update_name()

from_dict(obj_dict) classmethod

Re-route the saved solvent_fraction Parameter onto _fraction.

:class:ModelBase.from_dict writes the saved Parameter to _solvent_fraction because that's the constructor-arg name, but the live solvent_fraction property returns self._fraction (the field MaterialMixture maintains). Without this override the saved fit metadata (fixed/bounds/etc.) is stranded on the unused _solvent_fraction attribute and the active parameter keeps the defaults from __init__.

Also re-runs _materials_constraints so the parent MaterialMixture's mixed _sld / _isld depend on the live _fraction, not the temporary Parameter created from the float kwarg.

Source code in src/easyreflectometry/sample/elements/materials/material_solvated.py 
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@classmethod
def from_dict(cls, obj_dict: dict) -> 'MaterialSolvated':
    """Re-route the saved ``solvent_fraction`` Parameter onto ``_fraction``.

    :class:`ModelBase.from_dict` writes the saved Parameter to
    ``_solvent_fraction`` because that's the constructor-arg name, but
    the live `solvent_fraction` property returns ``self._fraction``
    (the field MaterialMixture maintains). Without this override the
    saved fit metadata (fixed/bounds/etc.) is stranded on the unused
    ``_solvent_fraction`` attribute and the active parameter keeps the
    defaults from `__init__`.

    Also re-runs `_materials_constraints` so the parent MaterialMixture's
    mixed `_sld` / `_isld` depend on the live `_fraction`, not the
    temporary Parameter created from the float kwarg.
    """
    instance = super().from_dict(obj_dict)
    saved = instance.__dict__.pop('_solvent_fraction', None)
    if saved is not None:
        old = instance._fraction
        instance._fraction = saved
        try:
            instance._global_object.map.prune(old.unique_name)
        except (AttributeError, KeyError):
            pass
        instance._materials_constraints()
    return instance

Layer

Bases: BaseCore

Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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class Layer(BaseCore):
    def __init__(
        self,
        material: Union[Material, None] = None,
        thickness: Union[Parameter, float, None] = None,
        roughness: Union[Parameter, float, None] = None,
        name: str = 'EasyLayer',
        unique_name: Optional[str] = None,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        material : Union[Material, None], optional
            The material for the layer. By default, None.
        thickness : Union[Parameter, float, None], optional
            Layer thickness in Angstrom. By default, None.
        roughness : Union[Parameter, float, None], optional
            Upper roughness on the layer in Angstrom. By default, None.
        name : str, optional
            Name of the layer. By default, 'EasyLayer'.
        interface :
            Interface object. By default, None.
        """
        if material is None:
            material = Material(interface=interface)

        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        thickness_value = thickness
        thickness = get_as_parameter(
            name='thickness',
            value=thickness,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Thickness',
        )
        thickness.default_limits_pending = not isinstance(thickness_value, Parameter)

        roughness_value = roughness
        roughness = get_as_parameter(
            name='roughness',
            value=roughness,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Roughness',
        )
        roughness.default_limits_pending = not isinstance(roughness_value, Parameter)

        super().__init__(name=name, unique_name=unique_name)
        self._material = material
        self._thickness = thickness
        self._roughness = roughness

        if interface is not None:
            self.interface = interface

    @property
    def material(self) -> Material:
        return self._material

    @material.setter
    def material(self, value: Material) -> None:
        self._material = value

    @property
    def thickness(self) -> Parameter:
        return self._thickness

    @thickness.setter
    def thickness(self, value: float) -> None:
        self._thickness.value = value

    @property
    def roughness(self) -> Parameter:
        return self._roughness

    @roughness.setter
    def roughness(self, value: float) -> None:
        self._roughness.value = value

    def assign_material(self, material: Material) -> None:
        """Assign a material to the layer interface.

        Parameters
        ----------
        material : Material
            The material to assign to the layer.
        """
        self._material = material
        if self.interface is not None:
            self.interface().assign_material_to_layer(self.material.unique_name, self.unique_name)

    # Representation
    @property
    def _dict_repr(self) -> dict[str, str]:
        """A simplified dict representation."""
        return {
            self.name: {
                'material': self.material._dict_repr,
                'thickness': f'{self.thickness.value:.3f} {self.thickness.unit}',
                'roughness': f'{self.roughness.value:.3f} {self.roughness.unit}',
            }
        }

__init__(material=None, thickness=None, roughness=None, name='EasyLayer', unique_name=None, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
material Union[Material, None]

The material for the layer. By default, None.

 None
thickness Union[Parameter, float, None]

Layer thickness in Angstrom. By default, None.

 None
roughness Union[Parameter, float, None]

Upper roughness on the layer in Angstrom. By default, None.

 None
name str

Name of the layer. By default, 'EasyLayer'.

 'EasyLayer'
interface

Interface object. By default, None.

 None
Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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def __init__(
    self,
    material: Union[Material, None] = None,
    thickness: Union[Parameter, float, None] = None,
    roughness: Union[Parameter, float, None] = None,
    name: str = 'EasyLayer',
    unique_name: Optional[str] = None,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    material : Union[Material, None], optional
        The material for the layer. By default, None.
    thickness : Union[Parameter, float, None], optional
        Layer thickness in Angstrom. By default, None.
    roughness : Union[Parameter, float, None], optional
        Upper roughness on the layer in Angstrom. By default, None.
    name : str, optional
        Name of the layer. By default, 'EasyLayer'.
    interface :
        Interface object. By default, None.
    """
    if material is None:
        material = Material(interface=interface)

    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    thickness_value = thickness
    thickness = get_as_parameter(
        name='thickness',
        value=thickness,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Thickness',
    )
    thickness.default_limits_pending = not isinstance(thickness_value, Parameter)

    roughness_value = roughness
    roughness = get_as_parameter(
        name='roughness',
        value=roughness,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Roughness',
    )
    roughness.default_limits_pending = not isinstance(roughness_value, Parameter)

    super().__init__(name=name, unique_name=unique_name)
    self._material = material
    self._thickness = thickness
    self._roughness = roughness

    if interface is not None:
        self.interface = interface

assign_material(material)

Assign a material to the layer interface.

Parameters:

Name Type Description Default
material Material

The material to assign to the layer.

 required
Source code in src/easyreflectometry/sample/elements/layers/layer.py 
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def assign_material(self, material: Material) -> None:
    """Assign a material to the layer interface.

    Parameters
    ----------
    material : Material
        The material to assign to the layer.
    """
    self._material = material
    if self.interface is not None:
        self.interface().assign_material_to_layer(self.material.unique_name, self.unique_name)

LayerAreaPerMolecule

Bases: Layer

The LayerAreaPerMolecule class allows a layer to be defined in terms of some molecular formula an area per molecule, and a solvent.

Source code in src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py 
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class LayerAreaPerMolecule(Layer):
    """The `LayerAreaPerMolecule` class allows a layer to be defined in terms of some
    molecular formula an area per molecule, and a solvent.
    """

    def __init__(
        self,
        molecular_formula: Union[str, None] = None,
        thickness: Union[Parameter, float, None] = None,
        solvent: Union[Material, None] = None,
        solvent_fraction: Union[Parameter, float, None] = None,
        area_per_molecule: Union[Parameter, float, None] = None,
        roughness: Union[Parameter, float, None] = None,
        name: str = 'EasyLayerAreaPerMolecule',
        unique_name: Optional[str] = None,
        interface=None,
    ):
        """Constructor.

        Parameters
        ----------
        unique_name : Optional[str], optional
            By default, None.
        molecular_formula : Union[str, None], optional
            Formula for the molecule in the layer. By default, None.
        thickness : Union[Parameter, float, None], optional
            Layer thickness in Angstrom. By default, None.
        solvent : Union[Material, None], optional
            Solvent containing the molecule. By default, None.
        solvent_fraction : Union[Parameter, float, None], optional
            Fraction of solvent in layer. Fx solvation or surface coverage. By default, None.
        area_per_molecule : Union[Parameter, float, None], optional
            Area per molecule in the layer. By default, None.
        roughness : Union[Parameter, float, None], optional
            Upper roughness on the layer in Angstrom. By default, None.
        name : str, optional
            Name of the layer. By default, 'EasyLayerAreaPerMolecule'.
        interface :
            Interface object. By default, None.
        """
        if unique_name is None:
            unique_name = global_object.generate_unique_name(self.__class__.__name__)

        if solvent is None:
            solvent = Material(
                sld=6.36,
                isld=0,
                name='D2O',
                unique_name=unique_name + '_MaterialSolvent',
                interface=interface,
            )

        if molecular_formula is None:
            molecular_formula = DEFAULTS['molecular_formula']
        molecule_material = Material(
            sld=0.0,
            isld=0.0,
            name=molecular_formula,
            unique_name=unique_name + '_MaterialMolecule',
            interface=interface,
        )

        thickness = get_as_parameter(
            name='thickness',
            value=thickness,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_Thickness',
        )
        area_per_molecule_param = get_as_parameter(
            name='area_per_molecule',
            value=area_per_molecule,
            default_dict=DEFAULTS,
            unique_name_prefix=f'{unique_name}_AreaPerMolecule',
        )
        scattering_length_real = get_as_parameter(
            name='scattering_length_real',
            value=0.0,
            default_dict=DEFAULTS['sl'],
            unique_name_prefix=f'{unique_name}_Sl',
        )
        scattering_length_imag = get_as_parameter(
            name='scattering_length_imag',
            value=0.0,
            default_dict=DEFAULTS['isl'],
            unique_name_prefix=f'{unique_name}_Isl',
        )

        # Constrain molecule.sld / .isld to scattering_length / (thickness * area_per_molecule).
        # `_setup_sld_constraints` rebuilds the same expression after from_dict, so keep the
        # variable names (`a`, `b`, `p`) consistent with that path.
        dependency_expression = 'a / (b*p) * 1e6'
        molecule_material.sld.make_dependent_on(
            dependency_expression=dependency_expression,
            dependency_map={'a': scattering_length_real, 'b': thickness, 'p': area_per_molecule_param},
        )
        molecule_material.isld.make_dependent_on(
            dependency_expression=dependency_expression,
            dependency_map={'a': scattering_length_imag, 'b': thickness, 'p': area_per_molecule_param},
        )

        solvated_molecule_material = MaterialSolvated(
            material=molecule_material,
            solvent=solvent,
            solvent_fraction=solvent_fraction,
            unique_name=unique_name + '_MaterialSolvated',
            interface=interface,
        )
        super().__init__(
            material=solvated_molecule_material,
            thickness=thickness,
            roughness=roughness,
            name=name,
            unique_name=unique_name,
            interface=None,
        )
        self._area_per_molecule = area_per_molecule_param
        self._scattering_length_real = scattering_length_real
        self._scattering_length_imag = scattering_length_imag

        scattering_length = neutron_scattering_length(molecular_formula)
        self._scattering_length_real.value = scattering_length.real
        self._scattering_length_imag.value = scattering_length.imag
        self._molecular_formula = molecular_formula

        if interface is not None:
            self.interface = interface

    # ----- constraint plumbing -----

    def _setup_sld_constraints(self) -> None:
        """Wire the inner molecule material's ``sld`` / ``isld`` to depend on
        the current scattering-length, thickness, and area-per-molecule
        parameters.

        Idempotent — called once from ``__init__`` and again from
        ``from_dict`` after the saved Parameter objects replace the
        constructor-time temporaries.
        """
        molecule_material = self.material.material
        for derived in (molecule_material.sld, molecule_material.isld):
            if not derived.independent:
                derived.make_independent()

        dependency_expression = 'a / (b*p) * 1e6'
        molecule_material.sld.make_dependent_on(
            dependency_expression=dependency_expression,
            dependency_map={
                'a': self._scattering_length_real,
                'b': self._thickness,
                'p': self._area_per_molecule,
            },
        )
        molecule_material.isld.make_dependent_on(
            dependency_expression=dependency_expression,
            dependency_map={
                'a': self._scattering_length_imag,
                'b': self._thickness,
                'p': self._area_per_molecule,
            },
        )

    # ----- deserialization -----

    @classmethod
    def from_dict(cls, obj_dict: dict) -> 'LayerAreaPerMolecule':
        """Re-route the saved ``solvent_fraction`` Parameter and rebuild the
        molecule-SLD constraint chain after :class:`ModelBase.from_dict`
        swaps in the persisted Parameter objects.

        `ModelBase.from_dict` writes the deserialized ``solvent_fraction``
        Parameter to ``self._solvent_fraction`` (orphan — the live property
        delegates to ``self.material.solvent_fraction``, which is
        ``self.material._fraction``). It also reassigns ``self._thickness``
        and ``self._area_per_molecule``, but the constraint graph built in
        ``__init__`` still references the temporary Parameters created from
        the float kwargs. We fix both here.
        """
        instance = super().from_dict(obj_dict)

        saved_solvent_fraction = instance.__dict__.pop('_solvent_fraction', None)
        if saved_solvent_fraction is not None:
            mixture = instance.material
            old = mixture._fraction
            mixture._fraction = saved_solvent_fraction
            try:
                instance._global_object.map.prune(old.unique_name)
            except (AttributeError, KeyError):
                pass
            mixture._materials_constraints()

        instance._setup_sld_constraints()
        return instance

    @property
    def area_per_molecule_parameter(self) -> Parameter:
        """Get the parameter for area per molecule."""
        return self._area_per_molecule

    @property
    def area_per_molecule(self) -> Parameter:
        """The Parameter that controls area per molecule."""
        return self._area_per_molecule

    @area_per_molecule.setter
    def area_per_molecule(self, value: float) -> None:
        if value < 0:
            raise ValueError('area_per_molecule must be greater than 0.0.')
        self._area_per_molecule.value = value

    @property
    def molecule(self) -> Material:
        """Get the molecule material."""
        return self.material.material

    @property
    def solvent(self) -> Material:
        """Get the solvent material."""
        return self.material.solvent

    @solvent.setter
    def solvent(self, new_solvent: Material) -> None:
        self.material.solvent = new_solvent

    @property
    def solvent_fraction_parameter(self) -> Parameter:
        """Get parameter for the fraction of the layer occupied by the solvent."""
        return self.material.solvent_fraction_parameter

    @property
    def solvent_fraction(self) -> Parameter:
        """The Parameter for the fraction of the layer occupied by the solvent."""
        return self.material.solvent_fraction

    @solvent_fraction.setter
    def solvent_fraction(self, value: float) -> None:
        self.material.solvent_fraction = value

    @property
    def molecular_formula(self) -> str:
        """Get the formula of molecule the layer."""
        return self._molecular_formula

    @molecular_formula.setter
    def molecular_formula(self, formula_string: str) -> None:
        self._molecular_formula = formula_string
        scattering_length = neutron_scattering_length(formula_string)
        self._scattering_length_real.value = scattering_length.real
        self._scattering_length_imag.value = scattering_length.imag

        self.molecule.name = formula_string
        self.material._update_name()

    @property
    def _dict_repr(self) -> dict[str, str]:
        """Dictionary representation of the `area_per_molecule` object."""
        dict_repr = super()._dict_repr
        dict_repr['molecular_formula'] = self._molecular_formula
        dict_repr['area_per_molecule'] = f'{self._area_per_molecule.value:.2f} {self._area_per_molecule.unit}'
        return dict_repr

area_per_molecule_parameter property

Get the parameter for area per molecule.

area_per_molecule property writable

The Parameter that controls area per molecule.

molecule property

Get the molecule material.

solvent property writable

Get the solvent material.

solvent_fraction_parameter property

Get parameter for the fraction of the layer occupied by the solvent.

solvent_fraction property writable

The Parameter for the fraction of the layer occupied by the solvent.

molecular_formula property writable

Get the formula of molecule the layer.

__init__(molecular_formula=None, thickness=None, solvent=None, solvent_fraction=None, area_per_molecule=None, roughness=None, name='EasyLayerAreaPerMolecule', unique_name=None, interface=None)

Constructor.

Parameters:

Name Type Description Default
unique_name Optional[str]

By default, None.

 None
molecular_formula Union[str, None]

Formula for the molecule in the layer. By default, None.

 None
thickness Union[Parameter, float, None]

Layer thickness in Angstrom. By default, None.

 None
solvent Union[Material, None]

Solvent containing the molecule. By default, None.

 None
solvent_fraction Union[Parameter, float, None]

Fraction of solvent in layer. Fx solvation or surface coverage. By default, None.

 None
area_per_molecule Union[Parameter, float, None]

Area per molecule in the layer. By default, None.

 None
roughness Union[Parameter, float, None]

Upper roughness on the layer in Angstrom. By default, None.

 None
name str

Name of the layer. By default, 'EasyLayerAreaPerMolecule'.

 'EasyLayerAreaPerMolecule'
interface

Interface object. By default, None.

 None
Source code in src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py 
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def __init__(
    self,
    molecular_formula: Union[str, None] = None,
    thickness: Union[Parameter, float, None] = None,
    solvent: Union[Material, None] = None,
    solvent_fraction: Union[Parameter, float, None] = None,
    area_per_molecule: Union[Parameter, float, None] = None,
    roughness: Union[Parameter, float, None] = None,
    name: str = 'EasyLayerAreaPerMolecule',
    unique_name: Optional[str] = None,
    interface=None,
):
    """Constructor.

    Parameters
    ----------
    unique_name : Optional[str], optional
        By default, None.
    molecular_formula : Union[str, None], optional
        Formula for the molecule in the layer. By default, None.
    thickness : Union[Parameter, float, None], optional
        Layer thickness in Angstrom. By default, None.
    solvent : Union[Material, None], optional
        Solvent containing the molecule. By default, None.
    solvent_fraction : Union[Parameter, float, None], optional
        Fraction of solvent in layer. Fx solvation or surface coverage. By default, None.
    area_per_molecule : Union[Parameter, float, None], optional
        Area per molecule in the layer. By default, None.
    roughness : Union[Parameter, float, None], optional
        Upper roughness on the layer in Angstrom. By default, None.
    name : str, optional
        Name of the layer. By default, 'EasyLayerAreaPerMolecule'.
    interface :
        Interface object. By default, None.
    """
    if unique_name is None:
        unique_name = global_object.generate_unique_name(self.__class__.__name__)

    if solvent is None:
        solvent = Material(
            sld=6.36,
            isld=0,
            name='D2O',
            unique_name=unique_name + '_MaterialSolvent',
            interface=interface,
        )

    if molecular_formula is None:
        molecular_formula = DEFAULTS['molecular_formula']
    molecule_material = Material(
        sld=0.0,
        isld=0.0,
        name=molecular_formula,
        unique_name=unique_name + '_MaterialMolecule',
        interface=interface,
    )

    thickness = get_as_parameter(
        name='thickness',
        value=thickness,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_Thickness',
    )
    area_per_molecule_param = get_as_parameter(
        name='area_per_molecule',
        value=area_per_molecule,
        default_dict=DEFAULTS,
        unique_name_prefix=f'{unique_name}_AreaPerMolecule',
    )
    scattering_length_real = get_as_parameter(
        name='scattering_length_real',
        value=0.0,
        default_dict=DEFAULTS['sl'],
        unique_name_prefix=f'{unique_name}_Sl',
    )
    scattering_length_imag = get_as_parameter(
        name='scattering_length_imag',
        value=0.0,
        default_dict=DEFAULTS['isl'],
        unique_name_prefix=f'{unique_name}_Isl',
    )

    # Constrain molecule.sld / .isld to scattering_length / (thickness * area_per_molecule).
    # `_setup_sld_constraints` rebuilds the same expression after from_dict, so keep the
    # variable names (`a`, `b`, `p`) consistent with that path.
    dependency_expression = 'a / (b*p) * 1e6'
    molecule_material.sld.make_dependent_on(
        dependency_expression=dependency_expression,
        dependency_map={'a': scattering_length_real, 'b': thickness, 'p': area_per_molecule_param},
    )
    molecule_material.isld.make_dependent_on(
        dependency_expression=dependency_expression,
        dependency_map={'a': scattering_length_imag, 'b': thickness, 'p': area_per_molecule_param},
    )

    solvated_molecule_material = MaterialSolvated(
        material=molecule_material,
        solvent=solvent,
        solvent_fraction=solvent_fraction,
        unique_name=unique_name + '_MaterialSolvated',
        interface=interface,
    )
    super().__init__(
        material=solvated_molecule_material,
        thickness=thickness,
        roughness=roughness,
        name=name,
        unique_name=unique_name,
        interface=None,
    )
    self._area_per_molecule = area_per_molecule_param
    self._scattering_length_real = scattering_length_real
    self._scattering_length_imag = scattering_length_imag

    scattering_length = neutron_scattering_length(molecular_formula)
    self._scattering_length_real.value = scattering_length.real
    self._scattering_length_imag.value = scattering_length.imag
    self._molecular_formula = molecular_formula

    if interface is not None:
        self.interface = interface

from_dict(obj_dict) classmethod

Re-route the saved solvent_fraction Parameter and rebuild the molecule-SLD constraint chain after :class:ModelBase.from_dict swaps in the persisted Parameter objects.

ModelBase.from_dict writes the deserialized solvent_fraction Parameter to self._solvent_fraction (orphan — the live property delegates to self.material.solvent_fraction, which is self.material._fraction). It also reassigns self._thickness and self._area_per_molecule, but the constraint graph built in __init__ still references the temporary Parameters created from the float kwargs. We fix both here.

Source code in src/easyreflectometry/sample/elements/layers/layer_area_per_molecule.py 
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@classmethod
def from_dict(cls, obj_dict: dict) -> 'LayerAreaPerMolecule':
    """Re-route the saved ``solvent_fraction`` Parameter and rebuild the
    molecule-SLD constraint chain after :class:`ModelBase.from_dict`
    swaps in the persisted Parameter objects.

    `ModelBase.from_dict` writes the deserialized ``solvent_fraction``
    Parameter to ``self._solvent_fraction`` (orphan — the live property
    delegates to ``self.material.solvent_fraction``, which is
    ``self.material._fraction``). It also reassigns ``self._thickness``
    and ``self._area_per_molecule``, but the constraint graph built in
    ``__init__`` still references the temporary Parameters created from
    the float kwargs. We fix both here.
    """
    instance = super().from_dict(obj_dict)

    saved_solvent_fraction = instance.__dict__.pop('_solvent_fraction', None)
    if saved_solvent_fraction is not None:
        mixture = instance.material
        old = mixture._fraction
        mixture._fraction = saved_solvent_fraction
        try:
            instance._global_object.map.prune(old.unique_name)
        except (AttributeError, KeyError):
            pass
        mixture._materials_constraints()

    instance._setup_sld_constraints()
    return instance

get_as_parameter(name, value, default_dict, unique_name_prefix=None)

This function creates a parameter for the variable name.

A parameter has a value and metadata.

If the value already is a parameter, it is returned. If the value is a number, a parameter is created with this value and metadata from the dictionary. If the value is None, a parameter is created with the default value and metadata from the dictionary.

param value: The value to use for the parameter.  If None, the default value in the dictionary is used.
param name: The name of the parameter
param default_dict: Dictionary with entry for `name` containing the default value and metadata for the parameter
Source code in src/easyreflectometry/utils.py 
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def get_as_parameter(
    name: str,
    value: Union[Parameter, Number, None],
    default_dict: dict,
    unique_name_prefix: Optional[str] = None,
) -> Parameter:
    """This function creates a parameter for the variable `name`.

        A parameter has a value and metadata.
    If the value already is a parameter, it is returned.
        If the value is a number, a parameter is created with this value and metadata from the dictionary.
        If the value is None, a parameter is created with the default value and metadata from the dictionary.

        param value: The value to use for the parameter.  If None, the default value in the dictionary is used.
        param name: The name of the parameter
        param default_dict: Dictionary with entry for `name` containing the default value and metadata for the parameter
    """
    # This is a parameter, return it
    if isinstance(value, Parameter):
        return value

    # Ensure we got the dictionary for the parameter with the given name
    # Should leave the passed dictionary unchanged
    if name not in default_dict:
        parameter_dict = deepcopy(default_dict)
    else:
        parameter_dict = deepcopy(default_dict[name])

    # Add specific unique name prefix if requested
    if unique_name_prefix is not None:
        parameter_dict['unique_name'] = global_object.generate_unique_name(unique_name_prefix + 'Parameter')

    if value is None:
        # Create a default parameter using both value and metadata from dictionary
        return Parameter(name, **parameter_dict)
    elif isinstance(value, Number):
        # Create a parameter using provided value and metadata from dictionary
        del parameter_dict['value']
        return Parameter(name, value, **parameter_dict)

    raise ValueError(f'{name} must be a Parameter, a number, or None.')