aragog.parser

@classmethod
def from_file(cls, *filenames) -> Self:
    """Parses the parameters in a configuration file(s)

    Args:
        *filenames: Filenames of the configuration data
    """
    parser: ConfigParser = ConfigParser()
    parser.read(*filenames)

    init_dict: dict[str, Any] = {}
    for section_name, dataclass_ in _get_dataclass_from_section_name().items():
        init_dict[section_name] = parser.parse_section(
            using_dataclass=dataclass_, section_name=section_name
        )
    radionuclides: list[_Radionuclide] = []
    for radionuclide_section in cls.radionuclide_sections(parser):
        radionuclide = parser.parse_section(
            using_dataclass=_Radionuclide, section_name=radionuclide_section
        )
        radionuclides.append(radionuclide)

    init_dict["radionuclides"] = radionuclides

    return cls(**init_dict)  # Unpacking gives required arguments so pylint: disable=E1125

@staticmethod
def radionuclide_sections(parser: ConfigParser) -> list[str]:
    """Section names relating to radionuclides

    Sections relating to radionuclides must have the prefix radionuclide_
    """
    return [
        parser[section].name
        for section in parser.sections()
        if section.startswith("radionuclide_")
    ]

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes.

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.equilibrium_temperature /= self.scalings_.temperature
    self.core_heat_capacity /= self.scalings_.heat_capacity
    self._scale_inner_boundary_condition()
    self._scale_outer_boundary_condition()

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes.

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.tidal_array /= self.scalings_.power_per_mass

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes.

    Initial condition method
        1: Linear profile
        2: User-defined temperature field (from file)
        3: Adiabatic profile

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.surface_temperature /= self.scalings_.temperature
    self.basal_temperature /= self.scalings_.temperature

    if self.initial_condition == 2:
        if self.init_file == "":
            msg: str = (f"you must provide an initial temperature file")
            raise ValueError(msg)
        self.init_temperature = np.loadtxt(self.init_file)
        self.init_temperature /= self.scalings_.temperature

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.outer_radius /= self.scalings_.radius
    self.inner_radius /= self.scalings_.radius
    self.core_density /= self.scalings_.density
    self.surface_density /= self.scalings_.density
    self.gravitational_acceleration /= self.scalings_.gravitational_acceleration
    self.adiabatic_bulk_modulus /= self.scalings_.pressure

    if self.eos_method == 2:
        if self.eos_file == "":
            msg: str = (f"you must provide a file for setting up equation of state")
            raise ValueError(msg)
        arr = np.loadtxt(self.eos_file)
        self.eos_radius = arr[:,0] / self.scalings_.radius
        self.eos_pressure = arr[:,1] / self.scalings_.pressure
        self.eos_density = arr[:,2] / self.scalings_.density
        self.eos_gravity = arr[:,3] / self.scalings_.gravitational_acceleration
        # Check that provided eos radius roughly match with Aragog mesh
        if ((self.eos_radius[0] < self.inner_radius) or
            (self.eos_radius[-1] > self.outer_radius) or
            (self.eos_radius[-1]-self.eos_radius[0]) < 0.75*(self.outer_radius-self.inner_radius)):
            msg: str = (f"Radius array in EOS file: Values out of range.")
            raise ValueError(msg)

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.latent_heat_of_fusion /= self.scalings_.latent_heat_per_mass
    self.grain_size /= self.scalings_.radius

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes if they are numbers.

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    cls_fields: tuple[Field, ...] = fields(self.__class__)
    for field_ in cls_fields:
        value: Any = getattr(self, field_.name)
        try:
            scaling: float = getattr(self.scalings_, field_.name)
            scaled_value = value / scaling
            setattr(self, field_.name, scaled_value)
            logger.info(
                "%s is a number (value = %s, scaling = %s, scaled_value = %s)",
                field_.name,
                value,
                scaling,
                scaled_value,
            )
        except AttributeError:
            logger.info("No scaling found for %s", field_.name)
        except TypeError:
            logger.info(
                "%s is a string (path to a filename) so the data will be scaled later",
                field_.name,
            )

def get_heating(self, time: npt.NDArray | float) -> npt.NDArray | float:
    """Radiogenic heating

    Args:
        time: Time

    Returns:
        Radiogenic heat production (power per unit mass) as a float if time is a float,
            otherwise a numpy row array where each entry in the row is associated
            with a single time in the time array.
    """
    arg: npt.NDArray | float = np.log(2) * (self.t0_years - time) / self.half_life_years
    heating: npt.NDArray | float = (
        self.heat_production * self.abundance * self.concentration * np.exp(arg)
    )

    return heating

def scale_attributes(self, scalings: _ScalingsParameters) -> None:
    """Scales the attributes.

    Args:
        scalings: scalings
    """
    self.scalings_ = scalings
    self.t0_years /= self.scalings_.time_years
    self.concentration *= 1e-6  # to mass fraction
    self.heat_production /= self.scalings_.power_per_mass
    self.half_life_years /= self.scalings_.time_years