Module diskchef.chemistry.andes

Classes

class ReadAndesData (physics: PhysicsBase = None, molar_mass: Unit("g / mol") = <Quantity 2.33 g / mol>, hydrogen_mass_fraction: float = 0.739, folder: Union[str, os.PathLike] = None, index: int = 0, read_uv: bool = False, read_ionization: bool = False, ionization_format: str = 'ascii.commented_header')

Class to read ANDES2 output for following usage in diskchef.maps

Expand source code

@dataclass
class ReadAndesData(ChemistryBase):
    """
    Class to read ANDES2 output for following usage in `diskchef.maps`
    """
    folder: PathLike = None
    index: int = 0
    read_uv: bool = False
    read_ionization: bool = False
    ionization_format: str = "ascii.commented_header"

    @property
    def table(self) -> CTable:
        return self._table

    def read(self, index: int = None) -> CTable:
        """Return the associated diskchef.CTable with r, z, and dust and gas properties"""
        if index is None:
            index = self.index
        reader = astropy.io.ascii.get_reader(Reader=astropy.io.ascii.CommentedHeader)
        reader.header.splitter.delimiter = '|'
        chemistry = reader.read(os.path.join(self.folder, f"Chemistry_{index:05d}"))
        physics = reader.read(os.path.join(self.folder, f"physical_structure_{index:05d}"))
        # if physics[["ir", "iz"]] != chemistry[["ir", "iz"]]:
        #     raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and chemistry tables do not match!")
        self._config = self._config_read(os.path.join(self.folder, "../config.ini"))
        table = CTable(
            [
                physics["Radius"] << u.au,
                physics["Height"] << u.au,
            ],
            names=["Radius", "Height"]
        )
        table["Height to radius"] = np.nan * u.dimensionless_unscaled
        for izr in physics["iz"]:
            indices = physics["iz"] == izr
            table["Height to radius"][indices] = np.nanmedian(physics["Height"][indices] / physics["Radius"][indices])

        table["Height"] = table.zr * table.r
        table["Gas density"] = physics["Gas density"] << (u.g / u.cm ** 3)
        table["Dust density"] = physics["Dust density"] << (u.g / u.cm ** 3)
        table["Gas temperature"] = physics["Gas temperature"] << (u.K)
        table["Dust temperature"] = physics["Dust temperature"] << (u.K)
        if "H2" not in chemistry.colnames and ("oH2" in chemistry.colnames and "pH2" in chemistry.colnames):
            chemistry["H2"] = chemistry["oH2"] + chemistry["pH2"]
        table["n(H+2H2)"] = (chemistry["H+"] + chemistry["H"] + 2 * chemistry["H2"]) << (u.cm ** (-3))
        for species in chemistry.colnames[3:]:
            table[species] = (chemistry[species] << (u.cm ** (-3))) / table["n(H+2H2)"]

        if self.read_uv:
            try:
                radiation = reader.read(os.path.join(self.folder, f"RadInt_StrengthTotal_{index:05d}"))
            except FileNotFoundError:
                self.logger.info("Radiation strength file %:05d not found! Trying 00000 instead", index)
                radiation = reader.read(os.path.join(self.folder, f"RadInt_StrengthTotal_00000"))
            if np.any(radiation[["ir", "iz"]] != physics[["ir", "iz"]]):
                raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and radiation tables do not match!")
            table["G_UV"] = radiation["G_UV"] << diskchef.maps.radiation_fields.ANDES2_G0

        if self.read_ionization:
            try:
                ionization = astropy.table.Table.read(os.path.join(self.folder, f"Ionization_Rate_{index:05d}"))
            except FileNotFoundError:
                if os.path.exists(os.path.join(self.folder, f"Ionization_Rate")):
                    self.logger.info("Ionization rate file %:05d not found! Ionization_Rate is found instead", index)
                    ionization = astropy.table.Table.read(
                        os.path.join(self.folder, f"Ionization_Rate"),
                        format=self.ionization_format
                    )
                else:
                    self.logger.info("Ionization rate file %:05d not found! Trying 00000 instead", index)
                    ionization = astropy.table.Table.read(
                        os.path.join(self.folder, f"Ionization_Rate_00000"),
                        format=self.ionization_format
                    )
            if np.any(ionization[["ir", "iz"]] != physics[["ir", "iz"]]):
                raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and ionization tables do not match!")
            table["X ray ionization rate"] = ionization["IR_XR[1/s]"] << u.s ** (-1)
            table["CR ionization rate"] = ionization["IR_CR[1/s]"] << u.s ** (-1)
            table["Ionization rate"] = ionization["IR_Total[1/s]"] << u.s ** (-1)

        self.physics = diskchef.physics.base.PhysicsBase(
            star_mass=float(self._config['stellar mass [MSun]']) * u.solMass,
        )
        self.physics.table = table

        return table

    def __post_init__(self):
        super().__post_init__()
        self._table = self.read()
        self.update_hydrogen_atom_number_density()

    def _config_read(self, path: PathLike) -> dict:
        out = {}
        with open(path, 'r') as configfile:
            for line in configfile.readlines():
                value, key = [entry.strip() for entry in line.split('::')]
                out[key] = value
        return out

Ancestors

• ChemistryBase

Class variables

var folder : Union[str, os.PathLike]

var index : int

var ionization_format : str

var read_ionization : bool

var read_uv : bool

Methods

def read(self, index: int = None) ‑> CTable

Return the associated diskchef.CTable with r, z, and dust and gas properties

Expand source code

def read(self, index: int = None) -> CTable:
    """Return the associated diskchef.CTable with r, z, and dust and gas properties"""
    if index is None:
        index = self.index
    reader = astropy.io.ascii.get_reader(Reader=astropy.io.ascii.CommentedHeader)
    reader.header.splitter.delimiter = '|'
    chemistry = reader.read(os.path.join(self.folder, f"Chemistry_{index:05d}"))
    physics = reader.read(os.path.join(self.folder, f"physical_structure_{index:05d}"))
    # if physics[["ir", "iz"]] != chemistry[["ir", "iz"]]:
    #     raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and chemistry tables do not match!")
    self._config = self._config_read(os.path.join(self.folder, "../config.ini"))
    table = CTable(
        [
            physics["Radius"] << u.au,
            physics["Height"] << u.au,
        ],
        names=["Radius", "Height"]
    )
    table["Height to radius"] = np.nan * u.dimensionless_unscaled
    for izr in physics["iz"]:
        indices = physics["iz"] == izr
        table["Height to radius"][indices] = np.nanmedian(physics["Height"][indices] / physics["Radius"][indices])

    table["Height"] = table.zr * table.r
    table["Gas density"] = physics["Gas density"] << (u.g / u.cm ** 3)
    table["Dust density"] = physics["Dust density"] << (u.g / u.cm ** 3)
    table["Gas temperature"] = physics["Gas temperature"] << (u.K)
    table["Dust temperature"] = physics["Dust temperature"] << (u.K)
    if "H2" not in chemistry.colnames and ("oH2" in chemistry.colnames and "pH2" in chemistry.colnames):
        chemistry["H2"] = chemistry["oH2"] + chemistry["pH2"]
    table["n(H+2H2)"] = (chemistry["H+"] + chemistry["H"] + 2 * chemistry["H2"]) << (u.cm ** (-3))
    for species in chemistry.colnames[3:]:
        table[species] = (chemistry[species] << (u.cm ** (-3))) / table["n(H+2H2)"]

    if self.read_uv:
        try:
            radiation = reader.read(os.path.join(self.folder, f"RadInt_StrengthTotal_{index:05d}"))
        except FileNotFoundError:
            self.logger.info("Radiation strength file %:05d not found! Trying 00000 instead", index)
            radiation = reader.read(os.path.join(self.folder, f"RadInt_StrengthTotal_00000"))
        if np.any(radiation[["ir", "iz"]] != physics[["ir", "iz"]]):
            raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and radiation tables do not match!")
        table["G_UV"] = radiation["G_UV"] << diskchef.maps.radiation_fields.ANDES2_G0

    if self.read_ionization:
        try:
            ionization = astropy.table.Table.read(os.path.join(self.folder, f"Ionization_Rate_{index:05d}"))
        except FileNotFoundError:
            if os.path.exists(os.path.join(self.folder, f"Ionization_Rate")):
                self.logger.info("Ionization rate file %:05d not found! Ionization_Rate is found instead", index)
                ionization = astropy.table.Table.read(
                    os.path.join(self.folder, f"Ionization_Rate"),
                    format=self.ionization_format
                )
            else:
                self.logger.info("Ionization rate file %:05d not found! Trying 00000 instead", index)
                ionization = astropy.table.Table.read(
                    os.path.join(self.folder, f"Ionization_Rate_00000"),
                    format=self.ionization_format
                )
        if np.any(ionization[["ir", "iz"]] != physics[["ir", "iz"]]):
            raise diskchef.engine.exceptions.CHEFRuntimeError("Physics and ionization tables do not match!")
        table["X ray ionization rate"] = ionization["IR_XR[1/s]"] << u.s ** (-1)
        table["CR ionization rate"] = ionization["IR_CR[1/s]"] << u.s ** (-1)
        table["Ionization rate"] = ionization["IR_Total[1/s]"] << u.s ** (-1)

    self.physics = diskchef.physics.base.PhysicsBase(
        star_mass=float(self._config['stellar mass [MSun]']) * u.solMass,
    )
    self.physics.table = table

    return table

Inherited members

• ChemistryBase:
  • add_co_isotopologues
  • calculate_column_density_towards_star
  • calculate_column_density_upwards
  • run_chemistry
  • table
  • update_hydrogen_atom_number_density