Module `diskchef.maps.radmc_lines`

Classes

class RadMCRT (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 1.38699672e-01, 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1.63322676e+03, 1.65230821e+03, 1.67161260e+03, 1.69114252e+03, 1.71090062e+03, 1.73088955e+03, 1.75111203e+03, 1.77157076e+03, 1.79226853e+03, 1.81320811e+03, 1.83439233e+03, 1.85582405e+03, 1.87750617e+03, 1.89944161e+03, 1.92163332e+03, 1.94408431e+03, 1.96679759e+03, 1.98977625e+03, 2.01302337e+03, 2.03654209e+03, 2.06033559e+03, 2.08440707e+03, 2.10875979e+03, 2.13339702e+03, 2.15832211e+03, 2.18353839e+03, 2.20904929e+03, 2.23485824e+03, 2.26096872e+03, 2.28738426e+03, 2.31410842e+03, 2.34114480e+03, 2.36849706e+03, 2.39616888e+03, 2.42416400e+03, 2.45248619e+03, 2.48113928e+03, 2.51012713e+03, 2.53945366e+03, 2.56912281e+03, 2.59913860e+03, 2.62950508e+03, 2.66022633e+03, 2.69130650e+03, 2.72274980e+03, 2.75456046e+03, 2.78674277e+03, 2.81930107e+03, 2.85223976e+03, 2.88556329e+03, 2.91927614e+03, 2.95338287e+03, 2.98788808e+03, 3.02279642e+03, 3.05811260e+03, 3.09384140e+03, 3.12998762e+03, 3.16655616e+03, 3.20355193e+03, 3.24097993e+03, 3.27884522e+03, 3.31715289e+03, 3.35590813e+03, 3.39511615e+03, 3.43478226e+03, 3.47491179e+03, 3.51551017e+03, 3.55658287e+03, 3.59813543e+03, 3.64017347e+03, 3.68270264e+03, 3.72572870e+03, 3.76925744e+03, 3.81329474e+03, 3.85784655e+03, 3.90291886e+03, 3.94851776e+03, 3.99464942e+03, 4.04132003e+03, 4.08853592e+03, 4.13630344e+03, 4.18462905e+03, 4.23351925e+03, 4.28298066e+03, 4.33301993e+03, 4.38364383e+03, 4.43485918e+03, 4.48667290e+03, 4.53909196e+03, 4.59212346e+03, 4.64577454e+03, 4.70005244e+03, 4.75496448e+03, 4.81051808e+03, 4.86672072e+03, 4.92357999e+03, 4.98110357e+03, 5.03929922e+03, 5.09817477e+03, 5.15773819e+03, 5.21799751e+03, 5.27896085e+03, 5.34063644e+03, 5.40303261e+03, 5.46615777e+03, 5.53002044e+03, 5.59462923e+03, 5.65999287e+03, 5.72612017e+03, 5.79302005e+03, 5.86070154e+03, 5.92917378e+03, 5.99844599e+03, 6.06852753e+03, 6.13942786e+03, 6.21115653e+03, 6.28372323e+03, 6.35713775e+03, 6.43140999e+03, 6.50654997e+03, 6.58256784e+03, 6.65947384e+03, 6.73727836e+03, 6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image'] = 'image', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>)

Class with interface to run RadMC3D by Cornelis Dullemond

By initialization creates the basic table (self.polar_table) with the grid in polar RadMC3D coordinates.

Runs a generation of a line cube

Expand source code

class RadMCRT(RadMCRTImage):
    """
    Class with interface to run RadMC3D by Cornelis Dullemond

    By initialization creates the basic table (`self.polar_table`) with the grid in polar RadMC3D coordinates.

    Runs a generation of a line cube
    """
    star_radius: typing.Union[None, u.Quantity] = None
    star_effective_temperature: typing.Union[None, u.Quantity] = None
    accretion_luminosity: typing.Union[None, u.Quantity] = None
    accretion_temperature: typing.Union[None, u.Quantity] = 2e4 * u.K

    def __post_init__(self):
        super().__post_init__()
        self.interpolate("n(H+2H2)")
        yb08 = diskchef.physics.yorke_bodenheimer.YorkeBodenheimer2008()
        if (self.star_radius is None) and (self.star_effective_temperature is not None):
            self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
            self.logger.warn(
                "Only star effective temperature was given, not star radius! Taking radius from trktime0210")
        elif (self.star_radius is not None) and (self.star_effective_temperature is None):
            self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
            self.logger.warn(
                "Only  star radius was given, not effective temperature! Taking effective temperature from trktime0210")
        elif (self.star_radius is None) and (self.star_effective_temperature is None):
            self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
            self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
            self.logger.info("Taking effective temperature and radius from trktime0210")

    def create_files(self, dopac: typing.List[str] = [], dust_mode: int = 1) -> None:
        """Creates all the files necessary to run RadMC3D for both lines and continuum"""
        super().create_files()
        self.lines()
        self.gas_velocity()
        self.gas_temperature()
        try:
            ndust = len(dopac)
            if ndust>0:
                self.dust_kappa(dopac=dopac, dust_mode=dust_mode)
                self.dust_temperature(ndust=ndust)
                self.dust_density(ndust=ndust)
                self.dust_ini(ndust=ndust)
                self.stars()
        except FileNotFoundError:
            self.logger.info("Dust opacity file not found. Assuming no dust.")
        # self.stars()

        for molecule in self.molecules_list:
            self.numberdens(species=molecule)
            self.molecule(species=molecule, lamda_file=self.lamda_files_dict[molecule])
        self.logger.info("Line files written to %s", self.folder)

    def gas_temperature(self, out_file: PathLike = None) -> None:
        """Writes the gas temperature files"""

        if out_file is None:
            out_file = os.path.join(self.folder, 'gas_temperature.inp')

        self.interpolate('Gas temperature')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print('\n'.join(f"{entry:.7e}" for entry in self.polar_table['Gas temperature'].to(u.K).value), file=file)

    def stars(self, out_file: PathLike = None) -> None:
        """Writes the `stars.inp` file"""
        if out_file is None:
            out_file = os.path.join(self.folder, 'stars.inp')
        with open(out_file, 'w') as file:
            if self.accretion_luminosity is None:
                print('2', file=file)  # Typically 2 at present
                print(f'1 {len(self.wavelengths)}', file=file)  # number of stars, wavelengths
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
            else:
                print('2', file=file)  # Typically 2 at present
                print(f'2 {len(self.wavelengths)}', file=file)
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                print(f'{self.accretion_effective_radius.to_value(u.cm)} '
                      f'0 '
                      f'0 0 0',
                      file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
                print(-self.accretion_temperature.to(u.K).value, file=file)

    def accretion_effective_radius(self):
        return np.sqrt(self.accretion_luminosity / (
                4 * np.pi * c.sigma_sb * self.accretion_temperature ** 4)).cgs

    def dust_temperature(self, ndust: int = 1) -> None:
        """Writes the dust temperature files"""

        out_file = os.path.join(self.folder, 'dust_temperature.dat')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust temperature {i}')
        else:
            self.interpolate('Dust temperature')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print(
                        '\n'.join(f"{entry:.7e}" for entry in self.polar_table[f'Dust temperature {i}'].to(u.K).value),
                        file=file)
            else:
                print('\n'.join(f"{entry:.7e}" for entry in self.polar_table['Dust temperature'].to(u.K).value),
                      file=file)

    def dust_ini(self, ndust: int = 1) -> None:
        """Writes the dust initialisation files"""

        out_file = os.path.join(self.folder, 'dustopac.inp')

        with open(out_file, 'w') as file:
            print('2', file=file)  # Typically 2 at present
            print(f'{ndust}', file=file)
            print('-----------------------------', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print('1', file=file)
                    print('0', file=file)
                    print(f'dust{i}', file=file)
                    print('-----------------------------', file=file)
            else:
                print('1', file=file)
                print('0', file=file)
                print(f'dust', file=file)
                print('-----------------------------', file=file)

    @u.quantity_input
    def camera_wavelength_micron(
            self,
            out_file: PathLike = None,
            wavs: u.Quantity = [500] * u.um
    ) -> None:
        """Creates a `camera_wavelength_micron.inp` file with all the frequencies for all the lines"""
        wavelengths = wavs.to(u.um).value
        if out_file is None:
            out_file = os.path.join(self.folder, 'camera_wavelength_micron.inp')
        with open(out_file, 'w') as file:
            print(len(wavelengths), file=file)
            print('\n'.join(f"{entry:.10e}" for entry in wavelengths), file=file)

    def dust_kappa(self, dopac: typing.List[str] = [], dust_mode: int = 1) -> None:
        """Writes the dust absorbance files"""

        ndust = len(dopac)

        if ndust > 1:
            for i in range(ndust):
                out_file = os.path.join(self.folder, f'dustkappa_dust{i}.inp')

                dust_opacity = astropy.io.ascii.read(os.path.join(dopac[i]))

                with open(out_file, 'w') as file:
                    print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                    print(len(dust_opacity), file=file)
                    if dust_mode == 1:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                    elif dust_mode == 2:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                            dust_opacity['sigma_dust'])), file=file)
                    elif dust_mode == 3:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                            dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                    else:
                        raise CHEFValueError(
                            "Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")
        else:
            out_file = os.path.join(self.folder, 'dustkappa_dust.inp')

            dust_opacity = astropy.io.ascii.read(os.path.join(dopac[0]))

            with open(out_file, 'w') as file:
                print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                print(len(dust_opacity), file=file)
                if dust_mode == 1:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                elif dust_mode == 2:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'])), file=file)
                elif dust_mode == 3:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                else:
                    raise CHEFValueError(
                        "Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")

    def dust_density(self, ndust: int = 1) -> None:
        """Writes the dust number density files"""

        out_file = os.path.join(self.folder, f'dust_density.inp')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust density {i}')
        else:
            self.interpolate('Dust density')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print(
                        '\n'.join(
                            f"{entry:.7e}" for entry
                            in self.polar_table[f'Dust density {i}'].to(u.g * u.cm ** (-3)).value),
                        file=file
                    )
            else:
                print(
                    '\n'.join(
                        f"{entry:.7e}" for entry
                        in self.polar_table['Dust density'].to(u.g * u.cm ** (-3)).value),
                    file=file
                )

    def numberdens(self, species: str, out_file: PathLike = None) -> None:
        """Writes the gas number density files"""

        if out_file is None:
            out_file = os.path.join(self.folder, f'numberdens_{species}.inp')

        self.interpolate(species)

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(
                '\n'.join(
                    f"{entry:.7e}" for entry
                    in self.polar_table['n(H+2H2)'].to(u.cm ** (-3)).value * self.polar_table[species]),
                file=file
            )

    def molecule(self, species: str, lamda_file: PathLike, out_file: PathLike = None) -> None:
        """
        Copies the molecule transition files into working directory

        species:    str     name of the molecule
        """

        if out_file is None:
            out_file = os.path.join(self.folder, f'molecule_{species}.inp')

        shutil.copyfile(lamda_file, out_file)

    def lines(self, out_file: PathLike = None) -> None:
        self.molecules_list = sorted(list(set([line.molecule for line in self.line_list])))
        self.lamda_files_dict = {
            line.molecule: line.lamda_file for line in self.line_list
        }

        if out_file is None:
            out_file = os.path.join(self.folder, 'lines.inp')
        with open(out_file, 'w') as file:
            print('2', file=file)  # 2 for molecules
            print(len(self.molecules_list), file=file)  # unique list of molecules

            for molecule in self.molecules_list:
                coll_partners = next(line for line in self.line_list if line.molecule == molecule).collision_partner
                print(f'{molecule} leiden 0 0 {len(coll_partners)}', file=file)
                print('\n'.join(coll_partners), file=file)

    def gas_velocity(self, out_file: PathLike = None) -> None:
        if out_file is None:
            out_file = os.path.join(self.folder, 'gas_velocity.inp')
        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            for vr, vtheta, vphi in zip(self.polar_table['Velocity R'].to(u.cm / u.s).value,
                                        self.polar_table['Velocity Theta'].to(u.cm / u.s).value,
                                        self.polar_table['Velocity Phi'].to(u.cm / u.s).value):
                print(f"{vr:.7e}", f"{vtheta:.7e}", f"{vphi:.7e}", file=file)

    @u.quantity_input
    def run(
            self,
            inclination: u.deg = 0 * u.deg, position_angle: u.deg = 0 * u.deg,
            distance: u.pc = 140 * u.pc, velocity_offset: u.km / u.s = 0 * u.km / u.s,
            threads: int = 1, npix: int = 100,
    ) -> None:
        """Run RadMC3D after files were created with `create_files()`"""
        self.logger.info("Running radmc3d")
        for line in self.line_list:
            self._run_single(
                molecule=self.molecules_list.index(line.molecule) + 1,
                line=line.transition,
                inclination=inclination.to(u.deg).value, position_angle=position_angle.to(u.deg).value,
                velocity_offset=velocity_offset.to(u.km / u.s).value,
                name=f"{line.name}_image.out",
                distance=distance.to(u.pc).value,
                threads=threads,
                lineobj=line,
                npix=npix,
                # coordinate=coordinate,
            )

    def _run_single(
            self, molecule: int, line: int, inclination: float = 0, position_angle: float = 0,
            name: PathLike = None, distance: float = 140, velocity_offset: float = 0,
            n_channels: int = 100, threads: int = 1, lineobj: Line = None, npix: int = 100,
    ) -> None:
        start = time.time()
        command = (self.command +
                   f"imolspec {molecule} "
                   f"iline {line} "
                   f"widthkms 10 "
                   f"incl {inclination} "
                   f"posang {position_angle} "
                   f"vkms {velocity_offset} "
                   f"linenlam {n_channels} "
                   f"setthreads {threads} "
                   f"npix {npix} "
                   )
        self.logger.info("Running radmc3d for molecule %d and transition %d: %s", molecule, line, command)
        proc = subprocess.run(
            command,
            cwd=self.folder,
            text=True,
            capture_output=True,
            shell=True
        )
        self.logger.info("radmc3d finished after %s", timedelta(seconds=time.time() - start))
        self.catch_radmc_messages(proc)
        output = RadMCOutput(lineobj, mode=self.mode)
        if name is not None:
            newname = os.path.join(self.folder, name)
            shutil.move(os.path.join(self.folder, "image.out"), newname)
            output.file_radmc = newname
            output.file_fits = self.radmc_to_fits(newname, self.line_list[line], distance * u.pc)
        self.outputs[lineobj] = output

    def copy_for_propype(self, folder: PathLike = None) -> None:
        """Creates a copy of `self.fitsfiles` in a format which is ready to run them through PRODIGE pipeline"""
        if folder is None:
            folder = os.path.join(self.folder, "propype")
        try:
            os.mkdir(folder)
        except FileExistsError as e:
            self.logger.debug("%s", e)
        for line, output in self.outputs.items():
            molecule = line.molecule
            fitsfile = output.file_fits
            transition = output.line.transition

            shutil.copyfile(fitsfile, os.path.join(folder, f"m-Line-00-{molecule}_{transition}+D.fits"))

Ancestors

Subclasses

RadMCRTLines

Class variables

var accretion_luminosity : Optional[None]
var accretion_temperature : Optional[None]
var star_effective_temperature : Optional[None]
var star_radius : Optional[None]

Methods

def accretion_effective_radius(self)
def camera_wavelength_micron(self, out_file: Union[str, os.PathLike] = None, wavs: astropy.units.quantity.Quantity = <Quantity [500.] um>) ‑> None: Creates a camera_wavelength_micron.inp file with all the frequencies for all the lines
def copy_for_propype(self, folder: Union[str, os.PathLike] = None) ‑> None: Creates a copy of self.fitsfiles in a format which is ready to run them through PRODIGE pipeline
def create_files(self, dopac: List[str] = [], dust_mode: int = 1) ‑> None: Creates all the files necessary to run RadMC3D for both lines and continuum
def dust_density(self, ndust: int = 1) ‑> None: Writes the dust number density files
def dust_ini(self, ndust: int = 1) ‑> None: Writes the dust initialisation files
def dust_kappa(self, dopac: List[str] = [], dust_mode: int = 1) ‑> None: Writes the dust absorbance files
def dust_temperature(self, ndust: int = 1) ‑> None: Writes the dust temperature files
def gas_temperature(self, out_file: Union[str, os.PathLike] = None) ‑> None: Writes the gas temperature files
def gas_velocity(self, out_file: Union[str, os.PathLike] = None) ‑> None
def lines(self, out_file: Union[str, os.PathLike] = None) ‑> None
def molecule(self, species: str, lamda_file: Union[str, os.PathLike], out_file: Union[str, os.PathLike] = None) ‑> None: Copies the molecule transition files into working directory

species: str name of the molecule
def numberdens(self, species: str, out_file: Union[str, os.PathLike] = None) ‑> None: Writes the gas number density files
def stars(self, out_file: Union[str, os.PathLike] = None) ‑> None: Writes the stars.inp file

Inherited members

RadMCRTImage:
- amr_grid
- catch_radmc_messages
- external_source
- factor
- fitsname_suffix
- interpolate
- interpolate_back
- radmc3d
- radmc_to_fits
- run
- unit
- wavelength_micron
RadMCBase:
- mode

class RadMCRTCont (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 1.38699672e-01, 1.40320140e-01, 1.41959539e-01, 1.43618093e-01, 1.45296024e-01, 1.46993558e-01, 1.48710926e-01, 1.50448358e-01, 1.52206088e-01, 1.53984355e-01, 1.55783398e-01, 1.57603459e-01, 1.59444785e-01, 1.61307624e-01, 1.63192226e-01, 1.65098847e-01, 1.67027744e-01, 1.68979176e-01, 1.70953408e-01, 1.72950705e-01, 1.74971337e-01, 1.77015577e-01, 1.79083700e-01, 1.81175985e-01, 1.83292715e-01, 1.85434176e-01, 1.87600656e-01, 1.89792448e-01, 1.92009847e-01, 1.94253152e-01, 1.96522666e-01, 1.98818696e-01, 2.01141551e-01, 2.03491545e-01, 2.05868994e-01, 2.08274220e-01, 2.10707547e-01, 2.13169303e-01, 2.15659820e-01, 2.18179435e-01, 2.20728487e-01, 2.23307320e-01, 2.25916283e-01, 2.28555727e-01, 2.31226008e-01, 2.33927487e-01, 2.36660528e-01, 2.39425500e-01, 2.42222776e-01, 2.45052733e-01, 2.47915753e-01, 2.50812223e-01, 2.53742533e-01, 2.56707079e-01, 2.59706261e-01, 2.62740482e-01, 2.65810154e-01, 2.68915689e-01, 2.72057507e-01, 2.75236032e-01, 2.78451692e-01, 2.81704922e-01, 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3.82362034e+02, 3.86829278e+02, 3.91348714e+02, 3.95920952e+02, 4.00546608e+02, 4.05226308e+02, 4.09960681e+02, 4.14750368e+02, 4.19596014e+02, 4.24498273e+02, 4.29457806e+02, 4.34475283e+02, 4.39551381e+02, 4.44686784e+02, 4.49882186e+02, 4.55138287e+02, 4.60455796e+02, 4.65835431e+02, 4.71277919e+02, 4.76783992e+02, 4.82354394e+02, 4.87989877e+02, 4.93691201e+02, 4.99459135e+02, 5.05294457e+02, 5.11197955e+02, 5.17170426e+02, 5.23212674e+02, 5.29325516e+02, 5.35509776e+02, 5.41766288e+02, 5.48095897e+02, 5.54499456e+02, 5.60977830e+02, 5.67531893e+02, 5.74162529e+02, 5.80870632e+02, 5.87657108e+02, 5.94522873e+02, 6.01468852e+02, 6.08495982e+02, 6.15605213e+02, 6.22797503e+02, 6.30073823e+02, 6.37435153e+02, 6.44882489e+02, 6.52416833e+02, 6.60039204e+02, 6.67750629e+02, 6.75552148e+02, 6.83444815e+02, 6.91429694e+02, 6.99507863e+02, 7.07680411e+02, 7.15948442e+02, 7.24313070e+02, 7.32775425e+02, 7.41336647e+02, 7.49997893e+02, 7.58760331e+02, 7.67625143e+02, 7.76593524e+02, 7.85666686e+02, 7.94845852e+02, 8.04132262e+02, 8.13527166e+02, 8.23031834e+02, 8.32647548e+02, 8.42375605e+02, 8.52217318e+02, 8.62174014e+02, 8.72247037e+02, 8.82437746e+02, 8.92747516e+02, 9.03177738e+02, 9.13729819e+02, 9.24405183e+02, 9.35205270e+02, 9.46131538e+02, 9.57185461e+02, 9.68368529e+02, 9.79682253e+02, 9.91128158e+02, 1.00270779e+03, 1.01442271e+03, 1.02627449e+03, 1.03826475e+03, 1.05039509e+03, 1.06266715e+03, 1.07508260e+03, 1.08764309e+03, 1.10035033e+03, 1.11320604e+03, 1.12621194e+03, 1.13936979e+03, 1.15268137e+03, 1.16614847e+03, 1.17977291e+03, 1.19355654e+03, 1.20750119e+03, 1.22160877e+03, 1.23588117e+03, 1.25032032e+03, 1.26492817e+03, 1.27970668e+03, 1.29465786e+03, 1.30978371e+03, 1.32508629e+03, 1.34056764e+03, 1.35622988e+03, 1.37207509e+03, 1.38810543e+03, 1.40432306e+03, 1.42073017e+03, 1.43732896e+03, 1.45412168e+03, 1.47111060e+03, 1.48829800e+03, 1.50568620e+03, 1.52327756e+03, 1.54107445e+03, 1.55907925e+03, 1.57729442e+03, 1.59572240e+03, 1.61436567e+03, 1.63322676e+03, 1.65230821e+03, 1.67161260e+03, 1.69114252e+03, 1.71090062e+03, 1.73088955e+03, 1.75111203e+03, 1.77157076e+03, 1.79226853e+03, 1.81320811e+03, 1.83439233e+03, 1.85582405e+03, 1.87750617e+03, 1.89944161e+03, 1.92163332e+03, 1.94408431e+03, 1.96679759e+03, 1.98977625e+03, 2.01302337e+03, 2.03654209e+03, 2.06033559e+03, 2.08440707e+03, 2.10875979e+03, 2.13339702e+03, 2.15832211e+03, 2.18353839e+03, 2.20904929e+03, 2.23485824e+03, 2.26096872e+03, 2.28738426e+03, 2.31410842e+03, 2.34114480e+03, 2.36849706e+03, 2.39616888e+03, 2.42416400e+03, 2.45248619e+03, 2.48113928e+03, 2.51012713e+03, 2.53945366e+03, 2.56912281e+03, 2.59913860e+03, 2.62950508e+03, 2.66022633e+03, 2.69130650e+03, 2.72274980e+03, 2.75456046e+03, 2.78674277e+03, 2.81930107e+03, 2.85223976e+03, 2.88556329e+03, 2.91927614e+03, 2.95338287e+03, 2.98788808e+03, 3.02279642e+03, 3.05811260e+03, 3.09384140e+03, 3.12998762e+03, 3.16655616e+03, 3.20355193e+03, 3.24097993e+03, 3.27884522e+03, 3.31715289e+03, 3.35590813e+03, 3.39511615e+03, 3.43478226e+03, 3.47491179e+03, 3.51551017e+03, 3.55658287e+03, 3.59813543e+03, 3.64017347e+03, 3.68270264e+03, 3.72572870e+03, 3.76925744e+03, 3.81329474e+03, 3.85784655e+03, 3.90291886e+03, 3.94851776e+03, 3.99464942e+03, 4.04132003e+03, 4.08853592e+03, 4.13630344e+03, 4.18462905e+03, 4.23351925e+03, 4.28298066e+03, 4.33301993e+03, 4.38364383e+03, 4.43485918e+03, 4.48667290e+03, 4.53909196e+03, 4.59212346e+03, 4.64577454e+03, 4.70005244e+03, 4.75496448e+03, 4.81051808e+03, 4.86672072e+03, 4.92357999e+03, 4.98110357e+03, 5.03929922e+03, 5.09817477e+03, 5.15773819e+03, 5.21799751e+03, 5.27896085e+03, 5.34063644e+03, 5.40303261e+03, 5.46615777e+03, 5.53002044e+03, 5.59462923e+03, 5.65999287e+03, 5.72612017e+03, 5.79302005e+03, 5.86070154e+03, 5.92917378e+03, 5.99844599e+03, 6.06852753e+03, 6.13942786e+03, 6.21115653e+03, 6.28372323e+03, 6.35713775e+03, 6.43140999e+03, 6.50654997e+03, 6.58256784e+03, 6.65947384e+03, 6.73727836e+03, 6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image'] = 'image', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>)

Class with interface to run RadMC3D by Cornelis Dullemond

By initialization creates the basic table (self.polar_table) with the grid in polar RadMC3D coordinates.

Runs a generation of a continuum image

Expand source code

class RadMCRTCont(RadMCRTImage):
    """
    Class with interface to run RadMC3D by Cornelis Dullemond

    By initialization creates the basic table (`self.polar_table`) with the grid in polar RadMC3D coordinates.

    Runs a generation of a continuum image
    """
    star_radius: typing.Union[None, u.Quantity] = None
    star_effective_temperature: typing.Union[None, u.Quantity] = None
    accretion_luminosity: typing.Union[None, u.Quantity] = None
    accretion_temperature: typing.Union[None, u.Quantity] = 2e4 * u.K

    def __post_init__(self):
        super().__post_init__()
        yb08 = diskchef.physics.yorke_bodenheimer.YorkeBodenheimer2008()
        if (self.star_radius is None) and (self.star_effective_temperature is not None):
            self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
            self.logger.warn(
                "Only star effective temperature was given, not star radius! Taking radius from trktime0210")
        elif (self.star_radius is not None) and (self.star_effective_temperature is None):
            self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
            self.logger.warn(
                "Only  star radius was given, not effective temperature! Taking effective temperature from trktime0210")
        elif (self.star_radius is None) and (self.star_effective_temperature is None):
            self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
            self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
            self.logger.info("Taking effective temperature and radius from trktime0210")

    def create_files(self, dopac: typing.List[str] = [], dust_mode: int = 1, wavs: u.Quantity = [500]*u.um) -> None:
        """Creates all the files necessary to run RadMC3D for both lines and continuum"""
        super().create_files()
        self.stars()
        ndust = len(dopac)
        self.dust_kappa(dopac=dopac, dust_mode=dust_mode)
        self.dust_temperature(ndust=ndust)
        self.dust_density(ndust=ndust)
        self.dust_ini(ndust=ndust)
        self.camera_wavelength_micron(wavs = wavs)

    def dust_temperature(self, ndust: int = 1) -> None:
        """Writes the dust temperature files"""

        out_file = os.path.join(self.folder, 'dust_temperature.dat')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust temperature {i}')
        else:
            self.interpolate('Dust temperature')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print('\n'.join(f"{entry:.7e}" for entry in self.polar_table[f'Dust temperature {i}'].to(u.K).value), file=file)
            else:
                print('\n'.join(f"{entry:.7e}" for entry in self.polar_table['Dust temperature'].to(u.K).value), file=file)


    def dust_ini(self, ndust: int = 1) -> None:
        """Writes the dust initialisation files"""

        out_file = os.path.join(self.folder, 'dustopac.inp')

        with open(out_file, 'w') as file:
            print('2', file=file)  # Typically 2 at present
            print(f'{ndust}', file=file)
            print('-----------------------------', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print('1', file=file)
                    print('0', file=file)
                    print(f'dust{i}', file=file)
                    print('-----------------------------', file=file)
            else:
                print('1', file=file)
                print('0', file=file)
                print(f'dust', file=file)
                print('-----------------------------', file=file)

    @u.quantity_input
    def camera_wavelength_micron(
            self,
            out_file: PathLike = None,
            wavs: u.Quantity = [500] * u.um
    ) -> None:
        """Creates a `camera_wavelength_micron.inp` file with all the frequencies for all the lines"""
        wavelengths = wavs.to(u.um).value
        if out_file is None:
            out_file = os.path.join(self.folder, 'camera_wavelength_micron.inp')
        with open(out_file, 'w') as file:
            print(len(wavelengths), file=file)
            print('\n'.join(f"{entry:.10e}" for entry in wavelengths), file=file)

    def dust_kappa(self, dopac: typing.List[str] = [], dust_mode: int = 1) -> None:
        """Writes the dust absorbance files"""

        ndust = len(dopac)

        if ndust > 1:
            for i in range(ndust):
                out_file = os.path.join(self.folder, f'dustkappa_dust{i}.inp')

                dust_opacity = astropy.io.ascii.read(os.path.join(dopac[i]))

                with open(out_file, 'w') as file:
                    print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                    print(len(dust_opacity), file=file)
                    if dust_mode == 1:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                    elif dust_mode == 2:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'])), file=file)
                    elif dust_mode == 3:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                            dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                    else:
                        raise CHEFValueError("Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")
        else:
            out_file = os.path.join(self.folder, 'dustkappa_dust.inp')

            dust_opacity = astropy.io.ascii.read(os.path.join(dopac[0]))

            with open(out_file, 'w') as file:
                print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                print(len(dust_opacity), file=file)
                if dust_mode == 1:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                elif dust_mode == 2:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'])), file=file)
                elif dust_mode == 3:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                else:
                    raise CHEFValueError(
                        "Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")

    def dust_density(self, ndust: int = 1) -> None:
        """Writes the dust number density files"""

        out_file = os.path.join(self.folder, f'dust_density.inp')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust density {i}')
        else:
            self.interpolate('Dust density')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print(
                        '\n'.join(
                            f"{entry:.7e}" for entry
                            in self.polar_table[f'Dust density {i}'].to(u.g * u.cm ** (-3)).value),
                        file=file
                    )
            else:
                print(
                    '\n'.join(
                        f"{entry:.7e}" for entry
                        in self.polar_table['Dust density'].to(u.g * u.cm ** (-3)).value),
                    file=file
                )

    def stars(self, out_file: PathLike = None) -> None:
        """Writes the `stars.inp` file"""
        if out_file is None:
            out_file = os.path.join(self.folder, 'stars.inp')
        with open(out_file, 'w') as file:
            if self.accretion_luminosity is None:
                print('2', file=file)  # Typically 2 at present
                print(f'1 {len(self.wavelengths)}', file=file)  # number of stars, wavelengths
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
            else:
                print('2', file=file)  # Typically 2 at present
                print(f'2 {len(self.wavelengths)}', file=file)
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                print(f'{self.accretion_effective_radius().to_value(u.cm)} '
                      f'0 '
                      f'0 0 0',
                      file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
                print(-self.accretion_temperature.to(u.K).value, file=file)

    @u.quantity_input
    def run(
            self, *,
            inclination: u.deg = 0 * u.deg, position_angle: u.deg = 0 * u.deg,
            distance: u.pc = 140 * u.pc,
            threads: int = 1, npix: int = 100, phi: u.deg = 0 * u.deg, see_radmc_warnings: bool = True,
            sizeau: float = None, sizepc: float = None, pointau = None, pointpc = None
    ) -> None:
        """Run RadMC3D after files were created with `create_files()`"""
        self.logger.info("Running radmc3d")
        start = time.time()
        command = (self.command +
                   f"incl {inclination.to_value(u.deg)} "
                   f"phi {phi.to_value(u.deg)} "
                   f"posang {position_angle.to_value(u.deg)} "
                   f"setthreads {threads} "
                   f"npix {npix} "
                   f"loadlambda"
                   )
        if sizeau is not None:
            command += f" sizeau {sizeau}"
        elif sizepc is not None:
            command += f" sizepc {sizepc}"
        if pointau is not None:
            command += f" pointau {pointau[0]} {pointau[1]} {pointau[2]}"
        elif pointpc is not None:
            command += f" pointpc {pointpc[0]} {pointpc[1]} {pointpc[2]}"
        self.logger.info("Running radmc3d for chosen wavelengths: %s", command)
        proc = subprocess.run(
            command,
            cwd=self.folder,
            text=True,
            capture_output=True,
            shell=True
        )
        self.logger.info("radmc3d finished after %s", timedelta(seconds=time.time() - start))
        if see_radmc_warnings:
            self.catch_radmc_messages(proc)

        name = os.path.join(self.folder, f"image.out")
        self.radmc_to_fits(
            name=name,
            line=None,
            distance=distance
        )

Ancestors

Class variables

var accretion_luminosity : Optional[None]
var accretion_temperature : Optional[None]
var star_effective_temperature : Optional[None]
var star_radius : Optional[None]

Methods

def camera_wavelength_micron(self, out_file: Union[str, os.PathLike] = None, wavs: astropy.units.quantity.Quantity = <Quantity [500.] um>) ‑> None: Creates a camera_wavelength_micron.inp file with all the frequencies for all the lines
def create_files(self, dopac: List[str] = [], dust_mode: int = 1, wavs: astropy.units.quantity.Quantity = <Quantity [500.] um>) ‑> None: Creates all the files necessary to run RadMC3D for both lines and continuum
def dust_density(self, ndust: int = 1) ‑> None: Writes the dust number density files
def dust_ini(self, ndust: int = 1) ‑> None: Writes the dust initialisation files
def dust_kappa(self, dopac: List[str] = [], dust_mode: int = 1) ‑> None: Writes the dust absorbance files
def dust_temperature(self, ndust: int = 1) ‑> None: Writes the dust temperature files
def stars(self, out_file: Union[str, os.PathLike] = None) ‑> None: Writes the stars.inp file

Inherited members

RadMCRTImage:
- amr_grid
- catch_radmc_messages
- external_source
- factor
- fitsname_suffix
- interpolate
- interpolate_back
- radmc3d
- radmc_to_fits
- run
- unit
- wavelength_micron
RadMCBase:
- mode

class RadMCRTImage (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 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7.85666686e+02, 7.94845852e+02, 8.04132262e+02, 8.13527166e+02, 8.23031834e+02, 8.32647548e+02, 8.42375605e+02, 8.52217318e+02, 8.62174014e+02, 8.72247037e+02, 8.82437746e+02, 8.92747516e+02, 9.03177738e+02, 9.13729819e+02, 9.24405183e+02, 9.35205270e+02, 9.46131538e+02, 9.57185461e+02, 9.68368529e+02, 9.79682253e+02, 9.91128158e+02, 1.00270779e+03, 1.01442271e+03, 1.02627449e+03, 1.03826475e+03, 1.05039509e+03, 1.06266715e+03, 1.07508260e+03, 1.08764309e+03, 1.10035033e+03, 1.11320604e+03, 1.12621194e+03, 1.13936979e+03, 1.15268137e+03, 1.16614847e+03, 1.17977291e+03, 1.19355654e+03, 1.20750119e+03, 1.22160877e+03, 1.23588117e+03, 1.25032032e+03, 1.26492817e+03, 1.27970668e+03, 1.29465786e+03, 1.30978371e+03, 1.32508629e+03, 1.34056764e+03, 1.35622988e+03, 1.37207509e+03, 1.38810543e+03, 1.40432306e+03, 1.42073017e+03, 1.43732896e+03, 1.45412168e+03, 1.47111060e+03, 1.48829800e+03, 1.50568620e+03, 1.52327756e+03, 1.54107445e+03, 1.55907925e+03, 1.57729442e+03, 1.59572240e+03, 1.61436567e+03, 1.63322676e+03, 1.65230821e+03, 1.67161260e+03, 1.69114252e+03, 1.71090062e+03, 1.73088955e+03, 1.75111203e+03, 1.77157076e+03, 1.79226853e+03, 1.81320811e+03, 1.83439233e+03, 1.85582405e+03, 1.87750617e+03, 1.89944161e+03, 1.92163332e+03, 1.94408431e+03, 1.96679759e+03, 1.98977625e+03, 2.01302337e+03, 2.03654209e+03, 2.06033559e+03, 2.08440707e+03, 2.10875979e+03, 2.13339702e+03, 2.15832211e+03, 2.18353839e+03, 2.20904929e+03, 2.23485824e+03, 2.26096872e+03, 2.28738426e+03, 2.31410842e+03, 2.34114480e+03, 2.36849706e+03, 2.39616888e+03, 2.42416400e+03, 2.45248619e+03, 2.48113928e+03, 2.51012713e+03, 2.53945366e+03, 2.56912281e+03, 2.59913860e+03, 2.62950508e+03, 2.66022633e+03, 2.69130650e+03, 2.72274980e+03, 2.75456046e+03, 2.78674277e+03, 2.81930107e+03, 2.85223976e+03, 2.88556329e+03, 2.91927614e+03, 2.95338287e+03, 2.98788808e+03, 3.02279642e+03, 3.05811260e+03, 3.09384140e+03, 3.12998762e+03, 3.16655616e+03, 3.20355193e+03, 3.24097993e+03, 3.27884522e+03, 3.31715289e+03, 3.35590813e+03, 3.39511615e+03, 3.43478226e+03, 3.47491179e+03, 3.51551017e+03, 3.55658287e+03, 3.59813543e+03, 3.64017347e+03, 3.68270264e+03, 3.72572870e+03, 3.76925744e+03, 3.81329474e+03, 3.85784655e+03, 3.90291886e+03, 3.94851776e+03, 3.99464942e+03, 4.04132003e+03, 4.08853592e+03, 4.13630344e+03, 4.18462905e+03, 4.23351925e+03, 4.28298066e+03, 4.33301993e+03, 4.38364383e+03, 4.43485918e+03, 4.48667290e+03, 4.53909196e+03, 4.59212346e+03, 4.64577454e+03, 4.70005244e+03, 4.75496448e+03, 4.81051808e+03, 4.86672072e+03, 4.92357999e+03, 4.98110357e+03, 5.03929922e+03, 5.09817477e+03, 5.15773819e+03, 5.21799751e+03, 5.27896085e+03, 5.34063644e+03, 5.40303261e+03, 5.46615777e+03, 5.53002044e+03, 5.59462923e+03, 5.65999287e+03, 5.72612017e+03, 5.79302005e+03, 5.86070154e+03, 5.92917378e+03, 5.99844599e+03, 6.06852753e+03, 6.13942786e+03, 6.21115653e+03, 6.28372323e+03, 6.35713775e+03, 6.43140999e+03, 6.50654997e+03, 6.58256784e+03, 6.65947384e+03, 6.73727836e+03, 6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image'] = 'image')

Class with interface to run RadMC3D by Cornelis Dullemond

By initialization creates the basic table (self.polar_table) with the grid in polar RadMC3D coordinates.

Runs a generation of a continuum image, can be subclassed for line cube

Expand source code

class RadMCRTImage(RadMCBase):
    """
    Class with interface to run RadMC3D by Cornelis Dullemond

    By initialization creates the basic table (`self.polar_table`) with the grid in polar RadMC3D coordinates.

    Runs a generation of a continuum image, can be subclassed for line cube
    """
    allowed_modes = ["image"]

    velocity: u.km / u.s = 0 * u.km / u.s
    mode: typing.Literal["image"] = 'image'

    def __post_init__(self):
        super().__post_init__()
        self.check_mode()

    def check_mode(self):
        if self.mode not in self.allowed_modes:
            self.logger.error(f"`mode` should be one of {self.allowed_modes}. Undefined behavior is expected")

    @property
    def command(self) -> str:
        return (
            f"{self.executable} {self.mode} "
        )

    @u.quantity_input
    def run(
            self, *,
            inclination: u.deg = 0 * u.deg, position_angle: u.deg = 0 * u.deg,
            distance: u.pc = 140 * u.pc, wav=1 * u.mm,
            threads: int = 1, npix: int = 100, phi:  u.deg = 0 * u.deg,
    ) -> None:
        """Run RadMC3D after files were created with `create_files()`"""
        self.logger.info("Running radmc3d")
        start = time.time()
        wavelength = wav.to(u.um, equivalencies=u.spectral())
        command = (self.command +
                   f"incl {inclination.to_value(u.deg)} "
                   f"phi {phi.to_value(u.deg)} "
                   f"posang {position_angle.to_value(u.deg)} "
                   f"setthreads {threads} "
                   f"npix {npix} "
                   f"lambda {wavelength.value}"
                   )
        self.logger.info("Running radmc3d for wavelength %.4e um: %s", wavelength.value, command)
        proc = subprocess.run(
            command,
            cwd=self.folder,
            text=True,
            capture_output=True,
            shell=True
        )
        self.logger.info("radmc3d finished after %s", timedelta(seconds=time.time() - start))
        self.catch_radmc_messages(proc)

        newname = os.path.join(self.folder, f"{wavelength.value:.4e}_um_image.out")
        shutil.move(os.path.join(self.folder, "image.out"), newname)
        self.radmc_to_fits(
            name=newname,
            line=wavelength,
            distance=distance
        )

    def radmc_to_fits(
            self, name: PathLike, line: typing.Union[Line, u.Quantity, None], distance,
    ) -> PathLike:
        """Saves RadMC3D `image.out` files as FITS files

        Args:
            name: PathLike -- image.out-like file to process
            line: Union[Line, wavelength-like u.Quantity]
        Returns:
            PathLike object of a newly created fits files
        """
        with redirect_stdout(io.StringIO()) as f:
            im = radmc3dPy.image.readImage(fname=name)
        self.logger.debug(f.getvalue())

        if line is None:
            restfreq = 'None'
        elif isinstance(line, Line):
            restfreq = line.frequency.to_value(u.Hz)
        else:
            restfreq = line.to_value(u.Hz, equivalencies=u.spectral())

        x_deg = ((im.x << u.cm) / distance).to(u.deg, equivalencies=u.dimensionless_angles())
        y_deg = ((im.y << u.cm) / distance).to(u.deg, equivalencies=u.dimensionless_angles())
        freq_hz = (im.freq << u.Hz)

        x_len = len(x_deg)
        midx_i = x_len // 2
        midx_val = x_deg[midx_i]
        mean_x_width = (x_deg[1:] - x_deg[:-1]).mean()

        y_len = len(y_deg)
        midy_i = y_len // 2
        midy_val = y_deg[midy_i]
        mean_y_width = (y_deg[1:] - y_deg[:-1]).mean()

        freq_len = len(freq_hz)
        midfreq_i = freq_len // 2
        midfreq_hz = freq_hz[midfreq_i]
        mean_channel_width = (freq_hz[1:] - freq_hz[:-1]).mean()

        coordinate = self.coordinate

        if coordinate is not None:
            try:
                coordinate = astropy.coordinates.SkyCoord(coordinate)
            except ValueError:
                coordinate = astropy.coordinates.SkyCoord.from_name(coordinate)
        else:
            coordinate = astropy.coordinates.SkyCoord("0h 0d")

        wcs_dict = {
            'CTYPE3': 'RA---TAN', 'CUNIT3': 'deg',
            'CDELT3': -mean_x_width.value, 'CRPIX3': midx_i + 1,
            'CRVAL3': midx_val.value + coordinate.ra.to_value(u.deg), 'NAXIS3': x_len,
            'CTYPE2': 'DEC--TAN', 'CUNIT2': 'deg',
            'CDELT2': mean_y_width.value, 'CRPIX2': midy_i + 1,
            'CRVAL2': midy_val.value + coordinate.dec.to_value(u.deg), 'NAXIS2': y_len,
            'CTYPE1': 'FREQ    ', 'CUNIT1': 'Hz',
            'CDELT1': mean_channel_width.value if np.isfinite(mean_channel_width.value) else 1,
            'CRPIX1': midfreq_i + 1, 'CRVAL1': (midfreq_hz * (1 - self.velocity / c.c)).to_value(u.Hz),
            'NAXIS1': freq_len,
        }

        header = WCS(wcs_dict).to_header()
        header["HISTORY"] = "Created with DiskCheF package"
        header["HISTORY"] = "(G.V. Smirnov-Pinchukov, Lis Zwicky, https://gitlab.com/SmirnGreg/diskchef)"
        header["HISTORY"] = "using RadMC3D (C. Dullemond, https://github.com/dullemond/radmc3d-2.0)"
        header["RESTFREQ"] = restfreq
        self._extra_header(header)

        cube = SpectralCube(
            data=np.rot90(im.image * self.factor, axes=[0, 1]) << self.unit,
            wcs=WCS(wcs_dict), header=header
        )

        fitsname = name.replace(".out", self.fitsname_suffix + ".fits")
        cube.write(fitsname, overwrite=True)

        self.fitsfiles.append(fitsname)
        self.logger.info("Saved as %s and %s", name, fitsname)
        self.logger.info("Saved as %s and %s", name, fitsname)
        return fitsname

    @property
    def unit(self) -> u.Unit:
        """Unit of the returned data"""
        return u.Jy / u.sr

    @property
    def factor(self) -> float:
        """Factor of the returned data relative to self.unit"""
        return 1e23

    def _extra_header(self, header: Header, **kwargs):
        """Add extra header items into the output fits files"""
        for key, value in kwargs.items():
            try:
                header[key] = value
            except Exception as e:
                self.logger.error(e)

    @property
    def fitsname_suffix(self) -> str:
        """Additional suffix of an output fits file"""
        return ""

Ancestors

Class variables

var allowed_modes
var velocity : Unit("km / s")

Instance variables

prop command : str

Expand source code

@property
def command(self) -> str:
    return (
        f"{self.executable} {self.mode} "
    )

prop factor : float

Factor of the returned data relative to self.unit

Expand source code

@property
def factor(self) -> float:
    """Factor of the returned data relative to self.unit"""
    return 1e23

prop fitsname_suffix : str

Additional suffix of an output fits file

Expand source code

@property
def fitsname_suffix(self) -> str:
    """Additional suffix of an output fits file"""
    return ""

prop unit : astropy.units.core.Unit

Unit of the returned data

Expand source code

@property
def unit(self) -> u.Unit:
    """Unit of the returned data"""
    return u.Jy / u.sr

Methods

def check_mode(self)

def radmc_to_fits(self, name: Union[str, os.PathLike], line: Union[Line, astropy.units.quantity.Quantity, None], distance) ‑> Union[str, os.PathLike]

Saves RadMC3D image.out files as FITS files

Args

name: PathLike – image.out-like file to process
line: Union[Line, wavelength-like u.Quantity]

Returns

PathLike object of a newly created fits files

Inherited members

RadMCBase:
- amr_grid
- catch_radmc_messages
- create_files
- external_source
- interpolate
- interpolate_back
- mode
- radmc3d
- run
- wavelength_micron

class RadMCRTLines (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 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1.61436567e+03, 1.63322676e+03, 1.65230821e+03, 1.67161260e+03, 1.69114252e+03, 1.71090062e+03, 1.73088955e+03, 1.75111203e+03, 1.77157076e+03, 1.79226853e+03, 1.81320811e+03, 1.83439233e+03, 1.85582405e+03, 1.87750617e+03, 1.89944161e+03, 1.92163332e+03, 1.94408431e+03, 1.96679759e+03, 1.98977625e+03, 2.01302337e+03, 2.03654209e+03, 2.06033559e+03, 2.08440707e+03, 2.10875979e+03, 2.13339702e+03, 2.15832211e+03, 2.18353839e+03, 2.20904929e+03, 2.23485824e+03, 2.26096872e+03, 2.28738426e+03, 2.31410842e+03, 2.34114480e+03, 2.36849706e+03, 2.39616888e+03, 2.42416400e+03, 2.45248619e+03, 2.48113928e+03, 2.51012713e+03, 2.53945366e+03, 2.56912281e+03, 2.59913860e+03, 2.62950508e+03, 2.66022633e+03, 2.69130650e+03, 2.72274980e+03, 2.75456046e+03, 2.78674277e+03, 2.81930107e+03, 2.85223976e+03, 2.88556329e+03, 2.91927614e+03, 2.95338287e+03, 2.98788808e+03, 3.02279642e+03, 3.05811260e+03, 3.09384140e+03, 3.12998762e+03, 3.16655616e+03, 3.20355193e+03, 3.24097993e+03, 3.27884522e+03, 3.31715289e+03, 3.35590813e+03, 3.39511615e+03, 3.43478226e+03, 3.47491179e+03, 3.51551017e+03, 3.55658287e+03, 3.59813543e+03, 3.64017347e+03, 3.68270264e+03, 3.72572870e+03, 3.76925744e+03, 3.81329474e+03, 3.85784655e+03, 3.90291886e+03, 3.94851776e+03, 3.99464942e+03, 4.04132003e+03, 4.08853592e+03, 4.13630344e+03, 4.18462905e+03, 4.23351925e+03, 4.28298066e+03, 4.33301993e+03, 4.38364383e+03, 4.43485918e+03, 4.48667290e+03, 4.53909196e+03, 4.59212346e+03, 4.64577454e+03, 4.70005244e+03, 4.75496448e+03, 4.81051808e+03, 4.86672072e+03, 4.92357999e+03, 4.98110357e+03, 5.03929922e+03, 5.09817477e+03, 5.15773819e+03, 5.21799751e+03, 5.27896085e+03, 5.34063644e+03, 5.40303261e+03, 5.46615777e+03, 5.53002044e+03, 5.59462923e+03, 5.65999287e+03, 5.72612017e+03, 5.79302005e+03, 5.86070154e+03, 5.92917378e+03, 5.99844599e+03, 6.06852753e+03, 6.13942786e+03, 6.21115653e+03, 6.28372323e+03, 6.35713775e+03, 6.43140999e+03, 6.50654997e+03, 6.58256784e+03, 6.65947384e+03, 6.73727836e+03, 6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image'] = 'image', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>)

Subclass of RadMCRT to run RadMC only once for all the required frequencies

Usage:

>>> physics = diskchef.physics.WilliamsBest2014(star_mass=0.52 * u.solMass, radial_bins=10, vertical_bins=10)
>>> chem = diskchef.chemistry.NonzeroChemistryWB2014(physics)
>>> chem.run_chemistry()
>>> mapping = RadMCRTLines(chemistry=chem, line_list=[
...     Line(name='CO J=2-1', transition=1, molecule='CO'),
...     Line(name='CO J=3-2', transition=2, molecule='CO'),
... ])
>>> mapping.wavelength_multiple_lines(channels_per_line=5, window_width=2 * u.km/u.s)  # doctest: +NORMALIZE_WHITESPACE
array([2600.76630869, 2600.76197107, 2600.75763346, 2600.75329588,
       2600.7489583 , 1300.40799349, 1300.40582464, 1300.4036558 ,
       1300.40148696, 1300.39931813])

Expand source code

class RadMCRTLines(RadMCRT):
    """
    Subclass of RadMCRT to run RadMC only once for all the required frequencies

    Usage:

    >>> physics = diskchef.physics.WilliamsBest2014(star_mass=0.52 * u.solMass, radial_bins=10, vertical_bins=10)
    >>> chem = diskchef.chemistry.NonzeroChemistryWB2014(physics)
    >>> chem.run_chemistry()
    >>> mapping = RadMCRTLines(chemistry=chem, line_list=[
    ...     Line(name='CO J=2-1', transition=1, molecule='CO'),
    ...     Line(name='CO J=3-2', transition=2, molecule='CO'),
    ... ])
    >>> mapping.wavelength_multiple_lines(channels_per_line=5, window_width=2 * u.km/u.s)  # doctest: +NORMALIZE_WHITESPACE
    array([2600.76630869, 2600.76197107, 2600.75763346, 2600.75329588,
           2600.7489583 , 1300.40799349, 1300.40582464, 1300.4036558 ,
           1300.40148696, 1300.39931813])
    """

    def frequency_centers(self) -> typing.List[u.Quantity]:
        """Fetches frequencies of lines from `self.line_list`"""
        for line in self.line_list:
            line.parse_lamda()
        self.ordered_line_list = sorted(self.line_list, key=lambda line: line.frequency)
        frequency_centers = [line.frequency for line in self.ordered_line_list]
        return frequency_centers

    def wavelength_multiple_lines(self, channels_per_line: int, window_width: u.km / u.s) -> np.ndarray:
        """
        Return a sorted array of wavelength for all the lines, in um (unitless)
        """
        frequencies_list = []
        self.channels_per_line = []
        for frequency_center in self.frequency_centers():
            width = np.abs(window_width.to(u.GHz, equivalencies=u.doppler_radio(frequency_center)) - frequency_center)
            frequencies_list.append(
                np.linspace(frequency_center - width / 2, frequency_center + width / 2, channels_per_line)
            )
            self.channels_per_line.append(channels_per_line)
        frequencies = np.hstack(frequencies_list)
        wavelengths = frequencies.to(u.um, equivalencies=u.spectral()).value
        return wavelengths

    @u.quantity_input
    def camera_wavelength_micron(
            self,
            out_file: PathLike = None,
            window_type: str = 'individual lines',
            window_width: u.km / u.s = 6 * u.km / u.s,
            window_lims: u.GHz = None,
            channels_per_line: int = 200
    ) -> None:
        """Creates a `camera_wavelength_micron.inp` file with all the frequencies for all the lines"""
        if window_type=='individual lines':
            wavelengths = self.wavelength_multiple_lines(channels_per_line, window_width)
        elif window_type=='spectral scan':
            wavelengths = np.linspace(np.min(window_lims.to(u.um, equivalencies=u.spectral()).value), np.max(window_lims.to(u.um, equivalencies=u.spectral()).value), channels_per_line)
        else:
            raise CHEFValueError("Unknown spectral window type. Choose one of the two: individual lines or spectral scan.")
        if out_file is None:
            out_file = os.path.join(self.folder, 'camera_wavelength_micron.inp')
        with open(out_file, 'w') as file:
            print(len(wavelengths), file=file)
            print('\n'.join(f"{entry:.10e}" for entry in wavelengths), file=file)

    def create_files(self,
                    window_type: str = 'individual lines',
                     window_width: u.km / u.s = 6 * u.km / u.s,
                     window_lims: u.GHz = None,
                     channels_per_line: int = 200,
                     dopac: typing.List[str] = [], dust_mode: int = 1) -> None:
        super().create_files(dopac=dopac, dust_mode=dust_mode)
        self.camera_wavelength_micron(window_width=window_width, channels_per_line=channels_per_line, window_lims=window_lims, window_type=window_type)

    @u.quantity_input
    def run(
            self,
            inclination: u.deg = 0 * u.deg, position_angle: u.deg = 0 * u.deg,
            distance: u.pc = 140 * u.pc, velocity_offset: u.km / u.s = 0 * u.km / u.s,
            threads: int = 1, npix: int = 100,
            mctherm: bool = False,
            is_split: bool = True
    ) -> None:
        """
        Run radmc3d to create the line emission cubes

        Args:
            inclination:
            position_angle:
            distance:
            velocity_offset:
            threads:
            npix:
        """
        self.logger.info("Running radmc3d")
        start = time.time()
        if mctherm:
            command = (f"radmc3d mctherm setthreads {threads}")
            proc = subprocess.run(
                command,
                cwd=self.folder,
                text=True,
                capture_output=True,
                shell=True
            )
            self.logger.info("radmc3d finished mctherm after %s", timedelta(seconds=time.time() - start))
            self.catch_radmc_messages(proc)
            shutil.copy(self.folder / 'dust_temperature.dat', self.folder / "gas_temperature.inp")
        command = (self.command +
                   f"incl {inclination.to(u.deg).value} "
                   f"posang {position_angle.to(u.deg).value} "
                   f"setthreads {threads} "
                   f"npix {npix} "
                   "loadlambda "
                   )
        self.logger.info("Running radmc3d for all transition at once: %s", command)
        proc = subprocess.run(
            command,
            cwd=self.folder,
            text=True,
            capture_output=True,
            shell=True
        )
        self.logger.info("radmc3d finished after %s", timedelta(seconds=time.time() - start))
        self.catch_radmc_messages(proc)
        if is_split:
            for line in self.ordered_line_list:
                Path(self.folder / f"../{line.name}_out").mkdir(parents=True, exist_ok=True)
            names = [os.path.join(self.folder, f"../{line.name}_out/{line.name}_image.out") for line in self.ordered_line_list]
            self.split(names=names)
            for line, name in zip(self.ordered_line_list, names):
                self.outputs[line] = RadMCOutput(line, file_radmc=name, distance=distance, mode=self.mode)
                self.outputs[line].file_fits = self.radmc_to_fits(name, line, distance)
        else:
            self.radmc_to_fits(os.path.join(self.folder, f"image.out"), None, distance)

    def channel_maps(
            self,
            filename: PathLike = None,
            extension: typing.Union[None, str] = 'png',
            distance: u.pc = None,
            **kwargs
    ) -> typing.List[Figure]:
        """
        Create channel maps for each line or just a given fits file

        This method is in unstable state and will be modified and fixed in future versions

        Args:
            filename: input fits file to create channel maps from
            extension: extension for the output figure, e.g. png, pdf, etc. Does not create any file if None
            distance (u.pc): distance to the source. If None, the distance will be searched with Simbad

        Returns:
            list of matplotlib figures containing the channel maps
        """
        if filename is None:
            outputs = self.outputs
        else:
            line = DummyLine(name=filename, molecule=filename)
            outputs: typing.Dict[DummyLine, RadMCOutput] = {
                line: RadMCOutput(line=line, file_fits=filename, distance=distance)
            }
        figures = []
        for output in outputs.values():
            fig = output.plot_channel_map(**kwargs)
            if extension is not None:
                fig.savefig(os.path.join(self.folder, f"{output.line.name}.{extension}"))
            figures.append(fig)
        return figures

    def split(
            self, filename=None,
            names: typing.List[PathLike] = None
    ):
        """Split the `image.out` file with all lines into multiple single-frequency files"""
        lengths = self.channels_per_line
        if filename is None:
            filename = os.path.join(self.folder, 'image.out')

        with open(filename, 'r') as bigfile:
            files = [open(name, 'w') for name in names]
            header = [next(bigfile) for _ in range(4)]
            px_number = [int(entry) for entry in header[1].split()]
            self.logger.info("Splitting %s in %s", filename, names)
            for file, length in zip(files, lengths):
                file.write(header[0])
                file.write(header[1])
                file.write(str(length) + "\n")
                file.write(header[3])
                for line in range(length):
                    file.write(next(bigfile))

            for file, length in zip(files, lengths):
                for line in range(length * (px_number[0] * px_number[1] + 1)):
                    file.write(next(bigfile))

            for file in files:
                file.close()

Ancestors

Subclasses

RadMCRTLinesTauSurf
RadMCRTLinesTraceTau
RadMCRTSingleCall

Class variables

var accretion_luminosity : Optional[None]
var accretion_temperature : Optional[None]
var star_effective_temperature : Optional[None]
var star_radius : Optional[None]

Methods

def channel_maps(self, filename: Union[str, os.PathLike] = None, extension: Optional[None] = 'png', distance: Unit("pc") = None, **kwargs)

Create channel maps for each line or just a given fits file

This method is in unstable state and will be modified and fixed in future versions

Args

filename: input fits file to create channel maps from
extension: extension for the output figure, e.g. png, pdf, etc. Does not create any file if None
distance : u.pc: distance to the source. If None, the distance will be searched with Simbad

Returns

list of matplotlib figures containing the channel maps

def frequency_centers(self) ‑> List[astropy.units.quantity.Quantity]

Fetches frequencies of lines from self.line_list

def run(self, inclination: Unit("deg") = <Quantity 0. deg>, position_angle: Unit("deg") = <Quantity 0. deg>, distance: Unit("pc") = <Quantity 140. pc>, velocity_offset: Unit("km / s") = <Quantity 0. km / s>, threads: int = 1, npix: int = 100, mctherm: bool = False, is_split: bool = True) ‑> None

Run radmc3d to create the line emission cubes

Args

inclination: position_angle: distance: velocity_offset: threads: npix:

def split(self, filename=None, names: List[Union[str, os.PathLike]] = None)

Split the image.out file with all lines into multiple single-frequency files

def wavelength_multiple_lines(self, channels_per_line: int, window_width: Unit("km / s")) ‑> numpy.ndarray

Return a sorted array of wavelength for all the lines, in um (unitless)

Inherited members

RadMCRT:
- amr_grid
- camera_wavelength_micron
- catch_radmc_messages
- copy_for_propype
- create_files
- dust_density
- dust_ini
- dust_kappa
- dust_temperature
- external_source
- factor
- fitsname_suffix
- gas_temperature
- interpolate
- interpolate_back
- mode
- molecule
- numberdens
- radmc3d
- radmc_to_fits
- stars
- unit
- wavelength_micron

class RadMCRTLinesTauSurf (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 1.38699672e-01, 1.40320140e-01, 1.41959539e-01, 1.43618093e-01, 1.45296024e-01, 1.46993558e-01, 1.48710926e-01, 1.50448358e-01, 1.52206088e-01, 1.53984355e-01, 1.55783398e-01, 1.57603459e-01, 1.59444785e-01, 1.61307624e-01, 1.63192226e-01, 1.65098847e-01, 1.67027744e-01, 1.68979176e-01, 1.70953408e-01, 1.72950705e-01, 1.74971337e-01, 1.77015577e-01, 1.79083700e-01, 1.81175985e-01, 1.83292715e-01, 1.85434176e-01, 1.87600656e-01, 1.89792448e-01, 1.92009847e-01, 1.94253152e-01, 1.96522666e-01, 1.98818696e-01, 2.01141551e-01, 2.03491545e-01, 2.05868994e-01, 2.08274220e-01, 2.10707547e-01, 2.13169303e-01, 2.15659820e-01, 2.18179435e-01, 2.20728487e-01, 2.23307320e-01, 2.25916283e-01, 2.28555727e-01, 2.31226008e-01, 2.33927487e-01, 2.36660528e-01, 2.39425500e-01, 2.42222776e-01, 2.45052733e-01, 2.47915753e-01, 2.50812223e-01, 2.53742533e-01, 2.56707079e-01, 2.59706261e-01, 2.62740482e-01, 2.65810154e-01, 2.68915689e-01, 2.72057507e-01, 2.75236032e-01, 2.78451692e-01, 2.81704922e-01, 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6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image tracetau'] = 'tausurf', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>, tau: float = 1)

Class to calculate optical depth map in lines

Expand source code

class RadMCRTLinesTauSurf(RadMCRTLines):
    """Class to calculate optical depth map in lines"""
    allowed_modes = ["tausurf"]
    mode: typing.Literal["image tracetau"] = "tausurf"
    tau: float = 1

    @property
    def unit(self) -> u.Unit:
        """Unit of the returned data"""
        return u.au

    @property
    def command(self) -> str:
        return super().command + f"{self.tau} "

    @property
    def factor(self) -> float:
        """Factor of the returned data relative to self.unit"""
        return (u.cm / u.au).si.scale

    def _extra_header(self, header: Header, **kwargs):
        """Add extra header items into the output fits files"""
        super()._extra_header(header, **{"HISTORY": f"Optical depth tau={self.tau: .2e} map"}, **kwargs)

    @property
    def fitsname_suffix(self) -> str:
        """Additional suffix of an output fits file"""
        return f"_tau_{self.tau:.2e}"

Ancestors

RadMCRTLines
RadMCRT
RadMCRTImage
RadMCBase
MapBase

Class variables

var allowed_modes
var tau : float

Instance variables

prop command : str

Expand source code

@property
def command(self) -> str:
    return super().command + f"{self.tau} "

Inherited members

RadMCRTLines:
- amr_grid
- camera_wavelength_micron
- catch_radmc_messages
- channel_maps
- copy_for_propype
- create_files
- dust_density
- dust_ini
- dust_kappa
- dust_temperature
- external_source
- factor
- fitsname_suffix
- frequency_centers
- gas_temperature
- interpolate
- interpolate_back
- mode
- molecule
- numberdens
- radmc3d
- radmc_to_fits
- run
- split
- stars
- unit
- wavelength_micron
- wavelength_multiple_lines

class RadMCRTLinesTraceTau (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 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external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image tracetau'] = 'image tracetau', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>)

Class to calculate optical depth map in lines

Expand source code

class RadMCRTLinesTraceTau(RadMCRTLines):
    """Class to calculate optical depth map in lines"""
    allowed_modes = ["image tracetau"]
    mode: typing.Literal["image tracetau"] = "image tracetau"

    @property
    def unit(self) -> u.Unit:
        """Unit of the returned data"""
        return u.dimensionless_unscaled

    @property
    def factor(self) -> float:
        """Factor of the returned data relative to self.unit"""
        return 1.

    def _extra_header(self, header: Header, **kwargs):
        """Add extra header items into the output fits files"""
        super()._extra_header(header, **{"HISTORY": "Optical depth map"}, **kwargs)

    @property
    def fitsname_suffix(self) -> str:
        """Additional suffix of an output fits file"""
        return "_tracetau"

Ancestors

RadMCRTLines
RadMCRT
RadMCRTImage
RadMCBase
MapBase

Class variables

var allowed_modes

Inherited members

RadMCRTLines:
- amr_grid
- camera_wavelength_micron
- catch_radmc_messages
- channel_maps
- copy_for_propype
- create_files
- dust_density
- dust_ini
- dust_kappa
- dust_temperature
- external_source
- factor
- fitsname_suffix
- frequency_centers
- gas_temperature
- interpolate
- interpolate_back
- mode
- molecule
- numberdens
- radmc3d
- radmc_to_fits
- run
- split
- stars
- unit
- wavelength_micron
- wavelength_multiple_lines

class RadMCRTSED (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 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1.61436567e+03, 1.63322676e+03, 1.65230821e+03, 1.67161260e+03, 1.69114252e+03, 1.71090062e+03, 1.73088955e+03, 1.75111203e+03, 1.77157076e+03, 1.79226853e+03, 1.81320811e+03, 1.83439233e+03, 1.85582405e+03, 1.87750617e+03, 1.89944161e+03, 1.92163332e+03, 1.94408431e+03, 1.96679759e+03, 1.98977625e+03, 2.01302337e+03, 2.03654209e+03, 2.06033559e+03, 2.08440707e+03, 2.10875979e+03, 2.13339702e+03, 2.15832211e+03, 2.18353839e+03, 2.20904929e+03, 2.23485824e+03, 2.26096872e+03, 2.28738426e+03, 2.31410842e+03, 2.34114480e+03, 2.36849706e+03, 2.39616888e+03, 2.42416400e+03, 2.45248619e+03, 2.48113928e+03, 2.51012713e+03, 2.53945366e+03, 2.56912281e+03, 2.59913860e+03, 2.62950508e+03, 2.66022633e+03, 2.69130650e+03, 2.72274980e+03, 2.75456046e+03, 2.78674277e+03, 2.81930107e+03, 2.85223976e+03, 2.88556329e+03, 2.91927614e+03, 2.95338287e+03, 2.98788808e+03, 3.02279642e+03, 3.05811260e+03, 3.09384140e+03, 3.12998762e+03, 3.16655616e+03, 3.20355193e+03, 3.24097993e+03, 3.27884522e+03, 3.31715289e+03, 3.35590813e+03, 3.39511615e+03, 3.43478226e+03, 3.47491179e+03, 3.51551017e+03, 3.55658287e+03, 3.59813543e+03, 3.64017347e+03, 3.68270264e+03, 3.72572870e+03, 3.76925744e+03, 3.81329474e+03, 3.85784655e+03, 3.90291886e+03, 3.94851776e+03, 3.99464942e+03, 4.04132003e+03, 4.08853592e+03, 4.13630344e+03, 4.18462905e+03, 4.23351925e+03, 4.28298066e+03, 4.33301993e+03, 4.38364383e+03, 4.43485918e+03, 4.48667290e+03, 4.53909196e+03, 4.59212346e+03, 4.64577454e+03, 4.70005244e+03, 4.75496448e+03, 4.81051808e+03, 4.86672072e+03, 4.92357999e+03, 4.98110357e+03, 5.03929922e+03, 5.09817477e+03, 5.15773819e+03, 5.21799751e+03, 5.27896085e+03, 5.34063644e+03, 5.40303261e+03, 5.46615777e+03, 5.53002044e+03, 5.59462923e+03, 5.65999287e+03, 5.72612017e+03, 5.79302005e+03, 5.86070154e+03, 5.92917378e+03, 5.99844599e+03, 6.06852753e+03, 6.13942786e+03, 6.21115653e+03, 6.28372323e+03, 6.35713775e+03, 6.43140999e+03, 6.50654997e+03, 6.58256784e+03, 6.65947384e+03, 6.73727836e+03, 6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Union[Literal['sed'], Literal['spectrum loadlambda']] = 'sed', star_number: int = 1, star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, add_luminosity: List[astropy.units.quantity.Quantity] = None, add_temperature: List[astropy.units.quantity.Quantity] = None)

Class with interface to run RadMC3D by Cornelis Dullemond

By initialization creates the basic table (self.polar_table) with the grid in polar RadMC3D coordinates.

Runs a generation of a continuum SED, maybe subclassed for spectrum (but maybe no?)

Expand source code

class RadMCRTSED(RadMCBase):
    """
    Class with interface to run RadMC3D by Cornelis Dullemond

    By initialization creates the basic table (`self.polar_table`) with the grid in polar RadMC3D coordinates.

    Runs a generation of a continuum SED, maybe subclassed for spectrum (but maybe no?)
    """
    allowed_modes = ["sed", "spectrum loadlambda"]

    velocity: u.km / u.s = 0 * u.km / u.s
    mode: typing.Union[typing.Literal["sed"], typing.Literal["spectrum loadlambda"]] = 'sed'

    star_number: int = 1
    star_radius: typing.Union[None, u.Quantity] = None
    star_effective_temperature: typing.Union[None, u.Quantity] = None
    add_luminosity: typing.List[u.Quantity] = None
    add_temperature: typing.List[u.Quantity] = None

    def __post_init__(self):
        super().__post_init__()
        self.check_mode()
        if self.star_number == 1:
            yb08 = diskchef.physics.yorke_bodenheimer.YorkeBodenheimer2008(lt = self.chemistry.age)
            if (self.star_radius is None) and (self.star_effective_temperature is not None):
                self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
                self.logger.warn(
                    f"Only star effective temperature was given, not star radius! Taking radius from {yb08.dfile}")
            elif (self.star_radius is not None) and (self.star_effective_temperature is None):
                self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
                self.logger.warn(
                    f"Only  star radius was given, not effective temperature! Taking effective temperature from {yb08.dfile}")
            elif (self.star_radius is None) and (self.star_effective_temperature is None):
                self.star_radius = yb08.radius(self.chemistry.physics.star_mass)
                self.star_effective_temperature = yb08.effective_temperature(self.chemistry.physics.star_mass)
                self.logger.info(f"Taking effective temperature and radius from {yb08.dfile}")
        elif self.star_number>1:
            pass #tbd

    def check_mode(self):
        if self.mode not in self.allowed_modes:
            self.logger.error(f"`mode` should be one of {self.allowed_modes}. Undefined behavior is expected")

    @property
    def command(self) -> str:
        return (
            f"{self.executable} {self.mode} "
        )

    def create_files(self, dopac: typing.List[str] = [], dust_mode: int = 1, wavs: u.Quantity = [500]*u.um) -> None:
        """Creates all the files necessary to run RadMC3D for both lines and continuum"""
        super().create_files()
        self.stars()
        try:
            ndust = len(dopac)
            if ndust>0:
                self.dust_kappa(dopac=dopac, dust_mode=dust_mode)
                self.dust_ini(ndust=ndust)
            else:
                self.logger.info("No dust files given. Hope you know what you are doing")
            self.dust_temperature(ndust=ndust)
            self.dust_density(ndust=ndust)
        except FileNotFoundError:
            self.logger.info("Dust opacity file not found. Please clarify it using dopac parameter.")



    def dust_temperature(self, ndust: int = 1) -> None:
        """Writes the dust temperature files"""

        out_file = os.path.join(self.folder, 'dust_temperature.dat')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust temperature {i}')
        else:
            ndust=1
            self.interpolate('Dust temperature')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print(
                        '\n'.join(f"{entry:.7e}" for entry in self.polar_table[f'Dust temperature {i}'].to(u.K).value),
                        file=file)
            else:
                print('\n'.join(f"{entry:.7e}" for entry in self.polar_table['Dust temperature'].to(u.K).value),
                      file=file)

    def dust_ini(self, ndust: int = 1) -> None:
        """Writes the dust initialisation files"""

        out_file = os.path.join(self.folder, 'dustopac.inp')

        with open(out_file, 'w') as file:
            print('2', file=file)  # Typically 2 at present
            print(f'{ndust}', file=file)
            print('-----------------------------', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print('1', file=file)
                    print('0', file=file)
                    print(f'dust{i}', file=file)
                    print('-----------------------------', file=file)
            else:
                print('1', file=file)
                print('0', file=file)
                print(f'dust', file=file)
                print('-----------------------------', file=file)

    def dust_kappa(self, dopac: typing.List[str] = [], dust_mode: int = 1) -> None:
        """Writes the dust absorbance files"""

        ndust = len(dopac)

        if ndust > 1:
            for i in range(ndust):
                out_file = os.path.join(self.folder, f'dustkappa_dust{i}.inp')

                dust_opacity = astropy.io.ascii.read(os.path.join(dopac[i]))

                with open(out_file, 'w') as file:
                    print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                    print(len(dust_opacity), file=file)
                    if dust_mode == 1:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                    elif dust_mode == 2:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                            dust_opacity['sigma_dust'])), file=file)
                    elif dust_mode == 3:
                        print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                        zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                            dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                    else:
                        raise CHEFValueError(
                            "Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")
        else:
            out_file = os.path.join(self.folder, 'dustkappa_dust.inp')

            dust_opacity = astropy.io.ascii.read(os.path.join(dopac[0]))

            with open(out_file, 'w') as file:
                print(f'{dust_mode}', file=file)  # 1 for kappa only, 2 for kappa & sigma, 3 for kappa, sigma & gcos
                print(len(dust_opacity), file=file)
                if dust_mode == 1:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}" for wav, kap in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'])), file=file)
                elif dust_mode == 2:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}" for wav, kap, sig in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'])), file=file)
                elif dust_mode == 3:
                    print('\n'.join(f"{wav:.6e}   {kap:.6e}   {sig:.6e}   {gcos:.6e}" for wav, kap, sig, gcos in
                                    zip(dust_opacity['wavelength'], dust_opacity['kappa_dust'],
                                        dust_opacity['sigma_dust'], dust_opacity['gcos'])), file=file)
                else:
                    raise CHEFValueError(
                        "Dust opacity files of RADMC support only 3 formats: 1 for wav+kappa_abs, 2 for +kappa_sca, 3 for +gcos")

    def dust_density(self, ndust: int = 1) -> None:
        """Writes the dust number density files"""

        out_file = os.path.join(self.folder, f'dust_density.inp')

        if ndust > 1:
            for i in range(ndust):
                self.interpolate(f'Dust density {i}')
        else:
            ndust=1
            self.interpolate('Dust density')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(f'{ndust}', file=file)
            if ndust > 1:
                for i in range(ndust):
                    print(
                        '\n'.join(
                            f"{entry:.7e}" for entry
                            in self.polar_table[f'Dust density {i}'].to(u.g * u.cm ** (-3)).value),
                        file=file
                    )
            else:
                print(
                    '\n'.join(
                        f"{entry:.7e}" for entry
                        in self.polar_table['Dust density'].to(u.g * u.cm ** (-3)).value),
                    file=file
                )

    @u.quantity_input
    def run(
            self, *,
            inclination: u.deg = 0 * u.deg, phi: u.deg = 0 * u.deg,
            distance: u.pc = 140 * u.pc,
            npix: int = 100, threads: int = 1,
            mctherm: bool = False, see_radmc_warnings: bool = True
    ) -> None:
        """Run RadMC3D after files were created with `create_files()`"""
        self.logger.info("Running radmc3d")
        start = time.time()
        temp_file = os.path.join(self.folder, 'dust_temperature.dat')
        if os.path.isfile(temp_file) == False:
            self.logger.info("No dust temperature file found. Running mctherm.")
            mctherm = True
        if mctherm:
            if os.path.isfile(temp_file) == True:
                os.remove(temp_file)
            command = (f"radmc3d mctherm setthreads {threads}")
            proc = subprocess.run(
                command,
                cwd=self.folder,
                text=True,
                capture_output=True,
                shell=True
            )
            self.logger.info("radmc3d finished mctherm after %s", timedelta(seconds=time.time() - start))
            if see_radmc_warnings:
                self.catch_radmc_messages(proc)
        command = (self.command +
                   f"incl {inclination.to_value(u.deg)} "
                   f"phi {phi.to_value(u.deg)} "
                   f"npix {npix} "
                   f"setthreads {threads} "
                   )
        proc = subprocess.run(
            command,
            cwd=self.folder,
            text=True,
            capture_output=True,
            shell=True
        )
        self.logger.info("radmc3d finished after %s", timedelta(seconds=time.time() - start))
        if see_radmc_warnings:
            self.catch_radmc_messages(proc)

        # self.radmc_to_fits(
        #     name=sedname,
        #     distance=distance
        # )


    def stars(self, out_file: PathLike = None) -> None:
        """Writes the `stars.inp` file"""
        if out_file is None:
            out_file = os.path.join(self.folder, 'stars.inp')

        with open(out_file, 'w') as file:
            if self.add_luminosity is None:
                print('2', file=file)  # Typically 2 at present
                print(f'1 {len(self.wavelengths)}', file=file)  # number of stars, wavelengths
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
            else:
                nsources = len(self.add_luminosity)
                print('2', file=file)  # Typically 2 at present
                print(f'{1+nsources} {len(self.wavelengths)}', file=file)
                print(f'{self.star_radius.to(u.cm).value} '
                      f'{self.chemistry.physics.star_mass.to(u.g).value} '
                      f'0 0 0',
                      file=file)
                for isource in range(nsources):
                    print(f'{self.source_effective_radius(isource).to_value(u.cm)} '
                          f'0 '
                          f'0 0 0',
                          file=file)
                print('\n'.join(f"{entry:.7e}" for entry in self.wavelengths.to_value(u.um)), file=file)
                print(-self.star_effective_temperature.to(u.K).value, file=file)
                for isource in range(nsources):
                    print(-self.add_temperature[isource].to(u.K).value, file=file)

    def source_effective_radius(self, isource):
        return np.sqrt(self.add_luminosity[isource] / (
                4 * np.pi * c.sigma_sb * self.add_temperature[isource] ** 4)).cgs

    def numberdens(self, species: str, out_file: PathLike = None) -> None:
        """Writes the gas number density files"""

        if out_file is None:
            out_file = os.path.join(self.folder, f'numberdens_{species}.inp')

        self.interpolate(species)
        self.interpolate("n(H+2H2)")

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print(
                '\n'.join(
                    f"{entry:.7e}" for entry
                    in self.polar_table['n(H+2H2)'].to(u.cm ** (-3)).value * self.polar_table[species]),
                file=file
            )

    def molecule(self, species: str, lamda_file: PathLike, out_file: PathLike = None) -> None:
        """
        Copies the molecule transition files into working directory

        species:    str     name of the molecule
        """

        if out_file is None:
            out_file = os.path.join(self.folder, f'molecule_{species}.inp')

        shutil.copyfile(lamda_file, out_file)

    def lines(self, out_file: PathLike = None) -> None:
        self.molecules_list = sorted(list(set([line.molecule for line in self.line_list])))
        self.lamda_files_dict = {
            line.molecule: line.lamda_file for line in self.line_list
        }

        if out_file is None:
            out_file = os.path.join(self.folder, 'lines.inp')
        with open(out_file, 'w') as file:
            print('2', file=file)  # 2 for molecules
            print(len(self.molecules_list), file=file)  # unique list of molecules

            for molecule in self.molecules_list:
                coll_partners = next(line for line in self.line_list if line.molecule == molecule).collision_partner
                print(f'{molecule} leiden 0 0 {len(coll_partners)}', file=file)
                print('\n'.join(coll_partners), file=file)

    def gas_velocity(self, out_file: PathLike = None) -> None:
        if out_file is None:
            out_file = os.path.join(self.folder, 'gas_velocity.inp')
        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            for vr, vtheta, vphi in zip(self.polar_table['Velocity R'].to(u.cm / u.s).value,
                                        self.polar_table['Velocity Theta'].to(u.cm / u.s).value,
                                        self.polar_table['Velocity Phi'].to(u.cm / u.s).value):
                print(f"{vr:.7e}", f"{vtheta:.7e}", f"{vphi:.7e}", file=file)

    def gas_temperature(self, out_file: PathLike = None) -> None:
        """Writes the gas temperature files"""

        if out_file is None:
            out_file = os.path.join(self.folder, 'gas_temperature.inp')

        self.interpolate('Gas temperature')

        with open(out_file, 'w') as file:
            print('1', file=file)  # Typically 1 at present
            print(self.nrcells, file=file)
            print('\n'.join(f"{entry:.7e}" for entry in self.polar_table['Gas temperature'].to(u.K).value), file=file)

    @u.quantity_input
    def camera_wavelength_micron(
            self,
            out_file: PathLike = None,
            wavs: u.Quantity = [500] * u.um
    ) -> None:
        """Creates a `camera_wavelength_micron.inp` file with all the frequencies for all the lines"""
        wavelengths = wavs.to(u.um).value
        if out_file is None:
            out_file = os.path.join(self.folder, 'camera_wavelength_micron.inp')
        with open(out_file, 'w') as file:
            print(len(wavelengths), file=file)
            print('\n'.join(f"{entry:.10e}" for entry in wavelengths), file=file)

    def radmc_to_fits(
            self, name: PathLike, line: typing.Union[Line, u.Quantity], distance,
    ) -> PathLike:
        """Saves RadMC3D `spectrum.out` files as FITS files
        to be done, currently copied from RadMCRTImage

        Args:
            name: PathLike -- image.out-like file to process
            line: Union[Line, wavelength-like u.Quantity]
        Returns:
            PathLike object of a newly created fits files
        """
        with redirect_stdout(io.StringIO()) as f:
            im = radmc3dPy.image.readImage(fname=name)
        self.logger.debug(f.getvalue())

        if isinstance(line, Line):
            restfreq = line.frequency.to_value(u.Hz)
        else:
            restfreq = line.to_value(u.Hz, equivalencies=u.spectral())

        x_deg = ((im.x << u.cm) / distance).to(u.deg, equivalencies=u.dimensionless_angles())
        y_deg = ((im.y << u.cm) / distance).to(u.deg, equivalencies=u.dimensionless_angles())
        freq_hz = (im.freq << u.Hz)

        x_len = len(x_deg)
        midx_i = x_len // 2
        midx_val = x_deg[midx_i]
        mean_x_width = (x_deg[1:] - x_deg[:-1]).mean()

        y_len = len(y_deg)
        midy_i = y_len // 2
        midy_val = y_deg[midy_i]
        mean_y_width = (y_deg[1:] - y_deg[:-1]).mean()

        freq_len = len(freq_hz)
        midfreq_i = freq_len // 2
        midfreq_hz = freq_hz[midfreq_i]
        mean_channel_width = (freq_hz[1:] - freq_hz[:-1]).mean()

        coordinate = self.coordinate

        if coordinate is not None:
            try:
                coordinate = astropy.coordinates.SkyCoord(coordinate)
            except ValueError:
                coordinate = astropy.coordinates.SkyCoord.from_name(coordinate)
        else:
            coordinate = astropy.coordinates.SkyCoord("0h 0d")

        wcs_dict = {
            'CTYPE3': 'RA---TAN', 'CUNIT3': 'deg',
            'CDELT3': -mean_x_width.value, 'CRPIX3': midx_i + 1,
            'CRVAL3': midx_val.value + coordinate.ra.to_value(u.deg), 'NAXIS3': x_len,
            'CTYPE2': 'DEC--TAN', 'CUNIT2': 'deg',
            'CDELT2': mean_y_width.value, 'CRPIX2': midy_i + 1,
            'CRVAL2': midy_val.value + coordinate.dec.to_value(u.deg), 'NAXIS2': y_len,
            'CTYPE1': 'FREQ    ', 'CUNIT1': 'Hz',
            'CDELT1': mean_channel_width.value if np.isfinite(mean_channel_width.value) else 1,
            'CRPIX1': midfreq_i + 1, 'CRVAL1': (midfreq_hz * (1 - self.velocity / c.c)).to_value(u.Hz),
            'NAXIS1': freq_len,
        }

        header = WCS(wcs_dict).to_header()
        header["HISTORY"] = "Created with DiskCheF package"
        header["HISTORY"] = "(G.V. Smirnov-Pinchukov, https://gitlab.com/SmirnGreg/diskchef)"
        header["HISTORY"] = "using RadMC3D (C. Dullemond, https://github.com/dullemond/radmc3d-2.0)"
        header["RESTFREQ"] = restfreq
        self._extra_header(header)

        cube = SpectralCube(
            data=np.rot90(im.image * self.factor, axes=[0, 1]) << self.unit,
            wcs=WCS(wcs_dict), header=header
        )

        fitsname = name.replace(".out", self.fitsname_suffix + ".fits")
        cube.write(fitsname, overwrite=True)

        self.fitsfiles.append(fitsname)
        self.logger.info("Saved as %s and %s", name, fitsname)
        self.logger.info("Saved as %s and %s", name, fitsname)
        return fitsname

    @property
    def unit(self) -> u.Unit:
        """Unit of the returned data"""
        return u.Jy / u.sr

    @property
    def factor(self) -> float:
        """Factor of the returned data relative to self.unit"""
        return 1e23

    def _extra_header(self, header: Header, **kwargs):
        """Add extra header items into the output fits files"""
        for key, value in kwargs.items():
            try:
                header[key] = value
            except Exception as e:
                self.logger.error(e)

    @property
    def fitsname_suffix(self) -> str:
        """Additional suffix of an output fits file"""
        return ""

Ancestors

Class variables

var add_luminosity : List[astropy.units.quantity.Quantity]
var add_temperature : List[astropy.units.quantity.Quantity]
var allowed_modes
var star_effective_temperature : Optional[None]
var star_number : int
var star_radius : Optional[None]
var velocity : Unit("km / s")

Instance variables

prop command : str

Expand source code

@property
def command(self) -> str:
    return (
        f"{self.executable} {self.mode} "
    )

prop factor : float

Factor of the returned data relative to self.unit

Expand source code

@property
def factor(self) -> float:
    """Factor of the returned data relative to self.unit"""
    return 1e23

prop fitsname_suffix : str

Additional suffix of an output fits file

Expand source code

@property
def fitsname_suffix(self) -> str:
    """Additional suffix of an output fits file"""
    return ""

prop unit : astropy.units.core.Unit

Unit of the returned data

Expand source code

@property
def unit(self) -> u.Unit:
    """Unit of the returned data"""
    return u.Jy / u.sr

Methods

def camera_wavelength_micron(self, out_file: Union[str, os.PathLike] = None, wavs: astropy.units.quantity.Quantity = <Quantity [500.] um>) ‑> None

Creates a camera_wavelength_micron.inp file with all the frequencies for all the lines

def check_mode(self)

def create_files(self, dopac: List[str] = [], dust_mode: int = 1, wavs: astropy.units.quantity.Quantity = <Quantity [500.] um>) ‑> None

Creates all the files necessary to run RadMC3D for both lines and continuum

def dust_density(self, ndust: int = 1) ‑> None

Writes the dust number density files

def dust_ini(self, ndust: int = 1) ‑> None

Writes the dust initialisation files

def dust_kappa(self, dopac: List[str] = [], dust_mode: int = 1) ‑> None

Writes the dust absorbance files

def dust_temperature(self, ndust: int = 1) ‑> None

Writes the dust temperature files

def gas_temperature(self, out_file: Union[str, os.PathLike] = None) ‑> None

Writes the gas temperature files

def gas_velocity(self, out_file: Union[str, os.PathLike] = None) ‑> None

def lines(self, out_file: Union[str, os.PathLike] = None) ‑> None

def molecule(self, species: str, lamda_file: Union[str, os.PathLike], out_file: Union[str, os.PathLike] = None) ‑> None

Copies the molecule transition files into working directory

species: str name of the molecule

def numberdens(self, species: str, out_file: Union[str, os.PathLike] = None) ‑> None

Writes the gas number density files

def radmc_to_fits(self, name: Union[str, os.PathLike], line: Union[Line, astropy.units.quantity.Quantity], distance) ‑> Union[str, os.PathLike]

Saves RadMC3D spectrum.out files as FITS files to be done, currently copied from RadMCRTImage

Args

name: PathLike – image.out-like file to process
line: Union[Line, wavelength-like u.Quantity]

Returns

PathLike object of a newly created fits files

def source_effective_radius(self, isource)

def stars(self, out_file: Union[str, os.PathLike] = None) ‑> None

Writes the stars.inp file

Inherited members

RadMCBase:
- amr_grid
- catch_radmc_messages
- external_source
- interpolate
- interpolate_back
- mode
- radmc3d
- run
- wavelength_micron

class RadMCRTSingleCall (chemistry: Union[ChemistryBase, PhysicsBase] = None, line_list: List[Line] = None, executable: Union[str, os.PathLike] = 'radmc3d', folder: Union[str, os.PathLike] = 'radmc', radii_bins: Optional[None] = None, theta_bins: Optional[None] = None, phi_bins: Optional[None] = None, outer_radius: Optional[None] = None, verbosity: int = 0, wavelengths: astropy.units.quantity.Quantity = <Quantity [9.13000000e-02, 9.23666837e-02, 9.34458298e-02, 9.45375839e-02, 9.56420933e-02, 9.67595069e-02, 9.78899756e-02, 9.90336519e-02, 1.00190690e-01, 1.01361246e-01, 1.02545478e-01, 1.03743546e-01, 1.04955611e-01, 1.06181838e-01, 1.07422390e-01, 1.08677436e-01, 1.09947145e-01, 1.11231689e-01, 1.12531240e-01, 1.13845975e-01, 1.15176069e-01, 1.16521704e-01, 1.17883060e-01, 1.19260321e-01, 1.20653673e-01, 1.22063304e-01, 1.23489404e-01, 1.24932166e-01, 1.26391784e-01, 1.27868455e-01, 1.29362378e-01, 1.30873756e-01, 1.32402791e-01, 1.33949690e-01, 1.35514662e-01, 1.37097918e-01, 1.38699672e-01, 1.40320140e-01, 1.41959539e-01, 1.43618093e-01, 1.45296024e-01, 1.46993558e-01, 1.48710926e-01, 1.50448358e-01, 1.52206088e-01, 1.53984355e-01, 1.55783398e-01, 1.57603459e-01, 1.59444785e-01, 1.61307624e-01, 1.63192226e-01, 1.65098847e-01, 1.67027744e-01, 1.68979176e-01, 1.70953408e-01, 1.72950705e-01, 1.74971337e-01, 1.77015577e-01, 1.79083700e-01, 1.81175985e-01, 1.83292715e-01, 1.85434176e-01, 1.87600656e-01, 1.89792448e-01, 1.92009847e-01, 1.94253152e-01, 1.96522666e-01, 1.98818696e-01, 2.01141551e-01, 2.03491545e-01, 2.05868994e-01, 2.08274220e-01, 2.10707547e-01, 2.13169303e-01, 2.15659820e-01, 2.18179435e-01, 2.20728487e-01, 2.23307320e-01, 2.25916283e-01, 2.28555727e-01, 2.31226008e-01, 2.33927487e-01, 2.36660528e-01, 2.39425500e-01, 2.42222776e-01, 2.45052733e-01, 2.47915753e-01, 2.50812223e-01, 2.53742533e-01, 2.56707079e-01, 2.59706261e-01, 2.62740482e-01, 2.65810154e-01, 2.68915689e-01, 2.72057507e-01, 2.75236032e-01, 2.78451692e-01, 2.81704922e-01, 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5.85602045e-01, 5.92443800e-01, 5.99365488e-01, 6.06368045e-01, 6.13452414e-01, 6.20619553e-01, 6.27870426e-01, 6.35206014e-01, 6.42627306e-01, 6.50135303e-01, 6.57731017e-01, 6.65415475e-01, 6.73189712e-01, 6.81054778e-01, 6.89011734e-01, 6.97061653e-01, 7.05205622e-01, 7.13444738e-01, 7.21780115e-01, 7.30212877e-01, 7.38744160e-01, 7.47375117e-01, 7.56106912e-01, 7.64940723e-01, 7.73877742e-01, 7.82919175e-01, 7.92066241e-01, 8.01320175e-01, 8.10682226e-01, 8.20153656e-01, 8.29735743e-01, 8.39429780e-01, 8.49237076e-01, 8.59158953e-01, 8.69196750e-01, 8.79351822e-01, 8.89625538e-01, 9.00019285e-01, 9.10534465e-01, 9.21172497e-01, 9.31934816e-01, 9.42822874e-01, 9.53838141e-01, 9.64982102e-01, 9.76256261e-01, 9.87662139e-01, 9.99201275e-01, 1.01087523e+00, 1.02268557e+00, 1.03463389e+00, 1.04672181e+00, 1.05895096e+00, 1.07132298e+00, 1.08383955e+00, 1.09650236e+00, 1.10931311e+00, 1.12227352e+00, 1.13538536e+00, 1.14865039e+00, 1.16207040e+00, 1.17564720e+00, 1.18938262e+00, 1.20327851e+00, 1.21733675e+00, 1.23155924e+00, 1.24594790e+00, 1.26050466e+00, 1.27523149e+00, 1.29013038e+00, 1.30520334e+00, 1.32045240e+00, 1.33587962e+00, 1.35148708e+00, 1.36727689e+00, 1.38325117e+00, 1.39941208e+00, 1.41576181e+00, 1.43230256e+00, 1.44903655e+00, 1.46596606e+00, 1.48309335e+00, 1.50042075e+00, 1.51795059e+00, 1.53568524e+00, 1.55362708e+00, 1.57177855e+00, 1.59014208e+00, 1.60872016e+00, 1.62751530e+00, 1.64653002e+00, 1.66576689e+00, 1.68522852e+00, 1.70491752e+00, 1.72483656e+00, 1.74498831e+00, 1.76537550e+00, 1.78600088e+00, 1.80686724e+00, 1.82797738e+00, 1.84933416e+00, 1.87094045e+00, 1.89279918e+00, 1.91491329e+00, 1.93728576e+00, 1.95991962e+00, 1.98281791e+00, 2.00598374e+00, 2.02942021e+00, 2.05313050e+00, 2.07711781e+00, 2.10138536e+00, 2.12593644e+00, 2.15077436e+00, 2.17590246e+00, 2.20132415e+00, 2.22704284e+00, 2.25306201e+00, 2.27938517e+00, 2.30601588e+00, 2.33295771e+00, 2.36021432e+00, 2.38778937e+00, 2.41568659e+00, 2.44390974e+00, 2.47246263e+00, 2.50134911e+00, 2.53057308e+00, 2.56013848e+00, 2.59004930e+00, 2.62030958e+00, 2.65092340e+00, 2.68189489e+00, 2.71322822e+00, 2.74492764e+00, 2.77699740e+00, 2.80944185e+00, 2.84226535e+00, 2.87547234e+00, 2.90906730e+00, 2.94305476e+00, 2.97743930e+00, 3.01222557e+00, 3.04741825e+00, 3.08302210e+00, 3.11904192e+00, 3.15548257e+00, 3.19234896e+00, 3.22964608e+00, 3.26737895e+00, 3.30555266e+00, 3.34417237e+00, 3.38324328e+00, 3.42277067e+00, 3.46275987e+00, 3.50321627e+00, 3.54414534e+00, 3.58555259e+00, 3.62744362e+00, 3.66982407e+00, 3.71269966e+00, 3.75607618e+00, 3.79995948e+00, 3.84435549e+00, 3.88927018e+00, 3.93470962e+00, 3.98067995e+00, 4.02718736e+00, 4.07423813e+00, 4.12183861e+00, 4.16999521e+00, 4.21871445e+00, 4.26800288e+00, 4.31786717e+00, 4.36831403e+00, 4.41935028e+00, 4.47098280e+00, 4.52321856e+00, 4.57606460e+00, 4.62952806e+00, 4.68361615e+00, 4.73833616e+00, 4.79369548e+00, 4.84970158e+00, 4.90636202e+00, 4.96368443e+00, 5.02167656e+00, 5.08034623e+00, 5.13970136e+00, 5.19974994e+00, 5.26050009e+00, 5.32196000e+00, 5.38413797e+00, 5.44704237e+00, 5.51068171e+00, 5.57506457e+00, 5.64019962e+00, 5.70609567e+00, 5.77276160e+00, 5.84020641e+00, 5.90843919e+00, 5.97746916e+00, 6.04730562e+00, 6.11795801e+00, 6.18943584e+00, 6.26174877e+00, 6.33490656e+00, 6.40891906e+00, 6.48379628e+00, 6.55954830e+00, 6.63618536e+00, 6.71371780e+00, 6.79215606e+00, 6.87151074e+00, 6.95179255e+00, 7.03301231e+00, 7.11518098e+00, 7.19830965e+00, 7.28240954e+00, 7.36749199e+00, 7.45356849e+00, 7.54065064e+00, 7.62875019e+00, 7.71787904e+00, 7.80804920e+00, 7.89927285e+00, 7.99156229e+00, 8.08492998e+00, 8.17938850e+00, 8.27495061e+00, 8.37162920e+00, 8.46943732e+00, 8.56838815e+00, 8.66849505e+00, 8.76977153e+00, 8.87223126e+00, 8.97588805e+00, 9.08075589e+00, 9.18684893e+00, 9.29418148e+00, 9.40276803e+00, 9.51262323e+00, 9.62376190e+00, 9.73619904e+00, 9.84994981e+00, 9.96502956e+00, 1.00814538e+01, 1.01992383e+01, 1.03183989e+01, 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6.81599189e+03, 6.89562505e+03, 6.97618859e+03, 7.05769337e+03, 7.14015040e+03, 7.22357080e+03, 7.30796582e+03, 7.39334685e+03, 7.47972542e+03, 7.56711317e+03, 7.65552189e+03, 7.74496352e+03, 7.83545012e+03, 7.92699390e+03, 8.01960721e+03, 8.11330256e+03, 8.20809257e+03, 8.30399003e+03, 8.40100790e+03, 8.49915925e+03, 8.59845733e+03, 8.69891555e+03, 8.80054744e+03, 8.90336672e+03, 9.00738728e+03, 9.11262313e+03, 9.21908849e+03, 9.32679771e+03, 9.43576532e+03, 9.54600604e+03, 9.65753473e+03, 9.77036644e+03, 9.88451640e+03, 1.00000000e+04] um>, modified_random_walk: bool = True, scattering_mode_max: int = None, istar_sphere: int = None, nphot_therm: int = None, nphotdiff: float = None, nphotdiff_type: int = None, nphot_mono: int = None, nphot_spec: int = None, mc_scat_maxtauabs: float = None, nphot_scat: int = None, coordinate: Union[str, astropy.coordinates.sky_coordinate.SkyCoord] = None, external_source_type: Literal['Draine1978', 'WeingartnerDraine2001', 'None'] = None, external_source_multiplier: float = 1, velocity: Unit("km / s") = <Quantity 0. km / s>, mode: Literal['image'] = 'image', star_radius: Optional[None] = None, star_effective_temperature: Optional[None] = None, accretion_luminosity: Optional[None] = None, accretion_temperature: Optional[None] = <Quantity 20000. K>)

Deprecated in favor of RadMCRTLines

Expand source code

class RadMCRTSingleCall(RadMCRTLines):
    """Deprecated in favor of RadMCRTLines"""

    def __post_init__(self):
        super().__post_init__()
        self.logger.warning("Deprecation warning. Renamed to RadMCRTLines!")

Ancestors

RadMCRTLines
RadMCRT
RadMCRTImage
RadMCBase
MapBase

Class variables

var accretion_luminosity : Optional[None]
var accretion_temperature : Optional[None]
var star_effective_temperature : Optional[None]
var star_radius : Optional[None]

Inherited members

RadMCRTLines:
- amr_grid
- camera_wavelength_micron
- catch_radmc_messages
- channel_maps
- copy_for_propype
- create_files
- dust_density
- dust_ini
- dust_kappa
- dust_temperature
- external_source
- factor
- fitsname_suffix
- frequency_centers
- gas_temperature
- interpolate
- interpolate_back
- mode
- molecule
- numberdens
- radmc3d
- radmc_to_fits
- run
- split
- stars
- unit
- wavelength_micron
- wavelength_multiple_lines