Molecule: Spectral line transition data for various molecules

Molecule: Spectral line transition data for various molecules#

For fitting of excitation diagrams, transition data (energy levels, wavelengths, temperatures, etc.) are manage via subclasses of the BaseMolecule class. Currently, $H_2, ^{12}CO, ^{13}CO, ^{12}C^{18}O, ^{13}C^{18}O, {\rm and}~ CH^{+}$ are supported.

class pdrtpy.molecule.BaseMolecule(name: str, path: Path | str, opr: float = 1, opr_can_vary: bool = False, **kwargs)[source]#

Bases: object

The base class for holding molecular transition data.

Parameters:

namestr: The descriptive name of the molecule, which will be used in displays. Can include LaTeX (without $ signs) e.g. ‘H_2’, ‘CO’, ‘^{13}CO’.
pathUnion[Path, str]: Path to the table of molecular transition data.
oprfloat: The canonical ortho-to-para ratio for molecules containing hydrogen. Default 1.
opr_can_varybool: Can the ortho-to-para ratio vary in this molecule under different physical conditions? Default:False
**kwargs: dict: Additional keywords to pass to Table.read

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function given an excitation temperature(s)

property canonical_opr: float#

The canonical ortho-to-para ratio of the molecule. Only used for molecules containing hydrogen (where canonical OPR=3).

Returns:

float: The ortho-to-para ratio

property line_ids: list#

The identifiers (names) of the spectral line transitions in the data. These should be used to identify your Measurement data for excitation fits.

Returns:

list: The spectral line IDs

property line_wavelengths: Quantity#

The wavelengths of the spectral line transitions in the data. These should be used to identify your Measurement data for excitation fits.

Returns:

Quantity: The spectral line wavelengths

property name#

The descriptive name of the molecule

Returns:

str: Descriptive name of the moelcule

property opr_can_vary#

Does the ortho-to-para ratio vary in this molecule under different physical conditions?

Returns:

bool: True if OPR can vary, False otherwise.

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function given an excitation temperature(s)

The default calculation is

$Q(T) = \sum g_j~e^{-E_j/kT}$

where $g_j$ is the statistical weight, $E_j$ is the transition energy, $T$ is the excitation temperature, and $k$ is Boltzmann’s constant.

Sub-classes should override this method for custom (and likely more accurate) partition function calculation.

Parameters:

temperatureQuantity: The excitation temperature(s)

Returns:

ndarray: The partition function evaluated at the given excitation temperatures

property transition_data: Table#

The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Returns:

Table: The table of transition data,

class pdrtpy.molecule.C13O(name='^{13}CO', path='13co_transition.tab', opr=1.0, opr_can_vary=False)[source]#

Bases: BaseMolecule

Carbon Monoxide isotopologue $^{13}C^{16}O$. This uses the molecular Lines and Levels data from the Meudon PDR7 code.

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function for 13CO at the given temperature using the HITRAN partition function.

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function for 13CO at the given temperature using the HITRAN partition function. https://hitran.org/data/Q/q27.txt The HITRAN function is evaluated at 1K intervals; this function performs a linear interpolation on those data.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

class pdrtpy.molecule.C13O18(name='^{13}C^{18}O', path='13c18o_transition.tab', opr=1.0, opr_can_vary=False)[source]#

Bases: BaseMolecule

Carbon Monoxide isotopologue $^{12}C^{18}O$. This uses the molecular Lines and Levels data from the Meudon PDR7 code.

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function for 13C18O at the given temperature using the HITRAN partition function.

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function for 13C18O at the given temperature using the HITRAN partition function. https://hitran.org/data/Q/q30.txt The HITRAN function is evaluated at 1K intervals; this function performs a linear interpolation on those data.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

class pdrtpy.molecule.CHplus(name='CH^+', path='CH_p_transition.tab', opr=3.0, opr_can_vary=True)[source]#

Bases: BaseMolecule

Methyl Cation isotopologue $^{12}CH^{+}$. This uses the molecular data from both the Meudon PDR7 code and EXOMOL database

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function for $^{12}CH^{+}$ at the given temperature using the EXOMOL partition function (Pearce et al., 2024, MNRAS, 527, 10736).

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function for $^{12}CH^{+}$ at the given temperature using the EXOMOL partition function (Pearce et al., 2024, MNRAS, 527, 10736). The EXOMOL function is evaluated at 1K intervals; this function performs a linear interpolation on those data.

Note

As described in Pearce+2024, “The ExoMol convention, in accordance with HITRAN (Gamache et al. 2017, J. Quant. Spectrosc. Radiat. Transfer, 203, 70) , is to provide partition functions that include full atomic nuclear spin degeneracy, $g_{nu}$.”

This results in a factor of 2 increase over the partition functions of Barklem and Collet (2016, A&A,588,A96) and of Godard and Cernicharo (2013) A&A, 550, A8. Be aware of this when comparing total column densities with papers that use those partition functions.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

class pdrtpy.molecule.CO(name='^{12}CO', path='12co_transition.tab.gz', opr=1.0, opr_can_vary=False)[source]#

Bases: BaseMolecule

Carbon Monoxide isotopologue $^{12}C^{16}O$. This uses the molecular Lines and Levels data from the Meudon PDR7 code.

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function for CO at the given temperature using the HITRAN partition function.

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function for CO at the given temperature using the HITRAN partition function. https://hitran.org/data/Q/q26.txt The HITRAN function is evaluated at 1K intervals; this function performs a linear interpolation on those data.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

class pdrtpy.molecule.CO18(name='^{12}C^{18}O', path='c18o_transition.tab', opr=1.0, opr_can_vary=False)[source]#

Bases: BaseMolecule

Carbon Monoxide isotopologue $^{12}C^{18}O$. This uses the molecular Lines and Levels data from the Meudon PDR7 code.

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the partition function for $^{12}C^{18}O$ at the given temperature using the HITRAN partition function.

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the partition function for $^{12}C^{18}O$ at the given temperature using the HITRAN partition function. https://hitran.org/data/Q/q28.txt The HITRAN function is evaluated at 1K intervals; this function performs a linear interpolation on those data.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

class pdrtpy.molecule.H2(name='H_2', path='RoueffEtAl.tab', opr=3.0, opr_can_vary=True)[source]#

Bases: BaseMolecule

Molecular hydrogen. This uses the $H_2$ line calculations from Roueff et al 2019, A&A, 630, 58, Table 2.

Attributes:

canonical_opr: The canonical ortho-to-para ratio of the molecule.
line_ids: The identifiers (names) of the spectral line transitions in the data.
line_wavelengths: The wavelengths of the spectral line transitions in the data.
name: The descriptive name of the molecule
opr_can_vary: Does the ortho-to-para ratio vary in this molecule under different physical conditions?
transition_data: The table fo transition data, containing columns such as transition energy, statistical weight, Einstein A coefficient, wavelength etc.

Methods

partition_function(temperature)

Calculate the $H_2$ partition function given an excitation temperature(s).

partition_function(temperature: Quantity) → ndarray[source]#

Calculate the $H_2$ partition function given an excitation temperature(s). This function uses the expression from Herbst et al 1996 http://articles.adsabs.harvard.edu/pdf/1996AJ….111.2403H

$Q(T) = 0.247 ~T / [1 - exp(6000 / T)]$

where $T$ is the excitation temperature.

Parameters:

temperatureQuantity: The excitation temperature(s) at which to evaluate the partition function

Returns:

Q: ndarray: The partition function evaluated at the given excitation temperature(s)

Molecule: Spectral line transition data for various molecules

Contents

Molecule: Spectral line transition data for various molecules#