Scale Linestrengths of carbon-monoxide

This example scales the linestrengths of CO to Tgas=300 from Tref = 296 and then plots the linestrengths against the wavenumbers. We are using fetch_hitemp() function to retrieve the dataframe from the HITEMP-CO databank.

References

\[S(T) = S_0 \frac{Q_{ref}}{Q_{gas}} \operatorname{exp}\left(-E_l \left(\frac{1}{T_{gas}}-\frac{1}{T_{ref}}\right)\right) \frac{1-\operatorname{exp}\left(\frac{-\omega_0}{Tgas}\right)}{1-\operatorname{exp}\left(\frac{-\omega_0}{T_{ref}}\right)}\]

See Eq.(A11) in [Rothman-1998]

Similar functions are used directly at the hearth of RADIS’s SpectrumFactory in the calc_linestrength_eq() and calc_linestrength_noneq() methods

Downloading 05_HITEMP2019.par.bz2 for CO (1/1).
Download complete. Parsing CO database to /home/docs/.radisdb/hitemp/CO-05_HITEMP2019.hdf5
/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/hitranapi.py:128: FutureWarning:

A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object.



/home/docs/checkouts/readthedocs.org/user_builds/radis/checkouts/latest/radis/api/tools.py:280: FutureWarning:

Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`

Added HITEMP-CO database in /home/docs/radis.json
Scaling equilibrium linestrength

from matplotlib import pyplot as plt
from numpy import exp

from radis.db.classes import get_molecule, get_molecule_identifier
from radis.io.hitemp import fetch_hitemp
from radis.levels.partfunc import PartFuncTIPS
from radis.phys.constants import hc_k


def get_Qgas(molecule, iso, T):

    M = get_molecule_identifier(molecule)

    Q = PartFuncTIPS(M, iso)
    return Q.at(T=T)


def scale_linestrength_eq(df, Tref, Tgas):

    print("Scaling equilibrium linestrength")

    # %% Load partition function values

    def _calc_Q(molecule, iso, T_ref, T_gas):

        Qref = get_Qgas(molecule, iso, T_ref)
        Qgas = get_Qgas(molecule, iso, T_gas)

        return Qref, Qgas

    id_set = df.id.unique()
    id = list(id_set)[0]
    molecule = get_molecule(id)  # retrieve the molecule
    iso_set = set(df.iso)  # df1.iso.unique()

    Qref_Qgas_ratio = {}

    for iso in iso_set:
        Qref, Qgas = _calc_Q(molecule, iso, Tref, Tgas)
        Qref_Qgas_ratio[iso] = Qref / Qgas

    # Scaling linestrength with the equations from Rothman's paper
    line_strength = df.int * df["iso"].map(Qref_Qgas_ratio)
    line_strength *= exp(-hc_k * df.El * (1 / Tgas - 1 / Tref))
    line_strength *= (1 - exp(-hc_k * df.wav / Tgas)) / (1 - exp(-hc_k * df.wav / Tref))
    # Add a fresh columns with the scaled linestrength
    df["S"] = line_strength  # [cm-1/(molecules/cm-2)]

    # Just to make sure linestrength is indeed added
    assert "S" in df

    return df


if __name__ == "__main__":
    Tref = 296
    df = fetch_hitemp(
        molecule="CO",
        isotope="1, 2, 3",
        load_wavenum_min=2000,
        load_wavenum_max=2250,
    )

    Tgas = 450

    df = scale_linestrength_eq(df, Tref, Tgas)
    plt.bar(df["wav"], df["S"])
    plt.xlabel("Wavenumbers in cm-1")
    plt.ylabel("Linestrengths in cm-1/(molecules/cm-2)")
    plt.show()