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- Cologne Database for Molecular Spectroscopy (CDMS) Queries (`astroquery.linelists.cdms`)

# Cologne Database for Molecular Spectroscopy (CDMS) Queries (`astroquery.linelists.cdms`)

## Getting Started

The CDMS module provides a query interface for the Search and Conversion Form of the Cologne Database for Molecular Spectroscopy. The module outputs the results that would arise from the browser form using similar search criteria as the ones found in the form, and presents the output as a `Table`. The module is similar in spirit and content to the JPLSpec module.

## Examples

### Querying the catalog

The default option to return the query payload is set to `False`. In the following examples we have explicitly set it to False and True to show the what each setting yields:

    >>> from astroquery.linelists.cdms import CDMS
    >>> import astropy.units as u
    >>> response = CDMS.query_lines(min_frequency=100 * u.GHz,
    ...                             max_frequency=1000 * u.GHz,
    ...                             min_strength=-500,
    ...                             molecule="028503 CO",
    ...                             get_query_payload=False)
    >>> response.pprint(max_width=120)
         FREQ     ERR    LGINT   DR   ELO    GUP MOLWT TAG QNFMT  Ju  Ku  vu F1u F2u F3u  Jl  Kl  vl F1l F2l F3l   name  Lab
         MHz      MHz   nm2 MHz      1 / cm        u
     ----------- ------ ------- --- -------- --- ----- --- ----- --- --- --- --- --- --- --- --- --- --- --- --- ------- ----
     115271.2018 0.0005 -5.0105   2      0.0   3    28 503   101   1  --  --  --  --  --   0  --  --  --  --  -- CO, v=0 True
        230538.0 0.0005 -4.1197   2    3.845   5    28 503   101   2  --  --  --  --  --   1  --  --  --  --  -- CO, v=0 True
     345795.9899 0.0005 -3.6118   2   11.535   7    28 503   101   3  --  --  --  --  --   2  --  --  --  --  -- CO, v=0 True
     461040.7682 0.0005 -3.2657   2  23.0695   9    28 503   101   4  --  --  --  --  --   3  --  --  --  --  -- CO, v=0 True
     576267.9305 0.0005 -3.0118   2  38.4481  11    28 503   101   5  --  --  --  --  --   4  --  --  --  --  -- CO, v=0 True
     691473.0763 0.0005 -2.8193   2  57.6704  13    28 503   101   6  --  --  --  --  --   5  --  --  --  --  -- CO, v=0 True
      806651.806  0.005 -2.6716   2  80.7354  15    28 503   101   7  --  --  --  --  --   6  --  --  --  --  -- CO, v=0 True
        921799.7  0.005  -2.559   2 107.6424  17    28 503   101   8  --  --  --  --  --   7  --  --  --  --  -- CO, v=0 True

The following example, with `get_query_payload = True`, returns the payload:

    >>> response = CDMS.query_lines(min_frequency=100 * u.GHz,
    ...                             max_frequency=1000 * u.GHz,
    ...                             min_strength=-500,
    ...                             molecule="028503 CO",
    ...                             get_query_payload=True)
    >>> print(response)
    {'MinNu': 100.0, 'MaxNu': 1000.0, 'UnitNu': 'GHz', 'StrLim': -500, 'temp': 300, 'logscale': 'yes', 'mol_sort_query': 'tag', 'sort': 'frequency', 'output': 'text', 'but_action': 'Submit', 'Molecules': '028503 CO'}

The units of the columns of the query can be displayed by calling `response.info`:

    >>> response = CDMS.query_lines(min_frequency=100 * u.GHz,
    ...                             max_frequency=1000 * u.GHz,
    ...                             min_strength=-500,
    ...                             molecule="028503 CO",
    ...                             get_query_payload=False)
    >>> print(response.info)
    <Table length=8>
     name  dtype    unit     class     n_bad
    ----- ------- ------- ------------ -----
     FREQ float64     MHz       Column     0
      ERR float64     MHz       Column     0
    LGINT float64 nm2 MHz       Column     0
       DR   int64               Column     0
      ELO float64  1 / cm       Column     0
      GUP   int64               Column     0
    MOLWT   int64       u       Column     0
      TAG   int64               Column     0
    QNFMT   int64               Column     0
       Ju   int64               Column     0
       Ku   int64         MaskedColumn     8
       vu   int64         MaskedColumn     8
      F1u   int64         MaskedColumn     8
      F2u   int64         MaskedColumn     8
      F3u   int64         MaskedColumn     8
       Jl   int64               Column     0
       Kl   int64         MaskedColumn     8
       vl   int64         MaskedColumn     8
      F1l   int64         MaskedColumn     8
      F2l   int64         MaskedColumn     8
      F3l   int64         MaskedColumn     8
     name    str7               Column     0
      Lab    bool               Column     0

These come in handy for converting to other units easily, an example using a simplified version of the data above is shown below:

    >>> print(response['FREQ', 'ERR', 'ELO'])
         FREQ     ERR     ELO
         MHz      MHz    1 / cm
     ----------- ------ --------
     115271.2018 0.0005      0.0
        230538.0 0.0005    3.845
     345795.9899 0.0005   11.535
     461040.7682 0.0005  23.0695
     576267.9305 0.0005  38.4481
     691473.0763 0.0005  57.6704
      806651.806  0.005  80.7354
        921799.7  0.005 107.6424
    >>> response['FREQ'].quantity
     <Quantity [115271.2018, 230538.    , 345795.9899, 461040.7682, 576267.9305,
                691473.0763, 806651.806 , 921799.7   ] MHz>
    >>> response['FREQ'].to('GHz')
     <Quantity [115.2712018, 230.538    , 345.7959899, 461.0407682, 576.2679305,
                691.4730763, 806.651806 , 921.7997   ] GHz>

The parameters and response keys are described in detail under the Reference/API section.

### Looking Up More Information from the partition function file

If you have found a molecule you are interested in, the `tag` column in the results provides enough information to access specific molecule information such as the partition functions at different temperatures. Keep in mind that a negative `tag` value signifies that the line frequency has been measured in the laboratory but not in space

    >>> import matplotlib.pyplot as plt
    >>> from astroquery.linelists.cdms import CDMS
    >>> result = CDMS.get_species_table()
    >>> mol = result[result['tag'] == 28503]
    >>> mol.pprint(max_width=160)
     tag  molecule    Name   #lines lg(Q(1000)) lg(Q(500)) lg(Q(300)) ... lg(Q(9.375)) lg(Q(5.000)) lg(Q(2.725)) Ver. Documentation Date of entry    Entry
    ----- -------- --------- ------ ----------- ---------- ---------- ... ------------ ------------ ------------ ---- ------------- ------------- -----------
    28503  CO, v=0 CO, v = 0     95      2.5595     2.2584     2.0369 ...       0.5733       0.3389       0.1478    1   e028503.cat     Oct. 2000 w028503.cat

One of the advantages of using CDMS is the availability in the catalog of the partition function at different temperatures for the molecules (just like for JPL). As a continuation of the example above, an example that accesses and plots the partition function against the temperatures found in the metadata is shown below:

    >>> import numpy as np
    >>> keys = [k for k in mol.keys() if 'lg' in k]
    >>> temp = np.array([float(k.split('(')[-1].split(')')[0]) for k in keys])
    >>> part = list(mol[keys][0])
    >>> plt.scatter(temp, part)
    >>> plt.xlabel('Temperature (K)')
    >>> plt.ylabel('Partition Function Value')
    >>> plt.title('Partition Function vs Temperature')

(`Source code`, `png`, `hires.png`, `pdf`)

For non-linear molecules like H2CO, curve fitting methods can be used to calculate production rates at different temperatures with the proportionality: `a*T**(3./2.)`. Calling the process above for the H2CO molecule (instead of for the CO molecule) we can continue to determine the partition function at other temperatures using curve fitting models:

    >>> import numpy as np
    >>> import matplotlib.pyplot as plt
    >>> from astroquery.linelists.cdms import CDMS
    >>> from scipy.optimize import curve_fit
    ...
    >>> result = CDMS.get_species_table()
    >>> mol = result[result['tag'] == 30501] #do not include signs of tag for this
    ...
    >>> def f(T, a):
            return np.log10(a*T**(1.5))
    >>> keys = [k for k in mol.keys() if 'lg' in k]
    >>> def tryfloat(x):
    ...     try:
    ...        return float(x)
    ...     except:
    ...        return np.nan
    >>> temp = np.array([float(k.split('(')[-1].split(')')[0]) for k in keys])
    >>> part = np.array([tryfloat(x) for x in mol[keys][0]])
    >>> param, cov = curve_fit(f, temp[np.isfinite(part)], part[np.isfinite(part)])
    >>> print(param)
    # array([0.51865074])
    >>> x = np.linspace(2.7,500)
    >>> y = f(x,param[0])
    >>> plt.scatter(temp,part,c='r')
    >>> plt.plot(x,y,'k')
    >>> plt.title('Partition Function vs Temperature')
    >>> plt.xlabel('Temperature')
    >>> plt.ylabel('Log10 of Partition Function')

(`Source code`)

We can then compare linear interpolation to the fitted interpolation above:

    >>> interp_Q = np.interp(x, temp, 10**part)
    >>> plt.plot(x, (10**y-interp_Q)/10**y)
    >>> plt.xlabel("Temperature")
    >>> plt.ylabel("Fractional difference between linear and fitted")

(`Source code`)

Linear interpolation is a good approximation, in this case, for any moderately high temperatures, but is increasingly poor at lower temperatures. It can be valuable to check this for any given molecule.

### Querying the Catalog with Regexes and Relative names

The regular expression parsing is analogous to that in the JPLSpec module.

## Troubleshooting

If you are repeatedly getting failed queries, or bad/out-of-date results, try clearing your cache:

    >>> from astroquery.linelists.cdms import CDMS
    >>> CDMS.clear_cache()

If this function is unavailable, upgrade your version of astroquery. The `clear_cache` function was introduced in version 0.4.7.dev8479.

## Reference/API

### astroquery.linelists.cdms Package

#### CDMS catalog

Cologne Database for Molecular Spectroscopy query tool

#### Classes

`CDMSClass`() |
`Conf`() | Configuration parameters for `astroquery.linelists.cdms`.