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https://github.com/migueldvb/cine

Calculate infrared pumping rates by solar radiation
https://github.com/migueldvb/cine

astronomy comets python science

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Calculate infrared pumping rates by solar radiation

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README 

          
===============================

CINE: Comet INfrared Excitation

===============================



``cine`` is a command-line tool for calculating infrared pumping efficiencies.

At large nucleocentric distances, one of the main mechanisms for molecular

excitation in comets is the fluorescence by the solar radiation followed by

radiative decay to the ground vibrational state.  This code calculates the

effective pumping rates for rotational levels in the ground vibrational state

scaled by the heliocentric distance of the comet.  These coefficients are

useful for modeling rotational emission lines observed in cometary spectra at

sub-millimeter wavelengths.



Code releases are available on `PyPI `_, and

development happens in the `github project page

`_.



Requirements

------------



The code requires the standard scientific Python packages (`numpy

`_, `scipy `_, and `pandas

`_) and astropy's affiliated package `astroquery

`_  to access the HITRAN and Lamda

databases. Running the tests requires `nose

`_.



Installation

------------



cine can be installed using `pip `_:



.. code-block:: bash



    $ pip install cine



or by cloning the github repository:



.. code-block:: bash



    $ # If you have a github account:

    $ git clone git@github.com:migueldvb/cine.git

    $ # If you do not:

    $ git clone https://github.com/migueldvb/cine.git

    $ cd cine

    $ python setup.py install

    $ # Or if you do not have root privileges:

    $ python setup.py install --user



When the package is installed using either method, the ``cine`` script will be

copied to a directory in the PATH environment variable and will be available

for general use.



Example

-------



``cine`` is a command-line tool that is included in the package to generate

pumping rates for several molecules. For example, to obtain the effective

pumping rates between the seven lowest rotational levels in the ground

vibrational state of HDO you can run the following command once ``CINE`` has

been installed:



.. code-block:: bash



    $ cine --mol HDO --nlevels 7



This should create a file named ``G_HDO.dat`` which contains the pumping rates

G :subscript:`ij` in units of s :superscript:`-1` between the rotational levels

i and j shown in the first two columns. Note that the levels use zero-based

indexing.



.. code-block:: bash



    0 3 2.568872e-05

    0 4 2.570305e-05

    0 5 1.552757e-05

    1 2 6.253229e-05

    1 6 2.987896e-05

    2 1 6.196215e-05

    2 6 4.410062e-05

    3 0 7.547422e-05

    3 4 3.103947e-05

    3 5 5.048423e-05

    4 0 1.253741e-04

    4 3 5.128064e-05

    4 5 4.679292e-05

    5 0 7.481781e-05

    5 3 8.287649e-05

    5 4 4.643613e-05

    6 1 4.820172e-05

    6 2 7.201329e-05



To include more levels in the calculation, change the ``-n/-nlevels`` command-line

option to a larger value.  cine has a ``-h/--help`` argument that presents an

usage explanation describing each optional argument.



These coefficients are useful for deriving molecular production rates from cometary

lines observed at sub-millimeter wavelengths combined with a code that

solves the radiative transfer equations such as `LIME

`_.



Downloading HITRAN data

-----------------------



To download the molecular data cine uses the ``astroquery.hitran`` and

``astroquery.lamda`` tools.  Set the ``LAMDA_DATA`` and ``HITRAN_DATA``

environment variables (otherwise, the default

``~/.astropy/cache/astroquery/Lamda``  and

``~/.astropy/cache/astroquery/hitran`` will be used),



Tests

-----



If ``nose`` is installed the tests can be run from the root of the repository as:



.. code-block:: bash



    $ python setup.py test



Contributing

------------



Any questions or bug reports can be raised in github's `issue tracker

`_ or `pull requests

`_.



Project Status

--------------



.. image:: https://travis-ci.org/migueldvb/cine.svg?branch=master

    :target: https://travis-ci.org/migueldvb/cine?branch=master



.. image:: https://coveralls.io/repos/github/migueldvb/cine/badge.svg?branch=master

    :target: https://coveralls.io/github/migueldvb/cine?branch=master



Citation

--------



.. image:: http://joss.theoj.org/papers/10.21105/joss.00182/status.svg

    :target: http://joss.theoj.org/papers/10.21105/joss.00182



If you wish to cite this work, please use this reference from `NASA's

Astrophysics Data System

`_:



.. code-block:: bibtex



    @ARTICLE{2017JOSS....2..182D,

           author = {{de Val-Borro}, Miguel and {Cordiner}, Martin A. and {Milam}, Stefanie

            N. and {Charnley}, Steven B.},

            title = "{Cine: Line excitation by infrared fluorescence in cometary atmospheres}",

          journal = {The Journal of Open Source Software},

             year = 2017,

            month = Mar,

           volume = {2},

            pages = {182},

              doi = {10.21105/joss.00182},

           adsurl = {https://ui.adsabs.harvard.edu/#abs/2017JOSS....2..182D},

          adsnote = {Provided by the SAO/NASA Astrophysics Data System}

    }



License

-------



Copyright 2017-2018 Miguel de Val-Borro



``CINE`` is free software made available under the MIT License.

For details see the LICENSE file.