Understanding the outputs
=========================

Output files are written to the ``sims/`` directory (unless specified otherwise) after the code has fully converged. The code generates multiple output files with different suffixes:

- **.pdr.fin**: Species abundances
- **.line.fin**: Line emission data
- **.cool.fin**: Cooling functions
- **.heat.fin**: Heating functions
- **.COOL.spop.fin**: Level populations for each coolant (where ``COOL`` is the coolant name)

.. note::
   Outputs are in ASCII format and can be plotted using standard tools like GNUPLOT or PYTHON.

One-dimensional Outputs
-----------------------

OUTPUT.pdr.fin
~~~~~~~~~~~~~~

+--------+---------------------+-----------------------------------+
| Column | Value               | Comments                          |
+========+=====================+===================================+
| 1      | ID                  | Cell identity (integer)           |
+--------+---------------------+-----------------------------------+
| 2      | x                   | Position (pc)                     |
+--------+---------------------+-----------------------------------+
| 3      | Av                  | Visual extinction (mag)           |
+--------+---------------------+-----------------------------------+
| 4      | Tgas                | Gas temperature (K)               |
+--------+---------------------+-----------------------------------+
| 5      | Tdust               | Dust temperature (K)              |
+--------+---------------------+-----------------------------------+
| 6      | etype               | Type of cell (integer)            |
+--------+---------------------+-----------------------------------+
| 7      | nH                  | Number density (cm⁻³)             |
+--------+---------------------+-----------------------------------+
| 8      | UV                  | FUV intensity (Draine units)      |
+--------+---------------------+-----------------------------------+
| 9+     | ...                 | Species abundances                |
+--------+---------------------+-----------------------------------+

Species abundances follow the sequence in ``species_NETWORK.d``.

OUTPUT.cool.fin
~~~~~~~~~~~~~~~

+--------+---------------------+-----------------------------------+
| Column | Value               | Comments                          |
+========+=====================+===================================+
| 1      | ID                  | Cell identity (integer)           |
+--------+---------------------+-----------------------------------+
| 2      | x                   | Position (pc)                     |
+--------+---------------------+-----------------------------------+
| 3      | Av                  | Visual extinction (mag)           |
+--------+---------------------+-----------------------------------+
| 4      | CO                  | CO cooling function               |
+--------+---------------------+-----------------------------------+
| 5      | C+                  | C+ cooling function               |
+--------+---------------------+-----------------------------------+
| 6      | C                   | C cooling function                |
+--------+---------------------+-----------------------------------+
| 7      | O                   | O cooling function                |
+--------+---------------------+-----------------------------------+
| 8+     | ...                 | Additional coolant cooling        |
+--------+---------------------+-----------------------------------+
| Last   | Total               | Total cooling (sum of all)        |
+--------+---------------------+-----------------------------------+

Coolant sequence matches the order in ``params.dat``. Without additional coolants, total cooling is column 8.

OUTPUT.heat.fin
~~~~~~~~~~~~~~~

+--------+---------------------+-----------------------------------+
| Column | Value               | Comments                          |
+========+=====================+===================================+
| 1      | ID                  | Cell identity (integer)           |
+--------+---------------------+-----------------------------------+
| 2      | x                   | Position (pc)                     |
+--------+---------------------+-----------------------------------+
| 3      | Av                  | Visual extinction (mag)           |
+--------+---------------------+-----------------------------------+
| 4      | HR01                | Not contributing                  |
+--------+---------------------+-----------------------------------+
| 5      | HR02                | Photoelectric heating             |
+--------+---------------------+-----------------------------------+
| 6      | HR03                | Not contributing                  |
+--------+---------------------+-----------------------------------+
| 7      | HR04                | Carbon ionization heating         |
+--------+---------------------+-----------------------------------+
| 8      | HR05                | H₂ formation heating              |
+--------+---------------------+-----------------------------------+
| 9      | HR06                | H₂ photodissociation heating      |
+--------+---------------------+-----------------------------------+
| 10     | HR07                | FUV pumping heating               |
+--------+---------------------+-----------------------------------+
| 11     | HR08                | Cosmic-ray heating                |
+--------+---------------------+-----------------------------------+
| 12     | HR09                | Turbulent heating                 |
+--------+---------------------+-----------------------------------+
| 13     | HR10                | Chemical heating                  |
+--------+---------------------+-----------------------------------+
| 14     | HR11                | Gas-grain heating                 |
+--------+---------------------+-----------------------------------+
| 15     | HR12                | Total heating (sum of all)        |
+--------+---------------------+-----------------------------------+

Three-dimensional Outputs
-------------------------

3D-OUTPUT.pdr.fin
~~~~~~~~~~~~~~~~~

+------------------+---------------------+-----------------------------------+
| Column           | Value               | Comments                          |
+==================+=====================+===================================+
| 1                | ID                  | Cell identity (integer)           |
+------------------+---------------------+-----------------------------------+
| 2                | x                   | x position (pc)                   |
+------------------+---------------------+-----------------------------------+
| 3                | y                   | y position (pc)                   |
+------------------+---------------------+-----------------------------------+
| 4                | z                   | z position (pc)                   |
+------------------+---------------------+-----------------------------------+
| 5                | Tgas                | Gas temperature (K)               |
+------------------+---------------------+-----------------------------------+
| 6                | Tdust               | Dust temperature (K)              |
+------------------+---------------------+-----------------------------------+
| 7                | etype               | Type of cell (integer)            |
+------------------+---------------------+-----------------------------------+
| 8                | nH                  | Number density (cm⁻³)             |
+------------------+---------------------+-----------------------------------+
| 9                | UV                  | FUV intensity (Draine units)      |
+------------------+---------------------+-----------------------------------+
| 10-10+species    | ...                 | Species abundances                |
+------------------+---------------------+-----------------------------------+
| 11+species-...   | Av                  | Visual extinction per HEALPix ray |
+------------------+---------------------+-----------------------------------+