TRANSP
======

**MITIM** can be used to run TRANSP, interpret results and plot revelant quantities.
This framework does not provide linceses or support to run TRANSP, therefore, please see :ref:`Installation` for information on how to get TRANSP working and how to configure your setup.

Once setup has been successful, the following regression test should run smoothly:

.. code-block:: console

	python3 MITIM-fusion/tests/TRANSP_workflow.py

.. contents:: Contents
    :local:
    :depth: 1

Run TRANSP
----------

For this tutorial we will need the following modules:

.. code-block:: python

	import os
	from pathlib import Path
	from mitim_tools.transp_tools import TRANSPtools

TRANSP runs are very personal and specific to each tokamak and plasma, as diagnostic availability strongly varies and namelist settings are not standarized.
For this reason, this workflow assumes that a folder exists with all the plasma information (UFILES) and namelist required to run TRANSP:

.. code-block:: python

	folder_original = Path("MITIM-fusion/tests/data/FolderTRANSP/")
	folder 			= Path("MITIM-fusion/tests/scratch/transp_tut/")
	os.system(f"rm -r {folder}")
	os.system(f"cp -r {folder_original} {folder}")

First, one would initialize the TRANSP class with the given folder and the tokamak name:

.. code-block:: python

	tokamak = "CMOD"
	transp  = TRANSPtools.TRANSP( folder, tokamak )

Then, select a shotnumber and run name, such that the TRANSP simulation will have the complete name `shotnumber+runname`, and the MPI settings for the TRANSP run:

.. code-block:: python

	shotnumber  = "12345"
	runname     = "X01"
	mpisettings = { "trmpi": 1, "toricmpi": 64, "ptrmpi": 1 }

	transp.defineRunParameters( shotnumber+runname, shotnumber, mpisettings = mpisettings )

Submit the TRANSP run:

.. code-block:: python

	transp.run()

Check every 5min if the run has finished, and grab final results when they are ready:

.. code-block:: python

	transp.checkUntilFinished( label = runname, checkMin = 5 )

Once the run has finished, results can be plotted:

.. code-block:: python

	transp.plot( label = runname ) 

As a result, a TRANSP notebook with different tabs will be opened with all relevant output quantities:

.. figure:: ./figs/TRANSPnotebook.png
	:align: center
	:alt: TRANSP_Notebook

.. raw:: html

   <br><br>

Read results from external TRANSP run
-------------------------------------

If TRANSP has already been run and the .CDF results file already exists (``cdf_file``), the workflow in the previous section is not needed and one can simply read and plot the results:

.. code-block:: python

	from mitim_tools.transp_tools import CDFtools

	transp_results = CDFtools.transp_output( cdf_file )

	transp_results.plot()

.. tip::

	``transp_results`` is a class that parses important TRANSP outputs.
	For example, to plot the electron temperature (in keV) as a function of the square root of the normalized toroidal flux coordinate at the top of the last simulated sawtooth (or last simulated time if no sawtooth present):

	.. code-block:: python

		import matplotlib.pyplot as plt

		plt.ion(); fig, ax = plt.subplots()

		index_sawtooth = transp_results.ind_saw
		rho            = transp_results.x[index_sawtooth,:]
		TeKeV          = transp_results.Te[index_sawtooth,:]

		ax.plot(rho,TeKeV)

	To plot all important time and spatial variables (at time ``t1`` seconds), simply do:

	.. code-block:: python

		transp_results.plot( time = t1 )

.. note::

	The contents of the TRANSP class ``transp_output`` can be found in ``transp_tools.CDFtools.py`` if one wants to understand what post-processing is applied to TRANSP outputs and the units of the variables.

TRANSP aliases
--------------

MITIM provides a few useful aliases, including for the TRANSP tools: :ref:`Shell Scripts`