XGC-S Output Parameters
=======================

At the moment XGC-S has a separate output from the main tokamak XGC code. The output is limited compared to main XGC, but we are continuously adding more ADIOS2 output. The available ADIOS2 output in XGC-S contains the same output parameters as main XGC, but there can be an additional dimension for the radial-poloidal plane number since each plane has a different mesh. Moreover, XGC-S also outputs files with ASCII data.

ASCII output
------------

XGC-S outputs ASCII files ``nnnnnn_*****_######.fd2D`` and ``nnnnnn_*****_######.tn2D`` where ``nnnnnn`` is the output files prefix given by ``sml_outfile_s`` in the `XGC-S Input Parameters <https://xgc.pppl.gov/html/inputs_xgc-s.html>`__, ``*****`` is the plane index and ``######`` is the time step.

.. New line 
.. |br| raw:: html

  <br/>

**nnnnnn_*****_######.fd2D file content** |br|
*(Mesh output)*  |br|

| line 1: Description to come
| line 2: Description to come
| line 3: Description to come
| line 4: Description to come
| line 5: Description to come
| line 6: Description to come
| line 7: Description to come
| line 8: Description to come
| line 9: Description to come

**nnnnnn_*****_######.tn2D file content** |br|
*(Physics quantities output)*  |br|

| line 1: node index
| line 2: :math:`R` coordinate of node [ :math:`\mathrm{m}` ].
| line 3: :math:`Z` coordinate of node [ :math:`\mathrm{m}` ].
| line 4: Flux-surface averaged electrostatic potential [ :math:`\mathrm{V}` ].
| line 5: Perturbed potential [ :math:`\mathrm{V}` ].
| line 6: Perturbed ion density [ :math:`{\mathrm{m}}^{-3}` ].
| line 7: Equilibrium ion density [ :math:`{\mathrm{m}}^{-3}` ].
| line 8: Equilibrium ion temperature [ :math:`\mathrm{eV}` ].
| line 9: Background radial electric field [ :math:`\mathrm{V}` ].
| line 10: Normalized minor radius :math:`\sqrt{\psi/\psi_a}`.

**Plot with gnuplot** |br|
The perturbed potential in a plane can plotted using gnuplot:

.. code-block:: bash

   > gnuplot --persist -e 'plot "w7x_te_00045_002000.tn2D" using 2:3:5 lc palette'

.. image:: ./img/xgc-s_test_run_w7x_te_00045_002000.png
         :width: 60%
         :align: center
         :alt: Alternative text

*Fig. 1: Example of the perturbed electrostatic potential illustrated with gnuplot.*

ADIOS2 output
-------------

At the moment the XGC-S ADIOS2 output includes quantities to plot the potential. We provide some Python scripts for plotting in `XGC-Devel/XGC-S/utils/python/ <https://github.com/PrincetonUniversity/XGC-Devel/tree/master/XGC-S/utils/python>`_. To be able to read ADIOS2 in Python

.. code-block:: python

   import adios2

follow the instructions `here <https://xgc.pppl.gov/html/xgc_output_scripts.html#python>`__.
On the Princeton Stellar cluster

.. code-block:: bash

   > module load anaconda3/2023.3
   > export PYTHONPATH=/projects/XGC/STELLAR/Software/install/adios2/2.8.3_python/gcc-8/lib/python3.10/site-packages/adios2

should be sufficient.

Use the Python scripts in the XGC-S run directory to plot perturbed quantities

.. code-block:: bash

   > python xgc_2D_dpot.py

.. image:: ./img/xgc-s_test_run_2D_dpot.png
         :width: 99%
         :align: center
         :alt: Alternative text

*Fig. 2: Example of perturbed quantities illustrated with Python.*

and linear growth rate

.. code-block:: bash

   > python xgc_linear_growth_rate.py

.. image:: ./img/xgc-s_test_run_linear_growth_rate.png
         :width: 80%
         :align: center
         :alt: Alternative text

*Fig. 3: Example of a linear growth rate calculation illustrated with Python.*

.. toctree::
   :maxdepth: 1