User Guide
==========

TOSCA uses ASCII input files, organized in files and dictionaries.  
The code provides some level of input checking, meaning that non-recognized inputs are followed by an error message that
lists available possibilities. 

TOSCA has a standardized case structure. The minimum-required case structure is depicted on the left of the following figure, 
while the case structure required to run e.g. atmospheric boundary layer (ABL) with potential 
temperature stratification is shown on the right (i.e. with the addition of the ``boundary/T`` and ``ABLProperties.dat`` files).
The principal control file for a TOSCA simulation is the `control.dat` file, located in the case directory (see 
:ref:`control-subsection` for details).
Depending on the type of simulation that one wishes to perform, flags can be activated in the `control.dat`, which prompt TOSCA 
to read additional input files and data. 

.. image:: ../images/structure_1.png
   :align: center
    
A complete list of entries to all TOSCA input files is contained in Sec. :ref:`input-files-section`. Sec. :ref:`spatial-mesh-section`
describes the two mesh formats available in TOSCA, and explains how boundary patches are identified using curvilinear coordinates,
in which TOSCA is formulated. Sec. :ref:`overset-section` explains how to set up TOSCA cases with one-way nested domains (i.e. the 
overset mesh technique) and Sec. :ref:`acquisition-section` details the various outputs that the user can extract from different kinds 
of simulations using TOSCA's acquisition system. Finally, Sec. :ref:`execution-section` shows a typical TOSCA workflow, where the 
solution is first performed using `tosca` executable, the simulation is then possibily restarted and `tosca2PV` is used in the end to 
convert output binary data into `.xmf` format to be inspected in *ParaView*. 

.. toctree::
   :maxdepth: 1
   
   01_user_guide/input_files.rst
   01_user_guide/spatial_mesh.rst
   01_user_guide/overset.rst
   01_user_guide/acquisition.rst
   01_user_guide/execution.rst