=============
User's Manual
=============

The MRChem program comes as two executables::

    <install-path>/bin/mrchem                   # Python input parser and launcher
    <install-path>/bin/mrchem.x                 # MRChem main executable

where the former is a Python script that reads and validates the *user input
file* and produces a new *program input file* which is then passed as argument
to the latter, which is the actual C++ executable.

The input and output of the program is thus organized as *three* separate files:

+-------------------+---------------------------+---------------+
| File extension    | Description               | Format        |
+===================+===========================+===============+
| ``.inp``          | User input file           | GETKW/JSON    | 
+-------------------+---------------------------+---------------+
| ``.json``         | Program input/output      | JSON          |
+-------------------+---------------------------+---------------+
| ``.out``          | User output file          | Text          |
+-------------------+---------------------------+---------------+

The name of the user input file can be anything, as long as it has the ``.inp``
extension, and the corresponding ``.json`` and ``.out`` files will get the
same name prefix. The JSON program file will get both an ``"input"`` and an
``"output"`` section. This ``"input"`` section is rather detailed and contains
very implementation specific keywords, but it is automatically generated by the
``mrchem`` script, based on the more generic keywords of the user input file.
The ``mrchem`` script will further launch the ``mrchem.x`` main executable,
which will produce the text output file as well as the ``"output"`` section
of the JSON in/out file. The contents of all these files will be discussed
in more detail in the sections below.

.. toctree::
   :maxdepth: 1

   running
   user_inp
   user_ref
   qcengine
   program_json
   geometry_optimization.rst
   pseudopotentials.rst