Running the program
===================

Running with default configurations can be achieved by running the below in a terminal::

  mango

This will run the program with the default values shown in the input file. See further examples in :ref:`examples`.
If not specified, the positions of the molecules will be the stable Leonard Jones configuration downloaded from http://doye.chem.ox.ac.uk/jon/structures/LJ/


Other commandline functions include:

MPI calculation command::

  mango_mpi

Running the mango test suite::

  mango_test

Restart and input file regenerators::

  mango_inputregen
  mango_restartregen

The rest have their own help with ``-h``::

  mango_plotsuscep
  mango_strings 
  mango_vars
  mango_vis

Jupyter Notebook or Module use
------------------------------

There are currently two functions designed for use as a module import or as part of a `jupyter notebook <https://jupyter.org/>`_ and they are::

  mango.run()
  mango.help()

Run takes a dictionary as input with the keys and values the same as the input file.
To run a simple simulation a python script would be;

.. code-block:: python3

  import mango
  mango.run({'SusceptibilityCalc': True, 'Iterations': 100000,
           'Repetitions': 1, 'NumberParticles': 5,
           'PositionFile': './Position_file'})

Help prints the help shown below.


Running with an Input or Restarting
-----------------------------------

To use an input file::

  -I Inputfile

To restart a run, specify the restart file as shown::

  -R Run1restart 

Saving Mechanism
----------------

Saving happens in two stages when running the main calculation as shown below. This reduces the amount of I/O to disk.

There are a two commands to deal with the saving. These are SkipSave (--skip) and SaveChunk (--savechunk). SkipSave deals with the number of iterations that are saved to memory and SaveChunk is the number of saved iterations to be collected before writing to disk.

.. figure:: _static/SavingMechanism.svg
   :target: _static/SavingMechanism.svg
   :width: 75 %

Errors
------

Errors are split into 2 categories, warning and critical. The program will still run under warnings but it will kill itself under critical errors.

Warning messages will be written like so::

    Warning: maximum number of iterations exceeded! [MD step 1] x10

The above message tells us that the error has happened 10 times on the first MD step.

Internal Help
-------------

To print the help from the commandline use the command ``mango -h``, to print the input file help from the commandline use ``mango -ifh`` or call ``mango.help()`` from an interactive prompt. For the full input file see :ref:`inputfile`. The commandline help is shown below.

.. program-output::  python3 helpout.py