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Add documentation for restarting from a seed mechanism
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amarkpayne committed Jul 23, 2019
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maxNumSpecies=100
)

Restarting from a Seed Mechanism
=================================
The preferred method for restarting an RMG-Py job is to restart the job from a seed mechanism. There are many scenarios
when the user might want to do this, including continuing on a job that ran out of time or crashed as the result of a
now fixed bug. To restart from a seed mechanism, the block below must be added on to the input file. ::

restartFromSeed(path='seed',
relative_path=True, # This by default is True, so you only have to include this if False
)

The ``path`` flag is the path to the seed mechanism folder, which contains three subfolders that must be titled as
follows: Filters, Seed, Seed_Edge. By default this path is relative to the location of the input.py file, but setting
the ``relative_path`` flag to False will instead treat the path as an absolute path on disk.

Then, to restart from the seed mechanism the input file is submitted as normal. ::

python rmg.py input.py

Once the restart job has begun, RMG will move the seed mechanism files to a new subfolder in the output directory
entitled ``restart``. This is to back-up the seed mechanism used for restarting, as everything in the ``seed`` subfolder
of the output directory is overwritten by RMG during the course of mechanism generation.

RMG also outputs a file entitled ``restart_from_seed.py`` the first time a seed mechanism is generated during the course
of an RMG job (so long as the RMG job was not itself a restarted job). This file is an exact duplicate of the original
input file with the exception that the restart block has been added on automatically for convenience. In this way this
file is treated in the exact way as a normal input file.

Finally, **note that it is advised to turn on generating the seed each iteration so that you can restart an RMG job right where it left off**.
This can be done by setting ``generateSeedEachIteration=True`` in the options block of the input file.

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