%load_ext autoreload
%autoreload 2

import osiris_utils as ou

Interface with Osiris Input Decks

For many tasks, it might be useful to read simulation parameters directly from the input deck, or algorithmically generate new Osiris input decks (e.g.to run large parameter scans).

The class InputDeckIO allows you to easily perform theses tasks. You need to provide it two inputs:

  • filename: path to OSIRIS input deck

  • verbose: if True will print auxiliary information when parsing the input deck

Reading an input deck

deck = ou.InputDeckIO('example_data/thermal.1d', verbose=True)

Not only does the object load the different module parameters, but also automatically determines other useful information for downstream tasks.

Examples include:

  • dim: number of dimensions

  • n_species: number of species

  • species: dictionary with Species objects with relevant information (e.g. charge, rqm, etc.)

print("Simulation Dimensions:", deck.dim)
print("Number of species:", deck.n_species)
print("Species:", deck.species)

InputDeckIO stores the state of the input deck in the parameter self._sections.

You should not access this value directly, instead you can use for example its getter function self.sections which returns a deepcopy.

The returned value corresponds to a list of pairs [section_name, dictionary] where the section_name matches the Osiris input deck section name and he dictionary contains the list of (key, values) for the parameters of the section.

print(deck.sections[0])
print(deck.sections[1])
print('Number of sections:', len(deck.sections))

Another option is to query the object as if it is an iterator, where the key is the section name.

This will return a list of dictionaries, since multiple sections can have the same name (e.g. you might have multiple species).

Once again, a deepcopy is being returned so editing the returned values of the dictionaries will not change the original InputDeckIO object.

print(deck['simulation'])
print(deck['node_conf'])

Finally you can also ask for a specific parameter directly with get_param()

# this one returns a list since there can be multiple sections with the same name
print(deck.get_param(section='simulation', param='random_seed')[0])
# which is equivalent to doing this
print(deck["simulation"][0]['random_seed'])

Editing an input deck

To safely edit the value of a parameter in an input deck you can use set_parameter().

Note: This re-writes the object values!

# edit a parameter already exists
print('Before', deck['simulation'])
deck.set_param('simulation', 'random_seed', value=42)
print('After', deck['simulation'])

# add a parameter
print("Before", deck["simulation"])
deck.set_param("simulation", "new_parameter", value='HI', unexistent_ok=True)
print("After", deck["simulation"])

And you can also delete the parameter using delete_param().

# delete a parameter
print("Before", deck["simulation"])
deck.delete_param("simulation", "new_parameter")
print("After", deck["simulation"])

Something slighlty more powerful, is the ability to edit a string in the whole input deck (use with care!)

This can be done for example to automatically change multiple parameter values that are shared / depend on an external quantity.

We can do this using the function set_tag().

Note: This only works on the parameter values, not section names / parameter names.

# this a dummy example where we change some values to #tag#
print("Before", deck["simulation"])
deck.set_tag(
    '42', # this has to be a string
    '#tag#',
)
deck.set_tag(
    '23:50:00', # this has to be a string
    '#tag#',
)
print("After 1", deck["simulation"])

# and here we change both values at once
deck.set_tag('#tag#', "BOTH CHANGED")
print("After 2", deck["simulation"])
# There is a reason why wall_clock_limit has an extra "" done worry
# it is because it should be a string, while random_seed is an int!
# InputDeckIO handles these things for you

Writing changes to file

Once you did your changes, you can simply generate a new input deck with print_to_file().

deck.print_to_file("edited-deck.1d")
with open("edited-deck.1d") as f:
    print(f.read())