Read Chimes¶

The read_chimes.py python module contains various dictionaries and functions that can be used to parse the abundance arrays that are output from the CHIMES module. These can be used to help the User find the abundance of a particular species in the abundance array, whether they are using the full CHIMES network or a reduced network with some of the elements switched off.

There are two dictionaries that define the names of the species in the full CHIMES network:

Dictionary Description

chimes_dict

This dictionary gives a series of {Key : Value} pairs where the
Key is the name of the species and the Value is the position of
that species in the full CHIMES abundance array. So the User can use
chimes_dict["<species_name>"] to get the position of the species
called "<species_name>" in the abundance array. Note that the name
given by the User must exactly match the name defined in this dictionary.
To see a list of all possible species names, you can do:
for k, v in sorted(chimes_dict.items(), key = lambda x: x[1]):
print(k)

chimes_dict_inv

This gives the inverse of the chimes-dict dictionary, i.e. where the
Key is the position in the full CHIMES abundance array and the
Value is the name of the species at that position. So the User can
use chimes_dict_inv[<position>] to find the name of the species that
is located at <position> in the abundance array.

The following functions can be used to construct dictionaries mapping species names to positions in the abundance array for a reduced network, and to read in the abundances of a given species from an HDF5 snapshot file:

Dictionary	Description
`create_reduced_` `chimes_dictionary(` `element_flags =` `np.zeros(9))`	Creates a dictionary mapping species names to their position in the CHIMES abundance array when using a reduced CHIMES network, i.e. when some of the elements have been switched off. It takes as an optional argument an array of integers of length 9, `element_flags`, that can be `0` or `1` that encode whether each metal element is included in the network. These are given in the order: C, N, O, Ne, Mg, Si, S, Ca, Fe. Note that H and He are always included in the network. If no `element_flags` array is given to the function, then it defaults to the primordial network with only H and He, i.e. with all metal elements switched off.
`create_reduced_` `inverse_chimes_` `dictionary(` `element_flags =` `np.zeros(9))`	Creates the inverse dictionary, i.e. mapping the species position in the CHIMES abundance array to the corresponding species name, when using a reduced CHIMES network, i.e. when some of the elements have been switched off. It takes as an optional argument an array of integers of length 9, `element_flags`, that encode which elements are included in the network (see above for details).
`read_chimes(` `filename,` `chimes_species,` `chimes_dataset =` `"PartType0/` `Abundances")`	Takes the HDF5 snapshot file specified by `filename` and reads the abundances of the species given by the string `chimes_species`. The optional argument `chimes_dataset` gives the name of the dataset in the HDF5 snapshot file containing the 2-dimensional CHIMES abundance array. If this is not specified by the User, it defaults to `PartType0/ChimesAbundances`. Returns a 1-dimensional array containing the abundance of `chimes_species` for each gas particle in the snapshot. This routine assumes that we are using the full CHIMES network.
`read_reduced_` `chimes(filename,` `chimes_species,` `chimes_dataset =` `"PartType0/` `Abundances",` `element_flags =` `np.zeros(9))`	As `read_chimes()`, but for when we are using a reduced network, i.e. with some of the elements switched off. The `filename`, `chimes_species` and `chimes_dataset` arguments are as described above. The optional `element_flags` argument gives an array of integers that encode which elements are included in the reduced network. See the `create_reduced_chimes_dictionary()` description above for details. If this is not specified by the User, it defaults to the primordial network with only H and He, i.e. with all metal elements switched off.