This package includes scripts and tools for generating grids for use by the synthesizer synthetic observations package. There are two main modules: scripts for creating incident grids (grids containing the theoretical spectra produced by a model) and scripts for creating cloudy input files and then combining them to form a synthesizer grid.
To use synthesizer-grids you'll first need to install it. To do this you can simply invoke the following at the root of the repo.
pip install .This will install all submodules containing tools needed by the grid generation scripts.
The first thing we need to do is create an incident grid. In some contexts this may be all you will need.
Unfortunately, since SPS codes adopt heterogenous approaches to everything the code for generating synthesizer incident grids is equally heterogenous. However, many helper tools are provided to standardise the process as much as possible. The result of running any of the generation scripts will be a standardised output file that can be further processed (e.g. by cloudy) or used within synthesizer.
The generation scripts can be found within src/synthesizer-grids/incident with sub-directories for each type of model (e.g. sps or blackholes). These generation scripts all take command line arguments. These commandline arguments can be seen by running the script with the help flag.
python <script>.py --helpMost models only take the standard arguments, but others can include other options. Here is an example --help output from the BC03 SPS model containing the default arguments.
usage: install_bc03.py [-h] --grid_dir GRID_DIR [--input_dir INPUT_DIR] [--download]
BC03 download and grid creation
options:
-h, --help show this help message and exit
--grid_dir GRID_DIR The grid file path
--input_dir INPUT_DIR The input file path
--download, -d Should the data be downloaded?Note that all scripts will only download the data needed for the model if the download flag is set. This means the data need only be downloaded once for each model.
In the cloudy/ directory are scripts to create cloudy input scripts and then process them to create synthesizer grids. There are two steps:
There are two approaches to creating cloudy input grids, using an incident grid (for example from an SPS model as above) or generating the grid using a cloudy shape command (e.g. blackbody). These scearnios are handled by two separate modules.
To create an input grid, we run make_cloudy_input_grid.py. This takes the following arguments:
-synthesizer_data_dir: The directory containing both the cloudy runs (cloudy/) and grids (grids/). Note by default new grids are placed in synthesizer_data_dir/grids/dev/.
-m (--machine): the type of HPC on which you are running. If not provided, no submission script will be written.
-incident_grid: The name of the synthesizer incident grid on which you wish to run cloudy.
-cloudy_params: the YAML file containing cloudy parameters for modelling. See the examples for more details. These can be single values or arrays resulting in the creating of higher-dimensionality grids. Also included is the cloudy version.
-cloudy_path: the path to the cloudy directory. Note this is not the path to executable. This was done to allow multiple versions of cloudy to exist simultanously.
As an alternative we can create a grid directly from using one of cloudy's in-built shape commands (e.g. blackbody). To do this we need to provide a yaml file containing the name of the model (at the moment this is limited to blackbody and agn) with all the parameters, including any that are to be varied as a list.
This contains the parameters that will be input into CLOUDY.
Users can provide arrays/lists of parameters they wish to iterate over. In this case, the code will create individual runs for each of the parameters specified, with the following naming convention:
{spsgrid}{imf}cloudy{param}_{value}
where {param} is the key in the param file of the parameter to be varied, and {value} is the value to be provided. If this is numeric, it will be converted to a string, and if it is negative, the '-' will be substituted for 'm'.
Next we need to combine the cloudy ouputs to create a new synthesizer grid. To do this we run create_synthesizer_grid.py. This takes the following arguments:
-synthesizer_data_dir: The directory containing both the cloudy runs (cloudy/) and grids (grids/).
-grid_name: The full grid name.
-include_spectra: Whether to include spectra or just include line properties. Depending on the science context for large grids it might be sensible to not save the full spectra.
-replace: Some models continuously fail. This is a last resort options to instead use the nearest model. I RECOMMEND NEVER SETTING THIS TO TRUE.
-line_calc_method: Change the way line quantities are calculated.
The cloudy directory also includes a script folder apollo_production_scripts/ for processing multiple grids automatically. Essentially there are two scripts, one for creating the cloudy inputs and a second for creating the ultimate synthesizer grids. These loop over the contents of incident.txt and grids.txt to get the input parameters.
These scripts will only work on Sussex's Apollo HPC system. Thus, if you want to use something similar please copy and adapt them as required. If you want them to form part of the package please make a new folder.
Contributions welcome. Please read the contributing guidelines here.