SÍGAME: SImulator of GAlaxy Millimeter/submillimeter Emission (v2)

Jump straigt to the auto-generated code documentation: https://kpolsen.github.io/SIGAME_dev/

Description

This is a code to simulate the emission lines of the ISM in galaxies from hydrodynamical codes for the interpretation and prediction of observations.

Obtaining the SÍGAME code

Clone this repository to an empty folder on your computer by giving the following command in the terminal:

git clone https://github.com/kpolsen/SIGAME_v2.git

OBS: For Linux users! If you're using the terminal, here the commands we found useful so far:

For updating from the master branch:

git pull origin master

When you make changes (before or after), please switch to your own personal branch with a name of your choice:

git branch -b NAME-OF-YOUR-BRANCH

For making a pull request with all your recent changes:

git add .
git commit -m "commmit message"
git push --set-upstream origin NAME-OF-YOUR-BRANCH
git request-pull origin/master NAME-OF-YOUR-BRANCH

where NAME-OF-YOUR-BRANCH is the name of your branch.

Running SÍGAME

All modules of SÍGAME are found in the sigame/ directory and loaded into python with:

import sigame as si

Importing sigame will ask you what redshift you're working at and who you are to set up a path for external large files not tracked by github. To change (or add) the path for your user, go into init.py and edit the relevant part.

Depending on the chosen redshift, a specific paramter file while be loaded and must be supplied with the general parameters for SÍGAME (redshift, resolution of datacubes etc.). See 'parameters_z0.txt' for an example and modify as needed. Whenever you change the parameter file, remember to reload sigame in order to get those changes into the code:

reload(si)

To create datacubes of line emission, you run SÍGAME with the command:

si.run()

which will call the program run() in the sigame/backend.py module. What will be executed depends on what you select at the bottom of the parameter file. For example setting:

+1 extract_galaxy
-1 subgrid
-1 interpolate
-1 datacubes

will only extract, center and cut out the selected model galaxies.

Making changes to SÍGAME modules

If you make changes to a module, say to the function histos() in the sigame/plot.py module, then you can try to load in those changes with:

import sigame.plot as siplot
reload(siplot)

Now you're ready to run e.g. plot.histos() with the changes implemented.

siplot.histos()

This will not always work though, so instead of loading submodules and reloading or exiting and re-entering python, I recommend changing the ipython configuration to reload by default everytime you type a python command. This is done by adding the two following lines to~/.ipython/profile_default/ipython_config.py (create this file if it doesn't exit):

c.InteractiveShellApp.extensions = ['autoreload']
c.InteractiveShellApp.exec_lines = ['%autoreload 2']

For more detail, see this discussion.

Coding rules

SÍGAME is a module under construction that may in the future be prepared for the stand-alone-use by anyone interested. But for the moment, it will only be viewed and used by people of this group, meaning that each has freedom to write functions/modules in the way that they prefer. However, we try to stick to these general rules:

• pull from the master before making edits
• docstrings in numpy format: http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html

... and let me know if you think of overall ways to improve the code! Happy python coding :)

Collaborators (active in developing the code)

Karen Pardos Olsen, kpolsen (at) asu.edu Daisy Leung, Thomas Greve, Lily Whitler, lwhitler (at) asu.edu

References

• 2018: Olsen, K. P., Greve, T. R., Narayanan, D., Thompson, R., Davé, Niebla Rios, L., Stawinsi, S.: "Erratum: SIGAME Simulations of the [CII], [OI], and [OIII] Line Emission from Star-forming Galaxies at z~6 (2018)", ApJ 857 2, ADS link
• 2017: Olsen, K. P., Greve, T. R., Narayanan, D., Thompson, R., Davé, Niebla Rios, L., Stawinsi, S.: "SIGAME Simulations of the [CII], [OI], and [OIII] Line Emission from Star-forming Galaxies at z~6 (2017)", ApJ 846 2, arXiv: 1708.04936
• 2017: Olsen, K. P., Greve, T. R., Brinch, C., Sommer-Larsen, J., Rasmussen, J., Toft, S., Zirm, A.: "SImulator of GAlaxy Millimeter/submillimeter Emission (SIGAME): CO emission from massive z=2 main sequence galaxies", arXiv: 1507.00012
• 2015: Olsen, K. P., Greve, T. R., Narayanan, D., Thompson, R., Toft, S. Brinch, C.: "Simulator of Galaxy Millimeter/Submillimeter Emission (SIGAME): The [CII]-SFR Relationship of Massive z=2 Main Sequence Galaxies", MNRAS 457 3, arXiv: 1507.00362