Running an isolated galaxy with all available COLIBRE physics. The default ICs for the colibre examples is the M5_disk.hdf5 IC file. This IC file is the default, there are also lower resolution files. The ICs are setup in such a way that they are setup using a assumed softening for the disk, the default runs are run without bulge as this causes a less strong ring formation in the stars and gas. Besides this the files contain a star formation history for the stars. Before we did not have old stars with an age. Now the ICs are setup such that the stars within 2.5 scale radii of the disk and not farther away than 1 kpc from the disk have a stellar age that is uniformly distributed over the last 100 Myr with a star formation rate of 10 Msun/yr for the default run. This means that some stars in this region still have an age of -1, given that the total stellar mass in the galaxy is not formed in the last 100 Myr alone. The default IC at different resolutions: Name IC file: eps: Mgas & Mstar: SFR init: M5_disk.hdf5 (fid) 0.2 (kpc) 10^5 Msun 10 Msun/yr M6_disk.hdf5 0.4 (kpc) 8*10^5 Msun 10 Msun/yr M4_disk.hdf5 0.1 (kpc) 10^5/8 Msun 10 Msun/yr The same galaxy with a lower gas fraction of 10%: Name IC file: eps: Mgas & Mstar: SFR init: M5_disk_f10.hdf5 0.2 (kpc) 10^5 Msun 10/3 Msun/yr M6_disk_f10.hdf5 0.4 (kpc) 8*10^5 Msun 10/3 Msun/yr M4_disk_f10.hdf5 0.1 (kpc) 10^5/8 Msun 10/3 Msun/yr The same galaxy with a higher gas fraction of 90%: Name IC file: eps: Mgas & Mstar: SFR init: M5_disk_f90.hdf5 0.2 (kpc) 10^5 Msun 30 Msun/yr M6_disk_f90.hdf5 0.4 (kpc) 8*10^5 Msun 30 Msun/yr M4_disk_f90.hdf5 0.1 (kpc) 10^5/8 Msun 30 Msun/yr Galaxies with different sizes (only at M5 resolution): Name IC file: Rdisk SFR M5_disk.hdf5 (fid) 4.0 kpc 10 Msun/yr M5_disk_compact.hdf5 2.0 kpc 10 Msun/yr M5_disk_diffuse.hdf5 8.0 kpc 10 Msun/yr These can be downloaded by editing the getIC.sh script. It is possible for me (Folkert) to generate new/modified ICs if necessary. By default the ICs are run with the overwrite_birth_time=0, such that the star formation histories are used. Recommendation when running isolated galaxies: Because the isolated galaxies are idealized setups the start of the simulation is not yet in equilibrium, for the inner region of the galaxy it is easier to reach equilibrium quickly in the galaxy, lets say around 100 Myr in the simulation. However for the lower density regions in the isolated galaxies it takes longer around 300 Myr for every feature at densities of 10^-2 cm^-3 to be completely gone. As a default we therefore by use a simulation time of 500 Myr. Softenings: It is important to use the appropriate softening in your runs, given that using a very small softening can cause unexpected crashes in the hydro and a too large softening can cause artificial ring formation around the center because gravity in that case gets softened too much at the center. --------------------------------------------------------------------- Running with old ICs if desired: Set the overwrite_birth_time to 1 instead of 0. 1) uncomment the relevant line in getIC.sh and run it 2) change the InitialConditions:file_name to the file that should be used 3) use a reasonable softening length for - Gravity:max_physical_baryon_softening - HernquistPotential:epsilon Suggested values for both are: fid.hdf5 0.2 lowres8.hdf5 0.4 lowres64.hdf5 0.8 lowres512.hdf5 1.6 --------------------------------------------------------------------- Recommended config option: ./configure --with-subgrid=COLIBRE --with-hydro=sphenix --with-kernel=wendland-C2 --with-ext-potential=hernquist --with-tbbmalloc --enable-ipo Other tested config options using different kernels: ./configure --with-subgrid=COLIBRE --with-hydro=sphenix --with-kernel=quintic-spline --with-ext-potential=hernquist --with-tbbmalloc --enable-ipo ./configure --with-subgrid=COLIBRE --with-hydro=sphenix --with-kernel=quartic-spline --with-ext-potential=hernquist --with-tbbmalloc --enable-ipo An isolated galaxy can also be run with other hydrodynamic schemes but we recommend to run with the sphenix scheme with a quintic-spline. The code can also be run with additional debug checks like: --enable-debug --enable-debugging-checks (code becomes slower) --disable-optimization (code becomes significanlty slower) --------------------------------------------------------------------- Plotting routines: face_on.py: uses py-sphviewer to create face on view of the galaxy and overplots the positions of HII regions left panel: total gas density (greyscale) and positions of HII region particles right panel: HII regions SPH smoothed (red) creates one plot for each output! plotindivHIIregions.py: plots some properties of all HII regions in the current snapshot creates one plot for each output! plot_phasespace.py: compares the density - temperature space for the hydro variables as well as the subgrid properties left panel: temperature and density as used by the hydro solver right panel: for particles close to and below the EOS the subgrid temperature and density differs from the hydro properties; the rgb colors refer to the hydrogen composition as indicated creates one plot for each output! plot_small_HII.py: face on view of the galaxy for HII model testing left panel: young stars that create HII regions (red) and gas particles that are in HII regions (grey) right panel: young star particles that create HII regions color coded by the number of gas particles they could ionize creates one plot for each output! plotSolution.py: argument: snapshot number produces an overview of different galaxy properties (mostly related to SF), needs to be better adapted to the COLIBRE models