Detailed Description of Parameters

There are two parameters files - parameters_master and parameters_model. The distinction between where a parameter goes is somewhat arbitrary, but is based on the following. Parameters_master tends to contain parameters that will likely be shared amongst all snapshots in a given galaxy run, while parameters_model are parameters that might change from run to run (like the snapshot name or the galaxy center).

The parameters files are (somewhat non-traditionally) written as python code files because this enables you to embed little snippets in them that may be particular to your galaxy run. For example, for gadget snapshot naming conventions, it can be useful to have a snippet along the lines of:

snapshot_num = 20
snapnum_str = '{:03d}'.format(snapshot_num)

snapshot_name = 'snapshot_'+snapnum_str+'.hdf5'

That ensures a 3 digit snapshot number, common to many gadget-style simulations.

parameters_master

Resolution Keywords

oref:Over Refinement of the Octree. For particle-based codes, 1 means each data holding cell (a False) gets refined one additional time, even after the octree refinement criteria has stopped. Very heavy on the memory but can enable higher pixel resolution for images. Default is 0.
n_ref:Refinement criteria for octree refinement for particle-based codes. This is the threshold number of particles to refine over. When nparticles > n_ref the octree refines further. Default is 64.
zoom_box_len:Side length to zoom in on. Is +/- zoom_box_len from the center. Units are proper kpc. So, a grid centered on [0,0,0] with zoom_box_len = 200 would extend from [-200,200] kpc in physical units at the redshift of the simulation.
bbox_lim:Initial bounding box of grid for particle simulations (+/- bbox_lim). Units are kpc. This must encompass all of the particles in a simulation currently. This just has to be a big number, but you want to be careful of making too large as precision limitations only allow for up to 20 levels of refinement.

Parallelization

n_processes:Number of pool processes to run the radiative transfer on. Note, the stellar population synthesis will only run on as many processors as are on a core since its parallelization is pool.map (not MPI)
n_MPI_processes:
 Number of MPI tasks to run. For TORQUE this is best set as the same as n_processes, while for SLURM this may not be the case.

RT Information

For all photon counts, a decent rule of thumb is 10-100x the number of grid cells that you have, though of course you should check the convergence properties of your simulation.

n_photons_initial:
 Number of photons to use in main iterations (for the whole grid) for specific energy and temperature calculations.
n_photons_imaging:
 Number of photons to use for the SED/image calculation
n_photons_raytracing_sources:
 If raytracing is set (which is the default hard-coded into the code), number of raytracing photons to use for source emission.
n_photons_raytracing_dust:
 Similar to n_photons_raytracing_sources but for dust emission.
FORCE_RANDOM_SEED:
 Boolean. True means the seed specified below will be used for random number generation in the Hyperion model. False means no seed will be set.
seed:The seed with which to initialize random number generation in Hyperion. Must be a negative integer.

Dust Information

dustdir:

String. Path to where your dust files are. String format - (e.g. ‘/home/desika/hyperion-dust-0.1.0/dust_files/’)

dustfile:

String. Name of your main dust file. String format - (e.g. ‘d03_3.1_6.0_A.hdf5’)

PAH:

Boolean - True means use model for PAHs, False means don’t.

dust_grid_type:

String that is of one of the following values: [‘dtm’,’rr’,’manual’,’li_bestfit’] that designates how we will determine the dust density in each octree grid cell. The choices are:

dtm:

A constant dust to metals ratio set by the keyword dusttometals_ratio

rr:

Follows the best fit relation from Remy Ruyer 2014A&A…563A..31R powerlaw relation between the the gas to dust ratio and metallicity (in which Xco is allowed to vary with the metallicity as well).

manual:

Looks for a dust mass associated with the hydrodynamic simulation (i.e. if the hydrodynamic simulation carries dust information with it, as some flavors of gizmo and arepo do). For gizmo and arepo currently assumes this information is stored in PartType0.

li_bestfit:

Takes the best fit relation from the cosmological simulations of Li, Narayanan & Dave 2019 (MNRAS, 490, 1425) that relates the dust to gas ratio to the metallicity for main sequence galaxies. note - this applies galaxy integrated properties to individual cells for the radiative transfer simulations.

li_ml:

Uses a the Extreme Randomized Trees learning algorithm from the aforementioned Li, Narayanan & Dave 2019 paper to predict the dust content based on the physical properties of the gas. The algorithm here is modified from the original LND2019 paper in that it is trained on particles, as opposed to the aggregated properties of galaxies.

Note, for this algorithm to work, one needs to download the training set datafile (a z=0 snapshot from the Simba cosmological simulation: Dave et al. 2019, MNRAS, 486, 282) and place it in the directory powderday/mlt. This snapshot is located here: https://www.astro.ufl.edu/~desika.narayanan/powderday_files

dusttometals_ratio:
 

Dust mass to metals mass ratio

enforce_energy_range:
 

Boolean. False ensures energy conservation. But the emisivities may not be strictly correct if the energy in a cell is out of range of the emissivities. True modifies the energy in the simulation, but ensures that the emissivities are consistent with the energy. See: <http://docs.hyperion-rt.org/en/latest/api/hyperion.model.Model.html?highlight=enforce#hyperion.model.Model.set_enforce_energy_range>

SUBLIMATION:

Boolean. If true, dust grains above the sublimation temperature are automatically killed. Fast mode is to set this to False.

SUBLIMATION_TEMPERATURE:
 

The temperature in Kelvin above which dust grains are automatically killed. Meaningless if SUBLIMATION == False.

Hydro Code Units

Currently these are actually not used in powderday). They remain in the parameters file as a placeholder though as we may need them as an over-ride if we find some HDF5 files don’t contain this information.

unit_mass:Mass code units for galaxy simulation. Units: Msun/h
unit_length:Length code unit for galaxy simulation. Units: kpc/h
unit_age:Stellar age units. Units: Gyr/h
unit_velocity:Velocity code unit for galaxy simulation. Units: cm/s

Stellar SEDs Info

Force_BINNED:

Boolean. True means force binning of the stellar SEDs (in bins of age and metallicity). False means don’t.

direct_add_stars:
 

Boolean. If True, since star particles below max_age_direct (next parameter) are individually represented in the stellar SED as opposed to broken up into bins. Note: This can be slow to run, and hard on the memory.

max_age_direct:

Age (in Gyr) below which star particles will not be binned for getting stellar SEDs (works only if both FORCE_BINNED and direct_add_stars is set to True)

imf_type:

IMF parameter for stellar pops calculations.

  1. Salpeter
  2. Chabrier
  3. Kroupa
  4. Van Dokkum
  5. Dave

Though note options 3 and 4 are currently not supported.

pagb:

Weight given to post AGB stars. 1 is the default.

Nebular Emission Info

add_neb_emission:
 

Boolean. If set to True, nebular line emission from Cloudy lookup tables (dev. by Nell Byler) will be added.

add_agb_dust_model:
 
use_cloudy_tables:
 

If True, CLOUDY look up tables will be used to calculate nebular emission. Otherwise CLOUDY models are generated individually for each young star particle (under active development)

FORCE_gas_logu:

If set, then we force the ionization parameter (gas_logu) of HII regions to be gas_logu (next parameter) else, it is taken to be variable and dependent on ionizing radiation from star particles. (Default: False)

gas_logu:

Gas ionization parameter for HII regions. This is only relevant if add_neb_emission is set to True and FORCE_gas_logu is set to True (Default: -2.0)

gas_logu_init:

Force the ionization parameter to increase/decrease by this value (Scale: log). Useful if you want to run tests (Default: 0.0)

FORCE_gas_logz:

If set, then we force the metallicity (gas_logz) of HII regions to be gas_logz (next parameter) else, it is taken to be the star particle’s metallicity. (Default: False)

gas_logz:

Metallicity of the HII region in units of log(Z/Z_sun) only relevant if add_neb_emission = True and FORCE_gas_logz = True (Default: 0.0)

FORCE_logq:

If set, then we force the number of ionizing photons to be source_logq (next parameter) else, it is taken to be variable and dependent on ionizing radiation from star particles. (Default: False)

source_logq:

The number of ionizing photons emitted by the source in units of s^-1. Only relevant if add_neb_emission = True, use_cloudy_tables = True and FORCE_gas_logq = True (Default: 1.e47)

FORCE_inner_radius:
 

If set, then we force the inner radius of the cloud to be inner_radius (next parameter) else, it is taken to be the Stromgren sphere radius. (Default: False)

inner_radius:

This sets the inner radius of the cloud in cm. This is used only when add_neb_emission = True, use_cloudy_tables = True and FORCE_inner_radius = True (Default: 1.e19)

neb_abund:

This sets the HII region elemental abundances for generating CLOUDY models. Available abundances are:

dopita:Abundabces from Dopita (2001) with old solar abundances = 0.019 and ISM grains.
newdopita:Abundances from Dopita (2013). Solar Abundances from Grevasse 2010 - z= 0.013 includes smooth polynomial for N/O, C/O relationship functional form for He(z), new depletion and factors in ISM grains.
gutkin:Abundances from Gutkin (2016) and PARSEC metallicity (Bressan+2012) based on Grevesse+Sauvel (1998) and Caffau+2011
direct:Abundances are taken directly from the simulation if possible. Defaults to using “dopita” if there is an error. (Note: Works only for star particles that are added directly without binning. Make sure to set direct_add_stars to True)

This is used only when add_neb_emission = True and use_cloudy_tables = True. (Default: dopita)

use_Q:

If True, we run CLOUDY by specifying the number of ionizing photons that are calculated based on the input sed and the inner radius which is set to the Strömgren radius. else, CLOUDY is run by specifying just the ionization parameter.Only relevant if add_neb_emission = True and use_cloudy_tables = True (Default: True)

HII_T:

Ionized gas temperature in K for calculating nebular emission. (Default = 1.e4)

HII_nh:

Gas hydrogen density for calcualting nebular emission in units if cm^-3. (Default = 1.e2)

HII_max_age:

Sets the maximum age limit for calculating nebular emission in units of Gyr. (Default = 1.e-2)

neb_dust:

If True dust is included in HII regions when calculating nebular emission. (Default = False)

HII_escape_fraction:
 

HII region escape fraction (Default = 0.0)

cmdf_min_mass:

While calulating nebular emission one star particle is broken down into smaller star cluster by assuming a cluster mass distribution function of the form dN/dM goes as M^(-2.0). This parameter sets the minimum mass of the star clusters in units of log(Msun). Note this value should not be set lower than 3.5. (Default = 3.5)

cmdf_max_mass:

Minimum mass of the star clusters in units of log(Msun). (Default = 5.0)

cmdf_bins:

The number of bins used for calulating the cluster mass distribution function (Default = 6.0)

cdmf_beta:

The power law exponent (beta) for calculating CMDF (dN/dM goes as M^(beta))

neb_file_output:
 

If set to True creates an output file with ionization parameter (LogU), number of ionizing photons (LogQ), inner radius, stellar mass, age and metallicity(zmet) for each particle. (Default: True)

stellar_cluster_mass:
 

Mass of star clusters in Msun (Default = 1.e4)

cloudy_cleanup:

If set to True, all the CLOUDY files will be deleted after the source addition is complete. This is used only when add_neb_emission = True and use_cloudy_tables = True. Note that in case an error occurs, the files are not deleted even if this value is set to True. (Default: True)

CF_on:

Boolean. If set to True, then enables the Charlot & Fall birthcloud models for all stars with age younger than birth_cloud_clearing_age.

birth_cloud_clearing_age:
 

Stars with age < birth_cloud_clearing_age have Charlot & Fall birthclouds (if CF_on == True). Meaningless if CF_on == False. Units: Gyr.

Z_init:

Forced metallicity increase in the newstar particles. Useful for idealized galaxy simulations where the stars can form out of pristine gas. Units are absolute (so 0.02 = Solar). Setting to 0 (default) means that you use the stellar metallicities as they come in the simulation (i.e. for Cosmological simulations).

disk_stars_age:

Age in Gyr of disk stars for idealized simulations. Meaningless for cosmological simulations. Note, if this is <=7, then these will live in Charlot & Fall birthclouds (if CF_on = True).

Note, for Gadget simulations, stars are divided into newstars, disk stars and bulge stars. For Tipsy outputs, the stars initalized with the simulation are auto-detected by their nonsensical ages, and assigned as disk stars. So, if there are stars initalized with your Tipsy simulation, assign their ages (and metallicities below) as disk stars.

bulge_stars_age:
 

As disk_stars_age but for bulge stars.

disk_stars_metals:
 

Metallicity of disk stars in FSPS metallicity units. See last page of FSPS manual for numbers. (e.g. 20 = Solar for Padova + BaSeL tracks). Meaningless for cosmological simulations.

bulge_stars_metals:
 

As disk_stars_metals but for bulge stars.

N_STELLAR_AGE_BINS:
 

Number of bins to bin the stellar ages in (boundaries are the oldest and youngest star particles; linear bins in log(age)).

N_MASS_BINS:

Meaningless parameter; place holder for future code additions.

metallicity_legend:
 

String. Location of the metallicity maps in FSPS for the stellar libraries you use. Currently Padova2007 is the default (hard coded into powderday), so this should point to something like: “/Users/desika/fsps/ISOCHRONES/Padova/Padova2007/zlegend_basel.dat”

Black Holes

BH_SED:If true, powderday will attempt to load black hole information from the snapshot.
BH_eta:Used in calculating the black hole luminosity (bhluminosity = BH_eta * mdot * c**2.)
BH_model:BH model type, either Nenkova or other.
BH_modelfile:The path to the Nenkova model file if BH_model is set to Nenkova. This file can be downloaded here and placed anywhere in the repository, as long as the correct path is set in parameters_master: <https://www.clumpy.org/downloads/clumpy_models_201410_tvavg.hdf5>
nenkova_params:Nenkova+ (2008) model parameters.

Images and SED Parameters

NTHETA:

Number of polar angles to view galaxy at

IMAGING:

Must be set to True for powderday to produce an image output file.

filterdir:

Directory where filter files are stored. They should be located in “/home/desika/powderday/filters/”.

filterfiles:

A list of the names of all filters to be used. powderday will run at each wavelength in all specified filter files, and will produce a .hdf5 file containing images convolved with each filter transmission function. Note that this can be quite computationally intensive and scales with the number of wavelengths. Following the example in parameters_master, additional filters can be added to this list. In bash, cd into your filterdir and use the following command to format the filenames for easy copying and pasting into this list.

>>> shopt -s globstar; printf "#    '%s'\n" *.filter
IMAGING_TRANSMISSION_FILTER:
 

If enabled, filter convolution will be performed through Hyperion instead of through powderday. This is much faster, but is still an experimental feature and does not seem to produce accurate convolved images.

DEBUGGING

You should probably never touch any of these.

parameters_model

snapshot_name:String - currently the snapshot name of your galaxy run. (Naming will change as other front ends built).
hydro_dir:Location of snapshots
PD_output_dir:String - location of where powderday output files should go.
Auto_TF_file:String - name of the TF logical file to be written (doesn’t need a path - will go into PD_output_dir)
Auto_dustdens_file:
 String - name of the dust density ascii file to be written (doesn’t need a path - will go into PD_output_dir)
inputfile:String - name of the input HDF5 (rtin) file for powderday to write before radiative transfer begins.
outputfile:String - name of the output HDF5 (rtout) file after radiative transfer
x_cent:Location in grid coordinates of the x-coordinate of the center of your galaxy. Only pertinenet if MANUAL_CENTERING==True. Otherwise ignored by powderday.
y_cent:As x_cent but for the y-coordinate
z_cent:As x_cent but for the z-coordinate.