Parameters and Data Files

Parameters

For all on/off integer flags, 0 is off and 1 is on.

int use_grackle

Flag to activate the grackle machinery. Default: 0.

int with_radiative_cooling

Flag to include radiative cooling and actually update the thermal energy during the chemistry solver. If off, the chemistry species will still be updated. The most common reason to set this to off is to iterate the chemistry network to an equilibrium state. Default: 1.

int primordial_chemistry

Flag to control which primordial chemistry network is used. Default: 0.

  • 0: no chemistry network. Radiative cooling for primordial species is solved by interpolating from lookup tables calculated with Cloudy.
  • 1: 6-species atomic H and He. Active species: H, H+, He, He+, ++, e-.
  • 2: 9-species network including atomic species above and species for molecular hydrogen formation. This network includes formation from the H- and H2+ channels, three-body formation (H+H+H and H+H+H2), H2 rotational transitions, chemical heating, and collision-induced emission (optional). Active species: above + H-, H2, H2+.
  • 3: 12-species network include all above plus HD rotation cooling. Active species: above + D, D+, HD.

Note

In order to make use of the non-equilibrium chemistry network (primordial_chemistry options 1-3), you must add and advect baryon fields for each of the species used by that particular option.

int h2_on_dust

Flag to enable H2 formation on dust grains, dust cooling, and dust-gas heat transfer follow Omukai (2000). This assumes that the dust to gas ratio scales with the metallicity. Default: 0.

int metal_cooling

Flag to enable metal cooling using the Cloudy tables. If enabled, the cooling table to be used must be specified with the grackle_data_file parameter. Default: 0.

Note

In order to use the metal cooling, you must add and advect a metal density field.

int cmb_temperature_floor

Flag to enable an effective CMB temperature floor. This is implemented by subtracting the value of the cooling rate at TCMB from the total cooling rate. Default: 1.

int UVbackground

Flag to enable a UV background. If enabled, the cooling table to be used must be specified with the grackle_data_file parameter. Default: 0.

float UVbackground_redshift_on

Used in combination with UVbackground_redshift_fullon, UVbackground_redshift_drop, and UVbackground_redshift_off to set an attenuation factor for the photo-heating and photo-ionization rates of the UV background model. See the figure below for an illustration its behavior. If not set, this parameter will be set to the highest redshift of the UV background data being used.

float UVbackground_redshift_fullon

Used in combination with UVbackground_redshift_on, UVbackground_redshift_drop, and UVbackground_redshift_off to set an attenuation factor for the photo-heating and photo-ionization rates of the UV background model. See the figure below for an illustration its behavior. If not set, this parameter will be set to the highest redshift of the UV background data being used.

float UVbackground_redshift_drop

Used in combination with UVbackground_redshift_on, UVbackground_redshift_fullon, and UVbackground_redshift_off to set an attenuation factor for the photo-heating and photo-ionization rates of the UV background model. See the figure below for an illustration its behavior. If not set, this parameter will be set to the lowest redshift of the UV background data being used.

float UVbackground_redshift_off

Used in combination with UVbackground_redshift_on, UVbackground_redshift_fullon, and UVbackground_redshift_drop to set an attenuation factor for the photo-heating and photo-ionization rates of the UV background model. See the figure below for an illustration its behavior. If not set, this parameter will be set to the lowest redshift of the UV background data being used.

_images/ramp.png
char* grackle_data_file

Path to the data file containing the metal cooling and UV background tables. Default: “”.

float Gamma

The ratio of specific heats for an ideal gas. A direct calculation for the molecular component is used if primordial_chemistry > 1. Default: 5/3.

int three_body_rate

Flag to control which three-body H2 formation rate is used.

The first five options are discussed in Turk et. al. (2011). Default: 0.

int cie_cooling

Flag to enable H2 collision-induced emission cooling from Ripamonti & Abel (2004). Default: 0.

int h2_optical_depth_approximation

Flag to enable H2 cooling attenuation from Ripamonti & Abel (2004). Default: 0.

int photoelectric_heating

Flag to enable a spatially uniform heating term approximating photo-electric heating from dust from Tasker & Bryan (2008). Default: 0.

int photoelectric_heating_rate

If photoelectric_heating enabled, the heating rate in units of erg cm-3 s-1. Default: 8.5e-26.

int Compton_xray_heating

Flag to enable Compton heating from an X-ray background following Madau & Efstathiou (1999). Default: 0.

float LWbackground_intensity

Intensity of a constant Lyman-Werner H2 photo-dissociating radiation field in units of 10-21 erg s-1 cm-2 Hz-1 sr-1. Default: 0.

int LWbackground_sawtooth_suppression

Flag to enable suppression of Lyman-Werner flux due to Lyman-series absorption (giving a sawtooth pattern), taken from Haiman & Abel, & Rees (2000). Default: 0.

int use_volumetric_heating_rate

Flag to signal that an array of volumetric heating rates is being provided in the volumetric_heating_rate field of the grackle_field_data struct. Default: 0.

int use_specific_heating_rate

Flag to signal that an array of specific heating rates is being provided in the specific_heating_rate field of the grackle_field_data struct. Default: 0.

use_radiative_transfer

Flag to signal that arrays of ionization and heating rates from radiative transfer solutions are being provided. Only available if primordial_chemistry is greater than 0. HI, HeI, and HeII ionization arrays are provided in RT_HI_ionization_rate, RT_HeI_ionization_rate, and RT_HeII_ionization_rate fields, respectively, of the grackle_field_data struct. Associated heating rate is provided in the RT_heating_rate field, and H2 photodissociation rate can also be provided in the RT_H2_dissociation_rate field when primordial_chemistry is set to either 2 or 3. Default: 0.

radiative_transfer_coupled_rate_solver

Flag that must be enabled to couple the passed radiative transfer fields to the chemistry solver. Default: 0.

radiative_transfer_intermediate_step

Flag to enable intermediate stepping in applying radiative transfer fields to chemistry solver. Default: 0.

radiative_transfer_hydrogen_only

Flag to only use hydrogen ionization and heating rates from the radiative transfer solutions. Default: 0.

H2_self_shielding

Switch to enable approximate H2 self-shielding from both the UV background dissociation rate and the H2 dissociation rate given by RT_H2_dissociation_rate (if present). This is a Sobolev-like, spherically averaged method from Wolcott-Green et. al. 2011 and is only valid for Cartesian grid codes in 3D. Default: 0.

self_shielding_method

Switch to enable approximate self-shielding from the UV background. All three of the below methods incorporate Eq. 13 and 14 from Rahmati et. al. 2013. These equations involve using the spectrum averaged photoabsorption cross for the given species (HI or HeI). These redshift dependent values are pre-computed for the HM2012 and FG2011 UV backgrounds and included in their respective cooling data tables. Care is advised in using any of these methods. Default: 0.

  • 0: No self shielding. Elements are optically thin to the UV background.
  • 1: Approximate self-shielding in HI only. HeI and HeII are left
    as optically thin.
  • 2: Approximate self-shielding in both HI and HeI. HeII remains
    optically thin.
  • 3: Approximate self-shielding in both HI and HeI, but ignoring
    HeII ionization and heating from the UV background entirely (setting HeII rates to zero).

These methods only work in conjunction with using updated Cloudy cooling tables, denoted with “_shielding”. These tables properly account for the decrease in metal line cooling rates in self-shielded regions, which can be significant.

int omp_nthreads

Sets the number of OpenMP threads. If not set, this will be set to the maximum number of threads possible, as determined by the system or as configured by setting the OMP_NUM_THREADS environment variable. Note, Grackle must be compiled with OpenMP support enabled. See Running with OpenMP.

Data Files

All data files are located in the input directory in the source.

The first three files contain the heating and cooling rates for both primordial and metal species as well as the UV background photo-heating and photo-ionization rates. For all three files, the valid density and temperature range is given below. Extrapolation is performed when outside of the data range. The metal cooling rates are stored for solar metallicity and scaled linearly with the metallicity of the gas.

Valid range:

  • number density: -10 < log10 (nH / cm-3) < 4
  • temperature: the temperature range is 1 < log10 (T / K) < 9.

Data files:

  • CloudyData_noUVB.h5 - cooling rates for collisional ionization equilibrium.
  • CloudyData_UVB=FG2011.h5 - heating and cooling rates and UV background rates from the work of Faucher-Giguere et. al. (2009), updated in 2011. The maxmimum redshift is 10.6. Above that, collisional ionization equilibrium is assumed.
  • CloudyData_UVB=HM2012.h5 - heating and cooling rates and UV background rates from the work of Haardt & Madau (2012). The maximum redshift is 15.13. Above that, collisional ionization equilibrium is assumed.

To use the self-shielding approximation (see self_shielding_method), one must properly account for the change in metal line cooling rates in self-shielded regions. Using the optically thin tables described above can result in an order of magnitude overestimation in the net cooling rate at certain densities. We have re-computed these tables by constructing Jeans-length depth models in Cloudy at each density - temperature pair, tabulating the cooling and heating rates from the core of each of these clouds. These models enforce a maximum depth of 100 pc. In addition, these tables contain the spectrum averaged absorption cross sections needed for the Rahmati et. al. 2013 self-shielding approximations. Currently only the HM2012 table has been recomputed.

  • CloudyData_UVB=HM2012_shielded.h5 - updated heating and cooling rates with the HM2012 UV background, accounting for self-shielding.

The final file includes only metal cooling rates under collisional ionization equilibrium, i.e., no incident radiation field. This table extends to higher densities and also varies in metallicity rather than scaling proportional to the solar value. This captures the thermalization of metal coolants occuring at high densities, making this table more appropriate for simulations of collapsing gas-clouds.

Valid range:

  • number density: -6 < log10 (nH / cm-3) < 12
  • metallicity: -6 < log10 (Z / Zsun) < 1
  • temperature: the temperature range is 1 < log10 (T / K) < 8.

Data file:

  • cloudy_metals_2008_3D.h5 - collisional ionization equilibrium, metal cooling rates only.