.. _parameters: Parameters and Data Files ========================= Parameters ---------- For all on/off integer flags, 0 is off and 1 is on. .. c:var:: int use_grackle Flag to activate the grackle machinery. Default: 0. .. c:var:: 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. .. c:var:: 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\ :sup:`+`, He, He\ :sup:`+`, \ :sup:`++`, e\ :sup:`-`. - 2: 9-species network including atomic species above and species for molecular hydrogen formation. This network includes formation from the H\ :sup:`-` and H\ :sub:`2`\ :sup:`+` channels, three-body formation (H+H+H and H+H+H\ :sub:`2`), H\ :sub:`2` rotational transitions, chemical heating, and collision-induced emission (optional). Active species: above + H\ :sup:`-`, H\ :sub:`2`, H\ :sub:`2`\ :sup:`+`. - 3: 12-species network include all above plus HD rotation cooling. Active species: above + D, D\ :sup:`+`, HD. .. note:: In order to make use of the non-equilibrium chemistry network (:c:data:`primordial_chemistry` options 1-3), you must add and advect baryon fields for each of the species used by that particular option. .. c:var:: int h2_on_dust Flag to enable H\ :sub:`2` 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. .. c:var:: 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 :c:data:`grackle_data_file` parameter. Default: 0. .. note:: In order to use the metal cooling, you must add and advect a metal density field. .. c:var:: int cmb_temperature_floor Flag to enable an effective CMB temperature floor. This is implemented by subtracting the value of the cooling rate at T\ :sub:`CMB` from the total cooling rate. Default: 1. .. c:var:: int UVbackground Flag to enable a UV background. If enabled, the cooling table to be used must be specified with the :c:data:`grackle_data_file` parameter. Default: 0. .. c:var:: float UVbackground_redshift_on Used in combination with :c:data:`UVbackground_redshift_fullon`, :c:data:`UVbackground_redshift_drop`, and :c:data:`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. .. c:var:: float UVbackground_redshift_fullon Used in combination with :c:data:`UVbackground_redshift_on`, :c:data:`UVbackground_redshift_drop`, and :c:data:`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. .. c:var:: float UVbackground_redshift_drop Used in combination with :c:data:`UVbackground_redshift_on`, :c:data:`UVbackground_redshift_fullon`, and :c:data:`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. .. c:var:: float UVbackground_redshift_off Used in combination with :c:data:`UVbackground_redshift_on`, :c:data:`UVbackground_redshift_fullon`, and :c:data:`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. .. image:: _images/ramp.png :width: 300 .. c:var:: char* grackle_data_file Path to the data file containing the metal cooling and UV background tables. Default: "". .. c:var:: float Gamma The ratio of specific heats for an ideal gas. A direct calculation for the molecular component is used if :c:data:`primordial_chemistry` > 1. Default: 5/3. .. c:var:: int three_body_rate Flag to control which three-body H\ :sub:`2` formation rate is used. - 0: `Abel, Bryan & Norman (2002) `_ - 1: `Palla, Salpeter & Stahler (1983) `_ - 2: `Cohen & Westberg (1983) `_ - 3: `Flower & Harris (2007) `_ - 4: `Glover (2008) `_ - 5: `Forrey (2013) `_. The first five options are discussed in `Turk et. al. (2011) `_. Default: 0. .. c:var:: int cie_cooling Flag to enable H\ :sub:`2` collision-induced emission cooling from `Ripamonti & Abel (2004) `_. Default: 0. .. c:var:: int h2_optical_depth_approximation Flag to enable H\ :sub:`2` cooling attenuation from `Ripamonti & Abel (2004) `_. Default: 0. .. c:var:: int photoelectric_heating Flag to enable a spatially uniform heating term approximating photo-electric heating from dust from `Tasker & Bryan (2008) `_. Default: 0. .. c:var:: int photoelectric_heating_rate If :c:data:`photoelectric_heating` enabled, the heating rate in units of erg cm\ :sup:`-3` s\ :sup:`-1`. Default: 8.5e-26. .. c:var:: int Compton_xray_heating Flag to enable Compton heating from an X-ray background following `Madau & Efstathiou (1999) `_. Default: 0. .. c:var:: float LWbackground_intensity Intensity of a constant Lyman-Werner H\ :sub:`2` photo-dissociating radiation field in units of 10\ :sup:`-21` erg s\ :sup:`-1` cm\ :sup:`-2` Hz\ :sup:`-1` sr\ :sup:`-1`. Default: 0. .. c:var:: 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. .. c:var:: int use_volumetric_heating_rate Flag to signal that an array of volumetric heating rates is being provided in the :c:data:`volumetric_heating_rate` field of the :c:data:`grackle_field_data` struct. Default: 0. .. c:var:: int use_specific_heating_rate Flag to signal that an array of specific heating rates is being provided in the :c:data:`specific_heating_rate` field of the :c:data:`grackle_field_data` struct. Default: 0. .. c:var:: use_radiative_transfer Flag to signal that arrays of ionization and heating rates from radiative transfer solutions are being provided. Only available if :c:data:`primordial_chemistry` is greater than 0. HI, HeI, and HeII ionization arrays are provided in :c:data:`RT_HI_ionization_rate`, :c:data:`RT_HeI_ionization_rate`, and :c:data:`RT_HeII_ionization_rate` fields, respectively, of the :c:data:`grackle_field_data` struct. Associated heating rate is provided in the :c:data:`RT_heating_rate` field, and H2 photodissociation rate can also be provided in the :c:data:`RT_H2_dissociation_rate` field when :c:data:`primordial_chemistry` is set to either 2 or 3. Default: 0. .. c:var:: radiative_transfer_coupled_rate_solver Flag that must be enabled to couple the passed radiative transfer fields to the chemistry solver. Default: 0. .. c:var:: radiative_transfer_intermediate_step Flag to enable intermediate stepping in applying radiative transfer fields to chemistry solver. Default: 0. .. c:var:: radiative_transfer_hydrogen_only Flag to only use hydrogen ionization and heating rates from the radiative transfer solutions. Default: 0. .. c:var:: H2_self_shielding Switch to enable approximate H\ :sub:`2`\ self-shielding from both the UV background dissociation rate and the H\ :sub:`2`\ dissociation rate given by :c:data:`RT_H2_dissociation_rate` (if present). Three options exist for the length scale used in calculating the H\ :sub:`2`\ column density. Default: 0. - 1: Use a Sobolev-like, spherically averaged method from `Wolcott-Green et. al. 2011 `_. This option is only valid for Cartesian grid codes in 3D. - 2: Supply an array of lengths using the :c:data:`H2_self_shielding_length` field. - 3: Use the local Jeans length. .. c:var:: 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. Default: 0 Care is advised in using any of these methods. The default behavior is to apply no self-shielding, but this is not necessarily the proper assumption, depending on the use case. If the user desires to turn on self-shielding, we strongly advise using option 3. All options include HI self-shielding, and vary only in treatment of HeI and HeII. In options 2 and 3, we approximately account for HeI self-shielding by applying the Rahmati et. al. 2013 relations, which are only strictly valid for HI, to HeI under the assumption that it behaves similarly to HI. None of these options are completely correct in practice, but option 3 has produced the most reasonable results in test simulations. Repeating the analysis of Rahmati et. al. 2013 to directly parameterize HeI and HeII self-shielding behavior would be a valuable avenue of future research in developing a more complete self-shielding model. Each self-shielding option is described below. - 0: No self shielding. Elements are optically thin to the UV background. - 1: Not Recommended. 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 (HeII ionization and heating rates are set 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. .. c:var:: 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 :ref:`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 < log\ :sub:`10` (n\ :sub:`H` / cm\ :sup:`-3`) < 4 - temperature: the temperature range is 1 < log\ :sub:`10` (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 < log\ :sub:`10` (n\ :sub:`H` / cm\ :sup:`-3`) < 12 - metallicity: -6 < log\ :sub:`10` (Z / Z\ :sub:`sun`) < 1 - temperature: the temperature range is 1 < log\ :sub:`10` (T / K) < 8. Data file: - **cloudy_metals_2008_3D.h5** - collisional ionization equilibrium, metal cooling rates only.