Configuring MORIA

The following is a complete list of MORIA’s configuration parameters, with some explanations below. See Run-time configuration parameters for the syntax of the config file. Parameters with default NONE must be set by the user or the code will throw an error.

Parameter	Type	Default	Explanation
Input
sparta_file	string	NONE	The path to the SPARTA output file
catalog_dir	string	<from sparta>	The path to the catalog dir (by default taken from SPARTA config)
main_def_catalog	string	M200m_bnd	The fiducial (host/sub) halo mass/radius definition of the input halo catalog
rockstar_strict_so	bool	NONE	If Rockstar catalog, was it run with the STRICT_SO_MASSES option turned on?
rockstar_bound_props	bool	NONE	If Rockstar catalog, was it run with the BOUND_PROPS option turned on?
cosmo_flat	int	1	Cosmology: flat?
cosmo_omega_b	float	NONE	Cosmology: baryon density of the universe
cosmo_sigma8	float	NONE	Cosmology: normalization of power spectrum
cosmo_ns	float	NONE	Cosmology: slope of the primordial power spectrum
cosmo_omega_r	float	0.0	Cosmology: energy density of radiation in the universe
cosmo_w	float	-1.0	Cosmology: dark energy equation of state parameter
cosmo_t_cmb	float	2.725	Cosmology: CMB temperature at z = 0 (in Kelvin)
cosmo_self_similar	bool	FALSE	Cosmology: if True, use power-law power spectrum P ~ k^ns, with -3 < ns < 0
Console output
log_level	int	1	Same meaning as in SPARTA config file
log_level_memory	int	2	Same meaning as in SPARTA config file
log_level_timing	int	1	Same meaning as in SPARTA config file
log_substatus_diff	bool	FALSE	Print detailed output about differences in subhalo assignment compared to catalog
Error levels
err_level_more_snaps_than_cat	int	1	Ignore/warning/error when more snapshots that catalog files are found
err_level_snap_outside_range	int	1	Ignore/warning/error when a requested snap is outside the redshift range of the sim.
err_level_main_def_not_200m	int	1	Ignore/warning/error when the main catalog definition is not R/M200m
err_level_acc_rate_undefined	int	1	Ignore/warning/error when the accretion rate at this snapshot cannot be det. at all
err_level_cat_field_changed	int	1	Ignore/warning/error when catalog field name changed in HDF5 file (for compatibility)
Algorithm
cut_def	string	Vmax_peak_cat	The halo mass/radius definition that determines the threshold for output
cut_threshold	int	1000	The threshold value in units of cut_units
cut_units	string	particles	Can be none, particles, particles_vmax depending on cut_def
order_def	string	Vmax	The halo mass/radius definition used to order halos during subhalo assignment
hostsub_assign_subparent_id	bool	FALSE	Give subhalos of subhalos the ID of that sub (TRUE) or of its host (FALSE)?
hostsub_restrict_to_output	bool	FALSE	Only consider halos written to file (that pass the cut) for host-sub relations
include_ghosts	bool	TRUE	Include ghost halos in the MORIA catalogs and tree
adjust_phantom_xv	bool	TRUE	Set the position and velocity to those measured by SPARTA, if available
max_mass_ratio_sparta	float	2.0	When SPARTA mass over catalog mass is greater, use the catalog mass for calculations
max_rsp_model_diff_factor	float	2.0	If interpolated/extrapolated Rsp/Msp fractionally differ more from model, do not use
max_rsp_model_diff_sigma	float	5.0	If interpolated/extrapolated Rsp/Msp differ more than x sigma from model, do not use
Output
output_dir_original	string	moria_original	Output directory for files in original format (filename is same as input)
output_dir_hdf5	string	moria_catalogs	Output directory for catalog files in hdf5 format (filename is auto-generated)
output_dir_tmp	string	.	Output directory for temporary files (restart and temporary tree files)
output_filename_tree	string	moria_tree.hdf5	Filename for tree output file (can contain a file path that will be created)
output_restart_files	bool	TRUE	Write restart files from which the code can restart if it crashes
output_restart_every	int	10	Number of snapshots between restart files
output_original	bool	TRUE	Whether catalogs are output in the format of the input halo catalog
output_hdf5	bool	TRUE	Whether catalogs are output in MORIA’s native HDF5 format
output_tree	bool	FALSE	Whether a tree file is output
output_compression_level	int	<from sparta>	Compression level for MORIA output files; by default the level set in SPARTA
output_a	list	-1 (all)	A scale factor or list of scale factors or -1 for all snapshots
output_rm_defs	list	NONE	A list of mass/radius definitions to output (see below)
output_sub_defs	list	NONE	A list of mass/radius definitions for which to compute subhalo assignments
output_cat_fields	list	NONE	A list of fields from the input catalog that are copied into the output catalog

What are strict-SO and bound-props?

The rockstar_strict_so parameter may seem a little esoterical, but is important and must be set by the user if Rockstar catalogs are used. This parameter, called STRICT_SO_MASSES in the Rockstar config, determines if Rockstar includes all particles in its SO calculation or only those bound to the FOF group. This setting is not apparent from the Rockstar output file, meaning that MORIA cannot know the true meaning of the definitions without this information.

Similarly, the BOUND_PROPS parameter in Rockstar determines what is output for certain halo properties, including the “main” mass definition in the catalog. By default, BOUND_PROPS is on, meaning that the main definition is bound-only even if STRICT_SO_MASSES makes the alternative mass definition include all particles.

Depending on these switches, requesting certain catalog definitions may lead to failure. For example, if STRICT_SO_MASSES = 1 and BOUND_PROPS = 0, the outputs include all particles and we cannot get any *_bnd masses. Similarly, if STRICT_SO_MASSES = 0, we cannot get any *_all definitions (from the catalog, we can from SPARTA).

Why so many cosmological parameters?

MORIA needs to compute certain power-spectrum related quantities such as peak height, which is why it needs more cosmological information than can be extracted from some simulation code outputs (e.g., Gadget2).

If cosmo_self_similar is turned on, the cosmology changes from a standard LCDM cosmology to a self-similar universe with a power-law spectrum. In this case, we assume that ns is the slope of that spectrum, P(k) ~ k^ns, with ns between -3 and 0. The matter density should typically be the critical density, Omega_m = 1, but this is set in SPARTA and not in the MORIA configuration.

Mass/radius definitions

All halo mass/radius definitions are given in the standard Halo radius and mass definitions format. Of course, the definition(s) requested must make sense in the respective context. In particular:

• The definitions chosen for cut_def and order_def must be catalog definitions, i.e., they must exist in the input halo catalog and for all halos.

• The main_def_catalog should, if at all possible, be a definition as close to M200m_all as possible. This field is used if (in some very rare cases) SPARTA failed to compute an internal M200m_all for the halo, or (more likely) if the halo does not exist in SPARTA.

• The definitions chosen for output_rm_defs and output_sub_defs can be definitions from either the input catalog or SPARTA, and must carry the _spa or _cat identifiers if they can be computed by both. For example, SO definitions must be listed as M200c_all_cat and M200c_all_spa because they can appear in both, whereas Rsp-apr-mn can only be computed by SPARTA and is thus unambiguous.

• For Rockstar catalogs, mass definitions are usually given as masses but not radii. MORIA automatically converts radii and masses into one another if necessary. For example, it is OK to demand R500c_all_cat if M500c is part of the catalog and STRICT_SO was on.

• The same goes for SO definitions from the SPARTA halo properties analysis. Here, the user can freely demand radii and masses as long as either one of the two is present in the SPARTA file.

Output threshold

The threshold for inclusion in the output catalog is important: only halos that are well-defined in the input catalog and that were output by SPARTA should be included. For example, if output_min_n200m is set to 500 in SPARTA (see Run-time configuration parameters), it does not make sense to set cut_def to M200m_all, cut_units to particles, and cut_threshold to 200: in that case, we would be including halos down to 200 particles even though they are not included in the SPARTA file.

The particles_vmax unit choice converts the given number of particles, that is, a minimum halo mass, into a circular velocity using the empirical fitting function of fitting function of Klypin et al. 2011,

\[v_{\rm max} \approx 2.8 \times 10^{-2} M_{\rm vir}^{0.316}\]

We note that this formula is only used to convert a particle limit into a \(v_{\rm max}\) limit, which is then compared to \(v_{\rm max}\) as measured by the halo finder for each individual halo. Thus, a limit of 100 particles means the \(v_{\rm max}\) that, on average, corresponds to a virial mass of 100 times the simulation’s particle mass.

Host-sub relations

MORIA assigns parent IDs by sorting the halos by order_def and the looking for subhalos within halos, starting with the first (largest) halo. By default, subhalos do not have subhalos themselves. However, there is a case where a subhalo is also the subhalo of a subhalo within the same host. In this case, we can assign either the host or the larger subhalo as parent. The latter is only done if hostsub_assign_subparent_id is turned on.

Another subtlety arises because the order definition is not necessarily the same as the cut definition, meaning that some halos might have subhalos but not be included in the output. By default, we still assign such halos as parents, especially because they may be output in the tree. This choice means that the results of running MORIA on a single snapshot are the same as creating a tree where we run on all snapshots and always consider all halos, whether they make the cut at a given snapshot or not. However, the user can change this behavior by turning on hostsub_restrict_to_output, which means that only halos in the catalog file at this redshift will be considered as hosts. Note that this can lead to small deviations in the host-sub assignment even if the same definition as in the original halo catalog is used.

Tree output

If output_tree is set, the list of scale factors in output_a is ignored because we need to run over all snapshots to construct the tree.

Compression level

The output_compression_level parameter has the same meaning as the corresponding parameter in the SPARTA config. Compared to no compression (0), a value of 1 provides almost all the benefit at very modest computational expense. In practice, raising the compression level does not lead to much smaller MORIA output files.

Example config file

The following file contains all currently supported MORIA parameters and their default values wherever applicable. The file can be found at /config/moria.cfg:

Rsp/Msp interpolation and extrapolation

MORIA increases the completeness of the splashback values in the catalogs by interpolating missing values between valid snapshots, or even extrapolating from past and/or future snapshots. For a snapshot to be considered, it must be within one dynamical time, the halo must have been a host, and a valid SPARTA value for all splashback definitions must have been computed. To avoid extreme values, we also check Rsp/R200m or Msp/M200m from that snapshot against the fitting function. If the values are far off, they may not be wrong – but we may not want to extrapolate them since the halo may have been in a unique situation, such as a merger event, mass loss etc. Thus, we accept a value only if it either differs less than max_rsp_model_diff_factor from the model (is either larger or smaller by that factor) or (!) if it is less than max_rsp_model_diff_sigma off the model. The sigma value is compared to the model scatter from the same fitting function. However, this model scatter is formally small (as low as 5%) depending on mass and accretion rate. Thus, we also introduce the absolute threshold.

#--------------------------------------------------------------------------------------------------
# 
# Complete config file for MORIA inclding all parameters. See the documentation for details.
#
#--------------------------------------------------------------------------------------------------

#--------------------------------------------------------------------------------------------------
# Input
#--------------------------------------------------------------------------------------------------

sparta_file                   <MUST BE SET BY USER>   # e.g., /my/dir/sparta.hdf5
catalog_dir                   # by default taken from SPARTA
main_def_catalog              M200m_bnd
rockstar_strict_so            <MUST BE SET BY USER> # If using Rockstar catalog
rockstar_bound_props          <MUST BE SET BY USER> # If using Rockstar catalog

cosmo_flat                    1
cosmo_omega_b                 <MUST BE SET BY USER>
cosmo_sigma8                  <MUST BE SET BY USER>
cosmo_ns                      <MUST BE SET BY USER>
cosmo_omega_r                 0.0
cosmo_w                       -1.0
cosmo_t_cmb                   2.725
cosmo_self_similar            0

#--------------------------------------------------------------------------------------------------
# Console output & Error levels
#--------------------------------------------------------------------------------------------------

log_level                     1
log_level_memory              2
log_level_timing              1
log_flush                     1
log_substatus_diff            0

err_level_more_snaps_than_cat 1
err_level_snap_outside_range  1
err_level_main_def_not_200m   1
err_level_acc_rate_undefined  1
err_level_cat_field_changed   1

#--------------------------------------------------------------------------------------------------
# Algorithm
#--------------------------------------------------------------------------------------------------

cut_def                       Vmax_peak_cat
cut_threshold                 1000
cut_units                     particles
order_def                     Vmax
hostsub_assign_subparent_id   0
hostsub_restrict_to_output    0
include_ghosts                1
adjust_phantom_xv             1
max_mass_ratio_sparta         2.0
max_rsp_model_diff_factor     2.0
max_rsp_model_diff_sigma      5.0

#--------------------------------------------------------------------------------------------------
# Output
#--------------------------------------------------------------------------------------------------

output_dir_original           moria_original
output_dir_hdf5               moria_catalogs
output_filename_tree          moria_tree.hdf5
output_dir_tmp                .
output_restart_files          1
output_restart_every          10
output_original               1
output_hdf5                   1
output_tree                   0
output_compression_level      1

output_a                      -1
output_rm_defs                <MUST BE SET BY USER>    # e.g., R200m_all_spa, R200c_bnd_cat, Rsp-apr-p75 etc
output_sub_defs               <MUST BE SET BY USER>    # e.g., R200m_all_spa, R200c_bnd_cat, Rsp-apr-p75 etc
output_cat_fields             # optionally set by user, e.g., rs, phantom etc