SUBFIND catalogs
Important
A reorganization of the data has been performed in 2024 in order to enhance its uniformity and simplicity. This will require slight changes to existing codes that access the data.
Folders in the 1P sets are now named
1P_pX_Yand each parameter only has 4 variations, rather than 10, such thatXranges from n2 to 2.Snapshot numbers in the IllustrisTNG and SIMBA suites, where simulations have only 34 snapshots, have been updated to match the numbering in the Astrid suite (and some TNG simulations) that have 91 snapshots. For example, where 33 used to be the z=0 snapshot, now it is 90 uniformly for all suites.
Snapshot files have been renamed from
snap_###.hdf5tosnapshot_###.hdf5and fof/subfind files fromfof_subhalo_tab_###.hdf5togroups_###.hdf5.
The FOF_Subfind folder contains the FOF+SUBFIND halo/subhalo/galaxy catalogs. The data is organized following the general hierarchical structure described in Suite folders.
The catalogs are stored as hdf5 files. h5py is needed in order to read these files using python. CAMELS provides a halo/subhalo catalog for each snapshot. The halos are identified through FOF and subhalos are identified through SUBFIND.
The easiest way to inspect the content of these files is:
>> h5ls -r SIMBA/CV_5/groups_031.hdf5
/ Group
/Config Group
/Group Group
/Group/GroupBHMass Dataset {32272}
/Group/GroupBHMdot Dataset {32272}
/Group/GroupCM Dataset {32272, 3}
/Group/GroupFirstSub Dataset {32272}
/Group/GroupGasMetalFractions Dataset {32272, 11}
/Group/GroupGasMetallicity Dataset {32272}
/Group/GroupLen Dataset {32272}
/Group/GroupLenType Dataset {32272, 6}
/Group/GroupMass Dataset {32272}
/Group/GroupMassType Dataset {32272, 6}
/Group/GroupNsubs Dataset {32272}
/Group/GroupPos Dataset {32272, 3}
/Group/GroupSFR Dataset {32272}
/Group/GroupStarMetalFractions Dataset {32272, 11}
/Group/GroupStarMetallicity Dataset {32272}
/Group/GroupVel Dataset {32272, 3}
/Group/GroupWindMass Dataset {32272}
/Group/Group_M_Crit200 Dataset {32272}
/Group/Group_M_Crit500 Dataset {32272}
/Group/Group_M_Mean200 Dataset {32272}
/Group/Group_M_TopHat200 Dataset {32272}
/Group/Group_R_Crit200 Dataset {32272}
/Group/Group_R_Crit500 Dataset {32272}
/Group/Group_R_Mean200 Dataset {32272}
/Group/Group_R_TopHat200 Dataset {32272}
/Header Group
/IDs Group
/IDs/ID Dataset {14575639}
/Parameters Group
/Subhalo Group
/Subhalo/SubhaloBHMass Dataset {22315}
/Subhalo/SubhaloBHMdot Dataset {22315}
/Subhalo/SubhaloBfldDisk Dataset {22315}
/Subhalo/SubhaloBfldHalo Dataset {22315}
/Subhalo/SubhaloCM Dataset {22315, 3}
/Subhalo/SubhaloGasMetalFractions Dataset {22315, 11}
/Subhalo/SubhaloGasMetalFractionsHalfRad Dataset {22315, 11}
/Subhalo/SubhaloGasMetalFractionsMaxRad Dataset {22315, 11}
/Subhalo/SubhaloGasMetalFractionsSfr Dataset {22315, 11}
/Subhalo/SubhaloGasMetalFractionsSfrWeighted Dataset {22315, 11}
/Subhalo/SubhaloGasMetallicity Dataset {22315}
/Subhalo/SubhaloGasMetallicityHalfRad Dataset {22315}
/Subhalo/SubhaloGasMetallicityMaxRad Dataset {22315}
/Subhalo/SubhaloGasMetallicitySfr Dataset {22315}
/Subhalo/SubhaloGasMetallicitySfrWeighted Dataset {22315}
/Subhalo/SubhaloGrNr Dataset {22315}
/Subhalo/SubhaloHalfmassRad Dataset {22315}
/Subhalo/SubhaloHalfmassRadType Dataset {22315, 6}
/Subhalo/SubhaloIDMostbound Dataset {22315}
/Subhalo/SubhaloLen Dataset {22315}
/Subhalo/SubhaloLenType Dataset {22315, 6}
/Subhalo/SubhaloMass Dataset {22315}
/Subhalo/SubhaloMassInHalfRad Dataset {22315}
/Subhalo/SubhaloMassInHalfRadType Dataset {22315, 6}
/Subhalo/SubhaloMassInMaxRad Dataset {22315}
/Subhalo/SubhaloMassInMaxRadType Dataset {22315, 6}
/Subhalo/SubhaloMassInRad Dataset {22315}
/Subhalo/SubhaloMassInRadType Dataset {22315, 6}
/Subhalo/SubhaloMassType Dataset {22315, 6}
/Subhalo/SubhaloParent Dataset {22315}
/Subhalo/SubhaloPos Dataset {22315, 3}
/Subhalo/SubhaloSFR Dataset {22315}
/Subhalo/SubhaloSFRinHalfRad Dataset {22315}
/Subhalo/SubhaloSFRinMaxRad Dataset {22315}
/Subhalo/SubhaloSFRinRad Dataset {22315}
/Subhalo/SubhaloSpin Dataset {22315, 3}
/Subhalo/SubhaloStarMetalFractions Dataset {22315, 11}
/Subhalo/SubhaloStarMetalFractionsHalfRad Dataset {22315, 11}
/Subhalo/SubhaloStarMetalFractionsMaxRad Dataset {22315, 11}
/Subhalo/SubhaloStarMetallicity Dataset {22315}
/Subhalo/SubhaloStarMetallicityHalfRad Dataset {22315}
/Subhalo/SubhaloStarMetallicityMaxRad Dataset {22315}
/Subhalo/SubhaloStellarPhotometrics Dataset {22315, 8}
/Subhalo/SubhaloStellarPhotometricsMassInRad Dataset {22315}
/Subhalo/SubhaloStellarPhotometricsRad Dataset {22315}
/Subhalo/SubhaloVel Dataset {22315, 3}
/Subhalo/SubhaloVelDisp Dataset {22315}
/Subhalo/SubhaloVmax Dataset {22315}
/Subhalo/SubhaloVmaxRad Dataset {22315}
/Subhalo/SubhaloWindMass Dataset {22315}
The catalogs contain two main groups:
Group. This group contains the properties of the halos.Subhalos. This group contains the properties of the subhalos. Galaxies are generally considered to be subhalos with stellar mass larger than 0.
A detailed description of the different blocks in the catalogs can be found here.
Note
For the IllustrisTNG suite, the particles in the snapshots are organized according to their FOF/Subfind group membership, as described here. However, for the snapshots in the other suites (e.g. IllustrisTNG_DM, SIMBA, Astrid), that is not the case. In those cases, instead, in order to access the particles of a specific FOF group or Subfind subhalo, a special hdf5 group called /IDs that exists in the group catalog files (as appears above for example for the SIMBA CV_5 case) needs to be used. This is a list of particle IDs (not ordered by type – all types mixed together) that is ordered according to the group membership in a similar way to how the particles are ordered in the native IllustrisTNG files. Namely, if one reorders the particles from e.g. an Astrid snapshot such that their IDs in the reordered list is the same as the IDs/ dataset from the corresponding group catalog, and then separates them by type, then by working with this reordered sets of particles, one can assign particles to groups in the standard IllustrisTNG-like approach. Note that there is an exception to the above with regards to SIMBA snapshots, which typically have duplicate IDs. There is no way to distinguish which of the particles with duplicate IDs truly belongs to a particular group except by sanity checks. For example, one in a pair of such particles may be physically too far away from the group center to plausibly truly belong to it. It is the user’s responsibility to apply such sanity checks and filtering.
Reading these files with python is straightforward:
import numpy as np
import h5py
# catalog name
catalog = 'SIMBA/CV_5/groups_090.hdf5'
# value of the scale factor
scale_factor = 1.0
# open the catalogue
f = h5py.File(catalog, 'r')
# read the positions, velocities and masses of the FoF halos
pos_h = f['Group/GroupPos'][:]/1e3 #positions in Mpc/h
vel_h = f['Group/GroupVel'][:]/scale_factor #velocities in km/s
mass_h = f['Group/GroupMass'][:]*1e10 #masses in Msun/h
# read the positions, black hole masses and stellar masses of the subhalos/galaxies
pos_g = f['Subhalo/SubhaloPos'][:]/1e3 #positions in Mpc/h
BH_g = f['Subhalo/SubhaloBHMass'][:]*1e10 #black-hole masses in Msun/h
M_star = f['Subhalo/SubhaloMassType'][:,4]*1e10 #stellar masses in Msun/h
# close file
f.close()
Note
Differently to the snapshots, the format of these files is identical across the simulations in the IllustrisTNG and SIMBA suites.
Suite differences
The halo/subhalo catalogs are designed to be as uniform as possible across the two suites. Thus, the metallicity field in the subfind catalogs of SIMBA differ from the metallicity field of the SIMBA snapshots. The Metallicity and MetalFraction fields in the subfind catalogs follow the same convention as those from the IllustrisTNG catalogs, except that the elements are the same as in the SIMBA snapshots.
In particular:
In IllustrisTNG snapshots and group catalogs,
Metallicityis the total content of elements heavier than H & He, andMetalsorMetalFractionsis a 10-element array with the elements in this order: [H, He, C, N, O, Ne, Mg, Si, Fe, other metals]In SIMBA snapshots,
Metallicityis an 11-element array with the elements in this order: [the total content of elements heavier than H & He, He,C,N,O,Ne,Mg,Si,S,Ca,Fe].In SIMBA FOF+Subfind catalogs, the structure is similar to IllustrisTNG:
Metallicityis the total content of elements heavier than H & He, andMetalsorMetalFractionsis a 11-element array with the elements in this (SIMBA-snapshot-like) order: [H,He,C,N,O,Ne,Mg,Si,S,Ca,Fe]
In the SIMBA catalogs, the SubhaloStellarPhotometrics and WindMass fields contain some irrelevant numbers as those quantities are not calculated within the SIMBA simulations.
Please also note the differences with respect to the ordering of the particles in the snapshots and its relation to the group catalogs, which are detailed in a blue Note box above in this page.