Outputs

This page documents the galaxy catalogues SAGE26 writes to disk: file layout, per-field units and descriptions, flag conventions, and the optional auxiliary datasets controlled by run parameters.

Sources: src/io/save_gals_hdf5.h, src/io/save_gals_hdf5.c, src/io/save_gals_binary.h, src/io/save_gals_binary.c.

Output formats

The OutputFormat parameter selects one of two writers:

Value	Format	Notes
`sage_binary`	Raw little-endian C struct dump	One file per task (`<FileNameGalaxies>_<filenr>`).
`sage_hdf5`	HDF5 column store with metadata	One file per task plus a master file linking them.

Both writers emit one file per output snapshot listed in FileWithOutputSnaps. Per-galaxy field content is the same in both formats, but field names and the on-disk layout differ – see the field reference below.

Code units used internally are:

Length: Mpc / h
Mass: 1.0e10 Msun / h
Velocity: km / s
Time: derived from length / velocity (UnitTime_in_Megayears stored in the header)

Where the writer converts to a more convenient unit (SFR, outflow rate, cooling/heating power, merger times) it is noted explicitly in the field reference. Everything else is in code units.

HDF5 layout

<FileNameGalaxies>_<N>.hdf5
+- Header/
|  +- Simulation/   (attributes: SimulationDir, FileWithSnapList,
|  |                              LastSnapshotNr, SimMaxSnaps,
|  |                              omega_matter, omega_lambda, particle_mass,
|  |                              hubble_h, num_simulation_tree_files,
|  |                              box_size, num_trees_this_file)
|  +- Runtime/      (every recipe flag and model parameter from the .par
|  |                 file, plus UnitLength_in_cm/UnitMass_in_g/
|  |                 UnitVelocity_in_cm_per_s and frac_volume_processed)
|  +- Misc/         (attributes: num_cores, sage_data_version,
|  |                              sage_version, git_SHA_reference)
|  +- snapshot_redshifts   (1-D dataset, length SimMaxSnaps)
|  +- output_snapshots     (1-D dataset, length NumOutputs)
+- TreeInfo/<snap>/  (per-tree galaxy counts for each output snapshot)
+- Snap_<N>/         (one group per output snapshot)
   +- SnapNum, Type, GalaxyIndex, ...   (one dataset per field)
   +- SFHMassDisk, SFHMassBulge          (only if SaveFullSFH = 1)

Each galaxy-property dataset has two HDF5 attributes:

Description – one-line text description.
Units – unit string.

The cumulative SFH datasets additionally carry a NumSnapshots attribute equal to SimMaxSnaps.

A separate master file (<FileNameGalaxies>.hdf5) is written at the end of the run; it contains the same Header group and uses HDF5 external links to expose each per-task file’s snapshot data under a single tree.

Binary layout

[int32  ntrees]
[int32  tot_ngals]
[int32  forest_ngals[ntrees]]
[GALAXY_OUTPUT  galaxies[tot_ngals]]

Galaxies are stored in snapshot order; the i-th block of forest_ngals[i] galaxies belongs to tree i. The GALAXY_OUTPUT struct layout is fixed at compile time – see src/io/save_gals_binary.h for the canonical definition. No header metadata, descriptions, or units are written; downstream tools must know the struct layout in advance.

The binary writer does not emit the cumulative SFH arrays; use HDF5 output if you need SFHMassDisk / SFHMassBulge.

Flag conventions

`Type` – galaxy hierarchy position

Value	Meaning
0	Central galaxy of the main FoF halo.
1	Central of a sub-halo (Type 1 satellite, still has its own subhalo).
2	Orphan satellite (subhalo lost; will merge or disrupt within the current timestep).

For Type 0 galaxies, all infall fields (infallMvir, infallVvir, infallVmax, infallStellarMass, TimeOfInfall) are zeroed on output – they are only meaningful for satellites.

`mergeType` – merger/disruption channel

Value	Meaning
0	None (galaxy still evolving).
1	Minor merger (mass ratio below `ThreshMajorMerger`).
2	Major merger (mass ratio above `ThreshMajorMerger`).
3	Reserved for disk instability (header documents it, but no code path sets this value).
4	Disrupted to intra-cluster stars.

`Regime` – CGM regime classification

Value	Meaning
0	CGM regime (cool flow / precipitation; cooling driven by `cooling_recipe_cgm()`).
1	Hot-halo regime (Mvir above the Dekel & Birnboim 2006 M_shock; cooling driven by `cooling_recipe_hot()`).

Set every snapshot in determine_and_store_regime() when CGMrecipeOn = 1. Left at zero (and unused) when CGMrecipeOn = 0.

`FFBRegime` – feedback-free burst classification

Value	Meaning
0	Normal halo (standard star formation + SN feedback).
1	FFB halo (Li+2024 / Boylan-Kolchin+2025 starburst path; disk-instability check skipped, SN feedback still applied).

Only set when FeedbackFreeModeOn = 1.

Galaxy property reference

The tables below list every per-galaxy field written to disk, with its HDF5 name (the binary writer uses the corresponding GALAXY_OUTPUT struct field name – see the “Binary vs HDF5 name differences” section below) and the unit actually written.

Identity and tree linkage

Field	Units	Description
`SnapNum`	–	Snapshot the galaxy is located at.
`Type`	–	Galaxy hierarchy position (see flag table above).
`GalaxyIndex`	–	Galaxy ID unique across all trees and files. Computed from local galaxy number, tree number, and file number.
`CentralGalaxyIndex`	–	`GalaxyIndex` of the central in this galaxy’s FoF group.
`SAGEHaloIndex`	–	Halo index from SAGE’s restructured tree (not the input tree’s).
`SAGETreeIndex`	–	Tree number (within file) this galaxy belongs to.
`SimulationHaloIndex`	–	`\|MostBoundID\|` from the input tree files.
`TaskForestNr`	–	HDF5 only. Task-local forest number used for parallel bookkeeping.
`mergeType`	–	Merger/disruption channel (see flag table above).
`mergeIntoID`	–	`GalaxyIndex` of the galaxy this one is merging into.
`mergeIntoSnapNum`	–	Snapshot of the merge target.
`dT`	Myr	Time since this galaxy was last evolved (snapshot interval / sub-step).

Halo properties

Field	Units	Description
`Posx`, `Posy`, `Posz`	Mpc / h	Galaxy spatial position. HDF5 splits into three 1-D datasets; binary stores as `Pos[3]`.
`Velx`, `Vely`, `Velz`	km / s	Galaxy peculiar velocity. HDF5 splits; binary stores as `Vel[3]`.
`Spinx`, `Spiny`, `Spinz`	Mpc * km / s	Halo specific angular momentum vector. HDF5 splits; binary stores as `Spin[3]`.
`Len`	–	Number of particles in the galaxy’s halo.
`Mvir`	1.0e10 Msun / h	Virial mass of this galaxy’s halo.
`CentralMvir`	1.0e10 Msun / h	Virial mass of the main FoF halo (central).
`Rvir`	Mpc / h	Virial radius of this galaxy’s halo.
`Vvir`	km / s	Virial velocity of this galaxy’s halo.
`Vmax`	km / s	Maximum circular velocity of this galaxy’s halo.
`VelDisp`	km / s	Velocity dispersion of this galaxy’s halo.
`Concentration`	–	NFW halo concentration from the Ishiyama+21 c-M relation (set when `ConcentrationOn = 1`).
`g_max`	–	Running maximum of the precipitation g-parameter across all snapshots for this halo (HDF5 dtype: float64).

Baryonic reservoirs

Field	Units	Description
`ColdGas`	1.0e10 Msun / h	Mass of gas in the cold reservoir (disk + bulge).
`StellarMass`	1.0e10 Msun / h	Total stellar mass (disk + bulge).
`BulgeMass`	1.0e10 Msun / h	Stellar mass in the bulge (= `MergerBulgeMass` + `InstabilityBulgeMass`).
`HotGas`	1.0e10 Msun / h	Mass of gas in the hot halo reservoir.
`EjectedMass`	1.0e10 Msun / h	Mass of gas ejected from the halo by SN feedback.
`BlackHoleMass`	1.0e10 Msun / h	Mass of the central black hole.
`IntraClusterStars` / `ICS`	1.0e10 Msun / h	Total ICS mass (HDF5 name `IntraClusterStars`; binary field `ICS`).
`CGMgas`	1.0e10 Msun / h	Mass of gas in the circum-galactic medium (Regime 0 reservoir).
`H2gas`	1.0e10 Msun / h	Mass of molecular hydrogen in the cold gas.
`H1gas`	1.0e10 Msun / h	Mass of atomic hydrogen in the cold gas.
`MergerBulgeMass`	1.0e10 Msun / h	Stellar mass in the merger-built classical bulge (Tonini+2016 channel A).
`InstabilityBulgeMass`	1.0e10 Msun / h	Stellar mass in the disk-instability pseudo-bulge (Tonini+2016 channel B).

Metals

Field	Units	Description
`MetalsColdGas`	1.0e10 Msun / h	Metals in the cold reservoir.
`MetalsStellarMass`	1.0e10 Msun / h	Metals locked in stars.
`MetalsBulgeMass`	1.0e10 Msun / h	Metals locked in bulge stars.
`MetalsHotGas`	1.0e10 Msun / h	Metals in the hot reservoir.
`MetalsEjectedMass`	1.0e10 Msun / h	Metals in the ejected reservoir.
`MetalsIntraClusterStars` / `MetalsICS`	1.0e10 Msun / h	Metals in intra-cluster stars (HDF5 name `MetalsIntraClusterStars`; binary field `MetalsICS`).
`MetalsCGMgas`	1.0e10 Msun / h	Metals in the CGM reservoir.

Star formation, feedback, and BH accretion

Field	Units	Description
`SfrDisk`	Msun / yr	Disk SFR averaged over the snapshot interval (mean over the STEPS sub-steps).
`SfrBulge`	Msun / yr	Bulge SFR averaged over the snapshot interval (starburst component).
`SfrDiskZ`	dimensionless	Mass-weighted metallicity of the star-forming disk gas (`MetalsColdGas / ColdGas` averaged over sub-steps). Despite the “Units” attribute saying `Msun/yr`, this field is a metallicity ratio, not a rate.
`SfrBulgeZ`	dimensionless	Mass-weighted metallicity of the star-forming bulge gas. Same caveat as `SfrDiskZ`.
`OutflowRate`	Msun / yr	Cold-gas reheating rate (cold -> hot) integrated over the substep.
`MassLoading`	dimensionless	SN mass-loading factor (outflow rate / SFR).
`Cooling`	log10(erg / s)	log10 of cooling energy rate. Stored as 0.0 when no cooling occurred (i.e. zero, not “1 erg/s”).
`Heating`	log10(erg / s)	log10 of AGN radio-mode heating energy rate. Stored as 0.0 when no heating occurred.
`QuasarModeBHaccretionMass`	1.0e10 Msun / h	Mass accreted by the black hole during the last sub-step via the quasar (merger-driven) mode.

Sizes

Field	Units	Description
`DiskRadius` / `DiskScaleRadius`	Mpc / h	Disk exponential scale length from Mo, Mao & White (1998). HDF5 name `DiskRadius`; binary field `DiskScaleRadius`.
`BulgeRadius`	Mpc / h	Bulge half-mass radius (Lange et al. 2015 / Shen et al. 2003 normalisation; updated by mergers and instabilities).
`MergerBulgeRadius`	Mpc / h	Sub-component bulge radius from the merger channel.
`InstabilityBulgeRadius`	Mpc / h	Sub-component bulge radius from the disk-instability channel (Tonini+2016 Eq. 15 incremental update).

Times

Field	Units	Description
`TimeOfLastMajorMerger`	Myr	Code-time of the last major merger, converted to Myr.
`TimeOfLastMinorMerger`	Myr	Code-time of the last minor merger, converted to Myr.
`TimeOfInfall`	Myr	Code-time at which this galaxy became a satellite (zero for Type 0).

Two-regime cooling (CGM model)

Field	Units	Description
`Regime`	–	CGM regime flag (see flag table above).
`tcool`	Myr	Cooling time of the CGM gas at the cooling radius.
`tff`	Myr	Free-fall time of the CGM gas at the cooling radius.
`tcool_over_tff`	dimensionless	Voit (2015) precipitation criterion ratio.
`tdeplete`	Myr	Depletion time of the CGM reservoir under the current cooling rate.
`H2DepletionTime_Gyr`	Gyr	H2 depletion time from the K13 prescription. Set to -1 when not applicable.
`RcoolToRvir`	dimensionless	Ratio of the cooling radius to the virial radius.
`mdot_cool`	Msun / yr	Hot-halo cooling rate (mass flowing from hot to cold).
`mdot_stream`	Msun / yr	Cold-stream accretion rate (CGM-regime mass flowing from CGM to cold).

Infall properties (Type > 0 only)

For Type 0 (central) galaxies, all five infall fields are zeroed on output. For satellites, they record the halo state at the snapshot just before infall:

Field	Units	Description
`infallMvir`	1.0e10 Msun / h	Virial mass of this halo at the previous timestep (the “infall snapshot”).
`infallVvir`	km / s	Virial velocity at the infall snapshot.
`infallVmax`	km / s	Maximum circular velocity at the infall snapshot.
`infallStellarMass`	1.0e10 Msun / h	Stellar mass at the moment of becoming a satellite.

Feedback-free burst diagnostic

Field	Units	Description
`FFBRegime`	–	FFB classification flag (see flag table above).

ICS assembly tracking (`TrackICSAssembly = 1`)

These three fields accumulate per-channel deposits into the ICS so that the mean assembly time can be reconstructed downstream:

Field	Units	Description
`ICS_disrupt`	1.0e10 Msun / h	Cumulative stellar mass disrupted to ICS via satellite disruption.
`ICS_accrete`	1.0e10 Msun / h	Cumulative ICS accreted from satellites via per-snapshot inheritance.
`ICS_sum_mt`	1.0e10 Msun / h * code_time	Mass-weighted sum of `mass * time_of_deposition` (code-time units).

Mean ICS assembly lookback for a given galaxy:

<t_assembly> = ICS_sum_mt / (ICS_disrupt + ICS_accrete)

The result is in code-time units; multiply by UnitTime_in_Megayears (read from the HDF5 header) to convert to Myr.

These fields are always present in both writers, but they only accumulate when TrackICSAssembly = 1. With the parameter off, they remain at zero.

Cumulative star formation history (`SaveFullSFH = 1`)

HDF5 output only. When SaveFullSFH = 1, two extra 2-D datasets are written per output snapshot:

Dataset	Shape	Units	Description
`SFHMassDisk`	(ngalaxies, SimMaxSnaps)	1.0e10 Msun / h	Stellar mass formed in the disk at each snapshot up to the current one.
`SFHMassBulge`	(ngalaxies, SimMaxSnaps)	1.0e10 Msun / h	Stellar mass formed in the bulge (starbursts) at each snapshot up to the current one.

Each dataset carries Description, Units, and NumSnapshots attributes. Entries for snapshots beyond the galaxy’s current SnapNum are zero. Reconstructing the SFR(z) curve for a galaxy amounts to differencing consecutive snapshot bins and dividing by the snapshot interval.

This option roughly doubles the per-galaxy footprint of the output file, so leave it off unless you need the full SFH.

Binary vs HDF5 name differences

A handful of fields use different names between the two writers. Otherwise the field set is identical:

Binary (GALAXY_OUTPUT)	HDF5 (HDF5_GALAXY_OUTPUT)
`Pos[3]`	`Posx`, `Posy`, `Posz`
`Vel[3]`	`Velx`, `Vely`, `Velz`
`Spin[3]`	`Spinx`, `Spiny`, `Spinz`
`DiskScaleRadius`	`DiskRadius`
`ICS`	`IntraClusterStars`
`MetalsICS`	`MetalsIntraClusterStars`
–	`TaskForestNr` (HDF5 only)

The HDF5 writer also lays out fields as struct-of-arrays (one dataset per field), whereas the binary writer lays them out as array-of-structs.

Parameter -> output mapping

Parameter	Effect on output
`OutputFormat`	Selects `sage_binary` or `sage_hdf5`.
`OutputDir`	Directory for the output files.
`FileNameGalaxies`	Filename stem; final names are `<stem>_<filenr>` (binary) or `<stem>_<filenr>.hdf5` (HDF5), plus `<stem>.hdf5` master.
`FileWithOutputSnaps`	Snapshot list to write. Each listed snap becomes either its own binary file or a `Snap_<N>` HDF5 group.
`SaveFullSFH`	Enables the cumulative `SFHMassDisk` / `SFHMassBulge` 2-D HDF5 datasets.
`TrackICSAssembly`	Activates accumulation into `ICS_disrupt`, `ICS_accrete`, `ICS_sum_mt`.
`ConcentrationOn`	Populates the `Concentration` field (otherwise 0).
`CGMrecipeOn`	Populates `Regime`, `CGMgas`, `MetalsCGMgas`, `tcool`, `tff`, `tcool_over_tff`, `tdeplete`, `RcoolToRvir`, `mdot_cool`, `mdot_stream`. With it off, these stay at their initialised values.
`FeedbackFreeModeOn`	Populates `FFBRegime`.

See parameters.md for full parameter descriptions and defaults.

Where to go next

getting_started.md – run SAGE26 and produce these outputs.
parameters.md – the parameter file that controls which fields are populated.
physics/ics.md – detail on the ICS assembly channels that feed ICS_disrupt / ICS_accrete / ICS_sum_mt.
physics/cooling_and_heating.md – what tcool, tff, tcool_over_tff, Regime, and Cooling / Heating actually measure.