Output files

For each snapshot of an execution, shark optionally outputs three different types of files:

  • galaxies.hdf5 contains the information of galaxies
  • star_formation_histories.hdf5 contains the star formation history of the galaxies

We list here each of the HDF5 groups and datasets found on each of these files. This list is automatically calculated from the files themselves.

Galaxies

cosmology

  • h: normalization of hubble parameter H0 = h * 100 (km/s)/Mpc
  • n_s: scalar spectral index assumed in simulation
  • omega_b: omega baryon assumed in simulation
  • omega_l: omega lambda assumed in simulation
  • omega_m: omega matter assumed in simulation
  • sigma8: fluctuation amplitude at 8 Mpc/h

galaxies

  • bh_accretion_rate_hh: accretion rate onto the black hole during the hot halo mode [Msun/Gyr/h]
  • bh_accretion_rate_sb: accretion rate onto the black hole during the starburst mode [Msun/Gyr/h]
  • bh_spin: black hole spin [dimensionless]
  • cnfw_subhalo: NFW concentration parameter of the dark matter subhalo in which this galaxy resides [dimensionless]. In the case of type 2 satellites, this corresponds to the concentration its subhalo had before disappearing from the subhalo catalogs.
  • cooling_rate: cooling rate of the hot halo component [Msun/Gyr/h].
  • descendant_id_galaxy: descendant galaxy ID. Different to galaxy id only if galaxy is type 2 and merges on the next snapshot.
  • id_galaxy: galaxy ID. Unique to this galaxy throughout time. If this galaxy never mergers onto a central, then its ID is always the same.
  • id_halo: halo ID. Unique to this snapshot.
  • id_halo_tree: halo id in the tree (unique to entire halo catalogue).
  • id_subhalo: subhalo ID. Unique to this snapshot.
  • id_subhalo_tree: subhalo id in the tree (unique to entire halo catalogue).
  • l_x: total angular momentum component x of galaxy [Msun pMpc km/s]. In the case of type 2 galaxies, the AM vector is randomly oriented.
  • l_y: total angular momentum component y of galaxy [Msun pMpc km/s]. In the case of type 2 galaxies, the AM vector is randomly oriented.
  • l_z: total angular momentum component z of galaxy [Msun pMpc km/s]. In the case of type 2 galaxies, the AM vector is randomly oriented.
  • lambda_subhalo: Spin parameter of the dark matter subhalo in which this galaxy resides [dimensionless]. In the case of type 2 satellites, this corresponds to the lambda its subhalo had before disappearing from the subhalo catalogs.
  • m_bh: black hole mass [Msun/h]
  • m_bh_assembly: black hole mass that comes from assembly (BH-BH mergers) [Msun/h]
  • matom_bulge: atomic gas mass (helium plus hydrogen) in the bulge [Msun/h]
  • matom_disk: atomic gas mass (helium plus hydrogen) in the disk [Msun/h]
  • mean_mstellar_galaxies_stellarhalo: mass weighted stellar mass of the galaxies that contributed to building the stellar halo [Msun/h]
  • mean_stellar_age: stellar mass-weighted stellar age [Gyr]
  • mgas_bulge: gas mass in the bulge [Msun/h]
  • mgas_disk: total gas mass in the disk [Msun/h]
  • mgas_metals_bulge: mass of metals locked in the gas of the bulge [Msun/h]
  • mgas_metals_disk: mass of metals locked in the gas of the disk [Msun/h]
  • mhot: hot gas mass in the halo [Msun/h]
  • mhot_metals: mass of metals locked in the hot halo gas [Msun/h]
  • mhot_metals_stripped: mass of metals that has been stripped out of this subhalo due to ram pressure stripping [Msun/h].
  • mhot_stripped: gas mass that has been stripped out of this subhalo due to ram pressure stripping [Msun/h].
  • mism_metals_stripped: mass of metals that has been stripped out of the ISM due to ram pressure stripping [Msun/h]
  • mism_stripped: gas mass that has been stripped out of the ISM due to ram pressure stripping [Msun/h]
  • mlost: gas mass in the lost gas component - due to QSO feedback [Msun/h]
  • mlost_metals: mass of metals locked in the lost gas component - due to QSO feedback [Msun/h]
  • mmol_bulge: molecular gas mass (helium plus hydrogen) in the bulge [Msun/h]
  • mmol_disk: molecular gas mass (helium plus hydrogen) in the disk [Msun/h]
  • mreheated: gas mass in the ejected gas component [Msun/h]
  • mreheated_metals: mass of metals locked in the ejected gas component [Msun/h]
  • mstars_bulge: stellar mass in the bulge [Msun/h]
  • mstars_bulge_diskins_assembly: stellar mass in the bulge brought via disk instabilities from the disk [Msun/h]
  • mstars_bulge_mergers_assembly: stellar mass in the bulge brought via galaxy mergers (but that formed in disks) [Msun/h]
  • mstars_burst_diskinstabilities: stellar mass formed via starbursts driven by disk instabilities [Msun/h]
  • mstars_burst_mergers: stellar mass formed via starbursts driven by galaxy mergers [Msun/h]
  • mstars_disk: stellar mass in the disk [Msun/h]
  • mstars_metals_bulge: mass of metals locked in stars in the bulge [Msun/h]
  • mstars_metals_bulge_diskins_assembly: mass of metals locked in stars in the bulge that was brought via disk instabilities from the disk [Msun/h]
  • mstars_metals_bulge_mergers_assembly: mass of metals locked in stars in the bulge that was brought via galaxy mergers (but that formed in disks) [Msun/h]
  • mstars_metals_burst_diskinstabilities: mass of metals locked in stars that formed via starbursts driven by disk instabilities [Msun/h]
  • mstars_metals_burst_mergers: mass of metals locked in stars that formed via starbursts driven by galaxy mergers [Msun/h]
  • mstars_metals_disk: mass of metals locked in stars in the disk [Msun/h]
  • mstars_metals_tidally_stripped: mass of metals locked in stars that was tidally stripped from this galaxy [Msun/h]
  • mstars_tidally_stripped: stellar mass that was tidally stripped from this galaxy [Msun/h]
  • mstellar_halo: stellar mass in the halo built by tidal stripping [Msun/h]
  • mstellar_halo_metals: mass of metals locked up in the stellar halo built by tidal stripping [Msun/h]
  • mvir_hosthalo: Dark matter mass of the host halo in which this galaxy resides [Msun/h]
  • mvir_infall_subhalo: Dark matter mass at infall of the host halo in which this galaxy reside when it was last central [Msun/h]
  • mvir_subhalo: Dark matter mass of the subhalo in which this galaxy resides [Msun/h]. In the case of type 2 satellites, this corresponds to the mass its subhalo had before disappearing from the subhalo catalogs.
  • on_hydrostatic_eq: is halo on quasi hydrostatic equilibrium (=1 for true, =0 for false).
  • position_x: position component x of galaxy [cMpc/h]. In the case of type 2 galaxies, the positions are generated to randomly sample an NFW halo with the concentration of the halo the galaxy lives in.
  • position_y: position component y of galaxy [cMpc/h]. In the case of type 2 galaxies, the positions are generated to randomly sample an NFW halo with the concentration of the halo the galaxy lives in.
  • position_z: position component z of galaxy [cMpc/h]. In the case of type 2 galaxies, the positions are generated to randomly sample an NFW halo with the concentration of the halo the galaxy lives in.
  • r_halo_stripped: ram pressure stripping radius of the halo gas [cMpc/h]
  • r_ism_stripped: ram pressure stripping radius of the ISM [cMpc/h]
  • redshift_merger: redshift at which this galaxy will merge onto a central galaxy (only relevant for type 2 galaxies)
  • rgas_bulge: half-mass radius of the gas bulge [cMpc/h]
  • rgas_disk: half-mass radius of the gas disk [cMpc/h]
  • rstar_bulge: half-mass radius of the stellar bulge [cMpc/h]
  • rstar_disk: half-mass radius of the stellar disk [cMpc/h]
  • sfr_burst: star formation rate in the bulge [Msun/Gyr/h]
  • sfr_burst_diskins: star formation rate in the bulge driven by disk instabilities [Msun/Gyr/h]
  • sfr_burst_mergers: star formation rate in the bulge driven by galaxy mergers [Msun/Gyr/h]
  • sfr_disk: star formation rate in the disk [Msun/Gyr/h]
  • specific_angular_momentum_bulge_gas: specific angular momentum of the gas bulge [km/s * cMpc/h]
  • specific_angular_momentum_bulge_star: specific angular momentum of the stellar bulge [km/s * cMpc/h]
  • specific_angular_momentum_disk_gas: specific angular momentum of the gas disk [km/s * cMpc/h]
  • specific_angular_momentum_disk_gas_atom: specific angular momentum of the atomic gas disk [km/s * cMpc/h]
  • specific_angular_momentum_disk_gas_mol: specific angular momentum of the molecular gas disk [km/s * cMpc/h]
  • specific_angular_momentum_disk_star: specific angular momentum of the stellar disk [km/s * cMpc/h]
  • type: galaxy type; =0 for centrals; =1 for satellites that reside in well identified subhalos; =2 for orphan satellites
  • velocity_x: peculiar velocity component x of galaxy [km/s]. In the case of type 2 galaxies, the velocity is generated to randomly sample the velocity dispersion of a NFW halo with the concentration of the halo the galaxy lives in.
  • velocity_y: peculiar velocity component y of galaxy [km/s]. In the case of type 2 galaxies, the velocity is generated to randomly sample the velocity dispersion of a NFW halo with the concentration of the halo the galaxy lives in.
  • velocity_z: peculiar velocity component z of galaxy [km/s]. In the case of type 2 galaxies, the velocity is generated to randomly sample the velocity dispersion of a NFW halo with the concentration of the halo the galaxy lives in.
  • vmax_subhalo: Maximum circular velocity of this galaxy [km/s]
  • vvir_hosthalo: Virial velocity of the dark matter host halo in which this galaxy resides [km/s].
  • vvir_subhalo: Virial velocity of the dark matter subhalo in which this galaxy resides [km/s]. In the case of type 2 satellites, this corresponds to the virial velocity its subhalo had before disappearing from the subhalo catalogs.

global

  • m_bh: total mass locked up in black holes in the simulated box [Msun/h]
  • m_dm: total dark matter mass locked up in halos in the simulated box [Msun/h].
  • m_h2: total molecular gas mass in the simulated box [Msun/h]
  • m_hi: total atomic gas mass in the simulated box [Msun/h]
  • mbar_created: total baryon mass in the simulated box [Msun/h]
  • mbar_lost: total baryons lost in the simulated box [Msun/h] (ideally this should be =0)
  • mcold: total cold gas mass (interstellar medium) in the simulated box [Msun/h]
  • mcold_halo: total halo cold gas in the simulated box [Msun/h]
  • mcold_halo_metals: total mass of metals in the halo cold gas mass in the simulated box [Msun/h]
  • mcold_metals: total mass of metals locked in cold gas in the simulated box [Msun/h]
  • mejected_halo: total gas mass ejected from halos due to stellar feedback (and that has not yet been reincorporated) in the simulated box [Msun/h]
  • mejected_halo_metals: total mass of metals in the ejected gas reservoir due to stellar feedback in the simulated box [Msun/h]
  • mhot_halo: total hot gas mass in halos in the simulated box [Msun/h]
  • mhot_metals: total mass of metals in the hot gas mass in halos in the simulated box [Msun/h]
  • mlost_halo: total gas mass ejected from halos due to QSO feedback in the simulated box [Msun/h]
  • mlost_halo_metals: total mass of metals in the ejected gas reservoir due to QSO feedback in the simulated box [Msun/h]
  • mstars: total stellar mass in the simulated box [Msun/h]
  • mstars_bursts_diskinstabilities: total stellar mass formed via starbursts triggered by disk instabilities in the simulated box [Msun/h]
  • mstars_bursts_mergers: total stellar mass formed via starbursts triggered by galaxy mergers in the simulated box [Msun/h]
  • mstars_metals: total mass of metals locked in stars in the simulated box [Msun/h]
  • mstars_metals_bursts_diskinstabilities: total mass of metals locked in stars that formed via starbursts triggered by disk instabilities in the simulated box [Msun/h]
  • mstars_metals_bursts_mergers: total mass of metals locked in stars that formed via starbursts triggered by galaxy mergers in the simulated box [Msun/h]
  • number_disk_instabilities: number of disk instability episodes taking place in the simulated box at this snapshot.
  • number_major_mergers: number of major mergers taking place in the simulated box at this snapshot.
  • number_minor_mergers: number of minor mergers taking place in the simulated box at this snapshot.
  • redshifts: redshifts of the global outputs.
  • sfr_burst: total star formation rate taking place in bulges in the simulated box [Msun/Gyr/h]
  • sfr_quiescent: total star formation rate taking place in disks in the simulated box [Msun/Gyr/h]
  • smbh_maximum: Maximum mass of the SMBHs in the simulated box [Msun/h]

halo

  • age_50: redshift at which the halo had 50% of its current mass
  • age_80: redshift at which the halo had 80% of its current mass
  • concentration: halo concentration
  • final_z0_mvir: virial mass of the halo in which this halo will end up in by z=0 [Msun/h]
  • halo_id: halo id in the tree (unique to entire halo catalogue)
  • lambda: halo spin
  • mvir: virial mass of halo [Msun/h]
  • vvir: virial velocity of halo [km/s]

run_info

  • batches: number of batches analysed
  • effective_volume: effective volume of this run [(cMpc/h)^3]
  • lbox: Box side size of the full simulated volume [Mpc/h]
  • ode_solver_precision: accuracy applied when solving the ODE system of the physical model.
  • particle_mass: dark matter particle mass of this simulation [Msun/h]
  • redshift: output redshift
  • seed: The seed value used in the random number engines
  • shark_git_has_local_changes: whether this shark instance had uncommitted local changes
  • shark_git_revision: the git revision of shark used to produce this data
  • shark_version: the shark version
  • skip_missing_descendants: boolean parameter that sets whether the code ignores subhalos that have no descendants.
  • snapshot: output snapshot
  • timestamp: time at which this shark execution started
  • tot_n_subvolumes: Total number of subvolumes in which the simulated box was divided into

subhalo

  • descendant_id: id of the subhalo that is the descendant of this subhalo
  • host_id: id of the host halo of this subhalo
  • id: Subhalo id
  • infall_time_subhalo: redshift at which the subhalo became a SATELLITE (only well defined for satellite subhalos)
  • l_x: total angular momentum component x of subhalo [Msun pMpc km/s]. From VELOCIraptor.
  • l_y: total angular momentum component y of galaxy [Msun pMpc km/s]. From VELOCIraptor.
  • l_z: total angular momentum component z of galaxy [Msun pMpc km/s]. From VELOCIraptor.
  • main_progenitor: =1 if subhalo is the main progenitor’ =0 otherwise.

Star formation histories

bulges_diskins

  • metallicity_histories: Stellar metallicity of the stars formed in a timestep that by this output time ends up in the bulge formed via disk instabilities
  • star_formation_rate_histories: Star formation history of stars formed that by this output time end up in the bulge formed via disk instabilities [Msun/yr/h]

bulges_mergers

  • metallicity_histories: Stellar metallicity of the stars formed in a timestep that by this output time ends up in the bulge formed via galaxy mergers
  • star_formation_rate_histories: Star formation history of stars formed that by this output time end up in the bulge formed via galaxy mergers [Msun/yr/h]

cosmology

  • h: normalization of hubble parameter H0 = h * 100 (km/s)/Mpc
  • n_s: scalar spectral index assumed in simulation
  • omega_b: omega baryon assumed in simulation
  • omega_l: omega lambda assumed in simulation
  • omega_m: omega matter assumed in simulation
  • sigma8: fluctuation amplitude at 8 Mpc/h
  • delta_t: Time interval covered between snapshots [Gyr]

disks

  • metallicity_histories: Stellar metallicity of the stars formed in a timestep that by this output time ends up in the disk
  • star_formation_rate_histories: Star formation history of stars formed that by this output time end up in the disk [Msun/yr/h]

galaxies

  • id_galaxy: galaxy ID. Unique to this galaxy throughout time. If this galaxy never mergers onto a central, then its ID is always the same.
  • lbt_mean: Look back time to mean time between snapshots [Gyr]
  • redshifts: Redshifts of the history outputs

run_info

  • batches: number of batches analysed
  • effective_volume: effective volume of this run [(cMpc/h)^3]
  • lbox: Box side size of the full simulated volume [Mpc/h]
  • ode_solver_precision: accuracy applied when solving the ODE system of the physical model.
  • particle_mass: dark matter particle mass of this simulation [Msun/h]
  • redshift: output redshift
  • seed: The seed value used in the random number engines
  • shark_git_has_local_changes: whether this shark instance had uncommitted local changes
  • shark_git_revision: the git revision of shark used to produce this data
  • shark_version: the shark version
  • skip_missing_descendants: boolean parameter that sets whether the code ignores subhalos that have no descendants.
  • snapshot: output snapshot
  • timestamp: time at which this shark execution started
  • tot_n_subvolumes: Total number of subvolumes in which the simulated box was divided into