L-Galaxies, Munich Galaxy Formation Model

Makefile & Input options
  1. Overview of Makefile and input options

    2. A number of usefull options are available in the makefile and input files. These range from running a completely different version of the galaxy formation model, changing the stellar populations used to compute photometric properties, use a different dark matter simulation, or simply changing the number of outputs snapshots or output properties. Below is a quicky overview of a few key options:

    • run different dark matter sub-volumes: change FirstFile and LastFile in input***.par.
    • change the output snapshots: OPT += -DNOUT changes the number and the list is in FileWithOutputRedshifts defined in the input***.par (./input/desired_output_redshifts.txt by default).
    • use diferent implementations of physical modules: different treatments of some processes are available as input options. These are listed under "Switches for different physical models" in input***.par.
    • change the model parameters: a variety of parameters can be changed under "Parameters of physical model" in input***.par
    • change stellar population models: choose between OPT += -DM05, OPT += -DBC03 and OPT += -DCB07 and change PhotPrefix and SpecPhotIMF in input***.par accordingly.
    • photometry: there are makefile options that control if rest-frame (OPT += -DOUTPUT_REST_MAGS) or observed-frame magnitudes (OPT += -DCOMPUTE_OBS_MAGS+OPT += -DOUTPUT_OBS_MAGS) are outputted. The number of bands written to the output file is controled by OPT += -DNMAG=40 (40 bands written by default). The list of bands is in FileWithFilterNames, defined in the input***.par.
    • use a different dark matter simulation: makefile options are available to run the code on MRII or PHOENIX. These must be used with the apropriate input***.par files (with the corresponding prefix on the name). Input files for other simulations can be created by changing the input variables under the "Simulation" and "Cosmological parameters" headers and the value for MAXSNAPS in allvars.h (number of snapshots of the dark matter simulation).

  2. My_Makefile_options

    3. Chaning the makefile options might change the output structure. Always make sure you are trying to read the correct LGalaxies_struct in your plotting routines.

    Options that control I/O and speed:

    • OPT += -DOVERWRITE_OUTPUT: overwrite output files if they exist
    • OPT += -DNOUT=28: define the number of output snapshots (read from /input/desired_output_redshifts.txt).
    • OPT += -DPARALLEL: if ON, the code will be run in parallel. Each processor will run on a different dark matter tree file.
    • OPT += -DGALAXYTREE: the entire galaxy tree (including long long IDs will be outputted)
    • OPT += -DLOADIDS: loads the tree_dbids files. This is needed for OPT += -DGALAXYTREE and is useful if one needs to follow progenitors/descendants while running the code.
    • OPT += -DUPDATETYPETWO: uses information from the most bounded particle at the time haloes get disrupted to track the dynamics of orphan galaxies. Crucial to properly track the dynamics of satellites in simulations with resolution below MRII.

    Options to choose the dark matter simulation:

    • OPT += -DMRII: run the model on the MillenniumII Simulation (when combined with input_MRII_***.par input files)
    • OPT += -DPHOENIX:

    Options to run pre-defined models:

    • OPT += -DGUO10: run the Guo2011 model (when combined with input_Guo11_***.par input files)
    • OPT += -DGUO13: run the Guo2013 model (when combined with input_Guo13_***.par input files)
    • OPT += -DHENRIQUES13: run the Henriques2013 model (when combined with input_Henriques13_***.par input files)

    Option to control the output of star formation histories:

    • OPT += -DSTAR_FORMATION_HISTORY: star formation histories are recorded. Option required in order to use OPT += -DPOST_PROCESS_MAGS and detailed chemical enrichment. The number of bins to be outputted is defined in allvars.h, default: SFH_NMERGE 3, SFH_NBIN 20.

    Options that control the output of emission properties

    • OPT += -DCOMPUTE_SPECPHOT_PROPERTIES: needs to be ON for any emission properties to be computed.

    • OPT += -DPOST_PROCESS_MAGS: Compute the magnitudes in post-processing. If ON, magnitudes are computed from star formation histories after galaxy evolution has been computed. It speeds up the code significantly and requires OPT += -DSTAR_FORMATION_HISTORY.

    Emission properties in the code are calculated from pre-computed photometry tables. These give the emission in different filters, per unit solar mass, as a function of age and metallicity. For a given episode of star formation, the metallicity and age of the population at the output redshifts are interpolated in the tables to give the right emission properties. For observed-frame magnitudes, it is also necessary to compute a table of redshifted emission, as a function of age and metallicity, for each filter and for each output redshift. For the list of snapshots in the Millennium and MillenniumII simulations, photometric tables are already available for WMAP1, WMAP7 and PLANCK cosmologies (you can use OPT += -DPHOTTABLES_PRECOMPUTED). For other simulations, or cosmologies, tables need to be computed on the fly using OPT += -DSPEC_PHOTABLES_ON_THE_FLY.

    • OPT += -DPHOTTABLES_PRECOMPUTED : use pre-computed photometry tables.
    • OPT += -DSPEC_PHOTABLES_ON_THE_FLY: compute photometry tables on the fly

    • OPT += -DFULL_SPECTRA: output full spectra, instead of magnitudes in different filters.
    • OPT += -DAB: compute emission properties in the AB reference system.
    • OPT += -DVEGA: compute emission properties in the Vega reference system.

    Type of photometric properties to be computed. The list of magnitudes is read from ./input/Filter_Names.txt and the number of magnitudes is given my the Makefile option NMAG.

    • OPT += -DOUTPUT_REST_MAGS: output rest-frame magnitudes.
    • OPT += -DCOMPUTE_OBS_MAGS: compute observed-frame magnitudes.
    • OPT += -DOUTPUT_OBS_MAGS: output observed-frame magnitudes.
    • OPT += -DICL: output luminosities for the intra-cluster light
    • OPT += -DOUTPUT_MOMAF_INPUTS: output luminosities for lightcone construction.
    • OPT += -DKITZBICHLER: output luminosities for lightcone construction.

    Choose the stellar population synthesis model to use. PhotPrefix in input_***.par needs to be changed accordingly.

    • OPT += -DM05: use Maraston 2005 stellar populations.
    • OPT += -DBC03: use Bruzual & Charlot 2003 stellar populations.
    • OPT += -DCB07: use Charlot & Bruzual 2007 stellar populations.

    • OPT += -DNMAG: number of filters for which luminosities will be computed.

    2.1 Detailed Chemical Enrichment:

    • OPT += -DDETAILED_METALS_AND_MASS_RETURN: Switches on the detailed chemical enrichment model described in Yates et al. 2013.

    This option incorporates a detailed calculation of chemical enrichment into the galaxy formation model. Instead of assuming that a fixed yield of metals is formed and immediately returned into the ISM in each star formation event, the mass of each element produced in stars of different masses (i.e. ages) and initial metallicities is computed. The fraction of mass and elements returned into the ISM is then computed over time taking into account stellar evolution. Stellar winds and the death of stars in different types of SN will then return different elements and inject energy into the surrounding medium.

    • OPT += -DFEEDBACK_COUPLED_WITH_MASS_RETURN: Switches on coupling between SN feedback and the chemical enrichment model. This option makes the SN feedback dependent on the actual amount of material released by SNe and stellar winds at time t, rather than on the amount of mass formed into stars at time t. This allows the feedback from an given stellar population to be more realistically delayed and distributed over time.

    • OPT += -DINDIVIDUAL_ELEMENTS: Switches on tracking of individual chemical elements. This option allows the 11 chemical elements (H, He, C , N, O, Ne, Mg, Si, S, Ca, and Fe) considered to be self-consistently tracked, as they are produced and distributioned through the various components of a galaxy. When switched off, only the total metal mass (i.e. the sum of the individual elements considered) is tracked.

    • OPT += -DMETALRICHWIND: Switches on galactic winds with a metallicity independent of that in the ISM. This option allows a user-defined (or see -DGASDENSITYWIND) fraction, f_wind, of the ejecta from SNe-II in the stellar disc to be deposited directly in the hot gas of a galaxy. If -DINDIVIDUAL_ELEMENTS is on, the chemical composition of this 'metal-rich wind' is identical to the composition of the SNe-II ejecta. Note that any SNe exploding in the stellar bulge directly enrich the hot gas (but see -DBULGE_TO_COLD). Direct depositing of ejecta from SN-Ia in the stellar disc into the hot gas is controlled by the -DSNIATOHOT option. Ejecta from AGB stars in the stellar disc is always assumed to only enrich the cold gas.

    • OPT += -DMAINELEMENTS: Switches on tracking of only five key chemical elements (H, He, O, Mg, and Fe). Only works when the -DINDIVIDUAL_ELEMENTS option is on.

    • OPT += -DSNIATOHOT: Switches on direct enrichment of the CGM/ICM by SNe-Ia in the stellar disc. This option allows 100% of the ejecta from SNe-Ia in the stellar disc to be directly deposited into the hot gas. When off, 100% of this ejecta is deposited into the cold gas. Note that any SNe exploding in the stellar bulge directly enrich the hot gas (but see -DBULGE_TO_COLD). Direct depositing of ejecta from SN-II in the stellar disc into the hot gas is controlled by the -DMETALRICHWIND option. Ejecta from AGB stars in the stellar disc is always assumed to only enrich the cold gas.

    • OPT += -DGASDENSITYFWIND: Switches on metal-rich galactic winds with a strength inversely proportional to the density of the ISM (see Yates et al. 2013, section 6.3.3). This option allows the value of f_wind (the fraction of SN-II ejecta directly deposited into the hot gas) to be inversely proportional to the gas density of the cold gas.

    • OPT += -DBULGE_TO_COLD: Switches on enrichment of the ISM by stars in the stellar bulge. This option allows SNe-Ia, SNe-II, and AGB stars in the stellar bulge to directly enrich the cold gas. When off, their ejecta directly enriches the hot gas.

    • OPT += -DPORTINARI: Switches on the SN-II stellar yields of Portinari et al. (1999). This option loads the SN-II stellar yield tables provided by Portinari et al. (1998) for use in the chemical enrichment model.

    • OPT += -DCHIEFFI: Switches on the SN-II stellar yields of Chieffi et al. (2004). This option loads the SN-II stellar yield tables provided by Chieffi et al. (2004) for use in the chemical enrichment model.

    • OPT += -DBIMODALDTD: Switches on the bi-modal SN-Ia DTD of Mannucci et al. (2006) (see Yates et al. 2013, section 4.1). This option makes the chemical enrichment model assume a bi-modal SN-Ia delay-time distribution (DTD) when calculating the amount of SN-Ia ejecta released at any given time after star formation.

    • OPT += -DGAUSSIANDTD: Switches on the narrow Gaussian SN-Ia DTD of Strolger et al. (2004) (see Yates et al. 2013, section 4.1). This option makes the chemical enrichment model assume a narrow Gaussian SN-Ia delay-time distribution (DTD) when calculating the amount of SN-Ia ejecta released at any given time after star formation.

    • OPT += -DPOWERLAWDTD: Switches on the power-law SN-Ia DTD of Maoz et al. (2012) (see Yates et al. 2013, section 4.1). This option makes the chemical enrichment model assume a power-law SN-Ia delay-time distribution (DTD) when calculating the amount of SN-Ia ejecta released at any given time after star formation.

    • OPT += -DRUITERDTD: Switches on the bi-modal SN-Ia DTD of Ruiter et al. (2011). This option makes the chemical enrichment model assume a bi-modal SN-Ia delay-time distribution (DTD), based on the sub-Chandrasekhar-mass detonation model described by Ruiter et al. (2011), when calculating the amount of SN-Ia ejecta released at any given time after star formation.

  3. Input Options
    4. 3.1 Available options in input_***.par:

    At run time, an input file (ending in .par) must be passed to the executable as an argument. The parameters and different options available in those files are described here.

    • FileNameGalaxies: specifies the pre-fix for the output files.
    • FirstFile: the millennium simulations are divided into 512 subvolumes. This variable specifies the first sub-volume to be computed.
    • LastFile: this variable specifies the last sub-volume to be computed (to compute galaxy properties in the entire simulation set FirstFile to 0 and LastFile to 511).
    • FileWithOutputRedshifts: specifies the name of the file containing the desired output redshifts, ./input/desired_output_redshifts.txt by default (see section Additional input files for a description of the file).
    • McFile: specifies the file containing inputs for the Okamoto2008 reionization model. Used if ReionizationModel=0 in input_***_.par
    • CoolFunctionsDir: file containing the cooling functions.

    Options related to emission properties:

    • SpecPhotDir: specifies the directory containing pre-computed photometry tables and full spectra from SPS models.
    • PhotPrefix: specifies the prefix of the photometry tables to be used. Should be adjusted according to the cosmology and stellar population synthesis model to be used (the former is defined by the input_***.par file, the latter in My_Makefile_options).
    • SpecPhotIMF: specifies the IMF to be used to compute luminosities. In order to get a fully consistent model, the values for the instantaneous recycled fraction, metal yield and SN energy should be adjusted when Chabrier is not selected.
    • FileWithFilterNames:specifies the name of the file containing the filters for which luminosities will be computed (see section Additional input files for a description of the file).

    Options related to the dark matter simulation and I/O:

    • SimulationDir: specifies the directory containing the dark matter merger trees (these must be placed in a subdirectory called /treedata/)
    • LastDarkMatterSnapShot: number of the last snapshot of the dark matter simulation (under sub-find naming this will be suffix of the files to be read).
    • Hashbits: used to generate peano-hilbert keys.
    • OutputDir: directory where the galaxy catalogues will be outputted.
    • MaxMemSize: maximum memory (in Mb) allocated for each core.

    Options related to the Cosmology assumed:

    • ScalePos: scale factor to be applied to lengths in order to scale the original cosmology of the dark matter simulation.
    • ScaleMass: scale factor to be applied to masses in order to scale the original cosmology of the dark matter simulation.

    Target Cosmology:

    • BaryonFrac: \( f_b\), Sigma8: \(\sigma_8\)
    • FileWithZList: file with scale factors for the outputs of the dark matter simulation (simulation dependent).
    • PartMass: particle mass of the dark matter simulation, original particle mass x ScaleMass (simulation dependent).
    • BoxSize: box size of the dark matter simulation, original box size x ScalePos (simulation dependent).
    • Omega: \(\Omega_m\), OmegaLambda: \(\Omega_{\Lambda}\), Hubble_h: \(h\)

    Original Cosmology:

    • FileWithZList_OriginalCosm: scale factors for the outputs of the dark matter simulation (simulation dependent).
    • PartMass_OriginalCosm: particle mass of the dark matter simulation (simulation dependent)
    • BoxSize_OriginalCosm: box size of the dark matter simulation(simulation dependent)
    • Omega_OriginalCosm: \(\Omega_m\), OmegaLambda_OriginalCosm: \(\Omega_{\Lambda}\), Hubble_h_OriginalCosm: \(h\)

    If you use a different cosmology you will need to adjust the BoxSize and Hubble_h used in your plotting routines.

    3.1.1 Switches for different physical models:

    A number of switches for different physical models are available in the input files. These will change the treatment of specific physical processes and are fully documented in the input files. In general the standard model is defined by the value 0 (except the last two of these variables).

    3.1.2 Parameters of the physical model:

    The free parameters of the physical model can be adjusted in the input files. These will change the efficiencies of different physical processes and are fully documented on the input files (including references to equations or sections in the supplementary material of Henriques et al. 2015).

    3.2 Additional input files in /input/:

    • desired_output_redshfits.txt: list of redshifts to be outputted (the closest available snapshots from the simulation will be selected). The number of values to be read, NOUT, is defined in My_Makefile_options, except if GALAXYTREE option is selected (in which case all snapshots are outputted).
    • Filter_Names.txt: Names and wavelengths for the filters for which magnitudes will be outputted. The number should match the value of NMAG defined in My_Makefile_options. Please see section Switches for different physical models for details on how to predict different photometric properties.
    • ./zlists/zlist_"cosmology"_"simulation".txt: list of scale factors for the snapshots of the dark matter simulation.
    • Mc.txt: file with inputs for the Okamoto2008 reionization model. Used if ReionizationModel=0 in input_***_.par