There is one main script for the galacticus matchup: lc_resample.py (light cone resample) There are several precompute scritps: All scirpts run with one argrument: their parameter file. i.e: "./lc_resample.py param_lc_resamp/v4.1.dust136.param" There are dependencies on dtk, Eve's galmatcher and the cosmoDC2 package.

Setup Scripts

1. lightcone_matchup.py param_lc_match/*.param: This script takes in parameters from param_lc_matchup folder This code takes in the binary outputs from the lightcone cutout cod and the UMachine + Color snapshot catalog and creates a lightcone catalog with all snapshot catalog properties. If the positions don't change, then all one has to do is change the "snapshot_galaxy_fname" parameter to point to the new UMachine + color snapshot catalog. This is a fast script.

2. k_cor_step.py param_kcorr/*.param: This scirpt generates the index to relate galaxies from step B to step A, where step B is later in time.

3. precompute_mask.py param_lc_resamp/*.param: This script precomputes the masks on snaps shot (eg: color cuts, mstar cuts, etc) It should run on teh same parameter file as lc_resamp

Main Script:

 ./lc_resample.py param_lc_resampe/*.param
 This function matches up the lightcone UMachine galaxies to Galacticus galaxies. 
 These are parameters for the script:
 
 #The output form lightcone_matchup.py
 lightcone_fname /cosmo/homes/dkorytov/data/cosmoDC2/protoDC2_v4.1/lc_mock/lc_mock_v4.1_${step}.hdf5
 #galacticus snapshots
 gltcs_fname     /cosmo/homes/dkorytov/proj/protoDC2/output/ANL_box_v2.1.3_nocut_steps/${step}.hdf5
 # a galacticus file from which the metadata is copied from
 gltcs_metadata_ref  /cosmo/homes/dkorytov/proj/protoDC2/output/ANL_box_v2.1.3_nocut_mod.hdf5
 # not sued
 gltcs_slope_fname output/k_corr_${step}.hdf5
 # host halo info
 halo_shape_fname     /cosmo/homes/dkorytov/data/AlphaQ/halo_shapes/m000-${step}.bighaloshapes
 halo_shape_red_fname /cosmo/homes/dkorytov/data/AlphaQ/halo_shapes/m000-${step}.bighaloshapes_red
 sod_fname /cosmo/homes/dkorytov/data/AlphaQ/M200/STEP${step}/m000-${step}.sodproperties
 # which steps to run on. 
 #steps       315     307      300      293      286      279      272      266      259      253      247
 #steps           487      475      464      453      442      432      421      411      401      392      382      373      365      355      347      338      331      323      315      307      300      293      286      279      272      266      259      253      247
 #steps  331      323      315     307     
 #steps     315     307     
 steps   432      421

 # output location 
 output_fname  /cosmo/homes/dkorytov/data/cosmoDC2/protoDC2_test/ptest${step}.hdf5

 # Where to load the precomputed galmatcher mask & if to load it
 load_mask true
 mask_loc output/masks/mask.hdf5

 # Where to load indexing to match galacticus snapshots
 index_loc output/index/index_${step}.hdf5

 # Use_slope must be ste to true. OTher paths are depricated.
 # Use_slope turns on the interpolation bewteen snapshots. Substeps indiciates
 # into how many slices each step is divided into. The kdtree match is done 
 # on each slice. "use_substep_redshift" controls if galaxies use the substep's 
 # redshift, which is discrete, or their own individual redshift. 
 use_slope true
 substeps  1
 use_substep_redshift true

 # assignes new colors to galaxies using the assign color function
 # in teh cosmodc2 repo.
 recolor false

 # The parameters are used to speed up the run of the catalog. if "short" and "supershort"
 # are turned on, all columns but SDSS filters, stellar mass and new calculated quantites
 # are not output to disk. "short" only excludes LSST and SEDs. Cut_small_galaxies cuts out
 # small galaxies from the KDTree & matchup so should speed things up as well. It hasn't been
 # carefuly tested. 
 short     true
 supershort true
 cut_small_galaxies true
 cut_small_galaxies_mass 8 

 # Use_dust_factor must be turned on. Other paths are depcripated
 # "dust_factors" list the extra multiplicitive factors of dust.
 # a x1 factor is automatically included. 
 use_dust_factor true
 dust_factors 

 # To match on stellar or not
 ignore_mstar true
 # To match on observed colors (g-r, r-i, i-z)  for red squence 
 # galaxies in clusters (M_halo > 10**13.5). 
 match_obs_color_red_seq true
 
 # "plot" plots after each step of the input UM catalog vs the catalog on disk.
 # "plot_substep" plots the input UM catalog vs the matched galacticus for each
 # substep whil matching. 
 plot      true
 plot_substep true
 
 # The version number to write into the catalog metadata
 version_major       4
 version_minor       1
 version_minor_minor 0