Merge changes to master into vimf

.github/workflows/main.yml

@@ -27,7 +27,7 @@ jobs:
 
       # Installs required Python modules
       - name: Install Python modules
-        run: python3 -m pip install black==22.1.0
+        run: python3 -m pip install click==8.0.4 black==19.3b0
 
       # Runs the formatting script
       - name: Formatting

colibre/auto_plotter/ages.yml

@@ -60,3 +60,67 @@ stellar_mass_ages_50:
     caption: Median age of stars within the 50 kpc 3D aperture of each galaxy.
   observational_data:
     - filename: GalaxyStellarMassStellarAges/Gallazzi2005_Data.hdf5
+
+stellar_mass_ages_centrals_50:
+  type: "scatter"
+  legend_loc: "lower right"
+  select_structure_type: 1
+  y:
+    quantity: "stellar_age.tage_star"
+    units: yr
+    start: 1e8
+    end: 3e10
+  x:
+    quantity: "apertures.mass_star_50_kpc"
+    units: solar_mass
+    start: 1e7
+    end: 1e12
+  median:
+    plot: true
+    log: true
+    number_of_bins: 25
+    adaptive: true
+    start:
+      value: 1e7
+      units: solar_mass
+    end:
+      value: 1e12
+      units: solar_mass
+  metadata:
+    title: "Stellar mass - Stellar age relation (50 kpc aperture, centrals only)"
+    section: Ages
+    caption: Median age of stars within the 50 kpc 3D aperture of each galaxy, showing central galaxies only.
+  observational_data:
+    - filename: GalaxyStellarMassStellarAges/Gallazzi2005_Data.hdf5
+
+stellar_mass_ages_satellites_50:
+  type: "scatter"
+  legend_loc: "lower right"
+  select_structure_type: 0
+  y:
+    quantity: "stellar_age.tage_star"
+    units: yr
+    start: 1e8
+    end: 3e10
+  x:
+    quantity: "apertures.mass_star_50_kpc"
+    units: solar_mass
+    start: 1e7
+    end: 1e12
+  median:
+    plot: true
+    log: true
+    number_of_bins: 25
+    adaptive: true
+    start:
+      value: 1e7
+      units: solar_mass
+    end:
+      value: 1e12
+      units: solar_mass
+  metadata:
+    title: "Stellar mass - Stellar age relation (50 kpc aperture, satellites only)"
+    section: Ages
+    caption: Median age of stars within the 50 kpc 3D aperture of each galaxy, showing satellite galaxies only.
+  observational_data:
+    - filename: GalaxyStellarMassStellarAges/Gallazzi2005_Data.hdf5

colibre/auto_plotter/baryon_fractions.yml

@@ -1,6 +1,6 @@
 baryon_fraction_500:
-  type: "2dhistogram"
-  select_structure_type: 10
+  type: "scatter"
+  select_structure_type: 1
   comment: "Centrals only"
   legend_loc: "upper left"
   x:
@@ -34,8 +34,8 @@ baryon_fraction_500:
     - filename: HaloMassBaryonFractions/Zhang2011.hdf5
 
 gas_fraction_500_no_bias:
-  type: "2dhistogram"
-  select_structure_type: 10
+  type: "scatter"
+  select_structure_type: 1
   comment: "Centrals only"
   legend_loc: "upper left"
   x:
@@ -72,9 +72,48 @@ gas_fraction_500_no_bias:
     - filename: HaloMassGasFractions/Eckert2016.hdf5
     - filename: HaloMassGasFractions/Lovisari2015.hdf5
 
+hot_gas_fraction_500_no_bias:
+  type: "scatter"
+  select_structure_type: 1
+  comment: "Centrals only"
+  legend_loc: "upper left"
+  x:
+    quantity: "spherical_overdensities.mass_500_rhocrit"
+    units: Solar_Mass
+    start: 1e10
+    end: 1e15
+  y:
+    quantity: "derived_quantities.hot_gas_fraction_true_R500"
+    units:  "dimensionless"
+    log: false
+    start: 0.
+    end: 1.2
+  median:
+    plot: true
+    log: true
+    min_num_points_highlight: 0
+    adaptive: true
+    number_of_bins: 25
+    start:
+      value: 1e10
+      units: Solar_Mass
+    end:
+      value: 1e15
+      units: Solar_Mass
+  metadata:
+    title: "Halo hot gas fractions within $R_{500}$ (no hydrostatic bias)"
+    caption: Fraction of halo mass within $R_{500}$ in hot ($T>10^5$K) gas, normalised by the cosmic mean. These are 'true' values, i.e. no cut or observational correction was applied. The observational data does not include any correction for hydrostatic bias.
+    section: Baryon Fractions
+  observational_data:
+    - filename: HaloMassGasFractions/Lin2012.hdf5
+    - filename: HaloMassGasFractions/Sun2009.hdf5
+    - filename: HaloMassGasFractions/Vikhlinin2006.hdf5
+    - filename: HaloMassGasFractions/Eckert2016.hdf5
+    - filename: HaloMassGasFractions/Lovisari2015.hdf5
+
 gas_fraction_500_with_bias:
-  type: "2dhistogram"
-  select_structure_type: 10
+  type: "scatter"
+  select_structure_type: 1
   comment: "Centrals only"
   legend_loc: "upper left"
   x:
@@ -108,8 +147,8 @@ gas_fraction_500_with_bias:
     - filename: HaloMassGasFractions/HSE-FLAMINGO.hdf5
 
 star_fraction_500:
-  type: "2dhistogram"
-  select_structure_type: 10
+  type: "scatter"
+  select_structure_type: 1
   comment: "Centrals only"
   legend_loc: "upper left"
   x:
@@ -145,8 +184,8 @@ star_fraction_500:
 
 
 gas_mass_500:
-  type: "2dhistogram"
-  select_structure_type: 10
+  type: "scatter"
+  select_structure_type: 1
   comment: "Centrals only"
   legend_loc: "upper left"
   x:

colibre/auto_plotter/black_holes.yml

@@ -108,7 +108,7 @@ stellar_mass_black_hole_mass_binned_50:
 
 stellar_mass_black_hole_mass_passive_30:
   type: "scatter"
-  select_structure_type: 10
+  select_structure_type: 1
   comment: "Passive centrals only"
   comment_loc: "lower right"
   legend_loc: "upper left"
@@ -144,7 +144,7 @@ stellar_mass_black_hole_mass_passive_30:
 
 stellar_mass_black_hole_mass_passive_50:
   type: "scatter"
-  select_structure_type: 10
+  select_structure_type: 1
   comment: "Passive centrals only"
   comment_loc: "lower right"
   legend_loc: "upper left"
@@ -179,7 +179,7 @@ stellar_mass_black_hole_mass_passive_50:
 
 stellar_mass_black_hole_mass_active_30:
   type: "scatter"
-  select_structure_type: 10
+  select_structure_type: 1
   comment: "Active centrals only"
   comment_loc: "lower right"
   legend_loc: "upper left"
@@ -215,7 +215,7 @@ stellar_mass_black_hole_mass_active_30:
 
 stellar_mass_black_hole_mass_active_50:
   type: "scatter"
-  select_structure_type: 10
+  select_structure_type: 1
   comment: "Active centrals only"
   comment_loc: "lower right"
   legend_loc: "upper left"
@@ -377,7 +377,7 @@ stellar_mass_stellar_veldisp_10:
 ssfr_rate_black_hole_mass_30:
   type: "scatter"
   legend_loc: "upper right"
-  select_structure_type: 10
+  select_structure_type: 1
   selection_mask: "derived_quantities.stellar_mass_is_bigger_than_1e10_msun_30_kpc"
   comment: "Centrals only, $M_* > 10^{10}$ solar masses"
   redshift_loc: "lower left"
@@ -414,7 +414,7 @@ ssfr_rate_black_hole_mass_30:
 ssfr_rate_black_hole_mass_50:
   type: "scatter"
   legend_loc: "upper right"
-  select_structure_type: 10
+  select_structure_type: 1
   selection_mask: "derived_quantities.stellar_mass_is_bigger_than_1e10_msun_50_kpc"
   comment: "Centrals only, $M_* > 10^{10}$ solar masses"
   redshift_loc: "lower left"

colibre/auto_plotter/dust_mass_function.yml

@@ -19,6 +19,8 @@ dust_mass_function:
     - filename: GalaxyDustMassFunction/Pozzi2020_z000p100.hdf5
     - filename: GalaxyDustMassFunction/Pozzi2020_z001p800.hdf5
     - filename: GalaxyDustMassFunction/Beeston2018_z000p000.hdf5
+    - filename: GalaxyDustMassFunction/Traina2024.hdf5
+    - filename: GalaxyDustMassFunction/Berta2025.hdf5
 
 adaptive_dust_mass_function:
   type: "adaptivemassfunction"
@@ -41,6 +43,8 @@ adaptive_dust_mass_function:
     - filename: GalaxyDustMassFunction/Pozzi2020_z000p100.hdf5
     - filename: GalaxyDustMassFunction/Pozzi2020_z001p800.hdf5
     - filename: GalaxyDustMassFunction/Beeston2018_z000p000.hdf5
+    - filename: GalaxyDustMassFunction/Traina2024.hdf5
+    - filename: GalaxyDustMassFunction/Berta2025.hdf5
 
 dust_mass_function_molecular:
   type: "massfunction"
@@ -63,6 +67,8 @@ dust_mass_function_molecular:
     - filename: GalaxyDustMassFunction/Pozzi2020_z000p100.hdf5
     - filename: GalaxyDustMassFunction/Pozzi2020_z001p800.hdf5
     - filename: GalaxyDustMassFunction/Beeston2018_z000p000.hdf5
+    - filename: GalaxyDustMassFunction/Traina2024.hdf5
+    - filename: GalaxyDustMassFunction/Berta2025.hdf5
 
 dust_mass_function_neutral:
   type: "massfunction"
@@ -85,6 +91,8 @@ dust_mass_function_neutral:
     - filename: GalaxyDustMassFunction/Pozzi2020_z000p100.hdf5
     - filename: GalaxyDustMassFunction/Pozzi2020_z001p800.hdf5
     - filename: GalaxyDustMassFunction/Beeston2018_z000p000.hdf5
+    - filename: GalaxyDustMassFunction/Traina2024.hdf5
+    - filename: GalaxyDustMassFunction/Berta2025.hdf5
 
 dust_mass_function_cold_dense:
   type: "massfunction"
@@ -107,4 +115,6 @@ dust_mass_function_cold_dense:
     - filename: GalaxyDustMassFunction/Pozzi2020_z000p100.hdf5
     - filename: GalaxyDustMassFunction/Pozzi2020_z001p800.hdf5
     - filename: GalaxyDustMassFunction/Beeston2018_z000p000.hdf5
+    - filename: GalaxyDustMassFunction/Traina2024.hdf5
+    - filename: GalaxyDustMassFunction/Berta2025.hdf5
 

colibre/auto_plotter/dust_mass_relations.yml

@@ -36,6 +36,14 @@ stellar_mass_v_dust_mass:
     - filename: GalaxyStellarMassDustMass/DaCunha2015_z004p000.hdf5
     - filename: GalaxyStellarMassDustMass/DaCunha2015_z005p000.hdf5
     - filename: GalaxyStellarMassDustMass/DaCunha2015_z006p000.hdf5
+    - filename: GalaxyStellarMassDustMass/Sommovigo2022.hdf5
+    - filename: GalaxyStellarMassDustMass/Jolly2024.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_HAPLESS.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_HIGH.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_HRS.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_HRS_HIdef.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_JINGLE.hdf5
+    - filename: GalaxyStellarMassDustMass/DeLooze20_KINGFISH.hdf5
 
 star_formation_rate_v_dust_mass:
   type: "scatter"
@@ -45,7 +53,7 @@ star_formation_rate_v_dust_mass:
     quantity: "apertures.sfr_gas_50_kpc"
     units: Solar_Mass / year
     start: 1e-3
-    end: 1e2
+    end: 3e2
     log: true
   y:
     quantity: "derived_quantities.total_dust_masses_50_kpc"
@@ -71,6 +79,7 @@ star_formation_rate_v_dust_mass:
     show_on_webpage: true
   observational_data:
     - filename: GalaxyStarFormationRateDustMass/Bianchi2018_Data_noerr.hdf5
+    - filename: GalaxyStarFormationRateDustMass/Jolly2024.hdf5
 
 neutral_mass_v_dust_mass:
   type: "scatter"

colibre/auto_plotter/gas_fraction_plots.yml

@@ -30,7 +30,7 @@ h2_frac_func_stellar_mass_xgass_selection:
   metadata:
     title: Stellar Mass-H$_2$ Fraction
     section: Cold Gas Data Comparison
-    caption: Galaxy H$_2$ mass (including Helium following the observations) over stellar mass as a function of stellar mass in 0.2 dex bins, measured in 50 kpc apertures. To include Helium we multiply $M_{\rm H_2}/M_{\rm star}$ by $(1+M_{\rm He}/M_{\rm H})$. The median values are shown. In Saintonge2017+ data, all galaxies with $10^9 < M_{\rm star} / \mathrm{M_\odot} < 10^{10}$ have $M_{\rm H_2}/M_{\rm star}$ fractions that cannot be lower than $0.025$, and for galaxies with $M_{\rm star} / \mathrm{M_\odot} > 10^{10}$ the floor value is $0.015$.
+    caption: Galaxy H$_2$ mass (including Helium following the observations) over stellar mass as a function of stellar mass in 0.2 dex bins, measured in 50 kpc apertures. To include Helium we multiply $M_{\rm H_2}/M_{\rm star}$ by $(1+M_{\rm He}/M_{\rm H})$. The median values are shown. In Saintonge2017+ data, all galaxies with $10^9 < M_{\rm star} / \mathrm{M_\odot} < 10^{10}$ have $M_{\rm H_2}/M_{\rm star}$ fractions that cannot be lower than $0.025$, and for galaxies with $M_{\rm star} / \mathrm{M_\odot} > 10^{10}$ the floor value is $0.015$. The median values ("Binning") are shown.
     show_on_webpage: false
   observational_data:
     - filename: GalaxyH2Fractions/Saintonge2017_abcissa_M_star.hdf5
@@ -246,7 +246,7 @@ h2_frac_func_stellar_mass:
   metadata:
     title: Stellar Mass-H$_2$ Fraction
     section: Cold Gas Data Comparison
-    caption: Galaxy H$_2$ mass (including Helium following the observations) over stellar mass as a function of stellar mass in 0.2 dex bins, measured in 50 kpc apertures. To include Helium we multiply $M_{\rm H_2}/M_{\rm star}$ by $(1+M_{\rm He}/M_{\rm H})$. The median values are shown. In Saintonge2017+ data, all galaxies with $10^9 < M_{\rm star} / \mathrm{M_\odot} < 10^{10}$ have $M_{\rm H_2}/M_{\rm star}$ fractions that cannot be lower than $0.025$, and for galaxies with $M_{\rm star} / \mathrm{M_\odot} > 10^{10}$ the floor value is $0.015$.
+    caption: Galaxy H$_2$ mass (including Helium following the observations) over stellar mass as a function of stellar mass in 0.2 dex bins, measured in 50 kpc apertures. To include Helium we multiply $M_{\rm H_2}/M_{\rm star}$ by $(1+M_{\rm He}/M_{\rm H})$. The median values are shown. In Saintonge2017+ data, all galaxies with $10^9 < M_{\rm star} / \mathrm{M_\odot} < 10^{10}$ have $M_{\rm H_2}/M_{\rm star}$ fractions that cannot be lower than $0.025$, and for galaxies with $M_{\rm star} / \mathrm{M_\odot} > 10^{10}$ the floor value is $0.015$. The median values ("Binning") are shown.
   observational_data:
     - filename: GalaxyH2Fractions/Saintonge2017_abcissa_M_star.hdf5
     - filename: GalaxyH2Fractions/Hunt2020_Data.hdf5
@@ -293,6 +293,43 @@ hi_frac_func_stellar_mass:
     - filename: GalaxyHIFractions/Lisenfeld2016_Data.hdf5
     - filename: GalaxyHIFractions/Gratier2010_Data.hdf5
     - filename: GalaxyHIFractions/FIREbox.hdf5
+    - filename: GalaxyHIFractions/Scholte2024_MassComplete.hdf5
+
+hi_frac_func_stellar_mass_active_only_50:
+  type: "scatter"
+  legend_loc: "lower left"
+  selection_mask: "derived_quantities.is_active_50_kpc"
+  comment: "Active only"
+  x:
+    quantity: "apertures.mass_star_50_kpc"
+    units: Solar_Mass
+    start: 1e5
+    end: 1e12
+  y:
+    quantity: "derived_quantities.hi_to_stellar_mass_50_kpc"
+    units: "Solar_Mass / Solar_Mass"
+    start: 1e-4
+    end: 100
+  median:
+    plot: true
+    adaptive: true
+    log: true
+    number_of_bins: 35
+    start:
+      value: 1e5
+      units: Solar_Mass
+    end:
+      value: 1e12
+      units: Solar_Mass
+    lower:
+      value: 1e-10
+      units: "Solar_Mass / Solar_Mass"
+  metadata:
+    title: Stellar Mass-HI Fraction (active galaxies)
+    section: Cold Gas Data Comparison
+    caption: Galaxy HI mass over stellar mass as a function of stellar mass in 0.2 dex bins, measured in 50 kpc apertures. Active galaxies only.
+  observational_data:
+    - filename: GalaxyHIFractions/Scholte2024_SF.hdf5
 
 cold_gas_frac_func_ssfr:
   type: "scatter"

colibre/auto_plotter/gas_mass_functions.yml

@@ -16,9 +16,13 @@ gas_HI_mass_function:
     caption: HIMF, showing all galaxies with a fixed bin-width of 0.2 dex (HI masses 50 kpc).
     section: Gas Mass Function
   observational_data:
-    - filename: GalaxyHIMassFunction/Zwaan2003.hdf5
-    - filename: GalaxyHIMassFunction/Jones2018.hdf5
+    - filename: GalaxyHIMassFunction/Zwaan2005.hdf5
+    - filename: GalaxyHIMassFunction/Xi2022.hdf5
+    - filename: GalaxyHIMassFunction/Guo2023.hdf5
     - filename: GalaxyHIMassFunction/Ponomareva2023.hdf5
+    - filename: GalaxyHIMassFunction/Ma2024_north.hdf5
+    - filename: GalaxyHIMassFunction/Ma2024_south.hdf5
+    - filename: GalaxyHIMassFunction/Chowdhury2024.hdf5
 
 adaptive_gas_HI_mass_function:
   type: "adaptivemassfunction"
@@ -38,9 +42,13 @@ adaptive_gas_HI_mass_function:
     caption: HIMF, showing all galaxies with an adaptive bin-width (HI masses 50 kpc).
     section: Gas Mass Function
   observational_data:
-    - filename: GalaxyHIMassFunction/Zwaan2003.hdf5
-    - filename: GalaxyHIMassFunction/Jones2018.hdf5
+    - filename: GalaxyHIMassFunction/Zwaan2005.hdf5
+    - filename: GalaxyHIMassFunction/Xi2022.hdf5
+    - filename: GalaxyHIMassFunction/Guo2023.hdf5
     - filename: GalaxyHIMassFunction/Ponomareva2023.hdf5
+    - filename: GalaxyHIMassFunction/Ma2024_north.hdf5
+    - filename: GalaxyHIMassFunction/Ma2024_south.hdf5
+    - filename: GalaxyHIMassFunction/Chowdhury2024.hdf5
 
 gas_H2_mass_function:
   type: "massfunction"