Specify the cosmology in terms of Omega_cdm and not Omega_m

doc/RTD/source/ParameterFiles/parameter_description.rst

@@ -33,9 +33,9 @@ parameters:
 .. code:: YAML
 
    Cosmology:    # Planck13
-     Omega_m:        0.307
+     Omega_cdm:      0.2587481
      Omega_lambda:   0.693
-     Omega_b:        0.0455
+     Omega_b:        0.0482519
      h:              0.6777
      a_begin:        0.0078125     # z = 127
 
@@ -146,7 +146,7 @@ cosmological model. The expanded :math:`\Lambda\rm{CDM}` parameters governing th
 background evolution of the Universe need to be specified here. These are:
 
 * The reduced Hubble constant: :math:`h`: ``h``,
-* The matter density parameter :math:`\Omega_m`: ``Omega_m``,
+* The cold dark matter density parameter :math:`\Omega_cdm`: ``Omega_cdm``,
 * The cosmological constant density parameter :math:`\Omega_\Lambda`: ``Omega_lambda``,
 * The baryon density parameter :math:`\Omega_b`: ``Omega_b``,
 * The radiation density parameter :math:`\Omega_r`: ``Omega_r``.
@@ -202,18 +202,18 @@ use the following parameters:
 
 .. code:: YAML
 
-   Cosmology:
+   Cosmology:        # Planck13 (EAGLE flavour)
      a_begin:        0.0078125     # z = 127
      a_end:          1.0           # z = 0
      h:              0.6777
-     Omega_m:        0.307
+     Omega_cdm:      0.2587481
      Omega_lambda:   0.693
      Omega_b:        0.0482519
      Omega_r:        0.            # (Optional)
      w_0:            -1.0          # (Optional)
      w_a:            0.            # (Optional)
 
-When running a non-cosmological simulation (i.e. without the ``-c`` run-time
+When running a non-cosmological simulation (i.e. without the ``--cosmology`` run-time
 flag) this section of the YAML file is entirely ignored.
 
 .. _Parameters_gravity:

examples/Cooling/ConstantCosmoTempEvolution/const_cosmo_temp_evol.yml

@@ -11,7 +11,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0099        # Initial scale-factor of the simulation (z = 100.0)
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/Cooling/CoolingRedshiftDependence/cooling_redshift_dependence_high_z.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.5        # Initial scale-factor of the simulation (z = 1.0)
   a_end:          0.5061559     # Final scale factor of the simulation (~ 100 myr)
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/Cooling/CoolingRedshiftDependence/cooling_redshift_dependence_low_z.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.99009       # Initial scale-factor of the simulation (z = 0.01)
   a_end:          0.99700       # Final scale factor of the simulation (~ 100 myr)
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/Cosmology/ComovingSodShock_1D/sodShock.yml

@@ -34,10 +34,10 @@ InitialConditions:
   periodic:   1
 
 Cosmology:
-  Omega_m: 1.
+  Omega_cdm:    0.
   Omega_lambda: 0.
-  Omega_b: 1.
-  h: 1.
+  Omega_b:      1.
+  h:            1.
   a_begin: 0.001
   a_end: 0.00106638
 

examples/Cosmology/ComovingSodShock_2D/sodShock.yml

@@ -34,10 +34,10 @@ InitialConditions:
   periodic:   1
 
 Cosmology:
-  Omega_m: 1.
+  Omega_cdm:    0.
   Omega_lambda: 0.
-  Omega_b: 1.
-  h: 1.
+  Omega_b:      1.
+  h:            1.
   a_begin: 0.001
   a_end: 0.00106638
 

examples/Cosmology/ComovingSodShock_3D/sodShock.yml

@@ -36,10 +36,10 @@ InitialConditions:
   periodic:   1
 
 Cosmology:
-  Omega_m: 1.
+  Omega_cdm:    0.
   Omega_lambda: 0.
-  Omega_b: 1.
-  h: 1.
+  Omega_b:      1.
+  h:            1.
   a_begin: 0.001
   a_end: 0.00106638
 

examples/Cosmology/ConstantCosmoVolume/constant_volume.yml

@@ -7,12 +7,12 @@ InternalUnitSystem:
   UnitTemp_in_cgs:     1   	     # Kelvin
 
 Cosmology:
-  Omega_m: 1.
+  Omega_cdm:    0.
   Omega_lambda: 0.
-  Omega_b: 1.
-  h: 1.
-  a_begin: 0.00990099	# z_ini = 100.
-  a_end: 1.0		# z_end = 0.
+  Omega_b:      1.
+  h:            1.
+  a_begin:  0.00990099	# z_ini = 100.
+  a_end:    1.0		# z_end = 0.
 
 # Parameters governing the time integration
 TimeIntegration:

examples/Cosmology/NeutrinoCosmo/neutrino_cosmo.yml

 InternalUnitSystem:
-  UnitMass_in_cgs:	1.9884350000e+43 # 1e10 M_sol
-  UnitLength_in_cgs:	3.0856775815e+24 # 1 Mpc
-  UnitVelocity_in_cgs:	9.7846194238e+07 # 1 Gyr
-  UnitCurrent_in_cgs:	1.0000000000e+00 # 1 A
-  UnitTemp_in_cgs:	1.0000000000e+00 # 1 K
+  UnitMass_in_cgs:     1.9884350000e+43 # 1e10 M_sol
+  UnitLength_in_cgs:   3.0856775815e+24 # 1 Mpc
+  UnitVelocity_in_cgs: 9.7846194238e+07 # 1 Gyr
+  UnitCurrent_in_cgs:  1.0000000000e+00 # 1 A
+  UnitTemp_in_cgs:     1.0000000000e+00 # 1 K
 
 Cosmology:
-  Omega_m:	0.3122685143
-  Omega_b:	0.0491989267
-  Omega_lambda:	0.6853646238
-  h:		0.6737000000
-  a_begin:	0.0250000000 # z = 39.000000
-  a_end:	1.0000000000
-  N_nu:		1
-  N_ur:         1.0196
-  T_nu_0:	1.9517578050
-  M_nu_eV:	0.0486000000
-  deg_nu:       2.0
+  Omega_cdm:     0.2630695876
+  Omega_b:       0.0491989267
+  Omega_lambda:  0.6853646238
+  h:             0.6737000000
+  a_begin:       0.0250000000 # z = 39.000000
+  a_end:         1.0000000000
+  N_nu:          1
+  N_ur:          1.0196
+  T_nu_0:        1.9517578050
+  M_nu_eV:       0.0486000000
+  deg_nu:        2.0
 
 TimeIntegration:
-  dt_min:	1.0000e-10
-  dt_max:	1.0000e-02
+  dt_min:    1.0000e-10
+  dt_max:    1.0000e-02
 
 Scheduler:
-  max_top_level_cells:	16
-  cell_split_size:	100
+  max_top_level_cells:    16
+  cell_split_size:        100
 
 Snapshots:
-  scale_factor_first:	0.0250000000 # z = 39.000000
-  delta_time:		1.2500
-  basename:		box
-  compression:		4
+  scale_factor_first:  0.0250000000 # z = 39.000000
+  delta_time:          1.2500
+  basename:            box
+  compression:         4
 
 Statistics:
-  scale_factor_first:	0.0250000000 # z = 39.000000
-  delta_time:		1.2500
+  scale_factor_first:  0.0250000000 # z = 39.000000
+  delta_time:          1.2500
 
 Restarts:
-  delta_hours:	4.00
+  delta_hours:    4.00
 
 InitialConditions:
-  file_name:	particles.hdf5
-  periodic:	1
+  file_name:    particles.hdf5
+  periodic:     1
 
 Neutrino:
-  use_delta_f: 1   # Use the delta-f method for shot noise reduction
+  use_delta_f:  1  # Use the delta-f method for shot noise reduction
   generate_ics: 1  # Generate new Fermi-Dirac velocities for the particles
 
 Gravity:
-  mesh_side_length:	32
-  MAC:			geometric
-  eta:			0.02500
-  theta_cr:		0.50000
-  rebuild_frequency:	0.00 # rebuild always
-  comoving_DM_softening:		0.0400000000 	# 0.0400 of the mean inter-particle separation
-  max_physical_DM_softening:		0.0400000000 	# 0.0400 of the mean inter-particle separation
-  comoving_nu_softening:		0.0400000000 	# 0.0400 of the mean inter-particle separation
-  max_physical_nu_softening:		0.0400000000 	# 0.0400 of the mean inter-particle separation
+  mesh_side_length:    32
+  MAC:            geometric
+  eta:            0.02500
+  theta_cr:        0.50000
+  rebuild_frequency:    0.00 # rebuild always
+  comoving_DM_softening:      0.0400000000  # Mpc
+  max_physical_DM_softening:  0.0400000000  # Mpc
+  comoving_nu_softening:      0.0400000000  # Mpc
+  max_physical_nu_softening:  0.0400000000  # Mpc

examples/Cosmology/ZeldovichPancake_3D/zeldovichPancake.yml

@@ -7,10 +7,10 @@ InternalUnitSystem:
   UnitTemp_in_cgs:     1   # Kelvin
 
 Cosmology:
-  Omega_m: 1.
+  Omega_cdm:    0.
   Omega_lambda: 0.
-  Omega_b: 1.
-  h: 1.
+  Omega_b:      1.
+  h:            1.
   a_begin: 0.00990099
   a_end: 1.0
 

examples/EAGLE_DMO_low_z/EAGLE_DMO_100/eagle_100.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.9090909     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/EAGLE_DMO_low_z/EAGLE_DMO_12/eagle_12.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.9090909     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/EAGLE_DMO_low_z/EAGLE_DMO_25/eagle_25.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.9090909     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/EAGLE_DMO_low_z/EAGLE_DMO_50/eagle_50.yml

@@ -11,9 +11,9 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.9090909     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
-  Omega_b:        0.0455        # Baryon density parameter
+  Omega_b:        0.0482519     # Baryon density parameter
 
 # Parameters governing the time integration
 TimeIntegration:

examples/EAGLE_ICs/EAGLE_100/eagle_100.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/EAGLE_ICs/EAGLE_12/eagle_12.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/EAGLE_ICs/EAGLE_25/eagle_25.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/EAGLE_ICs/EAGLE_25_low_res/eagle_25.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/EAGLE_ICs/EAGLE_50/eagle_50.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter
 

examples/EAGLE_ICs/EAGLE_50_low_res/eagle_50.yml

@@ -15,7 +15,7 @@ Cosmology:
   h:              0.6777        # Reduced Hubble constant
   a_begin:        0.0078125     # Initial scale-factor of the simulation
   a_end:          1.0           # Final scale factor of the simulation
-  Omega_m:        0.307         # Matter density parameter
+  Omega_cdm:      0.2587481     # Cold Dark Matter density parameter
   Omega_lambda:   0.693         # Dark-energy density parameter
   Omega_b:        0.0482519     # Baryon density parameter