Add a small cosmological volume example with gas and a script to plot the...

Add a small cosmological volume example with gas and a script to plot the temperature evolution of the Universe.

examples/SmallCosmoVolume/README

@@ -4,6 +4,11 @@ We use a softening length of 1/25th of the mean inter-particle separation.
 
 The ICs have been generated to run with Gadget-2 so we need to switch
 on the options to cancel the h-factors and a-factors at reading time.
+We generate gas from the ICs using SWIFT's internal mechanism and set the
+temperature to the expected gas temperature at this redshift.
+
+The 'plotTempEvolution.py' plots the temperature evolution of the gas
+in the simulated volume.
 
 MD5 checksum of the ICs:
 08736c3101fd738e22f5159f78e6022b  small_cosmo_volume.hdf5

examples/SmallCosmoVolume/run.sh

@@ -7,5 +7,8 @@ then
     ./getIC.sh
 fi
 
-../swift -c -G -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
+# Run SWIFT
+../swift -c -s -G -t 8 small_cosmo_volume.yml 2>&1 | tee output.log
 
+# Plot the temperature evolution
+python plotTempEvolution.py

examples/SmallCosmoVolume/small_cosmo_volume.yml

@@ -6,14 +6,6 @@ InternalUnitSystem:
   UnitCurrent_in_cgs:  1             # Amperes
   UnitTemp_in_cgs:     1             # Kelvin
 
-# Structure finding options
-StructureFinding:
-  config_file_name:     stf_input_6dfof_dmonly_sub.cfg
-  basename:             ./stf
-  output_time_format:   1
-  scale_factor_first:   0.02
-  delta_time:           1.02
-
 Cosmology:                      # WMAP9 cosmology
   Omega_m:        0.276
   Omega_lambda:   0.724
@@ -34,7 +26,14 @@ Gravity:
   comoving_softening:     0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
   max_physical_softening: 0.0889     # 1/25th of the mean inter-particle separation: 88.9 kpc
   mesh_side_length:       64
-  
+
+# Parameters of the hydro scheme
+SPH:
+  resolution_eta:      1.2348   # "48 Ngb" with the cubic spline kernel
+  CFL_condition:       0.1
+  initial_temperature: 7075.    # (1 + z_ini)^2 * 2.72K
+  minimal_temperature: 100.
+
 # Parameters governing the snapshots
 Snapshots:
   basename:            snap
@@ -55,3 +54,5 @@ InitialConditions:
   file_name:  small_cosmo_volume.hdf5
   cleanup_h_factors:           1    
   cleanup_velocity_factors:    1  
+  generate_gas_in_ics: 1            # Generate gas particles from the DM-only ICs
+  cleanup_smoothing_lengths: 1      # Since we generate gas, make use of the (expensive) cleaning-up procedure.

src/hydro_properties.c

@@ -219,7 +219,7 @@ void hydro_props_print_snapshot(hid_t h_grpsph, const struct hydro_props *p) {
   io_write_attribute_f(h_grpsph, "Hydrogen mass fraction",
                        p->hydrogen_mass_fraction);
   io_write_attribute_f(h_grpsph, "Hydrogen ionization transition temperature",
-		       p->hydrogen_ionization_temperature);
+                       p->hydrogen_ionization_temperature);
   io_write_attribute_f(h_grpsph, "Alpha viscosity", const_viscosity_alpha);
 }
 #endif