Expanded the HydrostaticHalo a little bit and added it to the 'make dist' target.

examples/HydrostaticHalo/README

+Hydrostatic halo in equilibrium in an isothermal potential. Running
+for 10 dynamical times.
 
 To make the initial conditions we distribute gas particles randomly in
 a cube with a side length twice that of the virial radius. The density
 profile of the gas is proportional to r^(-2) where r is the distance
 from the centre of the cube.
 
-The parameter v_rot (in makeIC.py and cooling.yml) sets the circular
+The parameter v_rot (in makeIC.py and hydrostatic.yml) sets the circular
 velocity of the halo, and by extension, the viral radius, viral mass,
 and the internal energy of the gas such that hydrostatic equilibrium
 is achieved.
@@ -12,10 +14,12 @@ is achieved.
 To run this example, make such that the code is compiled with either
 the isothermal potential or softened isothermal potential set in
 src/const.h. In the latter case, a (small) value of epsilon needs to
-be set in cooling.yml.  0.1 kpc should work well.
+be set in hydrostatic.yml.  ~1 kpc should work well.
 
 The plotting scripts produce a plot of the density, internal energy
-and radial velocity profile for each
-snapshot. test_energy_conservation.py shows the evolution of energy
+and radial velocity profile for each snapshot and divides the profile
+by the expected profile. 
+
+The script test_energy_conservation.py shows the evolution of energy
 with time. These can be used to check if the example has run properly.
 

examples/HydrostaticHalo/hydrostatic.yml

@@ -9,7 +9,7 @@ InternalUnitSystem:
 # Parameters governing the time integration
 TimeIntegration:
   time_begin: 0.    # The starting time of the simulation (in internal units).
-  time_end:   1.0    # The end time of the simulation (in internal units).
+  time_end:   30.   # The end time of the simulation (in internal units).
   dt_min:     1e-6  # The minimal time-step size of the simulation (in internal units).
   dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
 
@@ -20,21 +20,18 @@ Statistics:
 # Parameters governing the snapshots
 Snapshots:
   basename:            Hydrostatic  # Common part of the name of output files
-  time_first:          0.               # Time of the first output (in internal units)
-  delta_time:          0.01             # Time difference between consecutive outputs (in internal units)
+  time_first:          0.           # Time of the first output (in internal units)
+  delta_time:          0.1          # Time difference between consecutive outputs (in internal units)
 
 # Parameters for the hydrodynamics scheme
 SPH:
   resolution_eta:        1.2349   # Target smoothing length in units of the mean inter-particle separation (1.2349 == 48Ngbs with the cubic spline kernel).
-  delta_neighbours:      1.       # The tolerance for the targetted number of neighbours.
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
 
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Hydrostatic.hdf5       # The file to read
-  shift_x:    0.                  # A shift to apply to all particles read from the ICs (in internal units).
-  shift_y:    0.
-  shift_z:    0.
  
 # External potential parameters
 SoftenedIsothermalPotential:
@@ -42,6 +39,6 @@ SoftenedIsothermalPotential:
   position_y:      0.
   position_z:      0.	
   vrot:            200.     # rotation speed of isothermal potential in internal units
-  epsilon:         0.1
+  epsilon:         1.0
   timestep_mult:   0.03     # controls time step
 

examples/HydrostaticHalo/makeIC.py

@@ -116,9 +116,9 @@ print "x range = (%f,%f)" %(np.min(coords[:,0]),np.max(coords[:,0]))
 print "y range = (%f,%f)" %(np.min(coords[:,1]),np.max(coords[:,1]))
 print "z range = (%f,%f)" %(np.min(coords[:,2]),np.max(coords[:,2]))
 
-print np.mean(coords[:,0])
-print np.mean(coords[:,1])
-print np.mean(coords[:,2])
+#print np.mean(coords[:,0])
+#print np.mean(coords[:,1])
+#print np.mean(coords[:,2])
 
 #now find the particles which are within the box
 

examples/HydrostaticHalo/run.sh

@@ -2,14 +2,23 @@
 
 # Generate the initial conditions if they are not present.
 echo "Generating initial conditions for the isothermal potential box example..."
-python makeIC.py 10000 
+python makeIC.py 100000
 
-../swift -g -s -t 16 hydrostatic.yml 2>&1 | tee output.log
+# Run for 10 dynamical times
+../swift -g -s -t 2 hydrostatic.yml 2>&1 | tee output.log
 
-python density_profile.py 2. 200 100
+echo "Plotting density profiles"
+mkdir plots
+mkdir plots/density_profile
+python density_profile.py 2. 200 300
 
-python internal_energy_profile.py 2. 200 100
+echo "Plotting internal energy profiles"
+mkdir plots/internal_energy
+python internal_energy_profile.py 2. 200 300
 
-python velocity_profile.py 2. 200 100
+echo "Plotting radial velocity profiles"
+mkdir plots/radial_velocity_profile
+python velocity_profile.py 2. 200 300
 
-python test_energy_conservation.py
+echo "Plotting energy as a function of time"
+python test_energy_conservation.py 300

examples/HydrostaticHalo/test_energy_conservation.py

@@ -3,7 +3,7 @@ import h5py as h5
 import matplotlib.pyplot as plt
 import sys
 
-n_snaps = 5
+n_snaps = int(sys.argv[1])
 
 #some constants
 OMEGA = 0.3 # Cosmological matter fraction at z = 0
@@ -24,7 +24,7 @@ unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
 unit_length_cgs = float(params.attrs["InternalUnitSystem:UnitLength_in_cgs"])
 unit_velocity_cgs = float(params.attrs["InternalUnitSystem:UnitVelocity_in_cgs"])
 unit_time_cgs = unit_length_cgs / unit_velocity_cgs
-v_c = float(params.attrs["IsothermalPotential:vrot"])
+v_c = float(params.attrs["SoftenedIsothermalPotential:vrot"])
 v_c_cgs = v_c * unit_velocity_cgs
 header = f["Header"]
 N = header.attrs["NumPart_Total"][0]

examples/Makefile.am

@@ -65,6 +65,8 @@ EXTRA_DIST = BigCosmoVolume/makeIC.py \
 	     EAGLE_50/eagle_50.yml EAGLE_50/getIC.sh EAGLE_50/README EAGLE_50/run.sh \
 	     ExternalPointMass/externalPointMass.yml ExternalPointMass/makeIC.py ExternalPointMass/run.sh ExternalPointMass/test.pro \
 	     GreshoVortex_2D/getGlass.sh GreshoVortex_2D/gresho.yml GreshoVortex_2D/makeIC.py GreshoVortex_2D/plotSolution.py GreshoVortex_2D/run.sh \
+	     HydrostaticHalo/README HydrostaticHalo/hydrostatic.yml HydrostaticHalo/makeIC.py HydrostaticHalo/run.sh \
+	     HydrostaticHalo/density_profile.py HydrostaticHalo/velocity_profile.py HydrostaticHalo/internal_energy_profile.py HydrostaticHalo/test_energy_conservation.py
 	     KelvinHelmholtz_2D/kelvinHelmholtz.yml KelvinHelmholtz_2D/makeIC.py KelvinHelmholtz_2D/plotSolution.py KelvinHelmholtz_2D/run.sh \
 	     MultiTypes/makeIC.py  MultiTypes/multiTypes.yml MultiTypes/run.sh \
 	     PerturbedBox_2D/makeIC.py PerturbedBox_2D/perturbedPlane.yml \