Merge branch 'eos_selection' into 'master'

Eos selection

Closes #743

See merge request !1290

doc/RTD/source/ParameterFiles/parameter_description.rst

@@ -909,15 +909,10 @@ The ``EoS`` section contains options for the equations of state.
 Multiple EoS can be used for :ref:`planetary`,
 see :ref:`planetary_eos` for more information. 
 
-To enable one or multiple of these EoS, the corresponding ``planetary_use_*:``
+To enable one or multiple EoS, the corresponding ``planetary_use_*:``
 flag(s) must be set to ``1`` in the parameter file for a simulation,
-along with the path to any table files, which are provided with the 
+along with the path to any table files, which are set by the 
 ``planetary_*_table_file:`` parameters.
-This currently means that all EoS within each base type are prepared at once, 
-which we intend to simplify in the future.
-
-The data files for the tabulated EoS can be downloaded using 
-the ``examples/EoSTables/get_eos_tables.sh`` script.
 
 For the (non-planetary) isothermal EoS, the ``isothermal_internal_energy:``
 parameter sets the thermal energy per unit mass.

doc/RTD/source/Planetary/equations_of_state.rst

@@ -5,7 +5,7 @@
 
 Planetary Equations of State
 ============================
-   
+
 Configuring SWIFT with the ``--with-equation-of-state=planetary`` and 
 ``--with-hydro=planetary`` options enables the use of multiple 
 equations of state (EoS).
@@ -29,6 +29,7 @@ The material's ID is set by a somewhat arbitrary base type ID
     + Iron: ``100``
     + Granite: ``101``
     + Water: ``102``
+    + Basalt: ``103``
 + Hubbard \& MacFarlane (1980): ``2``
     + Hydrogen-helium atmosphere: ``200``
     + Ice H20-CH4-NH3 mix: ``201``
@@ -48,18 +49,19 @@ the ``examples/Planetary/EoSTables/get_eos_tables.sh`` script.
 
 To enable one or multiple EoS, the corresponding ``planetary_use_*:``
 flag(s) must be set to ``1`` in the parameter file for a simulation,
-along with the path to any table files, which are provided with the 
+along with the path to any table files, which are set by the 
 ``planetary_*_table_file:`` parameters,
 as detailed in :ref:`Parameters_eos` and ``examples/parameter_example.yml``.
-This currently means that all EoS within each base type are prepared at once, 
-which we intend to simplify in the future.
+
+The data files for the tabulated EoS can be downloaded using 
+the ``examples/EoSTables/get_eos_tables.sh`` script.
 
 Unlike the EoS for an ideal or isothermal gas, these more complicated materials 
 do not always include transformations between the internal energy, 
 temperature, and entropy. At the moment, we have implemented 
 \\(P(\\rho, u)\\) and \\(c_s(\\rho, u)\\), 
 which is sufficient for the :ref:`planetary_sph` hydro scheme, 
-but makes most materials currently incompatible with entropy-based schemes.
+but makes most materials currently incompatible with e.g. entropy-based schemes.
 
 The Tillotson sound speed was derived using 
 \\(c_s^2 = \\left. ( \\partial P / \\partial \\rho ) \\right|_S \\)

examples/Planetary/EarthImpact/earth_impact.yml

 # Define the system of units to use internally.
 InternalUnitSystem:
-    UnitMass_in_cgs:        5.9724e27   # Grams
-    UnitLength_in_cgs:      6.371e8     # Centimeters
-    UnitVelocity_in_cgs:    6.371e8     # Centimeters per second
+    UnitMass_in_cgs:        1e27        # Sets Earth mass = 5.972
+    UnitLength_in_cgs:      1e8         # Sets Earth radius = 6.371
+    UnitVelocity_in_cgs:    1e8         # Sets time in seconds
     UnitCurrent_in_cgs:     1           # Amperes
     UnitTemp_in_cgs:        1           # Kelvin
 
@@ -38,17 +38,16 @@ SPH:
     resolution_eta:     1.2348          # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
     delta_neighbours:   0.1             # The tolerance for the targetted number of neighbours.
     CFL_condition:      0.2             # Courant-Friedrich-Levy condition for time integration.
-    h_max:              0.2             # Maximal allowed smoothing length (in internal units).
+    h_max:              1.2             # Maximal allowed smoothing length (in internal units).
     viscosity_alpha:    1.5             # Override for the initial value of the artificial viscosity.
 
 # Parameters for the self-gravity scheme
 Gravity:
-    eta:                            0.025   # Constant dimensionless multiplier for time integration.
-    MAC:                            adaptive
-    theta_cr:                       0.7     
-    epsilon_fmm:                    0.001
-    use_tree_below_softening:       1
-    max_physical_baryon_softening:  0.003   # Physical softening length (in internal units).
+    eta:                            0.025       # Constant dimensionless multiplier for time integration.
+    MAC:                            adaptive    # Choice of mulitpole acceptance criterion: 'adaptive' OR 'geometric'.
+    epsilon_fmm:                    0.001       # Tolerance parameter for the adaptive multipole acceptance criterion.
+    theta_cr:                       0.7         # Opening angle for the purely gemoetric criterion.
+    max_physical_baryon_softening:  0.02        # Physical softening length (in internal units).
 
 # Parameters for the task scheduling
 Scheduler:
@@ -56,11 +55,6 @@ Scheduler:
 
 # Parameters related to the equation of state
 EoS:
-    planetary_use_Til:  1               # Whether to initialise the Tillotson EOS
-
-# Parameters governing the logger snapshot system
-Logger:
-  delta_step:           10     # Update the particle log every this many updates
-  basename:             index  # Common part of the filenames
-  initial_buffer_size:  0.01      # (Optional) Buffer size in GB
-  buffer_scale:	        10     # (Optional) When buffer size is too small, update it with required memory times buffer_scale
+    # Select which planetary EoS material(s) to enable for use.
+    planetary_use_Til_iron:       1     # Tillotson iron, material ID 100
+    planetary_use_Til_granite:    1     # Tillotson granite, material ID 101

examples/Planetary/EarthImpact/make_anim.sh

@@ -2,6 +2,6 @@
 
 # Make a simple animation of the snapshots
 out="earth_impact.mp4"
-ffmpeg -framerate 5 -i earth_impact_%?%?%?%?%?%?.png $out -y
+ffmpeg -framerate 5 -i earth_impact_%?%?%?%?.png $out -y
 
-echo Saved $out
\ No newline at end of file
+echo Saved $out

examples/Planetary/EarthImpact/plot_solution.py

@@ -57,10 +57,10 @@ Di_mat_colour = {
 Di_id_colour = {Di_mat_id[mat]: colour for mat, colour in Di_mat_colour.items()}
 
 
-def load_snapshot(snapshot_time, ax_lim):
+def load_snapshot(snapshot_id, ax_lim):
     """ Select and load the particles to plot. """
     # Snapshot to load
-    snapshot = "earth_impact_%06d.hdf5" % snapshot_time
+    snapshot = "earth_impact_%04d.hdf5" % snapshot_id
 
     # Only load data with the axis limits and below z=0
     ax_lim = 0.1
@@ -131,15 +131,15 @@ if __name__ == "__main__":
     ax_lim = 3.4
 
     # Plot each snapshot
-    for snapshot_time in range(0, 36000 + 1, 1000):
+    for snapshot_id in range(37):
         # Load the data
-        pos, mat_id = load_snapshot(snapshot_time, ax_lim)
+        pos, mat_id = load_snapshot(snapshot_id, ax_lim)
 
         # Plot the data
         plot_snapshot(pos, mat_id, ax_lim)
 
         # Save the figure
-        save = "earth_impact_%06d.png" % snapshot_time
+        save = "earth_impact_%04d.png" % snapshot_id
         plt.savefig(save, dpi=100)
 
         print("\rSaved %s" % save)

examples/parameter_example.yml

@@ -266,20 +266,31 @@ LineOfSight:
 # Parameters related to the equation of state ------------------------------------------
 
 EoS:
-  isothermal_internal_energy: 20.26784  # Thermal energy per unit mass for the case of isothermal equation of state (in internal units).
-
-  planetary_use_Til:    1   # (Optional) Whether to prepare the Tillotson EoS
-  planetary_use_HM80:   0   # (Optional) Whether to prepare the Hubbard & MacFarlane (1980) EoS
-  planetary_use_SESAME: 0   # (Optional) Whether to prepare the SESAME EoS
-  planetary_use_ANEOS:  0   # (Optional) Whether to prepare the ANEOS EoS
-                            # (Optional) Table file paths
-  planetary_HM80_HHe_table_file:            ./EoSTables/HM80_HHe.txt
-  planetary_HM80_ice_table_file:            ./EoSTables/HM80_ice.txt
-  planetary_HM80_rock_table_file:           ./EoSTables/HM80_rock.txt
-  planetary_SESAME_iron_table_file:         ./EoSTables/SESAME_iron_2140.txt
-  planetary_SESAME_basalt_table_file:       ./EoSTables/SESAME_basalt_7530.txt
-  planetary_SESAME_water_table_file:        ./EoSTables/SESAME_water_7154.txt
-  planetary_SS08_water_table_file:          ./EoSTables/SS08_water.txt
+  isothermal_internal_energy: 20.26784      # Thermal energy per unit mass for the case of isothermal equation of state (in internal units).
+  # Select which planetary EoS material(s) to enable for use.
+  planetary_use_idg_def:    0               # Default ideal gas, material ID 0
+  planetary_use_Til_iron:       1           # Tillotson iron, material ID 100
+  planetary_use_Til_granite:    1           # Tillotson granite, material ID 101
+  planetary_use_Til_water:      0           # Tillotson water, material ID 102
+  planetary_use_Til_basalt:     0           # Tillotson basalt, material ID 103
+  planetary_use_HM80_HHe:   0               # Hubbard & MacFarlane (1980) hydrogen-helium atmosphere, material ID 200
+  planetary_use_HM80_ice:   0               # Hubbard & MacFarlane (1980) H20-CH4-NH3 ice mix, material ID 201
+  planetary_use_HM80_rock:  0               # Hubbard & MacFarlane (1980) SiO2-MgO-FeS-FeO rock mix, material ID 202
+  planetary_use_SESAME_iron:    0           # SESAME iron 2140, material ID 300
+  planetary_use_SESAME_basalt:  0           # SESAME basalt 7530, material ID 301
+  planetary_use_SESAME_water:   0           # SESAME water 7154, material ID 302
+  planetary_use_SS08_water:     0           # Senft & Stewart (2008) SESAME-like water, material ID 303
+  planetary_use_ANEOS_forsterite:   0       # ANEOS forsterite (Stewart et al. 2019), material ID 400
+  planetary_use_ANEOS_iron:         0       # ANEOS iron (Stewart 2020), material ID 401
+  planetary_use_ANEOS_Fe85Si15:     0       # ANEOS Fe85Si15 (Stewart 2020), material ID 402
+  # Tablulated EoS file paths.
+  planetary_HM80_HHe_table_file:    ./EoSTables/HM80_HHe.txt
+  planetary_HM80_ice_table_file:    ./EoSTables/HM80_ice.txt
+  planetary_HM80_rock_table_file:   ./EoSTables/HM80_rock.txt
+  planetary_SESAME_iron_table_file:     ./EoSTables/SESAME_iron_2140.txt
+  planetary_SESAME_basalt_table_file:   ./EoSTables/SESAME_basalt_7530.txt
+  planetary_SESAME_water_table_file:    ./EoSTables/SESAME_water_7154.txt
+  planetary_SS08_water_table_file:      ./EoSTables/SS08_water.txt
   planetary_ANEOS_forsterite_table_file:    ./EoSTables/ANEOS_forsterite_S19.txt
   planetary_ANEOS_iron_table_file:          ./EoSTables/ANEOS_iron_S20.txt
   planetary_ANEOS_Fe85Si15_table_file:      ./EoSTables/ANEOS_Fe85Si15_S20.txt