Merge branch 'periodic_flag_in_yaml_file' into 'master'

Read the periodicity flag from the YAML file

Closes #466

See merge request !642

doc/RTD/source/InitialConditions/index.rst

@@ -117,15 +117,6 @@ GADGET-2 based analysis programs:
 + ``Time``, time of the start of the simulation in internal units or expressed
   as a scale-factor for cosmological runs. SWIFT ignores this and reads it from
   the parameter file.
-  
-RuntimePars
-~~~~~~~~~~~
-
-In the ``/RuntimePars/``, the following attributes are required:
-
-+ ``PeriodicBoundariesOn``, a flag to tell the code whether or not you
-  have periodic boundaries switched on. Again, this is historical; it should be
-  set to 1 (default) if you have the code running in periodic mode, or 0 otherwise.
 
 
 Particle Data
@@ -145,7 +136,7 @@ individual particle type (e.g. ``/PartType0/``) that have the following *dataset
   velocities divided by ``sqrt(a)`` (see below for a fix).
 + ``ParticleIDs``, an array of length N that are unique identifying numbers for
   each particle. Note that these have to be unique to a particle, and cannot be
-  the same even between particle types. The **IDs must be >1**. 0 or negative
+  the same even between particle types. The **IDs must be >= 0**. Negative
   IDs will be rejected by the code.
 + ``Masses``, an array of length N that gives the masses of the particles.
 
@@ -216,8 +207,6 @@ You should have an HDF5 file with the following structure:
      Flag_Entropy_ICs=0
      NumPart_Total=[0, 1, 0, 0, 4, 5]
      NumPart_Total_HighWord=[0, 0, 0, 0, 0, 0]
-   RuntimePars/
-     PeriodicBoundariesOn=1
    Units/
      Unit current in cgs (U_I)=1.0
      Unit length in cgs (U_L)=1.0

examples/AgoraDisk/agora_disk.yml

@@ -44,8 +44,9 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./agora_disk.hdf5     # The file to read
-  cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
-  shift:    [674.1175, 674.1175, 674.1175]   # (Optional) A shift to apply to all particles read from the ICs (in internal units).
+  periodic:   0                     # Non-periodic BCs
+  cleanup_h_factors: 1              # Remove the h-factors inherited from Gadget
+  shift:    [674.1175, 674.1175, 674.1175]   # Centre the box
 
 # Dimensionless pre-factor for the time-step condition
 LambdaCooling:

examples/AgoraDisk/getIC.sh

@@ -6,4 +6,4 @@ if [ "$#" -ne 1 ]; then
     exit
 fi
 
-wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/$1
+wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/$1.hdf5

examples/ConstantCosmoVolume/constant_volume.yml

@@ -39,7 +39,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./constantBox.hdf5
-
+  periodic:   1
+  
 Scheduler:
   max_top_level_cells: 8
   cell_split_size:     50

examples/CoolingBox/coolingBox.yml

@@ -32,7 +32,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./coolingBox.hdf5     # The file to read
-
+  periodic:   1
+  
 # Dimensionless pre-factor for the time-step condition
 LambdaCooling:
   lambda_nH2_cgs:              1e-22 # Cooling rate divided by square Hydrogen number density (in cgs units [erg * s^-1 * cm^3])

examples/CoolingHalo/cooling_halo.yml

@@ -32,7 +32,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  CoolingHalo.hdf5       # The file to read
- 
+  periodic:   1
+  
 # External potential parameters
 IsothermalPotential:
   vrot:            200.     # rotation speed of isothermal potential in internal units

examples/CoolingHalo/makeIC.py

@@ -91,10 +91,6 @@ grp.attrs["Unit current in cgs (U_I)"] = 1.
 grp.attrs["Unit temperature in cgs (U_T)"] = 1.
 
 
-# Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 # set seed for random number
 np.random.seed(1234)
 

examples/CoolingHalo/makeIC_random_box.py

@@ -102,10 +102,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["Dimension"] = 3
 
-# Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 # set seed for random number
 np.random.seed(1234)
 

examples/CoolingHaloWithSpin/cooling_halo.yml

@@ -32,7 +32,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  CoolingHalo.hdf5       # The file to read
- 
+  periodic:   1
+  
 # External potential parameters
 IsothermalPotential:
   vrot:            200.   # Rotation speed of isothermal potential in internal units

examples/CoolingHaloWithSpin/makeIC.py

@@ -92,11 +92,6 @@ grp.attrs["Unit time in cgs (U_t)"] = const_unit_length_in_cgs / const_unit_velo
 grp.attrs["Unit current in cgs (U_I)"] = 1.
 grp.attrs["Unit temperature in cgs (U_T)"] = 1.
 
-
-# Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 # set seed for random number
 np.random.seed(1234)
 

examples/CoolingHaloWithSpin/makeIC_random_box.py

@@ -102,10 +102,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["Dimension"] = 3
 
-# Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 # set seed for random number
 np.random.seed(1234)
 

examples/DiscPatch/GravityOnly/disc-patch.yml

@@ -34,7 +34,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Disc-Patch.hdf5       # The file to read
-
+  periodic:   1
+  
 # External potential parameters
 DiscPatchPotential:
   surface_density: 10.

examples/DiscPatch/GravityOnly/makeIC.py

@@ -111,10 +111,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["Dimension"] = 3
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 # set seed for random number
 numpy.random.seed(1234)
 

examples/DiscPatch/HydroStatic/disc-patch-icc.yml

@@ -37,7 +37,8 @@ EoS:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Disc-Patch.hdf5       # The file to read
-
+  periodic:   1
+  
 # External potential parameters
 DiscPatchPotential:
   surface_density: 10.

examples/DiscPatch/HydroStatic/disc-patch.yml

@@ -34,7 +34,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Disc-Patch-dynamic.hdf5       # The file to read
-
+  periodic:   1
+  
 # External potential parameters
 DiscPatchPotential:
   surface_density: 10.

examples/DiscPatch/HydroStatic/makeIC.py

@@ -182,10 +182,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["Dimension"] = 3
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
 # write gas particles
 grp0   = file.create_group("/PartType0")
 

examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml

@@ -34,7 +34,8 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  Disc-Patch.hdf5       # The file to read
-
+  periodic:   1
+  
 # External potential parameters
 DiscPatchPotential:
   surface_density: 10.

examples/DiscPatch/HydroStatic_1D/makeIC.py

@@ -168,10 +168,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
 grp.attrs["Dimension"] = 1
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
 # write gas particles
 grp0   = file.create_group("/PartType0")