Merge branch 'periodic_flag_in_yaml_file' into 'master'

Read the periodicity flag from the YAML file

Closes #466

See merge request !642

examples/DwarfGalaxy/dwarf_galaxy.yml

@@ -66,6 +66,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./dwarf_galaxy.hdf5     # The file to read
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_100/eagle_100.yml

@@ -55,6 +55,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_100.hdf5   # The file to read
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_12/eagle_12.yml

@@ -53,6 +53,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_12.hdf5    # The file to read
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_25/eagle_25.yml

@@ -62,6 +62,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_25.hdf5    # The file to read
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_50/eagle_50.yml

@@ -55,6 +55,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_50.hdf5     # The file to read
+  periodic:   1
   cleanup_h_factors: 1                # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1         # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_6/eagle_6.yml

@@ -66,6 +66,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./EAGLE_ICs_6.hdf5     # The file to read
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_DMO_100/eagle_100.yml

@@ -49,6 +49,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  EAGLE_DMO_ICs_100.hdf5
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_DMO_12/eagle_12.yml

@@ -51,6 +51,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  EAGLE_DMO_ICs_12.hdf5
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_DMO_25/eagle_25.yml

@@ -50,6 +50,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  EAGLE_DMO_ICs_25.hdf5
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EAGLE_DMO_50/eagle_50.yml

@@ -49,6 +49,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  EAGLE_DMO_ICs_50.hdf5
+  periodic:   1
   cleanup_h_factors: 1               # Remove the h-factors inherited from Gadget
   cleanup_velocity_factors: 1        # Remove the sqrt(a) factor in the velocities inherited from Gadget
 

examples/EvrardCollapse_3D/evrard.yml

@@ -39,6 +39,7 @@ Gravity:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./evrard.hdf5       # The file to read
-
+  periodic:   0
+  
 PhysicalConstants:
   G: 1.

examples/EvrardCollapse_3D/makeIC.py

@@ -86,10 +86,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = 0
 grp.attrs["Dimension"] = 3
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 0
-
 #Units
 grp = file.create_group("/Units")
 grp.attrs["Unit length in cgs (U_L)"] = 1.

examples/ExternalPointMass/externalPointMass.yml

@@ -31,6 +31,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  PointMass.hdf5        # The file to read
+  periodic:   0
   shift:      [50.,50.,50.]         # A shift to apply to all particles read from the ICs (in internal units).
 
 # External potential parameters

examples/ExternalPointMass/makeIC.py

@@ -79,9 +79,6 @@ 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
 
 #Units
 grp = file.create_group("/Units")

examples/Gradients/gradientsCartesian.yml

@@ -31,4 +31,4 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./Gradients_cartesian.hdf5       # The file to read
-
+  periodic:   1

examples/Gradients/gradientsRandom.yml

@@ -31,4 +31,4 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./Gradients_random.hdf5       # The file to read
-
+  periodic:   1

examples/Gradients/makeICs.py

@@ -26,7 +26,6 @@ import sys
 # reconstruction
 
 # Parameters
-periodic= 1      # 1 For periodic box
 gamma = 5./3.     # Gas adiabatic index
 gridtype = "cartesian"
 if len(sys.argv) > 1:
@@ -153,10 +152,6 @@ grp.attrs["NumFilesPerSnapshot"] = 1
 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]
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 #Particle group
 grp = file.create_group("/PartType0")
 ds = grp.create_dataset('Coordinates', (npart, 3), 'd')

examples/Gravity_glass/makeIC.py

@@ -53,10 +53,6 @@ grp.attrs["MassTable"] = [0.0, mass, 0.0, 0.0, 0.0, 0.0]
 grp.attrs["Flag_Entropy_ICs"] = 0
 grp.attrs["Dimension"] = 3
 
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
-
 #Units
 grp = file.create_group("/Units")
 grp.attrs["Unit length in cgs (U_L)"] = 1.