From 7e172373a869aed32c86ab8e2d2345aada75f974 Mon Sep 17 00:00:00 2001
From: Matthieu Schaller <schaller@strw.leidenuniv.nl>
Date: Sat, 20 Oct 2018 18:58:56 +0200
Subject: [PATCH] Updated all the examples' YAML files to use the new periodic
flag.
---
examples/AgoraDisk/agora_disk.yml | 5 +++--
examples/AgoraDisk/getIC.sh | 2 +-
examples/AgoraDisk/getSolution.sh | 0
examples/AgoraDisk/run.sh | 0
examples/ConstantCosmoVolume/constant_volume.yml | 3 ++-
examples/CoolingBox/coolingBox.yml | 3 ++-
examples/CoolingHalo/cooling_halo.yml | 3 ++-
examples/CoolingHalo/makeIC.py | 4 ----
examples/CoolingHalo/makeIC_random_box.py | 4 ----
examples/CoolingHaloWithSpin/cooling_halo.yml | 3 ++-
examples/CoolingHaloWithSpin/makeIC.py | 5 -----
examples/CoolingHaloWithSpin/makeIC_random_box.py | 4 ----
examples/DiscPatch/GravityOnly/disc-patch.yml | 3 ++-
examples/DiscPatch/GravityOnly/makeIC.py | 4 ----
examples/DiscPatch/HydroStatic/disc-patch-icc.yml | 3 ++-
examples/DiscPatch/HydroStatic/disc-patch.yml | 3 ++-
examples/DiscPatch/HydroStatic/makeIC.py | 4 ----
examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml | 3 ++-
examples/DiscPatch/HydroStatic_1D/makeIC.py | 4 ----
examples/DwarfGalaxy/dwarf_galaxy.yml | 1 +
examples/DwarfGalaxy/getIC.sh | 0
examples/DwarfGalaxy/run.sh | 0
examples/EAGLE_100/eagle_100.yml | 1 +
examples/EAGLE_12/eagle_12.yml | 1 +
examples/EAGLE_25/eagle_25.yml | 1 +
examples/EAGLE_50/eagle_50.yml | 1 +
examples/EAGLE_6/eagle_6.yml | 1 +
examples/EAGLE_DMO_100/eagle_100.yml | 1 +
examples/EAGLE_DMO_12/eagle_12.yml | 1 +
examples/EAGLE_DMO_25/eagle_25.yml | 1 +
examples/EAGLE_DMO_50/eagle_50.yml | 1 +
examples/EvrardCollapse_3D/evrard.yml | 3 ++-
examples/EvrardCollapse_3D/makeIC.py | 4 ----
examples/ExternalPointMass/externalPointMass.yml | 1 +
examples/ExternalPointMass/makeIC.py | 3 ---
examples/Gradients/gradientsCartesian.yml | 2 +-
examples/Gradients/gradientsRandom.yml | 2 +-
examples/Gradients/makeICs.py | 5 -----
examples/Gravity_glass/makeIC.py | 4 ----
examples/Gravity_glass/uniform_DM_box.yml | 1 +
examples/GreshoVortex_2D/gresho.yml | 1 +
examples/GreshoVortex_2D/makeIC.py | 4 ----
examples/GreshoVortex_3D/gresho.yml | 1 +
examples/GreshoVortex_3D/makeIC.py | 4 ----
examples/HydrostaticHalo/hydrostatic.yml | 3 ++-
examples/HydrostaticHalo/makeIC.py | 4 ----
examples/InteractingBlastWaves_1D/interactingBlastWaves.yml | 1 +
examples/InteractingBlastWaves_1D/makeIC.py | 4 ----
examples/IsothermalPotential/isothermal.yml | 1 +
examples/IsothermalPotential/makeIC.py | 4 ----
.../kelvinHelmholtzGrowthRate.yml | 1 +
examples/KelvinHelmholtzGrowthRate_2D/makeIC.py | 4 ----
examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py | 4 ----
.../kelvinHelmholtzGrowthRate.yml | 1 +
examples/KelvinHelmholtzGrowthRate_3D/makeIC.py | 4 ----
examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py | 4 ----
examples/KelvinHelmholtz_2D/kelvinHelmholtz.yml | 1 +
examples/KelvinHelmholtz_2D/makeIC.py | 4 ----
examples/KeplerianRing/keplerian_ring.yml | 3 ++-
examples/MultiTypes/makeIC.py | 4 ----
examples/MultiTypes/multiTypes.yml | 1 +
examples/Noh_1D/makeIC.py | 4 ----
examples/Noh_1D/noh.yml | 2 ++
examples/Noh_2D/makeIC.py | 4 ----
examples/Noh_2D/noh.yml | 1 +
examples/Noh_3D/makeIC.py | 4 ----
examples/Noh_3D/noh.yml | 1 +
examples/PMillennium-384/p-mill-384.yml | 1 +
examples/PMillennium-768/p-mill-768.yml | 1 +
examples/PerturbedBox_2D/makeIC.py | 4 ----
examples/PerturbedBox_2D/perturbedPlane.yml | 1 +
examples/PerturbedBox_3D/makeIC.py | 4 ----
examples/PerturbedBox_3D/perturbedBox.yml | 1 +
examples/SantaBarbara/santa_barbara.yml | 1 +
examples/SedovBlast_1D/makeIC.py | 4 ----
examples/SedovBlast_1D/sedov.yml | 2 +-
examples/SedovBlast_2D/makeIC.py | 4 ----
examples/SedovBlast_2D/sedov.yml | 2 +-
examples/SedovBlast_3D/makeIC.py | 4 ----
examples/SedovBlast_3D/sedov.yml | 1 +
examples/SineWavePotential_1D/makeIC.py | 4 ----
examples/SineWavePotential_1D/sineWavePotential.yml | 3 ++-
examples/SineWavePotential_2D/makeIC.py | 4 ----
examples/SineWavePotential_2D/sineWavePotential.yml | 3 ++-
examples/SineWavePotential_3D/makeIC.py | 4 ----
examples/SineWavePotential_3D/sineWavePotential.yml | 3 ++-
examples/SmallCosmoVolume/small_cosmo_volume.yml | 5 +++--
examples/SmallCosmoVolume_DM/small_cosmo_volume_dm.yml | 1 +
examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml | 5 +++--
examples/SmoothedMetallicity/makeIC.py | 4 ----
examples/SmoothedMetallicity/smoothed_metallicity.yml | 1 +
examples/SodShockSpherical_2D/makeIC.py | 4 ----
examples/SodShockSpherical_2D/sodShock.yml | 1 +
examples/SodShockSpherical_3D/makeIC.py | 4 ----
examples/SodShockSpherical_3D/sodShock.yml | 1 +
examples/SodShock_1D/makeIC.py | 4 ----
examples/SodShock_1D/sodShock.yml | 2 +-
examples/SodShock_2D/makeIC.py | 4 ----
examples/SodShock_2D/sodShock.yml | 1 +
examples/SodShock_3D/makeIC.py | 4 ----
examples/SodShock_3D/sodShock.yml | 1 +
examples/SquareTest_2D/makeIC.py | 4 ----
examples/SquareTest_2D/square.yml | 1 +
examples/UniformBox_2D/makeIC.py | 4 ----
examples/UniformBox_2D/uniformPlane.yml | 1 +
examples/UniformBox_3D/makeIC.py | 4 ----
examples/UniformBox_3D/uniformBox.yml | 1 +
examples/VacuumSpherical_2D/makeIC.py | 4 ----
examples/VacuumSpherical_2D/vacuum.yml | 2 +-
examples/VacuumSpherical_3D/makeIC.py | 4 ----
examples/VacuumSpherical_3D/vacuum.yml | 2 ++
examples/Vacuum_1D/makeIC.py | 4 ----
examples/Vacuum_1D/vacuum.yml | 1 +
examples/Vacuum_2D/makeIC.py | 4 ----
examples/Vacuum_2D/vacuum.yml | 1 +
examples/Vacuum_3D/makeIC.py | 4 ----
examples/Vacuum_3D/vacuum.yml | 1 +
examples/ZeldovichPancake_3D/makeIC.py | 4 ----
examples/ZeldovichPancake_3D/zeldovichPancake.yml | 3 ++-
examples/ZoomIn/getIC.sh | 0
examples/ZoomIn/run.sh | 0
examples/ZoomIn/zoom_in.yml | 1 +
examples/getCoolingTable.sh | 0
123 files changed, 91 insertions(+), 221 deletions(-)
mode change 100644 => 100755 examples/AgoraDisk/getIC.sh
mode change 100644 => 100755 examples/AgoraDisk/getSolution.sh
mode change 100644 => 100755 examples/AgoraDisk/run.sh
mode change 100644 => 100755 examples/DwarfGalaxy/getIC.sh
mode change 100644 => 100755 examples/DwarfGalaxy/run.sh
mode change 100644 => 100755 examples/ZoomIn/getIC.sh
mode change 100644 => 100755 examples/ZoomIn/run.sh
mode change 100644 => 100755 examples/getCoolingTable.sh
diff --git a/examples/AgoraDisk/agora_disk.yml b/examples/AgoraDisk/agora_disk.yml
index f1bd57b13c..92f2532b31 100644
--- a/examples/AgoraDisk/agora_disk.yml
+++ b/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:
diff --git a/examples/AgoraDisk/getIC.sh b/examples/AgoraDisk/getIC.sh
old mode 100644
new mode 100755
index 620a751bed..c234b52b94
--- a/examples/AgoraDisk/getIC.sh
+++ b/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
diff --git a/examples/AgoraDisk/getSolution.sh b/examples/AgoraDisk/getSolution.sh
old mode 100644
new mode 100755
diff --git a/examples/AgoraDisk/run.sh b/examples/AgoraDisk/run.sh
old mode 100644
new mode 100755
diff --git a/examples/ConstantCosmoVolume/constant_volume.yml b/examples/ConstantCosmoVolume/constant_volume.yml
index db5b3de536..ebfcc4ffd7 100644
--- a/examples/ConstantCosmoVolume/constant_volume.yml
+++ b/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
diff --git a/examples/CoolingBox/coolingBox.yml b/examples/CoolingBox/coolingBox.yml
index 99313e1a20..1a06168cef 100644
--- a/examples/CoolingBox/coolingBox.yml
+++ b/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])
diff --git a/examples/CoolingHalo/cooling_halo.yml b/examples/CoolingHalo/cooling_halo.yml
index c13c392571..3d6e44ae3e 100644
--- a/examples/CoolingHalo/cooling_halo.yml
+++ b/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
diff --git a/examples/CoolingHalo/makeIC.py b/examples/CoolingHalo/makeIC.py
index 3ec1be6f7b..046e5d619f 100644
--- a/examples/CoolingHalo/makeIC.py
+++ b/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)
diff --git a/examples/CoolingHalo/makeIC_random_box.py b/examples/CoolingHalo/makeIC_random_box.py
index 4295cb1352..be8f2f172e 100644
--- a/examples/CoolingHalo/makeIC_random_box.py
+++ b/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)
diff --git a/examples/CoolingHaloWithSpin/cooling_halo.yml b/examples/CoolingHaloWithSpin/cooling_halo.yml
index 7a6cd4eedb..1b29e1376e 100644
--- a/examples/CoolingHaloWithSpin/cooling_halo.yml
+++ b/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
diff --git a/examples/CoolingHaloWithSpin/makeIC.py b/examples/CoolingHaloWithSpin/makeIC.py
index 2cf3127c74..9a839bfd01 100644
--- a/examples/CoolingHaloWithSpin/makeIC.py
+++ b/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)
diff --git a/examples/CoolingHaloWithSpin/makeIC_random_box.py b/examples/CoolingHaloWithSpin/makeIC_random_box.py
index 4295cb1352..be8f2f172e 100644
--- a/examples/CoolingHaloWithSpin/makeIC_random_box.py
+++ b/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)
diff --git a/examples/DiscPatch/GravityOnly/disc-patch.yml b/examples/DiscPatch/GravityOnly/disc-patch.yml
index 4ec061add9..bcc7d1a3de 100644
--- a/examples/DiscPatch/GravityOnly/disc-patch.yml
+++ b/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.
diff --git a/examples/DiscPatch/GravityOnly/makeIC.py b/examples/DiscPatch/GravityOnly/makeIC.py
index 5f9650f442..3abf4f87fc 100644
--- a/examples/DiscPatch/GravityOnly/makeIC.py
+++ b/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)
diff --git a/examples/DiscPatch/HydroStatic/disc-patch-icc.yml b/examples/DiscPatch/HydroStatic/disc-patch-icc.yml
index 983a7dcc10..aee54057cf 100644
--- a/examples/DiscPatch/HydroStatic/disc-patch-icc.yml
+++ b/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.
diff --git a/examples/DiscPatch/HydroStatic/disc-patch.yml b/examples/DiscPatch/HydroStatic/disc-patch.yml
index 422e1cf910..8651ac09db 100644
--- a/examples/DiscPatch/HydroStatic/disc-patch.yml
+++ b/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.
diff --git a/examples/DiscPatch/HydroStatic/makeIC.py b/examples/DiscPatch/HydroStatic/makeIC.py
index 8b4c55560c..dd50a821a2 100644
--- a/examples/DiscPatch/HydroStatic/makeIC.py
+++ b/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")
diff --git a/examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml b/examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml
index 450689034f..ea5d2e24eb 100644
--- a/examples/DiscPatch/HydroStatic_1D/disc-patch-icc.yml
+++ b/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.
diff --git a/examples/DiscPatch/HydroStatic_1D/makeIC.py b/examples/DiscPatch/HydroStatic_1D/makeIC.py
index 983a550a34..b193c85e50 100644
--- a/examples/DiscPatch/HydroStatic_1D/makeIC.py
+++ b/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")
diff --git a/examples/DwarfGalaxy/dwarf_galaxy.yml b/examples/DwarfGalaxy/dwarf_galaxy.yml
index 655d41a928..0d815a99c4 100644
--- a/examples/DwarfGalaxy/dwarf_galaxy.yml
+++ b/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
diff --git a/examples/DwarfGalaxy/getIC.sh b/examples/DwarfGalaxy/getIC.sh
old mode 100644
new mode 100755
diff --git a/examples/DwarfGalaxy/run.sh b/examples/DwarfGalaxy/run.sh
old mode 100644
new mode 100755
diff --git a/examples/EAGLE_100/eagle_100.yml b/examples/EAGLE_100/eagle_100.yml
index dc2b814e0a..3bcda091bd 100644
--- a/examples/EAGLE_100/eagle_100.yml
+++ b/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
diff --git a/examples/EAGLE_12/eagle_12.yml b/examples/EAGLE_12/eagle_12.yml
index c567fa91fc..43593a05bc 100644
--- a/examples/EAGLE_12/eagle_12.yml
+++ b/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
diff --git a/examples/EAGLE_25/eagle_25.yml b/examples/EAGLE_25/eagle_25.yml
index 4e59eb3b9f..905906a0ef 100644
--- a/examples/EAGLE_25/eagle_25.yml
+++ b/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
diff --git a/examples/EAGLE_50/eagle_50.yml b/examples/EAGLE_50/eagle_50.yml
index 515b757741..7f03dce10a 100644
--- a/examples/EAGLE_50/eagle_50.yml
+++ b/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
diff --git a/examples/EAGLE_6/eagle_6.yml b/examples/EAGLE_6/eagle_6.yml
index eb374df964..e3b9e59331 100644
--- a/examples/EAGLE_6/eagle_6.yml
+++ b/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
diff --git a/examples/EAGLE_DMO_100/eagle_100.yml b/examples/EAGLE_DMO_100/eagle_100.yml
index f04c32c8d0..5a30661956 100644
--- a/examples/EAGLE_DMO_100/eagle_100.yml
+++ b/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
diff --git a/examples/EAGLE_DMO_12/eagle_12.yml b/examples/EAGLE_DMO_12/eagle_12.yml
index 2354216a5b..0660d98e87 100644
--- a/examples/EAGLE_DMO_12/eagle_12.yml
+++ b/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
diff --git a/examples/EAGLE_DMO_25/eagle_25.yml b/examples/EAGLE_DMO_25/eagle_25.yml
index b02f9742a5..558c68ffaa 100644
--- a/examples/EAGLE_DMO_25/eagle_25.yml
+++ b/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
diff --git a/examples/EAGLE_DMO_50/eagle_50.yml b/examples/EAGLE_DMO_50/eagle_50.yml
index 97299df063..3cab2b1dc8 100644
--- a/examples/EAGLE_DMO_50/eagle_50.yml
+++ b/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
diff --git a/examples/EvrardCollapse_3D/evrard.yml b/examples/EvrardCollapse_3D/evrard.yml
index f9a4e69f72..c14f9151b5 100644
--- a/examples/EvrardCollapse_3D/evrard.yml
+++ b/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.
diff --git a/examples/EvrardCollapse_3D/makeIC.py b/examples/EvrardCollapse_3D/makeIC.py
index f4d3c4c5bf..29c4acd69e 100644
--- a/examples/EvrardCollapse_3D/makeIC.py
+++ b/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.
diff --git a/examples/ExternalPointMass/externalPointMass.yml b/examples/ExternalPointMass/externalPointMass.yml
index de05a9ff3c..83c4b4fd1b 100644
--- a/examples/ExternalPointMass/externalPointMass.yml
+++ b/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
diff --git a/examples/ExternalPointMass/makeIC.py b/examples/ExternalPointMass/makeIC.py
index fdc5b1fd67..7a9e2e1fd5 100644
--- a/examples/ExternalPointMass/makeIC.py
+++ b/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")
diff --git a/examples/Gradients/gradientsCartesian.yml b/examples/Gradients/gradientsCartesian.yml
index b2131bdd4d..0264e9ced8 100644
--- a/examples/Gradients/gradientsCartesian.yml
+++ b/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
diff --git a/examples/Gradients/gradientsRandom.yml b/examples/Gradients/gradientsRandom.yml
index 57ae849898..1c6fcc1d07 100644
--- a/examples/Gradients/gradientsRandom.yml
+++ b/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
diff --git a/examples/Gradients/makeICs.py b/examples/Gradients/makeICs.py
index 38d035d2ad..be70a9e614 100644
--- a/examples/Gradients/makeICs.py
+++ b/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')
diff --git a/examples/Gravity_glass/makeIC.py b/examples/Gravity_glass/makeIC.py
index 1a3fde9e28..f573c79b19 100644
--- a/examples/Gravity_glass/makeIC.py
+++ b/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.
diff --git a/examples/Gravity_glass/uniform_DM_box.yml b/examples/Gravity_glass/uniform_DM_box.yml
index 8f3ef6f025..00a5864cdb 100644
--- a/examples/Gravity_glass/uniform_DM_box.yml
+++ b/examples/Gravity_glass/uniform_DM_box.yml
@@ -42,3 +42,4 @@ Statistics:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./uniform_DM_box.hdf5
+ periodic: 1
\ No newline at end of file
diff --git a/examples/GreshoVortex_2D/gresho.yml b/examples/GreshoVortex_2D/gresho.yml
index df94145019..2006bb4511 100644
--- a/examples/GreshoVortex_2D/gresho.yml
+++ b/examples/GreshoVortex_2D/gresho.yml
@@ -34,3 +34,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./greshoVortex.hdf5 # The file to read
+ periodic: 1
\ No newline at end of file
diff --git a/examples/GreshoVortex_2D/makeIC.py b/examples/GreshoVortex_2D/makeIC.py
index 4f4ec3407b..4fb382925e 100644
--- a/examples/GreshoVortex_2D/makeIC.py
+++ b/examples/GreshoVortex_2D/makeIC.py
@@ -89,10 +89,6 @@ 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"] = 2
-#Runtime parameters
-grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/GreshoVortex_3D/gresho.yml b/examples/GreshoVortex_3D/gresho.yml
index 113c03b9bd..a95a0eae32 100644
--- a/examples/GreshoVortex_3D/gresho.yml
+++ b/examples/GreshoVortex_3D/gresho.yml
@@ -35,3 +35,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./greshoVortex.hdf5 # The file to read
+ periodic: 1
\ No newline at end of file
diff --git a/examples/GreshoVortex_3D/makeIC.py b/examples/GreshoVortex_3D/makeIC.py
index cba2158016..03f99df108 100644
--- a/examples/GreshoVortex_3D/makeIC.py
+++ b/examples/GreshoVortex_3D/makeIC.py
@@ -90,10 +90,6 @@ 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 = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/HydrostaticHalo/hydrostatic.yml b/examples/HydrostaticHalo/hydrostatic.yml
index 0cc11d0d87..874d6344cf 100644
--- a/examples/HydrostaticHalo/hydrostatic.yml
+++ b/examples/HydrostaticHalo/hydrostatic.yml
@@ -31,7 +31,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: Hydrostatic.hdf5 # The file to read
-
+ periodic: 1
+
# External potential parameters
IsothermalPotential:
vrot: 200. # rotation speed of isothermal potential in internal units
diff --git a/examples/HydrostaticHalo/makeIC.py b/examples/HydrostaticHalo/makeIC.py
index d5081ac844..b8a4036b77 100644
--- a/examples/HydrostaticHalo/makeIC.py
+++ b/examples/HydrostaticHalo/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)
diff --git a/examples/InteractingBlastWaves_1D/interactingBlastWaves.yml b/examples/InteractingBlastWaves_1D/interactingBlastWaves.yml
index e845599730..c4960dfa2c 100644
--- a/examples/InteractingBlastWaves_1D/interactingBlastWaves.yml
+++ b/examples/InteractingBlastWaves_1D/interactingBlastWaves.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./interactingBlastWaves.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/InteractingBlastWaves_1D/makeIC.py b/examples/InteractingBlastWaves_1D/makeIC.py
index bed0e20c83..3a47bf7c42 100644
--- a/examples/InteractingBlastWaves_1D/makeIC.py
+++ b/examples/InteractingBlastWaves_1D/makeIC.py
@@ -62,10 +62,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/IsothermalPotential/isothermal.yml b/examples/IsothermalPotential/isothermal.yml
index 5f626ff72e..f9cae4d3b4 100644
--- a/examples/IsothermalPotential/isothermal.yml
+++ b/examples/IsothermalPotential/isothermal.yml
@@ -26,6 +26,7 @@ Snapshots:
# Parameters related to the initial conditions
InitialConditions:
file_name: Isothermal.hdf5 # The file to read
+ periodic: 1
shift: [200.,200.,200.] # Shift all particles to be in the potential
# External potential parameters
diff --git a/examples/IsothermalPotential/makeIC.py b/examples/IsothermalPotential/makeIC.py
index eab16d21e6..ebcbb6dda1 100644
--- a/examples/IsothermalPotential/makeIC.py
+++ b/examples/IsothermalPotential/makeIC.py
@@ -97,10 +97,6 @@ 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)
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml b/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml
index 380dc2ab3a..e5a46cca1a 100644
--- a/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml
+++ b/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./kelvinHelmholtzGrowthRate.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py b/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py
index f21d0c0abf..25ef65fd75 100644
--- a/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py
+++ b/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py
@@ -76,10 +76,6 @@ 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"] = 2
-#Runtime parameters
-grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py b/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py
index 5029165a6a..55cd17823a 100644
--- a/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py
+++ b/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py
@@ -82,10 +82,6 @@ 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"] = 2
-#Runtime parameters
-grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
index e39c01645b..f5f7157f7d 100644
--- a/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
+++ b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
@@ -32,3 +32,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./kelvinHelmholtzGrowthRate.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py b/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py
index a9bc20559b..d28f361721 100644
--- a/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py
+++ b/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py
@@ -76,10 +76,6 @@ 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 = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py b/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py
index aa7dd8f214..51ab694f38 100644
--- a/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py
+++ b/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py
@@ -84,10 +84,6 @@ 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 = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/KelvinHelmholtz_2D/kelvinHelmholtz.yml b/examples/KelvinHelmholtz_2D/kelvinHelmholtz.yml
index ccc7526b39..6e4e2bd43c 100644
--- a/examples/KelvinHelmholtz_2D/kelvinHelmholtz.yml
+++ b/examples/KelvinHelmholtz_2D/kelvinHelmholtz.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./kelvinHelmholtz.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/KelvinHelmholtz_2D/makeIC.py b/examples/KelvinHelmholtz_2D/makeIC.py
index 744b39de82..919066955c 100644
--- a/examples/KelvinHelmholtz_2D/makeIC.py
+++ b/examples/KelvinHelmholtz_2D/makeIC.py
@@ -122,10 +122,6 @@ 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"] = 2
-#Runtime parameters
-grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/KeplerianRing/keplerian_ring.yml b/examples/KeplerianRing/keplerian_ring.yml
index cc5db2a06a..2195acfb55 100644
--- a/examples/KeplerianRing/keplerian_ring.yml
+++ b/examples/KeplerianRing/keplerian_ring.yml
@@ -32,7 +32,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: initial_conditions.hdf5 # The file to read
-
+ periodic: 1
+
# External potential parameters
PointMassPotential:
position: [5.,5.,5.] # location of external point mass in internal units
diff --git a/examples/MultiTypes/makeIC.py b/examples/MultiTypes/makeIC.py
index 41a5ef5f2f..80d49c762b 100644
--- a/examples/MultiTypes/makeIC.py
+++ b/examples/MultiTypes/makeIC.py
@@ -93,10 +93,6 @@ for n in range(num_files):
grp.attrs["MassTable"] = [0.0, massDM, 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")
diff --git a/examples/MultiTypes/multiTypes.yml b/examples/MultiTypes/multiTypes.yml
index 04647f0f00..121a15b083 100644
--- a/examples/MultiTypes/multiTypes.yml
+++ b/examples/MultiTypes/multiTypes.yml
@@ -31,6 +31,7 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./multiTypes.hdf5 # The file to read
+ periodic: 1
replicate: 2 # Replicate all particles twice along each axis
# External potential parameters
diff --git a/examples/Noh_1D/makeIC.py b/examples/Noh_1D/makeIC.py
index 176f351745..9d9a5e5b62 100644
--- a/examples/Noh_1D/makeIC.py
+++ b/examples/Noh_1D/makeIC.py
@@ -66,10 +66,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Noh_1D/noh.yml b/examples/Noh_1D/noh.yml
index 1d126f19ba..58e13ddda8 100644
--- a/examples/Noh_1D/noh.yml
+++ b/examples/Noh_1D/noh.yml
@@ -31,4 +31,6 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./noh.hdf5 # The file to read
+ periodic: 1
+
\ No newline at end of file
diff --git a/examples/Noh_2D/makeIC.py b/examples/Noh_2D/makeIC.py
index f7239fa3cd..83bb1ac677 100644
--- a/examples/Noh_2D/makeIC.py
+++ b/examples/Noh_2D/makeIC.py
@@ -73,10 +73,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Noh_2D/noh.yml b/examples/Noh_2D/noh.yml
index 1d126f19ba..eaf9916318 100644
--- a/examples/Noh_2D/noh.yml
+++ b/examples/Noh_2D/noh.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./noh.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/Noh_3D/makeIC.py b/examples/Noh_3D/makeIC.py
index 0c25a5c8b3..2d560a1e86 100644
--- a/examples/Noh_3D/makeIC.py
+++ b/examples/Noh_3D/makeIC.py
@@ -75,10 +75,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Noh_3D/noh.yml b/examples/Noh_3D/noh.yml
index cc15af7ec1..e005d394a6 100644
--- a/examples/Noh_3D/noh.yml
+++ b/examples/Noh_3D/noh.yml
@@ -32,4 +32,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./noh.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/PMillennium-384/p-mill-384.yml b/examples/PMillennium-384/p-mill-384.yml
index b7fc6f7622..4aede77c0c 100644
--- a/examples/PMillennium-384/p-mill-384.yml
+++ b/examples/PMillennium-384/p-mill-384.yml
@@ -46,5 +46,6 @@ Gravity:
# Parameters related to the initial conditions
InitialConditions:
file_name: ics.hdf5
+ periodic: 1
cleanup_h_factors: 1
cleanup_velocity_factors: 1
diff --git a/examples/PMillennium-768/p-mill-768.yml b/examples/PMillennium-768/p-mill-768.yml
index 8b93a7752d..a70c9c7083 100644
--- a/examples/PMillennium-768/p-mill-768.yml
+++ b/examples/PMillennium-768/p-mill-768.yml
@@ -46,5 +46,6 @@ Gravity:
# Parameters related to the initial conditions
InitialConditions:
file_name: ics.hdf5
+ periodic: 1
cleanup_h_factors: 1
cleanup_velocity_factors: 1
diff --git a/examples/PerturbedBox_2D/makeIC.py b/examples/PerturbedBox_2D/makeIC.py
index 87a4151777..7f52525bdf 100644
--- a/examples/PerturbedBox_2D/makeIC.py
+++ b/examples/PerturbedBox_2D/makeIC.py
@@ -86,10 +86,6 @@ grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
grp.attrs["NumPart_Total"] = numPart
grp.attrs["Dimension"] = 2
-#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.
diff --git a/examples/PerturbedBox_2D/perturbedPlane.yml b/examples/PerturbedBox_2D/perturbedPlane.yml
index a0c6b6d9db..4d03b30398 100644
--- a/examples/PerturbedBox_2D/perturbedPlane.yml
+++ b/examples/PerturbedBox_2D/perturbedPlane.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./perturbedPlane.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/PerturbedBox_3D/makeIC.py b/examples/PerturbedBox_3D/makeIC.py
index 1b0fc284e4..f2d8357f2f 100644
--- a/examples/PerturbedBox_3D/makeIC.py
+++ b/examples/PerturbedBox_3D/makeIC.py
@@ -88,10 +88,6 @@ grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
grp.attrs["NumPart_Total"] = numPart
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.
diff --git a/examples/PerturbedBox_3D/perturbedBox.yml b/examples/PerturbedBox_3D/perturbedBox.yml
index 3148510979..6010cf457b 100644
--- a/examples/PerturbedBox_3D/perturbedBox.yml
+++ b/examples/PerturbedBox_3D/perturbedBox.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./perturbedBox.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SantaBarbara/santa_barbara.yml b/examples/SantaBarbara/santa_barbara.yml
index b01321c521..65e6c239e1 100644
--- a/examples/SantaBarbara/santa_barbara.yml
+++ b/examples/SantaBarbara/santa_barbara.yml
@@ -53,6 +53,7 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./SantaBarbara.hdf5
+ periodic: 1
cleanup_h_factors: 1 # ICs were generated for Gadget, we need to get rid of h-factors
cleanup_velocity_factors: 1 # ICs were generated for Gadget, we need to get rid of sqrt(a) factors in the velocity
generate_gas_in_ics: 1 # Generate gas particles from the DM-only ICs
diff --git a/examples/SedovBlast_1D/makeIC.py b/examples/SedovBlast_1D/makeIC.py
index 7177f3a767..28b9c4bfd6 100644
--- a/examples/SedovBlast_1D/makeIC.py
+++ b/examples/SedovBlast_1D/makeIC.py
@@ -72,10 +72,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SedovBlast_1D/sedov.yml b/examples/SedovBlast_1D/sedov.yml
index 5ef105b06c..b4912a95e7 100644
--- a/examples/SedovBlast_1D/sedov.yml
+++ b/examples/SedovBlast_1D/sedov.yml
@@ -31,4 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sedov.hdf5 # The file to read
-
+ periodic: 1
diff --git a/examples/SedovBlast_2D/makeIC.py b/examples/SedovBlast_2D/makeIC.py
index 0e83c7b19b..cd1e433c10 100644
--- a/examples/SedovBlast_2D/makeIC.py
+++ b/examples/SedovBlast_2D/makeIC.py
@@ -72,10 +72,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SedovBlast_2D/sedov.yml b/examples/SedovBlast_2D/sedov.yml
index 098ca7a0d6..84177ece31 100644
--- a/examples/SedovBlast_2D/sedov.yml
+++ b/examples/SedovBlast_2D/sedov.yml
@@ -31,4 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sedov.hdf5 # The file to read
-
+ periodic: 1
diff --git a/examples/SedovBlast_3D/makeIC.py b/examples/SedovBlast_3D/makeIC.py
index e1b743c6cd..30e0e31927 100644
--- a/examples/SedovBlast_3D/makeIC.py
+++ b/examples/SedovBlast_3D/makeIC.py
@@ -72,10 +72,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SedovBlast_3D/sedov.yml b/examples/SedovBlast_3D/sedov.yml
index 75849e33c0..e91601f3e1 100644
--- a/examples/SedovBlast_3D/sedov.yml
+++ b/examples/SedovBlast_3D/sedov.yml
@@ -32,5 +32,6 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sedov.hdf5
+ periodic: 1
smoothing_length_scaling: 3.33
diff --git a/examples/SineWavePotential_1D/makeIC.py b/examples/SineWavePotential_1D/makeIC.py
index afbf1bc0fa..39a7839365 100644
--- a/examples/SineWavePotential_1D/makeIC.py
+++ b/examples/SineWavePotential_1D/makeIC.py
@@ -74,10 +74,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SineWavePotential_1D/sineWavePotential.yml b/examples/SineWavePotential_1D/sineWavePotential.yml
index e628578509..a21a0b5936 100644
--- a/examples/SineWavePotential_1D/sineWavePotential.yml
+++ b/examples/SineWavePotential_1D/sineWavePotential.yml
@@ -31,7 +31,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: sineWavePotential.hdf5 # The file to read
-
+ periodic: 1
+
# External potential parameters
SineWavePotential:
amplitude: 10.
diff --git a/examples/SineWavePotential_2D/makeIC.py b/examples/SineWavePotential_2D/makeIC.py
index 62ae89f8f5..057760502e 100644
--- a/examples/SineWavePotential_2D/makeIC.py
+++ b/examples/SineWavePotential_2D/makeIC.py
@@ -70,10 +70,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SineWavePotential_2D/sineWavePotential.yml b/examples/SineWavePotential_2D/sineWavePotential.yml
index 9107652f65..63d575e7e2 100644
--- a/examples/SineWavePotential_2D/sineWavePotential.yml
+++ b/examples/SineWavePotential_2D/sineWavePotential.yml
@@ -31,7 +31,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: sineWavePotential.hdf5 # The file to read
-
+ periodic: 1
+
# External potential parameters
SineWavePotential:
amplitude: 10.
diff --git a/examples/SineWavePotential_3D/makeIC.py b/examples/SineWavePotential_3D/makeIC.py
index 4833ec1b05..a4f39238ba 100644
--- a/examples/SineWavePotential_3D/makeIC.py
+++ b/examples/SineWavePotential_3D/makeIC.py
@@ -81,10 +81,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SineWavePotential_3D/sineWavePotential.yml b/examples/SineWavePotential_3D/sineWavePotential.yml
index 8a49d8bc40..5b91feae0e 100644
--- a/examples/SineWavePotential_3D/sineWavePotential.yml
+++ b/examples/SineWavePotential_3D/sineWavePotential.yml
@@ -31,7 +31,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: sineWavePotential.hdf5 # The file to read
-
+ periodic: 1
+
# External potential parameters
SineWavePotential:
amplitude: 10.
diff --git a/examples/SmallCosmoVolume/small_cosmo_volume.yml b/examples/SmallCosmoVolume/small_cosmo_volume.yml
index 353ab469c8..a6ce1f2819 100644
--- a/examples/SmallCosmoVolume/small_cosmo_volume.yml
+++ b/examples/SmallCosmoVolume/small_cosmo_volume.yml
@@ -52,7 +52,8 @@ Scheduler:
# Parameters related to the initial conditions
InitialConditions:
file_name: small_cosmo_volume.hdf5
+ periodic: 1
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.
+ 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.
diff --git a/examples/SmallCosmoVolume_DM/small_cosmo_volume_dm.yml b/examples/SmallCosmoVolume_DM/small_cosmo_volume_dm.yml
index ae4cb62c8d..910137edc4 100644
--- a/examples/SmallCosmoVolume_DM/small_cosmo_volume_dm.yml
+++ b/examples/SmallCosmoVolume_DM/small_cosmo_volume_dm.yml
@@ -53,5 +53,6 @@ Scheduler:
# Parameters related to the initial conditions
InitialConditions:
file_name: small_cosmo_volume.hdf5
+ periodic: 1
cleanup_h_factors: 1
cleanup_velocity_factors: 1
diff --git a/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml b/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml
index a765c9860d..b091207fa9 100644
--- a/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml
+++ b/examples/SmallCosmoVolume_cooling/small_cosmo_volume.yml
@@ -52,10 +52,11 @@ Scheduler:
# Parameters related to the initial conditions
InitialConditions:
file_name: small_cosmo_volume.hdf5
+ periodic: 1
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.
+ 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.
# Constant lambda cooling function
LambdaCooling:
diff --git a/examples/SmoothedMetallicity/makeIC.py b/examples/SmoothedMetallicity/makeIC.py
index 86679d5efe..542b4c5911 100644
--- a/examples/SmoothedMetallicity/makeIC.py
+++ b/examples/SmoothedMetallicity/makeIC.py
@@ -84,10 +84,6 @@ 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"] = 1
-
# Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SmoothedMetallicity/smoothed_metallicity.yml b/examples/SmoothedMetallicity/smoothed_metallicity.yml
index 2e37695392..f6841c6bd0 100644
--- a/examples/SmoothedMetallicity/smoothed_metallicity.yml
+++ b/examples/SmoothedMetallicity/smoothed_metallicity.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./smoothed_metallicity.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SodShockSpherical_2D/makeIC.py b/examples/SodShockSpherical_2D/makeIC.py
index ac9f6e1937..bc2c7ed1dc 100644
--- a/examples/SodShockSpherical_2D/makeIC.py
+++ b/examples/SodShockSpherical_2D/makeIC.py
@@ -100,10 +100,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SodShockSpherical_2D/sodShock.yml b/examples/SodShockSpherical_2D/sodShock.yml
index a26ab95b21..4ef13c26cc 100644
--- a/examples/SodShockSpherical_2D/sodShock.yml
+++ b/examples/SodShockSpherical_2D/sodShock.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sodShock.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SodShockSpherical_3D/makeIC.py b/examples/SodShockSpherical_3D/makeIC.py
index be8f9b61a1..3884fc2928 100644
--- a/examples/SodShockSpherical_3D/makeIC.py
+++ b/examples/SodShockSpherical_3D/makeIC.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
grp.attrs["Dimension"] = 3
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SodShockSpherical_3D/sodShock.yml b/examples/SodShockSpherical_3D/sodShock.yml
index 3fc4a1fb2b..16d3bd313c 100644
--- a/examples/SodShockSpherical_3D/sodShock.yml
+++ b/examples/SodShockSpherical_3D/sodShock.yml
@@ -32,4 +32,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sodShock.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SodShock_1D/makeIC.py b/examples/SodShock_1D/makeIC.py
index a5c7f03b24..d26bbbb4db 100644
--- a/examples/SodShock_1D/makeIC.py
+++ b/examples/SodShock_1D/makeIC.py
@@ -92,10 +92,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SodShock_1D/sodShock.yml b/examples/SodShock_1D/sodShock.yml
index e827edadb9..69554b4db7 100644
--- a/examples/SodShock_1D/sodShock.yml
+++ b/examples/SodShock_1D/sodShock.yml
@@ -31,4 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sodShock.hdf5 # The file to read
-
+ periodic: 1
diff --git a/examples/SodShock_2D/makeIC.py b/examples/SodShock_2D/makeIC.py
index 850ca24f54..2d3bd75fcc 100644
--- a/examples/SodShock_2D/makeIC.py
+++ b/examples/SodShock_2D/makeIC.py
@@ -98,10 +98,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SodShock_2D/sodShock.yml b/examples/SodShock_2D/sodShock.yml
index 51a188b6d4..b831dd7827 100644
--- a/examples/SodShock_2D/sodShock.yml
+++ b/examples/SodShock_2D/sodShock.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sodShock.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SodShock_3D/makeIC.py b/examples/SodShock_3D/makeIC.py
index c71c07c6c9..69f1bc5066 100644
--- a/examples/SodShock_3D/makeIC.py
+++ b/examples/SodShock_3D/makeIC.py
@@ -98,10 +98,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SodShock_3D/sodShock.yml b/examples/SodShock_3D/sodShock.yml
index 6042c8090d..b2d783cd74 100644
--- a/examples/SodShock_3D/sodShock.yml
+++ b/examples/SodShock_3D/sodShock.yml
@@ -32,4 +32,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./sodShock.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/SquareTest_2D/makeIC.py b/examples/SquareTest_2D/makeIC.py
index 186e653124..12a394873e 100644
--- a/examples/SquareTest_2D/makeIC.py
+++ b/examples/SquareTest_2D/makeIC.py
@@ -96,10 +96,6 @@ 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"] = 2
-#Runtime parameters
-grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = fileOutput.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/SquareTest_2D/square.yml b/examples/SquareTest_2D/square.yml
index b700c441a6..54e0effa67 100644
--- a/examples/SquareTest_2D/square.yml
+++ b/examples/SquareTest_2D/square.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./square.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/UniformBox_2D/makeIC.py b/examples/UniformBox_2D/makeIC.py
index 642896c6ec..36bb1ba611 100644
--- a/examples/UniformBox_2D/makeIC.py
+++ b/examples/UniformBox_2D/makeIC.py
@@ -85,10 +85,6 @@ grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
grp.attrs["NumPart_Total"] = numPart
grp.attrs["Dimension"] = 2
-#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.
diff --git a/examples/UniformBox_2D/uniformPlane.yml b/examples/UniformBox_2D/uniformPlane.yml
index 58fe0d5055..77f53d59c4 100644
--- a/examples/UniformBox_2D/uniformPlane.yml
+++ b/examples/UniformBox_2D/uniformPlane.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./uniformPlane.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/UniformBox_3D/makeIC.py b/examples/UniformBox_3D/makeIC.py
index 01e37c67b6..8311aae951 100644
--- a/examples/UniformBox_3D/makeIC.py
+++ b/examples/UniformBox_3D/makeIC.py
@@ -57,10 +57,6 @@ 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"] = periodic
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/UniformBox_3D/uniformBox.yml b/examples/UniformBox_3D/uniformBox.yml
index 17dd5632ed..202ff8298f 100644
--- a/examples/UniformBox_3D/uniformBox.yml
+++ b/examples/UniformBox_3D/uniformBox.yml
@@ -31,3 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./uniformBox.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/VacuumSpherical_2D/makeIC.py b/examples/VacuumSpherical_2D/makeIC.py
index 498f1b5bc5..05f0d8414c 100644
--- a/examples/VacuumSpherical_2D/makeIC.py
+++ b/examples/VacuumSpherical_2D/makeIC.py
@@ -77,10 +77,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/VacuumSpherical_2D/vacuum.yml b/examples/VacuumSpherical_2D/vacuum.yml
index 881b155b62..1d5642d5c1 100644
--- a/examples/VacuumSpherical_2D/vacuum.yml
+++ b/examples/VacuumSpherical_2D/vacuum.yml
@@ -31,4 +31,4 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./vacuum.hdf5 # The file to read
-
+ periodic: 1
diff --git a/examples/VacuumSpherical_3D/makeIC.py b/examples/VacuumSpherical_3D/makeIC.py
index d67a30707a..dd4ddd7e8a 100644
--- a/examples/VacuumSpherical_3D/makeIC.py
+++ b/examples/VacuumSpherical_3D/makeIC.py
@@ -80,10 +80,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/VacuumSpherical_3D/vacuum.yml b/examples/VacuumSpherical_3D/vacuum.yml
index 8792f029d9..851abf7444 100644
--- a/examples/VacuumSpherical_3D/vacuum.yml
+++ b/examples/VacuumSpherical_3D/vacuum.yml
@@ -32,4 +32,6 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./vacuum.hdf5 # The file to read
+ periodic: 1
+
\ No newline at end of file
diff --git a/examples/Vacuum_1D/makeIC.py b/examples/Vacuum_1D/makeIC.py
index 067304ec95..5b057b340c 100644
--- a/examples/Vacuum_1D/makeIC.py
+++ b/examples/Vacuum_1D/makeIC.py
@@ -63,10 +63,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 1
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Vacuum_1D/vacuum.yml b/examples/Vacuum_1D/vacuum.yml
index 5ef5ce3da6..0be6427e50 100644
--- a/examples/Vacuum_1D/vacuum.yml
+++ b/examples/Vacuum_1D/vacuum.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./vacuum.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/Vacuum_2D/makeIC.py b/examples/Vacuum_2D/makeIC.py
index ef267c092c..4d9181b83c 100644
--- a/examples/Vacuum_2D/makeIC.py
+++ b/examples/Vacuum_2D/makeIC.py
@@ -71,10 +71,6 @@ grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
grp.attrs["Flag_Entropy_ICs"] = 0
grp.attrs["Dimension"] = 2
-#Runtime parameters
-grp = file.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Vacuum_2D/vacuum.yml b/examples/Vacuum_2D/vacuum.yml
index 5ef5ce3da6..0be6427e50 100644
--- a/examples/Vacuum_2D/vacuum.yml
+++ b/examples/Vacuum_2D/vacuum.yml
@@ -31,4 +31,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./vacuum.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/Vacuum_3D/makeIC.py b/examples/Vacuum_3D/makeIC.py
index 09c3cb4d6f..cee2d28d51 100644
--- a/examples/Vacuum_3D/makeIC.py
+++ b/examples/Vacuum_3D/makeIC.py
@@ -73,10 +73,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 1.
diff --git a/examples/Vacuum_3D/vacuum.yml b/examples/Vacuum_3D/vacuum.yml
index cf44d2441f..49bd9747d6 100644
--- a/examples/Vacuum_3D/vacuum.yml
+++ b/examples/Vacuum_3D/vacuum.yml
@@ -32,4 +32,5 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./vacuum.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/ZeldovichPancake_3D/makeIC.py b/examples/ZeldovichPancake_3D/makeIC.py
index 79ed7e71e9..efce60f128 100644
--- a/examples/ZeldovichPancake_3D/makeIC.py
+++ b/examples/ZeldovichPancake_3D/makeIC.py
@@ -123,10 +123,6 @@ 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"] = 1
-
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = 100. * unit_l_in_si
diff --git a/examples/ZeldovichPancake_3D/zeldovichPancake.yml b/examples/ZeldovichPancake_3D/zeldovichPancake.yml
index 4d83d805cf..a1d2342b56 100644
--- a/examples/ZeldovichPancake_3D/zeldovichPancake.yml
+++ b/examples/ZeldovichPancake_3D/zeldovichPancake.yml
@@ -39,7 +39,8 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./zeldovichPancake.hdf5 # The file to read
-
+ periodic: 1
+
Scheduler:
max_top_level_cells: 8
cell_split_size: 50
diff --git a/examples/ZoomIn/getIC.sh b/examples/ZoomIn/getIC.sh
old mode 100644
new mode 100755
diff --git a/examples/ZoomIn/run.sh b/examples/ZoomIn/run.sh
old mode 100644
new mode 100755
diff --git a/examples/ZoomIn/zoom_in.yml b/examples/ZoomIn/zoom_in.yml
index 5f0fa4958b..8e5763c4af 100644
--- a/examples/ZoomIn/zoom_in.yml
+++ b/examples/ZoomIn/zoom_in.yml
@@ -56,6 +56,7 @@ SPH:
# Parameters related to the initial conditions
InitialConditions:
file_name: ./zoom_in.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
diff --git a/examples/getCoolingTable.sh b/examples/getCoolingTable.sh
old mode 100644
new mode 100755
--
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