examples/EAGLE_ICs/EAGLE_12/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0012N0188_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0012N0188_ICs.hdf5

examples/EAGLE_ICs/EAGLE_25/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0025N0376_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0025N0376_ICs.hdf5

examples/EAGLE_ICs/EAGLE_25_low_res/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0025N0188_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0025N0188_ICs.hdf5

examples/EAGLE_ICs/EAGLE_50/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0752_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0752_ICs.hdf5

examples/EAGLE_ICs/EAGLE_50_low_res/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0376_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0050N0376_ICs.hdf5

examples/EAGLE_ICs/EAGLE_6/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0006N0094_ICs.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_ICs/EAGLE_L0006N0094_ICs.hdf5

examples/EAGLE_ICs/getEagleCoolingTable.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/EAGLE/coolingtables.tar.gz
-tar -xf coolingtables.tar.gz 
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/EAGLE/coolingtables.tar.gz
+tar -xf coolingtables.tar.gz

examples/EAGLE_ICs/getEaglePhotometryTable.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/photometry.tar.gz
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/photometry.tar.gz
 tar -xf photometry.tar.gz

examples/EAGLE_ICs/getEagleYieldTable.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/yieldtables.tar.gz
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/YieldTables/EAGLE/yieldtables.tar.gz
 tar -xf yieldtables.tar.gz

examples/EAGLE_ICs/getPS2020CoolingTables.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/COLIBRE/UV_dust1_CR1_G1_shield1.hdf5
-
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/COLIBRE/UV_dust1_CR1_G1_shield1.hdf5

examples/EAGLE_low_z/EAGLE_100/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_100.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_100.hdf5

examples/EAGLE_low_z/EAGLE_12/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_12.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_12.hdf5

examples/EAGLE_low_z/EAGLE_25/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_25.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_25.hdf5

examples/EAGLE_low_z/EAGLE_50/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_50.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_50.hdf5

examples/EAGLE_low_z/EAGLE_6/check_fof.py

@@ -4,9 +4,9 @@ from tqdm import tqdm
 from numba import jit, prange
 
 snapname = "eagle_0000/eagle_0000.hdf5"
-fofname = "fof_output_0000/fof_output_0000.0.hdf5"
+# fofname = "fof_output_0000/fof_output_0000.0.hdf5"
 # snapname = "eagle_0000.hdf5"
-# fofname = "fof_output_0000.hdf5"
+fofname = "fof_output_0000.hdf5"
 
 ######################################################
 
@@ -40,26 +40,36 @@ fof_grp = np.zeros(num_groups, dtype=np.int32)
 fof_size = np.zeros(num_groups, dtype=np.int32)
 fof_mass = np.zeros(num_groups)
 
-# Read the distributed catalog
-offset = 0
-for i in range(num_files):
+if num_files == 1:
 
-    my_filename = fofname[:-6]
-    my_filename = my_filename + str(i) + ".hdf5"
-    fof = h5.File(my_filename, "r")
+    fof = h5.File(fofname, "r")
+    fof_grp = fof["/Groups/GroupIDs"][:]
+    fof_size = fof["/Groups/Sizes"][:]
+    fof_mass = fof["/Groups/Masses"][:]
+    fof.close()
 
-    my_fof_grp = fof["/Groups/GroupIDs"][:]
-    my_fof_size = fof["/Groups/Sizes"][:]
-    my_fof_mass = fof["/Groups/Masses"][:]
+else:
 
-    num_this_file = fof["/Header"].attrs["NumGroups_ThisFile"][0]
-    fof.close()
+    # Read the distributed catalog
+    offset = 0
+    for i in range(num_files):
+
+        my_filename = fofname[:-6]
+        my_filename = my_filename + str(i) + ".hdf5"
+        fof = h5.File(my_filename, "r")
+
+        my_fof_grp = fof["/Groups/GroupIDs"][:]
+        my_fof_size = fof["/Groups/Sizes"][:]
+        my_fof_mass = fof["/Groups/Masses"][:]
+
+        num_this_file = fof["/Header"].attrs["NumGroups_ThisFile"][0]
+        fof.close()
 
-    fof_grp[offset : offset + num_this_file] = my_fof_grp
-    fof_size[offset : offset + num_this_file] = my_fof_size
-    fof_mass[offset : offset + num_this_file] = my_fof_mass
+        fof_grp[offset : offset + num_this_file] = my_fof_grp
+        fof_size[offset : offset + num_this_file] = my_fof_size
+        fof_mass[offset : offset + num_this_file] = my_fof_mass
 
-    offset += num_this_file
+        offset += num_this_file
 
 ####################################################
 

examples/EAGLE_low_z/EAGLE_6/getIC.sh

 #!/bin/bash
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_6.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/EAGLE_low_z/EAGLE_ICs_6.hdf5

examples/GEAR/AgoraCosmo/agora_cosmo.yml

@@ -86,14 +86,15 @@ GrackleCooling:
   max_steps: 1000
   convergence_limit: 1e-2
   thermal_time_myr: 5
+  maximal_density_Hpcm3: -1 # Maximal density (in hydrogen atoms/cm^3) for cooling. Higher densities are floored to this value to ensure grackle works properly when interpolating beyond the cloudy_table maximal density. A value < 0 deactivates this parameter.
 
 
 GEARStarFormation:
   star_formation_efficiency: 0.01   # star formation efficiency (c_*)
-  maximal_temperature:  3e4         # Upper limit to the temperature of a star forming particle
+  maximal_temperature_K:     3e4    # Upper limit to the temperature of a star forming particle
+  density_threshold_Hpcm3:   1e-6   # Density threshold (in addition to the pressure floor) in Hydrogen atoms/cm3
   n_stars_per_particle: 1
   min_mass_frac: 0.5
-  density_threshold:   1e-30       # Density threashold (in addition to the pressure floor) in g/cm3
 
 GEARPressureFloor:
   jeans_factor: 8.75

examples/GEAR/AgoraCosmo/getChemistryTable.sh

 #!/bin/bash
 
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/FeedbackTables/POPIIsw.h5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/FeedbackTables/POPIIsw.h5

examples/GEAR/AgoraCosmo/getGrackleCoolingTable.sh

 #!/bin/bash
 
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/GEAR/CloudyData_UVB=HM2012_shielded.h5
-
-
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/GEAR/CloudyData_UVB=HM2012_shielded.h5

examples/GEAR/AgoraCosmo/getIC.sh

 #!/bin/bash
 
-wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraCosmo/agora_swift.hdf5
-
-
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraCosmo/agora_swift.hdf5