Merge branch 'update_agora' into 'master'

Update agora

See merge request !809

examples/GEAR/AgoraDisk/cleanupSwift.py

@@ -13,9 +13,10 @@ copyfile(filename, out)
 
 f = File(out)
 
-name = "PartType0/ElementAbundance"
-if name in f:
-    del f[name]
+for i in range(6):
+    name = "PartType{}/ElementAbundance".format(i)
+    if name in f:
+        del f[name]
 
 for i in range(NPartType):
     name = "PartType%i" % i
@@ -25,4 +26,10 @@ for i in range(NPartType):
     grp = f[name + "/SmoothingLength"]
     grp[:] *= 1.823
 
+cosmo = f["Cosmology"].attrs
+head = f["Header"].attrs
+head["OmegaLambda"] = cosmo["Omega_lambda"]
+head["Omega0"] = cosmo["Omega_b"]
+head["HubbleParam"] = cosmo["H0 [internal units]"]
+
 f.close()

examples/GEAR/AgoraDisk/getSolution.sh

 #!/bin/bash
 
-OPTIND=1
-
-with_cooling=0
-
-function show_help {
-    echo "Valid options are:"
-    echo "\t -h \t Show this help"
-    echo "\t -C \t Download solution with cooling"
-}
-
-while getopts "h?C" opt; do
-    case "$opt" in
-	h|\?)
-	    show_help
-	    exit
-	    ;;
-	C)
-	    with_cooling=1
-	    ;;
-    esac
-done
-
 # cleanup work space
 rm snapshot_0000.hdf5 snapshot_0500.hdf5
 
-if [ $with_cooling -eq 1 ]; then
-    wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/with_cooling/snapshot_0000.hdf5
-    wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/with_cooling/snapshot_0500.hdf5
-else
-    wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/without_cooling/snapshot_0000.hdf5
-    wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/without_cooling/snapshot_0500.hdf5
-fi
+wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/with_cooling/snapshot_0000.hdf5
+wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/with_cooling/snapshot_0500.hdf5
+
+# wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/without_cooling/snapshot_0000.hdf5
+# wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/Gear/without_cooling/snapshot_0500.hdf5
 
 

examples/GEAR/AgoraDisk/run.sh

@@ -5,31 +5,21 @@
 # currently only the low resolution is available
 sim=low
 
-# enable cooling or not
-cooling=0
-
 # make run.sh fail if a subcommand fails
 set -e
 
-# define flags
-flag=
-if [ $cooling -eq 1 ]
-then
-    flag=-C
-fi
-
 # Generate the initial conditions if they are not present.
 if [ ! -e $sim.hdf5 ]
 then
     echo "Fetching initial glass file for the Sedov blast example..."
-    ./getIC.sh $sim.hdf5
+    ./getIC.sh $sim
 fi
 
 # Get the Grackle cooling table
 if [ ! -e CloudyData_UVB=HM2012.h5 ]
 then
     echo "Fetching the Cloudy tables required by Grackle..."
-    ../getCoolingTable.sh
+    ../../Cooling/getGrackleCoolingTable.sh 
 fi
 
 # copy the initial conditions
@@ -38,7 +28,7 @@ cp $sim.hdf5 agora_disk.hdf5
 python3 changeType.py agora_disk.hdf5
 
 # Run SWIFT
-#../../swift $flag --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
+../../swift --cooling --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
 
 
 echo "Changing smoothing length to be Gadget compatible"
@@ -46,7 +36,8 @@ python3 cleanupSwift.py agora_disk_0000.hdf5 agora_disk_IC.hdf5
 python3 cleanupSwift.py agora_disk_0050.hdf5 agora_disk_500Myr.hdf5
 
 echo "Fetching GEAR solution..."
-./getSolution.sh $flag
+./getSolution.sh
+
 
 echo "Plotting..."
-python3 plotSolution.py $flag
+python3 plotSolution.py