examples/GEAR/AgoraCosmo/getChemistryTable.sh

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

examples/GEAR/AgoraCosmo/getGrackleCoolingTable.sh

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

examples/GEAR/AgoraCosmo/getIC.sh

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

examples/GEAR/AgoraCosmo/music.conf

+################################################
+## AGORA IC file for the 1e12q halo ############
+################################################
+
+[setup]
+boxlength               = 60
+zstart                  = 100
+levelmin                = 7
+levelmin_TF             = 9
+levelmax                = 12
+
+padding                 = 16  # try reduce it at your own risk
+overlap                 = 4
+baryons                 = yes  # switch on for baryon runs
+use_2LPT                = no
+use_LLA                 = no  # AMR codes might want to enable this
+
+#Ellipsoidal refinement region defined on unity cube
+region                     = ellipsoid
+region_ellipsoid_matrix[0] = 822.07,  -86.84, -661.59
+region_ellipsoid_matrix[1] = -86.84,  673.36, 243.17
+region_ellipsoid_matrix[2] = -661.59, 243.17, 1295.95
+region_ellipsoid_center    = 0.527531, 0.522087, 0.449525
+
+
+[cosmology]
+Omega_m                 = 0.272
+Omega_L                 = 0.728
+Omega_b                 = 0.0455
+H0                              = 70.2
+sigma_8                 = 0.807
+nspec                   = 0.961
+transfer                = eisenstein
+
+#below are MUSIC defaults to initialize gas temperature for some codes
+#YHe				= 0.248     # primordial He abundance
+#gamma				= 1.6667    # adiabatic exponent (=5/3)
+
+
+[random]
+cubesize                = 256
+seed[8]                 = 95064
+seed[9]                 = 31415
+seed[10]                = 27183
+
+
+[poisson]
+fft_fine                = yes
+accuracy                = 1e-4
+grad_order      = 6
+laplace_order   = 6
+
+
+[output]
+## AREPO
+format = arepo
+filename = agora_arepo.hdf5
+
+## GENERIC
+#format			= generic
+#filename		= debug.hdf5
+
+## ENZO
+#format			= enzo
+#filename		= ic.enzo
+##enzo_refine_region_fraction = 0.8
+
+## GADGET-2
+#format			= gadget2
+#filename		= ics_gadget.dat
+#gadget_spreadcoarse	= yes
+#gadget_write_conn	= yes
+##gadget_num_files	= 8
+##gadget_longids	= no
+##gadget_usekpc		= no
+##gadget_usemsol	= no
+##gadget_coarsetype	= 5
+
+## RAMSES
+#ramses_nml		= yes
+#format			= grafic2
+#filename		= ics_ramses
+
+## TIPSY
+#format			= tipsy
+#filename		= ics_tipsy.dat
+
+## ART
+#format			= art
+#filename		= ics_art.dat
+##art_swap_endian	= yes
+##astep			= ...
+
+## CART
+#format			= cart
+#filename		= ics_cart.dat
\ No newline at end of file

examples/GEAR/AgoraCosmo/output_list.txt

+# Scale Factor
+0.02
+0.025
+0.03
+0.035
+0.04
+0.045
+0.05
+0.055
+0.06
+0.0625
+0.065
+0.07
+0.075
+0.0769231
+0.08
+0.085
+0.09
+0.0909091
+0.095
+0.1
+0.105
+0.11
+0.111111
+0.115
+0.12
+0.125
+0.13
+0.135
+0.14
+0.142857
+0.145
+0.15
+0.155
+0.16
+0.165
+0.166667
+0.17
+0.175
+0.18
+0.185
+0.19
+0.195
+0.2
+0.205
+0.21
+0.215
+0.22
+0.225
+0.23
+0.235
+0.24
+0.245
+0.25
+0.255
+0.26
+0.265
+0.27
+0.275
+0.28
+0.285
+0.285714
+0.29
+0.295
+0.3
+0.305
+0.31
+0.315
+0.32
+0.325
+0.33
+0.333333
+0.335
+0.34
+0.345
+0.35
+0.355
+0.36
+0.365
+0.37
+0.375
+0.38
+0.385
+0.39
+0.395
+0.4
+0.405
+0.41
+0.415
+0.42
+0.425
+0.43
+0.435
+0.44
+0.445
+0.45
+0.455
+0.46
+0.465
+0.47
+0.475
+0.48
+0.485
+0.49
+0.495
+0.5
+0.505
+0.51
+0.515
+0.52
+0.525
+0.53
+0.535
+0.54
+0.545
+0.55
+0.555
+0.56
+0.565
+0.57
+0.571429
+0.575
+0.58
+0.585
+0.59
+0.595
+0.6
+0.605
+0.61
+0.615
+0.62
+0.625
+0.63
+0.635
+0.64
+0.645
+0.65
+0.655
+0.66
+0.665
+0.666667
+0.67
+0.675
+0.68
+0.685
+0.69
+0.695
+0.7
+0.705
+0.71
+0.715
+0.72
+0.725
+0.73
+0.735
+0.74
+0.745
+0.75
+0.755
+0.76
+0.765
+0.77
+0.775
+0.78
+0.785
+0.79
+0.795
+0.8
+0.805
+0.81
+0.815
+0.82
+0.825
+0.83
+0.835
+0.84
+0.845
+0.85
+0.855
+0.86
+0.865
+0.87
+0.875
+0.88
+0.885
+0.89
+0.895
+0.9
+0.905
+0.91
+0.915
+0.92
+0.925
+0.93
+0.935
+0.94
+0.945
+0.95
+0.955
+0.96
+0.965
+0.97
+0.975
+0.98
+0.985
+0.99
+0.995
+1

examples/GEAR/AgoraCosmo/run.sh

+#!/bin/bash
+
+# Get the initial conditions
+if [ ! -e agora_swift.hdf5 ]
+then
+    echo "Fetching the initial conditions"
+    ./getIC.sh
+fi
+
+
+# Get the Grackle cooling table
+if [ ! -e CloudyData_UVB=HM2012_shielded.h5 ]
+then
+    echo "Fetching the Cloudy tables required by Grackle..."
+    ./getGrackleCoolingTable.sh
+fi
+
+
+if [ ! -e POPIIsw.h5 ]
+then
+    echo "Fetching the chemistry tables..."
+    ./getChemistryTable.sh
+fi
+
+
+
+
+../../../swift --cooling --feedback --cosmology  --limiter --sync --self-gravity --hydro --stars --star-formation --threads=24 agora_cosmo.yml 2>&1 | tee output.log
+
+
+

examples/GEAR/AgoraDisk/README

+To run this example, SWIFT must be configured with the following options:
+
+./configure --with-chemistry=GEAR_10  --with-cooling=grackle_0  --with-pressure-floor=GEAR --with-stars=GEAR --with-star-formation=GEAR --with-feedback=GEAR
+
+An analysis script for this test case can be found in the AGORA project repository:
+https://bitbucket.org/mornkr/agora-analysis-script/
+
+A modified version of the script able to read in SWIFT data is available upon request.
+
+(Note to the SWIFT authors: The modified script is stored with the other reference solutions.)

examples/GEAR/AgoraDisk/agora_disk.yml

@@ -7,18 +7,29 @@ InternalUnitSystem:
   UnitTemp_in_cgs:     1             # Kelvin
 
 Scheduler:
-  max_top_level_cells: 8
+  max_top_level_cells: 16
+  cell_extra_sparts:  5000       # (Optional) Number of spare sparts per top-level allocated at rebuild time for on-the-fly creation.
+  cell_extra_gparts:  5000       # (Optional) Number of spare sparts per top-level allocated at rebuild time for on-the-fly creation.
+  cell_max_size:             8000   # (Optional) Maximal number of interactions per task if we force the split (this is the default value).
+  cell_sub_size_pair_hydro:  2560 # (Optional) Maximal number of hydro-hydro interactions per sub-pair hydro/star task (this is the default value).
+  cell_sub_size_self_hydro:  3200     # (Optional) Maximal number of hydro-hydro interactions per sub-self hydro/star task (this is the default value).
+  cell_sub_size_pair_stars:  2560 # (Optional) Maximal number of hydro-star interactions per sub-pair hydro/star task (this is the default value).
+  cell_sub_size_self_stars:  3200     # (Optional) Maximal number of hydro-star interactions per sub-self hydro/star task (this is the default value).
+  cell_sub_size_pair_grav:   2560 # (Optional) Maximal number of interactions per sub-pair gravity task  (this is the default value).
+  cell_sub_size_self_grav:   3200     # (Optional) Maximal number of interactions per sub-self gravity task  (this is the default value).
+  cell_split_size:           100       # (Optional) Maximal number of particles per cell (this is the default value).
   
 # Parameters governing the time integration
 TimeIntegration:
   time_begin: 0.    # The starting time of the simulation (in internal units).
-  time_end:   0.5  # The end time of the simulation (in internal units).
+  time_end:   0.25  # The end time of the simulation (in internal units).
   dt_min:     1e-10 # The minimal time-step size of the simulation (in internal units).
-  dt_max:     1e-4  # The maximal time-step size of the simulation (in internal units).
-  
+  dt_max:     0.1  # The maximal time-step size of the simulation (in internal units).
+  max_dt_RMS_factor: 0.25  # (Optional) Dimensionless factor for the maximal displacement allowed based on the RMS velocities.
+
 # Parameters governing the snapshots
 Snapshots:
-  basename:            agora_disk # Common part of the name of output files
+  basename:            snapshot # Common part of the name of output files
   time_first:          0.    # Time of the first output (in internal units)
   delta_time:          1e-2  # Time difference between consecutive outputs (in internal units)
   compression:         4
@@ -29,10 +40,14 @@ Statistics:
 
 # Parameters for the self-gravity scheme
 Gravity:
-  eta:                    0.025    # Constant dimensionless multiplier for time integration.
-  theta:                  0.7     # Opening angle (Multipole acceptance criterion)
-  comoving_softening:     0.08 # Comoving softening length (in internal units).
-  max_physical_softening: 0.08    # Physical softening length (in internal units).
+  eta:                       0.05    # Constant dimensionless multiplier for time integration.
+  MAC:                       geometric
+  theta_cr:                  0.7     
+  use_tree_below_softening:  1
+  comoving_DM_softening:     0.08 # Comoving softening length (in internal units).
+  max_physical_DM_softening: 0.08    # Physical softening length (in internal units).
+  comoving_baryon_softening:     0.08 # Comoving softening length (in internal units).
+  max_physical_baryon_softening: 0.08    # Physical softening length (in internal units).
   mesh_side_length:       32        # Number of cells along each axis for the periodic gravity mesh.
   
 # Parameters for the hydrodynamics scheme
@@ -40,6 +55,8 @@ SPH:
   resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
   minimal_temperature:   10.      # Kelvin
+  h_min_ratio:           0.1095       # (Optional) Minimal allowed smoothing length in units of the softening. Defaults to 0 if unspecified.
+  h_max:                     10.      # (Optional) Maximal allowed smoothing length in internal units. Defaults to FLT_MAX if unspecified.
 
 # Parameters related to the initial conditions
 InitialConditions:
@@ -55,13 +72,44 @@ LambdaCooling:
 
 # Cooling with Grackle 2.0
 GrackleCooling:
-  CloudyTable: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
-  WithUVbackground: 1 # Enable or not the UV background
-  Redshift: 0 # Redshift to use (-1 means time based redshift)
-  WithMetalCooling: 1 # Enable or not the metal cooling
-  ProvideVolumetricHeatingRates: 0 # User provide volumetric heating rates
-  ProvideSpecificHeatingRates: 0 # User provide specific heating rates
-  SelfShieldingMethod: 0 # Grackle (<= 3) or Gear self shielding method
-  OutputMode: 1 # Write in output corresponding primordial chemistry mode
-  MaxSteps: 1000
-  ConvergenceLimit: 1e-2
+  cloudy_table: CloudyData_UVB=HM2012.h5 # Name of the Cloudy Table (available on the grackle bitbucket repository)
+  with_UV_background: 1 # Enable or not the UV background
+  redshift: 0 # Redshift to use (-1 means time based redshift)
+  with_metal_cooling: 1 # Enable or not the metal cooling
+  provide_volumetric_heating_rates: 0 # User provide volumetric heating rates
+  provide_specific_heating_rates: 0 # User provide specific heating rates
+  self_shielding_method: -1 # Grackle (<= 3) or Gear self shielding method
+  self_shielding_threshold_atom_per_cm3: 0.007  # Required only with GEAR's self shielding. Density threshold of the self shielding
+  max_steps: 1000
+  convergence_limit: 1e-2
+  thermal_time_myr: 0
+  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_K:     1e10   # Upper limit to the temperature of a star forming particle
+  density_threshold_Hpcm3:   10     # Density threshold in Hydrogen atoms/cm3
+  n_stars_per_particle: 1
+  min_mass_frac: 0.5
+
+
+GEARPressureFloor:
+  jeans_factor: 10
+
+GEARFeedback:
+  supernovae_energy_erg: 1e51
+  supernovae_efficiency: 0.1
+  yields_table: POPIIsw.h5
+  discrete_yields: 0
+  yields_table_first_stars: POPIIsw.h5          # Table containing the yields of the first stars.
+  metallicity_max_first_stars: -5                          # Maximal metallicity (in mass fraction) for a first star (-1 to deactivate).
+  elements: [Fe, Mg, O, C, Al, Ca, Ba, Zn, Eu]             # Elements to read in the yields table. The number of element should be one less than the number of elements (N) requested during the configuration (--with-chemistry=GEAR_N).
+
+GEARChemistry:
+  initial_metallicity: 1
+  scale_initial_metallicity: 1
+
+Restarts:
+  delta_hours:   1.        # (Optional) decimal hours between dumps of restart files.
+

examples/GEAR/AgoraDisk/changeType.py

-#!/usr/bin/env python3
-
-from h5py import File
-from sys import argv
-import numpy as np
-
-"""
-Change particle types in order to match the implemented types
-"""
-
-# number of particle type
-N_type = 6
-
-debug = 0
-
-
-def getOption():
-    if len(argv) != 2:
-        raise IOError("You need to provide a filename")
-
-    # get filename and read it
-    filename = argv[-1]
-
-    return filename
-
-
-def groupName(part_type):
-    return "PartType%i" % part_type
-
-
-def changeType(f, old, new):
-    # check if directory exists
-    old_group = groupName(old)
-    if old_group not in f:
-        raise IOError("Cannot find group '%s'" % old)
-    old = f[old_group]
-
-    new_group = groupName(new)
-    if new_group not in f:
-        f.create_group(new_group)
-    new = f[new_group]
-
-    for name in old:
-        if debug:
-            print("Moving '%s' from '%s' to '%s'"
-                  % (name, old_group, new_group))
-
-        tmp = old[name][:]
-        del old[name]
-        if name in new:
-            new_tmp = new[name][:]
-            if debug:
-                print("Found previous data:", tmp.shape, new_tmp.shape)
-            tmp = np.append(tmp, new_tmp, axis=0)
-            del new[name]
-
-        if debug:
-            print("With new shape:", tmp.shape)
-        new.create_dataset(name, tmp.shape)
-        new[name][:] = tmp
-
-    del f[old_group]
-
-
-def countPart(f):
-    npart = []
-    for i in range(N_type):
-        name = groupName(i)
-        if name in f:
-            grp = f[groupName(i)]
-            N = grp["Masses"].shape[0]
-        else:
-            N = 0
-        npart.append(N)
-
-    f["Header"].attrs["NumPart_ThisFile"] = npart
-    f["Header"].attrs["NumPart_Total"] = npart
-    f["Header"].attrs["NumPart_Total_HighWord"] = [0]*N_type
-
-
-if __name__ == "__main__":
-    filename = getOption()
-
-    f = File(filename)
-
-    changeType(f, 2, 1)
-    changeType(f, 3, 1)
-    changeType(f, 4, 1)
-
-    countPart(f)
-
-    f.close()

examples/GEAR/AgoraDisk/checkSolution.py

+import h5py
+import numpy as np
+
+expected_total_mass = 227413100.0
+
+f = h5py.File("snapshot_0025.hdf5", "r")
+
+# get the total stellar mass
+mass = f["StarsParticles/Masses"]
+total_mass = sum(mass) * 1e10
+
+error = np.fabs((expected_total_mass - total_mass) / expected_total_mass)
+
+if error < 0.01:
+    print(48 * "!")
+    print(r"Well done !")
+    print(r"The stellar mass is %g Msol," % (total_mass))
+    print(r"The expected stellar mass is %g Msol" % (expected_total_mass))
+    print(r"This represents an error of %d %% !" % (100 * error))
+    print(48 * "!")
+else:
+    print(48 * "!")
+    print(r"Too bad !")
+    print(r"The stellar mass is %g Msol," % (total_mass))
+    print(r"While the expected stellar mass is %g Msol" % (expected_total_mass))
+    print(r"This represents an error of %d %% !" % (100 * error))
+    print(r"This is beyond the requirements.")
+    print(48 * "!")

examples/GEAR/AgoraDisk/cleanupSwift.py

-#!/usr/bin/env python3
-
-# ./translate_particles.py filename output_name
-from h5py import File
-import sys
-from shutil import copyfile
-
-NPartType = 1
-filename = sys.argv[-2]
-out = sys.argv[-1]
-
-copyfile(filename, out)
-
-f = File(out)
-
-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
-    if name not in f:
-        continue
-
-    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/getChemistryTable.sh

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

examples/GEAR/AgoraDisk/getGrackleCoolingTable.sh

+#!/bin/bash
+
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5

examples/GEAR/AgoraDisk/getIC.sh

 #!/bin/bash
 
 if [ "$#" -ne 1 ]; then
-    echo "You need to provide the resolution (e.g. ./getIC.sh low)."
-    echo "The possible options are low, med and high."
+    echo "You need to provide the resolution (e.g. ./getIC.sh LOW)."
+    echo "The possible options are LOW and MED."
     exit
 fi
 
-wget https://obswww.unige.ch/~lhausamm/swift/IC/AgoraDisk/$1.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk/snap.$1.hdf5
+mv snap.$1.hdf5 agora_disk.hdf5

examples/GEAR/AgoraDisk/getSolution.sh

 #!/bin/bash
 
-# cleanup work space
-rm snapshot_0000.hdf5 snapshot_0500.hdf5
-
-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
-
-
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk/Gear/snapshot_0000.hdf5
+wget https://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraDisk/Gear/snapshot_0050.hdf5

examples/GEAR/AgoraDisk/run.sh

@@ -2,14 +2,15 @@
 
 # This example is based on the AGORA disk article (DOI: 10.3847/1538-4357/833/2/202)
 
-# currently only the low resolution is available
-sim=low
+# set the resolution (LOW or MED)
+sim=LOW
+
 
 # make run.sh fail if a subcommand fails
 set -e
 
 # Generate the initial conditions if they are not present.
-if [ ! -e $sim.hdf5 ]
+if [ ! -e agora_disk.hdf5 ]
 then
     echo "Fetching initial glass file for the Sedov blast example..."
     ./getIC.sh $sim
@@ -19,25 +20,22 @@ fi
 if [ ! -e CloudyData_UVB=HM2012.h5 ]
 then
     echo "Fetching the Cloudy tables required by Grackle..."
-    ../../Cooling/getGrackleCoolingTable.sh 
+    ./getGrackleCoolingTable.sh
 fi
 
-# copy the initial conditions
-cp $sim.hdf5 agora_disk.hdf5
-# Update the particle types
-python3 changeType.py agora_disk.hdf5
 
-# Run SWIFT
-../../swift --cooling --hydro --self-gravity --threads=4 agora_disk.yml 2>&1 | tee output.log
+if [ ! -e POPIIsw.h5 ]
+then
+    echo "Fetching the chemistry tables..."
+    ./getChemistryTable.sh
+fi
+
 
+# Run SWIFT
+../../../swift --sync --limiter --cooling --hydro --self-gravity --star-formation --feedback --stars --threads=8 agora_disk.yml 2>&1 | tee output.log
 
-echo "Changing smoothing length to be Gadget compatible"
-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
 
 
-echo "Plotting..."
-python3 plotSolution.py
+echo "check solution..."
+python3 checkSolution.py

examples/GEAR/DwarfGalaxy/README

-This example is a galaxy extracted from the example "ZoomIn". It allows
-to test SWIFT on a smaller problem. See the README in "ZoomIn" for more
-information.
-
-
-MD5 check-sum of the ICS: 
-ae2af84d88f30011b6a8af3f37d140cf  dwarf_galaxy.hdf5
\ No newline at end of file

examples/GEAR/DwarfGalaxy/getIC.sh

-#!/bin/bash
-wget https://obswww.unige.ch/~lhausamm/swift/IC/DwarfGalaxy/dwarf_galaxy.hdf5

examples/GEAR/DwarfGalaxy/run.sh

-#!/bin/bash
-
- # Generate the initial conditions if they are not present.
-if [ ! -e dwarf_galaxy.hdf5 ]
-then
-    echo "Fetching initial conditions for the dwarf galaxy example..."
-    ./getIC.sh
-fi
-
-../../swift --feedback --self-gravity --hydro --stars --threads=8 $@ dwarf_galaxy.yml 2>&1 | tee output.log
-