Fix GEAR pressure floor

.gitignore

@@ -26,6 +26,8 @@ doc/html/
 doc/latex/
 doc/man/
 doc/Doxyfile
+doc/RTD/source/SubgridModels/*/*.png
+doc/RTD/source/RadiativeTransfer/full_dependency_graph_RT.png
 
 examples/*/*/*.xmf
 examples/*/*/*.dat
@@ -73,6 +75,14 @@ examples/SmallCosmoVolume/SmallCosmoVolume_cooling/snapshots/
 examples/SmallCosmoVolume/SmallCosmoVolume_hydro/snapshots/
 examples/SmallCosmoVolume/SmallCosmoVolume_cooling/CloudyData_UVB=HM2012.h5
 examples/SmallCosmoVolume/SmallCosmoVolume_cooling/CloudyData_UVB=HM2012_shielded.h5
+examples/GEAR/AgoraDisk/CloudyData_UVB=HM2012.h5
+examples/GEAR/AgoraDisk/CloudyData_UVB=HM2012_shielded.h5
+examples/GEAR/AgoraDisk/chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
+examples/GEAR/AgoraCosmo/CloudyData_UVB=HM2012_shielded.h5
+examples/GEAR/AgoraCosmo/POPIIsw.h5
+examples/GEAR/ZoomIn/CloudyData_UVB=HM2012.h5
+examples/GEAR/ZoomIn/POPIIsw.h5
+examples/GEAR/ZoomIn/snap/
 
 tests/testActivePair
 tests/testActivePair.sh
@@ -198,6 +208,10 @@ theory/SPH/Flavours/sph_flavours.pdf
 theory/SPH/EoS/eos.pdf
 theory/SPH/*.pdf
 theory/paper_pasc/pasc_paper.pdf
+theory/Multipoles/alpha_derivatives.pdf
+theory/Multipoles/alpha_powers.pdf
+theory/Multipoles/chi_derivatives.pdf
+theory/Multipoles/sigma_derivatives.pdf
 theory/Multipoles/fmm.pdf
 theory/Multipoles/fmm_standalone.pdf
 theory/Multipoles/potential.pdf

configure.ac

@@ -2240,7 +2240,7 @@ fi
 #  chemistry function
 AC_ARG_WITH([chemistry],
    [AS_HELP_STRING([--with-chemistry=<function>],
-      [chemistry function @<:@none, GEAR_*, GEAR_DIFFUSION_*, QLA, EAGLE default: none@:>@
+      [chemistry function @<:@none, GEAR_*, QLA, EAGLE default: none@:>@
       For GEAR, you need to provide the number of elements (e.g. GEAR_10)]
    )],
    [with_chemistry="$withval"],
@@ -2260,13 +2260,6 @@ case "$with_chemistry" in
    none)
       AC_DEFINE([CHEMISTRY_NONE], [1], [No chemistry function])
    ;;
-   GEAR_DIFFUSION_*)
-      AC_DEFINE([CHEMISTRY_GEAR_DIFFUSION], [1], [Chemistry taken from the GEAR model including the metal diffusion])
-      number_element=${with_chemistry##*_}
-      AC_DEFINE_UNQUOTED([GEAR_CHEMISTRY_ELEMENT_COUNT], [$number_element], [Number of element to follow])
-      with_chemistry_name="GEAR (with $number_element elements and diffusion)"
-      with_chemistry="GEAR_DIFFUSION"
-   ;;
    GEAR_*)
       AC_DEFINE([CHEMISTRY_GEAR], [1], [Chemistry taken from the GEAR model])
       number_element=${with_chemistry#*_}

examples/Cooling/CoolingRates/cooling_rates.c

@@ -226,6 +226,9 @@ int main(int argc, char **argv) {
   // Init cosmology
   cosmology_init(params, &us, &internal_const, &cosmo);
 
+  // Init pressure floor
+  struct pressure_floor_props pressure_floor;
+
   // Set redshift and associated quantities
   const float scale_factor = 1.0 / (1.0 + redshift);
   integertime_t ti_current =
@@ -237,7 +240,7 @@ int main(int argc, char **argv) {
   cooling_init(params, &us, &internal_const, &hydro_properties, &cooling);
   cooling.H_reion_done = 1;
   cooling_print(&cooling);
-  cooling_update(&cosmo, &cooling, &s);
+  cooling_update(&cosmo, &pressure_floor, &cooling, &s);
 
   // Copy over the raw metals into the smoothed metals
   memcpy(&p.chemistry_data.smoothed_metal_mass_fraction,
@@ -323,7 +326,9 @@ int main(int argc, char **argv) {
   unsigned long long cpufreq = 0;
   clocks_set_cpufreq(cpufreq);
 
-  message("This test is only defined for the EAGLE cooling model.");
+  message(
+      "This test is only defined for the EAGLE cooling model and with Gadget-2 "
+      "SPH.");
   return 0;
 }
 #endif

examples/GEAR/AgoraCosmo/README

@@ -7,3 +7,7 @@ We will use SWIFT to cancel the h- and a-factors from the ICs.
 The IC consists in a halo evolving to a virial mass of ∼ 1e12 Msun at z = 0 with a relatively
 quiescent merger history between z = 2 and 0. The cosmological parameters are taken from WMAP7/9+SNe+BAO.
 The target halo contains the highest-resolution dark matter particles particles of masses = 2.8e5 Msun.
+
+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

examples/GEAR/AgoraCosmo/agora_cosmo.yml

@@ -93,17 +93,19 @@ GEARStarFormation:
   maximal_temperature:  3e4         # Upper limit to the temperature of a star forming particle
   n_stars_per_particle: 1
   min_mass_frac: 0.5
+  density_threashold:   1e-30       # Density threashold (in addition to the pressure floor) in g/cm3
 
 GEARPressureFloor:
   jeans_factor: 8.75
 
 GEARFeedback:
-  supernovae_energy_erg: 2.3e51
-  yields_table: chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
+  supernovae_energy_erg: 1e51
+  supernovae_efficiency: 2.3
+  yields_table: POPIIsw.h5
   discrete_yields: 0
-  yields_table_first_stars: chemistry-PopIII.hdf5          # Table containing the yields of the first stars.
+  yields_table_first_stars: POPIIsw.h5          # Table containing the yields of the first stars.
   metallicity_max_first_stars: -1                          # Maximal metallicity (in mass fraction) for a first star (-1 to deactivate).
-  elements: [Fe, Mg, O, S, Zn, Sr, Y, Ba, 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).
+  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: 1e-4

examples/GEAR/AgoraCosmo/getChemistryTable.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/FeedbackTables/POPIIsw.h5

examples/GEAR/AgoraCosmo/getGrackleCoolingTable.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/CoolingTables/GEAR/CloudyData_UVB=HM2012_shielded.h5
+
+

examples/GEAR/AgoraCosmo/getIC.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/AgoraCosmo/agora_swift.hdf5
+
+

examples/GEAR/AgoraCosmo/run.sh

@@ -1,29 +1,31 @@
 #!/bin/bash
 
-set -e
-
-# MUSIC binary
-music=~/music/MUSIC
-if test -f $music; then
-    echo "Using the following version of MUSIC $music."
-else
-    echo "MUSIC is not found."
-    exit
+# Get the initial conditions
+if [ ! -e agora_swift.hdf5 ]
+then
+    echo "Fetching the initial conditions"
+    ./getIC.sh
 fi
 
-# Grab the cooling and yield tables if they are not present.
+
+# Get the Grackle cooling table
 if [ ! -e CloudyData_UVB=HM2012_shielded.h5 ]
 then
-    echo "Fetching tables..."
-    ../getChemistryTable.sh
-    ../../Cooling/getGrackleCoolingTable.sh
+    echo "Fetching the Cloudy tables required by Grackle..."
+    ./getGrackleCoolingTable.sh
+fi
+
+
+if [ ! -e POPIIsw.h5 ]
+then
+    echo "Fetching the chemistry tables..."
+    ./getChemistryTable.sh
 fi
 
-echo "Generating the initial conditions"
-$music music.conf
 
-echo "Converting the initial conditions into a SWIFT compatible format"
-python3 convert_ic.py
 
-echo "Running SWIFT"
+
 ../../../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

@@ -1,3 +1,7 @@
+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/
 

examples/GEAR/AgoraDisk/agora_disk.yml

@@ -22,14 +22,14 @@ Scheduler:
 # 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:     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
@@ -82,26 +82,28 @@ GrackleCooling:
   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: 5
+  thermal_time_myr: 0
 
 
 GEARStarFormation:
   star_formation_efficiency: 0.01   # star formation efficiency (c_*)
   maximal_temperature:  1e10         # Upper limit to the temperature of a star forming particle
   n_stars_per_particle: 1
   min_mass_frac: 0.5
+  density_threashold:   1.67e-23   # Density threashold in g/cm3
+
 
 GEARPressureFloor:
   jeans_factor: 10
 
 GEARFeedback:
-  supernovae_efficiency: 1.0
-  supernovae_energy_erg: 0.1e51
-  yields_table: chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5
+  supernovae_energy_erg: 1e51
+  supernovae_efficiency: 0.1
+  yields_table: POPIIsw.h5
   discrete_yields: 0
-  yields_table_first_stars: chemistry-PopIII.hdf5          # Table containing the yields of the first stars.
-  metallicity_max_first_stars: -1                          # Maximal metallicity (in mass fraction) for a first star (-1 to deactivate).
-  elements: [Fe, Mg, O, S, Zn, Sr, Y, Ba, 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).
+  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

examples/GEAR/AgoraDisk/checkSolution.py

@@ -0,0 +1,28 @@
+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 * "!")