Merge branch 'master' into fix_h_max

configure.ac

@@ -60,6 +60,10 @@ if test "x$ax_enable_debug" != "xno"; then
    AC_DEFINE([SWIFT_DEVELOP_MODE],1,[Enable developer code options])
 fi
 
+# C++ in GCC 6 and above has an issue with undefined the min() and max()
+# macros. This hack works around that.
+AC_DEFINE([_GLIBCXX_INCLUDE_NEXT_C_HEADERS],1,[Hack for min() and max() using g++ 6+])
+
 # Enable POSIX and platform extension preprocessor macros.
 AC_USE_SYSTEM_EXTENSIONS
 
@@ -361,6 +365,18 @@ fi
 # Check whether we have any of the ARM v8.1 tick timers
 AX_ASM_ARM_PMCCNTR
 AX_ASM_ARM_CNTVCT
+# See if we want memuse reporting.
+AC_ARG_ENABLE([memuse-reports],
+   [AS_HELP_STRING([--enable-memuse-reports],
+     [Output reports about significant memory allocations@<:@yes/no@:>@]
+   )],
+   [enable_memuse_reports="$enableval"],
+   [enable_memuse_reports="no"]
+)
+if test "$enable_memuse_reports" = "yes"; then
+   AC_DEFINE([SWIFT_MEMUSE_REPORTS],1,[Enable memory usage reports])
+fi
+
 
 # Define HAVE_POSIX_MEMALIGN if it works.
 AX_FUNC_POSIX_MEMALIGN

doc/RTD/source/AnalysisTools/index.rst

 .. AnalysisTools
    Loic Hausammann 20th March 2019
+   Peter W. Draper 28th March 2019
 
 .. _analysistools:
 
@@ -33,3 +34,48 @@ or install ``npm`` and then run the following commands
    http-server .
 
 Now you can open the web page ``http://localhost:8080/cell_hierarchy.html``.
+
+Memory usage reports
+--------------------
+
+When SWIFT is configured using the ``--enable-memuse-reports`` flag it will
+log any calls to allocate or free memory that make use of the
+``swift_memalign()``, ``swift_malloc()``, ``swift_calloc()`` and
+``swift_free()`` functions and will generate a report at the end of each
+step. It will also attempt to dump the current memory use when SWIFT is
+aborted by calling the ``error()`` function. Failed memory allocations will be
+reported in these logs.
+
+These functions should be used by developers when allocating significant
+amounts of memory -- so don't use these for high frequency small allocations.
+Each call to the ``swift_`` functions differs to the standard calls by the
+inclusion of a "label", this should match between allocations and frees and
+ideally should be a short label that describes the use of the memory, i.e.
+"parts", "gparts", "hydro.sort" etc.
+
+Calls to external libraries that make allocations you'd also like to log
+can be made by calling the ``memuse_log_allocation()`` function directly.
+
+The output files are called ``memuse_report-step<n>.dat`` or
+``memuse_report-rank<m>-step<n>.dat`` if running using MPI. These have a line
+for each allocation or free that records the time, memory address, step,
+whether an allocation or free, the label and when an allocation, the amount of
+memory. The comments in this file also record the actual memory use of the
+process (including threads) as reported by the operating system at the end of
+the step.
+
+To post process these files into a memory used timeline and get a report of
+the peak memory use, as well as the memory still in use at the end of the step
+there is an basic analysis script ``analyse_memuse_logs.py`` and two wrappers
+that process a directory of logs, these are ``./process_memuse_logs.sh`` and
+``./process_memuse_logs_MPI.sh`` for non-MPI and MPI runs respectively.
+
+Note that the process scripts process each step individually and also process
+all the logs as a single sequence. When interpreting these some care should be
+taken as they are not all the memory allocated, just important allocations in
+SWIFT and when looking at a single step the context of any previous steps is
+not used, so you only see allocations made in that step and the effect of any
+matching frees (so allocations made in previous steps that are freed in this
+step will not be understood and will be ignored, you need the global analysis
+to understand that).
+

doc/RTD/source/SubgridModels/EAGLE/index.rst

@@ -17,9 +17,10 @@ Entropy floors
 The gas particles in the EAGLE model are prevented from cooling below a
 certain temperature. The temperature limit depends on the density of the
 particles. Two floors are used in conjonction. Both are implemented as
-polytropic "equations of states" :math:`P = P_c
-\left(\rho/\rho_c\right)^\gamma`, with the constants derived from the user
-input given in terms of temperature and Hydrogen number density.
+polytropic "equations of states":math:`P = P_c
+\left(\rho/\rho_c\right)^\gamma` (all done in physical coordinates), with
+the constants derived from the user input given in terms of temperature and
+Hydrogen number density.
 
 The first limit, labelled as ``Cool``, is typically used to prevent
 low-density high-metallicity particles to cool below the warm phase because
@@ -27,12 +28,7 @@ of over-cooling induced by the absence of metal diffusion. This limit plays
 only a small role in practice. The second limit, labelled as ``Jeans``, is
 used to prevent the fragmentation of high-density gas into clumps that
 cannot be resolved by the coupled hydro+gravity solver. The two limits are
-sketched on the following figure. An additional over-density criterion is
-applied to prevent gas not collapsed into structures from being
-affected. This criterion demands that :math:`\rho > \Delta_{\rm floor}
-\Omega_b \rho_{\rm crit}`, with :math:`\Delta_{\rm floor}` specified by the
-user and :math:`\rho_{\rm crit}` the critical density at that redshift
-[#f1]_.
+sketched on the following figure.
 
 .. figure:: EAGLE_entropy_floor.svg
     :width: 400px
@@ -51,6 +47,15 @@ user and :math:`\rho_{\rm crit}` the critical density at that redshift
     the figure for clarity reasons, typical values for EAGLE runs place
     both anchors at the same temperature.
 
+An additional over-density criterion above the mean baryonic density is
+applied to prevent gas not collapsed into structures from being
+affected. To be precise, this criterion demands that the floor is applied
+only if :math:`\rho_{\rm com} > \Delta_{\rm floor}\bar{\rho_b} =
+\Delta_{\rm floor} \Omega_b \rho_{\rm crit,0}`, with :math:`\Delta_{\rm
+floor}` specified by the user, :math:`\rho_{\rm crit,0} = 3H_0/8\pi G` the
+critical density at redshift zero [#f1]_, and :math:`\rho_{\rm com}` the
+gas co-moving density. Typical values for :math:`\Delta_{\rm floor}` are of
+order 10.
 
 The model is governed by 4 parameters for each of the two
 limits. These are given in the ``EAGLEEntropyFloor`` section of the
@@ -389,8 +394,61 @@ the snapshots for each gas and star particle:
 
 .. _EAGLE_star_formation:
 
-Star formation: Schaye+2008
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Star formation: Schaye+2008 modified for EAGLE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. figure:: EAGLE_SF_Z_dep.svg
+    :width: 400px
+    :align: center
+    :figclass: align-center
+    :alt: Metal-dependance of the threshold for star formation in the
+	  EAGLE model.
+
+    The dependency of the SF threshold density on the metallicty of the gas
+    in the EAGLE model (black line). The function is described by the four
+    parameters indicated on the figure. These are the slope of the
+    dependency, its position on the metallicity-axis and normalisation
+    (black circle) as well as the maximal threshold density allowed. For
+    reference, the black arrow indicates the value typically assumed for
+    solar metallicity :math:`Z_\odot=0.014` (note, however, that this value
+    does *not* enter the model at all). The values used to produce this
+    figure are the ones assumed in the reference EAGLE model.
+
+.. figure:: EAGLE_SF_EOS.svg
+    :width: 400px
+    :align: center
+    :figclass: align-center
+    :alt: Equation-of-state assumed for the star-forming gas
+
+    The equation-of-state assumed for the star-forming gas in the EAGLE
+    model (black line). The function is described by the three parameters
+    indicated on the figure. These are the slope of the relation, the
+    position of the normalisation point on the density axis and the
+    temperature expected at this density. Note that this is a normalisation
+    and *not* a threshold. Gas at densities lower than the normalisation
+    point will also be put on this equation of state when computing its
+    star formation rate. The values used to produce this figure are the
+    ones assumed in the reference EAGLE model.
+    
+.. code:: YAML
+
+   # EAGLE star formation parameters
+   EAGLEStarFormation:
+     EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
+     EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
+     EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
+     KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
+     KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
+     KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+     KS_high_density_threshold_H_p_cm3: 1e3       # Hydrogen number density above which the Kennicut-Schmidt law changes slope in Hydrogen atoms per cm^3.
+     KS_high_density_exponent:          2.0       # Slope of the Kennicut-Schmidt law above the high-density threshold.
+     KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+     KS_max_density_threshold_H_p_cm3:  1e5       # Hydrogen number density above which a particle gets automatically turned into a star in Hydrogen atoms per cm^3.
+     threshold_norm_H_p_cm3:            0.1       # Normalisation of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+     threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
+     threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
+     threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+     gas_fraction:                      0.1       # The gas fraction used internally by the model.
 
 .. _EAGLE_enrichment:
 

doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_EOS.py

+import matplotlib
+
+matplotlib.use("Agg")
+from pylab import *
+from scipy import stats
+
+# Plot parameters
+params = {
+    "axes.labelsize": 10,
+    "axes.titlesize": 10,
+    "font.size": 9,
+    "font.sans-serif": [
+        "Computer Modern",
+        "Computer Modern Roman",
+        "CMU Serif",
+        "cmunrm",
+        "DejaVu Sans",
+    ],
+    "mathtext.fontset": "cm",
+    "legend.fontsize": 9,
+    "xtick.labelsize": 10,
+    "ytick.labelsize": 10,
+    "text.usetex": False,
+    "figure.figsize": (3.15, 3.15),
+    "lines.markersize": 6,
+    "figure.subplot.left": 0.15,
+    "figure.subplot.right": 0.99,
+    "figure.subplot.bottom": 0.13,
+    "figure.subplot.top": 0.99,
+    "figure.subplot.wspace": 0.15,
+    "figure.subplot.hspace": 0.12,
+    "lines.linewidth": 2.0,
+}
+
+rcParams.update(params)
+
+# Equations of state
+eos_SF_rho = np.logspace(-10, 5, 1000)
+eos_SF_T = (eos_SF_rho / 10 ** (-1)) ** (1.0 / 3.0) * 8000.0
+
+# Plot the phase space diagram
+figure()
+subplot(111, xscale="log", yscale="log")
+plot(eos_SF_rho, eos_SF_T, "k-", lw=1.0)
+
+plot([1e-10, 1e-1], [8000, 8000], "k:", lw=0.6)
+plot([1e-1, 1e-1], [20, 8000], "k:", lw=0.6)
+plot([1e-1, 1e1], [20000.0, 20000.0 * 10.0 ** (2.0 / 3.0)], "k--", lw=0.6)
+text(
+    0.5e-1,
+    200000,
+    "$n_{\\rm H}$^EOS_gamma_effective",
+    va="top",
+    rotation=43,
+    fontsize=6.5,
+    family="monospace",
+)
+text(
+    0.95e-1,
+    25,
+    "EOS_density_norm_H_p_cm3",
+    rotation=90,
+    va="bottom",
+    ha="right",
+    fontsize=7,
+    family="monospace",
+)
+text(5e-8, 8400, "EOS_temperature_norm_K", va="bottom", fontsize=7, family="monospace")
+
+scatter([1e-1], [8000], s=4, color="k")
+
+xlabel("Hydrogen number density $n_{\\rm H}$ [cm$^{-3}$]", labelpad=0)
+ylabel("Temperature $T$ [K]", labelpad=2)
+xlim(3e-8, 3e3)
+ylim(20.0, 2e5)
+
+
+savefig("EAGLE_SF_EOS.svg", dpi=200)

doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_Z_dep.py

+import matplotlib
+
+matplotlib.use("Agg")
+from pylab import *
+from scipy import stats
+
+# Plot parameters
+params = {
+    "axes.labelsize": 10,
+    "axes.titlesize": 10,
+    "font.size": 9,
+    "font.sans-serif": [
+        "Computer Modern",
+        "Computer Modern Roman",
+        "CMU Serif",
+        "cmunrm",
+        "DejaVu Sans",
+    ],
+    "mathtext.fontset": "cm",
+    "legend.fontsize": 9,
+    "xtick.labelsize": 10,
+    "ytick.labelsize": 10,
+    "text.usetex": False,
+    "figure.figsize": (3.15, 3.15),
+    "lines.markersize": 6,
+    "figure.subplot.left": 0.15,
+    "figure.subplot.right": 0.99,
+    "figure.subplot.bottom": 0.13,
+    "figure.subplot.top": 0.99,
+    "figure.subplot.wspace": 0.15,
+    "figure.subplot.hspace": 0.12,
+    "lines.linewidth": 2.0,
+}
+
+rcParams.update(params)
+
+# Metal dependance parameters
+Z_0 = 0.002
+norm = 0.1
+slope = -0.64
+max_n = 10.0
+
+# Function
+Z = logspace(-8, 3, 1000)
+n = norm * (Z / Z_0) ** slope
+n = np.minimum(n, np.ones(np.size(n)) * (max_n))
+
+
+# Plot the phase space diagram
+figure()
+subplot(111, xscale="log", yscale="log")
+
+plot(Z, n, "k-", lw=1.0)
+
+plot([3e-4, 3e-2], [1.0, 1.0 * 100.0 ** (slope)], "k--", lw=0.6)
+plot([1e-10, 1e10], [max_n, max_n], "k:", lw=0.6)
+plot([Z_0, Z_0], [1e-10, norm], "k:", lw=0.6)
+plot([1e-10, Z_0], [norm, norm], "k:", lw=0.6)
+scatter([Z_0], [norm], s=4, color="k")
+
+annotate(
+    "",
+    xy=(0.014, 1e-3),
+    xytext=(0.014, 3e-4),
+    arrowprops=dict(
+        facecolor="black", shrink=0.0, width=0.1, headwidth=3.0, headlength=5.0
+    ),
+)
+text(0.016, 3.5e-4, "${Z_\\odot}$", fontsize=9)
+
+text(
+    3e-4,
+    1.45,
+    "Z^threshold_slope",
+    va="top",
+    rotation=-40,
+    fontsize=7,
+    family="monospace",
+)
+text(3e-5, 12.0, "threshold_max_density_H_p_cm3", fontsize=7, family="monospace")
+text(3e-7, 0.12, "threshold_norm_H_p_cm3", fontsize=7, family="monospace")
+text(
+    0.0018,
+    0.0004,
+    "threshold_Z0",
+    rotation=90,
+    va="bottom",
+    ha="right",
+    fontsize=7,
+    family="monospace",
+)
+
+xlabel("Metallicity (metal mass fraction) $Z$ [-]", labelpad=2)
+ylabel("SF threshold number density $n_{\\rm H, thresh}$ [cm$^{-3}$]", labelpad=-1)
+
+xlim(1e-7, 1.0)
+ylim(0.0002, 50)
+
+savefig("EAGLE_SF_Z_dep.svg", dpi=200)

doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_entropy_floor.py

 import matplotlib
+
 matplotlib.use("Agg")
 from pylab import *
 from scipy import stats
@@ -8,53 +9,97 @@ params = {
     "axes.labelsize": 10,
     "axes.titlesize": 10,
     "font.size": 9,
+    "font.sans-serif": [
+        "Computer Modern",
+        "Computer Modern Roman",
+        "CMU Serif",
+        "cmunrm",
+        "DejaVu Sans",
+    ],
+    "mathtext.fontset": "cm",
     "legend.fontsize": 9,
     "xtick.labelsize": 10,
     "ytick.labelsize": 10,
-    "text.usetex": True,
+    "text.usetex": False,
     "figure.figsize": (3.15, 3.15),
+    "lines.markersize": 6,
     "figure.subplot.left": 0.15,
     "figure.subplot.right": 0.99,
     "figure.subplot.bottom": 0.13,
     "figure.subplot.top": 0.99,
     "figure.subplot.wspace": 0.15,
     "figure.subplot.hspace": 0.12,
-    "lines.markersize": 6,
     "lines.linewidth": 2.0,
-    "text.latex.unicode": True,
 }
+
 rcParams.update(params)
-rc("font", **{"family": "sans-serif", "sans-serif": ["Times"]})
 
 # Equations of state
 eos_cool_rho = np.logspace(-5, 5, 1000)
-eos_cool_T = eos_cool_rho**0. * 8000.
+eos_cool_T = eos_cool_rho ** 0.0 * 8000.0
 eos_Jeans_rho = np.logspace(-1, 5, 1000)
-eos_Jeans_T = (eos_Jeans_rho/ 10**(-1))**(1./3.) * 4000.
+eos_Jeans_T = (eos_Jeans_rho / 10 ** (-1)) ** (1.0 / 3.0) * 4000.0
 
 # Plot the phase space diagram
 figure()
 subplot(111, xscale="log", yscale="log")
-plot(eos_cool_rho, eos_cool_T, 'k-', lw=1.)
-plot(eos_Jeans_rho, eos_Jeans_T, 'k-', lw=1.)
-plot([1e-10, 1e-5], [8000, 8000], 'k:', lw=0.6)
-plot([1e-10, 1e-1], [4000, 4000], 'k:', lw=0.6)
-plot([1e-5, 1e-5], [20, 8000], 'k:', lw=0.6)
-plot([1e-1, 1e-1], [20, 4000], 'k:', lw=0.6)
-plot([3e-6, 3e-4], [28000, 28000], 'k--', lw=0.6)
-text(3e-6, 22500, "$n_{\\rm H}~\\widehat{}~{\\tt Cool\\_gamma\\_effective}$", va="top", fontsize=7)
-plot([3e-1, 3e1], [15000., 15000.*10.**(2./3.)], 'k--', lw=0.6)
-text(3e-1, 200000, "$n_{\\rm H}~\\widehat{}~{\\tt Jeans\\_gamma\\_effective}$", va="top", rotation=43, fontsize=7)
-text(0.95e-5, 25, "${\\tt Cool\\_density\\_threshold\\_H\\_p\\_cm3}$", rotation=90, va="bottom", ha="right", fontsize=7)
-text(0.95e-1, 25, "${\\tt Jeans\\_density\\_threshold\\_H\\_p\\_cm3}$", rotation=90, va="bottom", ha="right", fontsize=7)
-text(5e-8, 8800, "${\\tt Cool\\_temperature\\_norm\\_K}$", va="bottom", fontsize=7)
-text(5e-8, 4400, "${\\tt Jeans\\_temperature\\_norm\\_K}$", va="bottom", fontsize=7)
-fill_between([1e-5, 1e5], [10, 10], [8000, 8000], color='0.9')
-fill_between([1e-1, 1e5], [4000, 400000], color='0.9')
-scatter([1e-5], [8000], s=4, color='k')
-scatter([1e-1], [4000], s=4, color='k')
-xlabel("${\\rm Density}~n_{\\rm H}~[{\\rm cm^{-3}}]$", labelpad=0)
-ylabel("${\\rm Temperature}~T~[{\\rm K}]$", labelpad=2)
+plot(eos_cool_rho, eos_cool_T, "k-", lw=1.0)
+plot(eos_Jeans_rho, eos_Jeans_T, "k-", lw=1.0)
+plot([1e-10, 1e-5], [8000, 8000], "k:", lw=0.6)
+plot([1e-10, 1e-1], [4000, 4000], "k:", lw=0.6)
+plot([1e-5, 1e-5], [20, 8000], "k:", lw=0.6)
+plot([1e-1, 1e-1], [20, 4000], "k:", lw=0.6)
+plot([3e-6, 3e-4], [28000, 28000], "k--", lw=0.6)
+
+text(
+    3e-6,
+    22500,
+    "$n_{\\rm H}$^Cool_gamma_effective",
+    va="top",
+    fontsize=6,
+    family="monospace",
+)
+plot([3e-1, 3e1], [15000.0, 15000.0 * 10.0 ** (2.0 / 3.0)], "k--", lw=0.6)
+text(
+    3e-1,
+    200000,
+    "$n_{\\rm H}$^Jeans_gamma_effective",
+    va="top",
+    rotation=43,
+    fontsize=6,
+    family="monospace",
+)
+text(
+    0.95e-5,
+    23,
+    "Cool_density_threshold_H_p_cm3",
+    rotation=90,
+    va="bottom",
+    ha="right",
+    fontsize=6,
+    family="monospace",
+)
+text(
+    0.95e-1,
+    23,
+    "Jeans_density_threshold_H_p_cm3",
+    rotation=90,
+    va="bottom",
+    ha="right",
+    fontsize=5.5,
+    family="monospace",
+)
+text(5e-8, 8800, "Cool_temperature_norm_K", va="bottom", fontsize=6, family="monospace")
+text(
+    5e-8, 4400, "Jeans_temperature_norm_K", va="bottom", fontsize=6, family="monospace"
+)
+fill_between([1e-5, 1e5], [10, 10], [8000, 8000], color="0.9")
+fill_between([1e-1, 1e5], [4000, 400000], color="0.9")
+scatter([1e-5], [8000], s=4, color="k")
+scatter([1e-1], [4000], s=4, color="k")
+xlabel("Hydrogen number density $n_{\\rm H}$ [cm$^{-3}$]", labelpad=0)
+ylabel("Temperature $T$ [K]", labelpad=2)
 xlim(3e-8, 3e3)
-ylim(20., 2e5)
-savefig("EAGLE_entropy_floor.png", dpi=200)
+ylim(20.0, 2e5)
+
+savefig("EAGLE_entropy_floor.svg", dpi=200)

examples/EAGLE_ICs/EAGLE_25/README

+Initial conditions corresponding to the 25 Mpc volume
+of the EAGLE suite. The ICs only contain DM particles. The
+gas particles will be generated in SWIFT.

examples/EAGLE_ICs/EAGLE_25/eagle_25.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun in grams
+  UnitLength_in_cgs:   3.08567758e24 # Mpc in centimeters
+  UnitVelocity_in_cgs: 1e5           # km/s in centimeters per second
+  UnitCurrent_in_cgs:  1             # Amperes
+  UnitTemp_in_cgs:     1             # Kelvin
+
+# Cosmological parameters
+Cosmology:
+  h:              0.6777        # Reduced Hubble constant
+  a_begin:        0.0078125     # Initial scale-factor of the simulation
+  a_end:          1.0           # Final scale factor of the simulation
+  Omega_m:        0.307         # Matter density parameter
+  Omega_lambda:   0.693         # Dark-energy density parameter
+  Omega_b:        0.0455        # Baryon density parameter
+
+# Parameters governing the time integration
+TimeIntegration:
+  dt_min:     1e-10 # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            eagle # Common part of the name of output files
+  scale_factor_first:  0.05
+  delta_time:          1.02
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:           1.02
+  scale_factor_first:   0.05
+
+# 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:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+  mesh_side_length:       128
+  
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  h_min_ratio:           0.1      # Minimal smoothing in units of softening.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100.0    # (internal units)
+  initial_temperature:   268.7
+
+Scheduler:
+  max_top_level_cells:   16
+  cell_split_size:       100
+  tasks_per_cell:        5
+
+Restarts:
+  delta_hours:  1.0
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  EAGLE_L0025N0376_ICs.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
+  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.
+
+# Impose primoridal metallicity
+EAGLEChemistry:
+  init_abundance_metal:     0.
+  init_abundance_Hydrogen:  0.752
+  init_abundance_Helium:    0.248
+  init_abundance_Carbon:    0.0
+  init_abundance_Nitrogen:  0.0
+  init_abundance_Oxygen:    0.0
+  init_abundance_Neon:      0.0
+  init_abundance_Magnesium: 0.0
+  init_abundance_Silicon:   0.0
+  init_abundance_Iron:      0.0
+
+# EAGLE cooling parameters
+EAGLECooling:
+  dir_name:                ./coolingtables/
+  H_reion_z:               11.5 
+  H_reion_eV_p_H:          2.0
+  He_reion_z_centre:       3.5
+  He_reion_z_sigma:        0.5
+  He_reion_eV_p_H:         2.0
+
+# EAGLE star formation parameters
+EAGLEStarFormation:
+  EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
+  EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
+  EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
+  KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
+  KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
+  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  KS_high_density_threshold_H_p_cm3: 1e3       # Hydrogen number density above which the Kennicut-Schmidt law changes slope in Hydrogen atoms per cm^3.
+  KS_high_density_exponent:          2.0       # Slope of the Kennicut-Schmidt law above the high-density threshold.
+  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  threshold_norm_H_p_cm3:            0.1       # Normalisation of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
+  threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
+  threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  
+# Parameters for the EAGLE "equation of state"
+EAGLEEntropyFloor:
+  Jeans_density_threshold_H_p_cm3: 0.1       # Physical density above which the EAGLE Jeans limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+  Jeans_over_density_threshold:    10.       # Overdensity above which the EAGLE Jeans limiter entropy floor can kick in.
+  Jeans_temperature_norm_K:        8000      # Temperature of the EAGLE Jeans limiter entropy floor at the density threshold expressed in Kelvin.
+  Jeans_gamma_effective:           1.3333333 # Slope the of the EAGLE Jeans limiter entropy floor
+  Cool_density_threshold_H_p_cm3: 1e-5       # Physical density above which the EAGLE Cool limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+  Cool_over_density_threshold:    10.        # Overdensity above which the EAGLE Cool limiter entropy floor can kick in.
+  Cool_temperature_norm_K:        8000       # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin.
+  Cool_gamma_effective:           1.         # Slope the of the EAGLE Cool limiter entropy floor
+

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

examples/EAGLE_ICs/EAGLE_25/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_L0025N0376_ICs.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 25Mpc example..."
+    ./getIC.sh
+fi
+
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_25.yml 2>&1 | tee output.log
+

examples/EAGLE_ICs/EAGLE_50/README

+Initial conditions corresponding to the 50 Mpc volume
+of the EAGLE suite. The ICs only contain DM particles. The
+gas particles will be generated in SWIFT.

examples/EAGLE_ICs/EAGLE_50/eagle_50.yml

+# Define the system of units to use internally. 
+InternalUnitSystem:
+  UnitMass_in_cgs:     1.98848e43    # 10^10 M_sun in grams
+  UnitLength_in_cgs:   3.08567758e24 # Mpc in centimeters
+  UnitVelocity_in_cgs: 1e5           # km/s in centimeters per second
+  UnitCurrent_in_cgs:  1             # Amperes
+  UnitTemp_in_cgs:     1             # Kelvin
+
+# Cosmological parameters
+Cosmology:
+  h:              0.6777        # Reduced Hubble constant
+  a_begin:        0.0078125     # Initial scale-factor of the simulation
+  a_end:          1.0           # Final scale factor of the simulation
+  Omega_m:        0.307         # Matter density parameter
+  Omega_lambda:   0.693         # Dark-energy density parameter
+  Omega_b:        0.0455        # Baryon density parameter
+
+# Parameters governing the time integration
+TimeIntegration:
+  dt_min:     1e-10 # The minimal time-step size of the simulation (in internal units).
+  dt_max:     1e-2  # The maximal time-step size of the simulation (in internal units).
+  
+# Parameters governing the snapshots
+Snapshots:
+  basename:            eagle # Common part of the name of output files
+  scale_factor_first:  0.05
+  delta_time:          1.02
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:           1.02
+  scale_factor_first:   0.05
+
+# 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:     0.0026994 # Comoving softening length (in internal units).
+  max_physical_softening: 0.0007    # Physical softening length (in internal units).
+  mesh_side_length:       256
+  
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  h_min_ratio:           0.1      # Minimal smoothing in units of softening.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+  minimal_temperature:   100.0    # (internal units)
+  initial_temperature:   268.7
+
+Scheduler:
+  max_top_level_cells:   32
+  cell_split_size:       100
+  tasks_per_cell:        5
+
+Restarts:
+  delta_hours:  1.0
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  EAGLE_L0050N0752_ICs.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
+  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.
+
+# Impose primoridal metallicity
+EAGLEChemistry:
+  init_abundance_metal:     0.
+  init_abundance_Hydrogen:  0.752
+  init_abundance_Helium:    0.248
+  init_abundance_Carbon:    0.0
+  init_abundance_Nitrogen:  0.0
+  init_abundance_Oxygen:    0.0
+  init_abundance_Neon:      0.0
+  init_abundance_Magnesium: 0.0
+  init_abundance_Silicon:   0.0
+  init_abundance_Iron:      0.0
+
+# EAGLE cooling parameters
+EAGLECooling:
+  dir_name:                ./coolingtables/
+  H_reion_z:               11.5 
+  H_reion_eV_p_H:          2.0
+  He_reion_z_centre:       3.5
+  He_reion_z_sigma:        0.5
+  He_reion_eV_p_H:         2.0
+
+# EAGLE star formation parameters
+EAGLEStarFormation:
+  EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
+  EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
+  EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
+  KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
+  KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
+  KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.
+  KS_high_density_threshold_H_p_cm3: 1e3       # Hydrogen number density above which the Kennicut-Schmidt law changes slope in Hydrogen atoms per cm^3.
+  KS_high_density_exponent:          2.0       # Slope of the Kennicut-Schmidt law above the high-density threshold.
+  KS_temperature_margin_dex:         0.5       # Logarithm base 10 of the maximal temperature difference above the EOS allowed to form stars.
+  threshold_norm_H_p_cm3:            0.1       # Normalisation of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  threshold_Z0:                      0.002     # Reference metallicity (metal mass fraction) for the metal-dependant threshold for star formation.
+  threshold_slope:                   -0.64     # Slope of the metal-dependant star formation threshold
+  threshold_max_density_H_p_cm3:     10.0      # Maximal density of the metal-dependant density threshold for star formation in Hydrogen atoms per cm^3.
+  
+# Parameters for the EAGLE "equation of state"
+EAGLEEntropyFloor:
+  Jeans_density_threshold_H_p_cm3: 0.1       # Physical density above which the EAGLE Jeans limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+  Jeans_over_density_threshold:    10.       # Overdensity above which the EAGLE Jeans limiter entropy floor can kick in.
+  Jeans_temperature_norm_K:        8000      # Temperature of the EAGLE Jeans limiter entropy floor at the density threshold expressed in Kelvin.
+  Jeans_gamma_effective:           1.3333333 # Slope the of the EAGLE Jeans limiter entropy floor
+  Cool_density_threshold_H_p_cm3: 1e-5       # Physical density above which the EAGLE Cool limiter entropy floor kicks in expressed in Hydrogen atoms per cm^3.
+  Cool_over_density_threshold:    10.        # Overdensity above which the EAGLE Cool limiter entropy floor can kick in.
+  Cool_temperature_norm_K:        8000       # Temperature of the EAGLE Cool limiter entropy floor at the density threshold expressed in Kelvin.
+  Cool_gamma_effective:           1.         # Slope the of the EAGLE Cool limiter entropy floor
+

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

examples/EAGLE_ICs/EAGLE_50/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e EAGLE_L0050N0752_ICs.hdf5 ]
+then
+    echo "Fetching initial conditions for the EAGLE 50Mpc example..."
+    ./getIC.sh
+fi
+
+../../swift --cosmology --hydro --self-gravity --stars --threads=16 eagle_50.yml 2>&1 | tee output.log
+

examples/EAGLE_low_z/EAGLE_12/README

@@ -13,4 +13,4 @@ The particle load of the main EAGLE simulation can be reproduced by
 running these ICs on 8 cores.
 
 MD5 checksum of the ICs: 
-88877f5bb0ee21488c20b8f065fc74db  EAGLE_ICs_12.hdf5
+d1ebf1c7ffb0488c3628e08ed6d2dbf4  EAGLE_ICs_12.hdf5

examples/EAGLE_low_z/EAGLE_12/eagle_12.yml

@@ -83,7 +83,6 @@ EAGLEStarFormation:
   EOS_density_norm_H_p_cm3:          0.1       # Physical density used for the normalisation of the EOS assumed for the star-forming gas in Hydrogen atoms per cm^3.
   EOS_temperature_norm_K:            8000      # Temperature om the polytropic EOS assumed for star-forming gas at the density normalisation in Kelvin.
   EOS_gamma_effective:               1.3333333 # Slope the of the polytropic EOS assumed for the star-forming gas.
-  gas_fraction:                      0.3       # The gas fraction used internally by the model.
   KS_normalisation:                  1.515e-4  # The normalization of the Kennicutt-Schmidt law in Msun / kpc^2 / yr.
   KS_exponent:                       1.4       # The exponent of the Kennicutt-Schmidt law.
   KS_min_over_density:               57.7      # The over-density above which star-formation is allowed.

examples/EAGLE_low_z/EAGLE_25/README

@@ -13,4 +13,4 @@ The particle load of the main EAGLE simulation can be reproduced by
 running these ICs on 64 cores.
 
 MD5 checksum of the ICs: 
-02cd1c353b86230af047b5d4ab22afcf  EAGLE_ICs_25.hdf5
+592faecfc51239a00396f5a4acc2fa4d  EAGLE_ICs_25.hdf5