diff --git a/configure.ac b/configure.ac
index c7f1df31d6148b568c22e6ed5ebc33fc9ff73abf..50619f589b9377001538f3c62870c72249b3f102 100644
--- a/configure.ac
+++ b/configure.ac
@@ -16,7 +16,7 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Init the project.
-AC_INIT([SWIFT],[0.8.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
+AC_INIT([SWIFT],[0.8.1],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
swift_config_flags="$*"
# We want to stop when given unrecognised options. No subdirs so this is safe.
@@ -60,6 +60,10 @@ if test "x$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
@@ -270,6 +274,18 @@ if test "$enable_debugging_checks" = "yes"; then
AC_DEFINE([SWIFT_DEBUG_CHECKS],1,[Enable expensive debugging])
fi
+# Check if cell graph is on.
+AC_ARG_ENABLE([cell-graph],
+ [AS_HELP_STRING([--enable-cell-graph],
+ [Activate the cell graph @<:@yes/no@:>@]
+ )],
+ [enable_cell_graph="$enableval"],
+ [enable_cell_graph="no"]
+)
+if test "$enable_cell_graph" = "yes"; then
+ AC_DEFINE([SWIFT_CELL_GRAPH],1,[Enable cell graph])
+fi
+
# Check if using our custom icbrtf is enalbled.
AC_ARG_ENABLE([custom-icbrtf],
[AS_HELP_STRING([--enable-custom-icbrtf],
@@ -294,6 +310,18 @@ if test "$enable_naive_interactions" = "yes"; then
AC_DEFINE([SWIFT_USE_NAIVE_INTERACTIONS],1,[Enable use of naive cell interaction functions])
fi
+# Check whether we want to default to naive cell interactions (stars)
+AC_ARG_ENABLE([naive-interactions-stars],
+ [AS_HELP_STRING([--enable-naive-interactions-stars],
+ [Activate use of naive cell interaction functions for stars @<:@yes/no@:>@]
+ )],
+ [enable_naive_interactions_stars="$enableval"],
+ [enable_naive_interactions_stars="no"]
+)
+if test "$enable_naive_interactions_stars" = "yes"; then
+ AC_DEFINE([SWIFT_USE_NAIVE_INTERACTIONS_STARS],1,[Enable use of naive cell interaction functions for stars])
+fi
+
# Check if gravity force checks are on for some particles.
AC_ARG_ENABLE([gravity-force-checks],
[AS_HELP_STRING([--enable-gravity-force-checks],
@@ -1185,6 +1213,16 @@ if test "$have_armv7apmccntr"x = "yes"x; then
AC_DEFINE(HAVE_ARMV7A_PMCCNTR,1,[Define if you have enabled the PMCCNTR cycle counter on ARMv7a])
fi
+# Check if we have native exp10 and exp10f functions. If not failback to our
+# implementations. On Apple/CLANG we have __exp10, so also check for that
+# if the compiler is clang.
+AC_CHECK_LIB([m],[exp10], [AC_DEFINE([HAVE_EXP10],1,[The exp10 function is present.])])
+AC_CHECK_LIB([m],[exp10f], [AC_DEFINE([HAVE_EXP10F],1,[The exp10f function is present.])])
+if test "$ax_cv_c_compiler_vendor" = "clang"; then
+ AC_CHECK_LIB([m],[__exp10], [AC_DEFINE([HAVE___EXP10],1,[The __exp10 function is present.])])
+ AC_CHECK_LIB([m],[__exp10f], [AC_DEFINE([HAVE___EXP10F],1,[The __exp10f function is present.])])
+fi
+
# Add warning flags by default, if these can be used. Option =error adds
# -Werror to GCC, clang and Intel. Note do this last as compiler tests may
# become errors, if that's an issue don't use CFLAGS for these, use an AC_SUBST().
@@ -1933,6 +1971,7 @@ AC_MSG_RESULT([
Interaction debugging : $enable_debug_interactions
Stars interaction debugging : $enable_debug_interactions_stars
Naive interactions : $enable_naive_interactions
+ Naive stars interactions : $enable_naive_interactions_stars
Gravity checks : $gravity_force_checks
Custom icbrtf : $enable_custom_icbrtf
diff --git a/doc/RTD/source/AnalysisTools/index.rst b/doc/RTD/source/AnalysisTools/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f68fa77536e77df48cd1acc44e98a3408e48b037
--- /dev/null
+++ b/doc/RTD/source/AnalysisTools/index.rst
@@ -0,0 +1,35 @@
+.. AnalysisTools
+ Loic Hausammann 20th March 2019
+
+.. _analysistools:
+
+Analysis Tools
+==============
+
+Task dependencies
+-----------------
+
+At the beginning of each simulation the file ``dependency_graph.csv`` is generated and can be transformed into a ``dot`` and a ``png`` file with the script ``tools/plot_task_dependencies.py``.
+It requires the ``dot`` package that is available in the library graphviz.
+This script has also the possibility to generate a list of function calls for each task with the option ``--with-calls`` (this list may be incomplete).
+You can convert the ``dot`` file into a ``png`` with the following command
+``dot -Tpng dependency_graph.dot -o dependency_graph.png`` or directly read it with the python module ``xdot`` with ``python -m xdot dependency_graph.dot``.
+
+
+Cell graph
+----------
+
+An interactive graph of the cells is available with the configuration option ``--enable-cell-graph``.
+During a run, SWIFT will generate a ``cell_hierarchy_*.csv`` file per MPI rank.
+The command ``tools/make_cell_hierarchy.sh cell_hierarchy_*.csv`` merges the files together and generates the file ``cell_hierarchy.html``
+that contains the graph and can be read with your favorite web browser.
+
+With chrome, you cannot access the files directly, you will need to either access them through an existing server (e.g. public http provided by your university)
+or install ``npm`` and then run the following commands
+
+.. code-block:: bash
+
+ npm install http-server -g
+ http-server .
+
+Now you can open the web page ``http://localhost:8080/cell_hierarchy.html``.
diff --git a/doc/RTD/source/SubgridModels/EAGLE/EAGLE_SF_EOS.svg b/doc/RTD/source/SubgridModels/EAGLE/EAGLE_SF_EOS.svg
new file mode 100644
index 0000000000000000000000000000000000000000..398c2bd88331cff072cd82590d4691f0c48bc148
--- /dev/null
+++ b/doc/RTD/source/SubgridModels/EAGLE/EAGLE_SF_EOS.svg
@@ -0,0 +1,2353 @@
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- <!-- ${\tt Jeans\_temperature\_norm\_K}$ -->
- <g transform="translate(37.862259 81.545055)scale(0.07 -0.07)">
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-L 1126.504703 0
-L 1126.504703 0.3985
-L 1098.398219 0.3985
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+ <!-- Jeans_temperature_norm_K -->
+ <g transform="translate(37.862259 81.680098)scale(0.06 -0.06)">
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+ <clipPath id="pf19aa30d2c">
<rect height="195.048" width="190.512" x="34.02" y="2.268"/>
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diff --git a/doc/RTD/source/SubgridModels/EAGLE/index.rst b/doc/RTD/source/SubgridModels/EAGLE/index.rst
index 620572f962948308884414622ca2ae7d555d158f..b9942628563f5ccc56bd44ee90270dd65cff2e44 100644
--- a/doc/RTD/source/SubgridModels/EAGLE/index.rst
+++ b/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
@@ -280,7 +285,7 @@ these elements from the abundance of `Si`. More specifically, we assume that
their abundance by mass relative to the table's solar abundance pattern is the
same as the relative abundance of `Si` (i.e. :math:`[Ca/Si] = 0` and
:math:`[S/Si] = 0`). Users can optionally modify the ratios used for `S` and
-`Ca`.
+`Ca`. Note that we use the *smoothed* abundances of elements for all calculations.
Above the redshift of Hydrogen re-ionization we use the extra table containing
net cooling rates for gas exposed to the CMB and a UV + X-ray background at
@@ -288,9 +293,13 @@ redshift nine truncated above 1 Rydberg. At the redshift or re-ionization, we
additionally inject a fixed user-defined amount of energy per unit mass to all
the gas particles.
-In addition to the tables we inject extra energy from Helium re-ionization using
-a Gaussian model with a user-defined redshift for the centre, width and total
-amount of energy injected per unit mass.
+In addition to the tables we inject extra energy from Helium II re-ionization
+using a Gaussian model with a user-defined redshift for the centre, width and
+total amount of energy injected per unit mass. Additional energy is also
+injected instantaneously for Hydrogen re-ionisation to all particles (active and
+inactive) to make sure the whole Universe reaches the expected temperature
+quickly (i.e not just via the interaction with the now much stronger UV
+background).
For non-cosmological run, we use the :math:`z = 0` table and the interpolation
along the redshift dimension then becomes a trivial operation.
@@ -326,7 +335,7 @@ they are listed for every gas particle:
+---------------------+-------------------------------------+-----------+-------------------------------------+
Note that if one is running without cooling switched on at runtime, the
-temperatures can be computed by passing the ``--temparature`` runtime flag (see
+temperatures can be computed by passing the ``--temperature`` runtime flag (see
:ref:`cmdline-options`). Note that the tables then have to be available as in
the case with cooling switched on.
@@ -341,9 +350,10 @@ implicit problem. A valid section of the YAML file looks like:
EAGLECooling:
dir_name: /path/to/the/Wiersma/tables/directory # Absolute or relative path
H_reion_z: 11.5 # Redhift of Hydrogen re-ionization
+ H_reion_ev_p_H: 2.0 # Energy injected in eV per Hydrogen atom for Hydrogen re-ionization.
He_reion_z_centre: 3.5 # Centre of the Gaussian used for Helium re-ionization
He_reion_z_sigma: 0.5 # Width of the Gaussian used for Helium re-ionization
- He_reion_ev_p_H: 2.0 # Energy injected in eV per Hydrogen atom for Helium re-ionization.
+ He_reion_ev_p_H: 2.0 # Energy injected in eV per Hydrogen atom for Helium II re-ionization.
And the optional parameters are:
@@ -384,8 +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:
diff --git a/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_EOS.py b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_EOS.py
new file mode 100644
index 0000000000000000000000000000000000000000..88ca56d750bf716fea8b4bf72b70c2b598953ac7
--- /dev/null
+++ b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_EOS.py
@@ -0,0 +1,78 @@
+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)
diff --git a/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_Z_dep.py b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_Z_dep.py
new file mode 100644
index 0000000000000000000000000000000000000000..26ae522947ecc9e75f6f287bafed0bb9acb9134a
--- /dev/null
+++ b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_SF_Z_dep.py
@@ -0,0 +1,99 @@
+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)
diff --git a/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_entropy_floor.py b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_entropy_floor.py
index 5b02dd657fdb32e411961f04d0d758119344b809..1e7dad6c95211a8e43805a904fb8d9901305b692 100644
--- a/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_entropy_floor.py
+++ b/doc/RTD/source/SubgridModels/EAGLE/plot_EAGLE_entropy_floor.py
@@ -1,4 +1,5 @@
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)
diff --git a/doc/RTD/source/Task/index.rst b/doc/RTD/source/Task/index.rst
index 82210895618618f87faaada472c72afe321b1d04..549a89c834570c45e7b4233f3c412fe8afba226d 100644
--- a/doc/RTD/source/Task/index.rst
+++ b/doc/RTD/source/Task/index.rst
@@ -9,11 +9,8 @@ Task System
This section of the documentation includes information on the task system
available in SWIFT, as well as how to implement your own task.
-SWIFT can produce a graph containing all the dependencies using graphviz.
-At the beginning of each simulation a ``csv`` file is generated and can be transformed into a ``png`` with the script ``tools/plot_task_dependencies.py``.
-This script has also the possibility to generate a list of function calls for each task with the option ``--with-calls``.
-You can convert the ``dot`` file into a ``png`` with the following command
-``dot -Tpng dependency_graph.dot -o dependency_graph.png`` or directly read it with the python module ``xdot`` with ``python -m xdot dependency_graph.dot``.
+SWIFT can produce a graph containing all the dependencies.
+Everything is described in :ref:`_analysistools`.
.. toctree::
diff --git a/doc/RTD/source/conf.py b/doc/RTD/source/conf.py
index fac755bbb4ee9cd25bf3526bc435c69be3a9d5b5..327c5524820772c4c891418cff72a3c22a4fb2b0 100644
--- a/doc/RTD/source/conf.py
+++ b/doc/RTD/source/conf.py
@@ -25,7 +25,7 @@ author = 'SWIFT Team'
# The short X.Y version
version = '0.8'
# The full version, including alpha/beta/rc tags
-release = '0.8.0'
+release = '0.8.1'
# -- General configuration ---------------------------------------------------
diff --git a/doc/RTD/source/index.rst b/doc/RTD/source/index.rst
index 83422b4e5caf05bacb3824d06426b9cdeba3921e..b7c4205b0ac45680ee14e4a3941f03d116ab8c69 100644
--- a/doc/RTD/source/index.rst
+++ b/doc/RTD/source/index.rst
@@ -26,3 +26,4 @@ difference is the parameter file that will need to be adapted for SWIFT.
NewOption/index
Task/index
VELOCIraptorInterface/index
+ AnalysisTools/index
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/README b/examples/Cooling/ConstantCosmoTempEvolution/README
new file mode 100644
index 0000000000000000000000000000000000000000..1ca1c87c06337fb3b44dfdf0227e99da3b79fdd0
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/README
@@ -0,0 +1,18 @@
+This example runs a cosmological simulation using 32^3 particles with
+the gas density set to the mean baryonic density and no fluctuations
+(i.e. sigma_8 == 0). The simulation is run without gravity to prevent
+any numerical fluctuation from growing.
+
+The gas is cooling/heating via its interaction with the UV background
+set by the cooling model. In practice, the gas will follow the
+equilibirum temperature of the model at all z and only be affected by
+reionization. Assuming primoridal abundance, the temperature of the
+gas at different redshifts can be compared to temperatures inferred
+from observations of the Lyman-alpha forrest. The plotting script runs
+this comparison once the simulation has completed.
+
+Within the EAGLE cooling model, interesting changes are to switch
+on/off the Helium II reionisation (or change its redshift) as well as
+the position and amount of energy injected by Hydrogen
+reionisation. The parameters given the YAML file are the ones used for
+actual EAGLE galaxy formation runs.
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/const_cosmo_temp_evol.yml b/examples/Cooling/ConstantCosmoTempEvolution/const_cosmo_temp_evol.yml
new file mode 100644
index 0000000000000000000000000000000000000000..01dcbc96fd329f53b1fd345bc198b05a53861982
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/const_cosmo_temp_evol.yml
@@ -0,0 +1,77 @@
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1.98848e43 # 10^10 M_sun
+ UnitLength_in_cgs: 3.08567758e24 # 1 Mpc
+ UnitVelocity_in_cgs: 1e5 # 1 km/s
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+# Cosmological parameters
+Cosmology:
+ h: 0.6777 # Reduced Hubble constant
+ a_begin: 0.0099 # Initial scale-factor of the simulation (z = 100.0)
+ 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-7
+ dt_max: 5e-3
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: cooling_box
+ delta_time: 1.04
+ scale_factor_first: 0.00991
+ compression: 4
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ scale_factor_first: 0.00991
+ delta_time: 1.1
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
+ minimal_temperature: 100 # K
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./constantBox.hdf5 # The file to read
+ periodic: 1
+
+# Parameters for the EAGLE chemistry
+EAGLEChemistry: # Solar abundances
+ init_abundance_metal: 0.
+ init_abundance_Hydrogen: 0.752
+ init_abundance_Helium: 0.248
+ init_abundance_Carbon: 0.
+ init_abundance_Nitrogen: 0.
+ init_abundance_Oxygen: 0.
+ init_abundance_Neon: 0.
+ init_abundance_Magnesium: 0.
+ init_abundance_Silicon: 0.
+ init_abundance_Iron: 0.
+
+# Parameters for the EAGLE cooling
+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
+
+# 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
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/datasets/schaye_et_al_2000_thermal_history.dat b/examples/Cooling/ConstantCosmoTempEvolution/datasets/schaye_et_al_2000_thermal_history.dat
new file mode 100644
index 0000000000000000000000000000000000000000..11c58fbc3255640b11269a95b9c7f00fc30fb4b1
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/datasets/schaye_et_al_2000_thermal_history.dat
@@ -0,0 +1,18 @@
+### Data from Figure 6 in Schaye et al. (2000) (2000MNRAS.318..817S)
+# z ########## z_lb ######### z_ub ######## T_0/1e4K ##### T_0_lb/1e4K ## T_0_ub/1e4K
+1.95804 1.84615 2.08042 1.09915 0.76847 2.27999
+2.20979 2.09790 2.32867 1.40112 0.90638 1.98188
+2.28322 2.22378 2.37762 1.19902 1.01236 1.36980
+2.49650 2.33217 2.62238 1.39889 1.15520 1.74657
+2.59441 2.48601 2.70629 1.60171 1.44953 1.76021
+2.65385 2.54895 2.87762 2.29650 1.57475 2.44105
+2.83916 2.70629 2.94056 1.72395 1.43950 2.30056
+3.00000 2.88462 3.13636 2.28574 1.89278 2.71473
+3.07343 2.90210 3.21329 2.01108 1.88150 2.13172
+3.23427 3.14685 3.41259 2.26386 1.40872 3.34756
+3.36014 3.22378 3.51748 1.53842 1.39604 1.69997
+3.54545 3.43007 3.69930 1.08649 0.88238 1.39077
+3.72028 3.61189 3.81469 1.25736 1.08243 1.62749
+3.83217 3.68531 4.01399 1.32092 1.03191 1.74809
+3.90909 3.81469 4.00350 1.55086 1.14616 2.01291
+4.30420 4.14685 4.42657 1.15002 0.92882 2.01412
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/datasets/walther_et_al_2019_thermal_history.dat b/examples/Cooling/ConstantCosmoTempEvolution/datasets/walther_et_al_2019_thermal_history.dat
new file mode 100644
index 0000000000000000000000000000000000000000..d11c770a710f970d50c08aa58db705018eb29aed
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/datasets/walther_et_al_2019_thermal_history.dat
@@ -0,0 +1,18 @@
+### Data from Figure 13 in Walther et al. (2019) (2019ApJ...872...13W)
+# z ######### T_0/1e4K ##### T_0_lb/1e4K ## T_0_ub/1e4K ########
+1.7793 0.77828 0.56109 1.1403
+1.9793 0.74208 0.65158 0.90950
+2.1793 1.0226 0.87330 1.2715
+2.3793 1.1719 0.98190 1.4570
+2.5793 1.2398 1.0995 1.4299
+2.7793 1.2941 1.1493 1.4796
+2.9793 1.3032 1.1538 1.4887
+3.1793 1.1900 1.0724 1.3258
+3.3770 1.4118 1.2443 1.6109
+3.5770 1.0452 0.78281 1.3575
+3.7770 1.2081 1.0181 1.4344
+3.9770 0.95023 0.77828 1.1674
+4.1770 0.89593 0.82805 0.99095
+4.5770 0.88688 0.77828 1.0136
+4.9770 0.54299 0.45701 0.66516
+5.3747 0.61086 0.47511 0.76018
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/getGlass.sh b/examples/Cooling/ConstantCosmoTempEvolution/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..01b4474ac21666c843b7abedfa39a76948934911
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/gravity_glassCube_32.hdf5
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/makeIC.py b/examples/Cooling/ConstantCosmoTempEvolution/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..c6ae39206e14770df590efb2d2d468bfc5c088fb
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/makeIC.py
@@ -0,0 +1,84 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2019 Stefan Arridge (stefan.arridge@durham.ac.uk)
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published
+# by the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+################################################################################
+
+from swiftsimio import Writer
+from swiftsimio.units import cosmo_units
+
+import unyt
+import numpy as np
+import h5py as h5
+
+
+# Parameters
+boxsize = 100 * unyt.Mpc
+T_i = 1000.0 # Initial temperature of the gas (in K)
+z_i = 100.0 # Initial redshift
+gamma = 5.0 / 3.0 # Gas adiabatic index
+n_p_1D = 32
+glassFile = "gravity_glassCube_32.hdf5"
+filename = "constantBox.hdf5"
+
+# Cosmology (must be same as param file)
+hubble_param = 0.6777 # same as in param file
+Omega_bar = 0.0455 # same as in param file
+
+
+# Read the glass file
+glass = h5.File(glassFile, "r")
+
+# Total number of particles
+n_p = n_p_1D ** 3
+# Read particle positions and from the glass
+glass_pos = glass["/PartType1/Coordinates"][:, :]
+glass.close()
+
+# Calculate mean baryon density today from comological parameters
+H_0 = 100.0 * hubble_param * unyt.km / unyt.s / unyt.Mpc
+rho_crit_0 = 3.0 * H_0 ** 2 / (8.0 * np.pi * unyt.G)
+rho_bar_0 = Omega_bar * rho_crit_0
+
+# From this, we calculate the mass of the gas particles
+gas_particle_mass = rho_bar_0 * boxsize ** 3 / (n_p_1D ** 3)
+
+# Generate object. cosmo_units corresponds to default Gadget-oid units
+# of 10^10 Msun, Mpc, and km/s
+x = Writer(cosmo_units, boxsize)
+
+# 32^3 particles.
+n_p = 32 ** 3
+
+# Make gas coordinates from 0, 100 Mpc in each direction
+x.gas.coordinates = glass_pos * boxsize
+
+# Random velocities from 0 to 1 km/s
+x.gas.velocities = np.zeros((n_p, 3)) * (unyt.km / unyt.s)
+
+# Generate uniform masses as 10^6 solar masses for each particle
+x.gas.masses = np.ones(n_p, dtype=float) * gas_particle_mass
+
+# Generate internal energy corresponding to 10^4 K
+x.gas.internal_energy = (
+ np.ones(n_p, dtype=float) * (T_i * unyt.kb * unyt.K) / (1e6 * unyt.msun)
+)
+
+# Generate initial guess for smoothing lengths based on MIPS
+x.gas.generate_smoothing_lengths(boxsize=boxsize, dimension=3)
+
+# If IDs are not present, this automatically generates
+x.write(filename)
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/plot_thermal_history.py b/examples/Cooling/ConstantCosmoTempEvolution/plot_thermal_history.py
new file mode 100644
index 0000000000000000000000000000000000000000..1494102531104b252e3edaa467920db7383ac6e6
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/plot_thermal_history.py
@@ -0,0 +1,184 @@
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+import h5py as h5
+import swiftsimio
+import sys
+import glob
+import unyt
+import numpy as np
+
+## read command line arguments
+snapshot_name = sys.argv[1]
+
+params = {'axes.labelsize': 10,
+'axes.titlesize': 10,
+'font.size': 9,
+'legend.fontsize': 9,
+'xtick.labelsize': 10,
+'ytick.labelsize': 10,
+'text.usetex': False,
+'figure.figsize' : (4.15,3.15),
+'figure.subplot.left' : 0.12,
+'figure.subplot.right' : 0.99,
+'figure.subplot.bottom' : 0.12,
+'figure.subplot.top' : 0.99,
+'figure.subplot.wspace' : 0.15,
+'figure.subplot.hspace' : 0.12,
+'lines.markersize' : 6,
+'lines.linewidth' : 2.,
+'text.latex.unicode': True
+}
+plt.rcParams.update(params)
+
+################# Read in observational data
+
+data_schaye = np.genfromtxt("./datasets/schaye_et_al_2000_thermal_history.dat",skip_header = 2)
+data_walther = np.genfromtxt("./datasets/walther_et_al_2019_thermal_history.dat",skip_header = 2)
+
+data_schaye = data_schaye.T
+data_walther = data_walther.T
+
+schaye_z_lower_error = data_schaye[0] - data_schaye[1]
+schaye_z_upper_error = data_schaye[2] - data_schaye[0]
+schaye_T_lower_error = np.log10(data_schaye[3]*1.0e4) - np.log10(data_schaye[4]*1.0e4)
+schaye_T_upper_error = np.log10(data_schaye[5]*1.0e4) - np.log10(data_schaye[3]*1.0e4)
+walther_T_lower_error = np.log10(data_walther[1]*1.0e4) - np.log10(data_walther[2]*1.0e4)
+walther_T_upper_error = np.log10(data_walther[3]*1.0e4) - np.log10(data_walther[1]*1.0e4)
+
+############### Read in simulation data
+
+## First, get list of all snapshots
+reg_exp = "%s*.hdf5" %snapshot_name
+snap_list = glob.glob(reg_exp)
+
+z = []
+T_mean = []
+T_std = []
+rho_mean = []
+rho_std = []
+
+## loop through list
+for snap in snap_list:
+
+ # This loads all metadata but explicitly does _not_ read any particle data yet
+ data = swiftsimio.load(snap)
+
+ # Get the redshift
+ z = np.append(z, data.metadata.z)
+
+ # Convert gas temperatures and densities to right units
+ data.gas.temperature.convert_to_cgs()
+
+ # Get mean and standard deviation of temperature
+ T_mean.append(np.mean(data.gas.temperature) * data.gas.temperature.units)
+ T_std.append(np.std(data.gas.temperature) * data.gas.temperature.units)
+
+ # Get mean and standard deviation of density
+ rho_mean.append(np.mean(data.gas.density) * data.gas.density.units)
+ rho_std.append(np.std(data.gas.density) * data.gas.density.units)
+
+## Turn into numpy arrays
+T_mean = np.array(T_mean) * data.gas.temperature.units
+T_std = np.array(T_std) * data.gas.temperature.units
+rho_mean = np.array(rho_mean) * data.gas.density.units
+rho_std = np.array(rho_std) * data.gas.density.units
+
+## Put Density into units of mean baryon density today
+
+# first calculate rho_bar_0 from snapshot metadata
+### from the first snapshot, get cosmology information
+d = swiftsimio.load(snap_list[0])
+cosmology = d.metadata.cosmology
+H0 = cosmology["H0 [internal units]"] / (d.units.time)
+Omega_bar = cosmology["Omega_b"]
+
+### now calculate rho_bar_0 and divide through
+rho_bar_0 = 3.0 * H0**2 / (8. * np.pi * unyt.G) * Omega_bar
+rho_mean /= rho_bar_0
+rho_std /= rho_bar_0
+
+### sort arrays into redshift order
+ind_sorted = np.argsort(z)
+z = z[ind_sorted]
+T_mean = T_mean[ind_sorted]
+T_std = T_std[ind_sorted]
+rho_mean = rho_mean[ind_sorted]
+rho_std = rho_std[ind_sorted]
+
+### from the first snapshot, get code information
+d = swiftsimio.load(snap_list[0])
+code_info = d.metadata.code
+git_branch = code_info["Git Branch"].decode('UTF-8')
+git_revision = code_info["Git Revision"].decode('UTF-8')
+hydro_metadata = d.metadata.hydro_scheme
+scheme = hydro_metadata["Scheme"].decode('UTF-8')
+params = d.metadata.parameters
+
+subgrid_metadata = d.metadata.subgrid_scheme
+cooling_model = subgrid_metadata["Cooling Model"].decode('UTF-8')
+chemistry_model = subgrid_metadata["Chemistry Model"].decode('UTF-8')
+
+if cooling_model == 'EAGLE':
+ z_r_H = float(params['EAGLECooling:H_reion_z'])
+ H_heat_input = float(params['EAGLECooling:H_reion_eV_p_H'])
+ z_r_He_centre = float(params['EAGLECooling:He_reion_z_centre'])
+ z_r_He_sigma = float(params['EAGLECooling:He_reion_z_sigma'])
+ He_heat_input = float(params['EAGLECooling:He_reion_eV_p_H'])
+
+metallicity = "Unknown"
+if chemistry_model == 'EAGLE':
+ metallicity = float(params['EAGLEChemistry:init_abundance_metal'])
+
+# Make plot of temperature evolution --------------------------------
+fig = plt.figure()
+
+# Plot sim properties
+if cooling_model == 'EAGLE':
+ plt.plot([z_r_H, z_r_H], [3.4, 4.4], 'k--', alpha=0.5, lw=0.7)
+ plt.text(z_r_H + 0.1, 3.55, "H reion.", rotation=90, alpha=0.5, fontsize=7, va="bottom")
+ plt.plot([z_r_He_centre, z_r_He_centre], [3.4, 4.4], 'k--', alpha=0.5, lw=0.7)
+ plt.text(z_r_He_centre + 0.1, 3.55, "HeII reion.", rotation=90, alpha=0.5, fontsize=7, va="bottom")
+
+# Plot observational data
+plt.errorbar(data_schaye[0],
+ np.log10(data_schaye[3]*1.0e4),
+ xerr = [schaye_z_lower_error,schaye_z_upper_error],
+ yerr = [schaye_T_lower_error,schaye_T_upper_error],
+ fmt='s', mec='0.3', color='0.3', markersize=4, markeredgewidth=0.5, linewidth=0.5, mfc='w', label="Schaye et al. (2000)")
+plt.errorbar(data_walther[0],
+ np.log10(data_walther[1]*1.0e4),
+ yerr = [walther_T_lower_error,walther_T_upper_error],
+ fmt='.', mec='0.3', color='0.3', markersize=7, markeredgewidth=0.5, linewidth=0.5, mfc='w', label = "Walther et al. (2019)")
+
+# Plot simulation
+plt.plot(z, np.log10(T_mean))
+
+# Legend
+plt.legend(loc="upper right", frameon=True, fontsize=8, handletextpad=0.1, facecolor="w", edgecolor="w", framealpha=1.)
+plt.text(0.2, 4.8, "SWIFT %s \nCooling model: %s \n$\\rho=%.3f$ $\\Omega_{b}\\rho_{crit,0}$\n$Z=%s$"%(git_revision, cooling_model, rho_mean[-1], metallicity), va="top", ha="left", fontsize=8)
+
+plt.xlim(0, 12.2)
+plt.ylim(3.5,4.85)
+plt.xlabel("Redshift", labelpad=-0.5)
+plt.ylabel(r"$\log_{10}(T/K)$", labelpad=0)
+plt.savefig("Temperature_evolution.png", dpi=200)
+
+
+# Make plot of denisty evolution --------------------------------
+plt.rcParams.update({'figure.subplot.left' : 0.14})
+fig = plt.figure()
+
+plt.text(0.2, 1.011, "SWIFT %s"%git_revision, va="top", ha="left", fontsize=8)
+
+plt.fill_between(z,rho_mean - rho_std,rho_mean + rho_std,alpha = 0.5)
+plt.plot(z,rho_mean)
+
+plt.axhline(y = 1.0, linestyle = '--', color='k', alpha=0.5, lw=1.)
+
+plt.xlim(0.0,12.2)
+plt.ylabel(r"$\delta_b = \rho / \Omega_b\rho_{crit,0}$", labelpad=0.)
+plt.ylim(0.988,1.012)
+plt.yticks([0.99, 1., 1.01])
+plt.xlabel("Redshift", labelpad=-0.5)
+plt.savefig("Density_evolution.png", dpi=200)
diff --git a/examples/Cooling/ConstantCosmoTempEvolution/run.sh b/examples/Cooling/ConstantCosmoTempEvolution/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..710613ec9a431a007ed7b83e2d5634ee24eea7ec
--- /dev/null
+++ b/examples/Cooling/ConstantCosmoTempEvolution/run.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e gravity_glassCube_32.hdf5 ]
+then
+ echo "Fetching initial gravity glass file for the constant cosmological box example..."
+ ./getGlass.sh
+fi
+if [ ! -e coolingtables ]
+then
+ echo "Fetching EAGLE Cooling Tables"
+ ../getEagleCoolingTable.sh
+fi
+
+# Fetch the cooling tables
+if [ ! -e constantBox.hdf5 ]
+then
+ echo "Generating initial conditions for the uniform cosmo box example..."
+ python3 makeIC.py
+fi
+
+# Run SWIFT
+../../swift --hydro --cosmology --cooling --threads=4 const_cosmo_temp_evol.yml 2>&1 | tee output.log
+
+# Plot the result
+python3 plot_thermal_history.py cooling_box
diff --git a/examples/Cooling/CoolingBox/coolingBox.yml b/examples/Cooling/CoolingBox/coolingBox.yml
index 853e480cd4ffba4baa659232e6d5f068b4ea2815..ca97793aa9b4de43872db38f55c4060a2b27ddc9 100644
--- a/examples/Cooling/CoolingBox/coolingBox.yml
+++ b/examples/Cooling/CoolingBox/coolingBox.yml
@@ -57,6 +57,7 @@ GearChemistry:
EAGLECooling:
dir_name: ./coolingtables/
H_reion_z: 11.5
+ H_reion_eV_p_H: 2.0
He_reion_z_center: 3.5
He_reion_z_sigma: 0.5
He_reion_eV_p_H: 2.0
diff --git a/examples/Cooling/CoolingRates/cooling_rates.c b/examples/Cooling/CoolingRates/cooling_rates.c
index e7ff0340853e5cd5361286bd8af5c547681b4f63..f23a987e3ae56db0811eb9997a8c1c48772f7f09 100644
--- a/examples/Cooling/CoolingRates/cooling_rates.c
+++ b/examples/Cooling/CoolingRates/cooling_rates.c
@@ -166,6 +166,7 @@ int main(int argc, char **argv) {
struct phys_const internal_const;
struct cooling_function_data cooling;
struct cosmology cosmo;
+ struct space s;
const char *parametersFileName = "./cooling_rates.yml";
/* Initialize CPU frequency, this also starts time. */
@@ -229,7 +230,7 @@ int main(int argc, char **argv) {
// Init cooling
cooling_init(params, &us, &internal_const, &cooling);
cooling_print(&cooling);
- cooling_update(&cosmo, &cooling);
+ cooling_update(&cosmo, &cooling, &s);
// Calculate abundance ratios
float abundance_ratio[(chemistry_element_count + 2)];
diff --git a/examples/Cooling/CoolingRates/cooling_rates.yml b/examples/Cooling/CoolingRates/cooling_rates.yml
index 1d67ad0af79368c39c24879b101a540d0bccb3d1..985eef220b24bd398deec09ea56630118d0bc5ab 100644
--- a/examples/Cooling/CoolingRates/cooling_rates.yml
+++ b/examples/Cooling/CoolingRates/cooling_rates.yml
@@ -30,6 +30,7 @@ EAGLEChemistry:
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
diff --git a/examples/Cooling/CoolingRates/getCoolingTable.sh b/examples/Cooling/getEagleCoolingTable.sh
similarity index 100%
rename from examples/Cooling/CoolingRates/getCoolingTable.sh
rename to examples/Cooling/getEagleCoolingTable.sh
diff --git a/examples/Cooling/getCoolingTable.sh b/examples/Cooling/getGrackleCoolingTable.sh
similarity index 100%
rename from examples/Cooling/getCoolingTable.sh
rename to examples/Cooling/getGrackleCoolingTable.sh
diff --git a/examples/Cosmology/ConstantCosmoVolume/run.sh b/examples/Cosmology/ConstantCosmoVolume/run.sh
index 4a30410e868aef58b1a9dac0a3225e5844c5873f..9c0e0ccdcbbdd52b14230d98393637e99d9ad80f 100755
--- a/examples/Cosmology/ConstantCosmoVolume/run.sh
+++ b/examples/Cosmology/ConstantCosmoVolume/run.sh
@@ -9,11 +9,11 @@ fi
if [ ! -e constantBox.hdf5 ]
then
echo "Generating initial conditions for the uniform cosmo box example..."
- python makeIC.py
+ python3 makeIC.py
fi
# Run SWIFT
../../swift --hydro --cosmology --self-gravity --threads=8 constant_volume.yml 2>&1 | tee output.log
# Plot the result
-python plotSolution.py $i
+python3 plotSolution.py $i
diff --git a/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml b/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
index 4c3d7f0a3516ea7919a7ecd28efa6808c2f0f046..df4c05811bae17a65b54e45c6625ff97a21357f6 100644
--- a/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
+++ b/examples/EAGLE_ICs/EAGLE_12/eagle_12.yml
@@ -80,6 +80,7 @@ EAGLEChemistry:
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
diff --git a/examples/EAGLE_low_z/EAGLE_12/eagle_12.yml b/examples/EAGLE_low_z/EAGLE_12/eagle_12.yml
index d09bbb51e90d843dd6731c5fcbd48b9c586713f9..ada36234d6a9691a8d78a33a047088920e2c6a11 100644
--- a/examples/EAGLE_low_z/EAGLE_12/eagle_12.yml
+++ b/examples/EAGLE_low_z/EAGLE_12/eagle_12.yml
@@ -73,6 +73,7 @@ EAGLEChemistry: # Solar abundances
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
diff --git a/examples/EAGLE_low_z/EAGLE_25/eagle_25.yml b/examples/EAGLE_low_z/EAGLE_25/eagle_25.yml
index 75799647b4e95ebd75202748c67a2c18c423f532..b1d897ec390ca0488229c460a4308c1ee793dbf7 100644
--- a/examples/EAGLE_low_z/EAGLE_25/eagle_25.yml
+++ b/examples/EAGLE_low_z/EAGLE_25/eagle_25.yml
@@ -80,6 +80,7 @@ EAGLEChemistry: # Solar abundances
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
diff --git a/examples/EAGLE_low_z/EAGLE_50/eagle_50.yml b/examples/EAGLE_low_z/EAGLE_50/eagle_50.yml
index 6c0c7421ba4f804437a8086b42fb2878bd3904b1..c837c88d870f21907b9fe7fc1408c5df8db5dd0c 100644
--- a/examples/EAGLE_low_z/EAGLE_50/eagle_50.yml
+++ b/examples/EAGLE_low_z/EAGLE_50/eagle_50.yml
@@ -75,6 +75,7 @@ EAGLEChemistry: # Solar abundances
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
diff --git a/examples/EAGLE_low_z/EAGLE_6/eagle_6.yml b/examples/EAGLE_low_z/EAGLE_6/eagle_6.yml
index 313a5a384324eecd56455ea22bbc96d147982d6b..4f68413fa4c69b8e2b9ff28e66f4f269d21a1a7b 100644
--- a/examples/EAGLE_low_z/EAGLE_6/eagle_6.yml
+++ b/examples/EAGLE_low_z/EAGLE_6/eagle_6.yml
@@ -84,9 +84,11 @@ EAGLEChemistry: # Solar abundances
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.
diff --git a/examples/HydroTests/Diffusion_1D/.gitignore b/examples/HydroTests/Diffusion_1D/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..dadfbc6e8ce185fc82169300e6f289ed8abc9bf2
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/.gitignore
@@ -0,0 +1 @@
+beta_*
diff --git a/examples/HydroTests/Diffusion_1D/README b/examples/HydroTests/Diffusion_1D/README
new file mode 100644
index 0000000000000000000000000000000000000000..6254e0ce9a7aa1af5f54ba388b2b08af6bb78739
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/README
@@ -0,0 +1,19 @@
+Diffusion 1D
+============
+
+This is a very simple, 1D test. It sets up a uniform density particle
+distribution, with energy discontinuities generated at every particle.
+Particles have their internal energy set in a binary manner, with them
+alternating between "low" and "high" states. Under a standard SPH
+scheme, we expect to see no evolution whatsoever in the box. However,
+under a scheme with thermal diffusion, we expect that there will be
+some diffusion between the particles and that the distribution of
+internal energy will equalise.
+
+Included are some scripts to create initial conditions (`makeIC.py`),
+plot a solution (`plotSolution.py`), and to run the code (`run.sh`).
+Also included is a script to run a convergence test by changing the
+`SPH:beta_diffusion` parameter (`run_set.sh`).
+
+To make the initial conditions and produce the plots, the `swiftsimio`
+library (http://gitlab.cosma.dur.ac.uk/jborrow/swiftsimio) is required.
\ No newline at end of file
diff --git a/examples/HydroTests/Diffusion_1D/diffusion.yml b/examples/HydroTests/Diffusion_1D/diffusion.yml
new file mode 100644
index 0000000000000000000000000000000000000000..099cad637bf947926baa3571a2b1361d16293547
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/diffusion.yml
@@ -0,0 +1,38 @@
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1 # Grams
+ UnitLength_in_cgs: 1 # Centimeters
+ UnitVelocity_in_cgs: 1 # Centimeters per second
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+# Parameters governing the time integration
+TimeIntegration:
+ time_begin: 0. # The starting time of the simulation (in internal units).
+ time_end: 1e-0 # The end time of the simulation (in internal units).
+ dt_min: 1e-7 # 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: diffusion # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 2e-2 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-1 # Time between statistics output
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
+ diffusion_alpha: 0.0 # (Optional) Override the initial value for the thermal diffusion coefficient in schemes with thermal diffusion.
+ diffusion_beta: 0.01 # (Optional) Override the decay/rise rate tuning parameter for the thermal diffusion.
+ diffusion_alpha_max: 1.0 # (Optional) Override the maximal thermal diffusion coefficient that is allowed for a given particle.
+ diffusion_alpha_min: 0.0 # (Optional) Override the minimal thermal diffusion coefficient that is allowed for a given particle.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./diffusion.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/HydroTests/Diffusion_1D/diffusion_fixed_alpha.yml b/examples/HydroTests/Diffusion_1D/diffusion_fixed_alpha.yml
new file mode 100644
index 0000000000000000000000000000000000000000..36f70e2492a05e90ab29496d4fc064cc2c35f62f
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/diffusion_fixed_alpha.yml
@@ -0,0 +1,38 @@
+# Define the system of units to use internally.
+InternalUnitSystem:
+ UnitMass_in_cgs: 1 # Grams
+ UnitLength_in_cgs: 1 # Centimeters
+ UnitVelocity_in_cgs: 1 # Centimeters per second
+ UnitCurrent_in_cgs: 1 # Amperes
+ UnitTemp_in_cgs: 1 # Kelvin
+
+# Parameters governing the time integration
+TimeIntegration:
+ time_begin: 0. # The starting time of the simulation (in internal units).
+ time_end: 1e-0 # The end time of the simulation (in internal units).
+ dt_min: 1e-7 # 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: diffusion_fixed_alpha # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 2e-2 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-1 # Time between statistics output
+
+# 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).
+ CFL_condition: 0.1 # Courant-Friedrich-Levy condition for time integration.
+ diffusion_alpha: 0.1 # (Optional) Override the initial value for the thermal diffusion coefficient in schemes with thermal diffusion.
+ diffusion_beta: 0.01 # (Optional) Override the decay/rise rate tuning parameter for the thermal diffusion.
+ diffusion_alpha_max: 0.1 # (Optional) Override the maximal thermal diffusion coefficient that is allowed for a given particle.
+ diffusion_alpha_min: 0.1 # (Optional) Override the minimal thermal diffusion coefficient that is allowed for a given particle.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./diffusion.hdf5 # The file to read
+ periodic: 1
diff --git a/examples/HydroTests/Diffusion_1D/makeIC.py b/examples/HydroTests/Diffusion_1D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..09a4b5c698c7351a8a08f53a268c2b333bfef991
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/makeIC.py
@@ -0,0 +1,143 @@
+"""
+This file is part of SWIFT.
+Copyright (c) 2019 Josh Borrow (joshua.borrow@durham.ac.uk)
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published
+by the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Creates initial conditiosn for the ContactDiscontinuty_1D test.
+Requires the swiftsimio library.
+"""
+
+import numpy as np
+import unyt
+
+
+def get_particle_positions(box_length: float, n_part: int) -> np.array:
+ """
+ Gets the particle positions evenly spaced along a _periodic_ box.
+ """
+
+ dx = box_length / float(n_part)
+ x = np.arange(n_part, dtype=float) * dx + (0.5 * dx)
+
+ return x
+
+
+def get_particle_u(low: float, high: float, n_part: int) -> np.array:
+ """
+ Gets the particle internal energies, which alternate between low
+ and high. Make sure n_part is even.
+ """
+
+ indicies = np.arange(n_part)
+ u = unyt.unyt_array(np.empty(n_part, dtype=float), low.units)
+ u[...] = low
+ u[(indicies % 2).astype(bool)] = high
+
+ return u
+
+
+def get_particle_masses(mass: float, n_part: int) -> np.array:
+ """
+ Gets the particle masses.
+ """
+
+ m = unyt.unyt_array(np.empty(n_part, dtype=float), mass.units)
+ m[...] = mass
+
+ return m
+
+
+def get_particle_hsml(box_length: float, n_part: int) -> np.array:
+ """
+ Gets the particle smoothing lengths based on their MIPS.
+ """
+
+ mips = box_length / float(n_part)
+ hsml = unyt.unyt_array(np.empty(n_part, dtype=float), box_length.units)
+ hsml[...] = mips
+
+ return hsml
+
+
+if __name__ == "__main__":
+ import argparse as ap
+ from swiftsimio import Writer
+
+ parser = ap.ArgumentParser(
+ description="Makes initial conditions for the ContactDiscontinuity_1D test."
+ )
+
+ parser.add_argument(
+ "-n",
+ "--npart",
+ help="Number of particles in the box. Make sure this is even. Default: 900",
+ type=int,
+ default=900,
+ )
+
+ parser.add_argument(
+ "-m",
+ "--mass",
+ help="Particle mass in grams. Default: 1e-4",
+ type=float,
+ default=1e-4,
+ )
+
+ parser.add_argument(
+ "-l",
+ "--low",
+ help="Low value for the internal energy (in ergs/g). Default: 1e-6",
+ type=float,
+ default=1e-6,
+ )
+
+ parser.add_argument(
+ "-t",
+ "--high",
+ help="Top/high value for the internal energy (in ergs/g). Default: 1e-4",
+ type=float,
+ default=1e-4,
+ )
+
+ parser.add_argument(
+ "-b", "--boxsize", help="Boxsize in cm. Default: 1.0", type=float, default=1.0
+ )
+
+ args = vars(parser.parse_args())
+ boxsize = args["boxsize"] * unyt.cm
+ n_part = args["npart"]
+ mass = args["mass"] * unyt.g
+ low = args["low"] * unyt.erg / unyt.g
+ high = args["high"] * unyt.erg / unyt.g
+
+ if not (n_part % 2 == 0):
+ raise AttributeError("Please ensure --npart is even.")
+
+ cgs = unyt.unit_systems.cgs_unit_system
+
+ boxsize = 1.0 * unyt.cm
+
+ writer = Writer(cgs, boxsize, dimension=1)
+
+ coordinates = np.zeros((n_part, 3), dtype=float) * unyt.cm
+ coordinates[:, 0] = get_particle_positions(boxsize, n_part)
+
+ writer.gas.coordinates = coordinates
+ writer.gas.velocities = np.zeros((n_part, 3), dtype=float) * unyt.cm / unyt.s
+ writer.gas.masses = get_particle_masses(mass, n_part)
+ writer.gas.internal_energy = get_particle_u(low, high, n_part)
+ writer.gas.smoothing_length = get_particle_hsml(boxsize, n_part)
+
+ writer.write("diffusion.hdf5")
diff --git a/examples/HydroTests/Diffusion_1D/plotSolution.py b/examples/HydroTests/Diffusion_1D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..66c8ffc6418f06589a2918ae4d8ed460b0081972
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/plotSolution.py
@@ -0,0 +1,341 @@
+"""
+This file is part of SWIFT.
+Copyright (c) 2019 Josh Borrow (joshua.borrow@durham.ac.uk)
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Lesser General Public License as published
+by the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Plots the solution for the ContactDiscontinuity_1D test.
+"""
+
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+
+try:
+ from scipy.integrate import solve_ivp
+ solve_ode = True
+except:
+ solve_ode = False
+
+from swiftsimio import load
+
+matplotlib.use("Agg")
+
+def solve_analytic(u_0, u_1, t_0, t_1, alpha=0.1):
+ """
+ Solves the analytic equation:
+
+ $$
+ \frac{d \Delta}{d t} = \kappa \alpha (
+ \sqrt{u_0 + \Delta} + \sqrt{u_1 + \Delta}
+ ) (
+ u_1 - u_0 - 2 \Delta
+ )
+ $$
+
+ from time t0 to t1.
+
+ + alpha is the gradient term
+ + u_0 is the "low" state
+ + u_1 is the "high" state.
+ """
+
+ if not solve_ode:
+ return [0.0], [0.0]
+
+ def gradient(t, u):
+ """
+ Returns du0/dt, du1/dt
+ """
+
+ common = alpha * (np.sqrt(u[0]) + np.sqrt(u[1])) * (u[0] - u[1])
+
+ return np.array([-1.0 * common, 1.0 * common])
+
+ ret = solve_ivp(gradient, t_span=[t_0.value, t_1.value], y0=[u_0.value, u_1.value], t_eval=np.linspace(t_0.value, t_1.value, 100))
+
+ t = ret.t
+ high = ret.y[1]
+ low = ret.y[0]
+
+ return t, (high - low) * u_0.units
+
+
+def get_data_dump(metadata):
+ """
+ Gets a big data dump from the SWIFT metadata
+ """
+
+ try:
+ viscosity = metadata.viscosity_info
+ except:
+ viscosity = "No info"
+
+ try:
+ diffusion = metadata.diffusion_info
+ except:
+ diffusion = "No info"
+
+ output = (
+ "SWIFT\n"
+ + metadata.code_info
+ + "\n\n"
+ + "Compiler\n"
+ + metadata.compiler_info
+ + "\n\n"
+ + "Hydrodynamics\n"
+ + metadata.hydro_info
+ + "\n\n"
+ + "Viscosity\n"
+ + viscosity
+ + "\n\n"
+ + "Diffusion\n"
+ + diffusion
+ )
+
+ return output
+
+
+def get_data_list(start: int, stop: int, handle: str):
+ """
+ Gets a list of swiftsimio objects that contains all of the data.
+ """
+
+ data = [load("{}_{:04d}.hdf5".format(handle, x)) for x in range(start, stop + 1)]
+
+ return data
+
+
+def setup_axes(size=[8, 8], dpi=300):
+ """
+ Sets up the axes with the correct labels, etc.
+ """
+ fig, ax = plt.subplots(ncols=2, nrows=2, figsize=size, dpi=dpi)
+
+ ax = ax.flatten()
+
+ ax[0].axis("off")
+ ax[1].set_xlabel("Time [s]")
+ ax[1].set_ylabel("Relative energy difference $u/\\left<u\\right>$")
+
+ ax[2].set_xlabel("Time [s]")
+ ax[2].set_ylabel("Deviation in position relative to MIPS [$\\times 10^{6}$]")
+
+ ax[3].set_xlabel("Time [s]")
+
+ return fig, ax
+
+def mean_std_max_min(data):
+ """
+ Returns:
+ mean, stdev, max, min
+ for your data.
+ """
+ means = np.array([np.mean(x) for x in data])
+ stdevs = np.array([np.std(x) for x in data])
+ maxs = np.array([np.max(x) for x in data])
+ mins = np.array([np.min(x) for x in data])
+
+ return means, stdevs, maxs, mins
+
+
+def extract_plottables_u(data_list):
+ """
+ Extracts the plottables for the internal energies. Returns:
+ mean, stdev, max, min differences between adjacent internal energies
+ """
+
+ data = [
+ np.diff(x.gas.internal_energy.value) / np.mean(x.gas.internal_energy.value)
+ for x in data_list
+ ]
+
+ return mean_std_max_min(data)
+
+
+def extract_plottables_x(data_list):
+ """
+ Extracts the plottables for positions. Returns:
+ mean, stdev, max, min * 1e6 deviations from original position
+ """
+
+ n_part = data_list[0].metadata.n_gas
+ boxsize = data_list[0].metadata.boxsize[0].value
+ dx = boxsize / n_part
+
+ original_x = np.arange(n_part, dtype=float) * dx + (0.5 * dx)
+
+ deviations = [1e6 * abs(original_x - x.gas.coordinates.value[:, 0]) / dx for x in data_list]
+
+ return mean_std_max_min(deviations)
+
+
+def extract_plottables_rho(data_list):
+ """
+ Extracts the plottables for pressure. Returns:
+ mean, stdev, max, min * 1e6 deviations from mean density
+ """
+
+ P = [x.gas.density.value for x in data_list]
+ mean_P = [np.mean(x) for x in P]
+ deviations = [1e6 * (x - y) / x for x, y in zip(mean_P, P)]
+
+ return mean_std_max_min(deviations)
+
+
+def extract_plottables_diff(data_list):
+ """
+ Extracts the plottables for pressure. Returns:
+ mean, stdev, max, min * 1e6 deviations from mean density
+ """
+
+ P = [x.gas.diffusion.value for x in data_list]
+
+ return mean_std_max_min(P)
+
+
+def make_plot(start: int, stop: int, handle: str):
+ """
+ Makes the plot and returns the figure and axes objects.
+ """
+ fig, ax = setup_axes()
+ data_list = get_data_list(start, stop, handle)
+ data_dump = get_data_dump(data_list[0].metadata)
+ t = [x.metadata.t for x in data_list]
+ means, stdevs, maxs, mins = extract_plottables_u(data_list)
+ x_means, x_stdevs, x_maxs, x_mins = extract_plottables_x(data_list)
+
+ try:
+ alpha = np.mean([np.mean(x.gas.diffusion) for x in data_list])
+ except AttributeError:
+ # Must be using a non-diffusive scheme.
+ alpha = 0.0
+
+ ax[0].text(
+ 0.5,
+ 0.5,
+ data_dump,
+ ha="center",
+ va="center",
+ fontsize=8,
+ transform=ax[0].transAxes,
+ )
+
+ ax[1].fill_between(
+ t, means - stdevs, means + stdevs, color="C0", alpha=0.5, edgecolor="none"
+ )
+ ax[1].plot(t, means, label="Mean", c="C0")
+ ax[1].plot(t, maxs, label="Max", linestyle="dashed", c="C1")
+ ax[1].plot(t, mins, label="Min", linestyle="dashed", c="C2")
+
+ if solve_ode:
+ times_ode, diff = solve_analytic(
+ u_0=data_list[0].gas.internal_energy.min(),
+ u_1=data_list[0].gas.internal_energy.max(),
+ t_0=t[0],
+ t_1=t[-1],
+ alpha=(
+ np.sqrt(5.0/3.0 * (5.0/3.0 - 1.0)) *
+ alpha / data_list[0].gas.smoothing_length[0].value
+ )
+ )
+
+ ax[1].plot(
+ times_ode,
+ (diff) / np.mean(data_list[0].gas.internal_energy),
+ label="Analytic",
+ linestyle="dotted",
+ c="C3"
+ )
+
+ #import pdb;pdb.set_trace()
+
+ ax[2].fill_between(
+ t, x_means - x_stdevs, x_means + x_stdevs, color="C0", alpha=0.5, edgecolor="none"
+ )
+ ax[2].plot(t, x_means, label="Mean", c="C0")
+ ax[2].plot(t, x_maxs, label="Max", linestyle="dashed", c="C1")
+ ax[2].plot(t, x_mins, label="Min", linestyle="dashed", c="C2")
+
+ try:
+ # Give diffusion info a go; this may not be present
+ diff_means, diff_stdevs, diff_maxs, diff_mins = extract_plottables_diff(data_list)
+
+ ax[3].set_ylabel(r"Diffusion parameter $\alpha_{diff}$")
+ ax[3].fill_between(
+ t, diff_means - diff_stdevs, diff_means + diff_stdevs, color="C0", alpha=0.5, edgecolor="none"
+ )
+ ax[3].plot(t, diff_means, label="Mean", c="C0")
+ ax[3].plot(t, diff_maxs, label="Max", linestyle="dashed", c="C1")
+ ax[3].plot(t, diff_mins, label="Min", linestyle="dashed", c="C2")
+
+ except:
+ # Diffusion info must not be present.
+ rho_means, rho_stdevs, rho_maxs, rho_mins = extract_plottables_rho(data_list)
+
+ ax[3].set_ylabel("Deviation from mean density $(\\rho_i - \\bar{\\rho}) / \\bar{\\rho}$ [$\\times 10^{6}$]")
+ ax[3].fill_between(
+ t, rho_means - rho_stdevs, rho_means + rho_stdevs, color="C0", alpha=0.5, edgecolor="none"
+ )
+ ax[3].plot(t, rho_means, label="Mean", c="C0")
+ ax[3].plot(t, rho_maxs, label="Max", linestyle="dashed", c="C1")
+ ax[3].plot(t, rho_mins, label="Min", linestyle="dashed", c="C2")
+
+ ax[1].legend(loc=1, markerfirst=False)
+
+ ax[1].set_xlim(t[0], t[-1])
+ ax[2].set_xlim(t[0], t[-1])
+ ax[3].set_xlim(t[0], t[-1])
+
+ fig.tight_layout()
+
+ return fig, ax
+
+
+if __name__ == "__main__":
+ import argparse as ap
+
+ parser = ap.ArgumentParser(
+ description="Makes a plot of the data from the ContactDiscontinuity_1D test."
+ )
+
+ parser.add_argument(
+ "-i", "--initial", help="Initial snapshot. Default: 0", type=int, default=0
+ )
+
+ parser.add_argument(
+ "-f", "--final", help="Final snapshot. Default: 50", type=int, default=50
+ )
+
+ parser.add_argument(
+ "-s",
+ "--snapshot",
+ help="First part of the snapshot filename. Default: diffusion",
+ type=str,
+ default="diffusion",
+ )
+
+ parser.add_argument(
+ "-o",
+ "--output",
+ help="Output filename. Default: diffusion.png",
+ type=str,
+ default="diffusion.png",
+ )
+
+ args = vars(parser.parse_args())
+
+ fig, ax = make_plot(args["initial"], args["final"], args["snapshot"])
+
+ fig.savefig(args["output"])
diff --git a/examples/HydroTests/Diffusion_1D/run.sh b/examples/HydroTests/Diffusion_1D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..fb70805ca01b96df20fff438b2141b03ccf6e7ab
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/run.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e diffusion.hdf5 ]
+then
+ echo "Generating initial conditions for the Sedov blast example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../../swift --hydro --limiter --threads=1 diffusion.yml 2>&1 | tee output.log
diff --git a/examples/HydroTests/Diffusion_1D/run_set.sh b/examples/HydroTests/Diffusion_1D/run_set.sh
new file mode 100644
index 0000000000000000000000000000000000000000..d6b1f233e65b4e7851f15cf3bc8aadceff4710d7
--- /dev/null
+++ b/examples/HydroTests/Diffusion_1D/run_set.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+beta=(1.0 0.1 0.01 0.001)
+swift_location="../../swift"
+flags="--hydro --limiter --threads=2"
+parameter="diffusion.yml"
+parameter_fixed="diffusion_fixed_alpha.yml"
+make_ic_script="makeIC.py"
+plot_script="plotSolution.py"
+
+for i in ${beta[@]};
+do
+ mkdir beta_$i
+ cd beta_$i
+
+ python ../$make_ic_script
+
+ ../$swift_location $flags -P "SPH:diffusion_beta:${i}" ../$parameter
+ python ../$plot_script
+ ../$swift_location $flags -P "SPH:diffusion_beta:${i}" ../$parameter_fixed
+ python ../$plot_script -s diffusion_fixed_alpha -o diffusion_fixed_alpha.png
+
+ rm *.hdf5
+
+ cd ..
+done
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/isolated_galaxy.yml b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/isolated_galaxy.yml
index 7ba1e601c764d9c12b93178efd8226601af8373c..7dac0a8a6c3b8d4c583ae6138513f0c5259227b1 100644
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/isolated_galaxy.yml
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/isolated_galaxy.yml
@@ -50,6 +50,7 @@ SPH:
EAGLECooling:
dir_name: ./coolingtables/ # Location of the Wiersma+08 cooling tables
H_reion_z: 11.5 # Redshift of Hydrogen re-ionization
+ H_reion_eV_p_H: 2.0
He_reion_z_centre: 3.5 # Redshift of the centre of the Helium re-ionization Gaussian
He_reion_z_sigma: 0.5 # Spread in redshift of the Helium re-ionization Gaussian
He_reion_eV_p_H: 2.0 # Energy inject by Helium re-ionization in electron-volt per Hydrogen atom
diff --git a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
index f2aa93fd0e11cd9b07be991187cf0780a82ebec8..dc0b49478cdabefbe4dbf3544e097f18593cfb16 100755
--- a/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
+++ b/examples/IsolatedGalaxy/IsolatedGalaxy_starformation/run.sh
@@ -6,7 +6,7 @@ then
./getIC.sh
fi
-../../swift --threads=32 --external-gravity --self-gravity --stars --star-formation --cooling --temperature --hydro isolated_galaxy.yml 2>&1 | tee output.log
+../../swift --threads=16 --external-gravity --self-gravity --stars --star-formation --cooling --hydro isolated_galaxy.yml -v 1 2>&1 | tee output.log
# Kennicutt-Schmidt law plot
python3 plotSolution.py
diff --git a/examples/SantaBarbara/SantaBarbara-256/santa_barbara.yml b/examples/SantaBarbara/SantaBarbara-256/santa_barbara.yml
index 0abbc91019957952276b51db01a3a1b71d6e4fdf..9f6585e0c589d3d016921eb85dd6af13a0643784 100644
--- a/examples/SantaBarbara/SantaBarbara-256/santa_barbara.yml
+++ b/examples/SantaBarbara/SantaBarbara-256/santa_barbara.yml
@@ -76,6 +76,7 @@ EAGLEChemistry:
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
diff --git a/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/small_cosmo_volume.yml b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/small_cosmo_volume.yml
index 96f10465410ac120b30904a8655da4d8133d09bd..b108290fcd146461827d5858742bd0971ac66945 100644
--- a/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/small_cosmo_volume.yml
+++ b/examples/SmallCosmoVolume/SmallCosmoVolume_cooling/small_cosmo_volume.yml
@@ -67,6 +67,7 @@ LambdaCooling:
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
diff --git a/src/cell.c b/src/cell.c
index 15ea5fc6981d671fff163b52efb3bc36e371aaba..a13a955a9bb61e0f3eaac39ff18555fc1ac5dc4f 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -3226,9 +3226,12 @@ int cell_unskip_hydro_tasks(struct cell *c, struct scheduler *s) {
if (c->timestep != NULL) scheduler_activate(s, c->timestep);
if (c->hydro.end_force != NULL) scheduler_activate(s, c->hydro.end_force);
if (c->hydro.cooling != NULL) scheduler_activate(s, c->hydro.cooling);
- if (c->hydro.star_formation != NULL)
- scheduler_activate(s, c->hydro.star_formation);
if (c->logger != NULL) scheduler_activate(s, c->logger);
+
+ if (c->hydro.star_formation != NULL) {
+ scheduler_activate(s, c->hydro.star_formation);
+ cell_activate_drift_spart(c, s);
+ }
}
return rebuild;
diff --git a/src/cell.h b/src/cell.h
index baae12e4a5797e3b1e00eee144635e41b52c157e..92f6bf95692bd01ddd2b6fe681ae159d72840917 100644
--- a/src/cell.h
+++ b/src/cell.h
@@ -687,9 +687,12 @@ struct cell {
/*! The maximal depth of this cell and its progenies */
char maxdepth;
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
/* Cell ID (for debugging) */
int cellID;
+#endif
+
+#ifdef SWIFT_DEBUG_CHECKS
/*! The list of tasks that have been executed on this cell */
char tasks_executed[64];
diff --git a/src/common_io.c b/src/common_io.c
index 733cf1dacac5f0c73ea401a584e2aa40eadd4a23..2b8a55f0eba047a6076a3023569d05ddf49b376b 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -557,7 +557,7 @@ void io_write_cell_offsets(hid_t h_grp, const int cdim[3],
H5Gclose(h_subgrp);
/* Write the centres to the group */
- hsize_t shape[2] = {nr_cells, 3};
+ hsize_t shape[2] = {(hsize_t)nr_cells, 3};
hid_t h_space = H5Screate(H5S_SIMPLE);
if (h_space < 0) error("Error while creating data space for cell centres");
hid_t h_err = H5Sset_extent_simple(h_space, 2, shape, shape);
diff --git a/src/cooling.h b/src/cooling.h
index 875ef5054491f783d526e7c8e2caf3e005c8a5a0..9b9b255dc7f845adeed8177b4385e08aaffbd977 100644
--- a/src/cooling.h
+++ b/src/cooling.h
@@ -31,6 +31,7 @@
#include "parser.h"
#include "physical_constants.h"
#include "restart.h"
+#include "space.h"
#include "units.h"
/* Import the right cooling definition */
diff --git a/src/cooling/Compton/cooling.h b/src/cooling/Compton/cooling.h
index c796375c33c586e2c9a95515f4124062a41640eb..9e5a5ad34a9086152b98a1f1709e3755d875fb83 100644
--- a/src/cooling/Compton/cooling.h
+++ b/src/cooling/Compton/cooling.h
@@ -49,9 +49,11 @@
*
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The #space containing all the particles.
*/
INLINE static void cooling_update(const struct cosmology* cosmo,
- struct cooling_function_data* cooling) {
+ struct cooling_function_data* cooling,
+ struct space* s) {
// Add content if required.
}
diff --git a/src/cooling/EAGLE/cooling.c b/src/cooling/EAGLE/cooling.c
index 87c12e73d970b4d1caa6ce33c20666556463e08c..2e829c9f1852d96f40a91e6c95cc8d803a8095a6 100644
--- a/src/cooling/EAGLE/cooling.c
+++ b/src/cooling/EAGLE/cooling.c
@@ -45,6 +45,7 @@
#include "parser.h"
#include "part.h"
#include "physical_constants.h"
+#include "space.h"
#include "units.h"
/* Maximum number of iterations for newton
@@ -57,8 +58,8 @@ static const float explicit_tolerance = 0.05;
static const float newton_tolerance = 1.0e-4;
static const float bisection_tolerance = 1.0e-6;
static const float rounding_tolerance = 1.0e-4;
-static const double bracket_factor = 1.5; /* sqrt(1.1) */
-static const double newton_log_u_guess_cgs = 12.30103; /* log10(2e12) */
+static const double bracket_factor = 1.5;
+static const double newton_log_u_guess_cgs = 12;
/**
* @brief Find the index of the current redshift along the redshift dimension
@@ -123,11 +124,14 @@ __attribute__((always_inline)) INLINE void get_redshift_index(
* given time-step or redshift. Predominantly used to read cooling tables
* above and below the current redshift, if not already read in.
*
+ * Also calls the additional H reionisation energy injection if need be.
+ *
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The space data, including a pointer to array of particles
*/
void cooling_update(const struct cosmology *cosmo,
- struct cooling_function_data *cooling) {
+ struct cooling_function_data *cooling, struct space *s) {
/* Current redshift */
const float redshift = cosmo->z;
@@ -138,6 +142,23 @@ void cooling_update(const struct cosmology *cosmo,
get_redshift_index(redshift, &z_index, &dz, cooling);
cooling->dz = dz;
+ /* Extra energy for reionization? */
+ if (!cooling->H_reion_done) {
+
+ /* Does this timestep straddle Hydrogen reionization? If so, we need to
+ * input extra heat */
+ if (cosmo->z <= cooling->H_reion_z && cosmo->z_old > cooling->H_reion_z) {
+
+ if (s == NULL) error("Trying to do H reionization on an empty space!");
+
+ /* Inject energy to all particles */
+ cooling_Hydrogen_reionization(cooling, cosmo, s);
+
+ /* Flag that reionization happened */
+ cooling->H_reion_done = 1;
+ }
+ }
+
/* Do we already have the correct tables loaded? */
if (cooling->z_index == z_index) return;
@@ -209,7 +230,8 @@ INLINE static float newton_iter(
const float log_table_bound_low = (cooling->Therm[0] + 0.05) / M_LOG10E;
/* convert Hydrogen mass fraction in Hydrogen number density */
- const float XH = p->chemistry_data.metal_mass_fraction[chemistry_element_H];
+ const float XH =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_H];
const double n_H =
hydro_get_physical_density(p, cosmo) * XH / phys_const->const_proton_mass;
const double n_H_cgs = n_H * cooling->number_density_to_cgs;
@@ -501,8 +523,10 @@ void cooling_cool_part(const struct phys_const *phys_const,
abundance_ratio_to_solar(p, cooling, abundance_ratio);
/* Get the Hydrogen and Helium mass fractions */
- const float XH = p->chemistry_data.metal_mass_fraction[chemistry_element_H];
- const float XHe = p->chemistry_data.metal_mass_fraction[chemistry_element_He];
+ const float XH =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_H];
+ const float XHe =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_He];
/* Get the Helium mass fraction. Note that this is He / (H + He), i.e. a
* metal-free Helium mass fraction as per the Wiersma+08 definition */
@@ -531,15 +555,17 @@ void cooling_cool_part(const struct phys_const *phys_const,
re-ionization as this needs to be added on no matter what */
/* Get helium and hydrogen reheating term */
- const double Helium_reion_heat_cgs = eagle_helium_reionization_extraheat(
- cooling->z_index, delta_redshift, cooling);
+ const double Helium_reion_heat_cgs =
+ eagle_helium_reionization_extraheat(cosmo->z, delta_redshift, cooling);
/* Convert this into a rate */
const double Lambda_He_reion_cgs =
Helium_reion_heat_cgs / (dt_cgs * ratefact_cgs);
/* Let's compute the internal energy at the end of the step */
- double u_final_cgs;
+ /* Initialise to the initial energy to appease compiler; this will never not
+ be overwritten. */
+ double u_final_cgs = u_0_cgs;
/* First try an explicit integration (note we ignore the derivative) */
const double LambdaNet_cgs =
@@ -719,8 +745,10 @@ float cooling_get_temperature(
const double u_cgs = u * cooling->internal_energy_to_cgs;
/* Get the Hydrogen and Helium mass fractions */
- const float XH = p->chemistry_data.metal_mass_fraction[chemistry_element_H];
- const float XHe = p->chemistry_data.metal_mass_fraction[chemistry_element_He];
+ const float XH =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_H];
+ const float XHe =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_He];
/* Get the Helium mass fraction. Note that this is He / (H + He), i.e. a
* metal-free Helium mass fraction as per the Wiersma+08 definition */
@@ -760,6 +788,41 @@ __attribute__((always_inline)) INLINE float cooling_get_radiated_energy(
return xp->cooling_data.radiated_energy;
}
+/**
+ * @brief Inject a fixed amount of energy to each particle in the simulation
+ * to mimic Hydrogen reionization.
+ *
+ * @param cooling The properties of the cooling model.
+ * @param cosmo The cosmological model.
+ * @param s The #space containing the particles.
+ */
+void cooling_Hydrogen_reionization(const struct cooling_function_data *cooling,
+ const struct cosmology *cosmo,
+ struct space *s) {
+
+ struct part *parts = s->parts;
+ struct xpart *xparts = s->xparts;
+
+ /* Energy to inject in internal units */
+ const float extra_heat =
+ cooling->H_reion_heat_cgs * cooling->internal_energy_from_cgs;
+
+ message("Applying extra energy for H reionization!");
+
+ /* Loop through particles and set new heat */
+ for (size_t i = 0; i < s->nr_parts; i++) {
+
+ struct part *p = &parts[i];
+ struct xpart *xp = &xparts[i];
+
+ const float old_u = hydro_get_physical_internal_energy(p, xp, cosmo);
+ const float new_u = old_u + extra_heat;
+
+ hydro_set_physical_internal_energy(p, xp, cosmo, new_u);
+ hydro_set_drifted_physical_internal_energy(p, cosmo, new_u);
+ }
+}
+
/**
* @brief Initialises properties stored in the cooling_function_data struct
*
@@ -774,10 +837,19 @@ void cooling_init_backend(struct swift_params *parameter_file,
struct cooling_function_data *cooling) {
/* read some parameters */
+
+ /* Despite the names, the values of H_reion_heat_cgs and He_reion_heat_cgs
+ * that are read in are actually in units of electron volts per proton mass.
+ * We later convert to units just below */
+
parser_get_param_string(parameter_file, "EAGLECooling:dir_name",
cooling->cooling_table_path);
+
+ cooling->H_reion_done = 0;
cooling->H_reion_z =
parser_get_param_float(parameter_file, "EAGLECooling:H_reion_z");
+ cooling->H_reion_heat_cgs =
+ parser_get_param_float(parameter_file, "EAGLECooling:H_reion_eV_p_H");
cooling->He_reion_z_centre =
parser_get_param_float(parameter_file, "EAGLECooling:He_reion_z_centre");
cooling->He_reion_z_sigma =
@@ -791,10 +863,19 @@ void cooling_init_backend(struct swift_params *parameter_file,
cooling->S_over_Si_ratio_in_solar = parser_get_opt_param_float(
parameter_file, "EAGLECooling:S_over_Si_in_solar", 1.f);
- /* Convert to cgs (units used internally by the cooling routines) */
+ /* Convert H_reion_heat_cgs and He_reion_heat_cgs to cgs
+ * (units used internally by the cooling routines). This is done by
+ * multiplying by 'eV/m_H' in internal units, then converting to cgs units.
+ * Note that the dimensions of these quantities are energy/mass = velocity^2
+ */
+
+ cooling->H_reion_heat_cgs *=
+ phys_const->const_electron_volt / phys_const->const_proton_mass *
+ units_cgs_conversion_factor(us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
+
cooling->He_reion_heat_cgs *=
- phys_const->const_electron_volt *
- units_cgs_conversion_factor(us, UNIT_CONV_ENERGY);
+ phys_const->const_electron_volt / phys_const->const_proton_mass *
+ units_cgs_conversion_factor(us, UNIT_CONV_ENERGY_PER_UNIT_MASS);
/* Read in the list of redshifts */
get_cooling_redshifts(cooling);
@@ -884,7 +965,7 @@ void cooling_restore_tables(struct cooling_function_data *cooling,
/* Force a re-read of the cooling tables */
cooling->z_index = -10;
cooling->previous_z_index = eagle_cooling_N_redshifts - 2;
- cooling_update(cosmo, cooling);
+ cooling_update(cosmo, cooling, /*space=*/NULL);
}
/**
diff --git a/src/cooling/EAGLE/cooling.h b/src/cooling/EAGLE/cooling.h
index d95c75e58aecfd8fb4816f1e50c7a3f379a08e51..eac3425d25f5f4c8fd0a5ed7656423379a3ad3f9 100644
--- a/src/cooling/EAGLE/cooling.h
+++ b/src/cooling/EAGLE/cooling.h
@@ -32,9 +32,10 @@ struct xpart;
struct cosmology;
struct hydro_props;
struct entropy_floor_properties;
+struct space;
void cooling_update(const struct cosmology *cosmo,
- struct cooling_function_data *cooling);
+ struct cooling_function_data *cooling, struct space *s);
void cooling_cool_part(const struct phys_const *phys_const,
const struct unit_system *us,
@@ -70,14 +71,15 @@ float cooling_get_temperature(
float cooling_get_radiated_energy(const struct xpart *restrict xp);
+void cooling_Hydrogen_reionization(const struct cooling_function_data *cooling,
+ const struct cosmology *cosmo,
+ struct space *s);
+
void cooling_init_backend(struct swift_params *parameter_file,
const struct unit_system *us,
const struct phys_const *phys_const,
struct cooling_function_data *cooling);
-void cooling_restore_tables(struct cooling_function_data *cooling,
- const struct cosmology *cosmo);
-
void cooling_print_backend(const struct cooling_function_data *cooling);
void cooling_clean(struct cooling_function_data *data);
diff --git a/src/cooling/EAGLE/cooling_rates.h b/src/cooling/EAGLE/cooling_rates.h
index d315a5ba339956828505c5f48165abdd2b2e0486..35a53b43fb26466686fa87704ec174a849667a78 100644
--- a/src/cooling/EAGLE/cooling_rates.h
+++ b/src/cooling/EAGLE/cooling_rates.h
@@ -54,39 +54,49 @@ __attribute__((always_inline)) INLINE void abundance_ratio_to_solar(
const struct part *p, const struct cooling_function_data *cooling,
float ratio_solar[chemistry_element_count + 2]) {
- ratio_solar[0] = p->chemistry_data.metal_mass_fraction[chemistry_element_H] *
- cooling->SolarAbundances_inv[0 /* H */];
+ ratio_solar[0] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_H] *
+ cooling->SolarAbundances_inv[0 /* H */];
- ratio_solar[1] = p->chemistry_data.metal_mass_fraction[chemistry_element_He] *
- cooling->SolarAbundances_inv[1 /* He */];
+ ratio_solar[1] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_He] *
+ cooling->SolarAbundances_inv[1 /* He */];
- ratio_solar[2] = p->chemistry_data.metal_mass_fraction[chemistry_element_C] *
- cooling->SolarAbundances_inv[2 /* C */];
+ ratio_solar[2] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_C] *
+ cooling->SolarAbundances_inv[2 /* C */];
- ratio_solar[3] = p->chemistry_data.metal_mass_fraction[chemistry_element_N] *
- cooling->SolarAbundances_inv[3 /* N */];
+ ratio_solar[3] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_N] *
+ cooling->SolarAbundances_inv[3 /* N */];
- ratio_solar[4] = p->chemistry_data.metal_mass_fraction[chemistry_element_O] *
- cooling->SolarAbundances_inv[4 /* O */];
+ ratio_solar[4] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_O] *
+ cooling->SolarAbundances_inv[4 /* O */];
- ratio_solar[5] = p->chemistry_data.metal_mass_fraction[chemistry_element_Ne] *
- cooling->SolarAbundances_inv[5 /* Ne */];
+ ratio_solar[5] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_Ne] *
+ cooling->SolarAbundances_inv[5 /* Ne */];
- ratio_solar[6] = p->chemistry_data.metal_mass_fraction[chemistry_element_Mg] *
- cooling->SolarAbundances_inv[6 /* Mg */];
+ ratio_solar[6] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_Mg] *
+ cooling->SolarAbundances_inv[6 /* Mg */];
- ratio_solar[7] = p->chemistry_data.metal_mass_fraction[chemistry_element_Si] *
- cooling->SolarAbundances_inv[7 /* Si */];
+ ratio_solar[7] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_Si] *
+ cooling->SolarAbundances_inv[7 /* Si */];
/* For S, we use the same ratio as Si */
- ratio_solar[8] = p->chemistry_data.metal_mass_fraction[chemistry_element_Si] *
- cooling->SolarAbundances_inv[7 /* Si */] *
- cooling->S_over_Si_ratio_in_solar;
+ ratio_solar[8] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_Si] *
+ cooling->SolarAbundances_inv[7 /* Si */] *
+ cooling->S_over_Si_ratio_in_solar;
/* For Ca, we use the same ratio as Si */
- ratio_solar[9] = p->chemistry_data.metal_mass_fraction[chemistry_element_Si] *
- cooling->SolarAbundances_inv[7 /* Si */] *
- cooling->Ca_over_Si_ratio_in_solar;
+ ratio_solar[9] =
+ p->chemistry_data.smoothed_metal_mass_fraction[chemistry_element_Si] *
+ cooling->SolarAbundances_inv[7 /* Si */] *
+ cooling->Ca_over_Si_ratio_in_solar;
ratio_solar[10] =
p->chemistry_data.metal_mass_fraction[chemistry_element_Fe] *
diff --git a/src/cooling/EAGLE/cooling_struct.h b/src/cooling/EAGLE/cooling_struct.h
index 0922bf74461c222bd6485bdc07cc35edc462ddba..88e49036f62962d35025f7fa81d5703a1245e3ce 100644
--- a/src/cooling/EAGLE/cooling_struct.h
+++ b/src/cooling/EAGLE/cooling_struct.h
@@ -74,9 +74,15 @@ struct cooling_function_data {
/*! Filepath to the directory containing the HDF5 cooling tables */
char cooling_table_path[eagle_table_path_name_length];
- /*! Redshit of H reionization */
+ /*! Redshift of H reionization */
float H_reion_z;
+ /*! H reionization energy in CGS units */
+ float H_reion_heat_cgs;
+
+ /*! Have we already done H reioisation? */
+ int H_reion_done;
+
/*! Ca over Si abundance divided by the solar ratio for these elements */
float Ca_over_Si_ratio_in_solar;
diff --git a/src/cooling/const_du/cooling.h b/src/cooling/const_du/cooling.h
index 15eecc43093e9cc571d166aa49392e7dfea60c11..c57ef4a6874e0314bcea672cd514d1419b1acdd8 100644
--- a/src/cooling/const_du/cooling.h
+++ b/src/cooling/const_du/cooling.h
@@ -54,9 +54,11 @@
*
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The #space containing all the particles.
*/
INLINE static void cooling_update(const struct cosmology* cosmo,
- struct cooling_function_data* cooling) {
+ struct cooling_function_data* cooling,
+ struct space* s) {
// Add content if required.
}
diff --git a/src/cooling/const_lambda/cooling.h b/src/cooling/const_lambda/cooling.h
index 974b055b1f8942f53b72e6ccf17389d8f85b666e..1e50c162d02e8c326f67978a7de73fda5c6aecd8 100644
--- a/src/cooling/const_lambda/cooling.h
+++ b/src/cooling/const_lambda/cooling.h
@@ -51,9 +51,11 @@
*
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The #space containing all the particles.
*/
INLINE static void cooling_update(const struct cosmology* cosmo,
- struct cooling_function_data* cooling) {
+ struct cooling_function_data* cooling,
+ struct space* s) {
// Add content if required.
}
diff --git a/src/cooling/grackle/cooling.h b/src/cooling/grackle/cooling.h
index 2632de7e223306a6c6400e350f8cb62a62e58206..edf8f0ca50cc498b8d1b235196addb5a694a0b80 100644
--- a/src/cooling/grackle/cooling.h
+++ b/src/cooling/grackle/cooling.h
@@ -66,9 +66,11 @@ static gr_float cooling_new_energy(
*
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The #space containing all the particles.
*/
INLINE static void cooling_update(const struct cosmology* cosmo,
- struct cooling_function_data* cooling) {
+ struct cooling_function_data* cooling,
+ struct space* s) {
/* set current time */
if (cooling->redshift == -1)
cooling->units.a_value = cosmo->a;
diff --git a/src/cooling/none/cooling.h b/src/cooling/none/cooling.h
index 3f90d357ad863da0525859f06e85a4cc492d3ae2..20aef187d912db379bb1c51ad9e8a4f16e47778c 100644
--- a/src/cooling/none/cooling.h
+++ b/src/cooling/none/cooling.h
@@ -41,13 +41,13 @@
* @brief Common operations performed on the cooling function at a
* given time-step or redshift.
*
- * @param phys_const The physical constants in internal units.
- * @param us The internal system of units.
* @param cosmo The current cosmological model.
* @param cooling The #cooling_function_data used in the run.
+ * @param s The #space containing all the particles.
*/
INLINE static void cooling_update(const struct cosmology* cosmo,
- struct cooling_function_data* cooling) {
+ struct cooling_function_data* cooling,
+ struct space* s) {
// Add content if required.
}
diff --git a/src/cosmology.c b/src/cosmology.c
index be23343d0d62584cd3a811e547b327120db744ef..a18f52b84da330238caaa0a16bb69de025e92046 100644
--- a/src/cosmology.c
+++ b/src/cosmology.c
@@ -140,6 +140,10 @@ double cosmology_get_time_since_big_bang(const struct cosmology *c, double a) {
void cosmology_update(struct cosmology *c, const struct phys_const *phys_const,
integertime_t ti_current) {
+ /* Save the previous state */
+ c->z_old = c->z;
+ c->a_old = c->a;
+
/* Get scale factor and powers of it */
const double a = c->a_begin * exp(ti_current * c->time_base);
const double a_inv = 1. / a;
@@ -527,6 +531,10 @@ void cosmology_init(struct swift_params *params, const struct unit_system *us,
/* Update the times */
c->time_begin = cosmology_get_time_since_big_bang(c, c->a_begin);
c->time_end = cosmology_get_time_since_big_bang(c, c->a_end);
+
+ /* Initialise the old values to a valid state */
+ c->a_old = c->a_begin;
+ c->z_old = 1. / c->a_old - 1.;
}
/**
@@ -568,6 +576,9 @@ void cosmology_init_no_cosmo(struct cosmology *c) {
c->a_factor_hydro_accel = 1.;
c->a_factor_grav_accel = 1.;
+ c->a_old = 1.;
+ c->z_old = 0.;
+
c->critical_density = 0.;
c->critical_density_0 = 0.;
diff --git a/src/cosmology.h b/src/cosmology.h
index d6b7dfbdc854a66f89c5511a5076c4fb4a7a5d3f..f2abdb6c62e7509c593b5edfbdb9dd8fe0c99e72 100644
--- a/src/cosmology.h
+++ b/src/cosmology.h
@@ -93,6 +93,12 @@ struct cosmology {
/*! Dark-energy equation of state at the current time */
double w;
+ /*! Scale-factor at the previous time-step */
+ double a_old;
+
+ /*! Redshit at the previous time-step */
+ double z_old;
+
/*------------------------------------------------------------------ */
/*! Starting expansion factor */
diff --git a/src/engine.c b/src/engine.c
index 17b4c50dae2b54cb749238bc100f216b975ff16e..38614c3ca2fb69142e7e5bd2f769e37326fc13a2 100644
--- a/src/engine.c
+++ b/src/engine.c
@@ -2878,7 +2878,7 @@ void engine_init_particles(struct engine *e, int flag_entropy_ICs,
/* Update the cooling function */
if ((e->policy & engine_policy_cooling) ||
(e->policy & engine_policy_temperature))
- cooling_update(e->cosmology, e->cooling_func);
+ cooling_update(e->cosmology, e->cooling_func, e->s);
#ifdef WITH_LOGGER
/* Mark the first time step in the particle logger file. */
@@ -2948,6 +2948,7 @@ void engine_init_particles(struct engine *e, int flag_entropy_ICs,
#endif
scheduler_write_dependencies(&e->sched, e->verbose);
+ space_write_cell_hierarchy(e->s);
if (e->nodeID == 0) scheduler_write_task_level(&e->sched);
/* Run the 0th time-step */
@@ -3143,7 +3144,7 @@ void engine_step(struct engine *e) {
/* Update the cooling function */
if ((e->policy & engine_policy_cooling) ||
(e->policy & engine_policy_temperature))
- cooling_update(e->cosmology, e->cooling_func);
+ cooling_update(e->cosmology, e->cooling_func, e->s);
/*****************************************************/
/* OK, we now know what the next end of time-step is */
@@ -4040,7 +4041,7 @@ void engine_collect_stars_counter(struct engine *e) {
}
free(n_sparts);
- free(n_sparts_in);
+ free(n_sparts_int);
swift_free("sparts", sparts);
#endif
}
diff --git a/src/engine_marktasks.c b/src/engine_marktasks.c
index c02eb5d2bd272111808701269faed07cef505449..9b34b3ea95a9ae8bc848a90113647b3e68b121b1 100644
--- a/src/engine_marktasks.c
+++ b/src/engine_marktasks.c
@@ -642,13 +642,17 @@ void engine_marktasks_mapper(void *map_data, int num_elements,
scheduler_activate(s, t);
}
- /* Subgrid tasks */
+ /* Subgrid tasks: cooling */
else if (t_type == task_type_cooling) {
- if (cell_is_active_hydro(t->ci, e) || cell_is_active_gravity(t->ci, e))
- scheduler_activate(s, t);
- } else if (t_type == task_type_star_formation) {
- if (cell_is_active_hydro(t->ci, e) || cell_is_active_gravity(t->ci, e))
+ if (cell_is_active_hydro(t->ci, e)) scheduler_activate(s, t);
+ }
+
+ /* Subgrid tasks: star formation */
+ else if (t_type == task_type_star_formation) {
+ if (cell_is_active_hydro(t->ci, e)) {
scheduler_activate(s, t);
+ cell_activate_drift_spart(t->ci, s);
+ }
}
}
}
diff --git a/src/entropy_floor/EAGLE/entropy_floor.h b/src/entropy_floor/EAGLE/entropy_floor.h
index 41d35fa0484cc1ee491a3c6293893ad5d2b5583f..5a53b3b39c9df3aa624b3fd93e82bed9d221204c 100644
--- a/src/entropy_floor/EAGLE/entropy_floor.h
+++ b/src/entropy_floor/EAGLE/entropy_floor.h
@@ -98,48 +98,117 @@ static INLINE float entropy_floor(
const struct part *p, const struct cosmology *cosmo,
const struct entropy_floor_properties *props) {
+ /* Comoving density in internal units */
+ const float rho_com = hydro_get_comoving_density(p);
+
/* Physical density in internal units */
- const float rho = hydro_get_physical_density(p, cosmo);
+ const float rho_phys = hydro_get_physical_density(p, cosmo);
- /* Critical density at this redshift.
- * Recall that this is 0 in a non-cosmological run */
- const float rho_crit = cosmo->critical_density;
- const float rho_crit_baryon = cosmo->Omega_b * rho_crit;
+ /* Mean baryon density in co-moving internal units for over-density condition
+ * (Recall cosmo->critical_density_0 is 0 in a non-cosmological run,
+ * making the over-density condition a no-op) */
+ const float rho_crit_0 = cosmo->critical_density_0;
+ const float rho_crit_baryon = cosmo->Omega_b * rho_crit_0;
/* Physical pressure */
float pressure = 0.f;
/* Are we in the regime of the Jeans equation of state? */
- if ((rho >= rho_crit_baryon * props->Jeans_over_density_threshold) &&
- (rho >= props->Jeans_density_threshold)) {
+ if ((rho_com >= rho_crit_baryon * props->Jeans_over_density_threshold) &&
+ (rho_phys >= props->Jeans_density_threshold)) {
- const float pressure_Jeans = props->Jeans_pressure_norm *
- powf(rho * props->Jeans_density_threshold_inv,
- props->Jeans_gamma_effective);
+ const float pressure_Jeans =
+ props->Jeans_pressure_norm *
+ powf(rho_phys * props->Jeans_density_threshold_inv,
+ props->Jeans_gamma_effective);
pressure = max(pressure, pressure_Jeans);
}
/* Are we in the regime of the Cool equation of state? */
- if ((rho >= rho_crit_baryon * props->Cool_over_density_threshold) &&
- (rho >= props->Cool_density_threshold)) {
+ if ((rho_com >= rho_crit_baryon * props->Cool_over_density_threshold) &&
+ (rho_phys >= props->Cool_density_threshold)) {
- const float pressure_Cool = props->Cool_pressure_norm *
- powf(rho * props->Cool_density_threshold_inv,
- props->Cool_gamma_effective);
+ const float pressure_Cool =
+ props->Cool_pressure_norm *
+ powf(rho_phys * props->Cool_density_threshold_inv,
+ props->Cool_gamma_effective);
pressure = max(pressure, pressure_Cool);
}
/* Convert to an entropy.
* (Recall that the entropy is the same in co-moving and phycial frames) */
- return gas_entropy_from_pressure(rho, pressure);
+ return gas_entropy_from_pressure(rho_phys, pressure);
+}
+
+/**
+ * @brief Compute the temperature from the entropy floor for a given #part
+ *
+ * Calculate the EoS temperature, the particle is not updated.
+ * This is the temperature exactly corresponding to the imposed EoS shape.
+ * It only matches the entropy returned by the entropy_floor() function
+ * for a neutral gas with primoridal abundance.
+ *
+ * @param p The #part.
+ * @param cosmo The cosmological model.
+ * @param props The properties of the entropy floor.
+ */
+static INLINE float entropy_floor_temperature(
+ const struct part *p, const struct cosmology *cosmo,
+ const struct entropy_floor_properties *props) {
+
+ /* Comoving density in internal units */
+ const float rho_com = hydro_get_comoving_density(p);
+
+ /* Physical density in internal units */
+ const float rho_phys = hydro_get_physical_density(p, cosmo);
+
+ /* Mean baryon density in co-moving internal units for over-density condition
+ * (Recall cosmo->critical_density_0 is 0 in a non-cosmological run,
+ * making the over-density condition a no-op) */
+ const float rho_crit_0 = cosmo->critical_density_0;
+ const float rho_crit_baryon = cosmo->Omega_b * rho_crit_0;
+
+ /* Physical */
+ float temperature = 0.f;
+
+ /* Are we in the regime of the Jeans equation of state? */
+ if ((rho_com >= rho_crit_baryon * props->Jeans_over_density_threshold) &&
+ (rho_phys >= props->Jeans_density_threshold)) {
+
+ const float jeans_slope = props->Jeans_gamma_effective - 1.f;
+
+ const float temperature_Jeans =
+ props->Jeans_temperature_norm *
+ pow(rho_phys * props->Jeans_density_threshold_inv, jeans_slope);
+
+ temperature = max(temperature, temperature_Jeans);
+ }
+
+ /* Are we in the regime of the Cool equation of state? */
+ if ((rho_com >= rho_crit_baryon * props->Cool_over_density_threshold) &&
+ (rho_phys >= props->Cool_density_threshold)) {
+
+ const float cool_slope = props->Cool_gamma_effective - 1.f;
+
+ const float temperature_Cool =
+ props->Cool_temperature_norm *
+ pow(rho_phys * props->Cool_density_threshold_inv, cool_slope);
+
+ temperature = max(temperature, temperature_Cool);
+ }
+
+ return temperature;
}
/**
* @brief Initialise the entropy floor by reading the parameters and converting
* to internal units.
*
+ * The input temperatures and number densities are converted to entropy and
+ * density assuming a neutral gas of primoridal abundance.
+ *
* @param params The YAML parameter file.
* @param us The system of units used internally.
* @param phys_const The physical constants.
diff --git a/src/entropy_floor/none/entropy_floor.h b/src/entropy_floor/none/entropy_floor.h
index 871ef8977e091841128e280184646e3be02957fd..6ce5319c8c76cf8f9e6dc1716f383452d7cce7d6 100644
--- a/src/entropy_floor/none/entropy_floor.h
+++ b/src/entropy_floor/none/entropy_floor.h
@@ -52,6 +52,21 @@ static INLINE float entropy_floor(
return 0.f;
}
+/**
+ * @brief Compute the temperature from the entropy floor for a given #part
+ *
+ * Simply return 0 (no floor).
+ *
+ * @param p The #part.
+ * @param cosmo The cosmological model.
+ * @param props The properties of the entropy floor.
+ */
+static INLINE float entropy_floor_temperature(
+ const struct part *p, const struct cosmology *cosmo,
+ const struct entropy_floor_properties *props) {
+ return 0.f;
+}
+
/**
* @brief Initialise the entropy floor by reading the parameters and converting
* to internal units.
diff --git a/src/exp10.h b/src/exp10.h
index b995bfdb3e1b6b1cb60bd4b60708413ea6c96f9f..fbae34af421c9d0bcc773fbfc50ac44df1e8fd42 100644
--- a/src/exp10.h
+++ b/src/exp10.h
@@ -25,11 +25,11 @@
/* Some standard headers. */
#include <math.h>
-#ifndef __GNUC__
-
/* Local headers. */
#include "inline.h"
+#if !defined(HAVE_EXP10) && !defined(HAVE___EXP10)
+
/**
* @brief Raises 10 to the power of the argument.
*
@@ -44,6 +44,10 @@ __attribute__((always_inline, const)) INLINE static double exp10(
return exp(x * M_LN10);
}
+#endif
+
+#if !defined(HAVE_EXP10F) && !defined(HAVE___EXP10F)
+
/**
* @brief Raises 10 to the power of the argument.
*
@@ -58,6 +62,15 @@ __attribute__((always_inline, const)) INLINE static float exp10f(
return expf(x * (float)M_LN10);
}
-#endif /* __GNUC__ */
+#endif
+
+/* Use the __exp10 and __exp10f versions if needed. */
+#if !defined(HAVE_EXP10) && defined(HAVE___EXP10)
+#define exp10(x) __exp10(x)
+#endif
+
+#if !defined(HAVE_EXP10F) && defined(HAVE___EXP10F)
+#define exp10f(x) __exp10f(x)
+#endif
#endif /* SWIFT_EXP10_H */
diff --git a/src/hydro/AnarchyPU/hydro.h b/src/hydro/AnarchyPU/hydro.h
index 9bb53f290acb16b4f9efc44e430a78a6d1f5c5ff..37d182889b703df9ea6d98b63a6daa5dc85274a8 100644
--- a/src/hydro/AnarchyPU/hydro.h
+++ b/src/hydro/AnarchyPU/hydro.h
@@ -379,6 +379,45 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
xp->u_full = gas_internal_energy_from_entropy(p->rho, comoving_entropy);
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
@@ -693,11 +732,18 @@ __attribute__((always_inline)) INLINE static void hydro_prepare_force(
const float sqrt_u = sqrtf(p->u);
/* Calculate initial value of alpha dt before bounding */
/* alpha_diff_dt is cosmology-less */
+ /* Evolution term: following Schaller+ 2015 */
float alpha_diff_dt =
hydro_props->diffusion.beta * p->h * p->diffusion.laplace_u / sqrt_u;
+ /* Decay term: not documented in Schaller+ 2015 but was present
+ * in the original EAGLE code and in Schaye+ 2015 */
+ alpha_diff_dt -=
+ (p->diffusion.alpha - hydro_props->diffusion.alpha_min) / tau;
- float new_diffusion_alpha = p->diffusion.alpha + alpha_diff_dt * dt_alpha;
+ float new_diffusion_alpha = p->diffusion.alpha;
+ new_diffusion_alpha += alpha_diff_dt * dt_alpha;
+ /* Consistency checks to ensure min < alpha < max */
if (new_diffusion_alpha > hydro_props->diffusion.alpha_max) {
new_diffusion_alpha = hydro_props->diffusion.alpha_max;
} else if (new_diffusion_alpha < hydro_props->diffusion.alpha_min) {
diff --git a/src/hydro/Default/hydro.h b/src/hydro/Default/hydro.h
index 2b1d19bc916889a5cfdc40b1357f1e3dfe9388af..175265dd4707be19e995e2ca6912629876ca2ca2 100644
--- a/src/hydro/Default/hydro.h
+++ b/src/hydro/Default/hydro.h
@@ -318,6 +318,62 @@ hydro_set_physical_internal_energy_dt(struct part *restrict p,
p->force.u_dt = du_dt * cosmo->a_factor_internal_energy;
}
+/**
+ * @brief Sets the physical entropy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param entropy The physical entropy
+ */
+__attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
+ struct part *p, struct xpart *xp, const struct cosmology *cosmo,
+ const float entropy) {
+
+ /* Note there is no conversion from physical to comoving entropy */
+ const float comoving_entropy = entropy;
+ xp->u_full = gas_internal_energy_from_entropy(p->rho, comoving_entropy);
+}
+
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
diff --git a/src/hydro/Default/hydro_part.h b/src/hydro/Default/hydro_part.h
index 21c0269f78c85b7d11ab5e838d45614161aee013..2ff41da0a7825d2ddba276c3d20a9d2d4aad3224 100644
--- a/src/hydro/Default/hydro_part.h
+++ b/src/hydro/Default/hydro_part.h
@@ -21,6 +21,7 @@
#include "chemistry_struct.h"
#include "cooling_struct.h"
+#include "star_formation_struct.h"
#include "tracers_struct.h"
/* Extra particle data not needed during the SPH loops over neighbours. */
@@ -44,6 +45,9 @@ struct xpart {
/* Additional data used by the tracers */
struct tracers_xpart_data tracers_data;
+ /* Additional data used by the star formation */
+ struct star_formation_xpart_data sf_data;
+
float u_full;
/* Old density. */
diff --git a/src/hydro/Gadget2/hydro.h b/src/hydro/Gadget2/hydro.h
index 9994be7dc6051b033c052d32a4ebf3d7b59f1a84..bcef2480810c807d61a6545f04fca6144f90e8fe 100644
--- a/src/hydro/Gadget2/hydro.h
+++ b/src/hydro/Gadget2/hydro.h
@@ -331,6 +331,7 @@ hydro_set_physical_internal_energy_dt(struct part *restrict p,
p->entropy_dt =
gas_entropy_from_internal_energy(p->rho * cosmo->a3_inv, du_dt);
}
+
/**
* @brief Sets the physical entropy of a particle
*
@@ -347,6 +348,56 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
xp->entropy_full = entropy;
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->entropy_full =
+ gas_entropy_from_internal_energy(p->rho * cosmo->a3_inv, u);
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->entropy = gas_entropy_from_internal_energy(p->rho * cosmo->a3_inv, u);
+
+ /* Now recompute the extra quantities */
+
+ /* Inverse of the co-moving density */
+ const float rho_inv = 1.f / p->rho;
+
+ /* Compute the pressure */
+ const float pressure = gas_pressure_from_entropy(p->rho, p->entropy);
+
+ /* Compute the sound speed */
+ const float soundspeed = gas_soundspeed_from_pressure(p->rho, pressure);
+
+ /* Divide the pressure by the density squared to get the SPH term */
+ const float P_over_rho2 = pressure * rho_inv * rho_inv;
+
+ /* Update variables. */
+ p->force.P_over_rho2 = P_over_rho2;
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
diff --git a/src/hydro/GizmoMFM/hydro.h b/src/hydro/GizmoMFM/hydro.h
index a4a54e7b551cc643bffedb8661f4fe269d348dc4..3456e6f9e0a4c1715951030a8b0a10c081d746bf 100644
--- a/src/hydro/GizmoMFM/hydro.h
+++ b/src/hydro/GizmoMFM/hydro.h
@@ -987,6 +987,35 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
error("Needs implementing");
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part* p, struct xpart* xp,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part* p,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
/**
* @brief Returns the comoving density of a particle
*
diff --git a/src/hydro/GizmoMFV/hydro.h b/src/hydro/GizmoMFV/hydro.h
index 974f57ed68bbc409697111c52c40f36d4a5cb9b1..526d84289554f7e2f4cd183bbf82484f0804be28 100644
--- a/src/hydro/GizmoMFV/hydro.h
+++ b/src/hydro/GizmoMFV/hydro.h
@@ -1061,6 +1061,35 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
error("Needs implementing");
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part* p, struct xpart* xp,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part* p,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
/**
* @brief Returns the comoving density of a particle
*
diff --git a/src/hydro/Minimal/hydro.h b/src/hydro/Minimal/hydro.h
index a5808468300da234a91a86feb897a9398e14db90..1d5d25f734acae72490ae42552abf65983463c07 100644
--- a/src/hydro/Minimal/hydro.h
+++ b/src/hydro/Minimal/hydro.h
@@ -354,6 +354,45 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
xp->u_full = gas_internal_energy_from_entropy(p->rho, comoving_entropy);
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
diff --git a/src/hydro/Planetary/hydro.h b/src/hydro/Planetary/hydro.h
index fbe0b6c8b9a8844cab3e38e485923fc7543ec528..e03b307bca754eb3a809613b20ebf3b1aae67a9f 100644
--- a/src/hydro/Planetary/hydro.h
+++ b/src/hydro/Planetary/hydro.h
@@ -378,6 +378,45 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
gas_internal_energy_from_entropy(p->rho, comoving_entropy, p->mat_id);
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
diff --git a/src/hydro/PressureEnergy/hydro.h b/src/hydro/PressureEnergy/hydro.h
index 4af00f7a657d61871dc0a82affb04d411e13e047..0e53b5f2ea12462fb1a618cda44934d113f655dd 100644
--- a/src/hydro/PressureEnergy/hydro.h
+++ b/src/hydro/PressureEnergy/hydro.h
@@ -379,6 +379,45 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
xp->u_full = gas_internal_energy_from_entropy(p->rho, comoving_entropy);
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
@@ -820,4 +859,22 @@ hydro_set_init_internal_energy(struct part *p, float u_init) {
__attribute__((always_inline)) INLINE static void hydro_remove_part(
const struct part *p, const struct xpart *xp) {}
+/**
+ * @brief Inputs extra heat to a particle at redshift of reionization
+ *
+ * We assume a constant density.
+ * @param p The particle of interest
+ * @param xp The extended particle data
+ * @param cosmo Cosmology data structure
+ * @param extra_heat The extra internal energy given to the particle.
+ */
+__attribute__((always_inline)) INLINE static void hydro_reion_heating(
+ struct part *p, struct xpart *xp, const struct cosmology *cosmo,
+ float extra_heat) {
+
+ const float old_u = xp->u_full * cosmo->a_factor_internal_energy;
+ const float new_u = old_u + extra_heat;
+ xp->u_full = new_u / cosmo->a_factor_internal_energy;
+}
+
#endif /* SWIFT_PRESSURE_ENERGY_HYDRO_H */
diff --git a/src/hydro/PressureEnergyMorrisMonaghanAV/hydro.h b/src/hydro/PressureEnergyMorrisMonaghanAV/hydro.h
index b50ca4e2543af94573ff34954c26a23200b78a1d..9f981569e80021774cebaf11066ebdac2afc6f94 100644
--- a/src/hydro/PressureEnergyMorrisMonaghanAV/hydro.h
+++ b/src/hydro/PressureEnergyMorrisMonaghanAV/hydro.h
@@ -376,6 +376,45 @@ __attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
xp->u_full = gas_internal_energy_from_entropy(p->rho, comoving_entropy);
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ xp->u_full = u / cosmo->a_factor_internal_energy;
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+
+ p->u = u / cosmo->a_factor_internal_energy;
+
+ /* Now recompute the extra quantities */
+
+ /* Compute the sound speed */
+ const float soundspeed = hydro_get_comoving_soundspeed(p);
+
+ /* Update variables. */
+ p->force.soundspeed = soundspeed;
+}
+
/**
* @brief Computes the hydro time-step of a given particle
*
diff --git a/src/hydro/PressureEntropy/hydro.h b/src/hydro/PressureEntropy/hydro.h
index 40b3f42eaed7cbff3c6503caa0fc8801d65ac8e3..578bebf635149fe29299800c2a4854c0158d3de9 100644
--- a/src/hydro/PressureEntropy/hydro.h
+++ b/src/hydro/PressureEntropy/hydro.h
@@ -150,6 +150,36 @@ __attribute__((always_inline)) INLINE static float hydro_get_physical_entropy(
return xp->entropy_full;
}
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical entropy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part *p, struct xpart *xp,
+ const struct cosmology *cosmo,
+ const float u) {
+ error("To be implemented");
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical entropy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part *p,
+ const struct cosmology *cosmo,
+ const float u) {
+ error("To be implemented");
+}
+
/**
* @brief Returns the comoving entropy of a particle drifted to the
* current time.
diff --git a/src/hydro/Shadowswift/hydro.h b/src/hydro/Shadowswift/hydro.h
index b0f3207dfce69ca79899b1134740d035d47251d1..9ac89fa02a3663e521f54b4df0f15884b041fad6 100644
--- a/src/hydro/Shadowswift/hydro.h
+++ b/src/hydro/Shadowswift/hydro.h
@@ -826,6 +826,50 @@ hydro_get_physical_soundspeed(const struct part* restrict p,
return cosmo->a_factor_sound_speed * hydro_get_comoving_soundspeed(p);
}
+/**
+ * @brief Sets the physical entropy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param entropy The physical entropy
+ */
+__attribute__((always_inline)) INLINE static void hydro_set_physical_entropy(
+ struct part* p, struct xpart* xp, const struct cosmology* cosmo,
+ const float entropy) {
+
+ error("Needs implementing");
+}
+
+/**
+ * @brief Sets the physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param xp The extended particle data.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_physical_internal_energy(struct part* p, struct xpart* xp,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
+/**
+ * @brief Sets the drifted physical internal energy of a particle
+ *
+ * @param p The particle of interest.
+ * @param cosmo Cosmology data structure
+ * @param u The physical internal energy
+ */
+__attribute__((always_inline)) INLINE static void
+hydro_set_drifted_physical_internal_energy(struct part* p,
+ const struct cosmology* cosmo,
+ const float u) {
+ error("Need implementing");
+}
+
/**
* @brief Returns the comoving pressure of a particle
*
diff --git a/src/hydro_properties.c b/src/hydro_properties.c
index f14c88bfb5128c1da17590f50698e5d038734b71..ff578aec139ad06cb80279d8d827a41975f9773f 100644
--- a/src/hydro_properties.c
+++ b/src/hydro_properties.c
@@ -317,6 +317,12 @@ void hydro_props_print_snapshot(hid_t h_grpsph, const struct hydro_props *p) {
io_write_attribute_f(h_grpsph, "Beta viscosity", const_viscosity_beta);
io_write_attribute_f(h_grpsph, "Max v_sig ratio (limiter)",
const_limiter_max_v_sig_ratio);
+ io_write_attribute_f(h_grpsph, "Diffusion alpha", p->diffusion.alpha);
+ io_write_attribute_f(h_grpsph, "Diffusion alpha (max)",
+ p->diffusion.alpha_max);
+ io_write_attribute_f(h_grpsph, "Diffusion alpha (min)",
+ p->diffusion.alpha_min);
+ io_write_attribute_f(h_grpsph, "Diffusion beta", p->diffusion.beta);
}
#endif
diff --git a/src/runner.c b/src/runner.c
index 4cac34538858da3882f1ac6a6c70d45d9842a022..75a181fa01fd8defbdc861f266fc892bd7bb60d9 100644
--- a/src/runner.c
+++ b/src/runner.c
@@ -75,6 +75,7 @@
#define TASK_LOOP_GRADIENT 1
#define TASK_LOOP_FORCE 2
#define TASK_LOOP_LIMITER 3
+#define TASK_LOOP_FEEDBACK 4
/* Import the density loop functions. */
#define FUNCTION density
@@ -111,14 +112,16 @@
/* Import the stars density loop functions. */
#define FUNCTION density
-#define UPDATE_STARS 1
+#define FUNCTION_TASK_LOOP TASK_LOOP_DENSITY
#include "runner_doiact_stars.h"
-#undef UPDATE_STARS
+#undef FUNCTION_TASK_LOOP
#undef FUNCTION
/* Import the stars feedback loop functions. */
#define FUNCTION feedback
+#define FUNCTION_TASK_LOOP TASK_LOOP_FEEDBACK
#include "runner_doiact_stars.h"
+#undef FUNCTION_TASK_LOOP
#undef FUNCTION
/**
@@ -578,6 +581,7 @@ void runner_do_star_formation(struct runner *r, struct cell *c, int timer) {
const struct hydro_props *restrict hydro_props = e->hydro_properties;
const struct unit_system *restrict us = e->internal_units;
struct cooling_function_data *restrict cooling = e->cooling_func;
+ const struct entropy_floor_properties *entropy_floor = e->entropy_floor;
const double time_base = e->time_base;
const integertime_t ti_current = e->ti_current;
const int current_stars_count = c->stars.count;
@@ -605,7 +609,8 @@ void runner_do_star_formation(struct runner *r, struct cell *c, int timer) {
/* Is this particle star forming? */
if (star_formation_is_star_forming(p, xp, sf_props, phys_const, cosmo,
- hydro_props, us, cooling)) {
+ hydro_props, us, cooling,
+ entropy_floor)) {
/* Time-step size for this particle */
double dt_star;
@@ -1446,9 +1451,9 @@ void runner_do_ghost(struct runner *r, struct cell *c, int timer) {
((p->h <= hydro_h_min) && (f > 0.f))) {
/* We have a particle whose smoothing length is already set (wants
- * to be larger but has already hit the maximum OR wants to be smaller
- * but has already reached the minimum). So, just tidy up as if the
- * smoothing length had converged correctly */
+ * to be larger but has already hit the maximum OR wants to be
+ * smaller but has already reached the minimum). So, just tidy up as
+ * if the smoothing length had converged correctly */
#ifdef EXTRA_HYDRO_LOOP
diff --git a/src/runner_doiact_stars.h b/src/runner_doiact_stars.h
index f208f14ac98a31a55df6741a2cc5f9cb0a829762..e56d3b9460381e8408f370cae33e64fb93ecd541 100644
--- a/src/runner_doiact_stars.h
+++ b/src/runner_doiact_stars.h
@@ -28,15 +28,23 @@
#define _DOSELF1_STARS(f) PASTE(runner_doself_stars, f)
#define DOSELF1_STARS _DOSELF1_STARS(FUNCTION)
-#define _DO_NONSYM_PAIR1_STARS(f) PASTE(runner_do_nonsym_pair_stars, f)
-#define DO_NONSYM_PAIR1_STARS _DO_NONSYM_PAIR1_STARS(FUNCTION)
+#define _DO_SYM_PAIR1_STARS(f) PASTE(runner_do_sym_pair_stars, f)
+#define DO_SYM_PAIR1_STARS _DO_SYM_PAIR1_STARS(FUNCTION)
-#define _DOPAIR1_STARS(f) PASTE(runner_dopair_stars, f)
-#define DOPAIR1_STARS _DOPAIR1_STARS(FUNCTION)
+#define _DO_NONSYM_PAIR1_STARS_NAIVE(f) \
+ PASTE(runner_do_nonsym_pair_stars_naive, f)
+#define DO_NONSYM_PAIR1_STARS_NAIVE _DO_NONSYM_PAIR1_STARS_NAIVE(FUNCTION)
+
+#define _DOPAIR1_STARS_NAIVE(f) PASTE(runner_dopair_stars_naive, f)
+#define DOPAIR1_STARS_NAIVE _DOPAIR1_STARS_NAIVE(FUNCTION)
#define _DOPAIR1_SUBSET_STARS(f) PASTE(runner_dopair_subset_stars, f)
#define DOPAIR1_SUBSET_STARS _DOPAIR1_SUBSET_STARS(FUNCTION)
+#define _DOPAIR1_SUBSET_STARS_NAIVE(f) \
+ PASTE(runner_dopair_subset_stars_naive, f)
+#define DOPAIR1_SUBSET_STARS_NAIVE _DOPAIR1_SUBSET_STARS_NAIVE(FUNCTION)
+
#define _DOSELF1_SUBSET_STARS(f) PASTE(runner_doself_subset_stars, f)
#define DOSELF1_SUBSET_STARS _DOSELF1_SUBSET_STARS(FUNCTION)
@@ -83,8 +91,8 @@ void DOSELF1_STARS(struct runner *r, struct cell *c, int timer) {
const struct cosmology *cosmo = e->cosmology;
/* Anything to do here? */
+ if (c->hydro.count == 0 || c->stars.count == 0) return;
if (!cell_is_active_stars(c, e)) return;
- if (c->hydro.count == 0 && c->stars.count == 0) return;
/* Cosmological terms */
const float a = cosmo->a;
@@ -100,7 +108,7 @@ void DOSELF1_STARS(struct runner *r, struct cell *c, int timer) {
/* Get a hold of the ith spart in ci. */
struct spart *restrict si = &sparts[sid];
- if (!spart_is_active(si, e) || spart_is_inhibited(si, e)) continue;
+ if (!spart_is_active(si, e)) continue;
const float hi = si->h;
const float hig2 = hi * hi * kernel_gamma2;
@@ -113,7 +121,9 @@ void DOSELF1_STARS(struct runner *r, struct cell *c, int timer) {
/* Get a pointer to the jth particle. */
struct part *restrict pj = &parts[pjd];
- const float hj = pj->h;
+
+ /* Early abort? */
+ if (part_is_inhibited(pj, e)) continue;
/* Compute the pairwise distance. */
const float pjx[3] = {(float)(pj->x[0] - c->loc[0]),
@@ -128,8 +138,8 @@ void DOSELF1_STARS(struct runner *r, struct cell *c, int timer) {
error("Particle pj not drifted to current time");
#endif
- if (r2 > 0.f && r2 < hig2) {
- IACT_STARS(r2, dx, hi, hj, si, pj, a, H);
+ if (r2 < hig2) {
+ IACT_STARS(r2, dx, hi, pj->h, si, pj, a, H);
}
} /* loop over the parts in ci. */
} /* loop over the sparts in ci. */
@@ -142,11 +152,11 @@ void DOSELF1_STARS(struct runner *r, struct cell *c, int timer) {
* @param ci The first #cell
* @param cj The second #cell
*/
-void DO_NONSYM_PAIR1_STARS(struct runner *r, struct cell *restrict ci,
- struct cell *restrict cj) {
+void DO_NONSYM_PAIR1_STARS_NAIVE(struct runner *r, struct cell *restrict ci,
+ struct cell *restrict cj) {
#ifdef SWIFT_DEBUG_CHECKS
-#ifdef UPDATE_STARS
+#if (FUNCTION_TASK_LOOP == TASK_LOOP_DENSITY)
if (ci->nodeID != engine_rank) error("Should be run on a different node");
#else
if (cj->nodeID != engine_rank) error("Should be run on a different node");
@@ -157,6 +167,7 @@ void DO_NONSYM_PAIR1_STARS(struct runner *r, struct cell *restrict ci,
const struct cosmology *cosmo = e->cosmology;
/* Anything to do here? */
+ if (cj->hydro.count == 0 || ci->stars.count == 0) return;
if (!cell_is_active_stars(ci, e)) return;
const int scount_i = ci->stars.count;
@@ -182,7 +193,8 @@ void DO_NONSYM_PAIR1_STARS(struct runner *r, struct cell *restrict ci,
/* Get a hold of the ith spart in ci. */
struct spart *restrict si = &sparts_i[sid];
- if (!spart_is_active(si, e) || spart_is_inhibited(si, e)) continue;
+ if (!spart_is_active(si, e)) continue;
+
const float hi = si->h;
const float hig2 = hi * hi * kernel_gamma2;
const float six[3] = {(float)(si->x[0] - (cj->loc[0] + shift[0])),
@@ -194,7 +206,9 @@ void DO_NONSYM_PAIR1_STARS(struct runner *r, struct cell *restrict ci,
/* Get a pointer to the jth particle. */
struct part *restrict pj = &parts_j[pjd];
- const float hj = pj->h;
+
+ /* Skip inhibited particles. */
+ if (part_is_inhibited(pj, e)) continue;
/* Compute the pairwise distance. */
const float pjx[3] = {(float)(pj->x[0] - cj->loc[0]),
@@ -209,27 +223,297 @@ void DO_NONSYM_PAIR1_STARS(struct runner *r, struct cell *restrict ci,
error("Particle pj not drifted to current time");
#endif
- if (r2 < hig2) IACT_STARS(r2, dx, hi, hj, si, pj, a, H);
+ if (r2 < hig2) IACT_STARS(r2, dx, hi, pj->h, si, pj, a, H);
} /* loop over the parts in cj. */
} /* loop over the parts in ci. */
}
-void DOPAIR1_STARS(struct runner *r, struct cell *restrict ci,
- struct cell *restrict cj, int timer) {
+/**
+ * @brief Compute the interactions between a cell pair.
+ *
+ * @param r The #runner.
+ * @param ci The first #cell.
+ * @param cj The second #cell.
+ * @param sid The direction of the pair.
+ * @param shift The shift vector to apply to the particles in ci.
+ */
+void DO_SYM_PAIR1_STARS(struct runner *r, struct cell *ci, struct cell *cj,
+ const int sid, const double *shift) {
+
+ const struct engine *restrict e = r->e;
+ const struct cosmology *restrict cosmo = e->cosmology;
+
+ /* Get the cutoff shift. */
+ double rshift = 0.0;
+ for (int k = 0; k < 3; k++) rshift += shift[k] * runner_shift[sid][k];
+
+ /* Cosmological terms */
+ const float a = cosmo->a;
+ const float H = cosmo->H;
+
+#if (FUNCTION_TASK_LOOP == TASK_LOOP_DENSITY)
+ const int do_ci_stars = (ci->nodeID == e->nodeID) && (ci->stars.count != 0) &&
+ (cj->hydro.count != 0) && cell_is_active_stars(ci, e);
+ const int do_cj_stars = (cj->nodeID == e->nodeID) && (cj->stars.count != 0) &&
+ (ci->hydro.count != 0) && cell_is_active_stars(cj, e);
+#else
+ /* here we are updating the hydro -> switch ci, cj for local */
+ const int do_ci_stars = (cj->nodeID == e->nodeID) && (ci->stars.count != 0) &&
+ (cj->hydro.count != 0) && cell_is_active_stars(ci, e);
+ const int do_cj_stars = (ci->nodeID == e->nodeID) && (cj->stars.count != 0) &&
+ (ci->hydro.count != 0) && cell_is_active_stars(cj, e);
+#endif
+
+ if (do_ci_stars) {
+
+ /* Pick-out the sorted lists. */
+ const struct entry *restrict sort_j = cj->hydro.sort[sid];
+ const struct entry *restrict sort_i = ci->stars.sort[sid];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Some constants used to checks that the parts are in the right frame */
+ const float shift_threshold_x =
+ 2. * ci->width[0] +
+ 2. * max(ci->stars.dx_max_part, cj->hydro.dx_max_part);
+ const float shift_threshold_y =
+ 2. * ci->width[1] +
+ 2. * max(ci->stars.dx_max_part, cj->hydro.dx_max_part);
+ const float shift_threshold_z =
+ 2. * ci->width[2] +
+ 2. * max(ci->stars.dx_max_part, cj->hydro.dx_max_part);
+#endif /* SWIFT_DEBUG_CHECKS */
+
+ /* Get some other useful values. */
+ const double hi_max = ci->stars.h_max * kernel_gamma - rshift;
+ const int count_i = ci->stars.count;
+ const int count_j = cj->hydro.count;
+ struct spart *restrict sparts_i = ci->stars.parts;
+ struct part *restrict parts_j = cj->hydro.parts;
+ const double dj_min = sort_j[0].d;
+ const float dx_max_rshift =
+ (ci->stars.dx_max_sort + cj->hydro.dx_max_sort) - rshift;
+ const float dx_max = (ci->stars.dx_max_sort + cj->hydro.dx_max_sort);
+
+ /* Loop over the sparts in ci. */
+ for (int pid = count_i - 1;
+ pid >= 0 && sort_i[pid].d + hi_max + dx_max > dj_min; pid--) {
+
+ /* Get a hold of the ith part in ci. */
+ struct spart *restrict spi = &sparts_i[sort_i[pid].i];
+ const float hi = spi->h;
+
+ /* Skip inactive particles */
+ if (!spart_is_active(spi, e)) continue;
+
+ /* Compute distance from the other cell. */
+ const double px[3] = {spi->x[0], spi->x[1], spi->x[2]};
+ float dist = px[0] * runner_shift[sid][0] + px[1] * runner_shift[sid][1] +
+ px[2] * runner_shift[sid][2];
+
+ /* Is there anything we need to interact with ? */
+ const double di = dist + hi * kernel_gamma + dx_max_rshift;
+ if (di < dj_min) continue;
+
+ /* Get some additional information about pi */
+ const float hig2 = hi * hi * kernel_gamma2;
+ const float pix = spi->x[0] - (cj->loc[0] + shift[0]);
+ const float piy = spi->x[1] - (cj->loc[1] + shift[1]);
+ const float piz = spi->x[2] - (cj->loc[2] + shift[2]);
+
+ /* Loop over the parts in cj. */
+ for (int pjd = 0; pjd < count_j && sort_j[pjd].d < di; pjd++) {
+
+ /* Recover pj */
+ struct part *pj = &parts_j[sort_j[pjd].i];
+
+ /* Skip inhibited particles. */
+ if (part_is_inhibited(pj, e)) continue;
+
+ const float hj = pj->h;
+ const float pjx = pj->x[0] - cj->loc[0];
+ const float pjy = pj->x[1] - cj->loc[1];
+ const float pjz = pj->x[2] - cj->loc[2];
+
+ /* Compute the pairwise distance. */
+ float dx[3] = {pix - pjx, piy - pjy, piz - pjz};
+ const float r2 = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Check that particles are in the correct frame after the shifts */
+ if (pix > shift_threshold_x || pix < -shift_threshold_x)
+ error(
+ "Invalid particle position in X for pi (pix=%e ci->width[0]=%e)",
+ pix, ci->width[0]);
+ if (piy > shift_threshold_y || piy < -shift_threshold_y)
+ error(
+ "Invalid particle position in Y for pi (piy=%e ci->width[1]=%e)",
+ piy, ci->width[1]);
+ if (piz > shift_threshold_z || piz < -shift_threshold_z)
+ error(
+ "Invalid particle position in Z for pi (piz=%e ci->width[2]=%e)",
+ piz, ci->width[2]);
+ if (pjx > shift_threshold_x || pjx < -shift_threshold_x)
+ error(
+ "Invalid particle position in X for pj (pjx=%e ci->width[0]=%e)",
+ pjx, ci->width[0]);
+ if (pjy > shift_threshold_y || pjy < -shift_threshold_y)
+ error(
+ "Invalid particle position in Y for pj (pjy=%e ci->width[1]=%e)",
+ pjy, ci->width[1]);
+ if (pjz > shift_threshold_z || pjz < -shift_threshold_z)
+ error(
+ "Invalid particle position in Z for pj (pjz=%e ci->width[2]=%e)",
+ pjz, ci->width[2]);
+
+ /* Check that particles have been drifted to the current time */
+ if (spi->ti_drift != e->ti_current)
+ error("Particle spi not drifted to current time");
+ if (pj->ti_drift != e->ti_current)
+ error("Particle pj not drifted to current time");
+#endif
+
+ /* Hit or miss? */
+ if (r2 < hig2) {
+
+ IACT_STARS(r2, dx, hi, hj, spi, pj, a, H);
+ }
+ } /* loop over the parts in cj. */
+ } /* loop over the parts in ci. */
+ } /* do_ci_stars */
+
+ if (do_cj_stars) {
+ /* Pick-out the sorted lists. */
+ const struct entry *restrict sort_i = ci->hydro.sort[sid];
+ const struct entry *restrict sort_j = cj->stars.sort[sid];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Some constants used to checks that the parts are in the right frame */
+ const float shift_threshold_x =
+ 2. * ci->width[0] +
+ 2. * max(ci->hydro.dx_max_part, cj->stars.dx_max_part);
+ const float shift_threshold_y =
+ 2. * ci->width[1] +
+ 2. * max(ci->hydro.dx_max_part, cj->stars.dx_max_part);
+ const float shift_threshold_z =
+ 2. * ci->width[2] +
+ 2. * max(ci->hydro.dx_max_part, cj->stars.dx_max_part);
+#endif /* SWIFT_DEBUG_CHECKS */
+
+ /* Get some other useful values. */
+ const double hj_max = cj->hydro.h_max * kernel_gamma;
+ const int count_i = ci->hydro.count;
+ const int count_j = cj->stars.count;
+ struct part *restrict parts_i = ci->hydro.parts;
+ struct spart *restrict sparts_j = cj->stars.parts;
+ const double di_max = sort_i[count_i - 1].d - rshift;
+ const float dx_max_rshift =
+ (ci->hydro.dx_max_sort + cj->stars.dx_max_sort) + rshift;
+ const float dx_max = (ci->hydro.dx_max_sort + cj->stars.dx_max_sort);
+
+ /* Loop over the parts in cj. */
+ for (int pjd = 0; pjd < count_j && sort_j[pjd].d - hj_max - dx_max < di_max;
+ pjd++) {
+
+ /* Get a hold of the jth part in cj. */
+ struct spart *spj = &sparts_j[sort_j[pjd].i];
+ const float hj = spj->h;
+
+ /* Skip inactive particles */
+ if (!spart_is_active(spj, e)) continue;
+
+ /* Compute distance from the other cell. */
+ const double px[3] = {spj->x[0], spj->x[1], spj->x[2]};
+ float dist = px[0] * runner_shift[sid][0] + px[1] * runner_shift[sid][1] +
+ px[2] * runner_shift[sid][2];
+
+ /* Is there anything we need to interact with ? */
+ const double dj = dist - hj * kernel_gamma - dx_max_rshift;
+ if (dj - rshift > di_max) continue;
+
+ /* Get some additional information about pj */
+ const float hjg2 = hj * hj * kernel_gamma2;
+ const float pjx = spj->x[0] - cj->loc[0];
+ const float pjy = spj->x[1] - cj->loc[1];
+ const float pjz = spj->x[2] - cj->loc[2];
+
+ /* Loop over the parts in ci. */
+ for (int pid = count_i - 1; pid >= 0 && sort_i[pid].d > dj; pid--) {
+
+ /* Recover pi */
+ struct part *pi = &parts_i[sort_i[pid].i];
+
+ /* Skip inhibited particles. */
+ if (part_is_inhibited(pi, e)) continue;
+
+ const float hi = pi->h;
+ const float pix = pi->x[0] - (cj->loc[0] + shift[0]);
+ const float piy = pi->x[1] - (cj->loc[1] + shift[1]);
+ const float piz = pi->x[2] - (cj->loc[2] + shift[2]);
+
+ /* Compute the pairwise distance. */
+ float dx[3] = {pjx - pix, pjy - piy, pjz - piz};
+ const float r2 = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Check that particles are in the correct frame after the shifts */
+ if (pix > shift_threshold_x || pix < -shift_threshold_x)
+ error(
+ "Invalid particle position in X for pi (pix=%e ci->width[0]=%e)",
+ pix, ci->width[0]);
+ if (piy > shift_threshold_y || piy < -shift_threshold_y)
+ error(
+ "Invalid particle position in Y for pi (piy=%e ci->width[1]=%e)",
+ piy, ci->width[1]);
+ if (piz > shift_threshold_z || piz < -shift_threshold_z)
+ error(
+ "Invalid particle position in Z for pi (piz=%e ci->width[2]=%e)",
+ piz, ci->width[2]);
+ if (pjx > shift_threshold_x || pjx < -shift_threshold_x)
+ error(
+ "Invalid particle position in X for pj (pjx=%e ci->width[0]=%e)",
+ pjx, ci->width[0]);
+ if (pjy > shift_threshold_y || pjy < -shift_threshold_y)
+ error(
+ "Invalid particle position in Y for pj (pjy=%e ci->width[1]=%e)",
+ pjy, ci->width[1]);
+ if (pjz > shift_threshold_z || pjz < -shift_threshold_z)
+ error(
+ "Invalid particle position in Z for pj (pjz=%e ci->width[2]=%e)",
+ pjz, ci->width[2]);
+
+ /* Check that particles have been drifted to the current time */
+ if (pi->ti_drift != e->ti_current)
+ error("Particle pi not drifted to current time");
+ if (spj->ti_drift != e->ti_current)
+ error("Particle spj not drifted to current time");
+#endif
+
+ /* Hit or miss? */
+ if (r2 < hjg2) {
+
+ IACT_STARS(r2, dx, hj, hi, spj, pi, a, H);
+ }
+ } /* loop over the parts in ci. */
+ } /* loop over the parts in cj. */
+ } /* Cell cj is active */
+}
+
+void DOPAIR1_STARS_NAIVE(struct runner *r, struct cell *restrict ci,
+ struct cell *restrict cj, int timer) {
-#ifdef UPDATE_STARS
- const int ci_local = ci->nodeID == engine_rank;
- const int cj_local = cj->nodeID == engine_rank;
+#if (FUNCTION_TASK_LOOP == TASK_LOOP_DENSITY)
+ const int do_ci_stars = ci->nodeID == r->e->nodeID;
+ const int do_cj_stars = cj->nodeID == r->e->nodeID;
#else
/* here we are updating the hydro -> switch ci, cj */
- const int ci_local = cj->nodeID == engine_rank;
- const int cj_local = ci->nodeID == engine_rank;
+ const int do_ci_stars = cj->nodeID == r->e->nodeID;
+ const int do_cj_stars = ci->nodeID == r->e->nodeID;
#endif
- if (ci_local && ci->stars.count != 0 && cj->hydro.count != 0)
- DO_NONSYM_PAIR1_STARS(r, ci, cj);
- if (cj_local && cj->stars.count != 0 && ci->hydro.count != 0)
- DO_NONSYM_PAIR1_STARS(r, cj, ci);
+ if (do_ci_stars && ci->stars.count != 0 && cj->hydro.count != 0)
+ DO_NONSYM_PAIR1_STARS_NAIVE(r, ci, cj);
+ if (do_cj_stars && cj->stars.count != 0 && ci->hydro.count != 0)
+ DO_NONSYM_PAIR1_STARS_NAIVE(r, cj, ci);
}
/**
@@ -244,12 +528,151 @@ void DOPAIR1_STARS(struct runner *r, struct cell *restrict ci,
* @param ind The list of indices of particles in @c ci to interact with.
* @param scount The number of particles in @c ind.
* @param cj The second #cell.
+ * @param sid The direction of the pair.
+ * @param flipped Flag to check whether the cells have been flipped or not.
* @param shift The shift vector to apply to the particles in ci.
*/
void DOPAIR1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
struct spart *restrict sparts_i, int *restrict ind,
- int scount, struct cell *restrict cj,
- const double *shift) {
+ int scount, struct cell *restrict cj, const int sid,
+ const int flipped, const double *shift) {
+
+ const struct engine *e = r->e;
+ const struct cosmology *cosmo = e->cosmology;
+
+ const int count_j = cj->hydro.count;
+ struct part *restrict parts_j = cj->hydro.parts;
+
+ /* Early abort? */
+ if (count_j == 0) return;
+
+ /* Cosmological terms */
+ const float a = cosmo->a;
+ const float H = cosmo->H;
+
+ /* Pick-out the sorted lists. */
+ const struct entry *restrict sort_j = cj->hydro.sort[sid];
+ const float dxj = cj->hydro.dx_max_sort;
+
+ /* Sparts are on the left? */
+ if (!flipped) {
+
+ /* Loop over the sparts_i. */
+ for (int pid = 0; pid < scount; pid++) {
+
+ /* Get a hold of the ith spart in ci. */
+ struct spart *restrict spi = &sparts_i[ind[pid]];
+ const double pix = spi->x[0] - (shift[0]);
+ const double piy = spi->x[1] - (shift[1]);
+ const double piz = spi->x[2] - (shift[2]);
+ const float hi = spi->h;
+ const float hig2 = hi * hi * kernel_gamma2;
+ const double di = hi * kernel_gamma + dxj + pix * runner_shift[sid][0] +
+ piy * runner_shift[sid][1] + piz * runner_shift[sid][2];
+
+ /* Loop over the parts in cj. */
+ for (int pjd = 0; pjd < count_j && sort_j[pjd].d < di; pjd++) {
+
+ /* Get a pointer to the jth particle. */
+ struct part *restrict pj = &parts_j[sort_j[pjd].i];
+
+ /* Skip inhibited particles. */
+ if (part_is_inhibited(pj, e)) continue;
+
+ const double pjx = pj->x[0];
+ const double pjy = pj->x[1];
+ const double pjz = pj->x[2];
+
+ /* Compute the pairwise distance. */
+ float dx[3] = {(float)(pix - pjx), (float)(piy - pjy),
+ (float)(piz - pjz)};
+ const float r2 = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Check that particles have been drifted to the current time */
+ if (spi->ti_drift != e->ti_current)
+ error("Particle pi not drifted to current time");
+ if (pj->ti_drift != e->ti_current)
+ error("Particle pj not drifted to current time");
+#endif
+
+ /* Hit or miss? */
+ if (r2 < hig2) {
+ IACT_STARS(r2, dx, hi, pj->h, spi, pj, a, H);
+ }
+ } /* loop over the parts in cj. */
+ } /* loop over the sparts in ci. */
+ }
+
+ /* Sparts are on the right. */
+ else {
+
+ /* Loop over the sparts_i. */
+ for (int pid = 0; pid < scount; pid++) {
+
+ /* Get a hold of the ith spart in ci. */
+ struct spart *restrict spi = &sparts_i[ind[pid]];
+ const double pix = spi->x[0] - (shift[0]);
+ const double piy = spi->x[1] - (shift[1]);
+ const double piz = spi->x[2] - (shift[2]);
+ const float hi = spi->h;
+ const float hig2 = hi * hi * kernel_gamma2;
+ const double di = -hi * kernel_gamma - dxj + pix * runner_shift[sid][0] +
+ piy * runner_shift[sid][1] + piz * runner_shift[sid][2];
+
+ /* Loop over the parts in cj. */
+ for (int pjd = count_j - 1; pjd >= 0 && di < sort_j[pjd].d; pjd--) {
+
+ /* Get a pointer to the jth particle. */
+ struct part *restrict pj = &parts_j[sort_j[pjd].i];
+
+ /* Skip inhibited particles. */
+ if (part_is_inhibited(pj, e)) continue;
+
+ const double pjx = pj->x[0];
+ const double pjy = pj->x[1];
+ const double pjz = pj->x[2];
+
+ /* Compute the pairwise distance. */
+ float dx[3] = {(float)(pix - pjx), (float)(piy - pjy),
+ (float)(piz - pjz)};
+ const float r2 = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+
+#ifdef SWIFT_DEBUG_CHECKS
+ /* Check that particles have been drifted to the current time */
+ if (spi->ti_drift != e->ti_current)
+ error("Particle pi not drifted to current time");
+ if (pj->ti_drift != e->ti_current)
+ error("Particle pj not drifted to current time");
+#endif
+
+ /* Hit or miss? */
+ if (r2 < hig2) {
+ IACT_STARS(r2, dx, hi, pj->h, spi, pj, a, H);
+ }
+ } /* loop over the parts in cj. */
+ } /* loop over the sparts in ci. */
+ }
+}
+
+/**
+ * @brief Compute the interactions between a cell pair, but only for the
+ * given indices in ci.
+ *
+ * Version using a brute-force algorithm.
+ *
+ * @param r The #runner.
+ * @param ci The first #cell.
+ * @param sparts_i The #part to interact with @c cj.
+ * @param ind The list of indices of particles in @c ci to interact with.
+ * @param scount The number of particles in @c ind.
+ * @param cj The second #cell.
+ * @param shift The shift vector to apply to the particles in ci.
+ */
+void DOPAIR1_SUBSET_STARS_NAIVE(struct runner *r, struct cell *restrict ci,
+ struct spart *restrict sparts_i,
+ int *restrict ind, int scount,
+ struct cell *restrict cj, const double *shift) {
#ifdef SWIFT_DEBUG_CHECKS
if (ci->nodeID != engine_rank) error("Should be run on a different node");
@@ -260,6 +683,9 @@ void DOPAIR1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
const int count_j = cj->hydro.count;
struct part *restrict parts_j = cj->hydro.parts;
+ /* Early abort? */
+ if (count_j == 0) return;
+
/* Cosmological terms */
const float a = cosmo->a;
const float H = cosmo->H;
@@ -285,6 +711,9 @@ void DOPAIR1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
/* Get a pointer to the jth particle. */
struct part *restrict pj = &parts_j[pjd];
+ /* Skip inhibited particles */
+ if (part_is_inhibited(pj, e)) continue;
+
/* Compute the pairwise distance. */
float r2 = 0.0f;
float dx[3];
@@ -334,6 +763,9 @@ void DOSELF1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
const int count_i = ci->hydro.count;
struct part *restrict parts_j = ci->hydro.parts;
+ /* Early abort? */
+ if (count_i == 0) return;
+
/* Loop over the parts in ci. */
for (int spid = 0; spid < scount; spid++) {
@@ -355,7 +787,9 @@ void DOSELF1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
/* Get a pointer to the jth particle. */
struct part *restrict pj = &parts_j[pjd];
- const float hj = pj->h;
+
+ /* Early abort? */
+ if (part_is_inhibited(pj, e)) continue;
/* Compute the pairwise distance. */
const float pjx[3] = {(float)(pj->x[0] - ci->loc[0]),
@@ -371,8 +805,8 @@ void DOSELF1_SUBSET_STARS(struct runner *r, struct cell *restrict ci,
#endif
/* Hit or miss? */
- if (r2 > 0.f && r2 < hig2) {
- IACT_STARS(r2, dx, hi, hj, spi, pj, a, H);
+ if (r2 < hig2) {
+ IACT_STARS(r2, dx, hi, pj->h, spi, pj, a, H);
}
} /* loop over the parts in cj. */
} /* loop over the parts in ci. */
@@ -414,6 +848,9 @@ void DOPAIR1_SUBSET_BRANCH_STARS(struct runner *r, struct cell *restrict ci,
const struct engine *e = r->e;
+ /* Anything to do here? */
+ if (cj->hydro.count == 0) return;
+
/* Get the relative distance between the pairs, wrapping. */
double shift[3] = {0.0, 0.0, 0.0};
for (int k = 0; k < 3; k++) {
@@ -423,7 +860,27 @@ void DOPAIR1_SUBSET_BRANCH_STARS(struct runner *r, struct cell *restrict ci,
shift[k] = -e->s->dim[k];
}
- DOPAIR1_SUBSET_STARS(r, ci, sparts_i, ind, scount, cj, shift);
+#ifdef SWIFT_USE_NAIVE_INTERACTIONS_STARS
+ DOPAIR1_SUBSET_STARS_NAIVE(r, ci, sparts_i, ind, scount, cj, shift);
+#else
+ /* Get the sorting index. */
+ int sid = 0;
+ for (int k = 0; k < 3; k++)
+ sid = 3 * sid + ((cj->loc[k] - ci->loc[k] + shift[k] < 0)
+ ? 0
+ : (cj->loc[k] - ci->loc[k] + shift[k] > 0) ? 2 : 1);
+
+ /* Switch the cells around? */
+ const int flipped = runner_flip[sid];
+ sid = sortlistID[sid];
+
+ /* Has the cell cj been sorted? */
+ if (!(cj->hydro.sorted & (1 << sid)) ||
+ cj->hydro.dx_max_sort_old > space_maxreldx * cj->dmin)
+ error("Interacting unsorted cells.");
+
+ DOPAIR1_SUBSET_STARS(r, ci, sparts_i, ind, scount, cj, sid, flipped, shift);
+#endif
}
void DOSUB_SUBSET_STARS(struct runner *r, struct cell *ci, struct spart *sparts,
@@ -1075,18 +1532,18 @@ void DOPAIR1_BRANCH_STARS(struct runner *r, struct cell *ci, struct cell *cj) {
const int ci_active = cell_is_active_stars(ci, e);
const int cj_active = cell_is_active_stars(cj, e);
-#ifdef UPDATE_STARS
- const int ci_local = ci->nodeID == engine_rank;
- const int cj_local = cj->nodeID == engine_rank;
+#if (FUNCTION_TASK_LOOP == TASK_LOOP_DENSITY)
+ const int do_ci_stars = ci->nodeID == e->nodeID;
+ const int do_cj_stars = cj->nodeID == e->nodeID;
#else
/* here we are updating the hydro -> switch ci, cj */
- const int ci_local = cj->nodeID == engine_rank;
- const int cj_local = ci->nodeID == engine_rank;
+ const int do_ci_stars = cj->nodeID == e->nodeID;
+ const int do_cj_stars = ci->nodeID == e->nodeID;
#endif
- const int do_ci =
- (ci->stars.count != 0 && cj->hydro.count != 0 && ci_active && ci_local);
- const int do_cj =
- (cj->stars.count != 0 && ci->hydro.count != 0 && cj_active && cj_local);
+ const int do_ci = (ci->stars.count != 0 && cj->hydro.count != 0 &&
+ ci_active && do_ci_stars);
+ const int do_cj = (cj->stars.count != 0 && ci->hydro.count != 0 &&
+ cj_active && do_cj_stars);
/* Anything to do here? */
if (!do_ci && !do_cj) return;
@@ -1130,7 +1587,11 @@ void DOPAIR1_BRANCH_STARS(struct runner *r, struct cell *ci, struct cell *cj) {
}
#endif /* SWIFT_DEBUG_CHECKS */
- DOPAIR1_STARS(r, ci, cj, 1);
+#ifdef SWIFT_USE_NAIVE_INTERACTIONS_STARS
+ DOPAIR1_STARS_NAIVE(r, ci, cj, 1);
+#else
+ DO_SYM_PAIR1_STARS(r, ci, cj, sid, shift);
+#endif
}
/**
@@ -1367,18 +1828,18 @@ void DOSUB_PAIR1_STARS(struct runner *r, struct cell *ci, struct cell *cj,
/* Otherwise, compute the pair directly. */
else {
-#ifdef UPDATE_STARS
- const int ci_local = ci->nodeID == engine_rank;
- const int cj_local = cj->nodeID == engine_rank;
+#if (FUNCTION_TASK_LOOP == TASK_LOOP_DENSITY)
+ const int do_ci_stars = ci->nodeID == e->nodeID;
+ const int do_cj_stars = cj->nodeID == e->nodeID;
#else
/* here we are updating the hydro -> switch ci, cj */
- const int ci_local = cj->nodeID == engine_rank;
- const int cj_local = ci->nodeID == engine_rank;
+ const int do_ci_stars = cj->nodeID == e->nodeID;
+ const int do_cj_stars = ci->nodeID == e->nodeID;
#endif
const int do_ci = ci->stars.count != 0 && cj->hydro.count != 0 &&
- cell_is_active_stars(ci, e) && ci_local;
+ cell_is_active_stars(ci, e) && do_ci_stars;
const int do_cj = cj->stars.count != 0 && ci->hydro.count != 0 &&
- cell_is_active_stars(cj, e) && cj_local;
+ cell_is_active_stars(cj, e) && do_cj_stars;
if (do_ci) {
diff --git a/src/scheduler.c b/src/scheduler.c
index 6187949c2e12e00a6caf51813aeaa46959dd0374..496d15ab302e6f0ea1280594ec16c433b117eb32 100644
--- a/src/scheduler.c
+++ b/src/scheduler.c
@@ -467,7 +467,7 @@ void scheduler_write_dependencies(struct scheduler *s, int verbose) {
if (s->nodeID == 0) {
/* Create file */
- char *filename = "dependency_graph.csv";
+ const char *filename = "dependency_graph.csv";
FILE *f = fopen(filename, "w");
if (f == NULL) error("Error opening dependency graph file.");
diff --git a/src/space.c b/src/space.c
index b98c1f86c3f1e01fa2553e6dc80a8bd857fb9fc5..bba6001ed63440747601f8abebd9f7a7076e847c 100644
--- a/src/space.c
+++ b/src/space.c
@@ -83,7 +83,7 @@ int space_extra_gparts = space_extra_gparts_default;
/*! Expected maximal number of strays received at a rebuild */
int space_expected_max_nr_strays = space_expected_max_nr_strays_default;
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
int last_cell_id;
#endif
@@ -256,7 +256,7 @@ void space_rebuild_recycle_mapper(void *map_data, int num_elements,
c->grav.ti_end_max = -1;
c->stars.ti_end_min = -1;
c->stars.ti_end_max = -1;
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
c->cellID = 0;
#endif
if (s->with_self_gravity)
@@ -569,7 +569,7 @@ void space_regrid(struct space *s, int verbose) {
c->mpi.grav.send = NULL;
#endif // WITH_MPI
if (s->with_self_gravity) c->grav.multipole = &s->multipoles_top[cid];
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
c->cellID = -last_cell_id;
last_cell_id++;
#endif
@@ -1551,7 +1551,7 @@ void space_rebuild(struct space *s, int repartitioned, int verbose) {
c->grav.ti_old_multipole = ti_current;
c->stars.ti_old_part = ti_current;
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
c->cellID = -last_cell_id;
last_cell_id++;
#endif
@@ -2744,7 +2744,7 @@ void space_split_recursive(struct space *s, struct cell *c,
#ifdef WITH_MPI
cp->mpi.tag = -1;
#endif // WITH_MPI
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
cp->cellID = last_cell_id++;
#endif
}
@@ -3977,7 +3977,7 @@ void space_init(struct space *s, struct swift_params *params,
/* Init the space lock. */
if (lock_init(&s->lock) != 0) error("Failed to create space spin-lock.");
-#ifdef SWIFT_DEBUG_CHECKS
+#if defined(SWIFT_DEBUG_CHECKS) || defined(SWIFT_CELL_GRAPH)
last_cell_id = 1;
#endif
@@ -4553,3 +4553,85 @@ void space_struct_restore(struct space *s, FILE *stream) {
s->nr_sparts, 1);
#endif
}
+
+#define root_cell_id 0
+/**
+ * @brief write a single cell in a csv file.
+ *
+ * @param s The #space.
+ * @param f The file to use (already open).
+ * @param c The current #cell.
+ */
+void space_write_cell(const struct space *s, FILE *f, const struct cell *c) {
+#ifdef SWIFT_CELL_GRAPH
+
+ if (c == NULL) return;
+
+ /* Get parent ID */
+ int parent = root_cell_id;
+ if (c->parent != NULL) parent = c->parent->cellID;
+
+ /* Get super ID */
+ char superID[100] = "";
+ if (c->super != NULL) sprintf(superID, "%i", c->super->cellID);
+
+ /* Get hydro super ID */
+ char hydro_superID[100] = "";
+ if (c->hydro.super != NULL)
+ sprintf(hydro_superID, "%i", c->hydro.super->cellID);
+
+ /* Write line for current cell */
+ fprintf(f, "%i,%i,%i,", c->cellID, parent, c->nodeID);
+ fprintf(f, "%i,%i,%i,%s,%s,%g,%g,%g,%g,%g,%g, ", c->hydro.count,
+ c->stars.count, c->grav.count, superID, hydro_superID, c->loc[0],
+ c->loc[1], c->loc[2], c->width[0], c->width[1], c->width[2]);
+ fprintf(f, "%g, %g\n", c->hydro.h_max, c->stars.h_max);
+
+ /* Write children */
+ for (int i = 0; i < 8; i++) {
+ space_write_cell(s, f, c->progeny[i]);
+ }
+#endif
+}
+
+/**
+ * @brief Write a csv file containing the cell hierarchy
+ *
+ * @param s The #space.
+ */
+void space_write_cell_hierarchy(const struct space *s) {
+
+#ifdef SWIFT_CELL_GRAPH
+
+ /* Open file */
+ char filename[200];
+ sprintf(filename, "cell_hierarchy_%04i.csv", engine_rank);
+ FILE *f = fopen(filename, "w");
+ if (f == NULL) error("Error opening task level file.");
+
+ const int root_id = root_cell_id;
+ /* Write header */
+ if (engine_rank == 0) {
+ fprintf(f, "name,parent,mpi_rank,");
+ fprintf(f,
+ "hydro_count,stars_count,gpart_count,super,hydro_super,"
+ "loc1,loc2,loc3,width1,width2,width3,");
+ fprintf(f, "hydro_h_max,stars_h_max\n");
+
+ /* Write root data */
+ fprintf(f, "%i, ,-1,", root_id);
+ fprintf(f, "%li,%li,%li, , , , , , , , , ", s->nr_parts, s->nr_sparts,
+ s->nr_gparts);
+ fprintf(f, ",\n");
+ }
+
+ /* Write all the top level cells (and their children) */
+ for (int i = 0; i < s->nr_cells; i++) {
+ struct cell *c = &s->cells_top[i];
+ if (c->nodeID == engine_rank) space_write_cell(s, f, c);
+ }
+
+ /* Cleanup */
+ fclose(f);
+#endif
+}
diff --git a/src/space.h b/src/space.h
index fe47a2b8b995e5872e79e755b5b8075a409795b8..924c3efaf81f88cb82a8c23707d42883832aa071 100644
--- a/src/space.h
+++ b/src/space.h
@@ -331,5 +331,6 @@ void space_free_cells(struct space *s);
void space_struct_dump(struct space *s, FILE *stream);
void space_struct_restore(struct space *s, FILE *stream);
+void space_write_cell_hierarchy(const struct space *s);
#endif /* SWIFT_SPACE_H */
diff --git a/src/star_formation/EAGLE/star_formation.h b/src/star_formation/EAGLE/star_formation.h
index b72bb38babaca51b3875147d04c46f2de95de1a7..43cc820189a117669aba30c36323a2aab840eadf 100644
--- a/src/star_formation/EAGLE/star_formation.h
+++ b/src/star_formation/EAGLE/star_formation.h
@@ -24,7 +24,9 @@
#include "cooling.h"
#include "cosmology.h"
#include "engine.h"
+#include "entropy_floor.h"
#include "equation_of_state.h"
+#include "exp10.h"
#include "hydro.h"
#include "parser.h"
#include "part.h"
@@ -187,23 +189,6 @@ INLINE static double EOS_pressure(const double n_H,
pow(n_H * starform->EOS_density_c_inv, starform->EOS_polytropic_index);
}
-/**
- * @brief Compute the temperarue on the polytropic equation of state for a given
- * Hydrogen number density.
- *
- * Schaye & Dalla Vecchia 2008, eq. 13 rewritten for temperature
- *
- * @param n_H The Hydrogen number density in internal units.
- * @param starform The properties of the star formation model.
- * @return The temperature on the equation of state in internal units.
- */
-INLINE static double EOS_temperature(const double n_H,
- const struct star_formation* starform) {
-
- return starform->EOS_temperature_c *
- pow(n_H, starform->EOS_polytropic_index - 1.);
-}
-
/**
* @brief Calculate if the gas has the potential of becoming
* a star.
@@ -216,7 +201,7 @@ INLINE static double EOS_temperature(const double n_H,
* @param hydro_props The properties of the hydro scheme.
* @param us The internal system of units.
* @param cooling The cooling data struct.
- *
+ * @param entropy_floor The entropy floor assumed in this run.
*/
INLINE static int star_formation_is_star_forming(
const struct part* restrict p, const struct xpart* restrict xp,
@@ -224,7 +209,8 @@ INLINE static int star_formation_is_star_forming(
const struct cosmology* cosmo,
const struct hydro_props* restrict hydro_props,
const struct unit_system* restrict us,
- const struct cooling_function_data* restrict cooling) {
+ const struct cooling_function_data* restrict cooling,
+ const struct entropy_floor_properties* restrict entropy_floor) {
/* Minimal density (converted from critical density) for star formation */
const double rho_crit_times_min_over_den =
@@ -261,7 +247,8 @@ INLINE static int star_formation_is_star_forming(
us, cosmo, cooling, p, xp);
/* Temperature on the equation of state */
- const double temperature_eos = EOS_temperature(n_H, starform);
+ const double temperature_eos =
+ entropy_floor_temperature(p, cosmo, entropy_floor);
/* Check the Scahye & Dalla Vecchia 2012 EOS-based temperature critrion */
return (temperature <
diff --git a/src/star_formation/GEAR/star_formation.h b/src/star_formation/GEAR/star_formation.h
index 420cecb6f6cdfa6be8d0803064122fa539131d0c..05bb584a5330002e610df9c1866c672f5ae1977f 100644
--- a/src/star_formation/GEAR/star_formation.h
+++ b/src/star_formation/GEAR/star_formation.h
@@ -21,6 +21,7 @@
/* Local includes */
#include "cosmology.h"
+#include "entropy_floor.h"
#include "error.h"
#include "hydro_properties.h"
#include "parser.h"
@@ -50,7 +51,8 @@ INLINE static int star_formation_is_star_forming(
const struct cosmology* cosmo,
const struct hydro_props* restrict hydro_props,
const struct unit_system* restrict us,
- const struct cooling_function_data* restrict cooling) {
+ const struct cooling_function_data* restrict cooling,
+ const struct entropy_floor_properties* restrict entropy_floor) {
return 0;
}
diff --git a/src/star_formation/none/star_formation.h b/src/star_formation/none/star_formation.h
index 7dbe5b20cc401c0284036f3c973c9b65fcec8d2e..25c0bcee6a8d2aa2f4be5479556eebc50027aa72 100644
--- a/src/star_formation/none/star_formation.h
+++ b/src/star_formation/none/star_formation.h
@@ -21,6 +21,7 @@
/* Local includes */
#include "cosmology.h"
+#include "entropy_floor.h"
#include "error.h"
#include "hydro_properties.h"
#include "parser.h"
@@ -53,7 +54,8 @@ INLINE static int star_formation_is_star_forming(
const struct cosmology* cosmo,
const struct hydro_props* restrict hydro_props,
const struct unit_system* restrict us,
- const struct cooling_function_data* restrict cooling) {
+ const struct cooling_function_data* restrict cooling,
+ const struct entropy_floor_properties* restrict entropy_floor) {
return 0;
}
diff --git a/src/stars/Default/stars.h b/src/stars/Default/stars.h
index 586a87f75600a08acfd84b0f7ecc57fc4573281f..1ff4936284c4d8913417c502db69a372fc83bc06 100644
--- a/src/stars/Default/stars.h
+++ b/src/stars/Default/stars.h
@@ -72,18 +72,7 @@ __attribute__((always_inline)) INLINE static void stars_init_spart(
* @param dt_drift The drift time-step for positions.
*/
__attribute__((always_inline)) INLINE static void stars_predict_extra(
- struct spart* restrict sp, float dt_drift) {
-
- // MATTHIEU
- /* const float h_inv = 1.f / sp->h; */
-
- /* /\* Predict smoothing length *\/ */
- /* const float w1 = sp->feedback.h_dt * h_inv * dt_drift; */
- /* if (fabsf(w1) < 0.2f) */
- /* sp->h *= approx_expf(w1); /\* 4th order expansion of exp(w) *\/ */
- /* else */
- /* sp->h *= expf(w1); */
-}
+ struct spart* restrict sp, float dt_drift) {}
/**
* @brief Sets the values to be predicted in the drifts to their values at a
diff --git a/src/tools.c b/src/tools.c
index 43ac0177daef171850ea325f9fa23770fb82ae13..a29408449600ad4b46bd73ba17e20adefdbcb613 100644
--- a/src/tools.c
+++ b/src/tools.c
@@ -442,6 +442,9 @@ void pairs_all_stars_density(struct runner *r, struct cell *ci,
struct part *pj = &cj->hydro.parts[j];
+ /* Early abort? */
+ if (part_is_inhibited(pj, e)) continue;
+
/* Pairwise distance */
r2 = 0.0f;
for (int k = 0; k < 3; k++) {
@@ -472,6 +475,9 @@ void pairs_all_stars_density(struct runner *r, struct cell *ci,
struct part *pi = &ci->hydro.parts[i];
+ /* Early abort? */
+ if (part_is_inhibited(pi, e)) continue;
+
/* Pairwise distance */
r2 = 0.0f;
for (int k = 0; k < 3; k++) {
@@ -660,6 +666,9 @@ void self_all_stars_density(struct runner *r, struct cell *ci) {
pj = &ci->hydro.parts[j];
hj = pj->h;
+ /* Early abort? */
+ if (part_is_inhibited(pj, e)) continue;
+
/* Pairwise distance */
r2 = 0.0f;
for (int k = 0; k < 3; k++) {
@@ -668,7 +677,7 @@ void self_all_stars_density(struct runner *r, struct cell *ci) {
}
/* Hit or miss? */
- if (r2 > 0.f && r2 < hig2) {
+ if (r2 < hig2) {
/* Interact */
runner_iact_nonsym_stars_density(r2, dxi, hi, hj, spi, pj, a, H);
}
diff --git a/tests/test27cellsStars.c b/tests/test27cellsStars.c
index e7e1b64b1cc99d8a51cf380fde1560bdd634ae20..e97aee278e4b34d7cb1904826aba7a5ff3ed5d67 100644
--- a/tests/test27cellsStars.c
+++ b/tests/test27cellsStars.c
@@ -70,6 +70,7 @@ struct cell *make_cell(size_t n, size_t n_stars, double *offset, double size,
const size_t count = n * n * n;
const size_t scount = n_stars * n_stars * n_stars;
float h_max = 0.f;
+ float stars_h_max = 0.f;
struct cell *cell = (struct cell *)malloc(sizeof(struct cell));
bzero(cell, sizeof(struct cell));
@@ -143,7 +144,7 @@ struct cell *make_cell(size_t n, size_t n_stars, double *offset, double size,
spart->h = size * h * random_uniform(1.f, h_pert) / (float)n_stars;
else
spart->h = size * h / (float)n_stars;
- h_max = fmaxf(h_max, spart->h);
+ stars_h_max = fmaxf(stars_h_max, spart->h);
spart->id = ++(*spartId);
spart->time_bin = 1;
@@ -161,6 +162,7 @@ struct cell *make_cell(size_t n, size_t n_stars, double *offset, double size,
cell->split = 0;
cell->hydro.h_max = h_max;
cell->hydro.count = count;
+ cell->stars.h_max = stars_h_max;
cell->stars.count = scount;
cell->hydro.dx_max_part = 0.;
cell->hydro.dx_max_sort = 0.;
diff --git a/tools/data/cell_hierarchy.html b/tools/data/cell_hierarchy.html
new file mode 100644
index 0000000000000000000000000000000000000000..6c9bcdb995be7970948cf9b9544ae0a59d41caf0
--- /dev/null
+++ b/tools/data/cell_hierarchy.html
@@ -0,0 +1,387 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+
+ <title>Cell Hierarchy</title>
+
+ <style>
+
+ div.tooltip {
+ position: absolute;
+ text-align: left;
+ width: 180px;
+ height: 80px;
+ padding: 2px;
+ font: 12px sans-serif;
+ background: lightsteelblue;
+ border: 0px;
+ border-radius: 8px;
+ pointer-events: none;
+ }
+ .node {
+ cursor: pointer;
+ }
+
+ .node circle {
+ fill: #fff;
+ stroke: steelblue;
+ stroke-width: 3px;
+ }
+
+ .node text {
+ font: 12px sans-serif;
+ }
+
+ .link {
+ fill: none;
+ stroke: #ccc;
+ stroke-width: 2px;
+ }
+
+ </style>
+
+ </head>
+
+ <div class="ui-widget">
+ <input id="search">
+ <button type="button" onclick="searchNode()">Search</button>
+ <progress value="0" max="100" id="progress">0</progress>
+ </div>
+ <body>
+
+<!-- load the d3.js library -->
+<script src="https://d3js.org/d3.v5.min.js"></script>
+
+<script>
+ // ************** Generate the tree diagram *****************
+ var margin = {top: 20, right: 60, bottom: 20, left: 60},
+ width = 1800 - margin.right - margin.left,
+ height = 900 - margin.top - margin.bottom;
+
+ var i = 0,
+ duration = 750,
+ root;
+
+ var tree = d3.tree()
+ .size([10*width, height]);
+
+ // append the svg object to the body of the page
+ // appends a 'group' element to 'svg'
+ // moves the 'group' element to the top left margin
+ var svg = d3.select("body").append("svg")
+ .attr("width", width + margin.right + margin.left)
+ .attr("height", height + margin.top + margin.bottom)
+ .call(d3.zoom().on("zoom", function () {
+ svg.attr("transform", d3.event.transform)
+ }))
+ .append("g")
+ .attr("transform", "translate("
+ + margin.left + "," + margin.top + ")")
+
+ // load the external data
+ d3.csv("cell_hierarchy.csv").then(function(data) {
+
+ // *********** Convert flat data into a nice tree ***************
+ // create a name: node map
+ var dataMap = data.reduce(function(map, node) {
+ map[node.name] = node;
+ return map;
+ }, {});
+
+ // create the tree array
+ var treeData = [];
+ data.forEach(function(node) {
+ // add to parent
+ var parent = dataMap[node.parent];
+ if (parent) {
+ // create child array if it doesn't exist
+ (parent.children || (parent.children = []))
+ // add node to child array
+ .push(node);
+ } else {
+ // parent is null or missing
+ treeData.push(node);
+ }
+ });
+
+ root = d3.hierarchy(treeData[0], function(d) { return d.children; });
+
+ root.x0 = width / 2;
+ root.y0 = 0;
+
+ // Collapse after the second level
+ root.children.forEach(collapse);
+ update(root);
+
+ var N = root.children.length
+ var size = 1.
+ if (N > 64)
+ size = 15 * N / 1664
+ tree = tree.size([size * width, height]);
+ update(root)
+
+ });
+
+ d3.select(self.frameElement).style("height", "500px");
+
+ function update(source) {
+
+ // Assigns the x and y position for the nodes
+ var treeData = tree(root);
+
+ // Compute the new tree layout.
+ var nodes = treeData.descendants(),
+ links = treeData.descendants().slice(1);
+
+ // Normalize for fixed-depth.
+ nodes.forEach(function(d){ d.y = d.depth * 100});
+
+ // ****************** Nodes section ***************************
+
+ // Update the nodes...
+ var node = svg.selectAll('g.node')
+ .data(nodes, function(d) {return d.id || (d.id = ++i); });
+
+ // Enter any new modes at the parent's previous position.
+ var nodeEnter = node.enter().append('g')
+ .attr('class', 'node')
+ .attr("transform", function(d) {
+ return "translate(" + source.x0 + "," + source.y0 + ")";
+ })
+ .on('click', click)
+
+ // add tool tip for ps -eo pid,ppid,pcpu,size,comm,ruser,s
+ .on("mouseover", function(d) {
+ var n = d.data
+ div.transition()
+ .duration(200)
+ .style("opacity", .9);
+ div .html(
+ "ID: " + n.name + "<br/>" +
+ "MPI rank:" + n.mpi_rank + "<br/>" +
+ "Part: " + n.hydro_count + "<br/>" +
+ "Spart: " + n.stars_count + "<br/>" +
+ "Super: " + n.super + "<br/>" +
+ "Super Hydro: " + n.hydro_super + "<br/>" +
+ "Loc: " + n.loc1 + ", " + n.loc2 + ", " + n.loc3 + "<br/>" +
+ "Width: " + n.width1 + ", " + n.width2 + ", " + n.width3 + "<br/>" +
+ "Hydro h_max: " + n.hydro_h_max + "<br/>" +
+ "Stars h_max: " + n.stars_h_max + "<br/>"
+ )
+ .style("left", (d3.event.pageX) + "px")
+ .style("top", (d3.event.pageY - 28) + "px")
+ // change here to change the tool tip box size
+ .style("height", 180 + "px");
+ })
+ .on("mouseout", function(d) {
+ div.transition()
+ .duration(500)
+ .style("opacity", 0);
+ });
+
+ // Add Circle for the nodes
+ nodeEnter.append('circle')
+ .attr('class', 'node')
+ .attr('r', 1e-6)
+ .style("fill", function(d) {
+ return d._children ? "lightsteelblue" : "#fff";
+ });
+
+ // Add labels for the nodes
+ nodeEnter.append('text')
+ .attr("dy", ".35em")
+ .attr("x", -55)
+ .attr("text-anchor", "start")
+ .attr("transform", "rotate(90)")
+ .text(function(d) { return d.data.name; });
+
+ // add the tool tip
+ var div = d3.select("body").append("div")
+ .attr("class", "tooltip")
+ .style("opacity", 0);
+
+ // UPDATE
+ var nodeUpdate = nodeEnter.merge(node);
+
+ // Transition to the proper position for the node
+ nodeUpdate.transition()
+ .duration(duration)
+ .attr("transform", function(d) {
+ return "translate(" + d.x + "," + d.y + ")";
+ });
+
+ // Update the node attributes and style
+ nodeUpdate.select('circle.node')
+ .attr('r', 10)
+ .style("fill", function(d) {
+ return d._children ? "lightsteelblue" : "#fff";
+ })
+ .attr('cursor', 'pointer');
+
+
+ // Remove any exiting nodes
+ var nodeExit = node.exit().transition()
+ .duration(duration)
+ .attr("transform", function(d) {
+ return "translate(" + source.x + "," + source.y + ")";
+ })
+ .remove();
+
+ // On exit reduce the node circles size to 0
+ nodeExit.select('circle')
+ .attr('r', 1e-6);
+
+ // On exit reduce the opacity of text labels
+ nodeExit.select('text')
+ .style('fill-opacity', 1e-6);
+
+ // ****************** links section ***************************
+
+ // Update the links...
+ var link = svg.selectAll('path.link')
+ .data(links, function(d) { return d.id; });
+
+ // Enter any new links at the parent's previous position.
+ var linkEnter = link.enter().insert('path', "g")
+ .attr("class", "link")
+ .attr('d', function(d){
+ var o = {x: source.x0, y: source.y0}
+ return diagonal(o, o)
+ });
+
+ // UPDATE
+ var linkUpdate = linkEnter.merge(link);
+
+ // Transition back to the parent element position
+ linkUpdate.transition()
+ .duration(duration)
+ .attr('d', function(d){ return diagonal(d, d.parent) });
+
+ // Remove any exiting links
+ var linkExit = link.exit().transition()
+ .duration(duration)
+ .attr('d', function(d) {
+ var o = {x: source.x, y: source.y}
+ return diagonal(o, o)
+ })
+ .remove();
+
+ // Store the old positions for transition.
+ nodes.forEach(function(d){
+ d.x0 = d.x;
+ d.y0 = d.y;
+ });
+
+ // Creates a curved (diagonal) path from parent to the child nodes
+ function diagonal(s, d) {
+
+ path = `M ${s.x} ${s.y}
+ C ${(s.x + d.x) / 2} ${s.y},
+ ${(s.x + d.x) / 2} ${d.y},
+ ${d.x} ${d.y}`
+
+ return path
+ }
+
+ // Toggle children on click.
+ function click(d) {
+ if (d.children) {
+ d._children = d.children;
+ d.children = null;
+ } else {
+ d.children = d._children;
+ d._children = null;
+ }
+ update(d);
+ }
+ }
+
+
+ // Collapse the node and all it's children
+ function collapse(d) {
+ if(d.children) {
+ d._children = d.children
+ d._children.forEach(collapse)
+ d.children = null
+ }
+ }
+
+ // open the node and all it's parent
+ function openNode(d) {
+ if (d._children) {
+ d.children = d._children
+ d._children = null
+ }
+ if (d.parent)
+ openNode(d.parent)
+ }
+
+ var selectedVal;
+
+ function searchSubNode(node) {
+ if (node.data.name == selectedVal) {
+ openNode(node)
+ update(root)
+ return true
+ }
+
+ var found = false
+ if (node.children) {
+ var N = node.children.length
+ for(var i = 0; i < N; i++) {
+ found = searchSubNode(node.children[i])
+ if (found) {
+ break
+ }
+ }
+ }
+
+ if (found)
+ return found
+
+ if (node._children) {
+ var N = node._children.length
+ for(var i = 0; i < N; i++) {
+ found = searchSubNode(node._children[i])
+ if (found) {
+ break
+ }
+ }
+
+ }
+
+ return found
+
+ }
+
+ function searchNode() {
+ //find the node
+ selectedVal = document.getElementById('search').value;
+ var progress = document.getElementById("progress");
+ progress.innerHTML = "0%"
+ progress.value = 0
+
+ var N = root.children.length
+ for(var i = 0; i < N; i++) {
+ var found = searchSubNode(root.children[i], selectedVal)
+
+ if (found) {
+ progress.innerHTML = "100%"
+ progress.value = 100
+ return
+ }
+ else {
+ progress.innerHTML = 100 * i / (N - 1.) + "%"
+ progress.value = 100 * i / (N - 1.)
+ }
+ }
+
+ console.log("Not found")
+ }
+
+
+</script>
+
+ </body>
+</html>
diff --git a/tools/make_cell_hierarchy.sh b/tools/make_cell_hierarchy.sh
new file mode 100644
index 0000000000000000000000000000000000000000..87fbe4c97f4aadcbb9be5867a62e8acb56415820
--- /dev/null
+++ b/tools/make_cell_hierarchy.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+output=cell_hierarchy.html
+
+# merge all mpi ranks together
+csv_output=cell_hierarchy.csv
+if [ -f $csv_output ]
+then
+ rm $csv_output
+fi
+
+for filename in ./cell_hierarchy_*.csv;
+do
+ cat $filename >> cell_hierarchy.csv
+done
+
+# copy HTML page to the repository
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cp $DIR/data/cell_hierarchy.html $output
+
+echo $output has been generated