Merge remote-tracking branch 'origin/master' into back_of_the_queue

configure.ac

@@ -407,6 +407,24 @@ if test "$enable_memuse_reports" = "yes"; then
    AC_DEFINE([SWIFT_MEMUSE_REPORTS],1,[Enable memory usage reports])
 fi
 
+# The system memory report depends on the presence of /proc/self/statm, i.e.
+# a linux OS, check for that.
+if test -f "/proc/self/statm"; then
+   AC_DEFINE([SWIFT_MEMUSE_STATM],1,[Have /proc/self/statm capability])
+fi
+
+# Check if we want to make the dumper thread active.
+AC_ARG_ENABLE([dumper],
+   [AS_HELP_STRING([--enable-dumper],
+     [Dump active tasks and memory use (if configured)@<:@yes/no@:>@]
+   )],
+   [enable_dumper="$enableval"],
+   [enable_dumper="no"]
+)
+if test "$enable_dumper" = "yes"; then
+   AC_DEFINE([SWIFT_DUMPER_THREAD],1,[Enable dumper thread])
+fi
+
 # See if we want mpi reporting.
 AC_ARG_ENABLE([mpiuse-reports],
    [AS_HELP_STRING([--enable-mpiuse-reports],
@@ -1208,6 +1226,17 @@ fi
 AC_SUBST([VELOCIRAPTOR_LIBS])
 AM_CONDITIONAL([HAVEVELOCIRAPTOR],[test -n "$VELOCIRAPTOR_LIBS"])
 
+# Now that we found VELOCIraptor, let's check how it was compiled.
+if test "$have_velociraptor" == "yes"; then
+    AC_CHECK_LIB(
+       [velociraptor],
+       [VR_NOMASS],
+       [AC_DEFINE([HAVE_VELOCIRAPTOR_WITH_NOMASS],1,[The VELOCIraptor library has been compiled with the NOMASS option. Only useful if running a uniform box.])],
+       [AC_MSG_RESULT(VELOCIraptor not compiled to so as to *not* store masses per particle.)],
+       [$VELOCIRAPTOR_LIBS $HDF5_LDFLAGS $HDF5_LIBS $GSL_LIBS]
+    )
+fi
+
 # Check for dummy VELOCIraptor.
 AC_ARG_ENABLE([dummy-velociraptor],
     [AS_HELP_STRING([--enable-dummy-velociraptor],
@@ -1899,7 +1928,7 @@ esac
 # Feedback model
 AC_ARG_WITH([feedback],
    [AS_HELP_STRING([--with-feedback=<model>],
-      [Feedback model to use @<:@none, EAGLE, debug default: none@:>@]
+      [Feedback model to use @<:@none, EAGLE, GEAR default: none@:>@]
    )],
    [with_feedback="$withval"],
    [with_feedback="none"]
@@ -1932,7 +1961,7 @@ esac
 # Black hole model.
 AC_ARG_WITH([black-holes],
    [AS_HELP_STRING([--with-black-holes=<model>],
-      [Black holes model to use @<:@none, default: none@:>@]
+      [Black holes model to use @<:@none, EAGLE default: none@:>@]
    )],
    [with_black_holes="$withval"],
    [with_black_holes="none"]
@@ -1961,14 +1990,14 @@ esac
 # Task order
 AC_ARG_WITH([task-order],
 [AS_HELP_STRING([--with-task-order=<model>],
-[Task order to use @<:@none, EAGLE, GEAR default: none@:>@]
+[Task order to use @<:@default, EAGLE, GEAR default: default@:>@]
 )],
 [with_task_order="$withval"],
-[with_task_order="none"]
+[with_task_order="default"]
 )
 
 if test "$with_subgrid" != "none"; then
-if test "$with_task_order" != "none"; then
+if test "$with_task_order" != "default"; then
 AC_MSG_ERROR([Cannot provide with-subgrid and with-task-order together])
 else
 with_task_order="$with_subgrid_task_order"
@@ -1979,8 +2008,8 @@ case "$with_task_order" in
 EAGLE)
 AC_DEFINE([TASK_ORDER_EAGLE], [1], [EAGLE task order])
 ;;
-none)
-AC_DEFINE([TASK_ORDER_NONE], [1], [Default task order])
+default)
+AC_DEFINE([TASK_ORDER_NONE], [1], [Default (i.e. EAGLE/OWLS) task order])
 ;;
 GEAR)
 AC_DEFINE([TASK_ORDER_GEAR], [1], [GEAR task order])

doc/RTD/source/EquationOfState/index.rst

@@ -7,18 +7,24 @@
 Equations of State
 ==================
 
-Currently (if the documentation was well updated), we have two different gas
-equations of state (EoS) implemented: ideal and isothermal; as well as a variety  
-of EoS for "planetary" materials. 
-The EoS describe the relations between our main thermodynamical variables: 
-the internal energy (\\(u\\)), the density (\\(\\rho\\)), the entropy (\\(A\\)) 
-and the pressure (\\(P\\)).
+Currently, SWIFT offers two different gas equations of state (EoS)
+implemented: ``ideal`` and ``isothermal``; as well as a variety of EoS for
+"planetary" materials.  The EoS describe the relations between our
+main thermodynamical variables: the internal energy per unit mass
+(\\(u\\)), the mass density (\\(\\rho\\)), the entropy (\\(A\\)) and
+the pressure (\\(P\\)).
 
 Gas EoS
 -------
 
-In the following section, the variables not yet defined are: \\(\\gamma\\) for
-the adiabatic index and \\( c_s \\) for the speed of sound.
+We write the adiabatic index as \\(\\gamma \\) and \\( c_s \\) denotes
+the speed of sound. The adiabatic index can be changed at configure
+time by choosing one of the allowed values of the option
+``--with-adiabatic-index``. The default value is \\(\\gamma = 5/3 \\).
+
+The tables below give the expression for the thermodynamic quantities
+on each row entry as a function of the gas density and the
+thermodynamical quantity given in the header of each column.
 
 .. csv-table:: Ideal Gas
    :header: "Variable", "A", "u", "P"
@@ -38,7 +44,11 @@ the adiabatic index and \\( c_s \\) for the speed of sound.
    "P", "", "\\(\\left( \\gamma - 1\\right) u \\rho \\)", ""
    "\\( c_s\\)", "", "\\(\\sqrt{ u \\gamma \\left( \\gamma - 1 \\right) } \\)", ""
 
-
+Note that when running with an isothermal equation of state, the value
+of the tracked thermodynamic variable (e.g. the entropy in a
+density-entropy scheme or the internal enegy in a density-energy SPH
+formulation) written to the snapshots is meaningless. The pressure,
+however, is always correct in all scheme.
 
 Planetary EoS
 -------------

doc/RTD/source/ParameterFiles/parameter_description.rst

@@ -986,26 +986,34 @@ should contain. The type of partitioning attempted is controlled by the::
   DomainDecomposition:
     initial_type:
 
-parameter. Which can have the values *memory*, *region*, *grid* or
+parameter. Which can have the values *memory*, *edgememory*, *region*, *grid* or
 *vectorized*:
 
+    * *edgememory*
+
+    This is the default if METIS or ParMETIS is available. It performs a
+    partition based on the memory use of all the particles in each cell.
+    The total memory per cell is used to weight the cell vertex and all the
+    associated edges. This attempts to equalize the memory used by all the
+    ranks but with some consideration given to the need to not cut dense
+    regions (by also minimizing the edge cut). How successful this
+    attempt is depends on the granularity of cells and particles and the
+    number of ranks, clearly if most of the particles are in one cell, or a
+    small region of the volume, balance is impossible or difficult. Having
+    more top-level cells makes it easier to calculate a good distribution
+    (but this comes at the cost of greater overheads).
 
     * *memory*
 
-    This is the default if METIS or ParMETIS is available. It performs a
-    partition based on the memory use of all the particles in each cell,
-    attempting to equalize the memory used by all the ranks.
-    How successful this attempt is depends on the granularity of cells and particles
-    and the number of ranks, clearly if most of the particles are in one cell,
-    or a small region of the volume, balance is impossible or
-    difficult. Having more top-level cells makes it easier to calculate a
-    good distribution (but this comes at the cost of greater overheads).
+    This is like *edgememory*, but doesn't include any edge weights, it should
+    balance the particle memory use per rank more exactly (but note effects
+    like the numbers of cells per rank will also have an effect, as that
+    changes the need for foreign cells).
 
     * *region*
 
     The one other METIS/ParMETIS option is "region". This attempts to assign equal
-    numbers of cells to each rank, with the surface area of the regions minimised
-    (so we get blobs, rather than rectangular volumes of cells).
+    numbers of cells to each rank, with the surface area of the regions minimised.
 
 If ParMETIS and METIS are not available two other options are possible, but
 will give a poorer partition:

examples/GravityTests/DiscPatch/HydroStatic/plotSolution.py

@@ -62,11 +62,9 @@ def get_analytic_pressure(x):
 def get_data(name):
   file = h5py.File(name, "r")
   coords = np.array(file["/PartType0/Coordinates"])
-  rho = np.array(file["/PartType0/Density"])
-  u = np.array(file["/PartType0/InternalEnergy"])
+  rho = np.array(file["/PartType0/Densities"])
   v = np.array(file["/PartType0/Velocities"])
-
-  P = (gamma - 1.) * rho * u
+  P = np.array(file["/PartType0/Pressures"])
 
   vtot = np.sqrt( v[:,0]**2 + v[:,1]**2 + v[:,2]**2 )
 
@@ -79,7 +77,7 @@ for f in sorted(glob.glob("Disc-Patch_*.hdf5")):
   if num < start or num > stop:
     continue
 
-  print "processing", f, "..."
+  print("processing", f, "...")
 
   xrange = np.linspace(0., 2. * x_disc, 1000)
   time, x, rho, P, v = get_data(f)

examples/HydroTests/GreshoVortex_2D/plotSolution.py

 ###############################################################################
- # This file is part of SWIFT.
- # Copyright (c) 2016  Matthieu Schaller (matthieu.schaller@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/>.
- # 
- ##############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016  Matthieu Schaller (matthieu.schaller@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/>.
+#
+##############################################################################
 
 # Computes the analytical solution of the Gresho-Chan vortex and plots the SPH answer
 
 # Parameters
-gas_gamma = 5./3.     # Gas adiabatic index
-rho0 = 1          # Gas density
-P0 = 0.           # Constant additional pressure (should have no impact on the dynamics)
+gas_gamma = 5.0 / 3.0  # Gas adiabatic index
+rho0 = 1  # Gas density
+P0 = 0.0  # Constant additional pressure (should have no impact on the dynamics)
 
 # ---------------------------------------------------------------
 # Don't touch anything after this.
 # ---------------------------------------------------------------
 
 import matplotlib
+
 matplotlib.use("Agg")
 from pylab import *
 from scipy import stats
 import h5py
 
-# Plot parameters
-params = {'axes.labelsize': 10,
-'axes.titlesize': 10,
-'font.size': 12,
-'legend.fontsize': 12,
-'xtick.labelsize': 10,
-'ytick.labelsize': 10,
-'text.usetex': True,
- 'figure.figsize' : (9.90,6.45),
-'figure.subplot.left'    : 0.045,
-'figure.subplot.right'   : 0.99,
-'figure.subplot.bottom'  : 0.05,
-'figure.subplot.top'     : 0.99,
-'figure.subplot.wspace'  : 0.15,
-'figure.subplot.hspace'  : 0.12,
-'lines.markersize' : 6,
-'lines.linewidth' : 3.,
-'text.latex.unicode': True
-}
-rcParams.update(params)
-rc('font',**{'family':'sans-serif','sans-serif':['Times']})
-
+style.use("../../../tools/stylesheets/mnras.mplstyle")
 
 snap = int(sys.argv[1])
 
@@ -69,21 +49,27 @@ solution_v_r = zeros(N)
 
 for i in range(N):
     if solution_r[i] < 0.2:
-        solution_P[i] = P0 + 5. + 12.5*solution_r[i]**2
-        solution_v_phi[i] = 5.*solution_r[i]
+        solution_P[i] = P0 + 5.0 + 12.5 * solution_r[i] ** 2
+        solution_v_phi[i] = 5.0 * solution_r[i]
     elif solution_r[i] < 0.4:
-        solution_P[i] = P0 + 9. + 12.5*solution_r[i]**2 - 20.*solution_r[i] + 4.*log(solution_r[i]/0.2)
-        solution_v_phi[i] = 2. -5.*solution_r[i]
+        solution_P[i] = (
+            P0
+            + 9.0
+            + 12.5 * solution_r[i] ** 2
+            - 20.0 * solution_r[i]
+            + 4.0 * log(solution_r[i] / 0.2)
+        )
+        solution_v_phi[i] = 2.0 - 5.0 * solution_r[i]
     else:
-        solution_P[i] = P0 + 3. + 4.*log(2.)
-        solution_v_phi[i] = 0.
+        solution_P[i] = P0 + 3.0 + 4.0 * log(2.0)
+        solution_v_phi[i] = 0.0
 
 solution_rho = ones(N) * rho0
-solution_s = solution_P / solution_rho**gas_gamma
-solution_u = solution_P /((gas_gamma - 1.)*solution_rho)
+solution_s = solution_P / solution_rho ** gas_gamma
+solution_u = solution_P / ((gas_gamma - 1.0) * solution_rho)
 
 # Read the simulation data
-sim = h5py.File("gresho_%04d.hdf5"%snap, "r")
+sim = h5py.File("gresho_%04d.hdf5" % snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]
@@ -92,133 +78,153 @@ neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"]
 eta = sim["/HydroScheme"].attrs["Kernel eta"]
 git = sim["Code"].attrs["Git Revision"]
 
-pos = sim["/PartType0/Coordinates"][:,:]
-x = pos[:,0] - boxSize / 2
-y = pos[:,1] - boxSize / 2
-vel = sim["/PartType0/Velocities"][:,:]
-r = sqrt(x**2 + y**2)
-v_r = (x * vel[:,0] + y * vel[:,1]) / r
-v_phi = (-y * vel[:,0] + x * vel[:,1]) / r
-v_norm = sqrt(vel[:,0]**2 + vel[:,1]**2)
+pos = sim["/PartType0/Coordinates"][:, :]
+x = pos[:, 0] - boxSize / 2
+y = pos[:, 1] - boxSize / 2
+vel = sim["/PartType0/Velocities"][:, :]
+r = sqrt(x ** 2 + y ** 2)
+v_r = (x * vel[:, 0] + y * vel[:, 1]) / r
+v_phi = (-y * vel[:, 0] + x * vel[:, 1]) / r
+v_norm = sqrt(vel[:, 0] ** 2 + vel[:, 1] ** 2)
 rho = sim["/PartType0/Densities"][:]
 u = sim["/PartType0/InternalEnergies"][:]
 S = sim["/PartType0/Entropies"][:]
 P = sim["/PartType0/Pressures"][:]
 
 # Bin te data
-r_bin_edge = np.arange(0., 1., 0.02)
-r_bin = 0.5*(r_bin_edge[1:] + r_bin_edge[:-1])
-rho_bin,_,_ = stats.binned_statistic(r, rho, statistic='mean', bins=r_bin_edge)
-v_bin,_,_ = stats.binned_statistic(r, v_phi, statistic='mean', bins=r_bin_edge)
-P_bin,_,_ = stats.binned_statistic(r, P, statistic='mean', bins=r_bin_edge)
-S_bin,_,_ = stats.binned_statistic(r, S, statistic='mean', bins=r_bin_edge)
-u_bin,_,_ = stats.binned_statistic(r, u, statistic='mean', bins=r_bin_edge)
-rho2_bin,_,_ = stats.binned_statistic(r, rho**2, statistic='mean', bins=r_bin_edge)
-v2_bin,_,_ = stats.binned_statistic(r, v_phi**2, statistic='mean', bins=r_bin_edge)
-P2_bin,_,_ = stats.binned_statistic(r, P**2, statistic='mean', bins=r_bin_edge)
-S2_bin,_,_ = stats.binned_statistic(r, S**2, statistic='mean', bins=r_bin_edge)
-u2_bin,_,_ = stats.binned_statistic(r, u**2, statistic='mean', bins=r_bin_edge)
-rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2)
-v_sigma_bin = np.sqrt(v2_bin - v_bin**2)
-P_sigma_bin = np.sqrt(P2_bin - P_bin**2)
-S_sigma_bin = np.sqrt(S2_bin - S_bin**2)
-u_sigma_bin = np.sqrt(u2_bin - u_bin**2)
+r_bin_edge = np.arange(0.0, 1.0, 0.02)
+r_bin = 0.5 * (r_bin_edge[1:] + r_bin_edge[:-1])
+rho_bin, _, _ = stats.binned_statistic(r, rho, statistic="mean", bins=r_bin_edge)
+v_bin, _, _ = stats.binned_statistic(r, v_phi, statistic="mean", bins=r_bin_edge)
+P_bin, _, _ = stats.binned_statistic(r, P, statistic="mean", bins=r_bin_edge)
+S_bin, _, _ = stats.binned_statistic(r, S, statistic="mean", bins=r_bin_edge)
+u_bin, _, _ = stats.binned_statistic(r, u, statistic="mean", bins=r_bin_edge)
+rho2_bin, _, _ = stats.binned_statistic(r, rho ** 2, statistic="mean", bins=r_bin_edge)
+v2_bin, _, _ = stats.binned_statistic(r, v_phi ** 2, statistic="mean", bins=r_bin_edge)
+P2_bin, _, _ = stats.binned_statistic(r, P ** 2, statistic="mean", bins=r_bin_edge)
+S2_bin, _, _ = stats.binned_statistic(r, S ** 2, statistic="mean", bins=r_bin_edge)
+u2_bin, _, _ = stats.binned_statistic(r, u ** 2, statistic="mean", bins=r_bin_edge)
+rho_sigma_bin = np.sqrt(rho2_bin - rho_bin ** 2)
+v_sigma_bin = np.sqrt(v2_bin - v_bin ** 2)
+P_sigma_bin = np.sqrt(P2_bin - P_bin ** 2)
+S_sigma_bin = np.sqrt(S2_bin - S_bin ** 2)
+u_sigma_bin = np.sqrt(u2_bin - u_bin ** 2)
 
 
 # Plot the interesting quantities
-figure()
+figure(figsize=(7, 7 / 1.6))
+
+line_color = "C4"
+binned_color = "C2"
+binned_marker_size = 4
 
+scatter_props = dict(
+    marker=".",
+    ms=1,
+    markeredgecolor="none",
+    alpha=0.5,
+    zorder=-1,
+    rasterized=True,
+    linestyle="none",
+)
+
+errorbar_props = dict(color=binned_color, ms=binned_marker_size, fmt=".", lw=1.2)
 
 # Azimuthal velocity profile -----------------------------
 subplot(231)
 
-plot(r, v_phi, '.', color='r', ms=0.5)
-plot(solution_r, solution_v_phi, '--', color='k', alpha=0.8, lw=1.2)
-errorbar(r_bin, v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
-plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-xlabel("${\\rm{Radius}}~r$", labelpad=0)
-ylabel("${\\rm{Azimuthal~velocity}}~v_\\phi$", labelpad=0)
-xlim(0,R_max)
+plot(r, v_phi, **scatter_props)
+plot(solution_r, solution_v_phi, "--", color=line_color, alpha=0.8, lw=1.2)
+errorbar(r_bin, v_bin, yerr=v_sigma_bin, **errorbar_props)
+plot([0.2, 0.2], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+plot([0.4, 0.4], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+xlabel("Radius $r$")
+ylabel("Azimuthal velocity $v_\\phi$")
+xlim(0, R_max)
 ylim(-0.1, 1.2)
 
 # Radial density profile --------------------------------
 subplot(232)
 
-plot(r, rho, '.', color='r', ms=0.5)
-plot(solution_r, solution_rho, '--', color='k', alpha=0.8, lw=1.2)
-errorbar(r_bin, rho_bin, yerr=rho_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
-plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-xlabel("${\\rm{Radius}}~r$", labelpad=0)
-ylabel("${\\rm{Density}}~\\rho$", labelpad=0)
-xlim(0,R_max)
-ylim(rho0-0.3, rho0 + 0.3)
-#yticks([-0.2, -0.1, 0., 0.1, 0.2])
+plot(r, rho, **scatter_props)
+plot(solution_r, solution_rho, "--", color=line_color, alpha=0.8, lw=1.2)
+errorbar(r_bin, rho_bin, yerr=rho_sigma_bin, **errorbar_props)
+plot([0.2, 0.2], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+plot([0.4, 0.4], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+xlabel("Radius $r$")
+ylabel("Density $\\rho$")
+xlim(0, R_max)
+ylim(rho0 - 0.3, rho0 + 0.3)
+# yticks([-0.2, -0.1, 0., 0.1, 0.2])
 
 # Radial pressure profile --------------------------------
 subplot(233)
 
-plot(r, P, '.', color='r', ms=0.5)
-plot(solution_r, solution_P, '--', color='k', alpha=0.8, lw=1.2)
-errorbar(r_bin, P_bin, yerr=P_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
-plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-xlabel("${\\rm{Radius}}~r$", labelpad=0)
-ylabel("${\\rm{Pressure}}~P$", labelpad=0)
+plot(r, P, **scatter_props)
+plot(solution_r, solution_P, "--", color=line_color, alpha=0.8, lw=1.2)
+errorbar(r_bin, P_bin, yerr=P_sigma_bin, **errorbar_props)
+plot([0.2, 0.2], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+plot([0.4, 0.4], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+xlabel("Radius $r$")
+ylabel("Pressure $P$")
 xlim(0, R_max)
 ylim(4.9 + P0, P0 + 6.1)
 
 # Internal energy profile --------------------------------
 subplot(234)
 
-plot(r, u, '.', color='r', ms=0.5)
-plot(solution_r, solution_u, '--', color='k', alpha=0.8, lw=1.2)
-errorbar(r_bin, u_bin, yerr=u_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
-plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-xlabel("${\\rm{Radius}}~r$", labelpad=0)
-ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0)
-xlim(0,R_max)
+plot(r, u, **scatter_props)
+plot(solution_r, solution_u, "--", color=line_color, alpha=0.8, lw=1.2)
+errorbar(r_bin, u_bin, yerr=u_sigma_bin, **errorbar_props)
+plot([0.2, 0.2], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+plot([0.4, 0.4], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+xlabel("$Radius $r$")
+ylabel("Internal Energy $u$")
+xlim(0, R_max)
 ylim(7.3, 9.1)
 
 
 # Radial entropy profile --------------------------------
 subplot(235)
 
-plot(r, S, '.', color='r', ms=0.5)
-plot(solution_r, solution_s, '--', color='k', alpha=0.8, lw=1.2)
-errorbar(r_bin, S_bin, yerr=S_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
-plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
-xlabel("${\\rm{Radius}}~r$", labelpad=0)
-ylabel("${\\rm{Entropy}}~S$", labelpad=0)
+plot(r, S, **scatter_props)
+plot(solution_r, solution_s, "--", color=line_color, alpha=0.8, lw=1.2)
+errorbar(r_bin, S_bin, yerr=S_sigma_bin, **errorbar_props)
+plot([0.2, 0.2], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+plot([0.4, 0.4], [-100, 100], ":", color=line_color, alpha=0.4, lw=1.2)
+xlabel("Radius $r$")
+ylabel("Entropy $S$")
 xlim(0, R_max)
 ylim(4.9 + P0, P0 + 6.1)
 
-# Image --------------------------------------------------
-#subplot(234)
-#scatter(pos[:,0], pos[:,1], c=v_norm, cmap="PuBu", edgecolors='face', s=4, vmin=0, vmax=1)
-#text(0.95, 0.95, "$|v|$", ha="right", va="top")
-#xlim(0,1)
-#ylim(0,1)
-#xlabel("$x$", labelpad=0)
-#ylabel("$y$", labelpad=0)
-
 # Information -------------------------------------
 subplot(236, frameon=False)
 
-text(-0.49, 0.9, "Gresho-Chan vortex with  $\\gamma=%.3f$ at $t=%.2f$"%(gas_gamma,time), fontsize=10)
-text(-0.49, 0.8, "Background $\\rho_0=%.3f$"%rho0, fontsize=10)
-text(-0.49, 0.7, "Background $P_0=%.3f$"%P0, fontsize=10)
-plot([-0.49, 0.1], [0.62, 0.62], 'k-', lw=1)
-text(-0.49, 0.5, "$\\textsc{Swift}$ %s"%git, fontsize=10)
-text(-0.49, 0.4, scheme, fontsize=10)
-text(-0.49, 0.3, kernel, fontsize=10)
-text(-0.49, 0.2, "$%.2f$ neighbours ($\\eta=%.3f$)"%(neighbours, eta), fontsize=10)
+text_fontsize = 5
+
+text(
+    -0.49,
+    0.9,
+    "Gresho-Chan vortex (2D) with $\\gamma=%.3f$ at $t=%.2f$" % (gas_gamma, time),
+    fontsize=text_fontsize,
+)
+text(-0.49, 0.8, "Background $\\rho_0=%.3f$" % rho0, fontsize=text_fontsize)
+text(-0.49, 0.7, "Background $P_0=%.3f$" % P0, fontsize=text_fontsize)
+plot([-0.49, 0.1], [0.62, 0.62], "k-", lw=1)
+text(-0.49, 0.5, "SWIFT %s" % git.decode("utf-8"), fontsize=text_fontsize)
+text(-0.49, 0.4, scheme.decode("utf-8"), fontsize=text_fontsize)
+text(-0.49, 0.3, kernel.decode("utf-8"), fontsize=text_fontsize)
+text(
+    -0.49,
+    0.2,
+    "$%.2f$ neighbours ($\\eta=%.3f$)" % (neighbours, eta),
+    fontsize=text_fontsize,
+)
 xlim(-0.5, 0.5)
 ylim(0, 1)
 xticks([])
 yticks([])
 
-savefig("GreshoVortex.png", dpi=200)
+tight_layout()
+
+savefig("GreshoVortex.png")

examples/HydroTests/GreshoVortex_3D/plotSolution.py

@@ -22,43 +22,23 @@
 # answer
 
 # Parameters
-gas_gamma = 5./3. # Gas adiabatic index
-rho0 = 1          # Gas density
-P0 = 0.           # Constant additional pressure (should have no impact on the
-                  # dynamics)
+gas_gamma = 5.0 / 3.0  # Gas adiabatic index