Merge branch 'gresho_vortex_plotSolution_update' into 'master'

Added improved plotting for the Gresho Vortex

See merge request !1013

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
+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])
 
@@ -72,21 +52,27 @@ 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"]
@@ -95,14 +81,14 @@ 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"][:]
@@ -121,144 +107,183 @@ except:
     plot_viscosity = False
 
 # 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)
 
 if plot_diffusion:
-    alpha_diff_bin,_,_ = stats.binned_statistic(r, diffusion, statistic='mean', bins=r_bin_edge)
-    alpha2_diff_bin,_,_ = stats.binned_statistic(r, diffusion**2, statistic='mean', bins=r_bin_edge)
-    alpha_diff_sigma_bin = np.sqrt(alpha2_diff_bin - alpha_diff_bin**2)
+    alpha_diff_bin, _, _ = stats.binned_statistic(
+        r, diffusion, statistic="mean", bins=r_bin_edge
+    )
+    alpha2_diff_bin, _, _ = stats.binned_statistic(
+        r, diffusion ** 2, statistic="mean", bins=r_bin_edge
+    )
+    alpha_diff_sigma_bin = np.sqrt(alpha2_diff_bin - alpha_diff_bin ** 2)
 
 if plot_viscosity:
-    alpha_visc_bin,_,_ = stats.binned_statistic(r, viscosity, statistic='mean', bins=r_bin_edge)
-    alpha2_visc_bin,_,_ = stats.binned_statistic(r, viscosity**2, statistic='mean', bins=r_bin_edge)
-    alpha_visc_sigma_bin = np.sqrt(alpha2_visc_bin - alpha_visc_bin**2)
+    alpha_visc_bin, _, _ = stats.binned_statistic(
+        r, viscosity, statistic="mean", bins=r_bin_edge
+    )
+    alpha2_visc_bin, _, _ = stats.binned_statistic(
+        r, viscosity ** 2, statistic="mean", bins=r_bin_edge
+    )
+    alpha_visc_sigma_bin = np.sqrt(alpha2_visc_bin - alpha_visc_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=0.1,
+    zorder=-1,
+    rasterized=True,