diff --git a/examples/EvrardCollapse_3D/evrard.yml b/examples/EvrardCollapse_3D/evrard.yml
new file mode 100644
index 0000000000000000000000000000000000000000..006a22e65d3f674f124ce6c4994e752ba39cd1e1
--- /dev/null
+++ b/examples/EvrardCollapse_3D/evrard.yml
@@ -0,0 +1,44 @@
+# 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: 0.8 # 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-3 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: evrard # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters for the self-gravity scheme
+Gravity:
+ eta: 0.025 # Constant dimensionless multiplier for time integration.
+ epsilon: 0.001 # Softening length (in internal units).
+ theta: 0.9
+ a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
+ r_cut: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./evrard.hdf5 # The file to read
+
+PhysicalConstants:
+ G: 1.
diff --git a/examples/EvrardCollapse_3D/getReference.sh b/examples/EvrardCollapse_3D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f8de6015c89ea78169c078217f04cc539f28efa8
--- /dev/null
+++ b/examples/EvrardCollapse_3D/getReference.sh
@@ -0,0 +1,2 @@
+#! /bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/evrardCollapse3D_exact.txt
diff --git a/examples/EvrardCollapse_3D/makeIC.py b/examples/EvrardCollapse_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..b68f0da0e1869ce54ae7ab2ad3b33b8c3deb8b51
--- /dev/null
+++ b/examples/EvrardCollapse_3D/makeIC.py
@@ -0,0 +1,95 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+from numpy import *
+
+# Generates a swift IC file for the Evrard collapse
+
+# Parameters
+gamma = 5. / 3. # Gas adiabatic index
+M = 1. # total mass of the sphere
+R = 1. # radius of the sphere
+u0 = 0.05 / M # initial thermal energy
+fileName = "evrard.hdf5"
+numPart = 100000
+
+r = R * sqrt(random.random(numPart))
+phi = 2. * pi * random.random(numPart)
+cos_theta = 2. * random.random(numPart) - 1.
+
+sin_theta = sqrt(1. - cos_theta**2)
+cos_phi = cos(phi)
+sin_phi = sin(phi)
+
+pos = zeros((numPart, 3))
+pos[:,0] = r * sin_theta * cos_phi
+pos[:,1] = r * sin_theta * sin_phi
+pos[:,2] = r * cos_theta
+
+# shift particles to put the sphere in the centre of the box
+pos += array([50. * R, 50. * R, 50. * R])
+
+h = ones(numPart) * 2. * R / numPart**(1. / 3.)
+
+# Generate extra arrays
+v = zeros((numPart, 3))
+ids = linspace(1, numPart, numPart)
+m = ones(numPart) * M / numPart
+u = ones(numPart) * u0
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [100. * R, 100. * R, 100. * R]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 0
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+file.close()
diff --git a/examples/EvrardCollapse_3D/plotSolution.py b/examples/EvrardCollapse_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..8422b9c45fd573f3d0ae36324d6e39ab23cceb25
--- /dev/null
+++ b/examples/EvrardCollapse_3D/plotSolution.py
@@ -0,0 +1,172 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+# Compares the swift result for the 2D spherical Sod shock with a high
+# resolution 2D reference result
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+from scipy import stats
+import h5py
+
+# Parameters
+gas_gamma = 5./3. # Polytropic index
+rho_L = 1. # Density left state
+rho_R = 0.125 # Density right state
+v_L = 0. # Velocity left state
+v_R = 0. # Velocity right state
+P_L = 1. # Pressure left state
+P_R = 0.1 # Pressure right state
+
+# 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']})
+
+snap = int(sys.argv[1])
+
+# Read the simulation data
+sim = h5py.File("evrard_%04d.hdf5"%snap, "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"]
+kernel = sim["/HydroScheme"].attrs["Kernel function"]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"]
+eta = sim["/HydroScheme"].attrs["Kernel eta"]
+git = sim["Code"].attrs["Git Revision"]
+
+coords = sim["/PartType0/Coordinates"]
+x = sqrt((coords[:,0] - 0.5 * boxSize)**2 + (coords[:,1] - 0.5 * boxSize)**2 + \
+ (coords[:,2] - 0.5 * boxSize)**2)
+vels = sim["/PartType0/Velocities"]
+v = sqrt(vels[:,0]**2 + vels[:,1]**2 + vels[:,2]**2)
+u = sim["/PartType0/InternalEnergy"][:]
+S = sim["/PartType0/Entropy"][:]
+P = sim["/PartType0/Pressure"][:]
+rho = sim["/PartType0/Density"][:]
+
+# Bin the data
+x_bin_edge = logspace(-3., log10(2.), 100)
+x_bin = 0.5*(x_bin_edge[1:] + x_bin_edge[:-1])
+rho_bin,_,_ = stats.binned_statistic(x, rho, statistic='mean', bins=x_bin_edge)
+v_bin,_,_ = stats.binned_statistic(x, v, statistic='mean', bins=x_bin_edge)
+P_bin,_,_ = stats.binned_statistic(x, P, statistic='mean', bins=x_bin_edge)
+S_bin,_,_ = stats.binned_statistic(x, S, statistic='mean', bins=x_bin_edge)
+u_bin,_,_ = stats.binned_statistic(x, u, statistic='mean', bins=x_bin_edge)
+rho2_bin,_,_ = stats.binned_statistic(x, rho**2, statistic='mean', bins=x_bin_edge)
+v2_bin,_,_ = stats.binned_statistic(x, v**2, statistic='mean', bins=x_bin_edge)
+P2_bin,_,_ = stats.binned_statistic(x, P**2, statistic='mean', bins=x_bin_edge)
+S2_bin,_,_ = stats.binned_statistic(x, S**2, statistic='mean', bins=x_bin_edge)
+u2_bin,_,_ = stats.binned_statistic(x, u**2, statistic='mean', bins=x_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)
+
+ref = loadtxt("evrardCollapse3D_exact.txt")
+
+# Plot the interesting quantities
+figure()
+
+# Velocity profile --------------------------------
+subplot(231)
+semilogx(x, -v, '.', color='r', ms=0.2)
+semilogx(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, -v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
+xlim(1.e-3, 2.)
+ylim(-1.7, 0.1)
+
+# Density profile --------------------------------
+subplot(232)
+loglog(x, rho, '.', color='r', ms=0.2)
+loglog(ref[:,0], ref[:,1], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, rho_bin, yerr=rho_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Density}}~\\rho$", labelpad=0)
+xlim(1.e-3, 2.)
+ylim(1.e-2, 1.e4)
+
+# Pressure profile --------------------------------
+subplot(233)
+loglog(x, P, '.', color='r', ms=0.2)
+loglog(ref[:,0], ref[:,3], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, P_bin, yerr=P_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Pressure}}~P$", labelpad=0)
+xlim(1.e-3, 2.)
+ylim(1.e-4, 1.e3)
+
+# Internal energy profile -------------------------
+subplot(234)
+loglog(x, u, '.', color='r', ms=0.2)
+loglog(ref[:,0], ref[:,3] / ref[:,1] / (gas_gamma - 1.), "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, u_bin, yerr=u_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0)
+xlim(1.e-3, 2.)
+ylim(1.e-2, 2.)
+
+# Entropy profile ---------------------------------
+subplot(235)
+semilogx(x, S, '.', color='r', ms=0.2)
+semilogx(ref[:,0], ref[:,3] / ref[:,1]**gas_gamma, "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, S_bin, yerr=S_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Entropy}}~S$", labelpad=0)
+xlim(1.e-3, 2.)
+ylim(0., 0.25)
+
+# Information -------------------------------------
+subplot(236, frameon=False)
+
+text(-0.49, 0.9, "Evrard collapse with $\\gamma=%.3f$ in 3D\nat $t=%.2f$"%(gas_gamma,time), 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)
+xlim(-0.5, 0.5)
+ylim(0, 1)
+xticks([])
+yticks([])
+
+tight_layout()
+savefig("EvrardCollapse.png", dpi=200)
diff --git a/examples/EvrardCollapse_3D/run.sh b/examples/EvrardCollapse_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..abb7614f66fc877aa670db9b0e1335fbfe2e85d2
--- /dev/null
+++ b/examples/EvrardCollapse_3D/run.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e evrard.hdf5 ]
+then
+ echo "Generating initial conditions for the Evrard collapse example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -G -t 4 evrard.yml 2>&1 | tee output.log
+
+# Get the high resolution 1D reference result if not present.
+if [ ! -e evrardCollapse3D_exact.txt ]
+then
+ echo "Fetching the reference result for the Evrard collapse example..."
+ ./getReference.sh
+fi
+
+# Plot the solution
+python plotSolution.py 8
diff --git a/examples/GreshoVortex_3D/getGlass.sh b/examples/GreshoVortex_3D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c
--- /dev/null
+++ b/examples/GreshoVortex_3D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
diff --git a/examples/GreshoVortex_3D/gresho.yml b/examples/GreshoVortex_3D/gresho.yml
new file mode 100644
index 0000000000000000000000000000000000000000..df941450196a7de6cd1471e1d258756ca8c36fb1
--- /dev/null
+++ b/examples/GreshoVortex_3D/gresho.yml
@@ -0,0 +1,36 @@
+# 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
+
+Scheduler:
+ max_top_level_cells: 15
+
+# Parameters governing the time integration
+TimeIntegration:
+ time_begin: 0. # The starting time of the simulation (in internal units).
+ time_end: 1. # The end time of the simulation (in internal units).
+ dt_min: 1e-6 # 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: gresho # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 1e-1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./greshoVortex.hdf5 # The file to read
diff --git a/examples/GreshoVortex_3D/makeIC.py b/examples/GreshoVortex_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..cba2158016bc86f58b6e89f83cbfb473798e1cf7
--- /dev/null
+++ b/examples/GreshoVortex_3D/makeIC.py
@@ -0,0 +1,120 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+from numpy import *
+
+# Generates a swift IC file for the Gresho-Chan vortex in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+rho0 = 1 # Gas density
+P0 = 0. # Constant additional pressure (should have no impact on the dynamics)
+fileOutputName = "greshoVortex.hdf5"
+fileGlass = "glassCube_64.hdf5"
+#---------------------------------------------------
+
+# Get position and smoothing lengths from the glass
+fileInput = h5py.File(fileGlass, 'r')
+coords = fileInput["/PartType0/Coordinates"][:,:]
+h = fileInput["/PartType0/SmoothingLength"][:]
+ids = fileInput["/PartType0/ParticleIDs"][:]
+boxSize = fileInput["/Header"].attrs["BoxSize"][0]
+numPart = size(h)
+fileInput.close()
+
+# Now generate the rest
+m = ones(numPart) * rho0 * boxSize**3 / numPart
+u = zeros(numPart)
+v = zeros((numPart, 3))
+
+for i in range(numPart):
+
+ x = coords[i,0]
+ y = coords[i,1]
+
+ r2 = (x - boxSize / 2)**2 + (y - boxSize / 2)**2
+ r = sqrt(r2)
+
+ v_phi = 0.
+ if r < 0.2:
+ v_phi = 5.*r
+ elif r < 0.4:
+ v_phi = 2. - 5.*r
+ else:
+ v_phi = 0.
+ v[i,0] = -v_phi * (y - boxSize / 2) / r
+ v[i,1] = v_phi * (x - boxSize / 2) / r
+ v[i,2] = 0.
+
+ P = P0
+ if r < 0.2:
+ P = P + 5. + 12.5*r2
+ elif r < 0.4:
+ P = P + 9. + 12.5*r2 - 20.*r + 4.*log(r/0.2)
+ else:
+ P = P + 3. + 4.*log(2.)
+ u[i] = P / ((gamma - 1.)*rho0)
+
+
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [boxSize, boxSize, boxSize]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFileOutputsPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = fileOutput.create_group("/PartType0")
+ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = coords
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = v
+ds = grp.create_dataset('Masses', (numPart, 1), 'f')
+ds[()] = m.reshape((numPart,1))
+ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
+ds[()] = h.reshape((numPart,1))
+ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
+ds[()] = u.reshape((numPart,1))
+ds = grp.create_dataset('ParticleIDs', (numPart,1), 'L')
+ds[()] = ids.reshape((numPart,1))
+
+fileOutput.close()
diff --git a/examples/GreshoVortex_3D/plotSolution.py b/examples/GreshoVortex_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..8fddf148bd169310d5e69ffbfa4a6de099068c69
--- /dev/null
+++ b/examples/GreshoVortex_3D/plotSolution.py
@@ -0,0 +1,227 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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)
+
+# ---------------------------------------------------------------
+# 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']})
+
+
+snap = int(sys.argv[1])
+
+# Generate the analytic solution at this time
+N = 200
+R_max = 0.8
+solution_r = arange(0, R_max, R_max / N)
+solution_P = zeros(N)
+solution_v_phi = zeros(N)
+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]
+ 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]
+ else:
+ solution_P[i] = P0 + 3. + 4.*log(2.)
+ solution_v_phi[i] = 0.
+
+solution_rho = ones(N) * rho0
+solution_s = solution_P / solution_rho**gas_gamma
+solution_u = solution_P /((gas_gamma - 1.)*solution_rho)
+
+# Read the simulation data
+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"]
+kernel = sim["/HydroScheme"].attrs["Kernel function"]
+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)
+rho = sim["/PartType0/Density"][:]
+u = sim["/PartType0/InternalEnergy"][:]
+S = sim["/PartType0/Entropy"][:]
+P = sim["/PartType0/Pressure"][:]
+
+# 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)
+
+
+# Plot the interesting quantities
+figure()
+
+
+# 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)
+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])
+
+# 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)
+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)
+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)
+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)
+xlim(-0.5, 0.5)
+ylim(0, 1)
+xticks([])
+yticks([])
+
+savefig("GreshoVortex.png", dpi=200)
diff --git a/examples/GreshoVortex_3D/run.sh b/examples/GreshoVortex_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..da7d6cee111aebcfd2fcb0f3508af80ef73cbeb0
--- /dev/null
+++ b/examples/GreshoVortex_3D/run.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e glassCube_64.hdf5 ]
+then
+ echo "Fetching initial glass file for the Gresho-Chan vortex example..."
+ ./getGlass.sh
+fi
+if [ ! -e greshoVortex.hdf5 ]
+then
+ echo "Generating initial conditions for the Gresho-Chan vortex example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 4 gresho.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 11
diff --git a/examples/InteractingBlastWaves_1D/getReference.sh b/examples/InteractingBlastWaves_1D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9b6e884850571f7dfbc3f2018235118447bc00be
--- /dev/null
+++ b/examples/InteractingBlastWaves_1D/getReference.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/interactingBlastWaves1D_exact.txt
diff --git a/examples/InteractingBlastWaves_1D/plotSolution.py b/examples/InteractingBlastWaves_1D/plotSolution.py
index 342b67eae1061a9a94675a59f53ebf9e4ba7717f..1719162dec34626d6f4ecb8267c4d06f85b3db26 100644
--- a/examples/InteractingBlastWaves_1D/plotSolution.py
+++ b/examples/InteractingBlastWaves_1D/plotSolution.py
@@ -17,21 +17,116 @@
#
##############################################################################
-import h5py
+import numpy as np
import matplotlib
matplotlib.use("Agg")
import pylab as pl
+import h5py
import sys
+# Parameters
+gamma = 1.4 # Polytropic index
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
snap = int(sys.argv[1])
-sim = h5py.File("interactingBlastWaves_%04d.hdf5" % snap, "r")
-coords = sim["/PartType0/Coordinates"]
-rho = sim["/PartType0/Density"]
+# Open the file and read the relevant data
+file = h5py.File("interactingBlastWaves_{0:04d}.hdf5".format(snap), "r")
+x = file["/PartType0/Coordinates"][:,0]
+rho = file["/PartType0/Density"]
+v = file["/PartType0/Velocities"][:,0]
+u = file["/PartType0/InternalEnergy"]
+S = file["/PartType0/Entropy"]
+P = file["/PartType0/Pressure"]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+ref = np.loadtxt("interactingBlastWaves1D_exact.txt")
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 4.)
+ax[0][0].plot(ref[:,0], ref[:,2], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0)
+ax[0][0].set_xlim(0., 1.)
+ax[0][0].set_ylim(-1., 15.)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 4.)
+ax[0][1].plot(ref[:,0], ref[:,1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+ax[0][1].set_xlim(0., 1.)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 4.)
+ax[0][2].plot(ref[:,0], ref[:,3], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+ax[0][2].set_xlim(0., 1.)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 4.)
+ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 1.), "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+ax[1][0].set_xlim(0., 1.)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 4.)
+ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+ax[1][1].set_xlim(0., 1.)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Interacting blast waves test\nwith $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
-pl.xlabel("$x$")
-pl.ylabel("$\\rho{}$")
-pl.xlim(0.4, 1.)
-pl.ylim(0., 7.)
-pl.plot(coords[:,0], rho, "k.")
-pl.savefig("InteractingBlastWaves.png")
+pl.tight_layout()
+pl.savefig("InteractingBlastWaves.png", dpi = 200)
diff --git a/examples/InteractingBlastWaves_1D/run.sh b/examples/InteractingBlastWaves_1D/run.sh
index 65a1a109857da6e32663451430b3284aa7207d5a..31717bd806ddd6c98c24dfc1def6f79dddff42ff 100755
--- a/examples/InteractingBlastWaves_1D/run.sh
+++ b/examples/InteractingBlastWaves_1D/run.sh
@@ -1,6 +1,6 @@
#!/bin/bash
- # Generate the initial conditions if they are not present.
+# Generate the initial conditions if they are not present.
if [ ! -e interactingBlastWaves.hdf5 ]
then
echo "Generating initial conditions for the Sedov blast example..."
@@ -10,5 +10,12 @@ fi
# Run SWIFT
../swift -s -t 1 interactingBlastWaves.yml 2>&1 | tee output.log
+# Get the high resolution reference solution if not present.
+if [ ! -e interactingBlastWaves1D_exact.txt ]
+then
+ echo "Fetching reference solution for the interacting blast waves test..."
+ ./getReference.sh
+fi
+
# Plot the solution
python plotSolution.py 4
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/getGlass.sh b/examples/KelvinHelmholtzGrowthRate_2D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ae3c977064f5e7a408aa249c5fd9089b3c52ecb1
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml b/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml
new file mode 100644
index 0000000000000000000000000000000000000000..380dc2ab3a530e89b952aa41f425e50709d73ee9
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.yml
@@ -0,0 +1,33 @@
+# 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: 4. # The end time of the simulation (in internal units).
+ dt_min: 1e-6 # 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: kelvinHelmholtzGrowthRate # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.04 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./kelvinHelmholtzGrowthRate.hdf5 # The file to read
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py b/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..f21d0c0abf9b15f8253f627bcb1da43ae276fb35
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/makeIC.py
@@ -0,0 +1,100 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+P0 = 2.5 # Pressure
+rho0 = 1. # Density
+d = 0.0317 # Thickness of the transition layer
+B = 0.0005 # Amplitude of the seed velocity
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+glass = h5py.File("glassPlane_128.hdf5", 'r')
+pos = glass["/PartType0/Coordinates"][:, :]
+h = glass["/PartType0/SmoothingLength"][:]
+
+N = len(h)
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+ -0.5 + \
+ 0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+ 0.5 - \
+ 0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+ (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+ np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFileOutputsPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = fileOutput.create_group("/PartType0")
+grp.create_dataset("Coordinates", data = pos, dtype = 'd')
+grp.create_dataset("Velocities", data = v, dtype = 'f')
+grp.create_dataset("Masses", data = m, dtype = 'f')
+grp.create_dataset("SmoothingLength", data = h, dtype = 'f')
+grp.create_dataset("InternalEnergy", data = u, dtype = 'f')
+grp.create_dataset("ParticleIDs", data = ids, dtype = 'L')
+
+fileOutput.close()
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py b/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py
new file mode 100644
index 0000000000000000000000000000000000000000..5029165a6a328b6c706d37b632b14cbcd51501d0
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py
@@ -0,0 +1,106 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+P0 = 2.5 # Pressure
+rho0 = 1. # Density
+d = 0.0317 # Thickness of the transition layer
+B = 0.0005 # Amplitude of the seed velocity
+N1D = 128 # Number of particles in one dimension
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+N = N1D ** 2
+x = np.linspace(0., 1., N1D + 1)
+x = 0.5 * (x[1:] + x[:-1])
+y = x
+xx, yy = np.meshgrid(x, y)
+pos = np.zeros((N, 3))
+pos[:, 0] = xx.reshape((N))
+pos[:, 1] = yy.reshape((N))
+h = np.ones(N) * 2. / N1D
+
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+ -0.5 + \
+ 0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+ 0.5 - \
+ 0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+ (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+ np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFileOutputsPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = fileOutput.create_group("/PartType0")
+grp.create_dataset("Coordinates", data = pos, dtype = 'd')
+grp.create_dataset("Velocities", data = v, dtype = 'f')
+grp.create_dataset("Masses", data = m, dtype = 'f')
+grp.create_dataset("SmoothingLength", data = h, dtype = 'f')
+grp.create_dataset("InternalEnergy", data = u, dtype = 'f')
+grp.create_dataset("ParticleIDs", data = ids, dtype = 'L')
+
+fileOutput.close()
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/plotSolution.py b/examples/KelvinHelmholtzGrowthRate_2D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..b2e3e1766a2b7d2618611aca9fb938ab87d78872
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/plotSolution.py
@@ -0,0 +1,47 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import numpy as np
+import h5py
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import sys
+
+if len(sys.argv) < 2:
+ print "No final snapshot number provided!"
+ exit()
+lastsnap = int(sys.argv[1])
+
+# Read the simulation data
+t = np.zeros(lastsnap + 1)
+ey = np.zeros(lastsnap + 1)
+for i in range(lastsnap + 1):
+ file = h5py.File("kelvinHelmholtzGrowthRate_{0:04d}.hdf5".format(i), 'r')
+ t_snap = float(file["/Header"].attrs["Time"])
+ vy = file["/PartType0/Velocities"][:,1]
+ m = file["/PartType0/Masses"][:]
+
+ ey_snap = 0.5 * m * vy**2
+
+ t[i] = t_snap
+ ey[i] = ey_snap.sum()
+
+pl.semilogy(t, ey, "k.")
+pl.savefig("kelvinHelmholtzGrowthRate.png")
diff --git a/examples/KelvinHelmholtzGrowthRate_2D/run.sh b/examples/KelvinHelmholtzGrowthRate_2D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3e6e026f66b14846a5c6e8e9daf99797dc3ff87a
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_2D/run.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e kelvinHelmholtzGrowthRate.hdf5 ]
+then
+ echo "Generating initial conditions for the Kelvin-Helmholtz growth rate " \
+ "example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 100
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/getGlass.sh b/examples/KelvinHelmholtzGrowthRate_3D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
new file mode 100644
index 0000000000000000000000000000000000000000..380dc2ab3a530e89b952aa41f425e50709d73ee9
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/kelvinHelmholtzGrowthRate.yml
@@ -0,0 +1,33 @@
+# 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: 4. # The end time of the simulation (in internal units).
+ dt_min: 1e-6 # 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: kelvinHelmholtzGrowthRate # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.04 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./kelvinHelmholtzGrowthRate.hdf5 # The file to read
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py b/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..a9bc20559b9fbb5da400ba5de2563cd715f473d5
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/makeIC.py
@@ -0,0 +1,100 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+P0 = 2.5 # Pressure
+rho0 = 1. # Density
+d = 0.0317 # Thickness of the transition layer
+B = 0.0005 # Amplitude of the seed velocity
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+glass = h5py.File("glassCube_64.hdf5", 'r')
+pos = glass["/PartType0/Coordinates"][:, :]
+h = glass["/PartType0/SmoothingLength"][:]
+
+N = len(h)
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+ -0.5 + \
+ 0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+ 0.5 - \
+ 0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+ (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+ np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFileOutputsPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = fileOutput.create_group("/PartType0")
+grp.create_dataset("Coordinates", data = pos, dtype = 'd')
+grp.create_dataset("Velocities", data = v, dtype = 'f')
+grp.create_dataset("Masses", data = m, dtype = 'f')
+grp.create_dataset("SmoothingLength", data = h, dtype = 'f')
+grp.create_dataset("InternalEnergy", data = u, dtype = 'f')
+grp.create_dataset("ParticleIDs", data = ids, dtype = 'L')
+
+fileOutput.close()
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py b/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py
new file mode 100644
index 0000000000000000000000000000000000000000..aa7dd8f214f8ece1c1d142bf02bd653cd35f9973
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/makeIC_regular.py
@@ -0,0 +1,108 @@
+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+P0 = 2.5 # Pressure
+rho0 = 1. # Density
+d = 0.0317 # Thickness of the transition layer
+B = 0.0005 # Amplitude of the seed velocity
+N1D = 64 # Number of particles in one dimension
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+N = N1D ** 3
+x = np.linspace(0., 1., N1D + 1)
+x = 0.5 * (x[1:] + x[:-1])
+y = x
+z = x
+xx, yy, zz = np.meshgrid(x, y, z)
+pos = np.zeros((N, 3))
+pos[:, 0] = xx.reshape((N))
+pos[:, 1] = yy.reshape((N))
+pos[:, 2] = zz.reshape((N))
+h = np.ones(N) * 2. / N1D
+
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+ -0.5 + \
+ 0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+ 0.5 - \
+ 0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+ (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+ np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFileOutputsPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = fileOutput.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = fileOutput.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = fileOutput.create_group("/PartType0")
+grp.create_dataset("Coordinates", data = pos, dtype = 'd')
+grp.create_dataset("Velocities", data = v, dtype = 'f')
+grp.create_dataset("Masses", data = m, dtype = 'f')
+grp.create_dataset("SmoothingLength", data = h, dtype = 'f')
+grp.create_dataset("InternalEnergy", data = u, dtype = 'f')
+grp.create_dataset("ParticleIDs", data = ids, dtype = 'L')
+
+fileOutput.close()
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/plotSolution.py b/examples/KelvinHelmholtzGrowthRate_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..b2e3e1766a2b7d2618611aca9fb938ab87d78872
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/plotSolution.py
@@ -0,0 +1,47 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+import numpy as np
+import h5py
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import sys
+
+if len(sys.argv) < 2:
+ print "No final snapshot number provided!"
+ exit()
+lastsnap = int(sys.argv[1])
+
+# Read the simulation data
+t = np.zeros(lastsnap + 1)
+ey = np.zeros(lastsnap + 1)
+for i in range(lastsnap + 1):
+ file = h5py.File("kelvinHelmholtzGrowthRate_{0:04d}.hdf5".format(i), 'r')
+ t_snap = float(file["/Header"].attrs["Time"])
+ vy = file["/PartType0/Velocities"][:,1]
+ m = file["/PartType0/Masses"][:]
+
+ ey_snap = 0.5 * m * vy**2
+
+ t[i] = t_snap
+ ey[i] = ey_snap.sum()
+
+pl.semilogy(t, ey, "k.")
+pl.savefig("kelvinHelmholtzGrowthRate.png")
diff --git a/examples/KelvinHelmholtzGrowthRate_3D/run.sh b/examples/KelvinHelmholtzGrowthRate_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3e6e026f66b14846a5c6e8e9daf99797dc3ff87a
--- /dev/null
+++ b/examples/KelvinHelmholtzGrowthRate_3D/run.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e kelvinHelmholtzGrowthRate.hdf5 ]
+then
+ echo "Generating initial conditions for the Kelvin-Helmholtz growth rate " \
+ "example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 100
diff --git a/examples/SodShockSpherical_2D/getGlass.sh b/examples/SodShockSpherical_2D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f4cb4ebcb4b452b2b123462bc97eed532f43ba25
--- /dev/null
+++ b/examples/SodShockSpherical_2D/getGlass.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_48.hdf5
diff --git a/examples/SodShockSpherical_2D/getReference.sh b/examples/SodShockSpherical_2D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..8b152badc65ece3b519fa660001acc792ee3f3dc
--- /dev/null
+++ b/examples/SodShockSpherical_2D/getReference.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/sodShockSpherical2D_exact.txt
diff --git a/examples/SodShockSpherical_2D/makeIC.py b/examples/SodShockSpherical_2D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..ac9f6e193769d7466f5b8e41a408da2350777be6
--- /dev/null
+++ b/examples/SodShockSpherical_2D/makeIC.py
@@ -0,0 +1,125 @@
+###############################################################################
+ # 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/>.
+ #
+ ##############################################################################
+
+import h5py
+from numpy import *
+
+# Generates a swift IC file for the 2D Sod Shock in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+x_min = -1.
+x_max = 1.
+rho_L = 1. # Density left state
+rho_R = 0.140625 # Density right state
+v_L = 0. # Velocity left state
+v_R = 0. # Velocity right state
+P_L = 1. # Pressure left state
+P_R = 0.1 # Pressure right state
+fileName = "sodShock.hdf5"
+
+
+#---------------------------------------------------
+boxSize = (x_max - x_min)
+
+glass_L = h5py.File("glassPlane_128.hdf5", "r")
+glass_R = h5py.File("glassPlane_48.hdf5", "r")
+
+pos_L = glass_L["/PartType0/Coordinates"][:,:]
+pos_R = glass_R["/PartType0/Coordinates"][:,:]
+h_L = glass_L["/PartType0/SmoothingLength"][:]
+h_R = glass_R["/PartType0/SmoothingLength"][:]
+
+radius_L = sqrt((pos_L[:,0] - 0.5)**2 + (pos_L[:,1] - 0.5)**2)
+index_L = radius_L < 0.25
+pos_LL = pos_L[index_L]
+h_LL = h_L[index_L]
+
+radius_R = sqrt((pos_R[:,0] - 0.5)**2 + (pos_R[:,1] - 0.5)**2)
+index_R = radius_R > 0.25
+pos_RR = pos_R[index_R]
+h_RR = h_R[index_R]
+
+# Merge things
+pos = append(pos_LL, pos_RR, axis=0)
+h = append(h_LL, h_RR)
+
+numPart_L = size(h_LL)
+numPart_R = size(h_RR)
+numPart = size(h)
+
+vol_L = pi * 0.25**2
+vol_R = 1. - pi * 0.25**2
+
+# Generate extra arrays
+v = zeros((numPart, 3))
+ids = linspace(1, numPart, numPart)
+m = zeros(numPart)
+u = zeros(numPart)
+
+for i in range(numPart):
+ x = sqrt((pos[i,0]-0.5)**2+(pos[i,1]-0.5)**2)
+
+ if x < 0.25: #left
+ u[i] = P_L / (rho_L * (gamma - 1.))
+ m[i] = rho_L * vol_L / numPart_L
+ v[i,0] = v_L
+ else: #right
+ u[i] = P_R / (rho_R * (gamma - 1.))
+ m[i] = rho_R * vol_R / numPart_R
+ v[i,0] = v_R
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+
+file.close()
diff --git a/examples/SodShockSpherical_2D/plotSolution.py b/examples/SodShockSpherical_2D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..57b7f7ddc64bc25df031eb0cba7547f40d46b31a
--- /dev/null
+++ b/examples/SodShockSpherical_2D/plotSolution.py
@@ -0,0 +1,163 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+# Compares the swift result for the 2D spherical Sod shock with a high
+# resolution 2D reference result
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+from scipy import stats
+import h5py
+
+# Parameters
+gas_gamma = 5./3. # Polytropic index
+rho_L = 1. # Density left state
+rho_R = 0.140625 # Density right state
+v_L = 0. # Velocity left state
+v_R = 0. # Velocity right state
+P_L = 1. # Pressure left state
+P_R = 0.1 # Pressure right state
+
+# 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']})
+
+snap = int(sys.argv[1])
+
+# Read the simulation data
+sim = h5py.File("sodShock_%04d.hdf5"%snap, "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"]
+kernel = sim["/HydroScheme"].attrs["Kernel function"]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"]
+eta = sim["/HydroScheme"].attrs["Kernel eta"]
+git = sim["Code"].attrs["Git Revision"]
+
+coords = sim["/PartType0/Coordinates"]
+x = sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2)
+vels = sim["/PartType0/Velocities"]
+v = sqrt(vels[:,0]**2 + vels[:,1]**2)
+u = sim["/PartType0/InternalEnergy"][:]
+S = sim["/PartType0/Entropy"][:]
+P = sim["/PartType0/Pressure"][:]
+rho = sim["/PartType0/Density"][:]
+
+# Bin the data
+rho_bin,x_bin_edge,_ = \
+ stats.binned_statistic(x, rho, statistic='mean', bins=100)
+x_bin = 0.5*(x_bin_edge[1:] + x_bin_edge[:-1])
+v_bin,_,_ = stats.binned_statistic(x, v, statistic='mean', bins=x_bin_edge)
+P_bin,_,_ = stats.binned_statistic(x, P, statistic='mean', bins=x_bin_edge)
+S_bin,_,_ = stats.binned_statistic(x, S, statistic='mean', bins=x_bin_edge)
+u_bin,_,_ = stats.binned_statistic(x, u, statistic='mean', bins=x_bin_edge)
+rho2_bin,_,_ = stats.binned_statistic(x, rho**2, statistic='mean', bins=x_bin_edge)
+v2_bin,_,_ = stats.binned_statistic(x, v**2, statistic='mean', bins=x_bin_edge)
+P2_bin,_,_ = stats.binned_statistic(x, P**2, statistic='mean', bins=x_bin_edge)
+S2_bin,_,_ = stats.binned_statistic(x, S**2, statistic='mean', bins=x_bin_edge)
+u2_bin,_,_ = stats.binned_statistic(x, u**2, statistic='mean', bins=x_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)
+
+ref = loadtxt("sodShockSpherical2D_exact.txt")
+
+# Plot the interesting quantities
+figure()
+
+# Velocity profile --------------------------------
+subplot(231)
+plot(x, v, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
+
+# Density profile --------------------------------
+subplot(232)
+plot(x, rho, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,1], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, rho_bin, yerr=rho_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Density}}~\\rho$", labelpad=0)
+
+# Pressure profile --------------------------------
+subplot(233)
+plot(x, P, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, P_bin, yerr=P_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Pressure}}~P$", labelpad=0)
+
+# Internal energy profile -------------------------
+subplot(234)
+plot(x, u, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3] / ref[:,1] / (gas_gamma - 1.), "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, u_bin, yerr=u_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0)
+
+# Entropy profile ---------------------------------
+subplot(235)
+plot(x, S, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3] / ref[:,1]**gas_gamma, "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, S_bin, yerr=S_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Entropy}}~S$", labelpad=0)
+
+# Information -------------------------------------
+subplot(236, frameon=False)
+
+text(-0.49, 0.9, "Sod shock with $\\gamma=%.3f$ in 2D at $t=%.2f$"%(gas_gamma,time), fontsize=10)
+text(-0.49, 0.8, "Left:~~ $(P_L, \\rho_L, v_L) = (%.3f, %.3f, %.3f)$"%(P_L, rho_L, v_L), fontsize=10)
+text(-0.49, 0.7, "Right: $(P_R, \\rho_R, v_R) = (%.3f, %.3f, %.3f)$"%(P_R, rho_R, v_R), 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)
+xlim(-0.5, 0.5)
+ylim(0, 1)
+xticks([])
+yticks([])
+
+
+savefig("SodShock.png", dpi=200)
diff --git a/examples/SodShockSpherical_2D/run.sh b/examples/SodShockSpherical_2D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d662d20f40ef9e221285d5820e867607804e9dbe
--- /dev/null
+++ b/examples/SodShockSpherical_2D/run.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassPlane_128.hdf5 ]
+then
+ echo "Fetching initial glass file for the Sod shock example..."
+ ./getGlass.sh
+fi
+if [ ! -e sodShock.hdf5 ]
+then
+ echo "Generating initial conditions for the Sod shock example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 sodShock.yml 2>&1 | tee output.log
+
+# Get the high resolution 1D reference solution if not present.
+if [ ! -e sodShockSpherical2D_exact.txt ]
+then
+ echo "Fetching reference solution for 2D spherical Sod shock example..."
+ ./getReference.sh
+fi
+python plotSolution.py 1
diff --git a/examples/SodShockSpherical_2D/sodShock.yml b/examples/SodShockSpherical_2D/sodShock.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a26ab95b21c782ce83310038432ac08df0e024c3
--- /dev/null
+++ b/examples/SodShockSpherical_2D/sodShock.yml
@@ -0,0 +1,34 @@
+# 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: 0.1 # 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: sodShock # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./sodShock.hdf5 # The file to read
+
diff --git a/examples/SodShockSpherical_3D/getGlass.sh b/examples/SodShockSpherical_3D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f61b61d4e6c51b44576fd7cdd6242cb9f0133039
--- /dev/null
+++ b/examples/SodShockSpherical_3D/getGlass.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_32.hdf5
diff --git a/examples/SodShockSpherical_3D/getReference.sh b/examples/SodShockSpherical_3D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..133d2fb8da9cbbfdc796140afc84a0859b9ca61e
--- /dev/null
+++ b/examples/SodShockSpherical_3D/getReference.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/sodShockSpherical3D_exact.txt
diff --git a/examples/SodShockSpherical_3D/makeIC.py b/examples/SodShockSpherical_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..be8f9b61a1beef00f49786860ce94287b30e2ab3
--- /dev/null
+++ b/examples/SodShockSpherical_3D/makeIC.py
@@ -0,0 +1,127 @@
+###############################################################################
+ # 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/>.
+ #
+ ##############################################################################
+
+import h5py
+from numpy import *
+
+# Generates a swift IC file for the 3D Sod Shock in a periodic box
+
+# Parameters
+gamma = 5./3. # Gas adiabatic index
+x_min = -1.
+x_max = 1.
+rho_L = 1. # Density left state
+rho_R = 0.125 # Density right state
+v_L = 0. # Velocity left state
+v_R = 0. # Velocity right state
+P_L = 1. # Pressure left state
+P_R = 0.1 # Pressure right state
+fileName = "sodShock.hdf5"
+
+
+#---------------------------------------------------
+boxSize = (x_max - x_min)
+
+glass_L = h5py.File("glassCube_64.hdf5", "r")
+glass_R = h5py.File("glassCube_32.hdf5", "r")
+
+pos_L = glass_L["/PartType0/Coordinates"][:,:]
+pos_R = glass_R["/PartType0/Coordinates"][:,:]
+h_L = glass_L["/PartType0/SmoothingLength"][:]
+h_R = glass_R["/PartType0/SmoothingLength"][:]
+
+radius_L = sqrt((pos_L[:,0] - 0.5)**2 + (pos_L[:,1] - 0.5)**2 + \
+ (pos_L[:,2] - 0.5)**2)
+index_L = radius_L < 0.25
+pos_LL = pos_L[index_L]
+h_LL = h_L[index_L]
+
+radius_R = sqrt((pos_R[:,0] - 0.5)**2 + (pos_R[:,1] - 0.5)**2 + \
+ (pos_R[:,2] - 0.5)**2)
+index_R = radius_R > 0.25
+pos_RR = pos_R[index_R]
+h_RR = h_R[index_R]
+
+# Merge things
+pos = append(pos_LL, pos_RR, axis=0)
+h = append(h_LL, h_RR)
+
+numPart_L = size(h_LL)
+numPart_R = size(h_RR)
+numPart = size(h)
+
+vol_L = 4. * pi / 3. * 0.25**3
+vol_R = 1. - 4. * pi / 3. * 0.25**3
+
+# Generate extra arrays
+v = zeros((numPart, 3))
+ids = linspace(1, numPart, numPart)
+m = zeros(numPart)
+u = zeros(numPart)
+
+for i in range(numPart):
+ x = sqrt((pos[i,0]-0.5)**2+(pos[i,1]-0.5)**2+(pos[i,2]-0.5)**2)
+
+ if x < 0.25: #left
+ u[i] = P_L / (rho_L * (gamma - 1.))
+ m[i] = rho_L * vol_L / numPart_L
+ v[i,0] = v_L
+ else: #right
+ u[i] = P_R / (rho_R * (gamma - 1.))
+ m[i] = rho_R * vol_R / numPart_R
+ v[i,0] = v_R
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+
+file.close()
diff --git a/examples/SodShockSpherical_3D/plotSolution.py b/examples/SodShockSpherical_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..539bfba799e3231bd26ae2eb39c271baa1fa6a4b
--- /dev/null
+++ b/examples/SodShockSpherical_3D/plotSolution.py
@@ -0,0 +1,164 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+# 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+################################################################################
+
+# Compares the swift result for the 2D spherical Sod shock with a high
+# resolution 2D reference result
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+from scipy import stats
+import h5py
+
+# Parameters
+gas_gamma = 5./3. # Polytropic index
+rho_L = 1. # Density left state
+rho_R = 0.125 # Density right state
+v_L = 0. # Velocity left state
+v_R = 0. # Velocity right state
+P_L = 1. # Pressure left state
+P_R = 0.1 # Pressure right state
+
+# 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']})
+
+snap = int(sys.argv[1])
+
+# Read the simulation data
+sim = h5py.File("sodShock_%04d.hdf5"%snap, "r")
+boxSize = sim["/Header"].attrs["BoxSize"][0]
+time = sim["/Header"].attrs["Time"][0]
+scheme = sim["/HydroScheme"].attrs["Scheme"]
+kernel = sim["/HydroScheme"].attrs["Kernel function"]
+neighbours = sim["/HydroScheme"].attrs["Kernel target N_ngb"]
+eta = sim["/HydroScheme"].attrs["Kernel eta"]
+git = sim["Code"].attrs["Git Revision"]
+
+coords = sim["/PartType0/Coordinates"]
+x = sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2 + \
+ (coords[:,2] - 0.5)**2)
+vels = sim["/PartType0/Velocities"]
+v = sqrt(vels[:,0]**2 + vels[:,1]**2 + vels[:,2]**2)
+u = sim["/PartType0/InternalEnergy"][:]
+S = sim["/PartType0/Entropy"][:]
+P = sim["/PartType0/Pressure"][:]
+rho = sim["/PartType0/Density"][:]
+
+# Bin the data
+rho_bin,x_bin_edge,_ = \
+ stats.binned_statistic(x, rho, statistic='mean', bins=100)
+x_bin = 0.5*(x_bin_edge[1:] + x_bin_edge[:-1])
+v_bin,_,_ = stats.binned_statistic(x, v, statistic='mean', bins=x_bin_edge)
+P_bin,_,_ = stats.binned_statistic(x, P, statistic='mean', bins=x_bin_edge)
+S_bin,_,_ = stats.binned_statistic(x, S, statistic='mean', bins=x_bin_edge)
+u_bin,_,_ = stats.binned_statistic(x, u, statistic='mean', bins=x_bin_edge)
+rho2_bin,_,_ = stats.binned_statistic(x, rho**2, statistic='mean', bins=x_bin_edge)
+v2_bin,_,_ = stats.binned_statistic(x, v**2, statistic='mean', bins=x_bin_edge)
+P2_bin,_,_ = stats.binned_statistic(x, P**2, statistic='mean', bins=x_bin_edge)
+S2_bin,_,_ = stats.binned_statistic(x, S**2, statistic='mean', bins=x_bin_edge)
+u2_bin,_,_ = stats.binned_statistic(x, u**2, statistic='mean', bins=x_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)
+
+ref = loadtxt("sodShockSpherical3D_exact.txt")
+
+# Plot the interesting quantities
+figure()
+
+# Velocity profile --------------------------------
+subplot(231)
+plot(x, v, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
+
+# Density profile --------------------------------
+subplot(232)
+plot(x, rho, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,1], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, rho_bin, yerr=rho_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Density}}~\\rho$", labelpad=0)
+
+# Pressure profile --------------------------------
+subplot(233)
+plot(x, P, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3], "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, P_bin, yerr=P_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Pressure}}~P$", labelpad=0)
+
+# Internal energy profile -------------------------
+subplot(234)
+plot(x, u, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3] / ref[:,1] / (gas_gamma - 1.), "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, u_bin, yerr=u_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0)
+
+# Entropy profile ---------------------------------
+subplot(235)
+plot(x, S, '.', color='r', ms=0.2)
+plot(ref[:,0], ref[:,3] / ref[:,1]**gas_gamma, "k--", alpha=0.8, lw=1.2)
+errorbar(x_bin, S_bin, yerr=S_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
+xlabel("${\\rm{Radius}}~r$", labelpad=0)
+ylabel("${\\rm{Entropy}}~S$", labelpad=0)
+
+# Information -------------------------------------
+subplot(236, frameon=False)
+
+text(-0.49, 0.9, "Sod shock with $\\gamma=%.3f$ in 3D at $t=%.2f$"%(gas_gamma,time), fontsize=10)
+text(-0.49, 0.8, "Left:~~ $(P_L, \\rho_L, v_L) = (%.3f, %.3f, %.3f)$"%(P_L, rho_L, v_L), fontsize=10)
+text(-0.49, 0.7, "Right: $(P_R, \\rho_R, v_R) = (%.3f, %.3f, %.3f)$"%(P_R, rho_R, v_R), 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)
+xlim(-0.5, 0.5)
+ylim(0, 1)
+xticks([])
+yticks([])
+
+
+savefig("SodShock.png", dpi=200)
diff --git a/examples/SodShockSpherical_3D/run.sh b/examples/SodShockSpherical_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..faf979869e175172ce31db6ac5021daf1758f3b0
--- /dev/null
+++ b/examples/SodShockSpherical_3D/run.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassCube_64.hdf5 ]
+then
+ echo "Fetching initial glass file for the Sod shock example..."
+ ./getGlass.sh
+fi
+if [ ! -e sodShock.hdf5 ]
+then
+ echo "Generating initial conditions for the Sod shock example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 4 sodShock.yml 2>&1 | tee output.log
+
+# Get the high resolution 1D reference solution if not present.
+if [ ! -e sodShockSpherical3D_exact.txt ]
+then
+ echo "Fetching reference solution for 3D spherical Sod shock example..."
+ ./getReference.sh
+fi
+python plotSolution.py 1
diff --git a/examples/SodShockSpherical_3D/sodShock.yml b/examples/SodShockSpherical_3D/sodShock.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a26ab95b21c782ce83310038432ac08df0e024c3
--- /dev/null
+++ b/examples/SodShockSpherical_3D/sodShock.yml
@@ -0,0 +1,34 @@
+# 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: 0.1 # 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: sodShock # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./sodShock.hdf5 # The file to read
+
diff --git a/examples/VacuumSpherical_2D/getGlass.sh b/examples/VacuumSpherical_2D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ae3c977064f5e7a408aa249c5fd9089b3c52ecb1
--- /dev/null
+++ b/examples/VacuumSpherical_2D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5
diff --git a/examples/VacuumSpherical_2D/getReference.sh b/examples/VacuumSpherical_2D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..01080400dba430852f0245d42fb5e30f971721a8
--- /dev/null
+++ b/examples/VacuumSpherical_2D/getReference.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/vacuumSpherical2D_exact.txt
diff --git a/examples/VacuumSpherical_2D/makeIC.py b/examples/VacuumSpherical_2D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..498f1b5bc5277188d8ff8d34a5ec24cd314332d4
--- /dev/null
+++ b/examples/VacuumSpherical_2D/makeIC.py
@@ -0,0 +1,101 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+###############################################################################
+
+import numpy as np
+import h5py
+
+# Generates an overdensity within a vacuum to test the vacuum resolving
+# capabilities of the code
+
+# Parameters
+gamma = 5. / 3. # Gas adiabatic index
+
+fileName = "vacuum.hdf5"
+
+#---------------------------------------------------
+glass = h5py.File("glassPlane_128.hdf5", "r")
+
+# Read particle positions and h from the glass
+pos = glass["/PartType0/Coordinates"][:,:]
+h = glass["/PartType0/SmoothingLength"][:] * 0.3
+
+# Make 4 copies of the glass to have more particles
+pos *= 0.5
+h *= 0.5
+pos = np.append(pos, pos + np.array([0.5, 0., 0.]), axis = 0)
+h = np.append(h, h)
+pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0)
+h = np.append(h, h)
+
+radius = np.sqrt((pos[:,0] - 0.5)**2 + (pos[:,1] - 0.5)**2)
+index = radius < 0.25
+pos = pos[index]
+h = h[index]
+
+numPart = len(h)
+vol = np.pi * 0.25**2
+
+# Generate extra arrays
+v = np.zeros((numPart, 3))
+ids = np.linspace(1, numPart, numPart)
+m = np.zeros(numPart)
+u = np.zeros(numPart)
+
+m[:] = 1. * vol / numPart
+u[:] = 1. / (1. * (gamma - 1.))
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+file.close()
diff --git a/examples/VacuumSpherical_2D/plotSolution.py b/examples/VacuumSpherical_2D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..6a65206ae20ccf79392054d047ba6be04f169f3e
--- /dev/null
+++ b/examples/VacuumSpherical_2D/plotSolution.py
@@ -0,0 +1,192 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import h5py
+import sys
+import scipy.stats as stats
+
+# Parameters
+gamma = 5. / 3. # Polytropic index
+rhoL = 1. # Initial density in the non vacuum state
+vL = 0. # Initial velocity in the non vacuum state
+PL = 1. # Initial pressure in the non vacuum state
+rhoR = 0. # Initial vacuum density
+vR = 0. # Initial vacuum velocity
+PR = 0. # Initial vacuum pressure
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
+snap = int(sys.argv[1])
+
+# Open the file and read the relevant data
+file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r")
+coords = file["/PartType0/Coordinates"]
+x = np.sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2)
+rho = file["/PartType0/Density"][:]
+vels = file["/PartType0/Velocities"]
+v = np.sqrt(vels[:,0]**2 + vels[:,1]**2)
+u = file["/PartType0/InternalEnergy"][:]
+S = file["/PartType0/Entropy"][:]
+P = file["/PartType0/Pressure"][:]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+# Bin the data values
+# We let scipy choose the bins and then reuse them for all other quantities
+rho_bin, x_bin_edge, _ = \
+ stats.binned_statistic(x, rho, statistic = "mean", bins = 50)
+rho2_bin, _, _ = \
+ stats.binned_statistic(x, rho**2, statistic = "mean", bins = x_bin_edge)
+rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2)
+
+v_bin, _, _ = \
+ stats.binned_statistic(x, v, statistic = "mean", bins = x_bin_edge)
+v2_bin, _, _ = \
+ stats.binned_statistic(x, v**2, statistic = "mean", bins = x_bin_edge)
+v_sigma_bin = np.sqrt(v2_bin - v_bin**2)
+
+P_bin, _, _ = \
+ stats.binned_statistic(x, P, statistic = "mean", bins = x_bin_edge)
+P2_bin, _, _ = \
+ stats.binned_statistic(x, P**2, statistic = "mean", bins = x_bin_edge)
+P_sigma_bin = np.sqrt(P2_bin - P_bin**2)
+
+u_bin, _, _ = \
+ stats.binned_statistic(x, u, statistic = "mean", bins = x_bin_edge)
+u2_bin, _, _ = \
+ stats.binned_statistic(x, u**2, statistic = "mean", bins = x_bin_edge)
+u_sigma_bin = np.sqrt(u2_bin - u_bin**2)
+
+S_bin, _, _ = \
+ stats.binned_statistic(x, S, statistic = "mean", bins = x_bin_edge)
+S2_bin, _, _ = \
+ stats.binned_statistic(x, S**2, statistic = "mean", bins = x_bin_edge)
+S_sigma_bin = np.sqrt(S2_bin - S_bin**2)
+
+x_bin = 0.5 * (x_bin_edge[1:] + x_bin_edge[:-1])
+
+ref = np.loadtxt("vacuumSpherical2D_exact.txt")
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 0.2)
+ax[0][0].plot(ref[:,0], ref[:,2], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].errorbar(x_bin, v_bin, yerr = v_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_r$", labelpad = 0)
+ax[0][0].set_xlim(0., 0.4)
+ax[0][0].set_ylim(-0.1, 3.2)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 0.2)
+ax[0][1].plot(ref[:,0], ref[:,1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].errorbar(x_bin, rho_bin, yerr = rho_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+ax[0][1].set_xlim(0., 0.4)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 0.2)
+ax[0][2].plot(ref[:,0], ref[:,3], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].errorbar(x_bin, P_bin, yerr = P_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+ax[0][2].set_xlim(0., 0.4)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 0.2)
+ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 1.), "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][0].errorbar(x_bin, u_bin, yerr = u_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+ax[1][0].set_xlim(0., 0.4)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 0.2)
+ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][1].errorbar(x_bin, S_bin, yerr = S_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+ax[1][1].set_xlim(0., 0.4)
+ax[1][1].set_ylim(0., 4.)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].text(-0.49, 0.8,
+ "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PL, rhoL, vL), fontsize = 10)
+ax[1][2].text(-0.49, 0.7,
+ "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PR, rhoR, vR), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
+
+pl.tight_layout()
+pl.savefig("Vacuum.png", dpi = 200)
diff --git a/examples/VacuumSpherical_2D/run.sh b/examples/VacuumSpherical_2D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..51d32b4de679877741b7ecd74238fecb785579e7
--- /dev/null
+++ b/examples/VacuumSpherical_2D/run.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassPlane_128.hdf5 ]
+then
+ echo "Fetching initial glass file for the 2D vacuum expansion example..."
+ ./getGlass.sh
+fi
+if [ ! -e vacuum.hdf5 ]
+then
+ echo "Generating initial conditions for the 2D vacuum expansion example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 4 vacuum.yml 2>&1 | tee output.log
+
+# Get the 1D high resolution reference result if not present.
+if [ ! -e vacuumSpherical2D_exact.txt ]
+then
+ echo "Fetching reference solution for the 2D vacuum expansion test..."
+ ./getReference.sh
+fi
+
+# Plot the result
+python plotSolution.py 1
diff --git a/examples/VacuumSpherical_2D/vacuum.yml b/examples/VacuumSpherical_2D/vacuum.yml
new file mode 100644
index 0000000000000000000000000000000000000000..881b155b62c7f1f2af12a1d013ff5c05f1c16a88
--- /dev/null
+++ b/examples/VacuumSpherical_2D/vacuum.yml
@@ -0,0 +1,34 @@
+# 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: 0.05 # The end time of the simulation (in internal units).
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: vacuum # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.05 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./vacuum.hdf5 # The file to read
+
diff --git a/examples/VacuumSpherical_3D/getGlass.sh b/examples/VacuumSpherical_3D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c
--- /dev/null
+++ b/examples/VacuumSpherical_3D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
diff --git a/examples/VacuumSpherical_3D/getReference.sh b/examples/VacuumSpherical_3D/getReference.sh
new file mode 100755
index 0000000000000000000000000000000000000000..49784c313f0c8758d88970169c30d39c58745ec4
--- /dev/null
+++ b/examples/VacuumSpherical_3D/getReference.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/vacuumSpherical3D_exact.txt
diff --git a/examples/VacuumSpherical_3D/makeIC.py b/examples/VacuumSpherical_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..d67a30707a904268a09641210a6a3bfcbf305dad
--- /dev/null
+++ b/examples/VacuumSpherical_3D/makeIC.py
@@ -0,0 +1,104 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+###############################################################################
+
+import numpy as np
+import h5py
+
+# Generates an overdensity within a vacuum to test the vacuum resolving
+# capabilities of the code
+
+# Parameters
+gamma = 5. / 3. # Gas adiabatic index
+
+fileName = "vacuum.hdf5"
+
+#---------------------------------------------------
+glass = h5py.File("glassCube_64.hdf5", "r")
+
+# Read particle positions and h from the glass
+pos = glass["/PartType0/Coordinates"][:,:]
+h = glass["/PartType0/SmoothingLength"][:] * 0.3
+
+# Make 8 copies of the glass to get more particles
+pos *= 0.5
+h *= 0.5
+pos = np.append(pos, pos + np.array([0.5, 0., 0.]), axis = 0)
+pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0)
+pos = np.append(pos, pos + np.array([0., 0., 0.5]), axis = 0)
+h = np.append(h, h)
+h = np.append(h, h)
+h = np.append(h, h)
+
+radius = np.sqrt((pos[:,0] - 0.5)**2 + (pos[:,1] - 0.5)**2 + \
+ (pos[:,2] - 0.5)**2)
+index = radius < 0.25
+pos = pos[index]
+h = h[index]
+
+numPart = len(h)
+vol = 4. * np.pi / 3. * 0.25**3
+
+# Generate extra arrays
+v = np.zeros((numPart, 3))
+ids = np.linspace(1, numPart, numPart)
+m = np.zeros(numPart)
+u = np.zeros(numPart)
+
+m[:] = 1. * vol / numPart
+u[:] = 1. / (1. * (gamma - 1.))
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+file.close()
diff --git a/examples/VacuumSpherical_3D/plotSolution.py b/examples/VacuumSpherical_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..c73e48ee2d311692cdf4aa3b0e52f4766b339df8
--- /dev/null
+++ b/examples/VacuumSpherical_3D/plotSolution.py
@@ -0,0 +1,193 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import h5py
+import sys
+import scipy.stats as stats
+
+# Parameters
+gamma = 5. / 3. # Polytropic index
+rhoL = 1. # Initial density in the non vacuum state
+vL = 0. # Initial velocity in the non vacuum state
+PL = 1. # Initial pressure in the non vacuum state
+rhoR = 0. # Initial vacuum density
+vR = 0. # Initial vacuum velocity
+PR = 0. # Initial vacuum pressure
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
+snap = int(sys.argv[1])
+
+# Open the file and read the relevant data
+file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r")
+coords = file["/PartType0/Coordinates"]
+x = np.sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2 + \
+ (coords[:,2] - 0.5)**2)
+rho = file["/PartType0/Density"][:]
+vels = file["/PartType0/Velocities"]
+v = np.sqrt(vels[:,0]**2 + vels[:,1]**2 + vels[:,2]**2)
+u = file["/PartType0/InternalEnergy"][:]
+S = file["/PartType0/Entropy"][:]
+P = file["/PartType0/Pressure"][:]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+# Bin the data values
+# We let scipy choose the bins and then reuse them for all other quantities
+rho_bin, x_bin_edge, _ = \
+ stats.binned_statistic(x, rho, statistic = "mean", bins = 50)
+rho2_bin, _, _ = \
+ stats.binned_statistic(x, rho**2, statistic = "mean", bins = x_bin_edge)
+rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2)
+
+v_bin, _, _ = \
+ stats.binned_statistic(x, v, statistic = "mean", bins = x_bin_edge)
+v2_bin, _, _ = \
+ stats.binned_statistic(x, v**2, statistic = "mean", bins = x_bin_edge)
+v_sigma_bin = np.sqrt(v2_bin - v_bin**2)
+
+P_bin, _, _ = \
+ stats.binned_statistic(x, P, statistic = "mean", bins = x_bin_edge)
+P2_bin, _, _ = \
+ stats.binned_statistic(x, P**2, statistic = "mean", bins = x_bin_edge)
+P_sigma_bin = np.sqrt(P2_bin - P_bin**2)
+
+u_bin, _, _ = \
+ stats.binned_statistic(x, u, statistic = "mean", bins = x_bin_edge)
+u2_bin, _, _ = \
+ stats.binned_statistic(x, u**2, statistic = "mean", bins = x_bin_edge)
+u_sigma_bin = np.sqrt(u2_bin - u_bin**2)
+
+S_bin, _, _ = \
+ stats.binned_statistic(x, S, statistic = "mean", bins = x_bin_edge)
+S2_bin, _, _ = \
+ stats.binned_statistic(x, S**2, statistic = "mean", bins = x_bin_edge)
+S_sigma_bin = np.sqrt(S2_bin - S_bin**2)
+
+x_bin = 0.5 * (x_bin_edge[1:] + x_bin_edge[:-1])
+
+ref = np.loadtxt("vacuumSpherical3D_exact.txt")
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 0.2)
+ax[0][0].plot(ref[:,0], ref[:,2], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].errorbar(x_bin, v_bin, yerr = v_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_r$", labelpad = 0)
+ax[0][0].set_xlim(0., 0.4)
+ax[0][0].set_ylim(-0.1, 3.2)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 0.2)
+ax[0][1].plot(ref[:,0], ref[:,1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].errorbar(x_bin, rho_bin, yerr = rho_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+ax[0][1].set_xlim(0., 0.4)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 0.2)
+ax[0][2].plot(ref[:,0], ref[:,3], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].errorbar(x_bin, P_bin, yerr = P_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+ax[0][2].set_xlim(0., 0.4)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 0.2)
+ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 1.), "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][0].errorbar(x_bin, u_bin, yerr = u_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+ax[1][0].set_xlim(0., 0.4)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 0.2)
+ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "k--", alpha = 0.8,
+ linewidth = 1.2)
+ax[1][1].errorbar(x_bin, S_bin, yerr = S_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Radius}}~r$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+ax[1][1].set_xlim(0., 0.4)
+ax[1][1].set_ylim(0., 4.)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].text(-0.49, 0.8,
+ "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PL, rhoL, vL), fontsize = 10)
+ax[1][2].text(-0.49, 0.7,
+ "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PR, rhoR, vR), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
+
+pl.tight_layout()
+pl.savefig("Vacuum.png", dpi = 200)
diff --git a/examples/VacuumSpherical_3D/run.sh b/examples/VacuumSpherical_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a136929678f745f6a3d0859ba146e1bc1c6c43d0
--- /dev/null
+++ b/examples/VacuumSpherical_3D/run.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassCube_64.hdf5 ]
+then
+ echo "Fetching initial glass file for the 3D vacuum expansion example..."
+ ./getGlass.sh
+fi
+if [ ! -e vacuum.hdf5 ]
+then
+ echo "Generating initial conditions for the 3D vacuum expansion example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 16 vacuum.yml 2>&1 | tee output.log
+
+# Get the reference solution if it is not present.
+if [ ! -e vacuumSpherical3D_exact.txt ]
+then
+ echo "Fetching reference solution for the 3D vacuum expansion test..."
+ ./getReference.sh
+fi
+
+# Plot the result
+python plotSolution.py 1
diff --git a/examples/VacuumSpherical_3D/vacuum.yml b/examples/VacuumSpherical_3D/vacuum.yml
new file mode 100644
index 0000000000000000000000000000000000000000..881b155b62c7f1f2af12a1d013ff5c05f1c16a88
--- /dev/null
+++ b/examples/VacuumSpherical_3D/vacuum.yml
@@ -0,0 +1,34 @@
+# 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: 0.05 # The end time of the simulation (in internal units).
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: vacuum # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.05 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./vacuum.hdf5 # The file to read
+
diff --git a/examples/Vacuum_1D/makeIC.py b/examples/Vacuum_1D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..067304ec951182da862cf2812cdc68a51a56d23b
--- /dev/null
+++ b/examples/Vacuum_1D/makeIC.py
@@ -0,0 +1,88 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+# Generates an overdensity within a vacuum to test the vacuum handling
+# capabilities of the code
+
+import numpy as np
+import h5py
+
+fileName = "vacuum.hdf5"
+numPart = 100
+boxSize = 1.
+gamma = 5. / 3.
+
+coords = np.zeros((numPart, 3))
+v = np.zeros((numPart, 3))
+m = np.zeros(numPart)
+h = np.zeros(numPart)
+u = np.zeros(numPart)
+ids = np.arange(numPart, dtype = 'L')
+rho = np.zeros(numPart)
+
+# first set the positions, as we try to do a reasonable volume estimate to
+# set the masses
+for i in range(numPart):
+ # we only generate particles in the range [0.25, 0.75]
+ coords[i,0] = 0.25 + 0.5 * (i + 0.5) / numPart
+ rho[i] = 1.
+ P = 1.
+ u[i] = P / (gamma - 1.) / rho[i]
+ m[i] = rho[i] * 0.5 / numPart
+ # reasonable smoothing length estimate
+ h[i] = 1. / numPart
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 1
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=coords, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+grp.create_dataset('Density', data=rho, dtype='f')
+
+file.close()
diff --git a/examples/Vacuum_1D/plotSolution.py b/examples/Vacuum_1D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..fceac10c25fd58b5bbcb6e31884cd62b4cfd61f5
--- /dev/null
+++ b/examples/Vacuum_1D/plotSolution.py
@@ -0,0 +1,180 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import h5py
+import sys
+
+# Parameters
+gamma = 5. / 3. # Polytropic index
+rhoL = 1. # Initial density in the non vacuum state
+vL = 0. # Initial velocity in the non vacuum state
+PL = 1. # Initial pressure in the non vacuum state
+rhoR = 0. # Initial vacuum density
+vR = 0. # Initial vacuum velocity
+PR = 0. # Initial vacuum pressure
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
+snap = int(sys.argv[1])
+
+# Open the file and read the relevant data
+file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r")
+x = file["/PartType0/Coordinates"][:,0]
+rho = file["/PartType0/Density"]
+v = file["/PartType0/Velocities"][:,0]
+u = file["/PartType0/InternalEnergy"]
+S = file["/PartType0/Entropy"]
+P = file["/PartType0/Pressure"]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+# Get the analytic solution, which is just the solution of the corresponding
+# vacuum Riemann problem evaluated at the correct time
+
+# left state sound speed (and rarefaction wave speed)
+aL = np.sqrt(gamma * PL / rhoL)
+
+# vacuum front speed
+SL = vL + 2. / (gamma - 1.) * aL
+
+# we evaluate the solution centred on 0., and shift to the correct position
+# afterwards
+xa = np.arange(-0.25, 0.25, 0.001)
+rhoa = np.zeros(len(xa))
+va = np.zeros(len(xa))
+Pa = np.zeros(len(xa))
+
+for i in range(len(xa)):
+ dxdt = xa[i] / time
+ if dxdt > vL - aL:
+ if dxdt < SL:
+ # rarefaction regime
+ # factor that appears in both the density and pressure expression
+ fac = 2. / (gamma + 1.) + \
+ (gamma - 1.) / (gamma + 1.) * (vL - dxdt) / aL
+ rhoa[i] = rhoL * fac**(2. / (gamma - 1.))
+ va[i] = 2. / (gamma + 1.) * (aL + 0.5 * (gamma - 1.) * vL + dxdt)
+ Pa[i] = PL * fac**(2. * gamma / (gamma - 1.))
+ else:
+ # vacuum regime
+ rhoa[i] = 0.
+ va[i] = 0.
+ Pa[i] = 0.
+ else:
+ # left state regime
+ rhoa[i] = rhoL
+ va[i] = vL
+ Pa[i] = PL
+
+ua = Pa / (gamma - 1.) / rhoa
+Sa = Pa / rhoa**gamma
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 4.)
+ax[0][0].plot(xa + 0.75, va, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].plot(xa + 0.25, -va[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 4.)
+ax[0][1].plot(xa + 0.75, rhoa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].plot(xa + 0.25, rhoa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 4.)
+ax[0][2].plot(xa + 0.75, Pa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].plot(xa + 0.25, Pa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 4.)
+ax[1][0].plot(xa + 0.75, ua, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].plot(xa + 0.25, ua[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 4.)
+ax[1][1].plot(xa + 0.75, Sa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].plot(xa + 0.25, Sa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].text(-0.49, 0.8,
+ "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PL, rhoL, vL), fontsize = 10)
+ax[1][2].text(-0.49, 0.7,
+ "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PR, rhoR, vR), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
+
+pl.tight_layout()
+pl.savefig("Vacuum.png", dpi = 200)
diff --git a/examples/Vacuum_1D/run.sh b/examples/Vacuum_1D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..b141f91f877c5b553281e53cdf02fbea948b0a97
--- /dev/null
+++ b/examples/Vacuum_1D/run.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e vacuum.hdf5 ]
+then
+ echo "Generating initial conditions for the 1D vacuum expansion example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 vacuum.yml 2>&1 | tee output.log
+
+# Plot the result
+python plotSolution.py 1
diff --git a/examples/Vacuum_1D/vacuum.yml b/examples/Vacuum_1D/vacuum.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5ef5ce3da68febb086a14ad1a2207711f680d9ff
--- /dev/null
+++ b/examples/Vacuum_1D/vacuum.yml
@@ -0,0 +1,34 @@
+# 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: 0.1 # The end time of the simulation (in internal units).
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: vacuum # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./vacuum.hdf5 # The file to read
+
diff --git a/examples/Vacuum_2D/getGlass.sh b/examples/Vacuum_2D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ae3c977064f5e7a408aa249c5fd9089b3c52ecb1
--- /dev/null
+++ b/examples/Vacuum_2D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5
diff --git a/examples/Vacuum_2D/makeIC.py b/examples/Vacuum_2D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..ef267c092cafdb95457d5adad1e6858df0e14bd3
--- /dev/null
+++ b/examples/Vacuum_2D/makeIC.py
@@ -0,0 +1,95 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+###############################################################################
+
+import numpy as np
+import h5py
+
+# Generates an overdensity within a vacuum to test the vacuum resolving
+# capabilities of the code
+
+# Parameters
+gamma = 5. / 3. # Gas adiabatic index
+
+fileName = "vacuum.hdf5"
+
+#---------------------------------------------------
+glass = h5py.File("glassPlane_128.hdf5", "r")
+
+# Read particle positions and h from the glass
+pos = glass["/PartType0/Coordinates"][:,:]
+h = glass["/PartType0/SmoothingLength"][:] * 0.3
+
+# Shrink the glass to half its size, move it to the centre of the box, and
+# clone it in the y direction
+pos = 0.5 * pos + np.array([0.25, 0., 0.])
+h *= 0.5
+pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0)
+h = np.append(h, h)
+
+numPart = len(h)
+vol = 0.5
+
+# Generate extra arrays
+v = np.zeros((numPart, 3))
+ids = np.linspace(1, numPart, numPart)
+m = np.zeros(numPart)
+u = np.zeros(numPart)
+
+m[:] = 1. * vol / numPart
+u[:] = 1. / (1. * (gamma - 1.))
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 2
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+file.close()
diff --git a/examples/Vacuum_2D/plotSolution.py b/examples/Vacuum_2D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..4d197234237df10b8cdbf197048a65991da023cf
--- /dev/null
+++ b/examples/Vacuum_2D/plotSolution.py
@@ -0,0 +1,225 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import h5py
+import sys
+import scipy.stats as stats
+
+# Parameters
+gamma = 5. / 3. # Polytropic index
+rhoL = 1. # Initial density in the non vacuum state
+vL = 0. # Initial velocity in the non vacuum state
+PL = 1. # Initial pressure in the non vacuum state
+rhoR = 0. # Initial vacuum density
+vR = 0. # Initial vacuum velocity
+PR = 0. # Initial vacuum pressure
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
+snap = int(sys.argv[1])
+
+# Open the file and read the relevant data
+file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r")
+x = file["/PartType0/Coordinates"][:,0]
+rho = file["/PartType0/Density"][:]
+v = file["/PartType0/Velocities"][:,0]
+u = file["/PartType0/InternalEnergy"][:]
+S = file["/PartType0/Entropy"][:]
+P = file["/PartType0/Pressure"][:]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+# Get the analytic solution, which is just the solution of the corresponding
+# vacuum Riemann problem evaluated at the correct time
+
+# left state sound speed (and rarefaction wave speed)
+aL = np.sqrt(gamma * PL / rhoL)
+
+# vacuum front speed
+SL = vL + 2. / (gamma - 1.) * aL
+
+# we evaluate the solution centred on 0., and shift to the correct position
+# afterwards
+xa = np.arange(-0.25, 0.25, 0.001)
+rhoa = np.zeros(len(xa))
+va = np.zeros(len(xa))
+Pa = np.zeros(len(xa))
+
+for i in range(len(xa)):
+ dxdt = xa[i] / time
+ if dxdt > vL - aL:
+ if dxdt < SL:
+ # rarefaction regime
+ # factor that appears in both the density and pressure expression
+ fac = 2. / (gamma + 1.) + \
+ (gamma - 1.) / (gamma + 1.) * (vL - dxdt) / aL
+ rhoa[i] = rhoL * fac**(2. / (gamma - 1.))
+ va[i] = 2. / (gamma + 1.) * (aL + 0.5 * (gamma - 1.) * vL + dxdt)
+ Pa[i] = PL * fac**(2. * gamma / (gamma - 1.))
+ else:
+ # vacuum regime
+ rhoa[i] = 0.
+ va[i] = 0.
+ Pa[i] = 0.
+ else:
+ # left state regime
+ rhoa[i] = rhoL
+ va[i] = vL
+ Pa[i] = PL
+
+ua = Pa / (gamma - 1.) / rhoa
+Sa = Pa / rhoa**gamma
+
+# Bin the data values
+# We let scipy choose the bins and then reuse them for all other quantities
+rho_bin, x_bin_edge, _ = \
+ stats.binned_statistic(x, rho, statistic = "mean", bins = 50)
+rho2_bin, _, _ = \
+ stats.binned_statistic(x, rho**2, statistic = "mean", bins = x_bin_edge)
+rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2)
+
+v_bin, _, _ = \
+ stats.binned_statistic(x, v, statistic = "mean", bins = x_bin_edge)
+v2_bin, _, _ = \
+ stats.binned_statistic(x, v**2, statistic = "mean", bins = x_bin_edge)
+v_sigma_bin = np.sqrt(v2_bin - v_bin**2)
+
+P_bin, _, _ = \
+ stats.binned_statistic(x, P, statistic = "mean", bins = x_bin_edge)
+P2_bin, _, _ = \
+ stats.binned_statistic(x, P**2, statistic = "mean", bins = x_bin_edge)
+P_sigma_bin = np.sqrt(P2_bin - P_bin**2)
+
+u_bin, _, _ = \
+ stats.binned_statistic(x, u, statistic = "mean", bins = x_bin_edge)
+u2_bin, _, _ = \
+ stats.binned_statistic(x, u**2, statistic = "mean", bins = x_bin_edge)
+u_sigma_bin = np.sqrt(u2_bin - u_bin**2)
+
+S_bin, _, _ = \
+ stats.binned_statistic(x, S, statistic = "mean", bins = x_bin_edge)
+S2_bin, _, _ = \
+ stats.binned_statistic(x, S**2, statistic = "mean", bins = x_bin_edge)
+S_sigma_bin = np.sqrt(S2_bin - S_bin**2)
+
+x_bin = 0.5 * (x_bin_edge[1:] + x_bin_edge[:-1])
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 0.2)
+ax[0][0].plot(xa + 0.75, va, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].plot(xa + 0.25, -va[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].errorbar(x_bin, v_bin, yerr = v_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 0.2)
+ax[0][1].plot(xa + 0.75, rhoa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].plot(xa + 0.25, rhoa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].errorbar(x_bin, rho_bin, yerr = rho_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 0.2)
+ax[0][2].plot(xa + 0.75, Pa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].plot(xa + 0.25, Pa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].errorbar(x_bin, P_bin, yerr = P_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 0.2)
+ax[1][0].plot(xa + 0.75, ua, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].plot(xa + 0.25, ua[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].errorbar(x_bin, u_bin, yerr = u_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 0.2)
+ax[1][1].plot(xa + 0.75, Sa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].plot(xa + 0.25, Sa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].errorbar(x_bin, S_bin, yerr = S_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].text(-0.49, 0.8,
+ "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PL, rhoL, vL), fontsize = 10)
+ax[1][2].text(-0.49, 0.7,
+ "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PR, rhoR, vR), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
+
+pl.tight_layout()
+pl.savefig("Vacuum.png", dpi = 200)
diff --git a/examples/Vacuum_2D/run.sh b/examples/Vacuum_2D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5c0b2ca5e19e33e813b7ff478ed4494752c0a2a5
--- /dev/null
+++ b/examples/Vacuum_2D/run.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassPlane_128.hdf5 ]
+then
+ echo "Fetching initial glass file for the 2D vacuum expansion example..."
+ ./getGlass.sh
+fi
+if [ ! -e vacuum.hdf5 ]
+then
+ echo "Generating initial conditions for the 2D vacuum expansion example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 4 vacuum.yml 2>&1 | tee output.log
+
+# Plot the result
+python plotSolution.py 1
diff --git a/examples/Vacuum_2D/vacuum.yml b/examples/Vacuum_2D/vacuum.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5ef5ce3da68febb086a14ad1a2207711f680d9ff
--- /dev/null
+++ b/examples/Vacuum_2D/vacuum.yml
@@ -0,0 +1,34 @@
+# 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: 0.1 # The end time of the simulation (in internal units).
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: vacuum # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./vacuum.hdf5 # The file to read
+
diff --git a/examples/Vacuum_3D/getGlass.sh b/examples/Vacuum_3D/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c
--- /dev/null
+++ b/examples/Vacuum_3D/getGlass.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
diff --git a/examples/Vacuum_3D/makeIC.py b/examples/Vacuum_3D/makeIC.py
new file mode 100644
index 0000000000000000000000000000000000000000..09c3cb4d6f5525d54fab59643ab4a7d0540a2a92
--- /dev/null
+++ b/examples/Vacuum_3D/makeIC.py
@@ -0,0 +1,97 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+###############################################################################
+
+import numpy as np
+import h5py
+
+# Generates an overdensity within a vacuum to test the vacuum resolving
+# capabilities of the code
+
+# Parameters
+gamma = 5. / 3. # Gas adiabatic index
+
+fileName = "vacuum.hdf5"
+
+#---------------------------------------------------
+glass = h5py.File("glassCube_64.hdf5", "r")
+
+# Read particle positions and h from the glass
+pos = glass["/PartType0/Coordinates"][:,:]
+h = glass["/PartType0/SmoothingLength"][:] * 0.3
+
+# Shrink the glass to half its size, move it to the centre of the box, and
+# clone it in the y and z directions
+pos = 0.5 * pos + np.array([0.25, 0., 0.])
+h *= 0.5
+pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0)
+pos = np.append(pos, pos + np.array([0., 0., 0.5]), axis = 0)
+h = np.append(h, h)
+h = np.append(h, h)
+
+numPart = len(h)
+vol = 0.5
+
+# Generate extra arrays
+v = np.zeros((numPart, 3))
+ids = np.linspace(1, numPart, numPart)
+m = np.zeros(numPart)
+u = np.zeros(numPart)
+
+m[:] = 1. * vol / numPart
+u[:] = 1. / (1. * (gamma - 1.))
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = 0
+grp.attrs["Dimension"] = 3
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = 1
+
+#Units
+grp = file.create_group("/Units")
+grp.attrs["Unit length in cgs (U_L)"] = 1.
+grp.attrs["Unit mass in cgs (U_M)"] = 1.
+grp.attrs["Unit time in cgs (U_t)"] = 1.
+grp.attrs["Unit current in cgs (U_I)"] = 1.
+grp.attrs["Unit temperature in cgs (U_T)"] = 1.
+
+#Particle group
+grp = file.create_group("/PartType0")
+grp.create_dataset('Coordinates', data=pos, dtype='d')
+grp.create_dataset('Velocities', data=v, dtype='f')
+grp.create_dataset('Masses', data=m, dtype='f')
+grp.create_dataset('SmoothingLength', data=h, dtype='f')
+grp.create_dataset('InternalEnergy', data=u, dtype='f')
+grp.create_dataset('ParticleIDs', data=ids, dtype='L')
+
+file.close()
diff --git a/examples/Vacuum_3D/plotSolution.py b/examples/Vacuum_3D/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..4d197234237df10b8cdbf197048a65991da023cf
--- /dev/null
+++ b/examples/Vacuum_3D/plotSolution.py
@@ -0,0 +1,225 @@
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2018 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
+#
+# 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/>.
+#
+##############################################################################
+
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import h5py
+import sys
+import scipy.stats as stats
+
+# Parameters
+gamma = 5. / 3. # Polytropic index
+rhoL = 1. # Initial density in the non vacuum state
+vL = 0. # Initial velocity in the non vacuum state
+PL = 1. # Initial pressure in the non vacuum state
+rhoR = 0. # Initial vacuum density
+vR = 0. # Initial vacuum velocity
+PR = 0. # Initial vacuum pressure
+
+# 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
+}
+pl.rcParams.update(params)
+pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']})
+
+# Read the snapshot index from the command line argument
+snap = int(sys.argv[1])
+
+# Open the file and read the relevant data
+file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r")
+x = file["/PartType0/Coordinates"][:,0]
+rho = file["/PartType0/Density"][:]
+v = file["/PartType0/Velocities"][:,0]
+u = file["/PartType0/InternalEnergy"][:]
+S = file["/PartType0/Entropy"][:]
+P = file["/PartType0/Pressure"][:]
+time = file["/Header"].attrs["Time"][0]
+
+scheme = file["/HydroScheme"].attrs["Scheme"]
+kernel = file["/HydroScheme"].attrs["Kernel function"]
+neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0]
+eta = file["/HydroScheme"].attrs["Kernel eta"][0]
+git = file["Code"].attrs["Git Revision"]
+
+# Get the analytic solution, which is just the solution of the corresponding
+# vacuum Riemann problem evaluated at the correct time
+
+# left state sound speed (and rarefaction wave speed)
+aL = np.sqrt(gamma * PL / rhoL)
+
+# vacuum front speed
+SL = vL + 2. / (gamma - 1.) * aL
+
+# we evaluate the solution centred on 0., and shift to the correct position
+# afterwards
+xa = np.arange(-0.25, 0.25, 0.001)
+rhoa = np.zeros(len(xa))
+va = np.zeros(len(xa))
+Pa = np.zeros(len(xa))
+
+for i in range(len(xa)):
+ dxdt = xa[i] / time
+ if dxdt > vL - aL:
+ if dxdt < SL:
+ # rarefaction regime
+ # factor that appears in both the density and pressure expression
+ fac = 2. / (gamma + 1.) + \
+ (gamma - 1.) / (gamma + 1.) * (vL - dxdt) / aL
+ rhoa[i] = rhoL * fac**(2. / (gamma - 1.))
+ va[i] = 2. / (gamma + 1.) * (aL + 0.5 * (gamma - 1.) * vL + dxdt)
+ Pa[i] = PL * fac**(2. * gamma / (gamma - 1.))
+ else:
+ # vacuum regime
+ rhoa[i] = 0.
+ va[i] = 0.
+ Pa[i] = 0.
+ else:
+ # left state regime
+ rhoa[i] = rhoL
+ va[i] = vL
+ Pa[i] = PL
+
+ua = Pa / (gamma - 1.) / rhoa
+Sa = Pa / rhoa**gamma
+
+# Bin the data values
+# We let scipy choose the bins and then reuse them for all other quantities
+rho_bin, x_bin_edge, _ = \
+ stats.binned_statistic(x, rho, statistic = "mean", bins = 50)
+rho2_bin, _, _ = \
+ stats.binned_statistic(x, rho**2, statistic = "mean", bins = x_bin_edge)
+rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2)
+
+v_bin, _, _ = \
+ stats.binned_statistic(x, v, statistic = "mean", bins = x_bin_edge)
+v2_bin, _, _ = \
+ stats.binned_statistic(x, v**2, statistic = "mean", bins = x_bin_edge)
+v_sigma_bin = np.sqrt(v2_bin - v_bin**2)
+
+P_bin, _, _ = \
+ stats.binned_statistic(x, P, statistic = "mean", bins = x_bin_edge)
+P2_bin, _, _ = \
+ stats.binned_statistic(x, P**2, statistic = "mean", bins = x_bin_edge)
+P_sigma_bin = np.sqrt(P2_bin - P_bin**2)
+
+u_bin, _, _ = \
+ stats.binned_statistic(x, u, statistic = "mean", bins = x_bin_edge)
+u2_bin, _, _ = \
+ stats.binned_statistic(x, u**2, statistic = "mean", bins = x_bin_edge)
+u_sigma_bin = np.sqrt(u2_bin - u_bin**2)
+
+S_bin, _, _ = \
+ stats.binned_statistic(x, S, statistic = "mean", bins = x_bin_edge)
+S2_bin, _, _ = \
+ stats.binned_statistic(x, S**2, statistic = "mean", bins = x_bin_edge)
+S_sigma_bin = np.sqrt(S2_bin - S_bin**2)
+
+x_bin = 0.5 * (x_bin_edge[1:] + x_bin_edge[:-1])
+
+# Plot the interesting quantities
+fig, ax = pl.subplots(2, 3)
+
+# Velocity profile
+ax[0][0].plot(x, v, "r.", markersize = 0.2)
+ax[0][0].plot(xa + 0.75, va, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].plot(xa + 0.25, -va[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][0].errorbar(x_bin, v_bin, yerr = v_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0)
+
+# Density profile
+ax[0][1].plot(x, rho, "r.", markersize = 0.2)
+ax[0][1].plot(xa + 0.75, rhoa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].plot(xa + 0.25, rhoa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][1].errorbar(x_bin, rho_bin, yerr = rho_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
+
+# Pressure profile
+ax[0][2].plot(x, P, "r.", markersize = 0.2)
+ax[0][2].plot(xa + 0.75, Pa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].plot(xa + 0.25, Pa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[0][2].errorbar(x_bin, P_bin, yerr = P_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
+
+# Internal energy profile
+ax[1][0].plot(x, u, "r.", markersize = 0.2)
+ax[1][0].plot(xa + 0.75, ua, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].plot(xa + 0.25, ua[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][0].errorbar(x_bin, u_bin, yerr = u_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
+
+# Entropy profile
+ax[1][1].plot(x, S, "r.", markersize = 0.2)
+ax[1][1].plot(xa + 0.75, Sa, "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].plot(xa + 0.25, Sa[::-1], "k--", alpha = 0.8, linewidth = 1.2)
+ax[1][1].errorbar(x_bin, S_bin, yerr = S_sigma_bin, fmt = ".",
+ markersize = 8., color = "b", linewidth = 1.2)
+ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
+ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
+
+# Run information
+ax[1][2].set_frame_on(False)
+ax[1][2].text(-0.49, 0.9,
+ "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
+ gamma, time), fontsize = 10)
+ax[1][2].text(-0.49, 0.8,
+ "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PL, rhoL, vL), fontsize = 10)
+ax[1][2].text(-0.49, 0.7,
+ "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format(
+ PR, rhoR, vR), fontsize = 10)
+ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1)
+ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10)
+ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10)
+ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10)
+ax[1][2].text(-0.49, 0.2,
+ "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta),
+ fontsize = 10)
+ax[1][2].set_xlim(-0.5, 0.5)
+ax[1][2].set_ylim(0., 1.)
+ax[1][2].set_xticks([])
+ax[1][2].set_yticks([])
+
+pl.tight_layout()
+pl.savefig("Vacuum.png", dpi = 200)
diff --git a/examples/Vacuum_3D/run.sh b/examples/Vacuum_3D/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5029626f67659bba1f22600bb5bd38859dd805ce
--- /dev/null
+++ b/examples/Vacuum_3D/run.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Generate the initial conditions if they are not present.
+if [ ! -e glassCube_64.hdf5 ]
+then
+ echo "Fetching initial glass file for the 3D vacuum expansion example..."
+ ./getGlass.sh
+fi
+if [ ! -e vacuum.hdf5 ]
+then
+ echo "Generating initial conditions for the 3D vacuum expansion example..."
+ python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 16 vacuum.yml 2>&1 | tee output.log
+
+# Plot the result
+python plotSolution.py 1
diff --git a/examples/Vacuum_3D/vacuum.yml b/examples/Vacuum_3D/vacuum.yml
new file mode 100644
index 0000000000000000000000000000000000000000..5ef5ce3da68febb086a14ad1a2207711f680d9ff
--- /dev/null
+++ b/examples/Vacuum_3D/vacuum.yml
@@ -0,0 +1,34 @@
+# 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: 0.1 # The end time of the simulation (in internal units).
+ dt_min: 1e-10 # The minimal time-step size of the simulation (in internal units).
+ dt_max: 1e-2 # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+ basename: vacuum # Common part of the name of output files
+ time_first: 0. # Time of the first output (in internal units)
+ delta_time: 0.1 # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+ delta_time: 1e-2 # 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.
+
+# Parameters related to the initial conditions
+InitialConditions:
+ file_name: ./vacuum.hdf5 # The file to read
+
diff --git a/src/const.h b/src/const.h
index dd7e1e267246c0f73e760191a071c6e24b96cfe8..85d64f5f3bf97b3f6ca6df8f230e0e0990687d34 100644
--- a/src/const.h
+++ b/src/const.h
@@ -68,7 +68,7 @@
#define GIZMO_UNPHYSICAL_RESCUE
/* Show a warning message if an unphysical value was reset (only works if
GIZMO_UNPHYSICAL_RESCUE is also selected). */
-//#define GIZMO_UNPHYSICAL_WARNING
+#define GIZMO_UNPHYSICAL_WARNING
/* Parameters that control how GIZMO handles pathological particle
configurations. */
diff --git a/src/hydro/Gizmo/hydro.h b/src/hydro/Gizmo/hydro.h
index a7ccde6a9bcd2ea87e16b89e07bcb4782e7044ad..b8c2c5e405e116acf5632b42b3b5fb60ae3e0d4e 100644
--- a/src/hydro/Gizmo/hydro.h
+++ b/src/hydro/Gizmo/hydro.h
@@ -645,18 +645,6 @@ __attribute__((always_inline)) INLINE static void hydro_kick_extra(
/* Make sure the gpart knows the mass has changed. */
p->gpart->mass = p->conserved.mass;
-#if !defined(EOS_ISOTHERMAL_GAS)
- /* If the energy needs to be updated, we need to do it before the momentum
- is updated, as the old value of the momentum enters the equations. */
- p->conserved.energy += dt * (p->conserved.momentum[0] * a_grav[0] +
- p->conserved.momentum[1] * a_grav[1] +
- p->conserved.momentum[2] * a_grav[2]);
-
- p->conserved.energy += dt * (a_grav[0] * p->gravity.mflux[0] +
- a_grav[1] * p->gravity.mflux[1] +
- a_grav[2] * p->gravity.mflux[2]);
-#endif
-
/* Kick the momentum for half a time step */
/* Note that this also affects the particle movement, as the velocity for
the particles is set after this. */