diff --git a/.gitignore b/.gitignore
index 3521b353ec4b1c4dea7192047e197596f083fe99..1a43373acd789366119becb30662be2855db4a51 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,6 +29,7 @@ examples/used_parameters.yml
examples/energy.txt
examples/*/*.xmf
examples/*/*.hdf5
+examples/*/*.png
examples/*/*.txt
examples/*/used_parameters.yml
examples/*/*/*.xmf
diff --git a/examples/GreshoVortex/getGlass.sh b/examples/GreshoVortex/getGlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..ae3c977064f5e7a408aa249c5fd9089b3c52ecb1
--- /dev/null
+++ b/examples/GreshoVortex/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/GreshoVortex/gresho.yml b/examples/GreshoVortex/gresho.yml
new file mode 100644
index 0000000000000000000000000000000000000000..9fb6af048e396878446fd9d6308a08ccf300a0d5
--- /dev/null
+++ b/examples/GreshoVortex/gresho.yml
@@ -0,0 +1,35 @@
+# 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: 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-2 # 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).
+ delta_neighbours: 0.1 # The tolerance for the targetted number of neighbours.
+ max_smoothing_length: 0.1 # Maximal smoothing length allowed (in internal units).
+ 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/makeIC.py b/examples/GreshoVortex/makeIC.py
index b3e0f641293feaf1b6274039fe2bcc82f80b186b..2f5bebc00ce0f86d3f4f3cccd030cfff5f90d51d 100644
--- a/examples/GreshoVortex/makeIC.py
+++ b/examples/GreshoVortex/makeIC.py
@@ -23,32 +23,32 @@ import random
from numpy import *
import sys
-# Generates a swift IC file for the Gresho Vortex in a periodic box
+# Generates a swift IC file for the Gresho-Chan vortex in a periodic box
# Parameters
-inputFile = "glass_256.hdf5"
-periodic= 1 # 1 For periodic box
gamma = 5./3. # Gas adiabatic index
-rho = 1 # Gas density
+rho0 = 1 # Gas density
P0 = 0. # Constant additional pressure (should have no impact on the dynamics)
fileOutputName = "greshoVortex.hdf5"
-
-
+fileGlass = "glassPlane_128.hdf5"
#---------------------------------------------------
-fileInput = h5py.File(inputFile, "r")
-header = fileInput["/Header"]
-boxSize = header.attrs["BoxSize"][0]
+
+# 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"][:]
-numPart = size(ids)
-
-m = ones(shape(ids)) * boxSize**2 / numPart
-u = zeros(shape(m))
-v = zeros(shape(coords))
+boxSize = fileInput["/Header"].attrs["BoxSize"][0]
+numPart = size(h)
+fileInput.close()
+# Now generate the rest
+m = ones(numPart) * rho0 * boxSize**2 / numPart
+u = zeros(numPart)
+v = zeros((numPart, 3))
for i in range(numPart):
+
x = coords[i,0]
y = coords[i,1]
z = coords[i,2]
@@ -74,7 +74,7 @@ for i in range(numPart):
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.)*rho)
+ u[i] = P / ((gamma - 1.)*rho0)
@@ -94,7 +94,7 @@ grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
#Runtime parameters
grp = fileOutput.create_group("/RuntimePars")
-grp.attrs["PeriodicBoundariesOn"] = periodic
+grp.attrs["PeriodicBoundariesOn"] = 1
#Units
grp = fileOutput.create_group("/Units")
diff --git a/examples/GreshoVortex/plotSolution.py b/examples/GreshoVortex/plotSolution.py
new file mode 100644
index 0000000000000000000000000000000000000000..db7ccceaaa21daed309654e2c59815b5c141cf15
--- /dev/null
+++ b/examples/GreshoVortex/plotSolution.py
@@ -0,0 +1,155 @@
+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ #
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ #
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ # GNU General Public License for more details.
+ #
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program. If not, see <http://www.gnu.org/licenses/>.
+ #
+ ##############################################################################
+
+# Computes the analytical solution of the Gresho-Chan vortex and plots the SPH answer
+
+# Parameters
+gas_gamma = 5./3. # Gas adiabatic index
+rho0 = 1 # Gas density
+P0 = 0. # Constant additional pressure (should have no impact on the dynamics)
+
+# ---------------------------------------------------------------
+# Don't touch anything after this.
+# ---------------------------------------------------------------
+
+import matplotlib
+matplotlib.use("Agg")
+from pylab import *
+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' : (6.45,6.45),
+'figure.subplot.left' : 0.07,
+'figure.subplot.right' : 0.985,
+'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_%03d.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"]
+
+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)
+u = sim["/PartType0/InternalEnergy"][:]
+
+# Plot the interesting quantities
+figure()
+
+# Internal energy profile --------------------------------
+subplot(221)
+
+plot(r, u, 'x', color='r')
+plot(solution_r, solution_u, '--', color='k', alpha=0.8, 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)
+text(0.02, 8.97, "%s"%scheme, fontsize=9, backgroundcolor="w")
+text(0.02, 8.82, "%s"%kernel, fontsize=9, backgroundcolor="w")
+xlim(0,R_max)
+ylim(7.3, 9.1)
+
+# Azimuthal velocity profile -----------------------------
+subplot(222)
+
+plot(r, v_phi, 'x', color='r')
+plot(solution_r, solution_v_phi, '--', color='k', alpha=0.8, 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)
+text(0.75, 1, "$t=%.3f$"%(time), ha="right", va="bottom")
+
+# Radial velocity profile --------------------------------
+subplot(223)
+
+plot(r, v_r, 'x', color='r', label="$\\texttt{SWIFT}$")
+plot(solution_r, solution_v_r, '--', color='k', alpha=0.8, lw=1.2, label="$\\rm{Solution}$")
+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("${\\rm{Radial~velocity}}~v_r$", labelpad=-5)
+legend(loc="upper right", fontsize=10, frameon=False, numpoints=1, handletextpad=0.1, handlelength=1.2)
+xlim(0,R_max)
+ylim(-0.2, 0.2)
+yticks([-0.2, -0.1, 0., 0.1, 0.2])
+
+
+# Image --------------------------------------------------
+subplot(224)
+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)
+
+savefig("greshoVortex_%03d.png"%snap)
diff --git a/examples/GreshoVortex/run.sh b/examples/GreshoVortex/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..9a312d0c161aab07c33c1bb7beb26a205e216a39
--- /dev/null
+++ b/examples/GreshoVortex/run.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e glass_128.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 1 gresho.yml
+
+# Plot the solution
+for i in {0..100}
+do
+ python plotSolution.py $i
+done
+
+# Make a movie
+mencoder mf://*.png -mf w=645:h=645:fps=12:type=png -ovc lavc -lavcopts vcodec=mpeg4:mbd=2:trell -oac copy -o gresho.avi
diff --git a/examples/GreshoVortex/solution.py b/examples/GreshoVortex/solution.py
deleted file mode 100644
index 5b282caf2d7f3311ddb595781fed74c51bb4819f..0000000000000000000000000000000000000000
--- a/examples/GreshoVortex/solution.py
+++ /dev/null
@@ -1,69 +0,0 @@
-###############################################################################
- # This file is part of SWIFT.
- # Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
- # 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 random
-from numpy import *
-
-# Computes the analytical solution of the Gresho-Chan vortex
-# The script works for a given initial box and background pressure and computes the solution for any time t (The solution is constant over time).
-# The code writes five files rho.dat, P.dat, v.dat, u.dat and s.dat with the density, pressure, internal energy and
-# entropic function on N radial points between r=0 and r=R_max.
-
-# Parameters
-rho0 = 1. # Background Density
-P0 = 0. # Background Pressure
-gamma = 5./3. # Gas polytropic index
-N = 1000 # Number of radial points
-R_max = 1. # Maximal radius
-
-# ---------------------------------------------------------------
-# Don't touch anything after this.
-# ---------------------------------------------------------------
-
-r = arange(0, R_max, R_max / N)
-rho = ones(N)
-P = zeros(N)
-v = zeros(N)
-u = zeros(N)
-s = zeros(N)
-
-
-for i in range(N):
- if r[i] < 0.2:
- P[i] = P0 + 5. + 12.5*r[i]**2
- v[i] = 5.*r[i]
- elif r[i] < 0.4:
- P[i] = P0 + 9. + 12.5*r[i]**2 - 20.*r[i] + 4.*log(r[i]/0.2)
- v[i] = 2. -5.*r[i]
- else:
- P[i] = P0 + 3. + 4.*log(2.)
- v[i] = 0.
- rho[i] = rho0
- s[i] = P[i] / rho[i]**gamma
- u[i] = P[i] /((gamma - 1.)*rho[i])
-
-savetxt("rho.dat", column_stack((r, rho)))
-savetxt("P.dat", column_stack((r, P)))
-savetxt("v.dat", column_stack((r, v)))
-savetxt("u.dat", column_stack((r, u)))
-savetxt("s.dat", column_stack((r, s)))
-
-
-