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

Conflicts:
	src/space.c

examples/SmoothedMetallicity/plotSolution.py

+#!/usr/bin/env python
+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2015 Bert Vandenbroucke (bert.vandenbroucke@ugent.be)
+#                    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 3D Smoothed Metallicity example.
+
+import h5py
+import sys
+import numpy as np
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+
+# Parameters
+low_metal = -6     # low metal abundance
+high_metal = -5    # High metal abundance
+sigma_metal = 0.1  # relative standard deviation for Z
+
+Nelem = 9
+# shift all metals in order to obtain nicer plots
+low_metal = [low_metal] * Nelem + np.linspace(0, 3, Nelem)
+high_metal = [high_metal] * Nelem + np.linspace(0, 3, Nelem)
+
+# ---------------------------------------------------------------
+# Don't touch anything after this.
+# ---------------------------------------------------------------
+
+# 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
+}
+
+plt.rcParams.update(params)
+plt.rc('font', **{'family': 'sans-serif', 'sans-serif': ['Times']})
+
+
+snap = int(sys.argv[1])
+
+
+# Read the simulation data
+sim = h5py.File("smoothed_metallicity_%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"]
+chemistry = sim["/SubgridScheme"].attrs["Chemistry Model"]
+git = sim["Code"].attrs["Git Revision"]
+
+pos = sim["/PartType0/Coordinates"][:, :]
+d = pos[:, 0] - boxSize / 2
+smooth_metal = sim["/PartType0/SmoothedElementAbundance"][:, :]
+metal = sim["/PartType0/ElementAbundance"][:, :]
+h = sim["/PartType0/SmoothingLength"][:]
+h = np.mean(h)
+
+if (Nelem != metal.shape[1]):
+    print("Unexpected number of element, please check makeIC.py"
+          " and plotSolution.py")
+    exit(1)
+
+N = 1000
+d_a = np.linspace(-boxSize / 2., boxSize / 2., N)
+
+# Now, work our the solution....
+
+
+def calc_a(d, high_metal, low_metal, std_dev, h):
+    """
+    Compute analytical solution:
+                        ___ High Metallicity
+    Low Metallicity ___/
+
+    where the linear part length is given by the smoothing length.
+
+    Parameters
+    ----------
+
+    d: np.array
+        Position to compute
+    high_metal: float
+        Value on the high metallicity side
+
+    low_metal: float
+        Value on the low metallicity side
+
+    std_dev: float
+        Standard deviation of the noise added
+
+    h: float
+        Mean smoothing length
+    """
+
+    # solution
+    a = np.zeros([len(d), Nelem])
+    # function at +- 1 sigma
+    sigma = np.zeros([len(d), Nelem, 2])
+
+    for i in range(Nelem):
+        # compute low metallicity side
+        s = d < -h
+        a[s, i] = low_metal[i]
+        # compute high metallicity side
+        s = d > h
+        a[s, i] = high_metal[i]
+
+        # compute non constant parts
+        m = (high_metal[i] - low_metal[i]) / (2.0 * h)
+        c = (high_metal[i] + low_metal[i]) / 2.0
+        # compute left linear part
+        s = d < - boxSize / 2.0 + h
+        a[s, i] = - m * (d[s] + boxSize / 2.0) + c
+        # compute middle linear part
+        s = np.logical_and(d >= -h, d <= h)
+        a[s, i] = m * d[s] + c
+        # compute right linear part
+        s = d > boxSize / 2.0 - h
+        a[s, i] = - m * (d[s] - boxSize / 2.0) + c
+
+    sigma[:, :, 0] = a * (1 + std_dev)
+    sigma[:, :, 1] = a * (1 - std_dev)
+    return a, sigma
+
+
+# compute solution
+sol, sig = calc_a(d_a, high_metal, low_metal, sigma_metal, h)
+
+# Plot the interesting quantities
+plt.figure()
+
+# Metallicity --------------------------------
+plt.subplot(221)
+for e in range(Nelem):
+    plt.plot(metal[:, e], smooth_metal[:, e], '.', ms=0.5, alpha=0.2)
+
+xmin, xmax = metal.min(), metal.max()
+ymin, ymax = smooth_metal.min(), smooth_metal.max()
+x = max(xmin, ymin)
+y = min(xmax, ymax)
+plt.plot([x, y], [x, y], "--k", lw=1.0)
+plt.xlabel("${\\rm{Metallicity}}~Z_\\textrm{part}$", labelpad=0)
+plt.ylabel("${\\rm{Smoothed~Metallicity}}~Z_\\textrm{sm}$", labelpad=0)
+
+# Metallicity --------------------------------
+e = 0
+plt.subplot(223)
+plt.plot(d, smooth_metal[:, e], '.', color='r', ms=0.5, alpha=0.2)
+plt.plot(d_a, sol[:, e], '--', color='b', alpha=0.8, lw=1.2)
+plt.fill_between(d_a, sig[:, e, 0], sig[:, e, 1], facecolor="b",
+                 interpolate=True, alpha=0.5)
+plt.xlabel("${\\rm{Distance}}~r$", labelpad=0)
+plt.ylabel("${\\rm{Smoothed~Metallicity}}~Z_\\textrm{sm}$", labelpad=0)
+plt.xlim(-0.5, 0.5)
+plt.ylim(low_metal[e]-1, high_metal[e]+1)
+
+# Information -------------------------------------
+plt.subplot(222, frameon=False)
+
+plt.text(-0.49, 0.9, "Smoothed Metallicity in 3D at $t=%.2f$" % time,
+         fontsize=10)
+plt.plot([-0.49, 0.1], [0.82, 0.82], 'k-', lw=1)
+plt.text(-0.49, 0.7, "$\\textsc{Swift}$ %s" % git, fontsize=10)
+plt.text(-0.49, 0.6, scheme, fontsize=10)
+plt.text(-0.49, 0.5, kernel, fontsize=10)
+plt.text(-0.49, 0.4, chemistry + "'s Chemistry", fontsize=10)
+plt.text(-0.49, 0.3, "$%.2f$ neighbours ($\\eta=%.3f$)" % (neighbours, eta),
+         fontsize=10)
+plt.xlim(-0.5, 0.5)
+plt.ylim(0, 1)
+plt.xticks([])
+plt.yticks([])
+
+plt.tight_layout()
+plt.savefig("SmoothedMetallicity.png", dpi=200)

examples/SmoothedMetallicity/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e glassCube_32.hdf5 ]
+then
+    echo "Fetching initial glass file for the SmoothedMetallicity example..."
+    ./getGlass.sh
+fi
+if [ ! -e smoothed_metallicity.hdf5 ]
+then
+    echo "Generating initial conditions for the SmoothedMetallicity example..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../swift -n 1 -s -t 4 smoothed_metallicity.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 1

examples/SmoothedMetallicity/smoothed_metallicity.yml

+# 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:   2e-4  # 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-4  # The maximal time-step size of the simulation (in internal units).
+
+# Parameters governing the snapshots
+Snapshots:
+  basename:            smoothed_metallicity # Common part of the name of output files
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          5e-5  # Time difference between consecutive outputs (in internal units)
+
+# Parameters governing the conserved quantities statistics
+Statistics:
+  delta_time:          1e-5 # 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:  ./smoothed_metallicity.hdf5          # The file to read
+

examples/SodShockSpherical_2D/getGlass.sh

+#!/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

examples/SodShockSpherical_2D/getReference.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/sodShockSpherical2D_exact.txt

examples/SodShockSpherical_2D/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ # GNU General Public License for more details.
+ # 
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+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()

examples/SodShockSpherical_2D/plotSolution.py

+###############################################################################
+# 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)

examples/SodShockSpherical_2D/run.sh

+#!/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

examples/SodShockSpherical_2D/sodShock.yml

+# 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
+

examples/SodShockSpherical_3D/getGlass.sh

+#!/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

examples/SodShockSpherical_3D/getReference.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/sodShockSpherical3D_exact.txt

examples/SodShockSpherical_3D/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ # GNU General Public License for more details.
+ # 
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+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()

examples/SodShockSpherical_3D/plotSolution.py

+###############################################################################
+# 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)

examples/SodShockSpherical_3D/run.sh

+#!/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

examples/SodShockSpherical_3D/sodShock.yml

+# 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
+

examples/VacuumSpherical_2D/getGlass.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5

examples/VacuumSpherical_2D/getReference.sh

+#!/bin/bash
+wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/vacuumSpherical2D_exact.txt

examples/VacuumSpherical_2D/makeIC.py

+###############################################################################
+# 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()

examples/VacuumSpherical_2D/plotSolution.py

+###############################################################################
+# 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)

examples/VacuumSpherical_2D/run.sh

+#!/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