Merge branch 'master' into dopair-vectorisation

Conflicts:
	src/Makefile.am
	src/cache.h

.gitignore

@@ -22,9 +22,6 @@ doc/Doxyfile
 
 examples/swift
 examples/swift_mpi
-examples/*.xmf
-examples/used_parameters.yml
-examples/energy.txt
 examples/*/*.xmf
 examples/*/*.hdf5
 examples/*/*.png

README

@@ -15,24 +15,26 @@ Usage: swift [OPTION]... PARAMFILE
        swift_mpi [OPTION]... PARAMFILE
 
 Valid options are:
-  -a          Pin runners using processor affinity
-  -c          Run with cosmological time integration
-  -C          Run with cooling
+  -a          Pin runners using processor affinity.
+  -c          Run with cosmological time integration.
+  -C          Run with cooling.
   -d          Dry run. Read the parameter file, allocate memory but does not read 
               the particles from ICs and exit before the start of time integration.
               Allows user to check validy of parameter and IC files as well as memory limits.
-  -D          Always drift all particles even the ones far from active particles.
-  -e          Enable floating-point exceptions (debugging mode)
-  -f    {int} Overwrite the CPU frequency (Hz) to be used for time measurements
-  -g          Run with an external gravitational potential
-  -G          Run with self-gravity
+  -D          Always drift all particles even the ones far from active particles. This emulates
+  	      Gadget-[23] and GIZMO's default behaviours.
+  -e          Enable floating-point exceptions (debugging mode).
+  -f    {int} Overwrite the CPU frequency (Hz) to be used for time measurements.
+  -g          Run with an external gravitational potential.
+  -G          Run with self-gravity.
   -n    {int} Execute a fixed number of time steps. When unset use the time_end parameter to stop. 
-  -s          Run with SPH
+  -s          Run with hydrodynamics.
+  -S          Run with stars.
   -t    {int} The number of threads to use on each MPI rank. Defaults to 1 if not specified.
   -v     [12] Increase the level of verbosity
   	      1: MPI-rank 0 writes
 	      2: All MPI-ranks write
-  -y    {int} Time-step frequency at which task graphs are dumped
-  -h          Print this help message and exit
+  -y    {int} Time-step frequency at which task graphs are dumped.
+  -h          Print this help message and exit.
 
 See the file examples/parameter_example.yml for an example of parameter file.

configure.ac

@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # Init the project.
-AC_INIT([SWIFT],[0.4.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
+AC_INIT([SWIFT],[0.5.0],[https://gitlab.cosma.dur.ac.uk/swift/swiftsim])
 swift_config_flags="$*"
 
 #  Need to define this, instead of using fifth argument of AC_INIT, until 2.64.

doc/Doxyfile.in

@@ -762,6 +762,7 @@ WARN_LOGFILE           =
 INPUT                  =  @top_srcdir@ @top_srcdir@/src @top_srcdir@/tests @top_srcdir@/examples
 INPUT		       += @top_srcdir@/src/hydro/Minimal
 INPUT		       += @top_srcdir@/src/gravity/Default
+INPUT		       += @top_srcdir@/src/stars/Default
 INPUT		       += @top_srcdir@/src/riemann
 INPUT		       += @top_srcdir@/src/potential/point_mass
 INPUT		       += @top_srcdir@/src/cooling/const_du

examples/ExternalPointMass/energy_plot.py

@@ -91,6 +91,9 @@ for i in range(402):
     E_tot_snap[i] = E_kin_snap[i] + E_pot_snap[i]
     Lz_snap[i] = np.sum(Lz)
 
+print "Starting energy:", E_kin_stats[0], E_pot_stats[0], E_tot_stats[0]
+print "Ending   energy:", E_kin_stats[-1], E_pot_stats[-1], E_tot_stats[-1]
+    
 # Plot energy evolution
 figure()
 plot(time_stats, E_kin_stats, "r-", lw=0.5, label="Kinetic energy")

examples/GreshoVortex_2D/plotSolution.py

@@ -31,6 +31,7 @@ P0 = 0.           # Constant additional pressure (should have no impact on the d
 import matplotlib
 matplotlib.use("Agg")
 from pylab import *
+from scipy import stats
 import h5py
 
 # Plot parameters
@@ -104,6 +105,26 @@ 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()
 
@@ -113,6 +134,7 @@ 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)
@@ -125,6 +147,7 @@ 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)
@@ -138,6 +161,7 @@ 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)
@@ -150,6 +174,7 @@ 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)
@@ -163,6 +188,7 @@ 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)

examples/IsothermalPotential/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e Isothermal.hdf5 ]
 then
     echo "Generating initial conditions for the isothermal potential box example..."
-    python makeIC.py 1000 1
+    python makeIC.py 1000 0
 fi
 
 rm -rf Isothermal_*.hdf5

examples/MultiTypes/makeIC.py

@@ -36,110 +36,154 @@ eta = 1.2349             # 48 ngbs with cubic spline kernel
 rhoDM = 1.
 Ldm = int(sys.argv[2])  # Number of particles along one axis
 
-fileName = "multiTypes.hdf5"
+massStars = 0.1
+Lstars = int(sys.argv[3])  # Number of particles along one axis
+
+fileBaseName = "multiTypes"
+num_files = int(sys.argv[4])
 
 #---------------------------------------------------
-numGas = Lgas**3
-massGas = boxSize**3 * rhoGas / numGas
+numGas_tot = Lgas**3
+massGas = boxSize**3 * rhoGas / numGas_tot
 internalEnergy = P / ((gamma - 1.)*rhoGas)
 
-numDM = Ldm**3
-massDM = boxSize**3 * rhoDM / numDM
+numDM_tot = Ldm**3
+massDM = boxSize**3 * rhoDM / numDM_tot
+
+numStars_tot = Lstars**3
+massStars = massDM * massStars
+
 
 #--------------------------------------------------
 
-#File
-file = h5py.File(fileName, 'w')
-
-# Header
-grp = file.create_group("/Header")
-grp.attrs["BoxSize"] = boxSize
-grp.attrs["NumPart_Total"] =  [numGas, numDM, 0, 0, 0, 0]
-grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
-grp.attrs["NumPart_ThisFile"] = [numGas, numDM, 0, 0, 0, 0]
-grp.attrs["Time"] = 0.0
-grp.attrs["NumFilesPerSnapshot"] = 1
-grp.attrs["MassTable"] = [0.0, massDM, 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"] = periodic
-
-#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.
-
-
-# Gas Particle group
-grp = file.create_group("/PartType0")
-
-v  = zeros((numGas, 3))
-ds = grp.create_dataset('Velocities', (numGas, 3), 'f')
-ds[()] = v
-v = zeros(1)
-
-m = full((numGas, 1), massGas)
-ds = grp.create_dataset('Masses', (numGas,1), 'f')
-ds[()] = m
-m = zeros(1)
-
-h = full((numGas, 1), eta * boxSize / Lgas)
-ds = grp.create_dataset('SmoothingLength', (numGas,1), 'f')
-ds[()] = h
-h = zeros(1)
-
-u = full((numGas, 1), internalEnergy)
-ds = grp.create_dataset('InternalEnergy', (numGas,1), 'f')
-ds[()] = u
-u = zeros(1)
-
-ids = linspace(0, numGas, numGas, endpoint=False).reshape((numGas,1))
-ds = grp.create_dataset('ParticleIDs', (numGas, 1), 'L')
-ds[()] = ids + 1
-x      = ids % Lgas;
-y      = ((ids - x) / Lgas) % Lgas;
-z      = (ids - x - Lgas * y) / Lgas**2;
-coords = zeros((numGas, 3))
-coords[:,0] = z[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
-coords[:,1] = y[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
-coords[:,2] = x[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
-ds = grp.create_dataset('Coordinates', (numGas, 3), 'd')
-ds[()] = coords
-
-
-
-
-
-# DM Particle group
-grp = file.create_group("/PartType1")
-
-v  = zeros((numDM, 3))
-ds = grp.create_dataset('Velocities', (numDM, 3), 'f')
-ds[()] = v
-v = zeros(1)
-
-m = full((numDM, 1), massDM)
-ds = grp.create_dataset('Masses', (numDM,1), 'f')
-ds[()] = m
-m = zeros(1)
-
-ids = linspace(0, numDM, numDM, endpoint=False).reshape((numDM,1))
-ds = grp.create_dataset('ParticleIDs', (numDM, 1), 'L')
-ds[()] = ids + Lgas**3 + 1
-x      = ids % Ldm;
-y      = ((ids - x) / Ldm) % Ldm;
-z      = (ids - x - Ldm * y) / Ldm**2;
-coords = zeros((numDM, 3))
-coords[:,0] = z[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
-coords[:,1] = y[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
-coords[:,2] = x[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
-ds = grp.create_dataset('Coordinates', (numDM, 3), 'd')
-ds[()] = coords
-
-file.close()
+offsetGas = 0
+offsetDM = 0
+offsetStars = 0
+
+for n in range(num_files):
+
+    # File name
+    if num_files == 1:
+        fileName = fileBaseName + ".hdf5"
+    else:
+        fileName = fileBaseName + ".%d.hdf5"%n
+        
+    # File
+    file = h5py.File(fileName, 'w')
+
+    # Number of particles
+    numGas = numGas_tot / num_files
+    numDM = numDM_tot / num_files
+    numStars = numStars_tot / num_files
+
+    if n == num_files - 1:
+        numGas += numGas_tot % num_files
+        numDM += numDM_tot % num_files
+        numStars += numStars_tot % num_files
+
+    
+    # Header
+    grp = file.create_group("/Header")
+    grp.attrs["BoxSize"] = boxSize
+    grp.attrs["NumPart_Total"] =  [numGas_tot, numDM_tot, 0, 0, numStars_tot, 0]
+    grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+    grp.attrs["NumPart_ThisFile"] = [numGas, numDM, 0, 0, numStars, 0]
+    grp.attrs["Time"] = 0.0
+    grp.attrs["NumFilesPerSnapshot"] = num_files
+    grp.attrs["MassTable"] = [0.0, massDM, 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"] = periodic
+    
+    #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.
+
+
+    # Gas Particle group
+    grp = file.create_group("/PartType0")
+
+    v  = zeros((numGas, 3))
+    ds = grp.create_dataset('Velocities', (numGas, 3), 'f', data=v)
+    
+    m = full((numGas, 1), massGas)
+    ds = grp.create_dataset('Masses', (numGas,1), 'f', data=m)
+    
+    h = full((numGas, 1), eta * boxSize / Lgas)
+    ds = grp.create_dataset('SmoothingLength', (numGas,1), 'f', data=h)
+    
+    u = full((numGas, 1), internalEnergy)
+    ds = grp.create_dataset('InternalEnergy', (numGas,1), 'f', data=u)
+
+    ids = linspace(offsetGas, offsetGas+numGas, numGas, endpoint=False).reshape((numGas,1))
+    ds = grp.create_dataset('ParticleIDs', (numGas, 1), 'L', data=ids+1)
+    x      = ids % Lgas;
+    y      = ((ids - x) / Lgas) % Lgas;
+    z      = (ids - x - Lgas * y) / Lgas**2;
+    coords = zeros((numGas, 3))
+    coords[:,0] = z[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+    coords[:,1] = y[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+    coords[:,2] = x[:,0] * boxSize / Lgas + boxSize / (2*Lgas)
+    ds = grp.create_dataset('Coordinates', (numGas, 3), 'd', data=coords)
+
+
+    
+    # DM Particle group
+    grp = file.create_group("/PartType1")
+
+    v  = zeros((numDM, 3))
+    ds = grp.create_dataset('Velocities', (numDM, 3), 'f', data=v)
+
+    m = full((numDM, 1), massDM)
+    ds = grp.create_dataset('Masses', (numDM,1), 'f', data=m)
+
+    ids = linspace(offsetDM, offsetDM+numDM, numDM, endpoint=False).reshape((numDM,1))
+    ds = grp.create_dataset('ParticleIDs', (numDM, 1), 'L', data=ids + numGas_tot + 1)
+    ds[()] = ids + Lgas**3 + 1
+    x      = ids % Ldm;
+    y      = ((ids - x) / Ldm) % Ldm;
+    z      = (ids - x - Ldm * y) / Ldm**2;
+    coords = zeros((numDM, 3))
+    coords[:,0] = z[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    coords[:,1] = y[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    coords[:,2] = x[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    ds = grp.create_dataset('Coordinates', (numDM, 3), 'd', data=coords)
+
+
+
+    # Star Particle group
+    grp = file.create_group("/PartType4")
+
+    v  = zeros((numStars, 3))
+    ds = grp.create_dataset('Velocities', (numStars, 3), 'f', data=v)
+
+    m = full((numStars, 1), massStars)
+    ds = grp.create_dataset('Masses', (numStars,1), 'f', data=m)
+
+    ids = linspace(0, numStars, numStars, endpoint=False).reshape((numStars,1))
+    ds = grp.create_dataset('ParticleIDs', (numStars, 1), 'L', data=ids + numGas_tot + numDM_tot + 1)
+    x      = ids % Ldm;
+    y      = ((ids - x) / Ldm) % Ldm;
+    z      = (ids - x - Ldm * y) / Ldm**2;
+    coords = zeros((numStars, 3))
+    coords[:,0] = z[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    coords[:,1] = y[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    coords[:,2] = x[:,0] * boxSize / Ldm + boxSize / (2*Ldm)
+    ds = grp.create_dataset('Coordinates', (numStars, 3), 'd', data=coords)
+
+
+    
+    # Shift stuff
+    offsetGas += numGas
+    offsetDM += numDM
+    offsetStars += numStars
+    
+    file.close()
+

examples/MultiTypes/multiTypes.yml

@@ -32,6 +32,7 @@ SPH:
 # Parameters related to the initial conditions
 InitialConditions:
   file_name:  ./multiTypes.hdf5     # The file to read
+  replicate:  2                     # Replicate all particles twice along each axis
 
 # External potential parameters
 PointMassPotential:

examples/MultiTypes/run.sh

@@ -4,7 +4,7 @@
 if [ ! -e multiTypes.hdf5 ]
 then
     echo "Generating initial conditions for the multitype box example..."
-    python makeIC.py 50 60
+    python makeIC.py 9 13 7 1
 fi
 
-../swift -s -g -t 16 multiTypes.yml 2>&1 | tee output.log
+../swift -s -g -S -t 1 multiTypes.yml 2>&1 | tee output.log

examples/Noh_1D/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 1D Noh problem test in a periodic box
+
+# Parameters
+numPart = 1001
+gamma = 5./3.      # Gas adiabatic index
+rho0 = 1.          # Background density
+P0 = 1.e-6         # Background pressure
+fileName = "noh.hdf5" 
+
+#---------------------------------------------------
+coords = zeros((numPart, 3))
+h = zeros(numPart)
+vol = 2.
+
+for i in range(numPart):
+    coords[i,0] = i * vol/numPart + vol/(2.*numPart)
+    h[i] = 1.2348 * vol / numPart
+
+# Generate extra arrays
+v = zeros((numPart, 3))
+ids = linspace(1, numPart, numPart)
+m = zeros(numPart)
+u = zeros(numPart)
+
+m[:] = rho0 * vol / numPart    
+u[:] = P0 / (rho0 * (gamma - 1))
+v[coords[:,0]<vol/2. ,0] = 1
+v[coords[:,0]>vol/2. ,0] = -1
+
+#--------------------------------------------------
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = [vol, vol, vol]
+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')
+
+file.close()

examples/Noh_1D/noh.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:   0.6   # 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:            noh # Common part of the name of output files
+  time_first:          0.    # Time of the first output (in internal units)
+  delta_time:          5e-2  # 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).
+  delta_neighbours:      0.1      # The tolerance for the targetted number of neighbours.
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
+
+# Parameters related to the initial conditions
+InitialConditions:
+  file_name:  ./noh.hdf5          # The file to read
+

examples/Noh_1D/plotSolution.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ # GNU General Public License for more details.
+ # 
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+# Computes the analytical solution of the Noh problem and plots the SPH answer
+ 
+
+# Parameters
+gas_gamma = 5./3.      # Polytropic index
+rho0 = 1.              # Background density
+P0 = 1.e-6             # Background pressure