Merge branch 'master' into tasks_cleanup

examples/CosmoVolume/run.sh

@@ -7,4 +7,4 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 cosmoVolume.yml
+../swift -s -t 16 cosmoVolume.yml 2>&1 | tee output.log

examples/EAGLE_12/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_12.yml
+../swift -s -t 16 eagle_12.yml 2>&1 | tee output.log
 

examples/EAGLE_25/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_25.yml
+../swift -s -t 16 eagle_25.yml 2>&1 | tee output.log
 

examples/EAGLE_50/run.sh

@@ -7,5 +7,5 @@ then
     ./getIC.sh
 fi
 
-../swift -s -t 16 eagle_50.yml
+../swift -s -t 16 eagle_50.yml 2>&1 | tee output.log
 

examples/ExternalPointMass/run.sh

@@ -7,4 +7,4 @@ then
     python makeIC.py 10000
 fi
 
-../swift -g -t 2 externalPointMass.yml
+../swift -g -t 2 externalPointMass.yml 2>&1 | tee output.log

examples/GreshoVortex/gresho.yml → examples/GreshoVortex_2D/gresho.yml

@@ -27,7 +27,7 @@ Statistics:
 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).
+  max_smoothing_length:  0.02     # Maximal smoothing length allowed (in internal units).
   CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.
   
 # Parameters related to the initial conditions

examples/GreshoVortex/makeIC.py → examples/GreshoVortex_2D/makeIC.py

 ###############################################################################
  # This file is part of SWIFT.
- # Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
- #                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 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
@@ -19,9 +18,7 @@
  ##############################################################################
 
 import h5py
-import random
 from numpy import *
-import sys
 
 # Generates a swift IC file for the Gresho-Chan vortex in a periodic box
 
@@ -51,7 +48,6 @@ for i in range(numPart):
     
     x = coords[i,0]
     y = coords[i,1]
-    z = coords[i,2]
 
     r2 = (x - boxSize / 2)**2 + (y - boxSize / 2)**2
     r = sqrt(r2)
@@ -83,7 +79,7 @@ fileOutput = h5py.File(fileOutputName, 'w')
 
 # Header
 grp = fileOutput.create_group("/Header")
-grp.attrs["BoxSize"] = boxSize
+grp.attrs["BoxSize"] = [boxSize, boxSize, 0.2]
 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]

examples/GreshoVortex/run.sh → examples/GreshoVortex_2D/run.sh

@@ -13,7 +13,7 @@ then
 fi
 
 # Run SWIFT
-../swift -s -t 1 gresho.yml
+../swift -s -t 1 gresho.yml 2>&1 | tee output.log
 
 # Plot the solution
 python plotSolution.py 11

examples/IsothermalPotential/GravityOnly/run.sh

@@ -7,4 +7,4 @@ then
     python makeIC.py 1000 1
 fi
 
-../../swift -g -t 2 isothermal.yml
+../../swift -g -t 2 isothermal.yml 2>&1 | tee output.log

examples/KelvinHelmholtz_2D/kelvinHelmholtz.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:   1.5   # 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:            kelvinHelmholtz  # Common part of the name of output files
+  time_first:          0.               # Time of the first output (in internal units)
+  delta_time:          0.25      # 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:  0.01      # 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:  ./kelvinHelmholtz.hdf5     # The file to read

examples/KelvinHelmholtz_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 *
+import sys
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+L2    = 128       # Particles along one edge in the low-density region
+gamma = 5./3.     # Gas adiabatic index
+P1    = 2.5       # Central region pressure
+P2    = 2.5       # Outskirts pressure
+v1    = 0.5       # Central region velocity
+v2    = -0.5      # Outskirts vlocity
+rho1  = 2         # Central density
+rho2  = 1         # Outskirts density
+omega0 = 0.1
+sigma = 0.05 / sqrt(2)
+fileOutputName = "kelvinHelmholtz.hdf5" 
+#---------------------------------------------------
+
+# Start by generating grids of particles at the two densities
+numPart2 = L2 * L2
+L1 = int(sqrt(numPart2 / rho2 * rho1))
+numPart1 = L1 * L1
+
+#print "N2 =", numPart2, "N1 =", numPart1
+#print "L2 =", L2, "L1 = ", L1
+#print "rho2 =", rho2, "rho1 =", (float(L1*L1)) / (float(L2*L2))
+
+coords1 = zeros((numPart1, 3))
+coords2 = zeros((numPart2, 3))
+h1 = ones(numPart1) * 1.2348 / L1
+h2 = ones(numPart2) * 1.2348 / L2
+m1 = zeros(numPart1)
+m2 = zeros(numPart2)
+u1 = zeros(numPart1)
+u2 = zeros(numPart2)
+vel1 = zeros((numPart1, 3))
+vel2 = zeros((numPart2, 3))
+
+# Particles in the central region
+for i in range(L1):
+    for j in range(L1):
+
+        index = i * L1 + j
+        
+        x = i / float(L1) + 1. / (2. * L1)
+        y = j / float(L1) + 1. / (2. * L1)
+
+        coords1[index, 0] = x
+        coords1[index, 1] = y
+        u1[index] = P1 / (rho1 * (gamma-1.))
+        vel1[index, 0] = v1
+        
+# Particles in the outskirts
+for i in range(L2):
+    for j in range(L2):
+
+        index = i * L2 + j
+        
+        x = i / float(L2) + 1. / (2. * L2)
+        y = j / float(L2) + 1. / (2. * L2)
+
+        coords2[index, 0] = x
+        coords2[index, 1] = y
+        u2[index] = P2 / (rho2 * (gamma-1.))
+        vel2[index, 0] = v2
+
+
+# Now concatenate arrays
+where1 = abs(coords1[:,1]-0.5) < 0.25
+where2 = abs(coords2[:,1]-0.5) > 0.25
+
+coords = append(coords1[where1, :], coords2[where2, :], axis=0)
+
+#print L2*(L2/2), L1*(L1/2)
+#print shape(coords), shape(coords1[where1,:]), shape(coords2[where2,:])
+#print shape(coords), shape(logical_not(coords1[where1,:])), shape(logical_not(coords2[where2,:]))
+
+vel = append(vel1[where1, :], vel2[where2, :], axis=0)
+h = append(h1[where1], h2[where2], axis=0)
+m = append(m1[where1], m2[where2], axis=0)
+u = append(u1[where1], u2[where2], axis=0)
+numPart = size(h)
+ids = linspace(1, numPart, numPart)
+m[:] = (0.5 * rho1 + 0.5 * rho2) / float(numPart)
+
+# Velocity perturbation
+vel[:,1] = omega0 * sin(4*pi*coords[:,0]) * (exp(-(coords[:,1]-0.25)**2 / (2 * sigma**2)) + exp(-(coords[:,1]-0.75)**2 / (2 * sigma**2)))
+            
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 0.1]
+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["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]
+
+#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[()] = vel
+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()
+
+

examples/KelvinHelmholtz_2D/plotSolution.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2016  Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # This program is distributed in the hope that it will be useful,
+ # but WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ # GNU General Public License for more details.
+ # 
+ # You should have received a copy of the GNU Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+# Computes the analytical solution of the Gresho-Chan vortex and plots the SPH answer
+
+# Parameters
+gas_gamma = 5./3.     # Gas adiabatic index
+P1    = 2.5       # Central region pressure
+P2    = 2.5       # Outskirts pressure
+v1    = 0.5       # Central region velocity
+v2    = -0.5      # Outskirts vlocity
+rho1  = 2         # Central density
+rho2  = 1         # Outskirts density
+
+# ---------------------------------------------------------------
+# 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' : (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("kelvinHelmholtz_%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"]
+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"][:,:]
+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"][:]
+
+# Plot the interesting quantities
+figure()
+
+
+# Azimuthal velocity profile -----------------------------
+subplot(231)
+scatter(pos[:,0], pos[:,1], c=vel[:,0], cmap="PuBu", edgecolors='face', s=4, vmin=-1., vmax=1.)
+text(0.97, 0.97, "${\\rm{Velocity~along}}~x$", ha="right", va="top", backgroundcolor="w")
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=0)
+xlim(0, 1)
+ylim(0, 1)
+
+# Radial density profile --------------------------------
+subplot(232)
+scatter(pos[:,0], pos[:,1], c=rho, cmap="PuBu", edgecolors='face', s=4, vmin=0.8, vmax=2.2)
+text(0.97, 0.97, "${\\rm{Density}}$", ha="right", va="top", backgroundcolor="w")
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=0)
+xlim(0, 1)
+ylim(0, 1)
+
+# Radial pressure profile --------------------------------
+subplot(233)
+scatter(pos[:,0], pos[:,1], c=P, cmap="PuBu", edgecolors='face', s=4, vmin=1, vmax=4)
+text(0.97, 0.97, "${\\rm{Pressure}}$", ha="right", va="top", backgroundcolor="w")
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=0)
+xlim(0, 1)
+ylim(0, 1)
+
+# Internal energy profile --------------------------------
+subplot(234)
+scatter(pos[:,0], pos[:,1], c=u, cmap="PuBu", edgecolors='face', s=4, vmin=1.5, vmax=5.)
+text(0.97, 0.97, "${\\rm{Internal~energy}}$", ha="right", va="top", backgroundcolor="w")
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=0)
+xlim(0, 1)
+ylim(0, 1)
+
+# Radial entropy profile --------------------------------
+subplot(235)
+scatter(pos[:,0], pos[:,1], c=S, cmap="PuBu", edgecolors='face', s=4, vmin=0.5, vmax=3.)
+text(0.97, 0.97, "${\\rm{Entropy}}$", ha="right", va="top", backgroundcolor="w")
+xlabel("${\\rm{Position}}~x$", labelpad=0)
+ylabel("${\\rm{Position}}~y$", labelpad=0)
+xlim(0, 1)
+ylim(0, 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, "Kelvin-Helmholtz instability at $t=%.2f$"%(time), fontsize=10)
+text(-0.49, 0.8, "Centre:~~~ $(P, \\rho, v) = (%.3f, %.3f, %.3f)$"%(P1, rho1, v1), fontsize=10)
+text(-0.49, 0.7, "Outskirts: $(P, \\rho, v) = (%.3f, %.3f, %.3f)$"%(P2, rho2, v2), 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("KelvinHelmholtz.png", dpi=200)

examples/KelvinHelmholtz_2D/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e kelvinHelmholtz.hdf5 ]
+then
+    echo "Generating initial conditions for the Kelvin-Helmholtz example..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 kelvinHelmholtz.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 6

examples/MultiTypes/run.sh

@@ -7,4 +7,4 @@ then
     python makeIC.py 50 60
 fi
 
-../swift -s -g -t 16 multiTypes.yml
+../swift -s -g -t 16 multiTypes.yml 2>&1 | tee output.log

examples/PerturbedBox_3D/run.sh

@@ -7,4 +7,4 @@ then
     python makeIC.py 50
 fi
 
-../swift -s -t 16 perturbedBox.yml
+../swift -s -t 16 perturbedBox.yml 2>&1 | tee output.log

examples/SedovBlast_3D/makeIC_fcc.py → examples/SedovBlast_1D/makeIC.py

 ###############################################################################
  # This file is part of SWIFT.
- # Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
- #                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 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
@@ -19,68 +18,42 @@
  ##############################################################################
 
 import h5py
-import random
 from numpy import *
 
 # Generates a swift IC file for the Sedov blast test in a periodic cubic box
 
 # Parameters
-periodic= 1      # 1 For periodic box
-boxSize = 5.
-L = 64            # Number of particles boxes along one axis
-rho = 1.          # Density
-P = 1.e-5         # Pressure
-E0= 1.e2          # Energy of the explosion
-pert = 0.025
-gamma = 5./3.     # Gas adiabatic index
-eta = 1.2349          # 48 ngbs with cubic spline kernel
+numPart = 1000   
+gamma = 5./3.      # Gas adiabatic index
+rho0 = 1.          # Background density
+P0 = 1.e-6         # Background pressure
+E0= 1.             # Energy of the explosion
+N_inject = 3     # Number of particles in which to inject energy
 fileName = "sedov.hdf5" 
 
-
 #---------------------------------------------------
-numPart = 4*(L**3) 
-mass = boxSize**3 * rho / numPart
-internalEnergy = P / ((gamma - 1.)*rho)
-off = array( [ [ 0.0 , 0.0 , 0.0 ] , [ 0.0 , 0.5 , 0.5 ] , [ 0.5 , 0.0 , 0.5 ] , [ 0.5 , 0.5 , 0.0 ] ] );
-hbox = boxSize / L
+coords = zeros((numPart, 3))
+h = zeros(numPart)
+vol = 1.
 
-# if L%2 == 0:
-#     print "Number of particles along each dimension must be odd."
-#     exit()
+for i in range(numPart):
+    coords[i,0] = i * vol/numPart + vol/(2.*numPart)
+    h[i] = 1.2348 * vol / numPart
 
-#Generate particles
-coords = zeros((numPart, 3))
-v      = zeros((numPart, 3))
-m      = zeros(numPart)
-h      = zeros(numPart)
-u      = zeros(numPart)
-ids    = zeros(numPart, dtype='L')
+# Generate extra arrays
+v = zeros((numPart, 3))
+ids = linspace(1, numPart, numPart)
+m = zeros(numPart)
+u = zeros(numPart)
+r = zeros(numPart)
 
-for i in range(L):
-    for j in range(L):
-        for k in range(L):
-            x = (i + 0.25) * hbox
-            y = (j + 0.25) * hbox
-            z = (k + 0.25) * hbox
-            for ell in range(4): 
-                index = 4*(i*L*L + j*L + k) + ell
-                coords[index,0] = x + off[ell,0] * hbox
-                coords[index,1] = y + off[ell,1] * hbox
-                coords[index,2] = z + off[ell,2] * hbox
-                v[index,0] = 0.
-                v[index,1] = 0.
-                v[index,2] = 0.
-                m[index] = mass
-                h[index] = eta * hbox
-                u[index] = internalEnergy
-                ids[index] = index + 1
-                if sqrt((x - boxSize/2.)**2 + (y - boxSize/2.)**2 + (z - boxSize/2.)**2) < 1.2 * hbox:
-                    u[index] = u[index] + E0 / (28. * mass)
-                    print "Particle " , index , " set to detonate."
-                coords[index,0] += random.random() * pert * hbox
-                coords[index,1] += random.random() * pert * hbox
-                coords[index,2] += random.random() * pert * hbox
+r = abs(coords[:,0] - 0.5)
+m[:] = rho0 * vol / numPart    
+u[:] = P0 / (rho0 * (gamma - 1))
 
+# Make the central particle detonate
+index = argsort(r)
+u[index[0:N_inject]] = E0 / (N_inject * m[0])
 
 #--------------------------------------------------
 
@@ -89,7 +62,7 @@ file = h5py.File(fileName, 'w')
 
 # Header
 grp = file.create_group("/Header")
-grp.attrs["BoxSize"] = boxSize
+grp.attrs["BoxSize"] = [1., 1., 1.]