Added the initial conditions for a Sod shock test following the description of...

Added the initial conditions for a Sod shock test following the description of arXiv:0808.1844. Better glass files will have to be generated to avoid suprious effects.


Former-commit-id: d084077eec18e58df653480a8c8f65996e4b8627

examples/SodShock/makeIC.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Coypright (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 h5py
+import random
+from numpy import *
+
+# Generates a swift IC file for the Sod Shock in a periodic box
+
+# Parameters
+periodic= 1      # 1 For periodic box
+boxSize = 1.
+L = 100           # Number of particles along one axis
+P1 = 1.           # Pressure left state
+P2 = 0.1795       # Pressure right state
+gamma = 5./3.     # Gas adiabatic index
+fileName = "sodShock.hdf5" 
+
+
+#---------------------------------------------------
+
+#Read in high density glass
+glass1 = h5py.File("../Glass/glass_12500.hdf5")
+pos1 = glass1["/PartType0/Coordinates"][:,:]
+pos1 = pos1 / 20. # Particles are in [0:0.5, 0:0.5, 0:0.5]
+
+#Read in high density glass
+glass2 = h5py.File("../Glass/glass_3125.hdf5")
+pos2 = glass2["/PartType0/Coordinates"][:,:]
+pos2 = pos2 / 20. # Particles are in [0:0.5, 0:0.5, 0:0.5]
+
+#Generate high density region
+rho1 = size(pos1) / size(pos2) 
+coord1 = append(pos1, pos1 + [0, 0.5, 0], 0)
+coord1 = append(coord1, pos1 + [0, 0, 0.5], 0)
+coord1 = append(coord1, pos1 + [0, 0.5, 0.5], 0)
+N1 = size(coord1)/3
+v1 = zeros((N1, 3))
+h1 = ones((N1, 1)) * 2.251 * 0.5 / (size(pos1)/3)**(1./3.)
+u1 = ones((N1, 1)) * P1 / ((gamma - 1.) * rho1)
+m1 = ones((N1, 1)) * 0.5 * rho1 / N1
+
+#Generate low density region
+rho2 = 1.
+coord2 = append(pos2, pos2 + [0, 0.5, 0], 0)
+coord2 = append(coord2, pos2 + [0, 0, 0.5], 0)
+coord2 = append(coord2, pos2 + [0, 0.5, 0.5], 0)
+N2 = size(coord2)/3
+v2 = zeros((N2, 3))
+h2 = ones((N2, 1)) * 2.251 * 0.5 / (size(pos2)/3)**(1./3.)
+u2 = ones((N2, 1)) * P2 / ((gamma - 1.) * rho2)
+m2 = ones((N2, 1)) * 0.5 * rho2 / N2
+
+#Merge arrays
+numPart = N1 + N2
+coords = append(coord1, coord2+[0.5, 0., 0.], 0)
+v = append(v1, v2,0)
+h = append(h1, h2,0)
+u = append(u1, u2,0)
+m = append(m1, m2,0)
+ids = zeros((numPart, 1), dtype='L')
+for i in range(numPart):
+    ids[i] = i
+
+#File
+file = h5py.File(fileName, 'w')
+
+# Header
+grp = file.create_group("/Header")
+grp.attrs["BoxSize"] = boxSize
+grp.attrs["NumPart_Total"] =  [numPart, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [numPart, 0, 0, 0, 0, 0]
+grp.attrs["Time"] = 0.0
+grp.attrs["NumFilesPerSnapshot"] = 1
+grp.attrs["MassTable"] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+grp.attrs["Flag_Entropy_ICs"] = [0, 0, 0, 0, 0, 0]
+
+#Runtime parameters
+grp = file.create_group("/RuntimePars")
+grp.attrs["PeriodicBoundariesOn"] = periodic
+
+#Particle group
+grp = file.create_group("/PartType0")
+ds = grp.create_dataset('Coordinates', (numPart, 3), 'd')
+ds[()] = coords
+ds = grp.create_dataset('Velocities', (numPart, 3), 'f')
+ds[()] = v
+ds = grp.create_dataset('Masses', (numPart,1), 'f')
+ds[()] = m
+ds = grp.create_dataset('SmoothingLength', (numPart,1), 'f')
+ds[()] = h
+ds = grp.create_dataset('InternalEnergy', (numPart,1), 'f')
+ds[()] = u
+ds = grp.create_dataset('ParticleIDs', (numPart,1), 'L')
+ds[()] = ids[:]
+
+file.close()
+
+