Added 2D Kelvin Helmholtz growth rate test.

examples/KelvinHelmholtzGrowthRate_2D/getGlass.sh

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

examples/KelvinHelmholtzGrowthRate_2D/kelvinHelmholtzGrowthRate.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:   4.   # 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:            kelvinHelmholtzGrowthRate  # Common part of the name of output files
+  time_first:          0.               # Time of the first output (in internal units)
+  delta_time:          0.04      # 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:  ./kelvinHelmholtzGrowthRate.hdf5     # The file to read

examples/KelvinHelmholtzGrowthRate_2D/makeIC.py

+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+#               2017 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 h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3.     # Gas adiabatic index
+P0    = 2.5       # Pressure
+rho0  = 1.        # Density
+d     = 0.0317    # Thickness of the transition layer
+B     = 0.0005    # Amplitude of the seed velocity
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+glass = h5py.File("glassPlane_128.hdf5", 'r')
+pos = glass["/PartType0/Coordinates"][:, :]
+h = glass["/PartType0/SmoothingLength"][:]
+
+N = len(h)
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+  -0.5 + \
+  0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+  0.5 - \
+  0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+          (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+           np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+            
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] =  [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 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]
+grp.attrs["Dimension"] = 2
+
+#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")
+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')
+
+fileOutput.close()

examples/KelvinHelmholtzGrowthRate_2D/makeIC_regular.py

+################################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+#               2017 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 h5py
+import numpy as np
+
+# Generates a swift IC file for the Kelvin-Helmholtz vortex in a periodic box
+
+# Parameters
+gamma = 5./3.     # Gas adiabatic index
+P0    = 2.5       # Pressure
+rho0  = 1.        # Density
+d     = 0.0317    # Thickness of the transition layer
+B     = 0.0005    # Amplitude of the seed velocity
+N1D   = 128       # Number of particles in one dimension
+
+fileOutputName = "kelvinHelmholtzGrowthRate.hdf5"
+
+#---------------------------------------------------
+
+N = N1D ** 2
+x = np.linspace(0., 1., N1D + 1)
+x = 0.5 * (x[1:] + x[:-1])
+y = x
+xx, yy = np.meshgrid(x, y)
+pos = np.zeros((N, 3))
+pos[:, 0] = xx.reshape((N))
+pos[:, 1] = yy.reshape((N))
+h = np.ones(N) * 2. / N1D
+
+vol = 1.
+
+# Generate extra arrays
+v = np.zeros((N, 3))
+ids = np.linspace(1, N, N)
+m = np.ones(N) * rho0 * vol / N
+u = np.ones(N) * P0 / (rho0 * (gamma - 1.))
+
+v[pos[:, 1] <= 0.25 - d, 0] = -0.5
+v[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 0] = \
+  -0.5 + \
+  0.5 * (pos[(pos[:, 1] < 0.25 + d) & (pos[:, 1] > 0.25 - d), 1] + d - 0.25) / d
+v[(pos[:, 1] <= 0.75 - d) & (pos[:, 1] >= 0.25 + d), 0] = 0.5
+v[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 0] = \
+  0.5 - \
+  0.5 * (pos[(pos[:, 1] < 0.75 + d) & (pos[:, 1] > 0.75 - d), 1] + d - 0.75) / d
+v[pos[:, 1] >= 0.75 + d, 0] = -0.5
+
+v[:, 1] = B * np.sin(4. * np.pi * pos[:, 0]) * \
+          (np.exp(-(pos[:, 1] - 0.25)**2 / 32. / d**2) + \
+           np.exp(-(pos[:, 1] - 0.75)**2 / 32. / d**2))
+            
+#File
+fileOutput = h5py.File(fileOutputName, 'w')
+
+# Header
+grp = fileOutput.create_group("/Header")
+grp.attrs["BoxSize"] = [1., 1., 1.]
+grp.attrs["NumPart_Total"] =  [N, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_Total_HighWord"] = [0, 0, 0, 0, 0, 0]
+grp.attrs["NumPart_ThisFile"] = [N, 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]
+grp.attrs["Dimension"] = 2
+
+#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")
+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')
+
+fileOutput.close()

examples/KelvinHelmholtzGrowthRate_2D/plotSolution.py

+###############################################################################
+# This file is part of SWIFT.
+# Copyright (c) 2017 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
+import matplotlib
+matplotlib.use("Agg")
+import pylab as pl
+import sys
+
+if len(sys.argv) < 2:
+  print "No final snapshot number provided!"
+  exit()
+lastsnap = int(sys.argv[1])
+
+# Read the simulation data
+t = np.zeros(lastsnap + 1)
+ey = np.zeros(lastsnap + 1)
+for i in range(lastsnap + 1):
+  file = h5py.File("kelvinHelmholtzGrowthRate_{0:04d}.hdf5".format(i), 'r')
+  t_snap = float(file["/Header"].attrs["Time"])
+  vy = file["/PartType0/Velocities"][:,1]
+  m = file["/PartType0/Masses"][:]
+
+  ey_snap = 0.5 * m * vy**2
+
+  t[i] = t_snap
+  ey[i] = ey_snap.sum()
+
+pl.semilogy(t, ey, "k.")
+pl.savefig("kelvinHelmholtzGrowthRate.png")

examples/KelvinHelmholtzGrowthRate_2D/run.sh

+#!/bin/bash
+
+ # Generate the initial conditions if they are not present.
+if [ ! -e kelvinHelmholtzGrowthRate.hdf5 ]
+then
+    echo "Generating initial conditions for the Kelvin-Helmholtz growth rate " \
+         "example..."
+    python makeIC.py
+fi
+
+# Run SWIFT
+../swift -s -t 1 kelvinHelmholtzGrowthRate.yml 2>&1 | tee output.log
+
+# Plot the solution
+python plotSolution.py 100