diff --git a/examples/GreshoVortex/makeIC.py b/examples/GreshoVortex/makeIC.py index 2f5bebc00ce0f86d3f4f3cccd030cfff5f90d51d..75af3a777682cb56dbd87bab9d125845d06fe153 100644 --- a/examples/GreshoVortex/makeIC.py +++ b/examples/GreshoVortex/makeIC.py @@ -1,7 +1,6 @@ ############################################################################### # 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 @@ -19,7 +18,6 @@ ############################################################################## import h5py -import random from numpy import * import sys @@ -51,7 +49,6 @@ 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) diff --git a/examples/KelvinHelmoltz/kelvinHelmholtz.yml b/examples/KelvinHelmoltz/kelvinHelmholtz.yml new file mode 100644 index 0000000000000000000000000000000000000000..38dd16880a209b885f7ad9c30c024988f4d8228f --- /dev/null +++ b/examples/KelvinHelmoltz/kelvinHelmholtz.yml @@ -0,0 +1,35 @@ +# 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 diff --git a/examples/KelvinHelmoltz/makeIC.py b/examples/KelvinHelmoltz/makeIC.py new file mode 100644 index 0000000000000000000000000000000000000000..5c8632dea52ef301c453cfbf21c35923f12e2d5a --- /dev/null +++ b/examples/KelvinHelmoltz/makeIC.py @@ -0,0 +1,153 @@ +############################################################################### + # 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() + + diff --git a/examples/KelvinHelmoltz/plotSolution.py b/examples/KelvinHelmoltz/plotSolution.py new file mode 100644 index 0000000000000000000000000000000000000000..9191f3ac7ec75c61d5fdab5d347c86222f787fab --- /dev/null +++ b/examples/KelvinHelmoltz/plotSolution.py @@ -0,0 +1,159 @@ +############################################################################### + # 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) diff --git a/examples/KelvinHelmoltz/run.sh b/examples/KelvinHelmoltz/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..4899ca89bc7bbbf72d15d6ecd3961c146a9c9821 --- /dev/null +++ b/examples/KelvinHelmoltz/run.sh @@ -0,0 +1,14 @@ +#!/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 + +# Plot the solution +python plotSolution.py 6