diff --git a/examples/Noh_2D/plotSolution.py b/examples/Noh_2D/plotSolution.py index 70ded94b9bc3b921de5a0ab62df1d632bdf13e1c..a01a712efd412488aea09c3f3c4e8d68323fc916 100644 --- a/examples/Noh_2D/plotSolution.py +++ b/examples/Noh_2D/plotSolution.py @@ -100,8 +100,6 @@ u_sigma_bin = np.sqrt(u2_bin - u_bin**2) # Analytic solution N = 1000 # Number of points -x_min = -1 -x_max = 1 x_s = np.arange(0, 2., 2./N) - 1. rho_s = np.ones(N) * rho0 diff --git a/examples/Noh_3D/getGlass.sh b/examples/Noh_3D/getGlass.sh new file mode 100755 index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c --- /dev/null +++ b/examples/Noh_3D/getGlass.sh @@ -0,0 +1,2 @@ +#!/bin/bash +wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5 diff --git a/examples/Noh_3D/makeIC.py b/examples/Noh_3D/makeIC.py new file mode 100644 index 0000000000000000000000000000000000000000..ec8d46639eecdefd55b917a955f13efc8ffe4126 --- /dev/null +++ b/examples/Noh_3D/makeIC.py @@ -0,0 +1,100 @@ + +############################################################################### + # 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 3D Noh problem in a periodic box + +# Parameters +gamma = 5./3. # Gas adiabatic index +gamma = 5./3. # Gas adiabatic index +rho0 = 1. # Background density +P0 = 1.e-6 # Background pressure +fileName = "noh.hdf5" + +#--------------------------------------------------- +glass = h5py.File("glassCube_64.hdf5", "r") + +vol = 8. + +pos = glass["/PartType0/Coordinates"][:,:] * cbrt(vol) +h = glass["/PartType0/SmoothingLength"][:] * cbrt(vol) +numPart = size(h) + +# 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)) + +# Make radial velocities +#r = sqrt((pos[:,0]-1.)**2 + (pos[:,1]-1.)**2) +#theta = arctan2((pos[:,1]-1.), (pos[:,0]-1.)) +v[:,0] = -(pos[:,0] - 1.) +v[:,1] = -(pos[:,1] - 1.) +v[:,2] = -(pos[:,2] - 1.) + +norm_v = sqrt(v[:,0]**2 + v[:,1]**2 + v[:,2]**2) +v[:,0] /= norm_v +v[:,1] /= norm_v +v[:,2] /= norm_v + +#File +file = h5py.File(fileName, 'w') + +# Header +grp = file.create_group("/Header") +grp.attrs["BoxSize"] = [cbrt(vol), cbrt(vol), cbrt(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"] = 3 + +#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=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') + + +file.close() diff --git a/examples/Noh_3D/noh.yml b/examples/Noh_3D/noh.yml new file mode 100644 index 0000000000000000000000000000000000000000..911ebbdc1ca82f9b5cf2f70841d848008cbc5f6c --- /dev/null +++ b/examples/Noh_3D/noh.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: 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 + diff --git a/examples/Noh_3D/plotSolution.py b/examples/Noh_3D/plotSolution.py new file mode 100644 index 0000000000000000000000000000000000000000..1742e13a5daeff392690a9804fb2831ef4304963 --- /dev/null +++ b/examples/Noh_3D/plotSolution.py @@ -0,0 +1,202 @@ +############################################################################### + # 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 +v0 = 1 + +import matplotlib +matplotlib.use("Agg") +from pylab import * +from scipy import stats +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("noh_%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"] + +x = sim["/PartType0/Coordinates"][:,0] +y = sim["/PartType0/Coordinates"][:,1] +z = sim["/PartType0/Coordinates"][:,2] +vx = sim["/PartType0/Velocities"][:,0] +vy = sim["/PartType0/Velocities"][:,1] +vz = sim["/PartType0/Velocities"][:,2] +u = sim["/PartType0/InternalEnergy"][:] +S = sim["/PartType0/Entropy"][:] +P = sim["/PartType0/Pressure"][:] +rho = sim["/PartType0/Density"][:] + +r = np.sqrt((x-1)**2 + (y-1)**2 + (z-1)**2) +v = -np.sqrt(vx**2 + vy**2 + vz**2) + +# 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, 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**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) + + +# Analytic solution +N = 1000 # Number of points + +x_s = np.arange(0, 2., 2./N) - 1. +rho_s = np.ones(N) * rho0 +P_s = np.ones(N) * rho0 +v_s = np.ones(N) * v0 + +# Shock position +u0 = rho0 * P0 * (gas_gamma-1) +us = 0.5 * (gas_gamma - 1) * v0 +rs = us * time + +# Post-shock values +rho_s[np.abs(x_s) < rs] = rho0 * ((gas_gamma + 1) / (gas_gamma - 1))**3 +P_s[np.abs(x_s) < rs] = 0.5 * rho0 * v0**2 * (gas_gamma + 1)**3 / (gas_gamma-1)**2 +v_s[np.abs(x_s) < rs] = 0. + +# Pre-shock values +rho_s[np.abs(x_s) >= rs] = rho0 * (1 + v0 * time/np.abs(x_s[np.abs(x_s) >=rs]))**2 +P_s[np.abs(x_s) >= rs] = 0 +v_s[x_s >= rs] = -v0 +v_s[x_s <= -rs] = v0 + +# Additional arrays +u_s = P_s / (rho_s * (gas_gamma - 1.)) #internal energy +s_s = P_s / rho_s**gas_gamma # entropic function + +# Plot the interesting quantities +figure() + +# Velocity profile -------------------------------- +subplot(231) +plot(r, v, '.', color='r', ms=0.5, alpha=0.2) +plot(x_s, v_s, '--', 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) +xlabel("${\\rm{Radius}}~r$", labelpad=0) +ylabel("${\\rm{Velocity}}~v_r$", labelpad=-4) +xlim(0, 0.5) +ylim(-1.2, 0.4) + +# Density profile -------------------------------- +subplot(232) +plot(r, rho, '.', color='r', ms=0.5, alpha=0.2) +plot(x_s, rho_s, '--', 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) +xlabel("${\\rm{Radius}}~r$", labelpad=0) +ylabel("${\\rm{Density}}~\\rho$", labelpad=0) +xlim(0, 0.5) +ylim(0.95, 71) + +# Pressure profile -------------------------------- +subplot(233) +plot(r, P, '.', color='r', ms=0.5, alpha=0.2) +plot(x_s, P_s, '--', 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) +xlabel("${\\rm{Radius}}~r$", labelpad=0) +ylabel("${\\rm{Pressure}}~P$", labelpad=0) +xlim(0, 0.5) +ylim(-0.5, 25) + +# Internal energy profile ------------------------- +subplot(234) +plot(r, u, '.', color='r', ms=0.5, alpha=0.2) +plot(x_s, u_s, '--', 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) +xlabel("${\\rm{Radius}}~r$", labelpad=0) +ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0) +xlim(0, 0.5) +ylim(-0.05, 0.8) + +# Entropy profile --------------------------------- +subplot(235) +plot(r, S, '.', color='r', ms=0.5, alpha=0.2) +plot(x_s, s_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) +xlabel("${\\rm{Radius}}~r$", labelpad=0) +ylabel("${\\rm{Entropy}}~S$", labelpad=-9) +xlim(0, 0.5) +ylim(-0.05, 0.2) + +# Information ------------------------------------- +subplot(236, frameon=False) + +text(-0.49, 0.9, "Noh problem with $\\gamma=%.3f$ in 3D at $t=%.2f$"%(gas_gamma,time), fontsize=10) +text(-0.49, 0.8, "ICs:~~ $(P_0, \\rho_0, v_0) = (%1.2e, %.3f, %.3f)$"%(1e-6, 1., -1.), 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("Noh.png", dpi=200) diff --git a/examples/Noh_3D/run.sh b/examples/Noh_3D/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..b9e4fb145b2465433aa2bc0362aba19cc1267461 --- /dev/null +++ b/examples/Noh_3D/run.sh @@ -0,0 +1,19 @@ +#!/bin/bash + + # Generate the initial conditions if they are not present. +if [ ! -e glassCube_64.hdf5 ] +then + echo "Fetching initial glass file for the Noh problem..." + ./getGlass.sh +fi +if [ ! -e noh.hdf5 ] +then + echo "Generating initial conditions for the Noh problem..." + python makeIC.py +fi + +# Run SWIFT +../swift -s -t 2 noh.yml 2>&1 | tee output.log + +# Plot the solution +python plotSolution.py 12