diff --git a/examples/Vacuum_2D/run.sh b/examples/Vacuum_2D/run.sh index 48f18f7878f0f17d62e6a16ae3a6dec883872bf0..5c0b2ca5e19e33e813b7ff478ed4494752c0a2a5 100755 --- a/examples/Vacuum_2D/run.sh +++ b/examples/Vacuum_2D/run.sh @@ -3,12 +3,12 @@ # Generate the initial conditions if they are not present. if [ ! -e glassPlane_128.hdf5 ] then - echo "Fetching initial glass file for the 1D vacuum expansion example..." + echo "Fetching initial glass file for the 2D vacuum expansion example..." ./getGlass.sh fi if [ ! -e vacuum.hdf5 ] then - echo "Generating initial conditions for the 1D vacuum expansion example..." + echo "Generating initial conditions for the 2D vacuum expansion example..." python makeIC.py fi diff --git a/examples/Vacuum_3D/getGlass.sh b/examples/Vacuum_3D/getGlass.sh new file mode 100755 index 0000000000000000000000000000000000000000..d5c5f590ac37c9c9431d626a2ea61b0c12c1513c --- /dev/null +++ b/examples/Vacuum_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/Vacuum_3D/makeIC.py b/examples/Vacuum_3D/makeIC.py new file mode 100644 index 0000000000000000000000000000000000000000..09c3cb4d6f5525d54fab59643ab4a7d0540a2a92 --- /dev/null +++ b/examples/Vacuum_3D/makeIC.py @@ -0,0 +1,97 @@ +############################################################################### +# This file is part of SWIFT. +# Copyright (c) 2018 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 + +# Generates an overdensity within a vacuum to test the vacuum resolving +# capabilities of the code + +# Parameters +gamma = 5. / 3. # Gas adiabatic index + +fileName = "vacuum.hdf5" + +#--------------------------------------------------- +glass = h5py.File("glassCube_64.hdf5", "r") + +# Read particle positions and h from the glass +pos = glass["/PartType0/Coordinates"][:,:] +h = glass["/PartType0/SmoothingLength"][:] * 0.3 + +# Shrink the glass to half its size, move it to the centre of the box, and +# clone it in the y and z directions +pos = 0.5 * pos + np.array([0.25, 0., 0.]) +h *= 0.5 +pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0) +pos = np.append(pos, pos + np.array([0., 0., 0.5]), axis = 0) +h = np.append(h, h) +h = np.append(h, h) + +numPart = len(h) +vol = 0.5 + +# Generate extra arrays +v = np.zeros((numPart, 3)) +ids = np.linspace(1, numPart, numPart) +m = np.zeros(numPart) +u = np.zeros(numPart) + +m[:] = 1. * vol / numPart +u[:] = 1. / (1. * (gamma - 1.)) + +#-------------------------------------------------- + +#File +file = h5py.File(fileName, 'w') + +# Header +grp = file.create_group("/Header") +grp.attrs["BoxSize"] = [1., 1., 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["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/Vacuum_3D/plotSolution.py b/examples/Vacuum_3D/plotSolution.py new file mode 100644 index 0000000000000000000000000000000000000000..4d197234237df10b8cdbf197048a65991da023cf --- /dev/null +++ b/examples/Vacuum_3D/plotSolution.py @@ -0,0 +1,225 @@ +############################################################################### +# This file is part of SWIFT. +# Copyright (c) 2018 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 matplotlib +matplotlib.use("Agg") +import pylab as pl +import h5py +import sys +import scipy.stats as stats + +# Parameters +gamma = 5. / 3. # Polytropic index +rhoL = 1. # Initial density in the non vacuum state +vL = 0. # Initial velocity in the non vacuum state +PL = 1. # Initial pressure in the non vacuum state +rhoR = 0. # Initial vacuum density +vR = 0. # Initial vacuum velocity +PR = 0. # Initial vacuum pressure + +# 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 +} +pl.rcParams.update(params) +pl.rc('font',**{'family':'sans-serif','sans-serif':['Times']}) + +# Read the snapshot index from the command line argument +snap = int(sys.argv[1]) + +# Open the file and read the relevant data +file = h5py.File("vacuum_{0:04d}.hdf5".format(snap), "r") +x = file["/PartType0/Coordinates"][:,0] +rho = file["/PartType0/Density"][:] +v = file["/PartType0/Velocities"][:,0] +u = file["/PartType0/InternalEnergy"][:] +S = file["/PartType0/Entropy"][:] +P = file["/PartType0/Pressure"][:] +time = file["/Header"].attrs["Time"][0] + +scheme = file["/HydroScheme"].attrs["Scheme"] +kernel = file["/HydroScheme"].attrs["Kernel function"] +neighbours = file["/HydroScheme"].attrs["Kernel target N_ngb"][0] +eta = file["/HydroScheme"].attrs["Kernel eta"][0] +git = file["Code"].attrs["Git Revision"] + +# Get the analytic solution, which is just the solution of the corresponding +# vacuum Riemann problem evaluated at the correct time + +# left state sound speed (and rarefaction wave speed) +aL = np.sqrt(gamma * PL / rhoL) + +# vacuum front speed +SL = vL + 2. / (gamma - 1.) * aL + +# we evaluate the solution centred on 0., and shift to the correct position +# afterwards +xa = np.arange(-0.25, 0.25, 0.001) +rhoa = np.zeros(len(xa)) +va = np.zeros(len(xa)) +Pa = np.zeros(len(xa)) + +for i in range(len(xa)): + dxdt = xa[i] / time + if dxdt > vL - aL: + if dxdt < SL: + # rarefaction regime + # factor that appears in both the density and pressure expression + fac = 2. / (gamma + 1.) + \ + (gamma - 1.) / (gamma + 1.) * (vL - dxdt) / aL + rhoa[i] = rhoL * fac**(2. / (gamma - 1.)) + va[i] = 2. / (gamma + 1.) * (aL + 0.5 * (gamma - 1.) * vL + dxdt) + Pa[i] = PL * fac**(2. * gamma / (gamma - 1.)) + else: + # vacuum regime + rhoa[i] = 0. + va[i] = 0. + Pa[i] = 0. + else: + # left state regime + rhoa[i] = rhoL + va[i] = vL + Pa[i] = PL + +ua = Pa / (gamma - 1.) / rhoa +Sa = Pa / rhoa**gamma + +# Bin the data values +# We let scipy choose the bins and then reuse them for all other quantities +rho_bin, x_bin_edge, _ = \ + stats.binned_statistic(x, rho, statistic = "mean", bins = 50) +rho2_bin, _, _ = \ + stats.binned_statistic(x, rho**2, statistic = "mean", bins = x_bin_edge) +rho_sigma_bin = np.sqrt(rho2_bin - rho_bin**2) + +v_bin, _, _ = \ + stats.binned_statistic(x, v, statistic = "mean", bins = x_bin_edge) +v2_bin, _, _ = \ + stats.binned_statistic(x, v**2, statistic = "mean", bins = x_bin_edge) +v_sigma_bin = np.sqrt(v2_bin - v_bin**2) + +P_bin, _, _ = \ + stats.binned_statistic(x, P, statistic = "mean", bins = x_bin_edge) +P2_bin, _, _ = \ + stats.binned_statistic(x, P**2, statistic = "mean", bins = x_bin_edge) +P_sigma_bin = np.sqrt(P2_bin - P_bin**2) + +u_bin, _, _ = \ + stats.binned_statistic(x, u, statistic = "mean", bins = x_bin_edge) +u2_bin, _, _ = \ + stats.binned_statistic(x, u**2, statistic = "mean", bins = x_bin_edge) +u_sigma_bin = np.sqrt(u2_bin - u_bin**2) + +S_bin, _, _ = \ + stats.binned_statistic(x, S, statistic = "mean", bins = x_bin_edge) +S2_bin, _, _ = \ + stats.binned_statistic(x, S**2, statistic = "mean", bins = x_bin_edge) +S_sigma_bin = np.sqrt(S2_bin - S_bin**2) + +x_bin = 0.5 * (x_bin_edge[1:] + x_bin_edge[:-1]) + +# Plot the interesting quantities +fig, ax = pl.subplots(2, 3) + +# Velocity profile +ax[0][0].plot(x, v, "r.", markersize = 0.2) +ax[0][0].plot(xa + 0.75, va, "k--", alpha = 0.8, linewidth = 1.2) +ax[0][0].plot(xa + 0.25, -va[::-1], "k--", alpha = 0.8, linewidth = 1.2) +ax[0][0].errorbar(x_bin, v_bin, yerr = v_sigma_bin, fmt = ".", + markersize = 8., color = "b", linewidth = 1.2) +ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0) +ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0) + +# Density profile +ax[0][1].plot(x, rho, "r.", markersize = 0.2) +ax[0][1].plot(xa + 0.75, rhoa, "k--", alpha = 0.8, linewidth = 1.2) +ax[0][1].plot(xa + 0.25, rhoa[::-1], "k--", alpha = 0.8, linewidth = 1.2) +ax[0][1].errorbar(x_bin, rho_bin, yerr = rho_sigma_bin, fmt = ".", + markersize = 8., color = "b", linewidth = 1.2) +ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0) +ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0) + +# Pressure profile +ax[0][2].plot(x, P, "r.", markersize = 0.2) +ax[0][2].plot(xa + 0.75, Pa, "k--", alpha = 0.8, linewidth = 1.2) +ax[0][2].plot(xa + 0.25, Pa[::-1], "k--", alpha = 0.8, linewidth = 1.2) +ax[0][2].errorbar(x_bin, P_bin, yerr = P_sigma_bin, fmt = ".", + markersize = 8., color = "b", linewidth = 1.2) +ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0) +ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0) + +# Internal energy profile +ax[1][0].plot(x, u, "r.", markersize = 0.2) +ax[1][0].plot(xa + 0.75, ua, "k--", alpha = 0.8, linewidth = 1.2) +ax[1][0].plot(xa + 0.25, ua[::-1], "k--", alpha = 0.8, linewidth = 1.2) +ax[1][0].errorbar(x_bin, u_bin, yerr = u_sigma_bin, fmt = ".", + markersize = 8., color = "b", linewidth = 1.2) +ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0) +ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0) + +# Entropy profile +ax[1][1].plot(x, S, "r.", markersize = 0.2) +ax[1][1].plot(xa + 0.75, Sa, "k--", alpha = 0.8, linewidth = 1.2) +ax[1][1].plot(xa + 0.25, Sa[::-1], "k--", alpha = 0.8, linewidth = 1.2) +ax[1][1].errorbar(x_bin, S_bin, yerr = S_sigma_bin, fmt = ".", + markersize = 8., color = "b", linewidth = 1.2) +ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0) +ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0) + +# Run information +ax[1][2].set_frame_on(False) +ax[1][2].text(-0.49, 0.9, + "Vacuum test with $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format( + gamma, time), fontsize = 10) +ax[1][2].text(-0.49, 0.8, + "Left:~~ $(P_L, \\rho_L, v_L) = ({0:.3f}, {1:.3f}, {2:.3f})$".format( + PL, rhoL, vL), fontsize = 10) +ax[1][2].text(-0.49, 0.7, + "Right: $(P_R, \\rho_R, v_R) = ({0:.3f}, {1:.3f}, {2:.3f})$".format( + PR, rhoR, vR), fontsize = 10) +ax[1][2].plot([-0.49, 0.1], [0.62, 0.62], "k-", lw = 1) +ax[1][2].text(-0.49, 0.5, "$\\textsc{{Swift}}$ {0}".format(git), fontsize = 10) +ax[1][2].text(-0.49, 0.4, scheme, fontsize = 10) +ax[1][2].text(-0.49, 0.3, kernel, fontsize = 10) +ax[1][2].text(-0.49, 0.2, + "${0:.2f}$ neighbours ($\\eta={1:.3f}$)".format(neighbours, eta), + fontsize = 10) +ax[1][2].set_xlim(-0.5, 0.5) +ax[1][2].set_ylim(0., 1.) +ax[1][2].set_xticks([]) +ax[1][2].set_yticks([]) + +pl.tight_layout() +pl.savefig("Vacuum.png", dpi = 200) diff --git a/examples/Vacuum_3D/run.sh b/examples/Vacuum_3D/run.sh new file mode 100755 index 0000000000000000000000000000000000000000..5029626f67659bba1f22600bb5bd38859dd805ce --- /dev/null +++ b/examples/Vacuum_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 3D vacuum expansion example..." + ./getGlass.sh +fi +if [ ! -e vacuum.hdf5 ] +then + echo "Generating initial conditions for the 3D vacuum expansion example..." + python makeIC.py +fi + +# Run SWIFT +../swift -s -t 16 vacuum.yml 2>&1 | tee output.log + +# Plot the result +python plotSolution.py 1 diff --git a/examples/Vacuum_3D/vacuum.yml b/examples/Vacuum_3D/vacuum.yml new file mode 100644 index 0000000000000000000000000000000000000000..5ef5ce3da68febb086a14ad1a2207711f680d9ff --- /dev/null +++ b/examples/Vacuum_3D/vacuum.yml @@ -0,0 +1,34 @@ +# 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: 0.1 # The end time of the simulation (in internal units). + dt_min: 1e-10 # 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: vacuum # Common part of the name of output files + time_first: 0. # Time of the first output (in internal units) + delta_time: 0.1 # 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: ./vacuum.hdf5 # The file to read +