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Commit aaae33e7 authored by Bert Vandenbroucke's avatar Bert Vandenbroucke
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Added reference result for interacting blast waves. Added 2D and 3D spherical...

Added reference result for interacting blast waves. Added 2D and 3D spherical vacuum expansion test. Disabled pathological particle configuration errors in GIZMO to make 3D vacuum test work.
parent eb2f2b4e
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1 merge request!508Evrard and other tests
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with 839 additions and 17 deletions
......@@ -110,7 +110,7 @@ semilogx(x, -v, '.', color='r', ms=0.2)
semilogx(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
errorbar(x_bin, -v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_x$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
xlim(1.e-3, 2.)
ylim(-1.7, 0.1)
......@@ -157,7 +157,7 @@ ylim(0., 0.25)
# Information -------------------------------------
subplot(236, frameon=False)
text(-0.49, 0.9, "Evrard collapse with $\\gamma=%.3f$ in 3D at $t=%.2f$"%(gas_gamma,time), fontsize=10)
text(-0.49, 0.9, "Evrard collapse with $\\gamma=%.3f$ in 3D\nat $t=%.2f$"%(gas_gamma,time), 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)
......@@ -168,5 +168,5 @@ ylim(0, 1)
xticks([])
yticks([])
tight_layout()
savefig("EvrardCollapse.png", dpi=200)
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/interactingBlastWaves1D_exact.txt
......@@ -17,21 +17,116 @@
#
##############################################################################
import h5py
import numpy as np
import matplotlib
matplotlib.use("Agg")
import pylab as pl
import h5py
import sys
# Parameters
gamma = 1.4 # Polytropic index
# 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])
sim = h5py.File("interactingBlastWaves_%04d.hdf5" % snap, "r")
coords = sim["/PartType0/Coordinates"]
rho = sim["/PartType0/Density"]
# Open the file and read the relevant data
file = h5py.File("interactingBlastWaves_{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"]
ref = np.loadtxt("interactingBlastWaves1D_exact.txt")
# Plot the interesting quantities
fig, ax = pl.subplots(2, 3)
# Velocity profile
ax[0][0].plot(x, v, "r.", markersize = 4.)
ax[0][0].plot(ref[:,0], ref[:,2], "k--", alpha = 0.8, linewidth = 1.2)
ax[0][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
ax[0][0].set_ylabel("${\\rm{Velocity}}~v_x$", labelpad = 0)
ax[0][0].set_xlim(0., 1.)
ax[0][0].set_ylim(-1., 15.)
# Density profile
ax[0][1].plot(x, rho, "r.", markersize = 4.)
ax[0][1].plot(ref[:,0], ref[:,1], "k--", alpha = 0.8, linewidth = 1.2)
ax[0][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
ax[0][1].set_xlim(0., 1.)
# Pressure profile
ax[0][2].plot(x, P, "r.", markersize = 4.)
ax[0][2].plot(ref[:,0], ref[:,3], "k--", alpha = 0.8, linewidth = 1.2)
ax[0][2].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
ax[0][2].set_xlim(0., 1.)
# Internal energy profile
ax[1][0].plot(x, u, "r.", markersize = 4.)
ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 1.), "k--", alpha = 0.8,
linewidth = 1.2)
ax[1][0].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
ax[1][0].set_xlim(0., 1.)
# Entropy profile
ax[1][1].plot(x, S, "r.", markersize = 4.)
ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "k--", alpha = 0.8,
linewidth = 1.2)
ax[1][1].set_xlabel("${\\rm{Position}}~x$", labelpad = 0)
ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
ax[1][1].set_xlim(0., 1.)
# Run information
ax[1][2].set_frame_on(False)
ax[1][2].text(-0.49, 0.9,
"Interacting blast waves test\nwith $\\gamma={0:.3f}$ in 1D at $t = {1:.2f}$".format(
gamma, time), 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.xlabel("$x$")
pl.ylabel("$\\rho{}$")
pl.xlim(0.4, 1.)
pl.ylim(0., 7.)
pl.plot(coords[:,0], rho, "k.")
pl.savefig("InteractingBlastWaves.png")
pl.tight_layout()
pl.savefig("InteractingBlastWaves.png", dpi = 200)
#!/bin/bash
# Generate the initial conditions if they are not present.
# Generate the initial conditions if they are not present.
if [ ! -e interactingBlastWaves.hdf5 ]
then
echo "Generating initial conditions for the Sedov blast example..."
......@@ -10,5 +10,12 @@ fi
# Run SWIFT
../swift -s -t 1 interactingBlastWaves.yml 2>&1 | tee output.log
# Get the high resolution reference solution if not present.
if [ ! -e interactingBlastWaves1D_exact.txt ]
then
echo "Fetching reference solution for the interacting blast waves test..."
./getReference.sh
fi
# Plot the solution
python plotSolution.py 4
......@@ -109,7 +109,7 @@ plot(x, v, '.', color='r', ms=0.2)
plot(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
errorbar(x_bin, v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_x$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
# Density profile --------------------------------
subplot(232)
......
......@@ -110,7 +110,7 @@ plot(x, v, '.', color='r', ms=0.2)
plot(ref[:,0], ref[:,2], "k--", alpha=0.8, lw=1.2)
errorbar(x_bin, v_bin, yerr=v_sigma_bin, fmt='.', ms=8.0, color='b', lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_x$", labelpad=0)
ylabel("${\\rm{Velocity}}~v_r$", labelpad=0)
# Density profile --------------------------------
subplot(232)
......
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.hdf5
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/vacuumSpherical2D_exact.txt
###############################################################################
# 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("glassPlane_128.hdf5", "r")
# Read particle positions and h from the glass
pos = glass["/PartType0/Coordinates"][:,:]
h = glass["/PartType0/SmoothingLength"][:] * 0.3
# Make 4 copies of the glass to have more particles
pos *= 0.5
h *= 0.5
pos = np.append(pos, pos + np.array([0.5, 0., 0.]), axis = 0)
h = np.append(h, h)
pos = np.append(pos, pos + np.array([0., 0.5, 0.]), axis = 0)
h = np.append(h, h)
radius = np.sqrt((pos[:,0] - 0.5)**2 + (pos[:,1] - 0.5)**2)
index = radius < 0.25
pos = pos[index]
h = h[index]
numPart = len(h)
vol = np.pi * 0.25**2
# 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"] = 2
#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()
###############################################################################
# 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")
coords = file["/PartType0/Coordinates"]
x = np.sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2)
rho = file["/PartType0/Density"][:]
vels = file["/PartType0/Velocities"]
v = np.sqrt(vels[:,0]**2 + vels[:,1]**2)
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"]
# 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])
ref = np.loadtxt("vacuumSpherical2D_exact.txt")
# 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(ref[:,0], ref[:,2], "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][0].set_ylabel("${\\rm{Velocity}}~v_r$", labelpad = 0)
ax[0][0].set_xlim(0., 0.4)
ax[0][0].set_ylim(-0.1, 3.2)
# Density profile
ax[0][1].plot(x, rho, "r.", markersize = 0.2)
ax[0][1].plot(ref[:,0], ref[:,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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
ax[0][1].set_xlim(0., 0.4)
# Pressure profile
ax[0][2].plot(x, P, "r.", markersize = 0.2)
ax[0][2].plot(ref[:,0], ref[:,3], "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
ax[0][2].set_xlim(0., 0.4)
# Internal energy profile
ax[1][0].plot(x, u, "r.", markersize = 0.2)
ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 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("${\\rm{Radius}}~r$", labelpad = 0)
ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
ax[1][0].set_xlim(0., 0.4)
# Entropy profile
ax[1][1].plot(x, S, "r.", markersize = 0.2)
ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
ax[1][1].set_xlim(0., 0.4)
ax[1][1].set_ylim(0., 4.)
# 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)
#!/bin/bash
# Generate the initial conditions if they are not present.
if [ ! -e glassPlane_128.hdf5 ]
then
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 2D vacuum expansion example..."
python makeIC.py
fi
# Run SWIFT
../swift -s -t 4 vacuum.yml 2>&1 | tee output.log
# Get the 1D high resolution reference result if not present.
if [ ! -e vacuumSpherical2D_exact.txt ]
then
echo "Fetching reference solution for the 2D vacuum expansion test..."
./getReference.sh
fi
# Plot the result
python plotSolution.py 1
# 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: 0.05 # 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: 0.05 # 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
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/vacuumSpherical3D_exact.txt
###############################################################################
# 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
# Make 8 copies of the glass to get more particles
pos *= 0.5
h *= 0.5
pos = np.append(pos, pos + np.array([0.5, 0., 0.]), axis = 0)
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)
h = np.append(h, h)
radius = np.sqrt((pos[:,0] - 0.5)**2 + (pos[:,1] - 0.5)**2 + \
(pos[:,2] - 0.5)**2)
index = radius < 0.25
pos = pos[index]
h = h[index]
numPart = len(h)
vol = 4. * np.pi / 3. * 0.25**3
# 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()
###############################################################################
# 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")
coords = file["/PartType0/Coordinates"]
x = np.sqrt((coords[:,0] - 0.5)**2 + (coords[:,1] - 0.5)**2 + \
(coords[:,2] - 0.5)**2)
rho = file["/PartType0/Density"][:]
vels = file["/PartType0/Velocities"]
v = np.sqrt(vels[:,0]**2 + vels[:,1]**2 + vels[:,2]**2)
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"]
# 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])
ref = np.loadtxt("vacuumSpherical3D_exact.txt")
# 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(ref[:,0], ref[:,2], "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][0].set_ylabel("${\\rm{Velocity}}~v_r$", labelpad = 0)
ax[0][0].set_xlim(0., 0.4)
ax[0][0].set_ylim(-0.1, 3.2)
# Density profile
ax[0][1].plot(x, rho, "r.", markersize = 0.2)
ax[0][1].plot(ref[:,0], ref[:,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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][1].set_ylabel("${\\rm{Density}}~\\rho$", labelpad = 0)
ax[0][1].set_xlim(0., 0.4)
# Pressure profile
ax[0][2].plot(x, P, "r.", markersize = 0.2)
ax[0][2].plot(ref[:,0], ref[:,3], "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[0][2].set_ylabel("${\\rm{Pressure}}~P$", labelpad = 0)
ax[0][2].set_xlim(0., 0.4)
# Internal energy profile
ax[1][0].plot(x, u, "r.", markersize = 0.2)
ax[1][0].plot(ref[:,0], ref[:,3] / ref[:,1] / (gamma - 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("${\\rm{Radius}}~r$", labelpad = 0)
ax[1][0].set_ylabel("${\\rm{Internal~Energy}}~u$", labelpad = 0)
ax[1][0].set_xlim(0., 0.4)
# Entropy profile
ax[1][1].plot(x, S, "r.", markersize = 0.2)
ax[1][1].plot(ref[:,0], ref[:,3] / ref[:,1]**gamma, "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("${\\rm{Radius}}~r$", labelpad = 0)
ax[1][1].set_ylabel("${\\rm{Entropy}}~S$", labelpad = 0)
ax[1][1].set_xlim(0., 0.4)
ax[1][1].set_ylim(0., 4.)
# 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)
#!/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
# Get the reference solution if it is not present.
if [ ! -e vacuumSpherical3D_exact.txt ]
then
echo "Fetching reference solution for the 3D vacuum expansion test..."
./getReference.sh
fi
# Plot the result
python plotSolution.py 1
# 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: 0.05 # 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: 0.05 # 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
......@@ -75,7 +75,7 @@
/* Show a warning message if a pathological configuration has been detected. */
//#define GIZMO_PATHOLOGICAL_WARNING
/* Crash if a pathological configuration has been detected. */
#define GIZMO_PATHOLOGICAL_ERROR
//#define GIZMO_PATHOLOGICAL_ERROR
/* Maximum allowed gradient matrix condition number. If the condition number of
the gradient matrix (defined in equation C1 in Hopkins, 2015) is larger than
this value, we artificially increase the number of neighbours to get a more
......
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