Commit b2d96158 authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Merge branch 'master' into smooth_metal

parents 2613add6 3cc0dba0
# 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: 0.8 # 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: evrard # 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 for the self-gravity scheme
Gravity:
eta: 0.025 # Constant dimensionless multiplier for time integration.
epsilon: 0.001 # Softening length (in internal units).
theta: 0.9
a_smooth: 1.25 # (Optional) Smoothing scale in top-level cell sizes to smooth the long-range forces over (this is the default value).
r_cut: 4.5 # (Optional) Cut-off in number of top-level cells beyond which no FMM forces are computed (this is the default value).
# Parameters related to the initial conditions
InitialConditions:
file_name: ./evrard.hdf5 # The file to read
PhysicalConstants:
G: 1.
#! /bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ReferenceSolutions/evrardCollapse3D_exact.txt
################################################################################
# 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 h5py
from numpy import *
# Generates a swift IC file for the Evrard collapse
# Parameters
gamma = 5. / 3. # Gas adiabatic index
M = 1. # total mass of the sphere
R = 1. # radius of the sphere
u0 = 0.05 / M # initial thermal energy
fileName = "evrard.hdf5"
numPart = 100000
r = R * sqrt(random.random(numPart))
phi = 2. * pi * random.random(numPart)
cos_theta = 2. * random.random(numPart) - 1.
sin_theta = sqrt(1. - cos_theta**2)
cos_phi = cos(phi)
sin_phi = sin(phi)
pos = zeros((numPart, 3))
pos[:,0] = r * sin_theta * cos_phi
pos[:,1] = r * sin_theta * sin_phi
pos[:,2] = r * cos_theta
# shift particles to put the sphere in the centre of the box
pos += array([50. * R, 50. * R, 50. * R])
h = ones(numPart) * 2. * R / numPart**(1. / 3.)
# Generate extra arrays
v = zeros((numPart, 3))
ids = linspace(1, numPart, numPart)
m = ones(numPart) * M / numPart
u = ones(numPart) * u0
#--------------------------------------------------
#File
file = h5py.File(fileName, 'w')
# Header
grp = file.create_group("/Header")
grp.attrs["BoxSize"] = [100. * R, 100. * R, 100. * R]
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"] = 0
#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) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
# 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/>.
#
################################################################################
# Compares the swift result for the 2D spherical Sod shock with a high
# resolution 2D reference result
import matplotlib
matplotlib.use("Agg")
from pylab import *
from scipy import stats
import h5py
# Parameters
gas_gamma = 5./3. # Polytropic index
rho_L = 1. # Density left state
rho_R = 0.125 # Density right state
v_L = 0. # Velocity left state
v_R = 0. # Velocity right state
P_L = 1. # Pressure left state
P_R = 0.1 # Pressure right state
# 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("evrard_%04d.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"]
coords = sim["/PartType0/Coordinates"]
x = sqrt((coords[:,0] - 0.5 * boxSize)**2 + (coords[:,1] - 0.5 * boxSize)**2 + \
(coords[:,2] - 0.5 * boxSize)**2)
vels = sim["/PartType0/Velocities"]
v = sqrt(vels[:,0]**2 + vels[:,1]**2 + vels[:,2]**2)
u = sim["/PartType0/InternalEnergy"][:]
S = sim["/PartType0/Entropy"][:]
P = sim["/PartType0/Pressure"][:]
rho = sim["/PartType0/Density"][:]
# Bin the data
x_bin_edge = logspace(-3., log10(2.), 100)
x_bin = 0.5*(x_bin_edge[1:] + x_bin_edge[:-1])
rho_bin,_,_ = stats.binned_statistic(x, rho, statistic='mean', bins=x_bin_edge)
v_bin,_,_ = stats.binned_statistic(x, v, statistic='mean', bins=x_bin_edge)
P_bin,_,_ = stats.binned_statistic(x, P, statistic='mean', bins=x_bin_edge)
S_bin,_,_ = stats.binned_statistic(x, S, statistic='mean', bins=x_bin_edge)
u_bin,_,_ = stats.binned_statistic(x, u, statistic='mean', bins=x_bin_edge)
rho2_bin,_,_ = stats.binned_statistic(x, rho**2, statistic='mean', bins=x_bin_edge)
v2_bin,_,_ = stats.binned_statistic(x, v**2, statistic='mean', bins=x_bin_edge)
P2_bin,_,_ = stats.binned_statistic(x, P**2, statistic='mean', bins=x_bin_edge)
S2_bin,_,_ = stats.binned_statistic(x, S**2, statistic='mean', bins=x_bin_edge)
u2_bin,_,_ = stats.binned_statistic(x, u**2, statistic='mean', bins=x_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)
ref = loadtxt("evrardCollapse3D_exact.txt")
# Plot the interesting quantities
figure()
# Velocity profile --------------------------------
subplot(231)
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("${\\rm{Velocity}}~v_r$", labelpad=0)
xlim(1.e-3, 2.)
ylim(-1.7, 0.1)
# Density profile --------------------------------
subplot(232)
loglog(x, rho, '.', color='r', ms=0.2)
loglog(ref[:,0], ref[:,1], "k--", alpha=0.8, lw=1.2)
errorbar(x_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(1.e-3, 2.)
ylim(1.e-2, 1.e4)
# Pressure profile --------------------------------
subplot(233)
loglog(x, P, '.', color='r', ms=0.2)
loglog(ref[:,0], ref[:,3], "k--", alpha=0.8, lw=1.2)
errorbar(x_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(1.e-3, 2.)
ylim(1.e-4, 1.e3)
# Internal energy profile -------------------------
subplot(234)
loglog(x, u, '.', color='r', ms=0.2)
loglog(ref[:,0], ref[:,3] / ref[:,1] / (gas_gamma - 1.), "k--", alpha=0.8, lw=1.2)
errorbar(x_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(1.e-3, 2.)
ylim(1.e-2, 2.)
# Entropy profile ---------------------------------
subplot(235)
semilogx(x, S, '.', color='r', ms=0.2)
semilogx(ref[:,0], ref[:,3] / ref[:,1]**gas_gamma, "k--", alpha=0.8, lw=1.2)
errorbar(x_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=0)
xlim(1.e-3, 2.)
ylim(0., 0.25)
# Information -------------------------------------
subplot(236, frameon=False)
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)
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([])
tight_layout()
savefig("EvrardCollapse.png", dpi=200)
#!/bin/bash
# Generate the initial conditions if they are not present.
if [ ! -e evrard.hdf5 ]
then
echo "Generating initial conditions for the Evrard collapse example..."
python makeIC.py
fi
# Run SWIFT
../swift -s -G -t 4 evrard.yml 2>&1 | tee output.log
# Get the high resolution 1D reference result if not present.
if [ ! -e evrardCollapse3D_exact.txt ]
then
echo "Fetching the reference result for the Evrard collapse example..."
./getReference.sh
fi
# Plot the solution
python plotSolution.py 8
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassCube_64.hdf5
# 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
Scheduler:
max_top_level_cells: 15
# Parameters governing the time integration
TimeIntegration:
time_begin: 0. # The starting time of the simulation (in internal units).
time_end: 1. # 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: gresho # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 1e-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: ./greshoVortex.hdf5 # The file to read
################################################################################
# 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
from numpy import *
# Generates a swift IC file for the Gresho-Chan vortex in a periodic box
# Parameters
gamma = 5./3. # Gas adiabatic index
rho0 = 1 # Gas density
P0 = 0. # Constant additional pressure (should have no impact on the dynamics)
fileOutputName = "greshoVortex.hdf5"
fileGlass = "glassCube_64.hdf5"
#---------------------------------------------------
# Get position and smoothing lengths from the glass
fileInput = h5py.File(fileGlass, 'r')
coords = fileInput["/PartType0/Coordinates"][:,:]
h = fileInput["/PartType0/SmoothingLength"][:]
ids = fileInput["/PartType0/ParticleIDs"][:]
boxSize = fileInput["/Header"].attrs["BoxSize"][0]
numPart = size(h)
fileInput.close()
# Now generate the rest
m = ones(numPart) * rho0 * boxSize**3 / numPart
u = zeros(numPart)
v = zeros((numPart, 3))
for i in range(numPart):
x = coords[i,0]
y = coords[i,1]
r2 = (x - boxSize / 2)**2 + (y - boxSize / 2)**2
r = sqrt(r2)
v_phi = 0.
if r < 0.2:
v_phi = 5.*r
elif r < 0.4:
v_phi = 2. - 5.*r
else:
v_phi = 0.
v[i,0] = -v_phi * (y - boxSize / 2) / r
v[i,1] = v_phi * (x - boxSize / 2) / r
v[i,2] = 0.
P = P0
if r < 0.2:
P = P + 5. + 12.5*r2
elif r < 0.4:
P = P + 9. + 12.5*r2 - 20.*r + 4.*log(r/0.2)
else:
P = P + 3. + 4.*log(2.)
u[i] = P / ((gamma - 1.)*rho0)
#File
fileOutput = h5py.File(fileOutputName, 'w')
# Header
grp = fileOutput.create_group("/Header")
grp.attrs["BoxSize"] = [boxSize, boxSize, boxSize]
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]
grp.attrs["Dimension"] = 3
#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[()] = v
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()
################################################################################
# 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/>.
#
################################################################################
# Computes the analytical solution of the Gresho-Chan vortex and plots the SPH
# answer
# Parameters
gas_gamma = 5./3. # Gas adiabatic index
rho0 = 1 # Gas density
P0 = 0. # Constant additional pressure (should have no impact on the
# dynamics)
# ---------------------------------------------------------------
# Don't touch anything after this.
# ---------------------------------------------------------------
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])
# Generate the analytic solution at this time
N = 200
R_max = 0.8
solution_r = arange(0, R_max, R_max / N)
solution_P = zeros(N)
solution_v_phi = zeros(N)
solution_v_r = zeros(N)
for i in range(N):
if solution_r[i] < 0.2:
solution_P[i] = P0 + 5. + 12.5*solution_r[i]**2
solution_v_phi[i] = 5.*solution_r[i]
elif solution_r[i] < 0.4:
solution_P[i] = P0 + 9. + 12.5*solution_r[i]**2 - 20.*solution_r[i] + 4.*log(solution_r[i]/0.2)
solution_v_phi[i] = 2. -5.*solution_r[i]
else:
solution_P[i] = P0 + 3. + 4.*log(2.)
solution_v_phi[i] = 0.
solution_rho = ones(N) * rho0
solution_s = solution_P / solution_rho**gas_gamma
solution_u = solution_P /((gas_gamma - 1.)*solution_rho)