Commit b2345b3c authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Merge branch 'master' into disk-patch

parents 911be52a 954b572d
......@@ -29,6 +29,7 @@ examples/used_parameters.yml
examples/energy.txt
examples/*/*.xmf
examples/*/*.hdf5
examples/*/*.png
examples/*/*.txt
examples/*/used_parameters.yml
examples/*/*/*.xmf
......
......@@ -469,7 +469,7 @@ if test "$enable_warn" != "no"; then
CFLAGS="$CFLAGS -Wall"
;;
intel)
CFLAGS="$CFLAGS -w2"
CFLAGS="$CFLAGS -w2 -Wunused-variable"
;;
*)
AX_CFLAGS_WARN_ALL
......
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2012 Pedro Gonnet (pedro.gonnet@durham.ac.uk),
# 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 random
from numpy import *
# Computes the analytical solution of the Gresho-Chan vortex
# The script works for a given initial box and background pressure and computes the solution for any time t (The solution is constant over time).
# The code writes five files rho.dat, P.dat, v.dat, u.dat and s.dat with the density, pressure, internal energy and
# entropic function on N radial points between r=0 and r=R_max.
# Parameters
rho0 = 1. # Background Density
P0 = 0. # Background Pressure
gamma = 5./3. # Gas polytropic index
N = 1000 # Number of radial points
R_max = 1. # Maximal radius
# ---------------------------------------------------------------
# Don't touch anything after this.
# ---------------------------------------------------------------
r = arange(0, R_max, R_max / N)
rho = ones(N)
P = zeros(N)
v = zeros(N)
u = zeros(N)
s = zeros(N)
for i in range(N):
if r[i] < 0.2:
P[i] = P0 + 5. + 12.5*r[i]**2
v[i] = 5.*r[i]
elif r[i] < 0.4:
P[i] = P0 + 9. + 12.5*r[i]**2 - 20.*r[i] + 4.*log(r[i]/0.2)
v[i] = 2. -5.*r[i]
else:
P[i] = P0 + 3. + 4.*log(2.)
v[i] = 0.
rho[i] = rho0
s[i] = P[i] / rho[i]**gamma
u[i] = P[i] /((gamma - 1.)*rho[i])
savetxt("rho.dat", column_stack((r, rho)))
savetxt("P.dat", column_stack((r, P)))
savetxt("v.dat", column_stack((r, v)))
savetxt("u.dat", column_stack((r, u)))
savetxt("s.dat", column_stack((r, s)))
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/glassPlane_128.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
# 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).
delta_neighbours: 0.1 # The tolerance for the targetted number of neighbours.
max_smoothing_length: 0.02 # 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: ./greshoVortex.hdf5 # The file to read
###############################################################################
# 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 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 = "glassPlane_128.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**2 / 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, 0.2]
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[()] = 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)
#
# 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 *
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)
# Read the simulation data
sim = h5py.File("gresho_%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"][:,:]
r = sqrt(x**2 + y**2)
v_r = (x * vel[:,0] + y * vel[:,1]) / r
v_phi = (-y * vel[:,0] + x * vel[:,1]) / r
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)
plot(r, v_phi, '.', color='r', ms=0.5)
plot(solution_r, solution_v_phi, '--', color='k', alpha=0.8, lw=1.2)
plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Azimuthal~velocity}}~v_\\phi$", labelpad=0)
xlim(0,R_max)
ylim(-0.1, 1.2)
# Radial density profile --------------------------------
subplot(232)
plot(r, rho, '.', color='r', ms=0.5)
plot(solution_r, solution_rho, '--', color='k', alpha=0.8, lw=1.2)
plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Density}}~\\rho$", labelpad=0)
xlim(0,R_max)
ylim(rho0-0.3, rho0 + 0.3)
#yticks([-0.2, -0.1, 0., 0.1, 0.2])
# Radial pressure profile --------------------------------
subplot(233)
plot(r, P, '.', color='r', ms=0.5)
plot(solution_r, solution_P, '--', color='k', alpha=0.8, lw=1.2)
plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Pressure}}~P$", labelpad=0)
xlim(0, R_max)
ylim(4.9 + P0, P0 + 6.1)
# Internal energy profile --------------------------------
subplot(234)
plot(r, u, '.', color='r', ms=0.5)
plot(solution_r, solution_u, '--', color='k', alpha=0.8, lw=1.2)
plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Internal~Energy}}~u$", labelpad=0)
xlim(0,R_max)
ylim(7.3, 9.1)
# Radial entropy profile --------------------------------
subplot(235)
plot(r, S, '.', color='r', ms=0.5)
plot(solution_r, solution_s, '--', color='k', alpha=0.8, lw=1.2)
plot([0.2, 0.2], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
plot([0.4, 0.4], [-100, 100], ':', color='k', alpha=0.4, lw=1.2)
xlabel("${\\rm{Radius}}~r$", labelpad=0)
ylabel("${\\rm{Entropy}}~S$", labelpad=0)
xlim(0, R_max)
ylim(4.9 + P0, P0 + 6.1)
# 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, "Gresho-Chan vortex with $\\gamma=%.3f$ at $t=%.2f$"%(gas_gamma,time), fontsize=10)
text(-0.49, 0.8, "Background $\\rho_0=%.3f$"%rho0, fontsize=10)
text(-0.49, 0.7, "Background $P_0=%.3f$"%P0, 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("GreshoVortex.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 Gresho-Chan vortex example..."
./getGlass.sh
fi
if [ ! -e greshoVortex.hdf5 ]
then
echo "Generating initial conditions for the Gresho-Chan vortex example..."
python makeIC.py
fi
# Run SWIFT
../swift -s -t 1 gresho.yml
# Plot the solution
python plotSolution.py 11
# 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
###############################################################################
# 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