Commit ecab068c authored by Bert Vandenbroucke's avatar Bert Vandenbroucke
Browse files

Added disc patch run script and 1D disc patch test.

parent eb586836
#!/bin/bash
# Generate the initial conditions if they are not present.
if [ ! -e glassCube_32.hdf5 ]
then
echo "Fetching initial glass file for the disc patch example..."
./getGlass.sh
fi
if [ ! -e Disc-Patch.hdf5 ]
then
echo "Generating initial conditions for the disc patch example..."
python makeIC.py
fi
# Run SWIFT
../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
python plotSolution.py
# Define the system of units to use internally.
InternalUnitSystem:
UnitMass_in_cgs: 1.9885e33 # Grams
UnitLength_in_cgs: 3.08567758149e18 # Centimeters
UnitVelocity_in_cgs: 1e5 # 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: 968. # The end time of the simulation (in internal units).
dt_min: 1e-4 # The minimal time-step size of the simulation (in internal units).
dt_max: 10. # The maximal time-step size of the simulation (in internal units).
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 12. # Time between statistics output
# Parameters governing the snapshots
Snapshots:
basename: Disc-Patch # Common part of the name of output files
time_first: 0. # Time of the first output (in internal units)
delta_time: 48. # Time difference between outputs (in internal units)
# Parameters for the hydrodynamics scheme
SPH:
resolution_eta: 1.2349 # Target smoothing length in units of the mean inter-particle separation (1.2349 == 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.
max_ghost_iterations: 30 # Maximal number of iterations allowed to converge towards the smoothing length.
h_max: 60. # Maximal smoothing length allowed (in internal units).
# Parameters related to the initial conditions
InitialConditions:
file_name: Disc-Patch.hdf5 # The file to read
# External potential parameters
DiscPatchPotential:
surface_density: 10.
scale_height: 100.
x_disc: 400.
x_trunc: 300.
x_max: 350.
timestep_mult: 0.03
growth_time: 5.
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2016 John A. Regan (john.a.regan@durham.ac.uk)
# Tom Theuns (tom.theuns@durham.ac.uk)
# 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk)
# 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
import sys
import numpy as np
import math
import random
# Generates a disc-patch in hydrostatic equilibrium
#
# See Creasey, Theuns & Bower, 2013, MNRAS, Volume 429, Issue 3, p.1922-1948
#
#
# Disc parameters are: surface density -- sigma
# scale height -- b
# gas adiabatic index -- gamma
#
# Problem parameters are: Ratio height/width of the box -- z_factor
# Size of the patch -- side_length
# Parameters of the gas disc
surface_density = 10.
scale_height = 100.
gas_gamma = 5./3.
# Parameters of the problem
x_factor = 2
side_length = 400.
numPart = 1000
# File
fileName = "Disc-Patch.hdf5"
####################################################################
# physical constants in cgs
NEWTON_GRAVITY_CGS = 6.67408e-8
SOLAR_MASS_IN_CGS = 1.9885e33
PARSEC_IN_CGS = 3.08567758149e18
PROTON_MASS_IN_CGS = 1.672621898e-24
BOLTZMANN_IN_CGS = 1.38064852e-16
YEAR_IN_CGS = 3.15569252e7
# choice of units
unit_length_in_cgs = (PARSEC_IN_CGS)
unit_mass_in_cgs = (SOLAR_MASS_IN_CGS)
unit_velocity_in_cgs = (1e5)
unit_time_in_cgs = unit_length_in_cgs / unit_velocity_in_cgs
print "UnitMass_in_cgs: %.5e"%unit_mass_in_cgs
print "UnitLength_in_cgs: %.5e"%unit_length_in_cgs
print "UnitVelocity_in_cgs: %.5e"%unit_velocity_in_cgs
print "UnitTime_in_cgs: %.5e"%unit_time_in_cgs
print ""
# Derived units
const_G = NEWTON_GRAVITY_CGS * unit_mass_in_cgs * unit_time_in_cgs**2 * \
unit_length_in_cgs**-3
const_mp = PROTON_MASS_IN_CGS * unit_mass_in_cgs**-1
const_kb = BOLTZMANN_IN_CGS * unit_mass_in_cgs**-1 * unit_length_in_cgs**-2 * \
unit_time_in_cgs**2
print "--- Some constants [internal units] ---"
print "G_Newton: %.5e"%const_G
print "m_proton: %.5e"%const_mp
print "k_boltzmann: %.5e"%const_kb
print ""
# derived quantities
temp = math.pi * const_G * surface_density * scale_height * const_mp / \
const_kb
u_therm = const_kb * temp / ((gas_gamma-1) * const_mp)
v_disp = math.sqrt(2 * u_therm)
soundspeed = math.sqrt(u_therm / (gas_gamma * (gas_gamma-1.)))
t_dyn = math.sqrt(scale_height / (const_G * surface_density))
t_cross = scale_height / soundspeed
print "--- Properties of the gas [internal units] ---"
print "Gas temperature: %.5e"%temp
print "Gas thermal_energy: %.5e"%u_therm
print "Dynamical time: %.5e"%t_dyn
print "Sound crossing time: %.5e"%t_cross
print "Gas sound speed: %.5e"%soundspeed
print "Gas 3D vel_disp: %.5e"%v_disp
print ""
# Problem properties
boxSize_x = side_length
boxSize_x *= x_factor
volume = boxSize_x
M_tot = surface_density * math.tanh(boxSize_x / (2. * scale_height))
density = M_tot / volume
entropy = (gas_gamma - 1.) * u_therm / density**(gas_gamma - 1.)
print "--- Problem properties [internal units] ---"
print "Box: %.1f"%boxSize_x
print "Volume: %.5e"%volume
print "Total mass: %.5e"%M_tot
print "Density: %.5e"%density
print "Entropy: %.5e"%entropy
print ""
####################################################################
# Now create enough copies to fill the volume in x
pos = np.zeros((numPart, 3))
h = np.zeros(numPart) + 2. * boxSize_x / numPart
for i in range(numPart):
pos[i, 0] = (i + 0.5) * boxSize_x / numPart
# Compute further properties of ICs
mass = M_tot / numPart
print "--- Particle properties [internal units] ---"
print "Number part.: ", numPart
print "Part. mass: %.5e"%mass
print ""
# Create additional arrays
u = np.ones(numPart) * u_therm
mass = np.ones(numPart) * mass
vel = np.zeros((numPart, 3))
ids = 1 + np.linspace(0, numPart, numPart, endpoint=False)
####################################################################
# Create and write output file
#File
file = h5py.File(fileName, 'w')
#Units
grp = file.create_group("/Units")
grp.attrs["Unit length in cgs (U_L)"] = unit_length_in_cgs
grp.attrs["Unit mass in cgs (U_M)"] = unit_mass_in_cgs
grp.attrs["Unit time in cgs (U_t)"] = unit_time_in_cgs
grp.attrs["Unit current in cgs (U_I)"] = 1.
grp.attrs["Unit temperature in cgs (U_T)"] = 1.
# Header
grp = file.create_group("/Header")
grp.attrs["BoxSize"] = [boxSize_x, 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, 0, 0, 0, 0, 0]
grp.attrs["Dimension"] = 1
#Runtime parameters
grp = file.create_group("/RuntimePars")
grp.attrs["PeriodicBoundariesOn"] = 1
# write gas particles
grp0 = file.create_group("/PartType0")
ds = grp0.create_dataset('Coordinates', (numPart, 3), 'f', data=pos)
ds = grp0.create_dataset('Velocities', (numPart, 3), 'f')
ds = grp0.create_dataset('Masses', (numPart,), 'f', data=mass)
ds = grp0.create_dataset('SmoothingLength', (numPart,), 'f', data=h)
ds = grp0.create_dataset('InternalEnergy', (numPart,), 'f', data=u)
ds = grp0.create_dataset('ParticleIDs', (numPart, ), 'L', data=ids)
####################################################################
print "--- Runtime parameters (YAML file): ---"
print "DiscPatchPotential:surface_density: ", surface_density
print "DiscPatchPotential:scale_height: ", scale_height
print "DiscPatchPotential:x_disc: ", 0.5 * boxSize_x
print ""
print "--- Constant parameters: ---"
print "const_isothermal_internal_energy: %ef"%u_therm
################################################################################
# This file is part of SWIFT.
# Copyright (c) 2017 Bert Vandenbroucke (bert.vandenbroucke@gmail.com)
# 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/>.
#
################################################################################
##
# This script plots the Disc-Patch_*.hdf5 snapshots.
# It takes two (optional) parameters: the counter value of the first and last
# snapshot to plot (default: 0 21).
##
import numpy as np
import h5py
import matplotlib
matplotlib.use("Agg")
import pylab as pl
import glob
import sys
# Parameters
surface_density = 10.
scale_height = 100.
x_disc = 400.
x_trunc = 300.
x_max = 350.
utherm = 20.2678457288
gamma = 5. / 3.
start = 0
stop = 21
if len(sys.argv) > 1:
start = int(sys.argv[1])
if len(sys.argv) > 2:
stop = int(sys.argv[2])
# Get the analytic solution for the density
def get_analytic_density(x):
return 0.5 * surface_density / scale_height / \
np.cosh( (x - x_disc) / scale_height )**2
# Get the analytic solution for the (isothermal) pressure
def get_analytic_pressure(x):
return (gamma - 1.) * utherm * get_analytic_density(x)
# Get the data fields to plot from the snapshot file with the given name:
# snapshot time, x-coord, density, pressure, velocity norm
def get_data(name):
file = h5py.File(name, "r")
coords = np.array(file["/PartType0/Coordinates"])
rho = np.array(file["/PartType0/Density"])
u = np.array(file["/PartType0/InternalEnergy"])
v = np.array(file["/PartType0/Velocities"])
P = (gamma - 1.) * rho * u
vtot = np.sqrt( v[:,0]**2 + v[:,1]**2 + v[:,2]**2 )
return float(file["/Header"].attrs["Time"]), coords[:,0], rho, P, vtot
# scan the folder for snapshot files and plot all of them (within the requested
# range)
for f in sorted(glob.glob("Disc-Patch_*.hdf5")):
num = int(f[-8:-5])
if num < start or num > stop:
continue
print "processing", f, "..."
xrange = np.linspace(0., 2. * x_disc, 1000)
time, x, rho, P, v = get_data(f)
fig, ax = pl.subplots(3, 1, sharex = True)
ax[0].plot(x, rho, "r.")
ax[0].plot(xrange, get_analytic_density(xrange), "k-")
ax[0].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
ax[0].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
ax[0].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
ax[0].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
ax[0].set_ylim(0., 1.2 * get_analytic_density(x_disc))
ax[0].set_ylabel("density")
ax[1].plot(x, v, "r.")
ax[1].plot(xrange, np.zeros(len(xrange)), "k-")
ax[1].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
ax[1].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
ax[1].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
ax[1].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
ax[1].set_ylim(-0.5, 10.)
ax[1].set_ylabel("velocity norm")
ax[2].plot(x, P, "r.")
ax[2].plot(xrange, get_analytic_pressure(xrange), "k-")
ax[2].plot([x_disc - x_max, x_disc - x_max], [0, 10], "k--", alpha=0.5)
ax[2].plot([x_disc + x_max, x_disc + x_max], [0, 10], "k--", alpha=0.5)
ax[2].plot([x_disc - x_trunc, x_disc - x_trunc], [0, 10], "k--", alpha=0.5)
ax[2].plot([x_disc + x_trunc, x_disc + x_trunc], [0, 10], "k--", alpha=0.5)
ax[2].set_xlim(0., 2. * x_disc)
ax[2].set_ylim(0., 1.2 * get_analytic_pressure(x_disc))
ax[2].set_xlabel("x")
ax[2].set_ylabel("pressure")
pl.suptitle("t = {0:.2f}".format(time))
pl.savefig("{name}.png".format(name = f[:-5]))
pl.close()
#!/bin/bash
# Generate the initial conditions if they are not present.
if [ ! -e Disc-Patch.hdf5 ]
then
echo "Generating initial conditions for the disc patch example..."
python makeIC.py
fi
# Run SWIFT
../../swift -g -s -t 4 disc-patch-icc.yml 2>&1 | tee output.log
python plotSolution.py
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