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Gear metal diffusion

Merged Loic Hausammann requested to merge gear_metal_diffusion into master
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###############################################################################
# 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
import numpy as np
# Generates a swift IC file for the Smoothed Metallicity test in a periodic cubic box
# Generates a swift IC file for the Smoothed Metallicity test
# in a periodic cubic box
# Parameters
gamma = 5./3. # Gas adiabatic index
rho0 = 1. # Background density
P0 = 1.e-6 # Background pressure
Nelem = 9 # Gear: 9, EAGLE: 9
P0 = 1e-6 # Background pressure
Nelem = 10 # Gear: 10, EAGLE: 9
low_metal = -6 # Low iron fraction
high_metal = -5 # high iron fraction
sigma_metal = 0.1 # relative standard deviation for the metallicities
high_metal = -5.5 # high iron fraction
max_shift = 1 # Shift between the different elements
sigma_metal = 0.2 # relative standard deviation for the metallicities
fileName = "smoothed_metallicity.hdf5"
# shift all metals in order to obtain nicer plots
low_metal = [low_metal] * Nelem + np.linspace(0, 3, Nelem)
high_metal = [high_metal] * Nelem + np.linspace(0, 3, Nelem)
low_metal = [low_metal] * Nelem + np.linspace(0, max_shift, Nelem)
low_metal = 10**low_metal
high_metal = [high_metal] * Nelem + np.linspace(0, max_shift, Nelem)
high_metal = 10**high_metal
# ---------------------------------------------------
glass = h5py.File("glassCube_32.hdf5", "r")
@@ -52,21 +57,24 @@ ids = np.linspace(1, numPart, numPart)
m = np.zeros(numPart)
u = np.zeros(numPart)
r = np.zeros(numPart)
Z = np.zeros((numPart, Nelem))
mass_frac = np.zeros((numPart, Nelem))
r = np.sqrt((pos[:, 0] - 0.5)**2 + (pos[:, 1] - 0.5)**2 + (pos[:, 2] - 0.5)**2)
m[:] = rho0 * vol / numPart
u[:] = P0 / (rho0 * (gamma - 1))
# set metallicities
select = pos[:, 0] < 0.5
nber = sum(select)
Z[select, :] = low_metal * (1 + np.random.normal(loc=0., scale=sigma_metal,
size=(nber, Nelem)))
mass_frac[select, :] = low_metal * (
1 + np.random.normal(loc=0., scale=sigma_metal,
size=(nber, Nelem)))
nber = numPart - nber
Z[np.logical_not(select), :] = high_metal * (1 + np.random.normal(
mass_frac[~select, :] = high_metal * (1 + np.random.normal(
loc=0., scale=sigma_metal, size=(nber, Nelem)))
v[select, 2] = 1
v[~select, 2] = -1
# --------------------------------------------------
# File
@@ -100,7 +108,8 @@ 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')
grp.create_dataset('ElementAbundance', data=Z, dtype='f')
grp.create_dataset('MetalMassFraction', data=mass_frac, dtype='d')
grp.create_dataset('ElementAbundance', data=mass_frac, dtype='d')
file.close()
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