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SWIFTsim
Commit 32516c49 authored by Jacob Kegerreis 's avatar Jacob Kegerreis Committed by Matthieu Schaller
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Big update for planetary stuff

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.gitignore
View file @ 32516c49
......@@ -165,6 +165,8 @@ m4/lt~obsolete.m4
/stamp-h1
/test-driver
src/equation_of_state/planetary/*.txt
# Intel compiler optimization reports
*.optrpt
......@@ -316,3 +318,6 @@ sympy-plots-for-*.tex/
#ctags
*tags
# vim
*.swp
configure.ac
View file @ 32516c49
......@@ -576,7 +576,7 @@ if test "x$with_profiler" != "xno"; then
proflibs="-lprofiler"
fi
AC_CHECK_LIB([profiler],[ProfilerFlush],
[have_profiler="yes"
[have_profiler="yes"
AC_DEFINE([WITH_PROFILER],1,[Link against the gperftools profiling library.])],
[have_profiler="no"], $proflibs)
......@@ -973,7 +973,7 @@ esac
# Hydro scheme.
AC_ARG_WITH([hydro],
[AS_HELP_STRING([--with-hydro=<scheme>],
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, default, gizmo-mfv, gizmo-mfm, shadowfax, minimal-multi-mat, debug default: gadget2@:>@]
[Hydro dynamics to use @<:@gadget2, minimal, pressure-entropy, pressure-energy, default, gizmo-mfv, gizmo-mfm, shadowfax, planetary, debug default: gadget2@:>@]
)],
[with_hydro="$withval"],
[with_hydro="gadget2"]
......@@ -1012,10 +1012,11 @@ case "$with_hydro" in
shadowfax)
AC_DEFINE([SHADOWFAX_SPH], [1], [Shadowfax SPH])
;;
minimal-multi-mat)
AC_DEFINE([MINIMAL_MULTI_MAT_SPH], [1], [Minimal Multiple Material SPH])
planetary)
AC_DEFINE([PLANETARY_SPH], [1], [Planetary SPH])
;;
*)
AC_MSG_ERROR([Unknown hydrodynamics scheme: $with_hydro])
;;
......
examples/MoonFormingImpact/README.md deleted 100644 → 0
View file @ 0fd491d2
Canonical Moon-Forming Giant Impact
===================================
NOTE: This doesn't really work because the EOS are different to Canup (2004) so
the impactor just glances then flies away!
A version of the canonical moon-forming giant impact of Theia onto the early
Earth (Canup 2004; Barr 2016). Both bodies are here made of a (Tillotson) iron
core and granite mantle. Only ~10,000 particles are used for a quick and crude
simulation.
Setup
-----
In `swiftsim/`:
`$ ./configure --with-hydro=minimal-multi-mat --with-equation-of-state=planetary`
`$ make`
In `swiftsim/examples/MoonFormingImpact/`:
`$ ./get_init_cond.sh`
Run
---
`$ ./run.sh`
Output
------
`$ python plot.py`
`$ mplayer anim.mpg`
examples/MoonFormingImpact/get_init_cond.sh deleted 100755 → 0
View file @ 0fd491d2
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/moon_forming_impact.hdf5
examples/MoonFormingImpact/moon_forming_impact.yml deleted 100644 → 0
View file @ 0fd491d2
# Define the system of units to use internally.
InternalUnitSystem:
UnitMass_in_cgs: 5.9724e27 # Grams
UnitLength_in_cgs: 6.371e8 # Centimeters
UnitVelocity_in_cgs: 6.371e8 # 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: 100000 # The end time of the simulation (in internal units).
dt_min: 0.001 # The minimal time-step size of the simulation (in internal units).
dt_max: 100 # The maximal time-step size of the simulation (in internal units).
# Parameters governing the snapshots
Snapshots:
# Common part of the name of output files
basename: snapshots/moon_forming_impact
time_first: 0 # Time of the first output (in internal units)
delta_time: 100 # Time difference between consecutive outputs (in internal units)
label_delta: 100 # Integer increment between snapshot output labels
# Parameters governing the conserved quantities statistics
Statistics:
delta_time: 500 # 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.
CFL_condition: 0.2 # Courant-Friedrich-Levy condition for time integration.
# Parameters for the self-gravity scheme
Gravity:
eta: 0.025 # Constant dimensionless multiplier for time integration.
theta: 0.7 # Opening angle (Multipole acceptance criterion)
comoving_softening: 0.005 # Comoving softening length (in internal units).
max_physical_softening: 0.005 # Physical softening length (in internal units).
# Parameters related to the initial conditions
InitialConditions:
# The initial conditions file to read
file_name: moon_forming_impact.hdf5
# Parameters related to the equation of state
EoS:
planetary_use_Til: 1 # Whether to prepare the Tillotson EOS
examples/MoonFormingImpact/plot.py deleted 100644 → 0
View file @ 0fd491d2
"""
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2018 Jacob Kegerreis (jacob.kegerreis@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/>.
#
###############################################################################
Plotting script for the Canonical Moon-Forming Giant Impact example.
Save a figure for each snapshot in `./plots/` then make them into a simple
animation with ffmpeg in `./`.
Usage:
`$ python plot.py time_end delta_time`
Sys args:
+ `time_end` | (opt) int | The time of the last snapshot to plot.
Default = 100000
+ `delta_time` | (opt) int | The time between successive snapshots.
Default = 100
"""
from __future__ import division
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import h5py
import sys
import subprocess
# Particle array fields
dtype_picle = [
('m', float), ('x', float), ('y', float), ('z', float), ('v_x', float),
('v_y', float), ('v_z', float), ('ID', int), ('rho', float), ('u', float),
('phi', float), ('P', float), ('h', float), ('mat_ID', int), ('r', float)
]
s_to_hour = 1 / 60**2
# Snapshot info
file_snap = "./snapshots/moon_forming_impact_"
file_plot = "./plots/moon_forming_impact_"
# Number of particles in the target body
num_target = 9496
# Material types (copied from src/equation_of_state/planetary/equation_of_state.h)
type_factor = 100
Di_type = {
'Til' : 1,
'HM80' : 2,
'ANEOS' : 3,
'SESAME' : 4,
}
Di_material = {
# Tillotson
'Til_iron' : Di_type['Til']*type_factor,
'Til_granite' : Di_type['Til']*type_factor + 1,
'Til_water' : Di_type['Til']*type_factor + 2,
# Hubbard & MacFarlane (1980) Uranus/Neptune
'HM80_HHe' : Di_type['HM80']*type_factor, # Hydrogen-helium atmosphere
'HM80_ice' : Di_type['HM80']*type_factor + 1, # H20-CH4-NH3 ice mix
'HM80_rock' : Di_type['HM80']*type_factor + 2, # SiO2-MgO-FeS-FeO rock mix
# ANEOS
'ANEOS_iron' : Di_type['ANEOS']*type_factor,
'MANEOS_forsterite' : Di_type['ANEOS']*type_factor + 1,
# SESAME
'SESAME_iron' : Di_type['SESAME']*type_factor,
}
# Material offset for impactor particles
ID_imp = 10000
# Material colours
Di_mat_colour = {
# Target
Di_material['Til_iron'] : 'orange',
Di_material['Til_granite'] : '#FFF0E0',
# Impactor
Di_material['Til_iron'] + ID_imp : 'dodgerblue',
Di_material['Til_granite'] + ID_imp : '#A080D0',
}
def load_snapshot(filename):
""" Load the hdf5 snapshot file and return the structured particle array.
"""
# Add extension if needed
if (filename[-5:] != ".hdf5"):
filename += ".hdf5"
# Load the hdf5 file
with h5py.File(filename, 'r') as f:
header = f['Header'].attrs
A2_pos = f['PartType0/Coordinates'].value
A2_vel = f['PartType0/Velocities'].value
# Structured array of all particle data
A2_picle = np.empty(header['NumPart_Total'][0],
dtype=dtype_picle)
A2_picle['x'] = A2_pos[:, 0]
A2_picle['y'] = A2_pos[:, 1]
A2_picle['z'] = A2_pos[:, 2]
A2_picle['v_x'] = A2_vel[:, 0]
A2_picle['v_y'] = A2_vel[:, 1]
A2_picle['v_z'] = A2_vel[:, 2]
A2_picle['m'] = f['PartType0/Masses'].value
A2_picle['ID'] = f['PartType0/ParticleIDs'].value
A2_picle['rho'] = f['PartType0/Density'].value
A2_picle['u'] = f['PartType0/InternalEnergy'].value
A2_picle['phi'] = f['PartType0/Potential'].value
A2_picle['P'] = f['PartType0/Pressure'].value
A2_picle['h'] = f['PartType0/SmoothingLength'].value
A2_picle['mat_ID'] = f['PartType0/MaterialID'].value
return A2_picle
def process_particles(A2_picle, num_target):
""" Modify things like particle units, material IDs, and coordinate origins.
"""
# Offset material IDs for impactor particles
A2_picle['mat_ID'][A2_picle['ID'] >= num_target] += ID_imp
# Shift coordinates to the centre of the target's core's mass and momentum
sel_tar = np.where(A2_picle['mat_ID'] == Di_material['Til_iron'])[0]
# Centre of mass
m_tot = np.sum(A2_picle[sel_tar]['m'])
x_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['x']) / m_tot
y_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['y']) / m_tot
z_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['z']) / m_tot
# Change origin to the centre-of-mass
A2_picle['x'] -= x_com
A2_picle['y'] -= y_com
A2_picle['z'] -= z_com
A2_picle['r'] = np.sqrt(
A2_picle['x']**2 + A2_picle['y']**2 + A2_picle['z']**2
)
# Centre of momentum
v_x_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_x']) / m_tot
v_y_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_y']) / m_tot
v_z_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_z']) / m_tot
# Change to the centre-of-momentum frame of reference
A2_picle['v_x'] -= v_x_com
A2_picle['v_y'] -= v_y_com
A2_picle['v_z'] -= v_z_com
return A2_picle
def plot_snapshot(A2_picle, filename, time, ax_lim=100, dz=0.1):
""" Plot the snapshot particles and save the figure.
"""
# Add extension if needed
if (filename[-5:] != ".png"):
filename += ".png"
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(111, aspect='equal')
# Plot slices in z below zero
for z in np.arange(-ax_lim, 0, dz):
sel_z = np.where((z < A2_picle['z']) & (A2_picle['z'] < z+dz))[0]
A2_picle_z = A2_picle[sel_z]
# Plot each material
for mat_ID, colour in Di_mat_colour.iteritems():
sel_col = np.where(A2_picle_z['mat_ID'] == mat_ID)[0]
ax.scatter(
A2_picle_z[sel_col]['x'], A2_picle_z[sel_col]['y'],
c=colour, edgecolors='none', marker='.', s=50, alpha=0.7
)
# Axes etc.
ax.set_axis_bgcolor('k')
ax.set_xlabel("x Position ($R_\oplus$)")
ax.set_ylabel("y Position ($R_\oplus$)")
ax.set_xlim(-ax_lim, ax_lim)
ax.set_ylim(-ax_lim, ax_lim)
plt.text(
-0.92*ax_lim, 0.85*ax_lim, "%.1f h" % (time*s_to_hour), fontsize=20,
color='w'
)
# Font sizes
for item in (
[ax.title, ax.xaxis.label, ax.yaxis.label] + ax.get_xticklabels() +
ax.get_yticklabels()
):
item.set_fontsize(20)
plt.tight_layout()
plt.savefig(filename)
plt.close()
if __name__ == '__main__':
# Sys args
try:
time_end = int(sys.argv[1])
try:
delta_time = int(sys.argv[2])
except IndexError:
delta_time = 100
except IndexError:
time_end = 100000
delta_time = 100
# Load and plot each snapshot
for i_snap in range(int(time_end/delta_time) + 1):
snap_time = i_snap * delta_time
print "\rPlotting snapshot %06d (%d of %d)" % (
snap_time, i_snap+1, int(time_end/delta_time)
),
sys.stdout.flush()
# Load particle data
filename = "%s%06d" % (file_snap, snap_time)
A2_picle = load_snapshot(filename)
# Process particle data
A2_picle = process_particles(A2_picle, num_target)
# Plot particles
filename = "%s%06d" % (file_plot, snap_time)
plot_snapshot(A2_picle, filename, snap_time)
# Animation
command = (
"ffmpeg -framerate 12 -i plots/moon_forming_impact_%*.png -r 25 "
"anim.mpg -y"
)
print "\n%s\n" % command
subprocess.check_output(command, shell=True)
examples/MoonFormingImpact/run.sh deleted 100755 → 0
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#!/bin/bash
../swift -G -s -t 8 moon_forming_impact.yml
examples/UranusImpact/README.md deleted 100644 → 0
View file @ 0fd491d2
Uranus Giant Impact
===================
A simple version of the low angular momentum impact onto the early Uranus shown
in Kegerreis et al. (2018), Fig. 2; with only ~10,000 particles for a quick and
crude simulation.
The collision of a 2 Earth mass impactor onto a proto-Uranus that can explain
the spin of the present-day planet, with an angular momentum of 2e36 kg m^2 s^-1
and velocity at infinity of 5 km s^-1 for a relatively head-on impact.
Both bodies have a rocky core and icy mantle, with a hydrogen-helium atmosphere
on the target as well. Although with this low number of particles it cannot be
modelled in any detail.
Setup
-----
In `swiftsim/`:
`$ ./configure --with-hydro=minimal-multi-mat --with-equation-of-state=planetary`
`$ make`
In `swiftsim/examples/UranusImpact/`:
`$ ./get_init_cond.sh`
Run
---
`$ ./run.sh`
Analysis
--------
`$ python plot.py`
`$ mplayer anim.mpg`
examples/UranusImpact/get_init_cond.sh deleted 100755 → 0
View file @ 0fd491d2
#!/bin/bash
wget http://virgodb.cosma.dur.ac.uk/swift-webstorage/ICs/uranus_impact.hdf5
examples/UranusImpact/plot.py deleted 100644 → 0
View file @ 0fd491d2
"""
###############################################################################
# This file is part of SWIFT.
# Copyright (c) 2018 Jacob Kegerreis (jacob.kegerreis@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/>.
#
###############################################################################
Plotting script for the Uranus Giant Impact example.
Save a figure for each snapshot in `./plots/` then make them into a simple
animation with ffmpeg in `./`.
The snapshot plots show all particles with z < 0, coloured by their material.
Usage:
`$ python plot.py time_end delta_time`
Sys args:
+ `time_end` | (opt) int | The time of the last snapshot to plot.
Default = 100000
+ `delta_time` | (opt) int | The time between successive snapshots.
Default = 500
"""
from __future__ import division
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import h5py
import sys
import subprocess
# Particle array fields
dtype_picle = [
('m', float), ('x', float), ('y', float), ('z', float), ('v_x', float),
('v_y', float), ('v_z', float), ('ID', int), ('rho', float), ('u', float),
('phi', float), ('P', float), ('h', float), ('mat_ID', int), ('r', float)
]
s_to_hour = 1 / 60**2
R_Ea = 6.371e6
# Default sys args
time_end_default = 100000
delta_time_default = 500
# Snapshot info
file_snap = "./snapshots/uranus_impact_"
file_plot = "./plots/uranus_impact_"
# Number of particles in the target body
num_target = 8992
# Material types (copied from src/equation_of_state/planetary/equation_of_state.h)
type_factor = 100
Di_type = {
'Til' : 1,
'HM80' : 2,
'ANEOS' : 3,
'SESAME' : 4,
}
Di_material = {
# Tillotson
'Til_iron' : Di_type['Til']*type_factor,
'Til_granite' : Di_type['Til']*type_factor + 1,
'Til_water' : Di_type['Til']*type_factor + 2,
# Hubbard & MacFarlane (1980) Uranus/Neptune
'HM80_HHe' : Di_type['HM80']*type_factor, # Hydrogen-helium atmosphere
'HM80_ice' : Di_type['HM80']*type_factor + 1, # H20-CH4-NH3 ice mix
'HM80_rock' : Di_type['HM80']*type_factor + 2, # SiO2-MgO-FeS-FeO rock mix
# ANEOS
'ANEOS_iron' : Di_type['ANEOS']*type_factor,
'MANEOS_forsterite' : Di_type['ANEOS']*type_factor + 1,
# SESAME
'SESAME_iron' : Di_type['SESAME']*type_factor,
}
# Material offset for impactor particles
ID_imp = 10000
# Material colours
Di_mat_colour = {
# Target
Di_material['HM80_HHe'] : '#33DDFF',
Di_material['HM80_ice'] : 'lightsteelblue',
Di_material['HM80_rock'] : 'slategrey',
# Impactor
Di_material['HM80_ice'] + ID_imp : '#A080D0',
Di_material['HM80_rock'] + ID_imp : '#706050',
}
def load_snapshot(filename):
""" Load the hdf5 snapshot file and return the structured particle array.
"""
# Add extension if needed
if (filename[-5:] != ".hdf5"):
filename += ".hdf5"
# Load the hdf5 file
with h5py.File(filename, 'r') as f:
header = f['Header'].attrs
A2_pos = f['PartType0/Coordinates'].value
A2_vel = f['PartType0/Velocities'].value
# Structured array of all particle data
A2_picle = np.empty(header['NumPart_Total'][0],
dtype=dtype_picle)
A2_picle['x'] = A2_pos[:, 0]
A2_picle['y'] = A2_pos[:, 1]
A2_picle['z'] = A2_pos[:, 2]
A2_picle['v_x'] = A2_vel[:, 0]
A2_picle['v_y'] = A2_vel[:, 1]
A2_picle['v_z'] = A2_vel[:, 2]
A2_picle['m'] = f['PartType0/Masses'].value
A2_picle['ID'] = f['PartType0/ParticleIDs'].value
A2_picle['rho'] = f['PartType0/Density'].value
A2_picle['u'] = f['PartType0/InternalEnergy'].value
A2_picle['phi'] = f['PartType0/Potential'].value
A2_picle['P'] = f['PartType0/Pressure'].value
A2_picle['h'] = f['PartType0/SmoothingLength'].value
A2_picle['mat_ID'] = f['PartType0/MaterialID'].value
return A2_picle
def process_particles(A2_picle, num_target):
""" Modify things like particle units, material IDs, and coordinate origins.
"""
# Offset material IDs for impactor particles
A2_picle['mat_ID'][A2_picle['ID'] >= num_target] += ID_imp
# Shift coordinates to the centre of the target's core's mass and momentum
sel_tar = np.where(A2_picle['mat_ID'] == Di_material['HM80_rock'])[0]
# Centre of mass
m_tot = np.sum(A2_picle[sel_tar]['m'])
x_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['x']) / m_tot
y_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['y']) / m_tot
z_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['z']) / m_tot
# Change origin to the centre-of-mass
A2_picle['x'] -= x_com
A2_picle['y'] -= y_com
A2_picle['z'] -= z_com
A2_picle['r'] = np.sqrt(
A2_picle['x']**2 + A2_picle['y']**2 + A2_picle['z']**2
)
# Centre of momentum
v_x_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_x']) / m_tot
v_y_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_y']) / m_tot
v_z_com = np.sum(A2_picle[sel_tar]['m'] * A2_picle[sel_tar]['v_z']) / m_tot
# Change to the centre-of-momentum frame of reference
A2_picle['v_x'] -= v_x_com
A2_picle['v_y'] -= v_y_com
A2_picle['v_z'] -= v_z_com
return A2_picle
def plot_snapshot(A2_picle, filename, time, ax_lim=13, dz=0.1):
""" Plot the snapshot particles and save the figure.
"""
# Add extension if needed
if (filename[-5:] != ".png"):
filename += ".png"
fig = plt.figure(figsize=(9, 9))
ax = fig.add_subplot(111, aspect='equal')
# Plot slices in z below zero
for z in np.arange(-ax_lim, 0, dz):
sel_z = np.where((z < A2_picle['z']) & (A2_picle['z'] < z+dz))[0]
A2_picle_z = A2_picle[sel_z]
# Plot each material
for mat_ID, colour in Di_mat_colour.iteritems():
sel_col = np.where(A2_picle_z['mat_ID'] == mat_ID)[0]
ax.scatter(
A2_picle_z[sel_col]['x'], A2_picle_z[sel_col]['y'],
c=colour, edgecolors='none', marker='.', s=50, alpha=0.7
)
# Axes etc.
ax.set_axis_bgcolor('k')
ax.set_xlabel("x Position ($R_\oplus$)")
ax.set_ylabel("y Position ($R_\oplus$)")
ax.set_xlim(-ax_lim, ax_lim)
ax.set_ylim(-ax_lim, ax_lim)
plt.text(
-0.92*ax_lim, 0.85*ax_lim, "%.1f h" % (time*s_to_hour), fontsize=20,
color='w'
)
# Font sizes
for item in (
[ax.title, ax.xaxis.label, ax.yaxis.label] + ax.get_xticklabels() +
ax.get_yticklabels()
):
item.set_fontsize(20)
plt.tight_layout()
plt.savefig(filename)
plt.close()
if __name__ == '__main__':
# Sys args
try:
time_end = int(sys.argv[1])
try:
delta_time = int(sys.argv[2])
except IndexError:
delta_time = delta_time_default
except IndexError: