Skip to content

GitLab

Commit 32516c49 authored by Jacob Kegerreis 's avatar Jacob Kegerreis Committed by Matthieu Schaller
Browse files

Big update for planetary stuff

parent 0fd491d2
Expand all Hide whitespace changes
Inline Side-by-side
.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
View file @ 0fd491d2
#!/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