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Jupyter example of four AMUSE tools - MASC, Multiples, Ekster and Fresco
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{ | |
"cells": [ | |
{ | |
"cell_type": "markdown", | |
"id": "a88c4196", | |
"metadata": {}, | |
"source": [ | |
"# Simulating dynamics of multiple stellar systems in clusters\n", | |
"**NOTE: this notebook will be updated during the week - please check for updates!**\n", | |
"\n", | |
"In this notebook, I show how to create a star cluster with binary stars using AMUSE with MASC.\n", | |
"\n", | |
"Then, I simulate an encounter of two binary stars using Multiples.\n", | |
"\n", | |
"Finally, I show how to make a visualisation of the cluster with Fresco.\n", | |
"\n", | |
"Please feel free to use and modify the code in this notebook if you find it useful - but please let me know if you do!\n", | |
"\n", | |
"~ Steven Rieder" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "6de1b5eb-dab5-44f2-888b-2e46ef561e7e", | |
"metadata": { | |
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"source": [ | |
"## MASC\n", | |
"*make a star cluster - choose an IMF and spatial distribution, supports initial binaries.*\n", | |
"\n", | |
"MASC is a tool that integrates several functions in AMUSE to facilitate creating initial conditions.\n", | |
"It supports multiple spatial distributions (like Plummer, King and Fractal models), initial mass functions (Kroupa, Salpeter, flat) and can now also create initial binaries with various properties (semi-major axis, eccentricity, mass relation between the primary and secondary).\n", | |
"It can be run from the command line to create an AMUSE file, or directly from an AMUSE script (with more functionality)." | |
] | |
}, | |
{ | |
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}, | |
"source": [ | |
"### Imports" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "8bee3a5e", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# The following Python packages and their dependencies are required for this notebook\n", | |
"# You can find installation instructions for AMUSE at https://www.amusecode.org\n", | |
"\n", | |
"# uncomment line below to install via pip - note that you must already have the dependencies!\n", | |
"#!pip install amuse-framework amuse-masc amuse-fractalcluster amuse-ph4 amuse-smalln amuse-kepler" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "3faa4895", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Imports used here - also needed for the examples below\n", | |
"import time\n", | |
"import numpy as np\n", | |
"import matplotlib as mpl\n", | |
"import matplotlib.pyplot as plt\n", | |
"%matplotlib inline\n", | |
"%config InlineBackend.figure_format='retina'\n", | |
"mpl.rcParams['figure.dpi'] = 144\n", | |
"\n", | |
"from amuse.datamodel import Particles\n", | |
"from amuse.units import units, nbody_system, constants\n", | |
"from amuse.ext.masc.cluster import new_star_cluster" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "cb86b904", | |
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"source": [ | |
"### Create a star cluster\n", | |
"The cell below sets up a star cluster, where the semi-major axis of the binaries kept constant.\n", | |
"The binaries can also be given different semi-major axes.\n", | |
"\n", | |
"More options are available (e.g. for mass distributions) and more can/will be added in the future." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "e4e4eb28", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"np.random.seed(1701)\n", | |
"number_of_binaries = 100\n", | |
"number_of_systems = 5000\n", | |
"semi_major_axis = np.ones(number_of_binaries) * (10 | units.au)\n", | |
"\n", | |
"single_stars, binary_stars, binary_systems = new_star_cluster(\n", | |
" star_distribution='fractal', # note that currently, fractal ignores pre-set random seeds... Known issue.\n", | |
" number_of_stars=number_of_systems, # note that this really means 'number of systems'\n", | |
" number_of_binaries=number_of_binaries,\n", | |
" return_binaries=True,\n", | |
" binary_semi_major_axis_distribution=semi_major_axis,\n", | |
" eccentricity_distribution=0,\n", | |
")" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "63023037", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"print(\n", | |
" f\"Singles: {len(single_stars)}, \"\n", | |
" f\"binary systems: {len(binary_systems)}, \"\n", | |
" f\"total stars: {len(single_stars)+len(binary_stars)}\"\n", | |
")" | |
] | |
}, | |
{ | |
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"jp-MarkdownHeadingCollapsed": true | |
}, | |
"source": [ | |
"### Helper functions for plotting" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "6b8675ab", | |
"metadata": { | |
"editable": true, | |
"slideshow": { | |
"slide_type": "" | |
}, | |
"tags": [] | |
}, | |
"outputs": [], | |
"source": [ | |
"# This cell contains plot functions\n", | |
"\n", | |
"figure_width_px = 1600\n", | |
"px = 1 / plt.rcParams['figure.dpi'] | units.inch # pixel in inches\n", | |
"\n", | |
"# Note the syntax used by AMUSE to create quantities (a variable with a unit)\n", | |
"# x.value_in(unit) will convert a quantity x back to a number\n", | |
"\n", | |
"figure_width_inch = figure_width_px * px # .value_in(units.inch)\n", | |
"\n", | |
"def plot_binary(b):\n", | |
" aspect = 1\n", | |
" figsize = (\n", | |
" figure_width_inch.value_in(units.inch),\n", | |
" aspect * figure_width_inch.value_in(units.inch),\n", | |
" )\n", | |
" l = (b[0].position - b[1].position).length()\n", | |
" fig = plt.figure(figsize=figsize, dpi=dpi.value_in(units.inch**-1))\n", | |
" ax_zoom = fig.add_subplot(111)\n", | |
" ax_zoom.scatter(\n", | |
" b.x.value_in(units.pc),\n", | |
" b.y.value_in(units.pc),\n", | |
" edgecolors=None, s=10,\n", | |
" )\n", | |
" ax_zoom.set_xlim(\n", | |
" (b[0].x - l).value_in(units.pc),\n", | |
" (b[0].x + l).value_in(units.pc),\n", | |
" )\n", | |
" ax_zoom.set_ylim(\n", | |
" (b[0].y - l).value_in(units.pc),\n", | |
" (b[0].y + l).value_in(units.pc),\n", | |
" )\n", | |
" ax_zoom.quiver(\n", | |
" b.x.value_in(units.pc),\n", | |
" b.y.value_in(units.pc),\n", | |
" b.vx.value_in(units.kms),\n", | |
" b.vy.value_in(units.kms),\n", | |
" scale=50\n", | |
" )\n", | |
" ax_zoom.set_aspect(1)\n", | |
" return fig\n", | |
"\n", | |
"\n", | |
"def plot_interaction(\n", | |
" stars,\n", | |
" length_unit=units.au,\n", | |
" speed_unit=units.kms,\n", | |
" time=0 | units.yr,\n", | |
" interactions=0,\n", | |
" time_requested=0 | units.yr,\n", | |
" min_width=100 | units.au,\n", | |
" return_width=False,\n", | |
"):\n", | |
" \"plot a set of interacting stars, seen from the center-of-mass frame\"\n", | |
" aspect = 1\n", | |
" figsize = (\n", | |
" 0.5 * figure_width_inch.value_in(units.inch),\n", | |
" 0.5 * aspect * figure_width_inch.value_in(units.inch),\n", | |
" )\n", | |
" fig = plt.figure(figsize=figsize)\n", | |
" ax = fig.add_subplot(111, aspect=aspect)\n", | |
" \n", | |
" com = stars.center_of_mass()\n", | |
" comv = stars.center_of_mass_velocity()\n", | |
"\n", | |
" minx = stars.x.min()\n", | |
" maxx = stars.x.max()\n", | |
" centerx = minx + (maxx-minx)/2\n", | |
" miny = stars.y.min()\n", | |
" maxy = stars.y.max()\n", | |
" centery = miny + (maxy-miny)/2\n", | |
" minz = stars.z.min()\n", | |
" maxz = stars.z.max()\n", | |
" centerz = minz + (maxz-minz)/2\n", | |
" width = max(\n", | |
" (\n", | |
" (maxx-minx)**2\n", | |
" + (maxy-miny)**2\n", | |
" + (maxz-minz)**2\n", | |
" )**0.5,\n", | |
" min_width\n", | |
" ).value_in(length_unit)\n", | |
"\n", | |
" ax.set_title(\n", | |
" f\"{time.value_in(units.yr):07.1f} yr \"\n", | |
" f\"({time_requested.value_in(units.yr):07.1f} yr), \"\n", | |
" f\"{interactions} interactions\"\n", | |
" )\n", | |
" stars = stars.sorted_by_attribute('z')\n", | |
" plt.scatter(\n", | |
" (stars.x - centerx).value_in(length_unit),\n", | |
" (stars.y - centery).value_in(length_unit),\n", | |
" c=stars.color,\n", | |
" )\n", | |
" plt.quiver(\n", | |
" (stars.x - centerx).value_in(length_unit),\n", | |
" (stars.y - centery).value_in(length_unit),\n", | |
" (stars.vx - comv.x).value_in(speed_unit),\n", | |
" (stars.vy - comv.y).value_in(speed_unit),\n", | |
" )\n", | |
" ax.set_xlim(\n", | |
" centerx.value_in(length_unit)-0.8*width,\n", | |
" centerx.value_in(length_unit)+0.8*width\n", | |
" )\n", | |
" ax.set_ylim(\n", | |
" centery.value_in(length_unit)-0.8*width,\n", | |
" centery.value_in(length_unit)+0.8*width\n", | |
" )\n", | |
" ax.set_xlabel(f'x [{length_unit}]')\n", | |
" ax.set_ylabel(f'y [{length_unit}]')\n", | |
" if return_width:\n", | |
" return fig, width\n", | |
" return fig\n", | |
"\n", | |
" \n", | |
"def plot_stars_binaries(s, b, width=5 | units.pc, title=''):\n", | |
" length_unit = width.unit\n", | |
" aspect = 1.7\n", | |
" figsize = (\n", | |
" figure_width_inch.value_in(units.inch),\n", | |
" figure_width_inch.value_in(units.inch) / aspect,\n", | |
" )\n", | |
" fig = plt.figure(figsize=figsize)\n", | |
" ax = fig.add_subplot(121)\n", | |
" ax.scatter(\n", | |
" s.x.value_in(length_unit),\n", | |
" s.y.value_in(length_unit),\n", | |
" edgecolors=None, s=1,\n", | |
" )\n", | |
" ax.set_xlim(-width.value_in(length_unit), width.value_in(length_unit))\n", | |
" ax.set_ylim(-width.value_in(length_unit), width.value_in(length_unit))\n", | |
" ax.set_xlabel(f'x [{length_unit}]')\n", | |
" ax.set_ylabel(f'y [{length_unit}]')\n", | |
" ax.set_title(title)\n", | |
" ax.set_aspect(1)\n", | |
" \n", | |
" ax_zoom = fig.add_subplot(122)\n", | |
" \n", | |
" n = s.nearest_neighbour()\n", | |
" d = (n.position - s.position).lengths()\n", | |
"\n", | |
" zoom_in_mass = (b[0].mass + n[0].mass)\n", | |
" zoom_in_position = (\n", | |
" b[0].mass * b[0].position\n", | |
" + n[0].mass * n[0].position\n", | |
" ) / zoom_in_mass\n", | |
" zoom_in_velocity = (\n", | |
" b[0].mass * b[0].velocity\n", | |
" + n[0].mass * n[0].velocity\n", | |
" ) / zoom_in_mass\n", | |
" system_projected_size = (\n", | |
" (b[0].x - n[0].x)**2\n", | |
" + (b[0].y - n[0].y)**2\n", | |
" )**0.5\n", | |
" \n", | |
" ax_zoom.scatter(\n", | |
" zoom_in_position.x.value_in(length_unit),\n", | |
" zoom_in_position.y.value_in(length_unit),\n", | |
" edgecolors=None, s=30,\n", | |
" label='Center-of-mass',\n", | |
" )\n", | |
" ax_zoom.scatter(\n", | |
" b.x.value_in(length_unit),\n", | |
" b.y.value_in(length_unit),\n", | |
" edgecolors=None, s=30,\n", | |
" label='Component stars',\n", | |
" )\n", | |
" ax_zoom.set_xlim(\n", | |
" (zoom_in_position.x - system_projected_size).value_in(length_unit),\n", | |
" (zoom_in_position.x + system_projected_size).value_in(length_unit)\n", | |
" )\n", | |
" ax_zoom.set_ylim(\n", | |
" (zoom_in_position.y - system_projected_size).value_in(length_unit),\n", | |
" (zoom_in_position.y + system_projected_size).value_in(length_unit)\n", | |
" )\n", | |
" ax_zoom.quiver(\n", | |
" zoom_in_position.x.value_in(length_unit),\n", | |
" zoom_in_position.y.value_in(length_unit),\n", | |
" (zoom_in_velocity.x).value_in(units.kms),\n", | |
" (zoom_in_velocity.y).value_in(units.kms),\n", | |
" scale=10,\n", | |
" )\n", | |
" ax_zoom.quiver(\n", | |
" b.x.value_in(length_unit),\n", | |
" b.y.value_in(length_unit),\n", | |
" (b.vx - zoom_in_velocity.x).value_in(units.kms),\n", | |
" (b.vy - zoom_in_velocity.y).value_in(units.kms),\n", | |
" scale=10,\n", | |
" )\n", | |
" ax_zoom.set_aspect(1)\n", | |
" ax_zoom.set_xlabel(f'x [{length_unit}]')\n", | |
" ax_zoom.set_ylabel(f'y [{length_unit}]')\n", | |
" ax_zoom.set_title('Zoom in on a binary pair')\n", | |
" ax_zoom.legend()\n", | |
" fig.tight_layout()\n", | |
" return fig" | |
] | |
}, | |
{ | |
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"id": "33bf48dc-66c7-4c36-919b-33920183d857", | |
"metadata": { | |
"jp-MarkdownHeadingCollapsed": true | |
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"source": [ | |
"### Plot the resulting cluster" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "a2435d3b", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"starplot = plot_stars_binaries(\n", | |
" (binary_stars | single_stars), # union of binary_stars and single_stars, i.e. all stars with the binaries first\n", | |
" binary_stars,\n", | |
" title='Fractal cluster'\n", | |
")\n", | |
"plt.savefig('masc_example.png', dpi=144)" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "0a6676b6-240b-4940-8aa3-883806be09bb", | |
"metadata": {}, | |
"source": [ | |
"## Multiples\n", | |
"*takes care of interactions between a binary pair and any system that could disrupt it.*\n", | |
"\n", | |
"Multiples is a solution to the problem encountered by gravitational dynamics codes when simulating large systems with hard binaries in them: the time step would get too short, slowing the code down to a crawl.\n", | |
"Multiples detects systems of two (or more) stars within a specified interaction radius, and replaces these for the gravity code by a single particle.\n", | |
"When this particle encounters another particle, Multiples calculates the orbital phase of the stars in the system with a Kepler integrator, and then handles the encounter to its conclusion, e.g. the formation of (a) new multiple system(s) or the dissolution into individual stars, using a gravity code optimized for a small number of particles.\n", | |
"In this way, gravitational dynamics are sped up by a large factor compared to using a pure N-body code.\n", | |
"\n", | |
"In the cells below I explain how to use Multiples, taking two binaries from the MASC cluster and putting them in a more convenient frame where they will collide within a short time." | |
] | |
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{ | |
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"source": [ | |
"### Imports and setup\n", | |
"The cell below imports the required AMUSE modules and creates a GravityWithMultiples class." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "8cc95995", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Now we simulate the system further using Multiples.\n", | |
"# This module uses Ph4 for the integration of the systems, \n", | |
"# but integrates the binaries using a Kepler integrator\n", | |
"# and interactions between stars and binary systems using a small-N integrator\n", | |
"# As a result, it can speed things up by a large factor when dealing with tight binaries.\n", | |
"# When this is not the case however, it can be much slower!\n", | |
"from amuse.community.ph4 import Ph4\n", | |
"from amuse.community.smalln import Smalln\n", | |
"from amuse.community.kepler import Kepler\n", | |
"import amuse.couple.multiples as multiples\n", | |
"\n", | |
"\n", | |
"# Multiples requires some setting up - you can use this class for that\n", | |
"class GravityWithMultiples:\n", | |
" def __init__(\n", | |
" self, stars,\n", | |
" gravity=Ph4, smalln=Smalln, kepler=Kepler,\n", | |
" converter=None, time_step=0.01 | units.Myr,\n", | |
" number_of_workers=1,\n", | |
" ):\n", | |
" self.smalln_code = smalln\n", | |
" if converter is None:\n", | |
" self.converter = nbody_system.nbody_to_si(stars.total_mass(), time_step)\n", | |
" else:\n", | |
" self.converter = converter\n", | |
" self.model_time = 0 | units.Myr\n", | |
"\n", | |
" self.smalln = None\n", | |
" self.gravity = gravity(convert_nbody=self.converter, number_of_workers=number_of_workers)\n", | |
" self.gravity.parameters.epsilon_squared = (self.converter.to_si(0.0 | nbody_system.length))**2\n", | |
" self.gravity.particles.add_particles(stars)\n", | |
"\n", | |
" stopping_condition = self.gravity.stopping_conditions.collision_detection\n", | |
" stopping_condition.enable()\n", | |
"\n", | |
" self.init_smalln()\n", | |
" self.kepler = kepler(unit_converter=self.converter)\n", | |
" self.kepler.initialize_code()\n", | |
" self.multiples_code = multiples.Multiples(\n", | |
" self.gravity, self.new_smalln, self.kepler, constants.G\n", | |
" )\n", | |
" self.multiples_code.neighbor_perturbation_limit = 0.05\n", | |
" self.multiples_code.global_debug = 0\n", | |
"\n", | |
" # global_debug = 0: no output from multiples\n", | |
" # 1: minimal output\n", | |
" # 2: debugging output\n", | |
" # 3: even more output\n", | |
"\n", | |
" print('Settings for Multiples:')\n", | |
" print(f'multiples_code.neighbor_veto = {self.multiples_code.neighbor_veto}')\n", | |
" print(f'multiples_code.neighbor_perturbation_limit = {self.multiples_code.neighbor_perturbation_limit}')\n", | |
" print(f'multiples_code.retain_binary_apocenter = {self.multiples_code.retain_binary_apocenter}')\n", | |
" print(f'multiples_code.wide_perturbation_limit = {self.multiples_code.wide_perturbation_limit}')\n", | |
"\n", | |
" self.energy_0 = self.print_diagnostics(self.multiples_code)\n", | |
"\n", | |
" @property\n", | |
" def stars(self):\n", | |
" return self.multiples_code.stars\n", | |
"\n", | |
" @property\n", | |
" def particles(self):\n", | |
" return self.multiples_code.particles\n", | |
"\n", | |
" def init_smalln(self):\n", | |
" self.smalln = self.smalln_code(convert_nbody=self.converter)\n", | |
"\n", | |
" def new_smalln(self):\n", | |
" self.smalln.reset()\n", | |
" return self.smalln\n", | |
"\n", | |
" def stop_smalln(self):\n", | |
" self.smalln.stop()\n", | |
"\n", | |
" def print_diagnostics(self, grav, energy_0=None):\n", | |
" # Simple diagnostics.\n", | |
" energy_kinetic = grav.kinetic_energy\n", | |
" energy_potential = grav.potential_energy\n", | |
" (\n", | |
" self.number_of_multiples,\n", | |
" self.number_of_binaries,\n", | |
" self.energy_in_multiples,\n", | |
" ) = grav.get_total_multiple_energy()\n", | |
" energy = energy_kinetic + energy_potential + self.energy_in_multiples\n", | |
" print(f'Time = {grav.get_time().in_(units.Myr)}')\n", | |
" print(f' top-level kinetic energy = {energy_kinetic}')\n", | |
" print(f' top-level potential energy = {energy_potential}')\n", | |
" print(f' total top-level energy = {energy_kinetic + energy_potential}')\n", | |
" print(f' {self.number_of_multiples} multiples, total energy = {self.energy_in_multiples}')\n", | |
" print(f' uncorrected total energy ={energy}')\n", | |
"\n", | |
" energy_tidal = (\n", | |
" grav.multiples_external_tidal_correction\n", | |
" + grav.multiples_internal_tidal_correction\n", | |
" ) # tidal error\n", | |
" energy_error = grav.multiples_integration_energy_error # integration error\n", | |
"\n", | |
" energy -= energy_tidal + energy_error\n", | |
" print(f' corrected total energy = {energy}')\n", | |
"\n", | |
" if energy_0 is not None: print(' relative energy error=', (energy-energy_0)/energy_0)\n", | |
"\n", | |
" return energy\n", | |
"\n", | |
" def evolve_model(self, t_end, return_number_of_encounters=False):\n", | |
" if return_number_of_encounters:\n", | |
" encounters_resolved, encounters_ignored = self.multiples_code.evolve_model(\n", | |
" t_end, return_number_of_encounters=return_number_of_encounters\n", | |
" )\n", | |
" else:\n", | |
" self.multiples_code.evolve_model(t_end)\n", | |
" # self.print_diagnostics(self.multiples_code, self.energy_0)\n", | |
" self.model_time = self.multiples_code.model_time\n", | |
" if return_number_of_encounters:\n", | |
" return encounters_resolved, encounters_ignored\n", | |
" \n", | |
"\n", | |
" def stop(self):\n", | |
" self.gravity.stop()\n", | |
" self.kepler.stop()\n", | |
" self.stop_smalln()" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "d4885a6b-942c-4965-a294-3f4b1b2d7e8a", | |
"metadata": { | |
"jp-MarkdownHeadingCollapsed": true | |
}, | |
"source": [ | |
"### Create a pair of binaries\n", | |
"These will collide after a short time." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "7b541dcb-c7be-47e8-b19b-2ce21bf08edc", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Use two binaries as a nice test case for Multiples.\n", | |
"# We create a copy of the binaries, so that we don't change the original particles.\n", | |
"colliding_binaries = Particles()\n", | |
"binary_pair_one = Particles()\n", | |
"binary_pair_one.add_particle(binary_stars[0].copy())\n", | |
"binary_pair_one.add_particle(binary_stars[number_of_binaries].copy())\n", | |
"binary_pair_two = Particles()\n", | |
"binary_pair_two.add_particle(binary_stars[1].copy())\n", | |
"binary_pair_two.add_particle(binary_stars[1+number_of_binaries].copy())\n", | |
"\n", | |
"# shift binaries to their respective center-of-mass coordinate frame\n", | |
"binary_pair_one.move_to_center()\n", | |
"binary_pair_two.move_to_center()\n", | |
"\n", | |
"# set the binaries 400 au apart - gravity will do the rest\n", | |
"binary_pair_one.x += 200 | units.au\n", | |
"binary_pair_two.x -= 200 | units.au\n", | |
"\n", | |
"# (setting a moderate vx helps the collision happen a bit sooner - it will also change the outcome though)\n", | |
"binary_pair_one.vx -= 1.1 | units.au / units.yr\n", | |
"binary_pair_two.vx += 1.1 | units.au / units.yr\n", | |
"binary_pair_one.vy -= 0.01 | units.au / units.yr\n", | |
"binary_pair_two.vy += 0.01 | units.au / units.yr\n", | |
"\n", | |
"# add them to a common particle set\n", | |
"colliding_binaries.add_particles(binary_pair_one)\n", | |
"colliding_binaries.add_particles(binary_pair_two)\n", | |
"\n", | |
"# give all stars their own color, so that we can uniquely identify them in plots\n", | |
"colliding_binaries.color = [\"red\", \"blue\", \"green\", \"orange\"]\n", | |
"\n", | |
"# The radius we set here is the *interaction* radius: Multiples will present systems smaller than this as a single star to the gravity code\n", | |
"# So don't set it too large or too small!\n", | |
"colliding_binaries.radius = 3 | units.au\n", | |
"# uncommenting the line below effectively disables Multiples\n", | |
"# colliding_binaries.radius = 2 | units.RSun" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "91244e6b-5cfa-421e-add8-dd34c7e3f0c6", | |
"metadata": { | |
"jp-MarkdownHeadingCollapsed": true | |
}, | |
"source": [ | |
"### Plot the initial setup" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "9507a7d4", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"colfig, width = plot_interaction(colliding_binaries, time=0 | units.yr, return_width=True)\n", | |
"plt.show()\n", | |
"colfig.clf()" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "ee23b2cf-fdb5-4c3d-aae7-2bfd3e155f2d", | |
"metadata": {}, | |
"source": [ | |
"### Simulate binary-binary interaction with Multiples\n", | |
"We now let the binary systems collide. Multiples will at times take over from the gravity code, each time this happens the 'interactions' counter will increase by 1.\n", | |
"This will create a lot of plots if save_plots is set to True!" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "434416b5", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# A converter sets the units used internally in the code, using two units out of mass, length and time.\n", | |
"converter_multiples = nbody_system.nbody_to_si(\n", | |
" 0.1 | units.au,\n", | |
" 0.1 | units.yr,\n", | |
")\n", | |
"grav = GravityWithMultiples(\n", | |
" colliding_binaries,\n", | |
" converter=converter_multiples,\n", | |
" number_of_workers=1, # if we simulate a large cluster, best increase this - but here we just do 4 stars\n", | |
")" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "bbc90e19", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"save_plots = True\n", | |
"i = 0\n", | |
"width = 0\n", | |
"time_step = 0.8 | units.yr\n", | |
"time_end = 1000 | units.yr\n", | |
"encounters_resolved = 0\n", | |
"encounters_ignored = 0\n", | |
"clock_start = time.time() | units.s\n", | |
"while grav.model_time < time_end:\n", | |
" t = i * time_step\n", | |
" res, ign = grav.evolve_model(t, return_number_of_encounters=True)\n", | |
" encounters_resolved += res\n", | |
" encounters_ignored += ign\n", | |
" channel = grav.stars.new_channel_to(colliding_binaries)\n", | |
" channel.copy_attributes([\"x\", \"y\", \"z\", \"vx\", \"vy\", \"vz\"])\n", | |
" if save_plots:\n", | |
" colfig, width = plot_interaction(\n", | |
" colliding_binaries, time=grav.model_time, interactions=encounters_resolved, time_requested=t,\n", | |
" return_width=True,\n", | |
" )\n", | |
" plt.savefig(f'interacting_binary_{i:06d}.png')\n", | |
" plt.close(colfig)\n", | |
" i += 1\n", | |
" print(f\"{encounters_resolved}, {encounters_ignored}, {width}, {grav.model_time.in_(units.yr)}\")\n", | |
"clock_finish = time.time() | units.s\n", | |
"print(f\"This took {(clock_finish-clock_start).in_(units.hour)}\")\n", | |
"print(f\"There are now {len(grav.particles)} particles in the gravity code\")\n", | |
"print(f\"There are however {len(grav.stars)} stars.\")\n", | |
"grav.stop()" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "cc6870c8-627c-4176-b8ba-a69b98f86e96", | |
"metadata": { | |
"jp-MarkdownHeadingCollapsed": true | |
}, | |
"source": [ | |
"## Fresco\n", | |
"*visualisation of stars with extinction from dust - create mock-observations from simulations.*\n", | |
"\n", | |
"Fresco (Rieder & Pelupessy, https://github.com/rieder/amuse-fresco) is a visualisation tool, that calculates the visual appearance of stars using their luminosity and temperature.\n", | |
"It calculates the stellar flux in several color bands, convolves this with a point-spread function (the PSF for Hubble's WFC3 is included) and combines the result to a color image (mimicking visual observation).\n", | |
"Additionally, Fresco supports calculating extinction and reflection by gas/dust." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "d768bb4d-9fbb-414c-a122-5f3dec93297d", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# uncomment to install Fresco\n", | |
"#!pip install amuse-fresco\n", | |
"from amuse.plot.fresco import make_fresco_image\n", | |
"from amuse.plot.fresco.fresco import evolve_to_age\n", | |
"\n", | |
"stars_for_fresco = (binary_stars | single_stars).copy()\n", | |
"evolve_to_age(stars_for_fresco, 1 | units.Myr)\n", | |
"\n", | |
"make_fresco_image(stars=stars_for_fresco, gas=None)" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "5724bff4-e7d4-46c0-9881-31fce341fd6e", | |
"metadata": {}, | |
"source": [ | |
"## Ekster\n", | |
"*star formation from molecular clouds at moderate mass resolution.*\n", | |
"\n", | |
"Ekster (Rieder et al. 2021) is a tool for simulating the formation of star clusters from molecular clouds.\n", | |
"It combines gravitational dynamics, hydrodynamics and stellar evolution with a recipe for star formation that forms stars on a proto-cluster basis, about 200 M<sub>☉</sub> at a time.\n", | |
"In Rieder et al. 2021, we used Ekster to simulate star formation in a spiral galaxy, while in Sills et al. 2022 we used it to simulate a possible future of the Orion nebula cluster based on observed gas- and star distributions.\n", | |
"\n", | |
"Ekster is still being developed, and currently requires some manual attention - please contact me if you want to try it!" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "7e6a9b1f-2884-4df7-9455-da578b2f6329", | |
"metadata": { | |
"jp-MarkdownHeadingCollapsed": true | |
}, | |
"source": [ | |
"## Extra cells" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "20b2e8c2-6db9-4bf6-8202-7575d441f682", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Extra cell - this is how to simulate a full star cluster with just a gravity code\n", | |
"\n", | |
"converter = nbody_system.nbody_to_si(\n", | |
" single_stars.total_mass() + binary_stars.total_mass(),\n", | |
" 0.01 | units.Myr\n", | |
")\n", | |
"\n", | |
"# We can simulate the cluster with the 'Ph4' code (Parallel Hermite 4th order),\n", | |
"# as long as the binaries aren't very tight.\n", | |
"# If they are, Ph4 will slow down to a crawl as the required timestep becomes too small.\n", | |
"# We then need to find another solution - like Multiples (below).\n", | |
"# The `number_of_workers` keyword indicates how many processes we will use for Ph4.\n", | |
"from amuse.community.ph4 import Ph4\n", | |
"grav = Ph4(converter, number_of_workers=6)\n", | |
"s_in_grav = grav.particles.add_particles(single_stars)\n", | |
"b_in_grav = grav.particles.add_particles(binary_stars)\n", | |
"\n", | |
"time_start = time.time() | units.s\n", | |
"grav.evolve_model(0.01 | units.Myr)\n", | |
"time_end = time.time() | units.s\n", | |
"print(f\"This took {time_end-time_start}\")\n", | |
"\n", | |
"# A channel is a way to copy updated properties from an in-code particle set back to our model.\n", | |
"\n", | |
"channel = b_in_grav.new_channel_to(binary_stars)\n", | |
"channel.copy()\n", | |
"channel = s_in_grav.new_channel_to(single_stars)\n", | |
"channel.copy()\n", | |
"grav.stop()\n", | |
"\n", | |
"# Note how the binary progressed in its orbit while the cluster as a whole is basically unchanged\n", | |
"# - this illustrates how much the timescales differ.\n", | |
"starplot = plot(binary_stars | single_stars, binary_stars)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "974ee08d", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Extra cell - this is how to simulate a full star cluster with Multiples\n", | |
"\n", | |
"converter = nbody_system.nbody_to_si(\n", | |
" single_stars.total_mass() + binary_stars.total_mass(),\n", | |
" 0.01 | units.Myr\n", | |
")\n", | |
"\n", | |
"grav = GravityWithMultiples(\n", | |
" binary_stars | single_stars,\n", | |
" gravity=Ph4, smalln=Smalln, kepler=Kepler,\n", | |
" converter=converter,\n", | |
" number_of_workers=6,\n", | |
")\n", | |
"time_start = time.time() | units.s\n", | |
"grav.evolve_model(0.01 | units.Myr)\n", | |
"time_end = time.time() | units.s\n", | |
"print(f\"This took {time_end-time_start}.\")\n", | |
"channel = grav.particles.new_channel_to(binary_stars)\n", | |
"channel.copy()\n", | |
"channel = grav.particles.new_channel_to(single_stars)\n", | |
"channel.copy()\n", | |
"grav.stop()" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "ea1a3fc8", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# Let's plot the system and the binary again\n", | |
"starplot = plot(binary_stars | single_stars, binary_stars)" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "fff11c43", | |
"metadata": {}, | |
"source": [ | |
"Below are some potentially useful methods/functions, without much explanation - mostly here to remember that they exist. Some are very slow so execute with caution!" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "99856d63", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# the 'get_binaries' method will search for binaries the hard way - use\n", | |
"# with caution and probably never use it on a large particle set!\n", | |
"# it will only return binaries of a specified (or default) 'hardness'\n", | |
"\n", | |
"stars_in_ph4 = grav.particles\n", | |
"q = stars_in_ph4.get_binaries() # control via 'hardness' keyword\n", | |
"print(len(q))" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"id": "7216706e", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"# use this function to extract the orbital parameters from a binary.\n", | |
"# the module has other useful functions for dealing with binaries.\n", | |
"from amuse.ext.orbital_elements import get_orbital_elements_from_binary\n", | |
"\n", | |
"mass1, mass2, a, e, c_o_ta, c_o_inc, c_o_lotan, c_o_aop = get_orbital_elements_from_binary(\n", | |
" binary_stars[0] + binary_stars[number_of_binaries]\n", | |
")\n", | |
"print(mass1, mass2, a.in_(units.au), e)" | |
] | |
} | |
], | |
"metadata": { | |
"kernelspec": { | |
"display_name": "Python 3 (ipykernel)", | |
"language": "python", | |
"name": "python3" | |
}, | |
"language_info": { | |
"codemirror_mode": { | |
"name": "ipython", | |
"version": 3 | |
}, | |
"file_extension": ".py", | |
"mimetype": "text/x-python", | |
"name": "python", | |
"nbconvert_exporter": "python", | |
"pygments_lexer": "ipython3", | |
"version": "3.10.10" | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 5 | |
} |
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