Astrophysical Recipes: The Art of AMUSE

Astrophysical Recipes: The Art of AMUSE
	Preface
	Acknowledgements
	Author biographies
		Simon Portegies Zwart
		Steve McMillan
Chapter 1: What is Computational Astrophysics?
	1.1 Computational Astrophysics
		1.1.1 Origin of This Book
		1.1.2 Hands-on is Hands-on
		1.1.3 What about the Math?
		1.1.4 Objective of This Book
		1.1.5 What is Missing from This Book
		1.1.6 Outline of the Book
	1.2 A Brief History of Simulations in Astrophysics
		1.2.1 The First Simulation Experiments
	1.3 Software Used in This Book
		1.3.1 Motivation for a Homogeneous Software Environment
		1.3.2 Choice of Programming Languages
		1.3.3 Design of AMUSE
		1.3.4 Terminology
		1.3.5 Installing AMUSE
		1.3.6 Running AMUSE
	1.4 Initial Conditions
		1.4.1 Particles and Particle Sets
		1.4.2 The Solar System
		1.4.3 The Plummer Sphere
		1.4.4 The Initial Mass Function
		1.4.5 Stellar Evolution
		1.4.6 Hydrodynamical Models
	References
Chapter 2: Gravitational Dynamics
	2.1 In a Nutshell
		2.1.1 Equations of Motion for a Self-gravitating System
		2.1.2 Gravitational Time Scales
		2.1.3 Star Cluster Dynamics
		2.1.4 Physics of the Integrator
	2.2 N-body Integration Strategies
		2.2.1 Global Structure of an N-body Code
		2.2.2 Types of N-body Code
		2.2.3 Discretization Strategies in N-body Simulations
	2.3 Gravity Solvers in AMUSE
		2.3.1 Generating Initial Conditions
		2.3.2 Specifying and Initializing the Gravity Solver
		2.3.3 Setting and Getting Parameters in a Community Code
		2.3.4 Feeding Particles to the N-body Code
		2.3.5 Evolving the Model to the Desired Time
		2.3.6 Retrieving Data from the N-body Code
		2.3.7 Storing and Recovering Data
		2.3.8 Using Other Units
		2.3.9 Interrupting the N-body Integrator
	2.4 Examples
		2.4.1 Integrating the Orbits of Venus and Earth
		2.4.2 Small Cluster with Stellar Collisions
		2.4.3 Secular Multiples
		2.4.4 Merging Galaxies
	2.5 Validation
		2.5.1 Error Propagation and Validation
	2.6 Assignments
		2.6.1 Orbital Trajectories
		2.6.2 Vostok
		2.6.3 Dynamical Binary Formation
		2.6.4 L1 Lagrangian Point
		2.6.5 Virial Equilibrium
	References
Chapter 3: Stellar Structure and Evolution
	3.1 In a Nutshell
		3.1.1 Stellar Time Scales
		3.1.2 Physics of the Interior
		3.1.3 Final Stages of Stellar Evolution
	3.2 Simulating Stellar Evolution
		3.2.1 Stellar Evolution Modules in AMUSE
		3.2.2 Improving the Stellar Evolution Solver
		3.2.3 Evolving an Inhomogeneous Stellar Population
		3.2.4 Multiprocessing Codes
		3.2.5 Enforcing Stellar Mass Loss/Gain
		3.2.6 Accessing Stellar Interiors
		3.2.7 Modeling Stellar Mergers
		3.2.8 Interrupting Stellar Evolution
		3.2.9 Binary Evolution
		3.2.10 Reading and Writing Binary Evolution Files
	3.3 Examples
		3.3.1 Response of a Star to Mass Loss
		3.3.2 Blue Stragglers in M67
	3.4 Validation
	3.5 Assignments
		3.5.1 Stellar Comparison
		3.5.2 Ages of the M67 Blue Stragglers
		3.5.3 Constructing Isochrones
	References
Chapter 4: Elementary Coupling Strategies
	4.1 Multiphysics Problems
	4.2 Combining Two or More Solvers
		4.2.1 Combining Gravity with Stellar Evolution
		4.2.2 Evolution of a Hierarchical Triple System
		4.2.3 Dedicated Channels and Copy Operations
		4.2.4 Particle Subsets and Supersets
	4.3 Analysis Tools
		4.3.1 The Hop Package
		4.3.2 The Kepler Package
	4.4 Multi-code Strategies
		4.4.1 Basic Collision Handling
		4.4.2 Using a Separate Code to Manage a Collision
		4.4.3 Recovering from a Code Crash
		4.4.4 Event-driven Simulations
	4.5 The multiples Module
	4.6 Examples
		4.6.1 Small Cluster with Disk-destroying Encounters
		4.6.2 Stellar and Binary Evolution with Stellar Dynamics
	4.7 Validation
	4.8 Assignments
		4.8.1 Interlaced Time-stepping
		4.8.2 Stellar Evolution and Dynamics
		4.8.3 Multiple Stellar Populations
	References
Chapter 5: Hydrodynamics
	5.1 In a Nutshell
		5.1.1 Underlying Equations
		5.1.2 Turbulence and Shocks
		5.1.3 Hydrodynamical Time Scales
		5.1.4 Hydrodynamical Instabilities
		5.1.5 Physics of the Integrator
	5.2 Hydrodynamics in AMUSE
		5.2.1 Types of Hydrodynamics Code
		5.2.2 Smoothed Particle Hydrodynamics
		5.2.3 Grid-based Methods
		5.2.4 Managing Shocks and Discontinuities
		5.2.5 Initializing a Grid from a Particle Distribution
		5.2.6 Using a Hydro Code to Simulate a Stellar Merger
		5.2.7. Continuing with Hydrodynamics after a Henyey Code Crash
		5.2.8 Extending the Hydrodynamics Solver
	5.3 Examples
		5.3.1 Collapsing Molecular Cloud
		5.3.2 Circumstellar Disk with a Bump
		5.3.3 Colliding Stars
		5.3.4 Accreting from the Wind of a Companion
	5.4 Validation
		5.4.1 Riemann Shock Tube Problem
		5.4.2 Kelvin–Helmholtz Test
		5.4.3 Cloud-shock Test
		5.4.4 Boss–Bodenheimer Test
	5.5 Assignments
		5.5.1 Convergence Test
		5.5.2 Testing the Boss–Bodenheimer Test
		5.5.3 The Dissolving Bump
		5.5.4 Collapsing Molecular Cloud with Sink Particles
		5.5.5 A Star-forming Region
		5.5.6 Neutron Star Hits Companion
		5.5.7 Supernova Explosion
		5.5.8 Hoag’s Object
	References
Chapter 6: Radiative Transfer
	6.1 In a Nutshell
		6.1.1 Underlying Equations
		6.1.2 Physics of the Integrator
	6.2 Radiative Transfer in AMUSE
		6.2.1 Radiative Transfer Modules
		6.2.2 Ionization of a Molecular Cloud
		6.2.3 Coupling Radiative Transfer with Hydrodynamics
	6.3 Examples
		6.3.1 Heating of a Protoplanetary Disk
		6.3.2 Ionization Front in an H2 Region
	6.4 Validation
	6.5 Assignments
		6.5.1 Habitability of a Protoplanetary Disk
		6.5.2 Bumpy disks
	References
Chapter 7: Hierarchical Coupling Strategies
	7.1 Code-coupling Strategies
		7.1.1 The Bridge Method
		7.1.2 Implementation of Bridge
		7.1.3 Higher-order Bridge
	7.2 Using Bridge
		7.2.1 Star Cluster in a Static Galactic Potential
		7.2.2 The Classic Bridge
	7.3 Bridging Other Codes
		7.3.1 Bridge Hierarchies and Hierarchical Bridges
		7.3.2 Bridging Gravity with Hydrodynamics
	7.4 Examples
		7.4.1 Dissolving Star Cluster in the Galactic Potential
		7.4.2 Did the Sun Originate in M67?
		7.4.3 Inspiral of a Binary Star into a Common Envelope
		7.4.4 Budding Planets in a Protoplanetary Disk
		7.4.5 Planetary Systems in Star Clusters
	7.5 Assignments
		7.5.1 Drift with Gravity Code
		7.5.2 How Did the Sun Escape from M67?
		7.5.3 Half Tree Code, Half Direct
		7.5.4 The Accreting Black Hole in HLX-1
		7.5.5 Forming the Widest Binary Stars
	References
Chapter 8: Case Studies
	8.1 Accretion in the Galactic Center from S-star Winds
		8.1.1 Initial Conditions
		8.1.2 The Combined Solver
		8.1.3 Results of the Simulation
	8.2 Supernova Impact on the Early Solar System
		8.2.1 Initial Conditions and Model Parameters
		8.2.2 The Combined Solver
		8.2.3 Radiative Hydrodynamics with Cooling and Heating
		8.2.4 Injection of the Supernova Blast Wave
		8.2.5 The Supernova Blast Wave Hits the Disk
	8.3 Closure
	References
Chapter 9: Epilogue
	Reference
Appendix A: AMUSE Fundamentals
	A.1 The AMUSE Framework
		A.1.1 The Community Module
		A.1.2 The User Script
		A.1.3 Inter-module Data Transfer and Unit Conversion
	A.2 Installing AMUSE
		A.2.1 Downloading AMUSE
		A.2.2 Installing the Prerequisites
		A.2.3 Compiling AMUSE
		A.2.4 Reproducibility with git
		A.2.5 Installing for Python3
		A.2.6 Installing Non-standard Codes
		A.2.7 Tuning Your AMUSE Installation
		A.2.8 Running AMUSE
	References
Appendix B: AMUSE Specifics
	B.1 Internal Parameters and Types
	B.2 Non-tunable Parameters
		B.2.1 Input/Output File Types
		B.2.2 Writing Composite Data Files
		B.2.3 Initial Conditions
		B.2.4 Alternative Converters
		B.2.5 The Huayno Multi-component Symplectic N-body Code
	B.3 Higher-order Bridges
		B.3.1 Hydrodynamical Boundary Conditions
		B.3.2 Debugging in AMUSE
		B.3.3 Stopping Conditions
		B.3.4 Galactic Potential Models
	B.4 Tricks with Units
		B.4.1 Setting Printing Strategies
		B.4.2 The Command-line Argument Parser
	B.5 Plotting
		B.5.1 Basic Plotting in Python
		B.5.2 Plotting with Units
		B.5.3 Additional Plotting Utilities
	B.6 AMUSE Community Modules
		B.6.1 Modules by Domain and Functionality
		B.6.2 Modules by Name
	References
Appendix C: Programming Primer
	C.1. Linux
		C.1.1. A Little awking and grepping
	C.2. Git
	C.3. Python
		C.3.1. Python Types and Printing
		C.3.2. Lists
		C.3.3. Dictionaries
		C.3.4. Flow Control
		C.3.5. Functions
		C.3.6. Lambda Functions
		C.3.7. Importing Packages
		C.3.8. Classes
		C.3.9. Operator Overloading
		C.3.10. Properties
		C.3.11. Testing and Debugging Python Scripts
	References