Contents

• List of figures
• List of tables
• 1. Introduction
• 2. Equations
  • 2.1 Basic equations
  • 2.2 Magnetohydrodynamics (W. Schaffenberger)
  • 2.3 A collection of thermodynamic relations (M. Steffen, AIP)
    • 2.3.1 Basic thermodynamic equations
    • 2.3.2 Definition of often-used thermodynamic coefficients
    • 2.3.3 CO5BOLD equation of state
    • 2.3.4 Derived thermodynamic coefficients
    • 2.3.5 Ideal gas with constant specific heats (polytropic gas)
  
  
• 3. CO5BOLD file overview
  • 3.1 Fortran directories
  • 3.2 Fortran files
  • 3.3 Script files
  • 3.4 Documentation files
  
  
• 4. Compilation & installation
  • 4.1 Quickstart: How to compile CO5BOLD
  • 4.2 Compilation procedure for CO5BOLD
  • 4.3 Configure script
    • 4.3.1 Control environment variables
  • 4.4 Compiler macros
    • 4.4.1 General
    • 4.4.2 Input/output with UIO
    • 4.4.3 Equation of state
    • 4.4.4 Opacity
    • 4.4.5 Hydrodynamics (Roe solver)
    • 4.4.6 Hydrodynamics (tensor viscosity)
    • 4.4.7 Radiation transport
    • 4.4.8 Obsolete macros
  • 4.5 Optimization, compiler switches
    • 4.5.1 OpenMP settings
    • 4.5.2 Vectorization
    • 4.5.3 Cache usage
    • 4.5.4 Inlining
    • 4.5.5 Single versus double precision
  • 4.6 Specific machines & compilers
    • 4.6.1 Cray: SV1
    • 4.6.2 Compaq: alpha
    • 4.6.3 Hewlett-Packard: V2500
    • 4.6.4 Hewlett-Packard: Itanium 2
    • 4.6.5 Hitachi SR8000
    • 4.6.6 IBM
    • 4.6.7 Linux: PGI compiler
    • 4.6.8 Linux: Intel compiler
    • 4.6.9 Linux: PathScale compiler
    • 4.6.10 Linux: GNU g95 compiler
    • 4.6.11 Linux: GNU gfortran compiler
    • 4.6.12 NEC SX-5, SX-6, SX-8
    • 4.6.13 SGI: Origin
    • 4.6.14 SGI: Origin 2000/3800 at UKAFF
    • 4.6.15 Sun: SunFire
  
  
• 5. Programmer's guide
  • 5.1 General code organization
  • 5.2 Indentation and spaces
    • 5.2.1 General layout and indentation recommendations
    • 5.2.2 Alignment of assignments and equations
    • 5.2.3 Normal code indentation
    • 5.2.4 Further recommendations
  • 5.3 Naming conventions
    • 5.3.1 File names
    • 5.3.2 Program names
    • 5.3.3 Names of modules, subroutines, and functions
    • 5.3.4 Variable names
  • 5.4 Comments
    • 5.4.1 Header of files
    • 5.4.2 Header of modules
    • 5.4.3 Header of subroutines and functions
    • 5.4.4 Comment lines
    • 5.4.5 Short comments after Fortran statements
  • 5.5 Compiler switches and directives
    • 5.5.1 OpenMP
    • 5.5.2 Compiler directives
    • 5.5.3 Compiler macros or switches
  • 5.6 Unit tests
    • 5.6.1 F90_UNIT
  
  
• 6. Data file types
  • 6.1 File overview
  • 6.2 UIO data format
    • 6.2.1 Quickstart: Introduction to UIO
    • 6.2.2 Example of UIO data file
    • 6.2.3 Structure of UIO files
    • 6.2.4 Files & directories & paths
    • 6.2.5 Fortran90
    • 6.2.6 UNIX scripts
    • 6.2.7 IDL UIO routines
  
  
• 7. Input and control files
  • 7.1 Parameter file: rhd.par
    • 7.1.1 Quickstart: How to make a proper parameter file
    • 7.1.2 Header
    • 7.1.3 Fundamental model parameters
    • 7.1.4 Boundary conditions (general)
    • 7.1.5 Boundary conditions (MHD only)
    • 7.1.6 Equation of state
    • 7.1.7 Opacities
    • 7.1.8 Hydrodynamics control (HD and MHD)
    • 7.1.9 Hydrodynamics control (HD only)
    • 7.1.10 Hydrodynamics control (MHD only)
    • 7.1.11 Tensor-viscosity control
    • 7.1.12 Dust/molecules/hydrogen ionization: General
    • 7.1.13 Dust: dustscheme=dust_moment04_c2
    • 7.1.14 Dust: dustscheme=dust_k3mon_03
    • 7.1.15 Dust: dustscheme=dust_bins_01
    • 7.1.16 Radiation-transport control (general)
    • 7.1.17 Radiation-transport control (MSrad only)
    • 7.1.18 Radiation-transport control (LHDrad only)
    • 7.1.19 Process-time management
    • 7.1.20 Time-step control
    • 7.1.21 Input/output control
    • 7.1.22 Scale and test parameters
    • 7.1.23 Additional information and obsolete parameters
  • 7.2 Input model file: rhd.sta
  • 7.3 EOS file
  • 7.4 Opacity file
  • 7.5 Chemistry input
  • 7.6 HION input
  • 7.7 More control files: rhd.stop, rhd.cont, rhd.dump
  
  
• 8. Output and status files
  • 8.1 Output model files: rhd.end, rhd.full
  • 8.2 Files with additional chunks of data: rhd.chu1, rhd.chu2, rhd.chu3
  • 8.3 Files with averaged data: rhd.mean
  • 8.4 File with azimuthally averaged data: rhd.mcyl
  • 8.5 HION output
  • 8.6 Text output: rhd.out
  • 8.7 Additional status and output files: rhd.done, rhd.snap
  
  
• 9. Running a simulation
  • 9.1 Quickstart: How to run CO5BOLD
  • 9.2 Using a batch system
  
  
• 10. Data analysis with IDL
  • 10.1 Preparations
  • 10.2 CO5BOLD data in IDL
    • 10.2.1 Loading the parameter file
    • 10.2.2 Loading CO5BOLD data (.full, .sta, .end, .chu1)
    • 10.2.3 Loading the equation of state
    • 10.2.4 Loading the opacity table
    • 10.2.5 Computation of deduced quantities
  • 10.3 IDL data structure
  • 10.4 More IDL routines
  
  
• 11. Document history
• 12. Glossary
• 13. Trademarks
• Bibliography
• Index