Contents

• List of Figures
• List of Tables
• 1 Introduction
• 2 Basic Equations
• 3 Program Files, Installation, Compilation
  • 3.1 Quickstart: How to Compile CO5BOLD
  • 3.2 Compilation Procedure for CO5BOLD
  • 3.3 Directory Structure
  • 3.4 Old Setup File for Paths
  • 3.5 Fortran Files
  • 3.6 Configure Script
  • 3.7 Compiler Macros
  • 3.8 Optimization, Compiler Switches
    • 3.8.1 Cray: SV1
    • 3.8.2 Compaq: alpha
    • 3.8.3 Hewlett-Packard: V2500
    • 3.8.4 Hewlett-Packard: Itanium 2
    • 3.8.5 Hitachi
    • 3.8.6 Linux: PGI Compiler
    • 3.8.7 Linux: Intel Compiler
    • 3.8.8 NEC SX-5
    • 3.8.9 SGI: Origin
    • 3.8.10 Sun: SunFire
  
  
• 4 UIO Data Format
  • 4.1 Quickstart: Introduction to UIO
  • 4.2 Example of UIO Data File
  • 4.3 Structure of UIO Files
    • 4.3.1 Data Representation: ASCII or Binary
    • 4.3.2 Data File Structure
    • 4.3.3 Tables
    • 4.3.4 Recommendations for Standard File Structure
  • 4.4 Files & Directories & Paths
  • 4.5 Fortran90
    • 4.5.1 Files
    • 4.5.2 Use of UIO Modules in Fortran90
    • 4.5.3 Compiling and Makefiles
    • 4.5.4 Sample Calls of Fortran UIO Routines
  • 4.6 UNIX Scripts
    • 4.6.1 Quick Examination of Files: uiolook
    • 4.6.2 Transformation of Files: uiocat
    • 4.6.3 Information about Conversion Types: uioinfo
  • 4.7 IDL UIO Routines
    • 4.7.1 Initialization of UIO Routines under IDL
    • 4.7.2 Reading Data with uio_data.pro
    • 4.7.3 Reading Data with uio_dataset_rd.pro or uio_datasetlist_rd.pro
  
  
• 5 Control and Data Files
  • 5.1 Model Files: rhd.sta, rhd.end, rhd.full
  • 5.2 File with Additional Data: rhd.mean
    • 5.2.1 Organization of rhd.mean File
    • 5.2.2 Contents of Individual rhd.mean File Entry
  • 5.3 Parameter File: rhd.par
    • 5.3.1 Quickstart: How to Make a Proper Parameter File
    • 5.3.2 Header
    • 5.3.3 Fundamental Model Parameters
    • 5.3.4 Boundary Conditions
    • 5.3.5 Equation of State
    • 5.3.6 Opacities
    • 5.3.7 Hydrodynamics Control
    • 5.3.8 Tensor Viscosity Control
    • 5.3.9 Dust/Molecules
    • 5.3.10 Radiation Transport Control
    • 5.3.11 Process Time Management
    • 5.3.12 Time Step Control
    • 5.3.13 Input/Output Control
    • 5.3.14 Additional Information, Obsolete and Test Parameters
  • 5.4 Additional Control and Status Files: rhd.stop, rhd.cont, and rhd.done
  • 5.5 Text Output: rhd.out
  
  
• 6 Running a Simulation
  • 6.1 Quickstart: How to Run CO5BOLD
  • 6.2 Running CO5BOLD on a Machine with Batch System
  
  
• 7 Data Analysis with IDL
  • 7.1 Preparations
  • 7.2 CO5BOLD Data in IDL
    • 7.2.1 Loading the Parameter File
    • 7.2.2 Loading CO5BOLD Data (.full, .sta, .end)
    • 7.2.3 Loading the Equation of State
    • 7.2.4 Loading the Opacity Table
    • 7.2.5 Computation of Deduced Quantities
  • 7.3 IDL Data Structure
  • 7.4 More IDL routines
  
  
• 8 Glossary
• Index
• About this document ...