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CO5BOLD User Manual
Bernd Freytag - Matthias Steffen - Sven Wedemeyer-Böhm - Hans-Günter Ludwig
3 May 2004
Contents
List of Figures
List of Tables
1 Introduction
2 Equations
2.1 Basic Equations
2.2 A collection of thermodynamic relations (M. Steffen, AIP)
2.2.1 Basic thermodynamic equations
2.2.2 Definition of often-used thermodynamic coefficients
2.2.3 CO5BOLD equation of state
2.2.4 Derived thermodynamic coefficients
2.2.5 Ideal gas with constant specific heats (polytropic gas)
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 General: OpenMP settings
3.8.2 General: Inlining
3.8.3 Cray: SV1
3.8.4 Compaq: alpha
3.8.5 Hewlett-Packard: V2500
3.8.6 Hewlett-Packard: Itanium 2
3.8.7 Hitachi SR8000
3.8.8 IBM
3.8.9 Linux: PGI Compiler
3.8.10 Linux: Intel Compiler
3.8.11 NEC SX-5
3.8.12 SGI: Origin
3.8.13 SGI: Origin 2000/3800 at UKAFF
3.8.14 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 Installation of UIO UNIX Scripts
4.6.2 Quick Examination of Files: uiolook
4.6.3 Transformation of Files: uiocat
4.6.4 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 Document history
9 Glossary
10 Trademarks
Index
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