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MCSim User' Manual

Table of Contents

1. Software License

1.1 PREAMBLE
1.2 TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

2. Overview

2.1 General procedure
2.2 Types of simulations
2.3 Major changes introduced with version 4.2.0

3. Installation

3.1 System requirements
3.2 Distribution
3.3 Machine-Specific Installation

4. Working Through an Example
5. Defining Models

5.1 Using Mod to process model description files
5.2 Syntax of the model description file

5.2.1 General syntax
5.2.2 Global parameter declarations
5.2.3 Special functions
5.2.4 Input functions
5.2.5 Dynamics specifications
5.2.6 Parameter scaling
5.2.7 Output calculations
5.2.8 Comments on style
5.2.9 Note about models

6. Specifying Simulations

6.1 Using the compiled program
6.2 Syntax of the simulation definition file
6.3 Global specifications

6.3.1 SimType() specification
6.3.2 Integrate() specification
6.3.3 OutputFile() specification
6.3.4 MonteCarlo() specification
6.3.5 Distrib() specification
6.3.6 MCMC() specification
6.3.7 SetPoints() specification

6.4 Specifying basic conditions to simulate

6.4.1 Experiment definition
6.4.2 StartTime() specification
6.4.3 Print() specification
6.4.4 PrintStep() specification
6.4.5 Data() specification

6.5 Specifying a statistical model

6.5.1 Level definition

6.6 Analyzing results
6.7 Error Handling

Bibliographic References
7. Common Pitfalls
A. Using make
B. Examples

B.1 `linear.model'
B.2 `1cpt.model': A sample model description file
B.3 `perc.model': A sample model description file
B.4 `perc.lsodes.in'

Concept Index