Command Line Interface Usage

In this form, we provide one executable named dune-copasi for running forward simulations from the command line. This executable is completely configurable from the command line arguments passed to it.

Configuration options

By running the program with the command line arguments --help or --help-full, it will result in the possible configuration options to run the program:

Command Line Interface of DuneCopasi

~$ dune-copasi --help
USAGE: dune-copasi [options]

Numerical simulator for diffusion-reaction systems on single or multiple compartments

Website: <https://dune-copasi.netlify.app>

OPTIONS:

-h / --help - Display this help.
--help-full - Display this help with long descriptions.
--version - Display the version of this program.
--parser-default - Display the default parser.
--parser-list - Display the parsers available for this program.
--dimension-list - Display the grid dimensions available for this program.
--dump-config - Dumps configuration in the INI format to stdout.
--config=<string> - Specifies a config file in INI format. See Configuration Options.
--{key}={value} - Overrides key=value sections of the config file. See Configuration Options.

...
~$

Alternatively, this online documentation also has the list of possible configuration options.

Version

By running the program with the command line argument --version, you can find out the installed version of DuneCopasi:

Getting DuneCopasi version

~$ dune-copasi --version
2.0.0
~$

Running the program

working directory

Be aware that the output files produced by DuneCopasi are relative to the directory where dune-copasi is started, hence, it is recommended to run the program within a working directory, for example ~/dune-copasi.

When passing configuration options to the command line arguments like --config={path}, or --{key}={value}, the simulation will start and the program will stream its log output into the terminal:

Running DuneCopasi

~/dune-copasi$ dune-copasi --config=config.ini
[2024-03-21 12:38:32.479] [info] Reading configuration file '~/dune-copasi/config.ini'
[2024-03-21 12:38:32.479] [info] Starting dune-copasi (version: 2.0.0)
[2024-03-21 12:38:32.580] [info] Axis names are set to: ["x", "y", "z"]
...
...
[2024-03-21 12:38:32.723] [info] dune-copasi successfully finished :)
~/dune-copasi$