A tool for exploring chemical kinetics and dynamics in elementary reaction systems.
Lines starting with the hash (#) is a single line comment.
# Comment
Species in excess, initial conditions, and numerical constants are defined as follows.
EXCESS H2O
INITIAL H 1.29
CONSTANT PI 3.14159
Reactions are defined in familiar-looking form which must be a single line.
A ==> B
Above reaction implies law of mass action with unity reaction rate. The reaction rate can be given explicitly by appending the line with the vertical bar (|) and the reaction rate, either a numeric or a constant.
A ==> B | 1E-5
Exceptions to mass action kinetics is also supported in the following form by using the at sign (@).
H2Q + BrO2 + BrO2 ==> HBrO2 + HBrO2 + Q @ K6*H2Q*BrO2
Numerical parameters for the simulation are defined by lines starting
with the SIMULATION keyword.
SIMULATION NAME example_simulation
SIMULATION PLOT X
SIMULATION RUN 1
SIMULATION T_END 55
SIMULATION T_POINTS 10
SIMULATION ATOL 1.1E-13
SIMULATION RTOL 1.1E-13
SIMULATION MAXIMUM_STEP_SIZE 0.01
In above example, the time range is equivalent to Octave syntax
linspace(0, 55, 55*10).
The LATEX keyword specifies formatting mapping.
LATEX H2O H_{2}O
Bibliography items can be specified as follows.
BIBITEM TestSet \url{https://www.dm.uniba.it/~testset}
Refer to the files in examples directory for complete simulations.
All contributions are welcome. Bug reports, suggestions and feature requests can be reported by creating a new issue. Code and documentation contributions should be provided by creating a pull request (here is a good tutorial). Use imperative in commit messages.
Licensed under the GNU General Public License Version 3, refer to the file LICENSE for more information.