Chemical Kinetics Simulator: solves the chemical master equation for concentrations over time in a reaction system using elementary chemical kinetic laws.
Consider a chemical system with a set of potential energy surface minima (or chemical species) and a set of transformations (reactions) between the minima.
Given a sufficient description of the transformations and an initial state, kinad solves for the concentration of each species at given points in time.
Uncertainty may be calculated via a monte-carlo method.
List of species/minima
Stoiciometry of transformation
Gibbs Free Activation barrier of transformation (enthalpy barrier may be sufficient but not rigorous [1])
[Optional Uncertainty of Activation Barriers]
Rate law exponents (order) of transformation
See the input template when setting up an input file
Temperature
Initial State
Points in time solved for
Concentration at each point in time
Conversion through each tranformation at each point in time
python kinad [OPTIONS]
-c, --config=CONFIG_FILE Specify configuration file, default is config.ini
All parameters are defined in config.ini and described below:
[parameters]
infile: Name of Input file located in kinad/. For formatting help see input_template.txt or tosh.in (an example)
runname: Name of output folder
tstart, tend, tstep: these three parameters define the points in time solved for. at t=0 the system state is equal to your initial state input.
temp: Temperature of the simulated reaction, a parameter in the rate law equation.
[montecarlo]
montecarlo: 1 to calculate uncertainty via monte-carlo trials, or 0 to run without calculating uncertainties. If 1, your input file must include uncertainty of every activation barrier on the same line separated by a space. [Activation barrier] [Uncertainty]
monteN: The number of monte-carlo trials to run. For rigorous statistics typically 1e3-1e6 trials are needed. Note: calculation time should scale linearly with this parameter
keepmonte: If 1, the results of each individual monte-carlo trial will be kept. If 0, these trial results are deleted.
Generate net flow diagram
[1]: For some systems, frequency calculations to obtain the Gibbs Free Energy barriers rather than Enthalpy barriers are rather expensive, and depending on the system the entropic factor may or may not be negligible. For more information on deciding between enthalpy and gibbs barriers see: http://pubs.acs.org/doi/abs/10.1021/acs.jpca.5b09447