Scripts Usage

pykinetic-model.py

Creates a {python|c++} script that contains a system of mass balance equations (that represent a certain Chemical System) and the tools to solve it numerically.

$ pykinetic-model.py compounds.txt reactions.txt model.py --writer python
$ # After editing the file and including the concentrations and simulation times
$ python model.py
$ # A fast approach to visualize the data generated is with xmgrace
$ # model.data is just a csv file where the first column is the time.
$ xmgrace -nxy model.data

$ pykinetic-model.py compounds.txt reactions.txt model.cpp --writer c++
$ # After editing the file and including the concentrations and simulation times
$ g++ model.cpp -o model.exe
$ ./model.exe

pykinetic-scan.py

Creates a {python|c++} script that contains a system of mass balance equations (that represent a certain Chemical System) and the tools to solve it numerically per each value of a scanned energy/energies of compounds/TSs. Currently it is recommended to do a --dryrun and run each generated model by itself.

$ # it is recommended to use a simulation parameters file
$ pykinetic-scan.py compounds.txt reactions.txt 0.0 0.5 5 --writer python --dryrun --I --simulation sim_params.txt