Package: pykinetic
Pykinetic is a project that aims to facilitate the automation and generation
of kinetic and microkinetic models. Pykinetic acts as an intermediate layer
between the user and the mathematical model that is then simulated to obtain the
kinetic data. This functionality can be done either through the use of the
pykinetic python library or through the use of the command line apps:
“pykinetic-model.py” and “pykinetic-scan.py”. The minimal source code to run the
simulation is the output of pykinetic and currently python and c++ are supported.
Compiling and executing that code leads to the simulation of the chemical system.Getting StartedPrerequisitesInstalling the dependenciesInstalling pykineticRunning the testsUninstalling pykineticDeveloped withExamplesAuthorsLicenseGetting StartedThese instructions will get you a copy of the project up and running on your
local machine.Prerequisitespython >= 3.6 (3.7.3 or higher recommended)python library: setuptoolspython library: numpy (optional, needed to run the generated python scripts)python library: scipy (optional, needed to run the generated python scripts)c++ library: boost (optional, needed to run the generated c++ scripts)Note: proper documentation installation of the c++ library is being
currently being reviewed.Installing the dependenciespython3.7 installation in Ubuntu 18.04 LTS$sudoapt-getupdate$sudoapt-getinstallpython3.7python3.7-devIf for any reason it is not reachable:$sudoadd-apt-repositoryppa:deadsnakes/ppa$sudoapt-getupdate$sudoapt-getinstallpython3.7python3.7-devNow you can skip the next step if you don’t want to set up a virtual environment
the lines below correspond to python3.7 but can be also applied to python3.6 or
higher (Remember to change “my_venv” for the actual path of the directory where
you want the virtual environment)$sudoapt-getinstallpython3.7-venv$python3.7-mvenvmy_venv$sourcemy_venv/bin/activateIn the case of creating a virtual environment and running the
previous “source” command, anytime you write “python” it will act as an alias
for “python3.7” or whichever python executable you used for the virtual environment.
(To leave the virtual environment run the “deactivate” command at anytime)If you have not created a virtual environment, all the following commands must
explicitly use the python executable in which you are going to install the
the package.
Now we install the python default installer pip in our virtual environment$python-mpipinstallpip$python-mpipinstall--upgradepip$python-mpipinstallsetuptoolsIf it proceeded without any errors (pip and setuptools should already be
installed) otherwise please check thepipdocumentationNow to install the optional dependencies (Skip if you do not want them):$python-mpipinstallnumpyscipy$sudoapt-getinstalllibboost-devInstalling pykineticGet the source code from github through git and install it.$gitclonehttps://github.com/maserasgroup-repo/pykinetic.gitpykinetic$python-mpipinstallpykinetic/If you do not have git or do prefer to download manually the source
code as a .zip or .tar.gz do it install it.$python-mpipinstallpykinetic-0.1.0.tar.gzNote: If you prefer to unpack it you can do it but it is not neededRunning the testsAfter installing you should be able to run the tests:$python-munittest-vpykinetic.testsUninstalling pykinetic$python-mpipuninstallpykineticDeveloped withpython 3.7.3Ubuntu 16.04 LTS and Ubuntu 18.04 LTSExamplesPlease open theExamples.rstfile in github to visualize the
basic usage examples or read the documentation.AuthorsList of main developers and contact emails:Raúl Pérez-Soto [ORCID,Github,email]Sergio Pablo-García [ORCID,Github,email]María Besora [ORCID,Github,email]Feliu Maseras [ORCID,Github,email]Licensepykinetic is freely available under anMITLicense