New Chemkin Webapp Github Repository
There are two ways to use our chemical kinetics library:
- Download and install this repository by following the instructions in the Library Installation section below.
- Visit our new Chemkin Webapp and upload your properly formatted .xml reactions file.
For more details about correctly formatting the input file, please refer to the sample input file.
Introduction:
Please refer to the table below for equation symbols and their meaning
For more in-depth information regarding chemical kinetics, please visit the "Chemical kinetics" Wikipedia page.
The purpose of this library is to return the reaction rate of a system of N species undergoing M reactions. The reactions can be reversible or irreversible, and should be elementary of the form:
Irreversible:
Reversible:
The progress rate for each reaction is given by:
The reaction rate of each specie i in an irreversible reaction can be written as:
The reaction rate coefficient for each specie in an elementary reversible reaction j can be written as:
where:
P0 is the pressure of the reactor (we will use 100,000 Pa in this library). Using the NASA polynomial coefficients and relationships between specific heat, enthalpy and entropy, we use the following equations to compute the backwards reaction rate coefficient for elementary reversible reactions:
This library will read in the relevant NASA polynomial coefficients from an SQL database and store them in a data structure based on which species the user specifies in the .xml input file. See more about input files below in the Input Format section.
All the code related to this library can be found in this repository. This includes the NASA polynomial coefficients stored as an SQL database, nasa.sqlite, used to calculate the backwards reaction rate coefficients for reversible elementary reactions.
To install this library and run the test suite:
- Download or clone this repository.
- Using your terminal, navigate to the local
cs207-FinalProjectfolder. - Enter
python setup.py install- This will install the library. - Enter
python setup.py test- This will run the library's test suite. - You are now ready to start calculating reaction rates.
See the Input Format and Basic Usage and Examples sections below for more step-by-step instructions.
The data of the relative reactions must be stored in an .xml file.
The user needs to have a <phase> tag to specify a list of species involved in the reaction. Pay particular attention to the reversible="no" or reversible="yes" in the <reaction> tag when specifying reaction types. The order should be consistent with the input for concentrations when a user calculates the reaction rates.
The second tag of the .xml file needs to store reaction information inside the <reactionData> tag. This library's parser supports multiple <reactionData> tags when parsing the .xml file.
The user also needs to specify reaction temperature.
For more details of correctly formatting the input file, please refer to this sample input file.
If the .xml file is not properly formatted, the parser.py will print a warning and return an empty data structure to the user.
After cloning this repository:
-
Follow installation instructions above:
python setup.py install,python setup.py test. -
Create the reaction system directly from an .xml data file (see 3.1), obtain reaction data by parsing a properly formatted .xml file using the
read_data()function (see 3.2), or manually create reactions using the constructor in theReaction()class.
3.1 To create a reaction system directly from a properly formatted .xml input file, use the following code. The 'rxns_reversible.xml' file is found in the 'tests' folder of this repository.
>>> from chem3.chemkin import *
>>> from chem3.parser import *
>>> concs = [2., 1., .5, 1., 1., .5, .5, .5] #reactant concentrations
>>> T = 900 #temperature
>>> system = ReactionSystem(filename='rxns_reversible.xml') #local reaction .xml file
>>> # calculate reaction rates
>>> reaction_rates = system.reaction_rate(concs, T)
>>> reaction_rates
[7.58794849e+15 -7.55388022e+15 -7.87055958e+15 3.01455401e+13 1.88251730e+14 7.73916703e+15 -8.79625439e+13 -3.31104554e+13]
3.2 To calculate the reaction rate of a system, you must specify the current concentration of each species and the temperature under which the reaction takes place. The order of the concentrations will be matched to the order of the reactants list obtained from the .xml file.
>>> from chem3.chemkin import *
>>> from chem3.parser import *
>>> import os
>>> # parse data from xml file
>>> db_file = os.path.join(os.path.dirname(chem3.__file__), 'nasa.sqlite')
>>> data = read_data('rxns_reversible.xml', db_file)
>>> # specify concentration list and current temperature
>>> concs = [2., 1., .5, 1., 1., .5, .5, .5]
>>> T = 1500
>>> # create a system of the reactions
>>> system = ReactionSystem(data['reactions']['hydrogen_air_mechanism'], data['species'], data['low'], data['high'], data['T_cutoff'], data['T_range'])
>>> # calculate reaction rates
>>> reaction_rates = system.reaction_rate(concs, T)
>>> reaction_rates
[2.23407833e+14 -3.53181969e+14 -2.11084849e+14 3.52252690e+13 4.70006140e+13 3.84606136e+14 -7.51713182e+13 -5.08017161e+13]
Note: The order the user inputs reaction concentrations will be matched to the reactants pulled from the <phase> tag in the .xml file.
To uninstall this library, open a terminal window and enter pip uninstall chem3.
The newest exciting feature of this library is an accompanying webapp found at http://chemkin.pythonanywhere.com/. The webapp includes all the code inherent to this library, but offers the convenience of a browser based application and eliminates the need to install this library ahead of time. You can upload a properly formatted .xml file just like with the library and receive the same reaction rate outputs as using this library.
Webapp Usage:
Navigate to the webapp homepage using your browser of choice:
Upload a properly formatted .xml file using the 'Choose File' button and click 'SUBMIT'. If your file is not properly formatted, you will receive an 'Incorrect file format!' message. After uploading, your reactions will be displayed in the 'REACTION SYSTEM' column as shown below:
Input temperatures (within the NASA coefficient temperature range for each species) as well as species concentrations (in the same order as the .xml input file) using the gray 'example' input as a guide and click 'CALCULATE.' You will receive applicable error messages if you leave an input box blank, your temperature is outside the coefficient range, or your concentrations are too short, long, or strings. Your system reaction rates will be displayed in the right column as shown below.
We hope you enjoy this new user-friendly feature.
Motivation and Description:
The primary motivation for providing users of this library a webapp is that it can offer users with little or no knowledge of python the ability to run their chemical kinetics calculations with confidence from a familiar looking web-based user-interface.
Our webapp is a user-friendly chemical kinetics reaction rate tool with the same underlying functionality of this python library. Users will be restricted to specific inputs and offered hints or recommendations directly in the webapp to ensure they use the underlying library correctly.
Most users will be familiar with webapps from their day-to-day use of modern operating systems and web browsers, so adding a webapp to accompany this library makes sense from a basic usability standpoint.
Implementation Details
All webapp implementation code can be found at this Github Repository. We used a separate repository for the webapp implementation in order to ensure proper indication from the Travis CI and Coveralls badges of this repository.
The webapp is hosted by pythonanywhere and uses their internal terminal to employ the same installation procedure as this library along with the necessary html and webapp-specific python files to allow it to function in the browser.
In order to implement our webapp, we relied heavily on the Flask python microframework. More information about Flask can be found here.
The webapp uses a combination of python, html, javascript, and css to both look nice and provide the same functionality as the underlying chemical kinetics python library. The app.py module was specifically written to interface with our 'chem3' library and feed the html and javascript information to render on the site. App.py includes new methods 'get_data(),' 'get_rates(),' 'allowed_file(),' 'home(),' and 'upload_data().' The 'base.html' and 'test.html' contain the basic web-design framework, and use the 'grascale.js' javascript library for overall website design and animation implementation.