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Python3 Script check #1840
Python3 Script check #1840
Commits on Dec 9, 2019
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delete the script and example files no longer use
Reduction example folder is deleted because /rmgpy/reduction/main.py no longer exists. convertFAME.py is also deleted because it is no longer used
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moved all the script example under example/scripts
All the examples related to scripts are moved under a new folder example/scripts. Each bash scripts are changed appropriately to have correct relative paths for each script file. Also, for the examples file that were throwing error, I made somes changes to make them work: 1. generateReactions - This example was origianlly throwing error because surface chemistry was included in the kinetic_family in the input file. The kinetic family is changed to 'default', so it no longer throws error 2. simulate/withoutSensitivity - This example had minor error with default temperature range in chem.inp file. The temperature range in chem.inp file is changed appropriately. 3. thermoEstimator - input.py (run.sh) example had QM on in input file when it was not supposed to. The QM thermoEstimator has its own example (input_QM.py). The quantumMechanics portion in the input.py is deleted.
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added example for generateChemkimHTML.py
An example for scripts/generateChemkimHTML.py is added
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added an example for mergeModels.py
An example for scripts/mergeModels.py is added. The run.sh file contains two examples: merging 2 models and merging 3 models.
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Example for generateFluxDiagram is added
An example for scripts/generateFluxDiagram.py is added
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added an example for standardizeModelSpeceisNames
An exmaple for scripts/standardizeModelSpeceisNames.py is added
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modified the description for generateTree script
A few more lines are added in the description
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