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Python3 Script check #1840

Merged
merged 7 commits into from Dec 9, 2019
Merged

Python3 Script check #1840

merged 7 commits into from Dec 9, 2019

Commits on Dec 9, 2019

  1. 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
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  2. 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.
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  3. added example for generateChemkimHTML.py 

    An example for scripts/generateChemkimHTML.py is added
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  4. 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.
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  5. Example for generateFluxDiagram is added 

    An example for scripts/generateFluxDiagram.py is added
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  6. added an example for standardizeModelSpeceisNames 

    An exmaple for scripts/standardizeModelSpeceisNames.py is added
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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  7. modified the description for generateTree script 

    A few more lines are added in the description
    @yunsiechung
    yunsiechung committed Dec 9, 2019
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