load input files from subfolder

[Xenhua Zhang]

Dear Toon,

I am loading the vasp files CONTCAR and OUTCAR from the sub-folders as you can see from the attached script.

I am getting an error:

Traceback (most recent call last):
  File "script_kinetics.py", line 30, in <module>
    tm = ThermodynamicModel(pf_IS, pf_FS)
  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/chemmod.py", line 315, in __init__
    self._add_pfs(pfs_react, -1)
  File "/home/xenhua/anaconda3/envs/py27/lib/python2.7/site-packages/tamkin/chemmod.py", line 77, in _add_pfs
    for pf in pfs:
TypeError: 'PartFun' object is not iterable

Could you please point me to where I am making a mistake in this script. Thank you so much.

Best regards

Xenhua

[Toon Verstraelen]

Dear Xenhau,

Could you try changing the following line:

tm = ThermodynamicModel(pf_IS, pf_FS)

into 

tm = ThermodynamicModel([pf_IS], pf_FS)

?

Best regards,

Toon

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[Xenhua Zhang]

Dear Toon,

I would like to inform you that I have made the script (attached) to work successfully for me. Thank you for your tips.

However, I would like to point out to you that the thermodynamic model line only worked when both the [pf_IS] and [pf_FS] are enclosed in square brackets. (are made into lists?)

It gets more complicated when the kinetic model method is introduced in the script. "km = KineticModel([pf_IS], [pf_TS])" does not work with both pfs included in square brackets. They don't work even when both are not in square brackets, "km = KineticModel(pf_IS, pf_TS)". It works only in the case when initial state pf is in square brackets and the pf of transition state isn't, "km = KineticModel([pf_IS], pf_TS)"

It will be much better to have similar syntax for both Thermodynamic and  Kinetic Model methods.

Best regards,

Xenhua

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CAB9k2Yk7bswzR34v0XDjC1vQH%2Bqum%3Dwry94%3DZFRWa_VPTErtkA%40mail.gmail.com.

[Toon Verstraelen]

Hi Xenhua,

I was indeed mixing up the two. This API is currently defined this way because (as far as I know), there is no case where multiple partition functions for a transition state would make sense. If you know exceptions, please let me know.

Best regards,

Toon

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CADzbQDD%2B9_W81As7Fo%2B3P52dy2X23Z1SOifq%2B4juhPrvUA8eFA%40mail.gmail.com.

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