Tamkin Shows Error "The rotational symmetry number can only be computed when the graph is fully conn

[Jeya Vimalan]

Dear All,

I am trying to work out some examples using TAMKIN+G09.

The reaction i am considering here is

H + CH4 --> H2 + CH3.

Level of calculation is B3LYP/6-31G(d).and used the reaction.py

The error i am seeing here is.

========================================

Traceback (most recent call last):

  File "./reaction.py", line 47, in <module>

    pf_react1 = PartFun(nma_react1, [ExtTrans(), ExtRot()])

  File "/user/e154414/.local/lib/python2.7/site-packages/tamkin/partf.py", line 1353, in __init__

    term.init_part_fun(nma, self)

  File "/user/e154414/.local/lib/python2.7/site-packages/tamkin/partf.py", line 1016, in init_part_fun

    self.symmetry_number = tmp_mol.compute_rotsym()

  File "/user/e154414/.local/lib/python2.7/site-packages/molmod/molecules.py", line 291, in compute_rotsym

    raise ValueError("The rotational symmetry number can only be computed when the graph is fully connected.")

ValueError: rotational: The rotational symmetry number can only be computed when the graph is fully connected.

========================================

Any help would be appreciated.

Best regards,

Vimal

[Toon Verstraelen]

Hi Vimal,

This may be a bug. Can you send me (directly to toon.ver...@gmail.com) the
Gaussian FCHK file that causes trouble? Then I can take a closer look. It is a bit
hard to guess what is exactly going wrong from just the error message.

Best Regards,

Toon

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--
Prof. Dr. ir. Toon Verstraelen
Center for Molecular Modeling
Ghent University
Technologiepark 903,
B9052 Zwijnaarde
Belgium
Tel: +32 9 264 65 56
GSM: +32 471 66 68 83
E-mail: Toon.Ver...@UGent.be
http://molmod.UGent.be/
http://molmod.UGent.be/software/

[Jeya Vimalan]

Prof. Toon, I have sent the files to the email you mentioned.

Thanks.

Vimal

[Mark Fuller]

Has this issue been resolved? I am also using Tamkin and G09 and receiving the same error message when I do not include a rotor in my partition function.

When I include the rotor, I get a different error: "FloatingPointError: hindered_rotor_5_6: invalid value encountered in sqrt"

Thank you,

Dr. Mark E. Fuller, Ph.D.
Physico-Chemical Fundamentals of Combustion
RWTH Aachen University
Schinkelstraße 8
52062 Aachen | GERMANY
Tel: +49 241 80 24239
www.pcfc.rwth-aachen.de

[Toon Verstraelen]

Hi Mark,

You can manually specify the rotational symmetry number if the automatic detection fails. See 

http://molmod.github.io/tamkin/reference/pf.html?highlight=rotational#tamkin.partf.Extort

The automatic procedure is only working well for relatively simple cases.

Does this fully address the issue?

Best regards,

Toon

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Prof. Dr. ir. Toon Verstraelen

Center for Molecular Modeling

Technologiepark-Zwijnaarde 46 (before Jan 1, 2019, this was building 903)

Ghent University

Tech Lane Ghent Science Park Campus A

9052 Zwijnaarde

Belgium

How to reach my office? See https://molmod.ugent.be/where-find-us (2nd floor, CMM, door next to Xerox)

Office: +32 9 264 65 56

Mobile: +32 471 66 68 83

E-mail: Toon.Ver...@UGent.be

http://molmod.UGent.be/

[Mark Fuller]

Explicitly giving the rotational symmetry resolves the error when I do not include a rotor in the partition function, i.e. pf_ts = PartFun(nma_ts, [ExtTrans(), ExtRot(symmetry_number=1.0)])

If I do want to use my rotor calculation, i.e. pf_ts = PartFun(nma_ts, [ExtTrans(), ExtRot(symmetry_number=1.0), rotor_ts]), then I still get the same error as before:

"""

scan_cancel_freq = np.sqrt(force_constant/moment)/(2*np.pi)

FloatingPointError: hindered_rotor_5_6: invalid value encountered in sqrt

"""

Is this perhaps due to Tamkin attempting to manipulate the imaginary frequency owing to this being a transition state?

That frequency would be negative in the log file, so it would be the source of a negative argument

Mark E. Fuller
Robensstraße 57
52070 Aachen
+49 (0)1577-1848188
mark.e...@gmail.com

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[Toon Verstraelen]

Hi Mark,

Sorry for the late reply. This issue you bring up is different from the original problem. 

Your problem is indeed caused by the fact that the curvature of the rotor degree of freedom is negative. This is normally not related to the negative curvature from the transition state. (That degree of freedom is normally never replaced by a rotor.) It rather points to an issue with the relaxed scan used to model the rotor. It could also point to a poorly converged TS optimization. For example, a typical pathology of a TS optimizer is to find an irrelevant TS corresponding to an internal rotation, rather than the reaction of interest.

Best regards,

Toon

To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/CAMxj0KeUPU1-YL07GREoyVVZs38ZOVfLFywL-RAYboVTwjD3sA%40mail.gmail.com.

--

Prof. Dr. ir. Toon Verstraelen

Center for Molecular Modeling

Technologiepark-Zwijnaarde 46 (before Jan 1, 2019, this was building 903)

Ghent University

Tech Lane Ghent Science Park Campus A

9052 Zwijnaarde

Belgium

How to reach my office? See https://molmod.ugent.be/where-find-us (2nd floor, CMM, door next to Xerox)

Office: +32 9 264 65 56

Mobile: +32 471 66 68 83 (Consider email instead. If you leave no message, I will not call you back.)

E-mail: Toon.Ver...@UGent.be

http://molmod.UGent.be/