Could you help with VASP data intake?

[Anne L]

Hi,

Could you help me with generating and importing data for vasp program? I've done an IBRION 5 frequency calculation, which should be generating the hessian matrix in the OUTCAR file. But I cannot get data successfully for TAMkin. 

I appreciate your help!

P.S. I'm using 

tamkin.io.vasp.load_molecule_vasp("test.xyz","OUTCAR","-285.195324","1","True")

according to the manual. Is this the correct command?

[Toon Verstraelen]

Hi Anne,

There is a development version of TAMkin that should fix the problem. It can be downloaded here:

https://github.com/tovrstra/tamkin/archive/vasp.zip

Can you try installing this one and give it a try? The new vasp reader is documented here:

https://github.com/tovrstra/tamkin/blob/vasp/tamkin/io/vasp.py#L49

I would really appreciate your feedback, also when it does work as expected. If it all works for you, I'll make a new stable release with the improved vasp reader.

Best Regards,

Toon

--
You received this message because you are subscribed to the Google Groups "TAMkin" group.
To unsubscribe from this group and stop receiving emails from it, send an email to tamkin+un...@googlegroups.com.
To post to this group, send email to tam...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/bf1103f3-e089-4cd8-bd53-178ab8577d32%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

-- 
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/

[Anne L]

Hi Toon,

I actually tried to play with the python script in TAMkin and got the data intake part working yesterday. I was able to let TAMkin successfully grab data from the vasp OUTCAR and xyz files (converted from a CONTCAR file).  The correct command for the stable release is like this:  

tamkin.io.vasp.load_molecule_vasp("test.xyz","OUTCAR",-285.195324)

The problem now I face is the following error message:

Traceback (most recent call last):

  File "test.py", line 8, in <module>

    pf = PartFun(nma, [ExtTrans(), ExtRot()])

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

    term.init_part_fun(nma, self)

  File "****/.local/lib/python2.7/site-packages/tamkin/partf.py", line 1006, in init_part_fun

    raise ValueError("There is no external rotation in periodic systems.")

ValueError: rotational: There is no external rotation in periodic systems.

I looked at the partf.py script and tried to find out how I could get off with this error. But I couldn't figure this out. Do you know what this error means? My system is a zeolite periodic supercell with ~40 atoms.

Thanks a lot!

Anne

[Toon Verstraelen]

Hi Anna,

You have to remove the ExtRot() item. It only makes sense for isolated molecules.

Best Regards,

Toon

-- You received this message because you are subscribed to the Google Groups "TAMkin" group. To unsubscribe from this group and stop receiving emails from it, send an email to tamkin+un...@googlegroups.com. To post to this group, send email to tam...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/tamkin/5aa69664-b344-4dc5-893a-9d78a1e5bca6%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.