VMD-L Mailing List

From: Haijun (huf11_at_psu.edu)
Date: Tue May 10 2011 - 13:58:07 CDT

Thanks.

Axel Kohlmeyer wrote:
> please always keep the VMD list in cc: so that people get to
> see the resolution of the issue. thanks.
>
> On Tue, May 10, 2011 at 2:43 PM, Haijun <huf11_at_psu.edu> wrote:
>
>> Hi Axel,
>>
>> When I read back the written out file, the structure is changed, it's not
>>
>
> then there is likely a bug in the output routine.
>
>
>> the same as before. Do you mean I have to turn to VASP author?
>>
>
> no. this was not written by the VASP folks. you can see the
> respective plugin authors in the molfile plugin documentation.
> in your case, check out:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/vaspplugin.html
>
> cheers,
> axel.
>
>
>> best,
>>
>> Hal
>>
>> Axel Kohlmeyer wrote:
>>
>>> On Tue, May 10, 2011 at 1:56 PM, Haijun <huf11_at_psu.edu> wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> I have a POSCAR file by VASP, I use VMD (1.8.7) to read it and then saved
>>>> coordinates, choose POSCAR, then the coordinate changed strangely, which
>>>> is
>>>> not what I want, the structure is changed. Just read in and save out, I
>>>> didn't do anything with the graph. I don't know whether it has something
>>>> to
>>>> do with the box. Does anybody have this problem. Thanks!!!
>>>>
>>>>
>>> it is not a problem. it is a feature.
>>>
>>> VMD cannot handle periodic display
>>> of coordinates unless the unitcell is rotated
>>> in a very specific orientation. most (classical)
>>> MD codes generate trajectories according to
>>> those conventions. however, most solid state
>>> electronic structure codes use rotated unit cells
>>> for computational efficiency.
>>>
>>> in order to give you the best visualization,
>>> most VMD plugins rotate your coordinates
>>> according to the VMD requirements on reading.
>>>
>>> if you read back the written out file, do you
>>> get the same structure as before?
>>> if yes, then this rotation is the cause,
>>> if not, then there may be a bug in the
>>> POSCAR writer. you'd have to contact the author,
>>> since this is code that was contributed to VMD.
>>>
>>> cheers,
>>> axel.
>>>
>>>
>>>
>>>
>>>> My input POSCAR file by VASP:
>>>>
>>>> **************************************************************************
>>>> pp 4.09000000000000 2.8284271247461898
>>>> 0.0000000000000000 0.0000000000000000
>>>> 1.4142135623730949 2.4494897427831779 0.0000000000000000
>>>> 0.0000000000000000 0.0000000000000000 8.0829037686547611
>>>> C N O 2 1 1 Selective dynamics
>>>> Direct
>>>> 0.3548963329056939 0.2386292361801097 0.4576784760662509 T T T
>>>> 0.2131006946456214 0.2624310721160927 0.4527066803041102 T T T
>>>> 0.3670230019904553 0.0336035425479118 0.4491527493994849 T T T
>>>> 0.5638996343219198 0.0347274618276919 0.4372277282656143 T T T
>>>>
>>>> ****************************************************************************
>>>>
>>>>
>>>> The output POSCAR file by VMD:
>>>>
>>>> ****************************************************************************
>>>>
>>>> C N O 1.000000000000
>>>> 11.568266868591 0.000000000000 0.000000000000
>>>> 5.784133434296 10.018414196966 0.000000000000
>>>> 0.000000000000 0.000000000000 33.059078216553
>>>> 2 1 1
>>>> Direct
>>>> 0.474210951223 -0.035156579115 0.457678469288
>>>> 0.344316238791 0.063640024296 0.452706704719
>>>> 0.383824777269 -0.187997768686 0.449152740883
>>>> 0.581263370032 -0.300865059006 0.437227729353
>>>>
>>>> ****************************************************************************
>>>>
>>>> best,
>>>>
>>>> Hal
>>>>
>>>>
>>>>
>>>
>>>
>>>
>
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