VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 10 2011 - 13:50:39 CDT

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
>>>
>>>
>>
>>
>>
>>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.