VMD-L Mailing List

From: Jaap Kroes (jaap.kroes_at_epfl.ch)
Date: Thu Sep 26 2013 - 04:10:58 CDT

Dear Axel,

Thanks! I confirm that it indeed works in the alpha test binary.
I was using 1.9.1 when I found the problem, but with 1.9.2alpha-33 the
file loads fine.

Best,
Jaap

2013/9/26 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> On Thu, Sep 26, 2013 at 3:14 AM, Jaap Kroes <jaap.kroes_at_epfl.ch> wrote:
>> Dear VMD developers,
>>
>> Likely you are already aware, but I believe there is a problem with
>> non-orthorhombic cells in VMD.
>> Upon looking trough the mailing list I only found some old topics,
>> where this problem already seemed to be present.
>> Is this still the case?
>>
>> The example at the end of this mail works fine in xcrysden but not in VMD.
>
> which version of VMD? have you tried the latest alpha test binary?
> there was an issue with the rotation of cell vectors (and coordinates)
> to comply with the requirements in VMD for correct PBC display. this
> was fixed in april.
>
> axel.
>
>> When manually specifying the unit vectors with the 'pbc' module
>> pbc set {4.26000000 0.00000000 0.00000000 0.00000000
>> 2.13000000 1.22975607 0.00000000 -3.30000000 5.71576766}
>> -namd
>> I get the error "vecdot needs vectors of the same size: 1.0 : 1 0 0".
>>
>> Thanks!
>>
>> Best,
>> Jaap
>>
>> Below is a rotated graphite xsf-file, which loads fine in xcrysden
>> ('graphite.xsf')
>>
>> CRYSTAL
>>
>> PRIMVEC
>> 4.26000000 0.00000000 0.00000000
>> 0.00000000 2.13000000 1.22975607
>> 0.00000000 -3.30000000 5.71576766
>>
>> PRIMCOORD
>> 8 1
>> 6 0.00000000 0.00000000 0.00000000
>> 6 1.42000000 0.00000000 0.00000000
>> 6 1.42000000 -1.65000000 2.85788383
>> 6 2.84000000 -1.65000000 2.85788383
>> 6 2.13000000 1.06500000 0.61487803
>> 6 3.55000000 1.06500000 0.61487803
>> 6 3.55000000 -0.58500000 3.47276187
>> 6 4.97000000 -0.58500000 3.47276187
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.