AW: vmd-l: non-orthorhombic PBCs

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Sep 26 2013 - 00:49:18 CDT

Isn't "pbc set" expecting only six values? You passed eight, so there might
be the problem.

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Jaap Kroes
> Gesendet: Donnerstag, 26. September 2013 03:15
> An: vmd-l_at_ks.uiuc.edu
> Betreff: vmd-l: non-orthorhombic PBCs
>
> 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.
> 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

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