VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 11 2013 - 12:08:32 CDT

Hi guys,
  I applied Roberto's patch to the xsfplugin in the VMD CVS tree, so it'll
be in the next round of test builds I produce.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 11, 2013 at 06:59:11PM +0200, Axel Kohlmeyer wrote:
> On Thu, Apr 11, 2013 at 6:50 PM, Roberto Guerra <robguerra_at_unimore.it> wrote:
> > afaik cube files treat only orthorhombic cells. If so, cube plugin shouldn't be affected by the bug.
>
> no, they can handle any kind of lattice. many plane wave
> pseudopotential DFT codes produce non-orthogonal cube files. i worked
> on some of that stuff myself back in the time. but the bug doesn't
> show.
>
> axel.
>
>
> >
> >
> > Roberto
> >
> >
> > On 11 April 2013, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >> john, roberto,
> >>
> >> i just double checked the patch and example files with xcrysden (which
> >> is *the* authoritative reference for the file format) and can confirm
> >> that the change is correct. since the xsf and the cube plugin share a
> >> lot of code, we need to double check whether the same problem exists
> >> for cubefiles as well. will look into this now.
> >>
> >> thanks for the patch.
> >>
> >> axel.
> >>
> >> On Wed, Apr 3, 2013 at 10:56 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> > Axel, Roberto,
> >> > If you can both test this and agree together that it works, I will
> >> > apply the requested chang to the plugin source code. Since Axel wrote
> >> > this plugin and I'm not familiar with xcrysden myself, I would prefer that
> >> > he has a chance to comment on the proposed change before I take action
> >> > on putting it into VMD. If you both agree, then I am happy to put the
> >> > changes in place and it would then be part of one of the upcoming test
> >> > builds of VMD.
> >> >
> >> > Cheers,
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> > On Sun, Mar 31, 2013 at 01:55:43AM +0100, Roberto Guerra wrote:
> >> >> Dear all,
> >> >>
> >> >> at present vmd does not visualize correclty the structure in a xsf file when the cell vectors don't form a simmetric matrix. You can verify this with the two simple examples attached, a.xsf and b.xsf, having monoclinic and fcc cells, respectively.
> >> >> In these, the atoms are aligned along the cell vectors, and you can see they are not correctly rotated by the xsfplugin. You can see the difference with xcrysden.
> >> >>
> >> >> It have fount that the bug was in the readbox routine of xsfplugin.C. This is the diff of original-vs-patched code:
> >> >>
> >> >> 167,169c167,169
> >> >> < box->cell[0][i] = x[i];
> >> >> < box->cell[1][i] = y[i];
> >> >> < box->cell[2][i] = z[i];
> >> >> ---
> >> >> > box->cell[i][0] = x[i];
> >> >> > box->cell[i][1] = y[i];
> >> >> > box->cell[i][2] = z[i];
> >> >> 908c910
> >> >> < plugin.minorv = 7;
> >> >> ---
> >> >> > plugin.minorv = 8;
> >> >>
> >> >> Clearly, for symmetric matrices one doesn't notice the difference.
> >> >> You can verify that the patched code visualizes correctly the attached examples.
> >> >>
> >> >>
> >> >> Best regards,
> >> >> Roberto Guerra
> >> >
> >> >> CRYSTAL
> >> >> PRIMVEC
> >> >> 22.80 0.000 0.000
> >> >> 11.40 19.75 0.000
> >> >> 0.000 0.000 20.30
> >> >> PRIMCOORD
> >> >> 7
> >> >> Au 0.01 0.01 0.01
> >> >> Si 3 0.01 0.01
> >> >> Si 6 0.01 0.01
> >> >> C 2.28 3.95 0.01
> >> >> C 4.56 7.90 0.01
> >> >> Ge 0.01 0.01 3
> >> >> Ge 0.01 0.01 6
> >> >
> >> >> CRYSTAL
> >> >> PRIMVEC
> >> >> -15.26 0.00 15.26
> >> >> 0.00 15.26 15.26
> >> >> -15.26 15.26 0.00
> >> >> PRIMCOORD
> >> >> 10
> >> >> Au 0 0 0
> >> >> Si -3 0.01 3
> >> >> Si -6 0.01 6
> >> >> Si -9 0.01 9
> >> >> C 0.01 3 3
> >> >> C 0.01 6 6
> >> >> C 0.01 9 9
> >> >> Ge -3 3 0.01
> >> >> Ge -6 6 0.01
> >> >> Ge -9 9 0.01
> >> >
> >> >
> >> > --
> >> > NIH Center for Macromolecular Modeling and Bioinformatics
> >> > Beckman Institute for Advanced Science and Technology
> >> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> >> > http://www.ks.uiuc.edu/Research/vmd/
> >>
> >>
> >>
> >>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/