VMD-L Mailing List

From: Roberto Guerra (robguerra_at_unimore.it)
Date: Sat Mar 30 2013 - 19:55:43 CDT

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

  • text/plain attachment: a.xsf
  • text/plain attachment: b.xsf