I figured out why XCrySDen wouldn't open the cube files that Denchar outputs when processing SIESTA output. There is a
formatting issue. One must edit the cube file so
that the third line contains the number of atoms, where it currently
prints zero. Then, after the lattice parameters on lines 4, 5 and 6,
one must insert 5 columns: the first being the atomic number of the
species, the second being 0.000000, and the third, fourth and fifth the
atomic coordinates.<br>If anyone could further clarify the significance of that second column of zeros that would be appreciated.<br>
Chris<br><br><div class="gmail_quote">On 6 August 2010 11:46, Christopher Rowan <span dir="ltr"><<a href="mailto:chriskrowan@gmail.com" target="_blank">chriskrowan@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br><br>I have been struggling at getting XCrySDen version 1.5.17
to open the cube files that Denchar outputs, which it claims is in Gaussian 98 cube file format and that XCrySDen can open. The files are labeled: SystemLabel.DRHO.cube, SystemLabel.RHO.cube and SystemLabel.WF1.cube. (I am doing some calculations with SIESTA, and interested in visualizing the orbitals.) The error message is:<br>
<br>ERROR: ERROR: An Error occured, while reading XSF file /home/chrisr/xcrys_tmp/xc_<div>32537/denpot.xsf.raw<br><br>and
nothing is loaded.<br><br>The cube file looks something like:<br><br> SystemLabel.RHO.cube<br> SystemLabel.RHO.cube<br> 0 -3.000000 -3.000000 -3.000000<br> 50 0.122449 0.000000 0.000000<br> 50 0.000000 0.122449 0.000000<br>
50 0.000000 0.000000 0.122449<br> 0.10791E+01 0.11755E+01 0.12777E+01 0.13812E+01 0.14787E+01 0.15659E+01<br> 0.16451E+01 0.17256E+01 0.18185E+01 0.19245E+01 0.20274E+01 0.20975E+01<br> 0.21064E+01 0.20423E+01 0.19136E+01 0.17422E+01 0.15509E+01 0.13576E+01<br>
0.11733E+01 0.10039E+01 0.85213E+00 0.71919E+00 0.60506E+00 0.50865E+00<br> 0.42832E+00 0.36211E+00 0.30796E+00 0.26397E+00 0.22794E+00 0.19846E+00<br> 0.17417E+00 0.15388E+00 0.13658E+00 0.12148E+00 0.10800E+00 0.95743E-01<br>
0.84450E-01 0.73978E-01 0.64256E-01 0.55330E-01 0.47290E-01 0.40346E-01<br> 0.34475E-01 0.29478E-01 0.25241E-01 0.21565E-01 0.18251E-01 0.15317E-01<br> 0.12762E-01 0.10603E-01<br> 0.10525E+01 0.11520E+01 0.12559E+01 0.13583E+01 0.14522E+01 0.15337E+01<br>
0.16067E+01 0.16837E+01 0.17780E+01 0.18920E+01 0.20079E+01 0.20919E+01<br> 0.21111E+01 0.20513E+01 0.19216E+01 0.17460E+01 0.15496E+01 0.13518E+01<br><br>
etc.<br><br>Any help/comments much appreciated,<br>Thank you,<br>Chris Rowan</div>
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