[xcrysden] Error Opening Cube File

[Christopher Rowan]

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.
If anyone could further clarify the significance of that second column of
zeros that would be appreciated.
Chris

On 6 August 2010 11:46, Christopher Rowan <chriskrowan at gmail.com> wrote:

> Hello,
>>
>> 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:
>>
>> ERROR: ERROR: An Error occured, while reading XSF file
>> /home/chrisr/xcrys_tmp/xc_
>> 32537/denpot.xsf.raw
>>
>> and nothing is loaded.
>>
>> The cube file looks something like:
>>
>>  SystemLabel.RHO.cube
>>  SystemLabel.RHO.cube
>>     0   -3.000000   -3.000000   -3.000000
>>    50    0.122449    0.000000    0.000000
>>    50    0.000000    0.122449    0.000000
>>    50    0.000000    0.000000    0.122449
>>   0.10791E+01  0.11755E+01  0.12777E+01  0.13812E+01  0.14787E+01
>> 0.15659E+01
>>   0.16451E+01  0.17256E+01  0.18185E+01  0.19245E+01  0.20274E+01
>> 0.20975E+01
>>   0.21064E+01  0.20423E+01  0.19136E+01  0.17422E+01  0.15509E+01
>> 0.13576E+01
>>   0.11733E+01  0.10039E+01  0.85213E+00  0.71919E+00  0.60506E+00
>> 0.50865E+00
>>   0.42832E+00  0.36211E+00  0.30796E+00  0.26397E+00  0.22794E+00
>> 0.19846E+00
>>   0.17417E+00  0.15388E+00  0.13658E+00  0.12148E+00  0.10800E+00
>> 0.95743E-01
>>   0.84450E-01  0.73978E-01  0.64256E-01  0.55330E-01  0.47290E-01
>> 0.40346E-01
>>   0.34475E-01  0.29478E-01  0.25241E-01  0.21565E-01  0.18251E-01
>> 0.15317E-01
>>   0.12762E-01  0.10603E-01
>>   0.10525E+01  0.11520E+01  0.12559E+01  0.13583E+01  0.14522E+01
>> 0.15337E+01
>>   0.16067E+01  0.16837E+01  0.17780E+01  0.18920E+01  0.20079E+01
>> 0.20919E+01
>>   0.21111E+01  0.20513E+01  0.19216E+01  0.17460E+01  0.15496E+01
>> 0.13518E+01
>>
>> etc.
>>
>> Any help/comments much appreciated,
>> Thank you,
>> Chris Rowan
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100825/302b7c35/attachment.htm