[Pw_forum] About gaussian cubic format
On Thu, 2009-10-29 at 10:52 +0100, Paolo Giannozzi wrote: > Tone Kokalj wrote: > > > Would you share the info of how you do the Bader analysis? > > maybe it is already shared I added the following paragraph > a few days ago to the user guide: Paolo - thank you for the info. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] About gaussian cubic format
Tone Kokalj wrote:
> Would you share the info of how you do the Bader analysis?
maybe it is already shared I added the following paragraph
a few days ago to the user guide:
---
Note for people interested in Bader's analysis: there is a software
(link here: \texttt{http://theory.cm.utexas.edu/bader/}) that performs
Bader's analysis starting from charge on a regular grid. The required
"cube" format can be produced by \qe\ using pp.x (info by G. Lapenna
who has successfully used this technique). This code should perform
decomposition into Voronoi polyhedra as well, in place of obsolete
code voronoy.x (removed from distribution after v.4.1).
---
Paolo
--
Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] About gaussian cubic format
On Wed, 2009-10-28 at 17:40 +0100, saqib javaid wrote: > with regards to the Tone comments, infact i am using guassian cubic so > that i can do bader population analysis. Would you share the info of how you do the Bader analysis? Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] About gaussian cubic format
with regards to the Tone comments, infact i am using guassian cubic so that i can do bader population analysis. I am thankful to all for your timely help. with best regards saqib University of strasbourg, France.
[Pw_forum] About gaussian cubic format
On Wed, 2009-10-28 at 16:55 +0100, Lorenzo Paulatto wrote: > In data 28 ottobre 2009 alle ore 16:49:42, saqib javaid > ha scritto: > > i found that > > inter atomic distances are the same as in SCF input file, but origin for > > plotting has changed. I hope i am clear enough this time... > > Dear Saqib, > it does not come from the Gaussian file, but from XCrysDen itself, which > translates all the atoms inside the primitive unit cell. If you want all > the atoms in they original positions follow the menu Displa -> Unit of > repetition -> translational asymmetric unit. To add to this comment, which raises two issues: (1) if your system is periodic (i.e. crystal or surface), use XSF file instead of gaussian cube file as to have the possibility to use/generate periodic images (2) if your system is a molecule "in the box", put the molecule in the center of the box, as this will avoid the "translational" problem discussed above. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] About gaussian cubic format
In data 28 ottobre 2009 alle ore 16:49:42, saqib javaid ha scritto: > i found that > inter atomic distances are the same as in SCF input file, but origin for > plotting has changed. I hope i am clear enough this time... Dear Saqib, it does not come from the Gaussian file, but from XCrysDen itself, which translates all the atoms inside the primitive unit cell. If you want all the atoms in they original positions follow the menu Displa -> Unit of repetition -> translational asymmetric unit. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/
[Pw_forum] About gaussian cubic format
saqib javaid wrote: > What i mean by "do not match" is the fact > that atomic coordinates are different from what i gave in SCF input atoms outside the cell are wrapped back into the cell P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] About gaussian cubic format
Thanks a lot for your reply. What i mean by "do not match" is the fact that atomic coordinates are different from what i gave in SCF input file. When i load the guassina cubic file in the Xcrysden, i found that inter atomic distances are the same as in SCF input file, but origin for plotting has changed. I hope i am clear enough this time... with best regards saqib javaid University of strasbourg, France
[Pw_forum] About gaussian cubic format
saqib javaid wrote: > the xyz coordinates of the atoms given in the output file (...) > do not match the coordinates used in SCF input file. what do you mean by "do not match"? if you visualize the charge and the atoms, do they look misplaced? > Secondly, is there any way to increase the no. of mesh points in this > format. the number of mesh points is determined by the size of the FFT grid. P. -- Paolo Giannozzi, Democritos and University of Udine, Italy
[Pw_forum] About gaussian cubic format
Dear PWSCF users, I have a question regarding gaussian cubic format (output_format=6 in pp input file). I have used this format to get charge density. However, the xyz coordinates of the atoms given in the output file (which should be in bohr as per a previous post) do not match the coordinates used in SCF input file. I would appreciate if you can clarify this problem. Secondly, is there any way to increase the no. of mesh points in this format. Thanks in advance for your kind reply with best regards, saqib Javaid Unviersity of Strasbourg, France
