Hi, 1. You have created issue here https://github.com/zerothi/sisl/issues/290, great! 2. You have to do some scripting, see tutorials here: http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_1.html and http://zerothi.github.io/sisl/docs/latest/tutorials/tutorial_siesta_2.html 3. You can read in the Hamiltonian from sisl, then do es = H.eigenstate() (produces Gamma-point eigenstates), then filter out the eigenvalues close to 0 (sisl automatically shifts electronic structure to Fermi-level) 4. See 2. 5. None, you have to write a small python script. :), but something like es_state4 = sisl.get_sile("RUN.fdf").read_hamiltonian().eigenstate(k=[0.25, 0.25, 0.25]).sub(3) # note C-indexing 6. I don't know what you mean here...
Den lør. 16. jan. 2021 kl. 22.04 skrev El-abed Haidar < ehai2...@uni.sydney.edu.au>: > Hello Nick, Thank you for the reply: > > > > 1. Sisl can do what denchar can? That’s fantastic, I was wondering how > because I will give you my feedback 😊 > 2. Can you let me know how though? As far I understand, sisl is made > of 3 parts: sdata, sgeom, and sgrid. My guess to do a denchar calculation > is to use sgrid. Then the real questions are: > 3. Which nc file should I use to get the homo and lumo as in denchar? > 4. Is there a specific sisl page tutorial for such? > 5. What are the main sisl commands that would be equivalent to*: d**enchar > -k 3 -w 4 file.fdf ??* > 6. Since there is no GitHub for denchar and since I could not find the > command in the denchar manual, where can I find the commands mentioned in > 4?? > > > > Thank you and eager to reading your reply. > > EL-abed > > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > *From: *Nick Papior <nickpap...@gmail.com> > *Sent: *Saturday, 16 January 2021 8:02 AM > *To: *siesta-l <siesta-l@uam.es> > *Subject: *Re: [SIESTA-L] FW: Concerning Denchar > > > > Hmm. > > > > Den tor. 14. jan. 2021 kl. 22.02 skrev ehai2584 < > ehai2...@uni.sydney.edu.au>: > > Good evening, > > 1. I was wondering if Denchar has problems with systems which are not > orthorhombic as it was in 1.3 version? Because when I studied a molecule > inside orthorhombic system, I could visualize cube files. When I study for > example graphene in an hexagonal system, even though the file is not empty > (13000 kb) I could not visualize it. > > I am pretty sure it works for other than orthorhombic cells. However, the > output can only be in an orthorhomic cell. > > > 1. > 2. Does Denchar have its own GitHub like sisl? Alberto once gave a > great advice of using denchar -k 3 -w 4 file.fdf which will plot only the > wave-function with (original) index 4 of the third k-point in the (WFSX) > file. An > > No, denchar is part of the siesta distribution. > > sisl can in principle do what denchar does, however it is not as tested as > denchar (so any feedback on them would be really nice!) > > > 1. > 2. May I convert the output cube file to xsf files in siesta? > > You can do this with sisl > > > > sgrid input.cube output.xsf > > or > > sdata input.cube output.xsf > > > > Denchar does not write out xsf files. > > > 1. > > > > Thank you and looking forward to your reply. > > EL-abed > > > > El-abed Haidar | Doctor of Philosophy (Science) > Condensed Matter Theory (CMT) Group| School of Physics > THE UNIVERSITY OF SYDNEY | NSW | 2006 > > > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/ > <https://protect-au.mimecast.com/s/3lWHC3QNPBiE3LELIgu0O3?domain=max-centre.eu/> > ) > > > > > -- > > Kind regards Nick > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
