Re: [SIESTA-L] Puzzle in Spin Polarized calculation in Siesta

[Dmitriy Muzychenko]

Dear Andrei, 

Thank you very much for the detailed answer.

Indeed, I discussed “total spin polarization”, which, as I assumed, should be 
mainly independent throughout the calculation method for the given system. 
Moreover, since in my system (Bi2Te3+Co) the spin polarization comes mainly 
from the Co atom, then I may conclude that the total spin polarization of the 
system corresponds to the magnetization of the Co atom. Luckily, Bi2Te3 system, 
itself, possess zero total spin polarization at all tested parameters 
(pseudopotentials, basis). However, the “opposite” values of magnetization for 
the Co atom are confused, i.e. either the Co atom have a strong magnetic moment 
(4μB), or does not have a magnetic moment at all (0μB).

Concerning the convergence problem. I don't think this is critical one in my 
case. Basically, I have no problem with convergence and all calculations were 
properly converged (10^-3 or 10^-4 for DM and H). Moreover, latest version of 
Siesta (from “master brunch”) allows you to monitor the total spin polarization 
value during SCF cycles. So, as I noticed, the total spin polarization value 
converges very quickly to some value (for example: 4, 3 or 2) within 20-30 SCF 
cycles and then it almost does not change (only within first or second decimal 
place) until the end of the calculations. Thus, k-mesh, mixing schema and 
weights, electronic temperature etc. do not affect at the final result if the 
convergence is achieved. I have also tried more hard convergence criteria (like 
10^-5 or 10^-6 for DM and H), but this is just a waste of time, because the 
main parameters of the system already almost not change after 10^-3.

I’m grateful for the idea that it is necessary to compare the Siesta results 
against an all-electron method. Perhaps, it really can provide some kind of 
reference point for magnetism in my system. I’m not sure that all-electron 
method will be able to calculate such large system, but most likely a smaller 
system may be sufficient for estimation of magnetism in such system.

Thank you one more time.

With kind regards,
Dmitriy Muzychenko




From: Andrei Postnikov
[SIESTA-L] Puzzle in Spin Polarized calculation in Siesta

> Dear Dmitriy,
> 
> as I understand, you are talking about total spin polarisation, which should
> normally
> be reproducible throughout the methods. Otherwise, in terms of local spin
> moments,
> expressed via Mulliken charges or whatever, the differences in the
> definition
> between methods (or, between basis sets) may substantially add to confusion.
> 
> 
> This said, I'd suggest you to try to separate, as possible sources of worry,
> the "local" issues (pseudopotentials, basis) from "global" ones (convergence
> in a large system with – probably – narrow bands). Your P.S. gives an
> impression that
> you are trying everything possible in different directions at the same time.
> For setting the "local" issues, I'd suggest a reasonable compact case,
> including
> your cobalt or whatever, to check against an all–electron method. Here
> you'd check
> the magnetism or whatever is essential for your problem to the accuracy
> needed,
> settle the XC etc., and then do not touch these issues anymore.
> 
> This settled, the instability of results may come from problematic
> convergence,
> as you have a large system and probably narrow bands which swap back and
> forth
> across the Fermi level. If you have no gap but a metal, then in a large
> system
> you need to be very careful about the dense enough k-mesh, mixing schema 
> and weights, electronic temperature etc., to see that your system really
> converges 
> and not fluctuates.
> 
> Good luck, best regards
> 
> Andrei
> 
> -- prof. Andrei Postnikov -- 
> University of Lorraine - Laboratoire de Chimie/Physique - A2MC
> ICPM, 1 Bd Arago - BP 95823, F-57078 Metz Cedex 03, France
> 
> 
> - Dmitriy Muzychenko  a écrit :
> > Dear Siesta Users and Developers
> > 
> > I’m really confused by the results of the Spin Polarized calculation in
> Siesta.
> > 
> > My system is Bi2Te3 slab with single Co atom substitutions of a Bi atom
> (typically concentration: 1 Co atom per 490-1100 Bi+Te atoms).
> > 
> > The confusion arises when I start to analyze the spin properties of this
> system. Depending on the pseudopotential or/and basis set I observe
> completely different value of total spin polarization (S_up-S_down). For
> example, numerous calculations have resulted in the following list of total
> spin polarization values: 4.33, 4.19, 4.00, 3.99, 3,77, 3.52, 3.00, 2,99,
> 2,90, 2.63, 2.59, 2.00, 1.99, 1.53 and 0.00. I note, that these values are
> for exactly the same system, just calculated with a different pseudo(s) or
> basis set(s).
> > 
> > Such a wide range of total spin (from 4.33 up to 0.00) raise a logical
> question, what value can I trust and why? The question is rather not in
> asking for some “perfect set” of 

Re: [SIESTA-L] FW: Concerning Denchar

[Nick Papior]

Hi,

Den lør. 23. jan. 2021 kl. 22.00 skrev El-abed Haidar <
ehai2...@uni.sydney.edu.au>:

> Thank you for the reply.
>
>1. Because it was a different issue concerning Denchar but you are
>right!
>2. Will try to understand whats going on with such scripts
>3. I assume that is in python correct?
>
> Yes :)

>
>1. NA
>2. I understand.
>3. I was wondering for denchar version 3, where did you get the
>command from? Denchar -w 3 -k 4 ?? There is a manual for which you got that
>command from right?
>
> It is written in the denchar manual. Ok, it seems it was added after
4.1-b4 was released. So the next release will have it :)

> Thank you!
>
>
>
>
>
> El-abed Haidar | Doctor of Philosophy (Science)
>  Condensed Matter Theory (CMT) Group| School of Physics
>  THE UNIVERSITY OF SYDNEY  | NSW | 2006
>
>
>
> *From: *Nick Papior 
> *Sent: *Saturday, 23 January 2021 8:02 AM
> *To: *siesta-l 
> *Subject: *Re: [SIESTA-L] FW: Concerning Denchar
>
>
>
> 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*:
>denchar -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 
> *Sent: *Saturday, 16 January 2021 8:02 AM
> *To: *siesta-l 
> *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/
>