Re: [Wien] error in exercise 6(MgO surface slab)

[Rubel, Oleg]

I see that the error occurs in the SCF cycle _before_ Wannier-related commands 
are called. This means that you cannot run GaAs with XC=LDA. You can test if Si 
runs with LDA (using identical initialization parameters).

Oleg

> On Apr 9, 2024, at 11:32 AM, harri...@sjtu.edu.cn wrote:
> 
> Caution: External email.
> 
> run_lapw
> 
> 发自我的手机

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Re: [Wien] error in exercise 6(MgO surface slab)

[Rubel, Oleg]

At which step (command) does the segmentation fault occur?

> On Apr 9, 2024, at 10:19 AM, 夏宇阳  wrote:
> 
> Caution: External email.
> 
> 
> Dear Oleg,
> i just follow the guide step by step.
> And the error is:
> 
> Program received signal SIGSEGV: Segmentation fault - invalid memory 
> reference.
> 
> Backtrace for this error:
> #0  0x817bc823960 in ???
> #1  0x817bc822ac5 in ???
> #2  0x817bc44251f in ???
>at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
> #3  0x817bc5a1082 in ???
>at ../sysdeps/x86_64/multiarch/memset-vec-unaligned-erms.S:394
> #4  0x57975d1a3c47 in ???
> #5  0x57975d13a80e in ???
> #6  0x817bc429d8f in __libc_start_call_main
>at ../sysdeps/nptl/libc_start_call_main.h:58
> #7  0x817bc429e3f in __libc_start_main_impl
>at ../csu/libc-start.c:392
> #8  0x57975d13a834 in ???
> #9  0x in ???
> Segmentation fault (core dumped)
> 
>>  stop error
> 
> This wont happen when use PBE and WC
> 
> With regards!
> 
> Yuyang Xia

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Re: [Wien] error in exercise 6(MgO surface slab)

[Rubel, Oleg]

Dear Yuyang,

I tested the tutorial and initialized the calculation with "init_lapw -b -vxc 5 
-numk 600”. It works on my end (Wien2k v23.2, Wannier90 v2.1.0). We also tested 
with Wannier 3.X for the workshop. Please be more specific about your steps 
leading to the error message and the message itself.

Thank you
Oleg

> On Apr 8, 2024, at 11:48 PM, harri...@sjtu.edu.cn wrote:
> 
> Caution: External email.
> 
> Dear Prof.Blaha,
> It is on my home computer with wien2k_23.
> 
> And there is another error existing when i do the scf of GaAs following the 
> guide of "wien2k + w2wannier+wannier90".
> 
> I can't use LDA for initialization, and it will lead an error in scf 
> calculation. But I can use PBE and WC.They perform well.
> 
> Looking forward to your reply.
> 
> With regards!
> 
> Yuyang Xia
> 
> 
> 
> 
> 
> 
> 
> 
> 发自我的手机
> 
> 
>  原始邮件 
> 发件人： Peter Blaha 
> 日期： 2024年4月9日周二 凌晨4:07
> 收件人： wien@zeus.theochem.tuwien.ac.at
> 主 题： Re: [Wien] error in exercise 6(MgO surface slab)
> Hi,
> 
> Where does this happen and with which version of WIEN2k.
> 
> It is on the workshop nodes or on your home computer with WIEN2k_23.
> 
> I'm aware of this problem and I think I fixed in on the workshop nodes. 
> Of course it will still happen when using  WIEN2k_23 and only the next 
> release will have fixed it.
> 
> Peter Blaha
> 
> Am 08.04.2024 um 16:43 schrieb 夏宇阳:
> > Dear all,
> > I am doing the latest exercise 6(MgO surface slab),and there is a error 
> > when do "init_lapw -prec 1n"
> >
> > STOP KGEN ENDS
> > NUMK: 1000
> > basic k-mesh: 12, 12, 2 = 288,  kfactor = .1000
> >NUMBER OF K-POINTS IN WHOLE CELL: (0 for 3 divisions of K, -1 for 
> > delta-K)
> > At line 243 of file main.f (unit = 5, file = 'stdin')
> > Fortran runtime error: Bad integer for item 1 in list input
> >
> > what should i do?
> > Looking forward to your reply.
> >
> > With regards!
> > ___
> > Wien mailing list
> > Wien@zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > SEARCH the MAILING-LIST at:  
> > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 
> -- 
> ---
> Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-158801165300
> Email: peter.bl...@tuwien.ac.at
> WWW:   http://www.imc.tuwien.ac.at  WIEN2k: http://www.wien2k.at
> -
> 
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Re: [Wien] how to choose the band indices in init_w2w of a parallel spin-polarized calculation

[Rubel, Oleg]

I would suggest starting by plotting the band structure and deciding which 
energy window you would like to get wannierized. For example, if we are 
describing sp3 bonding in GaAs or Si and would like to model the valence and 
conduction band, then I would ask for 4xN Wannier functions (4=1s+3p, N=number 
of atoms in the primitive cell).

Oleg

> On Apr 7, 2024, at 4:37 PM, 夏宇阳  wrote:
> 
> Caution: External email.
> 
> 
> Dear all,
> i am doing the MLWF calculation of KFe2As2. and i wonder know how to set band 
> indices.
> Here are the band data(They have two parts):
> spin up:
>   TEMP.-SMEARING WITH0.00200 Ry
>  -S / Kb   =  -1.23098122
>  -(T*S)/2  =  -0.00061549
>  Chem Pot  =   0.21595875
> Bandranges (emin - emax) and occupancy:
> :BAN00138: 1380.1062260.203958  0.8232
> :BAN00139: 1390.100.204162  0.8040
> :BAN00140: 1400.1109640.207976  0.99987160
> :BAN00141: 1410.1246190.222401  0.94618996
> :BAN00142: 1420.1246200.224598  0.92998833
> :BAN00143: 1430.1280980.237002  0.49531848
> :BAN00144: 1440.1280980.244802  0.36415663
> :BAN00145: 1450.1399460.256809  0.31798703
> :BAN00146: 1460.1399540.268867  0.26439317
> :BAN00147: 1470.1410060.275217  0.20029264
> :BAN00148: 1480.1411940.280018  0.15643532
> :BAN00149: 1490.2442340.323306  0.0001
> :BAN00150: 1500.2466710.323513  0.
> :BAN00151: 1510.2586180.361356  0.
> :BAN00152: 1520.2586560.363918  0.
> :BAN00153: 1530.2702970.388945  0.
>Energy to separate low and high energystates:   -0.22906
> 
> 
> :NOE  : NUMBER OF ELECTRONS  =  277.000
> 
> spin down:
>  TEMP.-SMEARING WITH0.00200 Ry
>  -S / Kb   =  -1.23098122
>  -(T*S)/2  =  -0.00061549
>  Chem Pot  =   0.21595875
> Bandranges (emin - emax) and occupancy:
> :BAN00128: 1280.1059870.189245  0.9992
> :BAN00129: 1290.1063500.200158  0.8569
> :BAN00130: 1300.1079010.202819  0.4998
> :BAN00131: 1310.1145250.214050  0.99489891
> :BAN00132: 1320.1146060.233903  0.93938606
> :BAN00133: 1330.1869730.246794  0.28420547
> :BAN00134: 1340.1870520.259525  0.27635539
> :BAN00135: 1350.1942970.277080  0.21643727
> :BAN00136: 1360.1943700.278194  0.21300873
> :BAN00137: 1370.1972380.280269  0.12860379
> :BAN00138: 1380.1972400.282380  0.12735150
> :BAN00139: 1390.2039940.282578  0.07262851
> :BAN00140: 1400.2039950.283249  0.07261446
> :BAN00141: 1410.2443300.285107  0.0002
> :BAN00142: 1420.2443350.288372  0.0002
> :BAN00143: 1430.2454030.298816  0.0001
>Energy to separate low and high energystates:   -0.22073
> 
> 
> :NOE  : NUMBER OF ELECTRONS  =  277.000
> 
> Looking for your reply
> 
> With regards!
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Re: [Wien] How to assign kz to slab bands?

[Rubel, Oleg]

Dear Lukasz ,

I am not aware of fold2Bloch ever being used for supercells with vacuum. So, 
you are welcome to try but I am skeptical (same as Peter). Another option would 
be to plot "fat" bands with a higher weight assigned to surface atoms.

Best regards,
Oleg

> -Original Message-
> From: Wien  On Behalf Of Peter
> Blaha
> Sent: Sunday, February 25, 2024 12:33 PM
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: Re: [Wien] How to assign kz to slab bands?
> 
> Caution: External email.
> 
> 
> Yes, I know.
> 
> But usually the model is to make a supercell (without vacuum) and put some
> impurity into it. Then you can fold the supercell back becaus it is a 
> multiple of
> the small unit cell, and find bulk and impurity bands.
> 
> In your case, you don't have just a supercell, but a supercell + vacuum.
> Thus c' is not just 3 x c (for a cell with 3 unitcells in c direction), but 
> vacuum has
> been added.
> 
> I don't know if backfolding would work in this case, maybe you can use the
> trick I mentioned last time.
> 
> Am 25.02.2024 um 12:45 schrieb pluto via Wien:
> > Dear Prof. Blaha,
> >
> > Thank you for the comment.
> >
> > fold2Bloch might be exactly what I need! There are papers where it is
> > mentioned in relation to ARPES.
> >
> > Best,
> > Lukasz
> >
> >
> >
> >
> >
> >
> > On 2024-02-24 16:05, Peter Blaha wrote:
> >> Hi,
> >>
> >> There is no automatic tool for this.
> >>
> >> I detected surface states by an analysis of the partial charges of
> >> the atoms in the various layers. A surface state should have charge
> >> only in the surface (maybe a bit in the subsurface layer).
> >>
> >> Note, there is   fold2bloch, which does backfolding of supercells, but
> >> I don't know what to do with the vacuum.
> >> One could try to give him a supercell in z direction without vacuum
> >> and still use the eigenvectors from the supercell+vacuum calculation,
> >> but it may give complete nonsense.
> >>
> >> Best regards
> >> Peter Blaha
> >>
> >> Am 23.02.2024 um 17:02 schrieb pluto via Wien:
> >>> Dear All,
> >>>
> >>> Everyone who has done a slab calculation knows that it contains some
> >>> surface states and some projected bulk bands.
> >>>
> >>> These projected bulk bands are typically nearly identical to the
> >>> bulk projected bands. If we have a 10ML slab, they will essentially
> >>> look like cutting the bulk BZ 10 times along kz. In case of bulk
> >>> bands obviously each cut is assigned to some kz.
> >>>
> >>> Now, we can compare bulk projected bands and slab bands, and then we
> >>> will more or less know which of the slab bands relate to which kz
> >>> (besides the surface states that don't have kz).
> >>>
> >>> Is there a simple way to automatically assign kz to the slab bands?
> >>>
> >>> One solution to this problem would be to calculate something like
> >>> , which is essentially a Fourier
> >>> transform of the initial wave function for some energy and k_paral,
> >>> i.e. for one eigenvalue point in the band structure. Is that kind of
> >>> matrix element hidden somewhere in the WIEN2k output files?
> >>>
> >>> Actually, this would also assign kz to the surface states, which
> >>> could also be useful in the photoemission context.
> >>>
> >>> Best,
> >>> Lukasz
> >>> ___
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> >>> SEARCH the MAILING-LIST at:
> >>> http://www.mail-
> archive.com/wien@zeus.theochem.tuwien.ac.at/index.ht
> >>> ml
> > ___
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> archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300
> Email: peter.bl...@tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at
> -
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Re: [Wien] Wannier

[Rubel, Oleg]

Dear Lukasz,

Let me try to address the Wannier part of your question. There is a tutorial on 
construction of maximally localized Wannier functions for GaAs with 
WIEN2k+w2w+wannier90. Please check one of the latest workshops at 
http://susi.theochem.tuwien.ac.at/events/index.html. In this tutorial, you will 
see a nice analogy with the sp3 LCAO model. This is because we got lucky, and 
the Wannier functions ended up centered at the atomic sites. However, this is 
not generally the case, even though you can initially place WFs at the atomic 
sites. Simple Si is an example where the centers of WFs stray away from the 
centers of atoms. In any case, we technically obtain a TB Hamiltonian that fits 
the band structure, but the LCAO interpretation (atomic orbitals) is not 
possible in most cases. (At least, this has been my experience.)

There are developments beyond "standard" wannierization, for instance, 
symmetry-constrained WFs. There was a good summer school on Wannier90 
(https://indico.ictp.it/event/9789/), so please check the program. I do not 
know if those developments allow for constraining the centers of WFs. I recall 
that symmetry-constrained WFs require additional input that is not 
automatically generated by WIEN2k.

If you find a solution on how to get an LCAO Hamiltonian for a generic 
material, please post it to the list.

Thank you in advance
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
Web: http://olegrubel.mcmaster.ca



> -Original Message-
> From: Wien  On Behalf Of pluto
> via Wien
> Sent: Wednesday, February 14, 2024 7:41 PM
> To: A Mailing list for WIEN2k users 
> Cc: pluto 
> Subject: [Wien] Wannier
> 
> Caution: External email.
> 
> 
> Dear All,
> 
> I am interested to project WIEN2k band structure onto atomic orbitals, but
> getting complex amplitudes. For example, for graphene Dirac band (formed
> primarily by C 2pz) I would get two k-dependent complex numbers
> A_C2pz(k) and B_C2pz(k), where A and B are the two inequivalent sites, and
> these coefficients for other orbitals (near the Dirac points) would be nearly
> zero. Of course, for graphene I can write a TB model and get these numbers,
> but already for WSe2 monolayer TB model has several bands (TB models for
> WSe2 are published but implementing would be time-consuming), and for a
> generic material there is often no simple TB model.
> 
> Some time ago I looked at the WIEN2k wave functions, but because of the
> way LAPW works, it is not a trivial task to project these onto atomic 
> orbitals.
> This is due to the radial wave functions, each one receiving its own 
> coefficient.
> 
> I was wondering if I can somehow get such projection automatically using
> Wien2Wannier, and later with some Wannier program. I thought it is good to
> ask before I invest any time into this.
> 
> And I would need it with spin, because I am interested with systems where
> SOC plays a role.
> 
> The reason I ask:
> Simple model of photoemission can be made by assuming coherent addition
> of atomic-like photoionization, with additional k-dependent initial band
> amplitudes/phases. One can assume that radial integrals in photoemission
> matrix elements don't have special structure and maybe just take atomic cross
> sections of Yeh-Lindau. But one still needs these complex coefficients to 
> allow
> for interference of the emission from different sites within the unit cell. I 
> think
> for a relatively simple material such as WSe2 monolayer, the qualitative 
> result
> of this might be reasonable. I am not aiming at anything quantitative since we
> have one-step-model codes for quantitative.
> 
> Any suggestion on how to do this projection (even approximately) within the
> realm of WIEN2k would be welcome.
> 
> Best,
> Lukasz
> 
> 
> PD Dr. Lukasz Plucinski
> Group Leader, FZJ PGI-6
> Phone: +49 2461 61 6684
> https://electronic-structure.fz-juelich.de/
> 
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Re: [Wien] effective mass calculation using mstar

[Rubel, Oleg]

Did the archive include the bi2se3.mommat2up file?

> On Dec 6, 2023, at 1:40 PM, Burhan Ahmed  wrote:
> 
> Caution: External email.
> 
>  bi2se3.tar.gz

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Re: [Wien] effective mass calculation using mstar

[Rubel, Oleg]

Hi Burhan,

It would be better if I could reproduce the error on my end. The easiest way 
would be to share a link to the tar.gz file of your complete case folder.

Thanks
Oleg

P.S. Your email did not come through the mailing list (need to register?)

> On Dec 6, 2023, at 7:08 AM, Rubel, Oleg  wrote:
> 
> Caution: External email.
> 
> Hi,
> 
> thank you for the interest in mstar code! Please send your support request 
> via WIEN2k mailing list for the benefit of other users.
> 
> Best regards 
> Oleg
> 
> --
> Oleg Rubel (PhD, PEng)
> Department of Materials Science and Engineering
> McMaster University
> JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
> Email: rub...@mcmaster.ca
> Tel: +1-905-525-9140, ext. 24094
> Web: http://olegrubel.mcmaster.ca
> 
>> On Dec 6, 2023, at 00:14, Burhan Ahmed  wrote:
>> 
>>  
>> Caution: External email.
>> 
>> dear experts, I want to calculate the effective mass by mstar script. I did 
>> the steps mentioned in the article "Perturbation approach to ab initio 
>> effective mass calculations" by Oleg Rubel. 
>> 
>> All the steps did works fine for me but when I run the final " x mstar -up 
>> -settol 1.0e-5" , I got the error that dM is not finite. I tried with 
>> 1.0e-1...1.0e-6 but got the same error. What may be a possible solution of 
>> this?
>> 
>> indrajit@Indrajit:~/Documents/bi2se3$ x mstar -up -settol 1.0e-5
>>  Detected input arguments = 2
>>  Input mommat file = ./bi2se3.mommat2up
>>  Degeneracy tolerance dEtol = 1.0e-5 [Ha]
>>  Confirming text-to-number conversion dEtol =  1.0E-05 [Ha]
>>  The input file ./bi2se3.mommat2up was found.
>>   number of lines in mommat file = 1276410
>>  Entering the main loop...
>>  ikpt =   1
>>  n =   1
>>  k =   3
>>  m =   1
>>  alpha =   1
>>  beta =   1
>>  pij(alpha,n,k) = (NaN,NaN)
>>  pij(beta,k,m) = (NaN,NaN)
>>  pij(beta,n,k) = (NaN,NaN)
>>  pij(alpha,k,m) = (NaN,NaN)
>>  dEij(n,k) =  4.6810001E-05
>>  dEij(m,k) =  4.6810001E-05
>>  dM =  (NaN,NaN)
>>  dE =  -4.6810001E-05
>>  p2 =  (NaN,NaN)
>> Error: dM is not finite
>> 0.232u 0.032s 0:00.26 100.0% 0+0k 0+32io 0pf+0w
>> 
>> 
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Re: [Wien] effective mass calculation using mstar

[Rubel, Oleg]

Hi,


thank you for the interest in mstar code! Please send your support request via WIEN2k mailing list for the benefit of other users.


Best regards 
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton,
 Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On Dec 6, 2023, at 00:14, Burhan Ahmed  wrote:










Caution:
External email. 






dear experts, I want to calculate the effective mass by mstar script. I did the steps
 mentioned in the article "Perturbation approach to
ab initio
effective mass calculations"
by Oleg Rubel. 


All the steps did works fine for me but when I run the final " x mstar -up -settol 1.0e-5" , I got the error that dM is not finite. I tried with 1.0e-1...1.0e-6
 but got the same error. What may be a possible solution of this?


indrajit@Indrajit:~/Documents/bi2se3$ x mstar -up -settol 1.0e-5
 Detected input arguments = 2
 Input mommat file = ./bi2se3.mommat2up
 Degeneracy tolerance dEtol = 1.0e-5 [Ha]
 Confirming text-to-number conversion dEtol =  1.0E-05 [Ha]
 The input file ./bi2se3.mommat2up was found.
  number of lines in mommat file = 1276410
 Entering the main loop...
 ikpt =           1
 n =           1
 k =           3
 m =           1
 alpha =           1
 beta =           1
 pij(alpha,n,k) = (NaN,NaN)
 pij(beta,k,m) = (NaN,NaN)
 pij(beta,n,k) = (NaN,NaN)
 pij(alpha,k,m) = (NaN,NaN)
 dEij(n,k) =  4.6810001E-05
 dEij(m,k) =  4.6810001E-05
 dM =  (NaN,NaN)
 dE =  -4.6810001E-05
 p2 =  (NaN,NaN)
Error: dM is not finite
0.232u 0.032s 0:00.26 100.0% 0+0k 0+32io 0pf+0w









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Re: [Wien] Berrypi Error

[Rubel, Oleg]

I reproduced the error on my end with Python 3.10. The GitHub version is 
updated to fix the error as Sharbano suggested and tested. To update your 
version please run those commands irrespective of the WIEN2k version:

cd $WIENROOT/SRC_BerryPI/BerryPI
git pull

This will update BerryPI to the most current version (including updates to the 
Chern number and hybrid Wannier charge center calculations for topological 
materials).

Thank you again, Sharbano!

Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Rubel, Oleg
> Sent: Friday, November 17, 2023 12:24 PM
> To: A Mailing list for WIEN2k users 
> Subject: Re: [Wien] Berrypi Error
> 
> Caution: External email.
> 
> 
> Dear Sharbano,
> 
> Many thanks for sharing the fix. I will take a closer look in the next couple 
> of
> days.
> 
> Best regards
> Oleg
> 
> > -Original Message-
> > From: Wien  On Behalf Of
> > shahrbano rahimi
> > Sent: Friday, November 17, 2023 11:17 AM
> > To: A Mailing list for WIEN2k users 
> > Subject: [Wien] Berrypi Error
> >
> >   Caution: External email.
> >
> >
> > Dear Prof. Peter Blaha and Prof. Oleg Rubel,
> >
> >
> > hope this email finds you in good health and spirits. I am reaching
> > out to respectfully report a technical challenge we recently
> > encountered in our Wien2k calculations using BerrypI, and to share the
> > solution we found in hopes that it might be helpful.
> >
> > Our team has been utilizing Wien2k version 23.2, along with Python
> > version
> > 3.10.9 and Numpy version 1.23.5. Initially, the electronic part of the
> > calculations proceeded without any issues. However, we stumbled upon a
> > snag in the ionic part, which resulted in the following error message:
> >
> > “Traceback (most recent call last): File
> > "/opt/codes/wien2k/v23.2/berrypi",
> > line 1081, in  theCalc =
> > postProcBerryPhase(configFile,phasesRaw,spCalc) File
> > "/opt/codes/wien2k/v23.2/berrypi", line 72, in postProcBerryPhase
> > mainCalculation = b_PyCalc.MainCalculationContainer( File
> > "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line
> > 338, in init ionP = self.determineIonPolarization(wrpFn,args) File
> > "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line
> > 621, in determineIonPolarization if isinstance(iValence, 
> > collections.Iterable):
> > AttributeError: module 'collections' has no attribute 'Iterable'”
> >
> > In our efforts to resolve this, we made the following changes in the
> > calculations.py file:
> >
> > 1.Altered the import statement from:
> >
> >   import collections
> >
> >   to:
> >
> >   from collections.abc import Iterable
> >
> > 2.Amended the following line:
> >
> >   from:
> >
> >   if isinstance(iValence, collections.Iterable):
> >
> >   to:
> >
> >   if isinstance(iValence, Iterable):
> >
> > These modifications have thankfully resolved the
> > 'collections.Iterable' error, allowing our calculations to proceed without
> further issues.
> >
> > I thought it prudent to share this experience with you, given your
> > profound expertise and significant contributions to the development of
> > Wien2k. Your guidance and insights have always been invaluable to our
> > work, and I hope this information might be of some utility in your ongoing
> endeavors.
> >
> > Thank you very much for your time and attention to this matter. Any
> > further insights or suggestions from your esteemed perspectives would
> > be greatly appreciated.
> >
> > With sincere respect and best regards,
> >
> > Sharbano Rahimi
> 
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> archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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Re: [Wien] Berrypi Error

[Rubel, Oleg]

Dear Sharbano,

Many thanks for sharing the fix. I will take a closer look in the next couple 
of days.

Best regards
Oleg

> -Original Message-
> From: Wien  On Behalf Of
> shahrbano rahimi
> Sent: Friday, November 17, 2023 11:17 AM
> To: A Mailing list for WIEN2k users 
> Subject: [Wien] Berrypi Error
> 
>   Caution: External email.
> 
> 
> Dear Prof. Peter Blaha and Prof. Oleg Rubel,
> 
> 
> hope this email finds you in good health and spirits. I am reaching out to
> respectfully report a technical challenge we recently encountered in our
> Wien2k calculations using BerrypI, and to share the solution we found in
> hopes that it might be helpful.
> 
> Our team has been utilizing Wien2k version 23.2, along with Python version
> 3.10.9 and Numpy version 1.23.5. Initially, the electronic part of the
> calculations proceeded without any issues. However, we stumbled upon a
> snag in the ionic part, which resulted in the following error message:
> 
> “Traceback (most recent call last): File "/opt/codes/wien2k/v23.2/berrypi",
> line 1081, in  theCalc =
> postProcBerryPhase(configFile,phasesRaw,spCalc) File
> "/opt/codes/wien2k/v23.2/berrypi", line 72, in postProcBerryPhase
> mainCalculation = b_PyCalc.MainCalculationContainer( File
> "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line 338, in
> init ionP = self.determineIonPolarization(wrpFn,args) File
> "/opt/codes/wien2k/v23.2/SRC_BerryPI/BerryPI/calculations.py", line 621, in
> determineIonPolarization if isinstance(iValence, collections.Iterable):
> AttributeError: module 'collections' has no attribute 'Iterable'”
> 
> In our efforts to resolve this, we made the following changes in the
> calculations.py file:
> 
> 1.Altered the import statement from:
> 
>   import collections
> 
>   to:
> 
>   from collections.abc import Iterable
> 
> 2.Amended the following line:
> 
>   from:
> 
>   if isinstance(iValence, collections.Iterable):
> 
>   to:
> 
>   if isinstance(iValence, Iterable):
> 
> These modifications have thankfully resolved the 'collections.Iterable' error,
> allowing our calculations to proceed without further issues.
> 
> I thought it prudent to share this experience with you, given your profound
> expertise and significant contributions to the development of Wien2k. Your
> guidance and insights have always been invaluable to our work, and I hope
> this information might be of some utility in your ongoing endeavors.
> 
> Thank you very much for your time and attention to this matter. Any further
> insights or suggestions from your esteemed perspectives would be greatly
> appreciated.
> 
> With sincere respect and best regards,
> 
> Sharbano Rahimi

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Re: [Wien] Confirming Chern z2 topological invariants using BerryPhase

[Rubel, Oleg]

Dear Burhan,

Thank you for trying wcc.py.

Fig. 4 in https://doi.org/10.48550/arXiv.2303.16306 plots evolution of Wannier 
charge centers (bands 61-78 gives that total of 18 WCCs) stored in wcc.csv file 
(the sample is shown and discussed on page 6 of the preprint paper). You can 
compare your result with our wcc.csv available from 
https://zenodo.org/record/7761199

Your table listed below gives the total phase (essentially a sum of those 18 
WCCs). Bi2Se3 is a centrosymmetric material and, thus, the total phase = 0. 
Therefore, this table is not useful here. But if you try a Chern insulator, the 
table should show a 2pi jump.

For the speed of light you need to search older posts in the mailing list. I 
found suggestions there.

I hope it will help
Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Burhan Ahmed
> Sent: Wednesday, July 26, 2023 1:40 PM
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: [Wien] Confirming Chern z2 topological invariants using BerryPhase
> 
>   Caution: External email.
> 
> 
> Dear experts, I want to reproduce the results for the confirmation of Chern
> and Z2 topological invariants as calculated in the manuscript “Software
> implementation for calculating Chern and ℤ2 topological invariants of
> crystalline solids with WIEN2k all-electron density functional package” by
> Gomez, et. al. https://doi.org/10.48550/arXiv.2303.16306 (DOI:
> 10.48550/arXiv.2303.16306).
> 
> 
> 
> For this I have tried with the tutorial by Rubel available in
> https://github.com/rubel75/BerryPI  When I run the wcc.py in my case
> directory (where I have done my PBE+SOC calculation)  I got the following
> results
> 
> Total Berry phase on each Wislon loop for bands 61-78:
> 
> --
> 
> i   kPhase wrap.Phase unwrap.
> 
> (rad)   (rad)
> 
> --
> 
> 1  [0.000, 0.000, ***] 56.549   0.000
> 
> 2  [0.000, 0.026, ***] 56.549  -0.000
> 
> 3  [0.000, 0.053, ***] 56.549  -0.000
> 
> 4  [0.000, 0.079, ***] 56.549   0.000
> 
> 5  [0.000, 0.105, ***] 56.549   0.000
> 
> 6  [0.000, 0.132, ***] 56.549  -0.000
> 
> 7  [0.000, 0.158, ***] 56.549  -0.000
> 
> 8  [0.000, 0.184, ***] 56.549  -0.000
> 
> 9  [0.000, 0.211, ***] 56.549   0.000
> 
> 10  [0.000, 0.237, ***] 56.549  -0.000
> 
> 11  [0.000, 0.263, ***] 56.549   0.000
> 
> 12  [0.000, 0.289, ***] 56.549  -0.000
> 
> 13  [0.000, 0.316, ***] 56.549  -0.000
> 
> 14  [0.000, 0.342, ***] 56.549  -0.000
> 
> 15  [0.000, 0.368, ***] 56.549  -0.000
> 
> 16  [0.000, 0.395, ***] 56.549  -0.000
> 
> 17  [0.000, 0.421, ***] 56.549  -0.000
> 
> 18  [0.000, 0.447, ***] 56.549   0.000
> 
> 19  [0.000, 0.474, ***] 56.549   0.000
> 
> 20  [0.000, 0.500, ***] 56.549   0.000
> 
> --
> 
> Here "***" refer to the direction of the Wilson loop.
> 
> 
> 
> Where the value of wrap. remains constant in my case. I don't know what the
> mistake I have done. Also in the manuscript by Gomez and Rubel there is a plot
> in Figure 4 (a,b,c,d). I want to know how to plot this graph (is it from .csv
> file?). Also they have performed a reduce SOC calculation by increasing the
> speed of light from 137 to 300. In which file/step we can change the value of
> c.
> 
> 
> 
> Dear experts if possible please upload a video tutorial my mentioning the 
> steps
> on how to confirm Chern and Z2 topological invariants by Berryphse. It will be
> a great help for the researchers.
> 
> 
> 
> 
> 
> 
> 
> Regards
> 
> Burhan Ahmed
> 
> Research Scholar, AUS
> 
> 

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Re: [Wien] Problem running fold2bloch interface with wien2k_17

[Rubel, Oleg]

I made the benchmarking on the same system (one of supercomputers) with 
pre-installed Matlab (2021a.5) and Octave (v5.2.0). I did not do the install 
and cannot comment on libraries. Both run on a single core of a compute node (I 
can see it in top). The Matlab runs through the task in 5-10 sec, while Octave 
needs 20 mins (!) for the same task. On my home desktop I do not have Octave, 
but Matlab timing is comparable with a standard installation.

I can provide files if anyone is interested in running the benchmark.

Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Laurence Marks
> Sent: Sunday, April 23, 2023 10:27 PM
> To: A Mailing list for WIEN2k users 
> Subject: Re: [Wien] Problem running fold2bloch interface with wien2k_17
> 
> A question out of curiosity. When you are comparing the Matlab and Octave
> versions, are you using mkl + OMP_NUM_THREADS for both?
> 
> 
> --
> Professor Laurence Marks (Laurie)
> Department of Materials Science and Engineering, Northwestern University
> www.numis.northwestern.edu <http://www.numis.northwestern.edu>
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought" Albert Szent-Györgyi
> 
> On Sun, Apr 23, 2023, 16:08 Rubel, Oleg  <mailto:rub...@mcmaster.ca> > wrote:
> 
> 
>   Dear Gavin,
> 
>   Many thanks for letting me know about all of those inconsistencies. I
> fixed the links. Also the ubs_dots_w2k_octave.m script was revisited to fix
> issues that you mentioned. I had to make some kind of a  progress bar
> because it takes relatively long to run for a realistic scenario. For some 
> reason
> the MATLAB version of the same (ubs_dots.m) runs an order of magnitude
> faster. All updates were pushed to GitHub.
> 
>   Thank you once again
>   Oleg
> 
>   > -Original Message-
>   > From: Wien  <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> > On Behalf Of
>   > Gavin Abo
>   > Sent: Wednesday, April 19, 2023 1:04 AM
>   > To: wien@zeus.theochem.tuwien.ac.at
> <mailto:wien@zeus.theochem.tuwien.ac.at>
>   > Subject: Re: [Wien] Problem running fold2bloch interface with
> wien2k_17
>   >
>   > Dear Oleg,
>   >
>   > The tutorial 1 at:
>   >
>   > https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-
> Lattice-of-
>   > Hydrogen-atoms
>   >
>   > It has:
>   >
>   >
>   > ~/fold2Bloch/fold2Bloch -c 6-atom2D.vector "''1 0 0:0 2 0:0 0 3''"
>   >
>   > Cannot remember for sure but that might not have worked starting
> with
>   > (double quote)(single quote)(single quote).  I think it needed to be
> (double
>   > quote)(single quote).  Similarly ending with (single quote)(double
> quote).
>   >
>   > The ubs_dot.m link seems to be broken pointing to:
>   >
>   >
>   >
> https://github.com/rubel75/fold2Bloch/blob/master/Utils/ubs_dots.m
>   >
>   >
>   > The working link now appears to be:
>   >
>   > https://github.com/rubel75/fold2Bloch-
>   > Wien2k/blob/master/utils/ubs_dots.m
>   >
>   > It might just be me, but instead of the matlab script, I like using 
> the
> octave
>   > script at:
>   >
>   >
>   > https://github.com/rubel75/fold2Bloch-
>   > Wien2k/blob/master/utils/ubs_dots_w2k_octave.m
>   >
>   >
>   > However, if I recall correctly, the script failed to run right.
>   >
>   > The ubs_dots.m has line 43:
>   >
>   > roundOffErrK = 0.01; % this is the round off error 1/3 =
> 0.33 + err
>   >
>   > and it has lines 70-72:
>   >
>   >
>   > epsk = [roundOffErrK roundOffErrK roundOffErrK]; % k rounding
> error epsk =
>   > coordTransform(epsk,G); % transform to Cart. coords epsk =
>   > sqrt(dot(epsk,epsk)); % get magnitude of the vector
>   >
>   >
>   > I believe I had to add line 43 after line 54 and lines 70-72 between
> lines 72 and
>   > 73 in the current ubs_dots_w2k_octave.m for it to work.
>   >
>   >
>   > Regarding Tutorial 2 at:
>   >
>   >
>   > https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-2:-
> Bismuth-in-
>   > GaAs
>   >
>   >
>   > It has:
>   >
>   > ~/fold2Bloch/fold2Bloch -c Ga8As7Bi1.vector 2:2:2
>   >
>   > According to your post below

Re: [Wien] Problem running fold2bloch interface with wien2k_17

[Rubel, Oleg]

Dear Gavin,

Many thanks for letting me know about all of those inconsistencies. I fixed the 
links. Also the ubs_dots_w2k_octave.m script was revisited to fix issues that 
you mentioned. I had to make some kind of a  progress bar because it takes 
relatively long to run for a realistic scenario. For some reason the MATLAB 
version of the same (ubs_dots.m) runs an order of magnitude faster. All updates 
were pushed to GitHub.

Thank you once again
Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Gavin Abo
> Sent: Wednesday, April 19, 2023 1:04 AM
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: Re: [Wien] Problem running fold2bloch interface with wien2k_17
> 
> Dear Oleg,
> 
> The tutorial 1 at:
> 
> https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-Lattice-of-
> Hydrogen-atoms
> 
> It has:
> 
> 
> ~/fold2Bloch/fold2Bloch -c 6-atom2D.vector "''1 0 0:0 2 0:0 0 3''"
> 
> Cannot remember for sure but that might not have worked starting with
> (double quote)(single quote)(single quote).  I think it needed to be (double
> quote)(single quote).  Similarly ending with (single quote)(double quote).
> 
> The ubs_dot.m link seems to be broken pointing to:
> 
> 
> https://github.com/rubel75/fold2Bloch/blob/master/Utils/ubs_dots.m
> 
> 
> The working link now appears to be:
> 
> https://github.com/rubel75/fold2Bloch-
> Wien2k/blob/master/utils/ubs_dots.m
> 
> It might just be me, but instead of the matlab script, I like using the octave
> script at:
> 
> 
> https://github.com/rubel75/fold2Bloch-
> Wien2k/blob/master/utils/ubs_dots_w2k_octave.m
> 
> 
> However, if I recall correctly, the script failed to run right.
> 
> The ubs_dots.m has line 43:
> 
> roundOffErrK = 0.01; % this is the round off error 1/3 = 0.33 + err
> 
> and it has lines 70-72:
> 
> 
> epsk = [roundOffErrK roundOffErrK roundOffErrK]; % k rounding error epsk =
> coordTransform(epsk,G); % transform to Cart. coords epsk =
> sqrt(dot(epsk,epsk)); % get magnitude of the vector
> 
> 
> I believe I had to add line 43 after line 54 and lines 70-72 between lines 72 
> and
> 73 in the current ubs_dots_w2k_octave.m for it to work.
> 
> 
> Regarding Tutorial 2 at:
> 
> 
> https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-2:-Bismuth-in-
> GaAs
> 
> 
> It has:
> 
> ~/fold2Bloch/fold2Bloch -c Ga8As7Bi1.vector 2:2:2
> 
> According to your post below, that needs to be:
> 
> 
> ~/fold2Bloch/fold2Bloch -c 6-atom2D.vector "'2 0 0:0 2 0:0 0 2'"
> 
> The link to ubs_dot.m for Ga8As7Bi1.unfolded for reproducing the tutorial 2
> plot seems to be broken (for me it leads me to a github page with a 404  
> error).
> 
> 
> Thanks,
> 
> Gavin
> WIEN2k user 

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Re: [Wien] Problem running fold2bloch interface with wien2k_17

[Rubel, Oleg]

Dear Dibya,

thanks for sharing the error. It is a nice case when the error message is 
helpful and tells you exactly what went wrong and how to fix (please read) 

The input arguments were changed (around Aug 2022) to accommodate a full 3x3 
transformation matrix P (not just multipliers for each lattice vector). Your 
matrix will, probably, be "'2 0 0:0 2 0:0 0 2'". Watch out for double quotes! 
It is strange, but I found them needed to pass the argument as a whole string. 
(Does anyone have better suggestion?)

If you need more insight, please check fold2Bloch Guide: 
https://github.com/rubel75/fold2Bloch-Wien2k/wiki/fold2Bloch-Guide
The ultimate level of details can be found in this manuscript: 
https://arxiv.org/abs/2301.02696

Good luck
Oleg

P.S. Please let me where you got the old format "~/fold2Bloch/fold2Bloch -c 
Ga8As7Bi1.vector 2:2:2", so we can go back and change the documentation where 
possible.

> -Original Message-
> From: Wien  On Behalf Of
> DibyaR Prakash
> Sent: Tuesday, April 18, 2023 10:29 AM
> To: wien@zeus.theochem.tuwien.ac.at
> Subject: [Wien] Problem running fold2bloch interface with wien2k_17
> 
> Dear Wien2K users,
> 
> I have a problem running fold2boch command . I install fold2bloch program
> using make command.
> fold2bloch excitable is generated.
> However when I run the tutorial.
> # ~/fold2Bloch/fold2Bloch -c Ga8As7Bi1.vector 2:2:2 I got the following error,
> 
> 
>  **
>  ** fold2Bloch   **
>  ** version Jul 12, 2022 **
>  **
> Detected 3 input arguments
> Checking prerequisite files...
> Ga8As7Bi1.vector  vector file found
>  Unable to read the Dp2s(1,:) matrix
>  Relevant input line = 2:2:1
>  Parsed input section = 2
>  while expected 3 numerical values separated by space.
> ERROR: Unable to recognize command line options. Possible options are:
> fold2Bloch -h # get help
> fold2Bloch -r case.vector[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" #
> real calculation (inversion symm.) no SO fold2Bloch -c case.vector[_1] "'P11
> P12 P13:P21 P22 P23:P31 P32 P33'" # complex calc. (no inv. symm.) no SO
> fold2Bloch case.vector[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" #
> complex calc. implied no SO fold2Bloch -so case.vectorso[_1]
> case.vectorsodn[_1] case.normsoup[_1] case.normsodn[_1] "'P11 P12
> P13:P21 P22 P23:P31 P32 P33'" # spin-orbit without -sp fold2Bloch -so
> case.vectorsoup[_1] case.vectorsodn[_1] case.normsoup[_1]
> case.normsodn[_1] "'P11 P12 P13:P21 P22 P23:P31 P32 P33'" # spin-orbit
> with -sp
> 
> Notes:
> (1) [P] matrix (internally called Dp2s) is used to transform primitive a_p to
> supercell a_s lattice vectors (same as in VESTA):
>a_s(i) = sum_j a_p(j)*P(j,i)  i,j = 1, 2, 3
> (2) Use quotations to input the [P] matrix _exactly_ as shown in this help
> (3) Tutorials can be found at https://github.com/rubel75/fold2Bloch-
> Wien2k/wiki
> 
> 
> The log file is attached.
> 
> 
> Thank you in advance.
> 
> 
> Dibya Prakash Rai
> -
> 
> Assistant Professor
> 
> Physical Sciences Research Center(PSRC)
> 
> Pachhunga University College
> 
> Aizawl,Mizoram
> 
> India-796001
> 
> Mobile:8132832252
> -
> https://www.researchgate.net/profile/Dibya_Rai
> https://scholar.google.co.in/citations?user=rQvHHw8J=en
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Re: [Wien] Difference between "x lapw2 -qtl" and "x qtl"

[Rubel, Oleg]

Dear Lukasz,

sorry, I do not have a direct answer, but you might consider checking files 
case.normsoup and case.normsodn. They contain alpha^2 (normsoup) and beta^2 
(normsodn) spinor components for each k point and each eigenvalue (check that 
alpha^2 + beta^2=1). I would compare alpha^2 vs beta^2 for a k point and 
eigenvalue of interest to see if one of them dominate. These are plane text 
files and easy to read. Here is the subroutine for reading used in fold2Bloch 
https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/read_norms.F90 It is 
called sequentially for each k point. The number of eigenstates (NE) sometimes 
changes from one k point to another.

Best regards
Oleg

> -Original Message-
> From: Wien  On Behalf Of
> pluto via Wien
> Sent: Tuesday, March 14, 2023 8:32 PM
> To: A Mailing list for WIEN2k users 
> Cc: pluto 
> Subject: [Wien] Difference between "x lapw2 -qtl" and "x qtl"
> 
> Dear All,
> 
> I am calculating one of the 1T TMDC materials. This material e.g. has a spin-
> polarized Dirac cone on the surface (see e.g. DOI
> 10.1088/2516-1075/ab09b7 for review of similar materials).
> 
> I calculated 10L (15 inequivalent atoms) and 20L (30 inequivalent atoms)
> slabs. I allowed sgroup to find the space group (no. 164) in order to speed up
> the calculation. In this case it means each inequivalent atom has 2 equivalent
> positions.
> 
> It is a spin polarized calculation with SOC. Band structures look good
> compared to the literature Wannier calculations.
> 
> One obvious test is to check spin polarization of the Dirac cone.
> 
> Band characters can be calculated either using x lapw2 -band -qtl -up/dn -so
> (default in w2web) or using x qtl -band -up/dn -so
> 
> Importantly, in order to make x qtl work I need to cp case.in1 case.in1c
> although the system does have inversion (otherwise qtl gives an error and
> nothing is calculated). Is this allowed?
> 
> Another problem is that for the 20L slab x spaghetti does not want to plot fat
> bands out of case.qtlup/dn produced by "x qtl". I didn't look at the
> case.qtlup/dn files in detail yet (I will, but it might take a while), but 
> either they
> are incomplete (i.e. x qtl cannot handle a big slab), or spaghetti cannot 
> handle
> these files beyond a certain size limit. On the other hand case.qtlup/dn
> produced by x lapw2 always work with fat bands. Of couse when using x qtl I
> limit the number of atoms in case.inq, and I typically only calculate 
> characters
> for 2 outermost atoms (my case.inq pasted below). For 10L slab everything
> works fine.
> 
> The plotted results (using w2web) for these two cases look very different. I
> tried plotting characters on couple of outermost atoms.
> 
> x lapw2 does not show any spin polarization of the Dirac cone x qtl shows
> clear very high polarization of the Dirac cone
> 
> This happens when I plot total character on a particular atom, is it not an
> effect related to some Y_lm character or things like that.
> 
> I think in general I should split all atoms in order to get correct spin
> polarization (the so-called hidden spin polarization introduced by
> Zunger/Freeman). This is what one had to do with the 2H MoS2 calculations
> several years back. But splitting all atoms would probably make 20L slab
> calculation prohibitive on my system (I think 20L would be unrealistic).
> 
> But perhaps the QTL program can somehow do the job of splitting the
> equivalent atoms even on slab with equivalent positions.
> 
> I also paste below case.inso, note that the direction of spin polarization 
> quant.
> axis is along 100, i.e. in-plane, as it should for these materials.
> 
> Best,
> Lukasz
> 
> 
> case.inq file:
> 
> -9.0   3.0   Emin  Emax
>2 number of atoms
> 1   1  0  1   iatom,qsplit,symmetrize,locrot
> 3   0  1  2  nL, l-values
> 0 0 1
>30   1  0  1   iatom,qsplit,symmetrize,locrot
> 3   0  1  2  nL, l-values
> 0 0 1
> 
> case.inso
> 
> WFFIL
> 4  0  0 llmax,ipr,kpot
> -10  1.9Emin, Emax
>  1 0 0   h,k,l (direction of magnetization)
>   30   number of atoms with RLO
> 1 -3.53 0.0001 STOP atom-number, E-param for RLO
> 2 -3.53 0.0001 STOP atom-number, E-param for RLO
> 3 -3.53 0.0001 STOP atom-number, E-param for RLO
> 4 -3.53 0.0001 STOP atom-number, E-param for RLO
> 5 -3.53 0.0001 STOP atom-number, E-param for RLO
> 6 -3.53 0.0001 STOP atom-number, E-param for RLO
> 7 -3.53 0.0001 STOP atom-number, E-param for RLO
> 8 -3.53 0.0001 STOP atom-number, E-param for RLO
> 9 -3.53 0.0001 STOP atom-number, E-param for RLO
> 10 -3.53 0.0001 STOP atom-number, E-param for RLO
> 11 0.30 0. CONT atom-number, E-param for RLO
> 12 0.30 0. CONT atom-number, E-param for RLO
> 13 0.30 0. CONT 

Re: [Wien] Finding the right plotting window for Wannier functions

[Rubel, Oleg]

Here is the UG for wien2wannier: 
https://github.com/wien2wannier/wien2wannier/blob/master/doc/wien2wannier_userguide.pdf
The case .inwplot file is discussed on Page 7. Fractional coordinates are 
mentioned there. Could it be that your result can be explained by fractional 
coordinates?

Oleg

> -Original Message-
> From: Wien  On Behalf Of
> Brandon Gunn via Wien
> Sent: Monday, February 27, 2023 5:20 PM
> To: wien@zeus.theochem.tuwien.ac.at
> Cc: Brandon Gunn 
> Subject: [Wien] Finding the right plotting window for Wannier functions
> 
> Hello,
> 
> I am attempting to plot a WF which is centered at (0 0 7.645) with a spread of
> 0.405.
> 
> For the GaAs example, to plot a WF centered at the origin, lines 2-5 of 
> inwplot
> read:
> 
>   -1 -1 -1 1
>   1 -1 -1 1
>   -1 1 -1 1
>   -1 -1 1 1
> 
> 
> Using the following lines to shift the the L=7 unit cell results in the WF
> displaying very far away from the displayed unit cell along the Z direction in
> Xcrysden:
> 
>   -1 -1 6 1
>   1 -1 6 1
>   -1 1 6 1
>   -1 -1 8 1
> 
> 
> However, if I use the same lines as for the origin-centered GaAs WF, my WF
> seems to plot only one unit cell away from the unit cell being displayed in
> Xcrysden. Trying to walk in the z-coordinate by 1 u.c. does not seem to move
> the WF.
> 
> Can someone please help explain which parameters to use in order to properly
> view the WF centered at (0 0 7.645)?
> 
> Thank you,
> Brandon
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Re: [Wien] Missing write_inwplot executable

[Rubel, Oleg]

Dear Brandon,

I checked tutorials from the workshop in 2019 
(http://www.wien2k.at/events/ws2019/Exercises_19-tot.pdf). Page 36 describes 
plotting of WFs. To generate 'case.inwplot
‘ we just copied it from a template:

cp $WIENROOT/SRC_templates/case.inwplot
 GaAs-WANN.inwplot

Maybe you do not need write_inwplot?

I hope it will help
Oleg

> On Feb 6, 2023, at 4:09 PM, Brandon Gunn via Wien 
>  wrote:
> 
> Hello,
> 
> I am running Wien2k v21 on an Ubuntu system. I am trying to work through a 
> tutorial to obtain the Wannier functions for GaAs. I receive an error stating 
> that the 'write_inwplot' command is not found. While investigating, I see in 
> the SRC_trig folder that I have a 'write_inwplot.f' file but there is no 
> corresponding 'write_inwplot.o' file or 'write_inwplot' executable. 
> 
> It looks like maybe this file was missed during the initial Wien2k 
> compilation or something? How can I obtain the missing executable?
> 
> Thank you,
> Brandon
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Re: [Wien] problem in compiling mstar with gfortran

[Rubel, Oleg]

Dear Halim,

it seems that something is wrong with 'lmkl_gf_lp64'. I did a test and compiled 
with GNU FORTRAN first with correct settings:

(base) [rubel@gra-login1 mstar]$ make veryclean
rm -f *.o *.mod *.MOD
rm -f *~
(base) [rubel@gra-login1 mstar]$ make
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_pij_vasp.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c mstar.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c eigvs.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_numlines_vasp.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_pij.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c kdelta.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_numlines.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c eigvz.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_nb.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c dgenen.f90
gfortran 
-L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/lib/intel64
 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread -fopenmp -ldl -g 
-fbacktrace -ffpe-summary=none  -o mstar read_mommat_pij_vasp.o mstar.o eigvs.o 
read_numlines_vasp.o read_mommat_pij.o kdelta.o read_numlines.o eigvz.o 
read_mommat_nb.o dgenen.o
(base) [rubel@gra-login1 mstar]$ gfortran --version
GNU Fortran (GCC) 9.3.0

Then I changed 'lmkl_gf_lp64' so something unrecognizable 'lmkl_ggf_lp64'. Here 
is the result:

(base) [rubel@gra-login1 mstar]$ make
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_pij_vasp.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c mstar.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c eigvs.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_numlines_vasp.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_pij.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c kdelta.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_numlines.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c eigvz.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c read_mommat_nb.f90
gfortran 
-I/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/include
 -fopenmp -g -fbacktrace -ffpe-summary=none  -c dgenen.f90
gfortran 
-L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/imkl/2020.1.217/mkl/lib/intel64
 -lmkl_ggf_lp64 -lmkl_sequential -lmkl_core -lpthread -fopenmp -ldl -g 
-fbacktrace -ffpe-summary=none  -o mstar read_mommat_pij_vasp.o mstar.o eigvs.o 
read_numlines_vasp.o read_mommat_pij.o kdelta.o read_numlines.o eigvz.o 
read_mommat_nb.o dgenen.o
/cvmfs/soft.computecanada.ca/gentoo/2020/usr/x86_64-pc-linux-gnu/binutils-bin/2.33.1/ld.gold:
 error: cannot find -lmkl_ggf_lp64
eigvs.f90:44: error: undefined reference to 'ssyevd_'
eigvs.f90:61: error: undefined reference to 'ssyevd_'
eigvz.f90:49: error: undefined reference to 'cheevd_'
eigvz.f90:67: error: undefined reference to 'cheevd_'
collect2: error: ld returned 1 exit status

I suspect that you have something else instead of 'lmkl_gf_lp64'. To find out 
more try to explore the mkl library folder:

(base) [rubel@gra-login1 mstar]$ cd 

Re: [Wien] Symmetry adapted wanniers using wien to wannier interface

[Rubel, Oleg]

Dear Banhi,

the current w2w interface does not create the .dmn file you need for the 
symmetry-adapted wannierization.
We recently started a discussion about adding new features to w2w (the dmn file 
was on the list), but there is no timeline yet.

Best regards
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca



From: Wien  On Behalf Of Banhi 
Chatterjee
Sent: Wednesday, July 6, 2022 1:42 PM
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Symmetry adapted wanniers using wien to wannier interface

Dear users,
I am interested in performing a symmetry adapted Wannierization using the 
keyword  "site_symmetry=.true." in the .win file. However, this needs an 
additional input file seedname.dmn (in addition to the amn, and mmn files) 
which the wien2wannier interface (version 19.1) do not produce.
Is there a way to do a symmetry adapted Wannier using the existing versions of 
Wien2k and wien2wannier codes?
Thanks a lot for your reply.
Regards
Banhi
-- 
Dr. Banhi Chatterjee
Post-doctoral researcher
Jozef stefan Institute, Ljubljana, Slovenia
e-mail: mailto:banhi.chatter...@ijs.si
mailto:banhi...@gmail.com
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Re: [Wien] How to calculate AHC in wien2k?

[Rubel, Oleg]

I see. Thanks for sharing. Many people complain about difficulties with MLWF, 
but the wannier90 community also tries to address issues to make wannierization 
easier. Maybe those lectures/tutorials will help (see 
https://indico.ictp.it/event/9789/other-view?view=ictptimetable )
"Selected columns of density matrix for Wannier functions…”, “Automated 
Wannierisation & SCDM”, “Spread-balanced Wannier functions and automated 
Wannierization with the ASE”.

Once again, I do not think we have a solution within the WIEN2k ecosystem.

All the best
Oleg

> On Jun 21, 2022, at 3:33 PM, Samir Rom  wrote:
> 
> Hi,
> Thanks for your reply. I am facing some problems in building an effective 
> model using the MLWF function as my band structure is not that clean and it 
> has several band crossings near Fermi level. That is why I am avoiding this 
> path and am thinking of calculating in a different way. I can get the Berry 
> curvature information by using the Kubo formula. Anomalous Hall conductivity 
> is nothing but the Berry curvature sum over the first BZ. Can you suggest 
> anything better than this?
> 
> Best regards,
> Samir Rom
>  
> SAMIR ROM
> Senior Research Fellow (SRF)
> Department of Condensed Matter Physics and Material Sciences.
> S N Bose National Centre for Basic Sciences
> JD Block, Sector-III, Salt lake City, Kolkata-700106
> West Bengal 
> India
> 
> 
> 
> On Tue, Jun 21, 2022 at 9:16 PM Rubel, Oleg  wrote:
> Dear Samir,
> 
> It is not possible to get AHC in WIEN2k without wannier90, as far as I know. 
> My understanding is that one needs to get the Berry curvature Omega(k) (we 
> only have the Berry phase). Also, we need a very fine k mesh (something like 
> 200x200x200 for iron) to resolve fast-changing Omega(k) on the Fermi surface.
> 
> Would you mind sharing your experience related to WIEN2k interface to 
> wannier90? What is your reason to avoid Wannier?
> 
> Thank you
> Oleg
> 
> --
> Oleg Rubel (PhD, PEng)
> Department of Materials Science and Engineering
> McMaster University
> JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
> Email: rub...@mcmaster.ca
> Tel: +1-905-525-9140, ext. 24094
> Web: http://olegrubel.mcmaster.ca
> 
> > On Jun 21, 2022, at 3:39 AM, Samir Rom  wrote:
> > 
> > Dear Wien2k users,
> > 
> > Is it possible to compute Anomalous Hall Conductivity (AHC) value in Wien2k 
> > self-consistently without first building an effective model using the 
> > maximally localised generalised Wannier function (MLWF)?
> > 
> > Best regards,
> > SAMIR ROM
> > Senior Research Fellow (SRF)
> > Department of Condensed Matter Physics and Material Sciences.
> > S N Bose National Centre for Basic Sciences
> > JD Block, Sector-III, Salt lake City, Kolkata-700106
> > West Bengal 
> > India
> > 
> > ___
> > Wien mailing list
> > Wien@zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> > SEARCH the MAILING-LIST at:  
> > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 
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> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
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Re: [Wien] How to calculate AHC in wien2k?

[Rubel, Oleg]

Dear Samir,

It is not possible to get AHC in WIEN2k without wannier90, as far as I know. My 
understanding is that one needs to get the Berry curvature Omega(k) (we only 
have the Berry phase). Also, we need a very fine k mesh (something like 
200x200x200 for iron) to resolve fast-changing Omega(k) on the Fermi surface.

Would you mind sharing your experience related to WIEN2k interface to 
wannier90? What is your reason to avoid Wannier?

Thank you
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

> On Jun 21, 2022, at 3:39 AM, Samir Rom  wrote:
> 
> Dear Wien2k users,
> 
> Is it possible to compute Anomalous Hall Conductivity (AHC) value in Wien2k 
> self-consistently without first building an effective model using the 
> maximally localised generalised Wannier function (MLWF)?
> 
> Best regards,
> SAMIR ROM
> Senior Research Fellow (SRF)
> Department of Condensed Matter Physics and Material Sciences.
> S N Bose National Centre for Basic Sciences
> JD Block, Sector-III, Salt lake City, Kolkata-700106
> West Bengal 
> India
> 
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

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Re: [Wien] Charged cell versus virtual atom?

[Rubel, Oleg]

I agree that Z=40.0625 was not a good suggestion. Then Z=22.0675 is reasonable 
to simulate n-doped STO. Would it be possible to verify that the additional 
charge accumulates at the surface? If I recall correctly, STO is cubic. It 
could be that the symmetry will be broken to respond to the surface dipole?

Also, I have heard about core-hole calculations. Is it completely irrelevant 
here?

Best regards
Oleg


From: Wien  on behalf of Laurence 
Marks 
Sent: Monday, May 2, 2022 10:35
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Charged cell versus virtual atom?

To clarify first: Nb-doped STO is commercial, with Nb on the Ti site doping the 
STO n-type -- Nb is 5+ valence versus 4+ for Ti. It is known that the carriers 
are delocalized.

I am interested in the near-surface band bending, both clean and with a Shottky 
contact to Pt/Pd under force. This models some of the terms in the 
trbolectricity of a moving Shottky diode contact. (This is bare-bones details.)

Band bending, but also energy (to get contact forces and bulk lattice) matter.

While having Z=22.0675 is more like V doped, it does balance the charge. 
Charged cells have approximations for the total energy, and add a background 
potential, which raises issues in my mind for the vacuum & Pd/Pt.

Simple approximations have ~80 total atoms, 25 unique; a more complete has 
~700/190 for total/unique.

To zero'th order the two look similar, but.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu<http://www.numis.northwestern.edu>
"Research is to see what everybody else has seen, and to think what nobody else 
has thought" Albert Szent-Györgyi

On Mon, May 2, 2022, 5:41 AM Fecher, Gerhard 
mailto:fec...@uni-mainz.de>> wrote:
Z=40.0625 means you replace all Ti by Zr + a little electrons, instead of Ti + 
1/16 e-, isn't it ?
I assume that changing the charge by epsilon e- works only for neighbouring 
elements, on top,  if you rplace the Z of Ti (22) by 22+1=23 then you have 
fully V and not Ti+1/2 Cr, etc..

==> supercell even if its vast (or some program that uses CPA to have a 
mean field behaviour).

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien 
[wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at>]
 im Auftrag von Rubel, Oleg [rub...@mcmaster.ca<mailto:rub...@mcmaster.ca>]
Gesendet: Montag, 2. Mai 2022 05:19
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Charged cell versus virtual atom?

I must admit that I do not have any experience with the fractional Z, but it 
seems that the option (b) could be better. At least it has some chemical 
specificity. Maybe it is better to use Z=40.0625 to differentiate between Nb 
and V?

Best regards
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Laurence Marks 
mailto:laurence.ma...@gmail.com>>
Sent: Sunday, May 1, 2022 16:59
To: A Mailing list for WIEN2k users
Subject: [Wien] Charged cell versus virtual atom?

As part of a larger problem, I need to simulate a Nb-doped SrTiO3 surface, 
where 1/16 Ti sites is Nb. To first order this is 1/16 extra electrons. There 
are two ways I can think of to do this:
a) Charged cell calculation, with extra electrons + background charge.
b) Virtual atom, where the Ti's have a Z of 22.0625.

Does anyone have any experience with something similar? I can think of reasons 
why both have issues, e.g. the extra potential in the vacuum in a).

N.B., doing a super-duper surface cell with 1/16 Ti changed is too vast.

--
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
http://www.numis.northwestern.edu<http://www.numis.northwestern.edu>
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Györgyi
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Re: [Wien] Charged cell versus virtual atom?

[Rubel, Oleg]

I must admit that I do not have any experience with the fractional Z, but it 
seems that the option (b) could be better. At least it has some chemical 
specificity. Maybe it is better to use Z=40.0625 to differentiate between Nb 
and V?

Best regards
Oleg


From: Wien  on behalf of Laurence 
Marks 
Sent: Sunday, May 1, 2022 16:59
To: A Mailing list for WIEN2k users
Subject: [Wien] Charged cell versus virtual atom?

As part of a larger problem, I need to simulate a Nb-doped SrTiO3 surface, 
where 1/16 Ti sites is Nb. To first order this is 1/16 extra electrons. There 
are two ways I can think of to do this:
a) Charged cell calculation, with extra electrons + background charge.
b) Virtual atom, where the Ti's have a Z of 22.0625.

Does anyone have any experience with something similar? I can think of reasons 
why both have issues, e.g. the extra potential in the vacuum in a).

N.B., doing a super-duper surface cell with 1/16 Ti changed is too vast.

--
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Györgyi
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Re: [Wien] amorphous binary rare-earth transition metal alloys

[Rubel, Oleg]

Here are my two cents:
Amorphous structures is an advanced topic, but not impossible. Our group has 
calculated the electronic structure of amorphous Se in the past with WIEN2k 
(https://olegrubel.mcmaster.ca/publications/2012/Darbandi_JPCM_24_2012.pdf), 
but we had to construct the structural model ourselves using a pre-existing 
recipe (see Refs. 21-23 therein). This recipe is not universal though. 
Alternatively, there should also be literature on the phase-change GST 
compound. I have seen amorphous structures created using ab initio MD by 
heating up (melting) and slowly cooling down, which is a more "universal" 
method.

In summary: I do not think WIEN2k has tools that are dedicated to facilitate 
creation of an amorphous structure. But if you manage to generate a reasonable 
structure somehow, it should be possible to calculate its electronic structure 
with WIEN2k.

I hope it will help
Oleg


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Re: [Wien] Problem with fold2Bloch in real calculations

[Rubel, Oleg]

Dear Veronique,

I fixed the 'allocatable array is already allocated' error. The updated version 
should be on the GitHub:
https://github.com/rubel75/fold2Bloch-Wien2k

I wonder if you can make a plot for FeSe (primitive vs unfolded) similar to 
what we just did for WS2 to make sure that f2b produces a reasonable result. It 
would be useful particularly in the [-r] mode since this option is not well 
tested.

Thank you in advance!

Best regards
Oleg


From: Wien  on behalf of Véronique 
BROUET 
Sent: Thursday, January 13, 2022 05:59
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Problem with fold2Bloch in real calculations

Dear Oleg,

Thanks a lot, it's working perfectly now in -r mode.

However, I still have a problem with spin-orbit calculations, namely the 
message "allocatable array is already allocated" when processing the second k 
point of the klist. Maybe I'm not using the right input ? As I'm not running a 
spin-polarized case, I only have a *.vectorso and *.vectorsodn files (they have 
same size). I have the *.normsoup and *.normsodn files.
So I have tried :

fold2Bloch -so case.vectorso case.vectorsodn case.normsoup case.normsodn 2:2:1

on FeSe case for example (the SO calculation itself is ok) and got the error 
message. I had same problem with other cases.
Do you see what's wrong ?

As for FeSe structure it is indeed sqrt(2)*sqrt(2) unit cell with 2 atoms (it 
is similar for other cases I mentioned as Sr2IrO4 and SrIrO3). It still works 
fine if I unfold in the larger unit cell and keep the part relevant for 1Fe 
unit cell.

Veronique

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Re: [Wien] Problem with fold2Bloch in real calculations

[Rubel, Oleg]

Dear Veronique,

the option [-r] should work now (you need to fetch the most recent version from 
GitHub and recompile the code). There was indeed a problem with array 
allocation that caused a segfault. Thanks for reporting that!

I tested you FeSe structure. Technically f2b runs, but this structure is _not_ 
a 2x2x1 supercell in a standard way of thinking. If the primitive cell contains 
1 Fe atom, the 2x2x1 should have 4 Fe atoms, while you have 2. Maybe this is a 
sqrt(2) supercell?

Best regards
Oleg


From: Wien  on behalf of Rubel, Oleg 

Sent: Tuesday, January 11, 2022 18:44
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Problem with fold2Bloch in real calculations

Dear Veronique,

the [-r] option is not much tested (if tested at all). The main reason is that 
typical supercells with disorder have a low symmetry. I do not exclude that 
some supercells can possess the inversion, but I did not have such before in 
practice. Would you mind sharing a simplest struct file of your supercell with 
inversion?

As a temporary solution, one can break the inversion symmetry with labels 
(e.g., Sr1, Sr2, ...). This will force the complex calculation.

Best regards
Oleg


From: Wien  on behalf of Véronique 
BROUET 
Sent: Tuesday, January 11, 2022 10:22
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Problem with fold2Bloch in real calculations

Dear Oleg,

It's not happening with only one case. I've tried it for the very simple FeSe 
(attached case), trying to unfold with 2:2:1, but also for Sr2IrO4 or SrIrO3 
(the case I'm interested in at the moment, also attached) or your examples. 
Everything works fine in complex mode, but not with another switch.

For example both FeSe and SrIrO3 have inversion symmetry and do not require 
complex calculation, but if I run the case in real mode, fold2Bloch recognizes 
well it's a real case.vector (it asks for the -r switch), but cannot process it 
(segmentation error).

Veronique

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Re: [Wien] fold2bloch: unfolded band-structure plot have addition bands

[Rubel, Oleg]

Dear Asif,

I am glad it worked for you. I think your unfolded band structure is OK. I am 
not sure what you refer to as "numerical precision of the unfolding procedure", 
but sometime weights go down to 0.0001. So, 0.2 is not so small. The plotting 
script has a weight threshold to display (wth = 0.05; % threshold weight). The 
default is 0.05. Everything less than that will not be displayed. You can set 
it to =0 and see what happens.

> ... bands with Bloch weight < 0.2 in just below the conduction band.

I see a low-weighted conduction band at K point, but it is not below the band 
edge, which is between K-Gamma. Maybe you can highlight the band in question 
and enclose the folded band structure you refer in the text.

> My question is that is this due to the numerical precision of the unfolding 
> procedure which leaves some bands behind or if it is real how to 
> confirm/check such a thing?

It would be beneficial to increase the supercell size to better represent a 
random structure, if this is what you aim at.

Thank you
Oleg


From: Wien  on behalf of Asif Ali 

Sent: Wednesday, January 12, 2022 04:52
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] fold2bloch: unfolded band-structure plot have addition bands

Dear Sir,

I am thankful for your help. I am able to plot the correct unfolded band 
structure with the update plotting script.

I have one more question regarding the bands with small Bloch vector weights. 
In my calculated band structure (M_0.5M'_0.5 X_2), there are bands with Bloch 
weight < 0.2 in just below the conduction band. However these bands are clearly 
seen in the folded band structure.
My question is that is this due to the numerical precision of the unfolding 
procedure which leaves some bands behind or if it is real how to confirm/check 
such a thing?
I am enclosing the figure for your reference. I have increased the marker size 
20 for a clear view of low weight bands.

Looking forward to hearing from you

Thankyou and Regards
Asif

On Wed, Jan 12, 2022 at 3:16 PM Asif Ali 
mailto:as...@iiserb.ac.in>> wrote:
Dear Sir,

I am thankful for your help. I am able to plot the correct unfolded band 
structure with the update plotting script.

I have one more question regarding the bands with small Bloch vector weights. 
In my calculated band structure (M_0.5M'_0.5 X_2), there are bands with bloch 
weight < 0.2 in just below the conduction band. However these bands are clearly 
seen in the folded band structure.
My question is that is this due to the numerical precision of the unfolding 
procedure which leaves some bands behind or if it is real how to confirm/check 
such a thing


I am enclosing the figure for your reference. I have increased the marker size 
20 for a clear view of low weight bands.

Looking forward to hearing from you

Thankyou and Regards
Asif


On Wed, Jan 12, 2022 at 12:41 PM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> wrote:
Resent from Oleg Rubel:

Dear Asif,

I reproduced your problem. It happens during plotting and related to the
way a distance is calculated between a segment in k space and a point.

The GitHub now contains an updated version of plotting scripts
(https://github.com/rubel75/fold2Bloch-Wien2k/tree/master/Utils).

There is _no_ need to recompile fold2bloch or redo WIEN2k calculation.

Enclosed is the unfolded band structure of 2H-WS2 (2x2x2 supercell) vs
WIEN2k primitive cell to verify that it works.

Thank you for the bug report!

Best regards
Oleg


Am 11.01.2022 um 17:53 schrieb Asif Ali:
> Dear Sir,
>
> Thankyou for your response. Yes, I am working with WS2 and similar
> systems. At the moment,  I was doing LDA calculation and I plan to do
> LDA+SO calculations.
>
> Regards
> Asif
>

--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at
WIEN2k: http://www.wien2k.at
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--
Thanks and Regards
Asif Ali


--
Thanks and Regards
Asif Ali
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Re: [Wien] Problem with fold2Bloch in real calculations

[Rubel, Oleg]

Dear Veronique,

the [-r] option is not much tested (if tested at all). The main reason is that 
typical supercells with disorder have a low symmetry. I do not exclude that 
some supercells can possess the inversion, but I did not have such before in 
practice. Would you mind sharing a simplest struct file of your supercell with 
inversion?

As a temporary solution, one can break the inversion symmetry with labels 
(e.g., Sr1, Sr2, ...). This will force the complex calculation.

Best regards
Oleg


From: Wien  on behalf of Véronique 
BROUET 
Sent: Tuesday, January 11, 2022 10:22
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Problem with fold2Bloch in real calculations

Dear Oleg,

It's not happening with only one case. I've tried it for the very simple FeSe 
(attached case), trying to unfold with 2:2:1, but also for Sr2IrO4 or SrIrO3 
(the case I'm interested in at the moment, also attached) or your examples. 
Everything works fine in complex mode, but not with another switch.

For example both FeSe and SrIrO3 have inversion symmetry and do not require 
complex calculation, but if I run the case in real mode, fold2Bloch recognizes 
well it's a real case.vector (it asks for the -r switch), but cannot process it 
(segmentation error).

Veronique

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Re: [Wien] Problem with fold2Bloch in real calculations

[Rubel, Oleg]

Dear Véroniqu,


thank you for sharing your experience! It would help to get a sample structure file and enough details to recreate the
 problematic case on my end.


Thank you
Oleg

On Jan 11, 2022, at 07:35, Véronique BROUET  wrote:




Dear users,

I have recently installed the fold2Bloch procedure from Oleg Rubel and it works beautifully for complex calculations. Thanks a lot for this procedure !

However, I have a problem when using a real case. I systematically get an error message at the processing of the first k point : "forrtl: severe (174):SIGSEV, segmentation fault occurred".

It is not a problem with the case.struct or memory, because if I force the same case in complex mode, it works fine.

Also for spin-orbit calculations, I have an error at the processing of the second k point : "allocatable array is already allocated".

I have no idea where the error could come from and would appreciate help. I compiled fold2Bloch with ifort.

Veronique

-- 

Véronique Brouet
Laboratoire de physique des Solides
Université Paris-Sud, Bât 510
91405 Orsay (France)
Tel : (+33) (0)1 69 15 53 34
Fax : (+33) (0)1 69 15 60 86

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Re: [Wien] fold2bloch: unfolded band-structure plot have addition bands

[Rubel, Oleg]

Dear Asif,


thank you for the detailed description! It will allow me to recreate the case on my end. I will get back soon.  I assume
 you deal with MoS2?


Best regards 
Oleg

On Jan 8, 2022, at 12:47, Asif Ali  wrote:







Dear Wien2k users,


I am calculating band structure for 2x2x2 supercell of hexagonal MX2 TMDC. The required K-path is G (0 0 0) - M (1/2 0 0) - K (1/3 1/3 0) - G. But the unfolded band plot has some additional bands in M-K direction.


Below I describe the steps used for unfolding using fold2bloch tool:


To get the folded k-path, fold.m file is used (https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/Utils/ubs_dots.m).

And used this path for "x lapw1 -band".


Copied the case.vector, case.struct, case.klist_band to f2b folder and successfully run " fold2Bloch -c case.vector 2:2:2"



The plotted band structure using matlab script looks fine (compared with the parent unit cell). 
But the problem is that there are some extra bands appearing in the K-M direction. For example, the band in M-K direction beginning from -0.4 eV, should not be present. 



--modification in fold.m 

kpath = [0 0 0;
1/2 0 0;

1/3 1/3 0;

0 0 0]; 
% desired k-path after unfolding



--generated case.klist_band is attached (LDA.klist)


--ubs_dots.m modified

%% Init. parameters

KPATH = [0 0 0;
1/2 0 0;

1/3 1/3 0;
0 0 0]; % k-point path
FOLDS = [2 2 2]; 
% multiplicity in the corresponding directions used when constructing the super-cell

KLABEL = {'G';
'M';'K';'G'};

finpt = 'LDA.f2b';
% input file name




--generated plot, unfoldedband.jpg (I can send a better quality figure by email)


Please help me to resolve this issue. 


Thankyou and Regards
Asif Ali



-- 






---

Asif Ali



PhD student, Department of Physics

Indian Institute of Science Education and Research Bhopal

Bhopal Bypass Road, Bhauri

Bhopal - 462 066, M.P. (INDIA)


---










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Re: [Wien] mstar: Error: dM is not finite

[Rubel, Oleg]

Even if the whole mommat file cannot be shared (too large size, many k points), 
it would be still interesting to see its part related to the problematic k 
point.

Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Monday, December 6, 2021 06:05
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mstar: Error: dM is not finite

with dEtol = 1e-3 I could finish it.

Thanks

On Mon, Dec 6, 2021 at 2:12 AM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
dE = 0 is very strange. This should no happen. Degenerate states (or nearly 
degenerate |dE| < dEtol) are sorted out from the beginning and treated 
separately within a degenerate perturbation theory to avoid "dM = p2/dE".

What is your dEtol? (A meaningful value is 1e-4 ... 1e-6 Ry).  What happens if 
you raise dEtol? Do you mind sharing a link with the mommat file?

Thank you
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Laurence Marks 
mailto:laurence.ma...@gmail.com>>
Sent: Sunday, December 5, 2021 14:41
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mstar: Error: dM is not finite

Obviously the line should be something like
dM = p2*dE/(dE*dE+1D-16)

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu<http://www.numis.northwestern.edu><http://www.numis.northwestern.edu>
"Research is to see what everybody else has seen, and to think what nobody else 
has thought" Albert Szent-Györgyi

On Sun, Dec 5, 2021, 7:23 PM Gavin Abo 
mailto:gabo13...@gmail.com><mailto:gabo13...@gmail.com<mailto:gabo13...@gmail.com>>>
 wrote:

According to the README.md at [1], read_mommat_pij.f90 has to be modified for 
WIEN2k 19.1.  Did you do that?  If you didn't do that it might explain why your 
dEij(n,k) and dEij(m,k) values are both zero.

In the mstar.f90 source code (from lines 422 and 423) [2], you can see that dE 
needs to be non-zero to have a computed value for dM.  If dE is zero then it 
causes a divide by zero [3] that is an incomputable computer mathematical 
operation such that dM would be undefined (which is why the "Error: dM is not 
finite").

line 422: dE = -dEij(n,k)/2 -dEij(m,k)/2
line 423: dM = p2/dE

[1] 
https://github.com/rubel75/mstar<https://urldefense.com/v3/__https://github.com/rubel75/mstar__;!!Dq0X2DkFhyF93HkjWTBQKhk!A1M4TMzDqdChWXiSrMbJ6jpLdUmIOs0RXkqPT-_6ags-PpPXOBVrkJMCVKaWO_6TYYaogQ$>
[2] 
https://github.com/rubel75/mstar/blob/master/mstar.f90<https://urldefense.com/v3/__https://github.com/rubel75/mstar/blob/master/mstar.f90__;!!Dq0X2DkFhyF93HkjWTBQKhk!A1M4TMzDqdChWXiSrMbJ6jpLdUmIOs0RXkqPT-_6ags-PpPXOBVrkJMCVKaWO_66qkrE4g$>
[3] 
https://www.math.utah.edu/~pa/math/0by0.html<https://urldefense.com/v3/__https://www.math.utah.edu/*pa/math/0by0.html__;fg!!Dq0X2DkFhyF93HkjWTBQKhk!A1M4TMzDqdChWXiSrMbJ6jpLdUmIOs0RXkqPT-_6ags-PpPXOBVrkJMCVKaWO_5w-17Opg$>

On 12/5/2021 1:30 AM, Dr. K. C. Bhamu wrote:
Dear Prof. Oleg,
I am running mstar with Wien2k_19.1 with PBE+SO (2 kpt, rkmax=8, lvns =6).
I am getting ebelow error:

 KP: 1876 bands: 856 progress:  75%
 KP: 1877 bands: 854 progress:  75%
 ikpt =  1878
 n =39
 k =40
 m =39
 alpha = 1
 beta = 1
 pij(alpha,n,k) = (-3.6972599E-06,1.5258900E-06)
 pij(beta,k,m) = (-3.6972599E-06,-1.5258900E-06)
 pij(beta,n,k) = (-3.6972599E-06,1.5258900E-06)
 pij(alpha,k,m) = (-3.6972599E-06,-1.5258900E-06)
 dEij(n,k) =  0.000E+00
 dEij(m,k) =  0.000E+00
 dM =  (-Infinity,NaN)
 dE =   0.000E+00
 p2 =  (3.1996142E-11,0.000E+00)
Error: dM is not finite

Should I do a fresh calculation with less number of k-points or the error is 
about something else?
Let me know if I need to share any files.

Thanks and regards
Bhamu
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Re: [Wien] mstar: Error: dM is not finite

[Rubel, Oleg]

dE = 0 is very strange. This should no happen. Degenerate states (or nearly 
degenerate |dE| < dEtol) are sorted out from the beginning and treated 
separately within a degenerate perturbation theory to avoid "dM = p2/dE".

What is your dEtol? (A meaningful value is 1e-4 ... 1e-6 Ry).  What happens if 
you raise dEtol? Do you mind sharing a link with the mommat file?

Thank you
Oleg


From: Wien  on behalf of Laurence 
Marks 
Sent: Sunday, December 5, 2021 14:41
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mstar: Error: dM is not finite

Obviously the line should be something like
dM = p2*dE/(dE*dE+1D-16)

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody else 
has thought" Albert Szent-Györgyi

On Sun, Dec 5, 2021, 7:23 PM Gavin Abo 
mailto:gabo13...@gmail.com>> wrote:

According to the README.md at [1], read_mommat_pij.f90 has to be modified for 
WIEN2k 19.1.  Did you do that?  If you didn't do that it might explain why your 
dEij(n,k) and dEij(m,k) values are both zero.

In the mstar.f90 source code (from lines 422 and 423) [2], you can see that dE 
needs to be non-zero to have a computed value for dM.  If dE is zero then it 
causes a divide by zero [3] that is an incomputable computer mathematical 
operation such that dM would be undefined (which is why the "Error: dM is not 
finite").

line 422: dE = -dEij(n,k)/2 -dEij(m,k)/2
line 423: dM = p2/dE

[1] 
https://github.com/rubel75/mstar
[2] 
https://github.com/rubel75/mstar/blob/master/mstar.f90
[3] 
https://www.math.utah.edu/~pa/math/0by0.html

On 12/5/2021 1:30 AM, Dr. K. C. Bhamu wrote:
Dear Prof. Oleg,
I am running mstar with Wien2k_19.1 with PBE+SO (2 kpt, rkmax=8, lvns =6).
I am getting ebelow error:

 KP: 1876 bands: 856 progress:  75%
 KP: 1877 bands: 854 progress:  75%
 ikpt =  1878
 n =39
 k =40
 m =39
 alpha = 1
 beta = 1
 pij(alpha,n,k) = (-3.6972599E-06,1.5258900E-06)
 pij(beta,k,m) = (-3.6972599E-06,-1.5258900E-06)
 pij(beta,n,k) = (-3.6972599E-06,1.5258900E-06)
 pij(alpha,k,m) = (-3.6972599E-06,-1.5258900E-06)
 dEij(n,k) =  0.000E+00
 dEij(m,k) =  0.000E+00
 dM =  (-Infinity,NaN)
 dE =   0.000E+00
 p2 =  (3.1996142E-11,0.000E+00)
Error: dM is not finite

Should I do a fresh calculation with less number of k-points or the error is 
about something else?
Let me know if I need to share any files.

Thanks and regards
Bhamu
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Re: [Wien] Error in BerryPI Ver. Mar 15, 2021

[Rubel, Oleg]

Dear Vitalii,

thanks again for reporting the issues. It pointed to some limitations in 
parsing the struct file related to writing the oxidation state along the side 
of the element name (e.g., Fe3+). It is OK from WIEN2k perspective, but BerryPI 
was not ready for that change. Also, I fixed reading of the angles (20 instead 
of 120 ged).

I suggest updating BerryPI (please see instructions here 
https://github.com/spichardo/BerryPI/wiki/Installation)

I encountered another issue trying to run your structure. The calculation 
yields a metal. Here are the band occupancies:

   TEMP.-SMEARING WITH0.00200 Ry
  -S / Kb   =  -7.03015466
  -(T*S)/2  =  -0.00351508
  Chem Pot  =   0.47784960
 Bandranges (emin - emax) and occupancy:
:BAN00276: 2760.4554930.471354  0.98266438
:BAN00277: 2770.4619540.473011  0.96308654
:BAN00278: 2780.4671570.473773  0.95117094
:BAN00279: 2790.4693440.476153  0.87986424
:BAN00280: 2800.4723170.476920  0.82870047
:BAN00281: 2810.4743860.479084  0.64359769
:BAN00282: 2820.4783690.480901  0.30835266
:BAN00283: 2830.4796050.481091  0.21542985
:BAN00284: 2840.4804180.482618  0.15653925
:BAN00285: 2850.4809010.482824  0.13158760
:BAN00286: 2860.4810490.482827  0.10831523
:BAN00287: 2870.4836180.484738  0.03915318
:BAN00288: 2880.4836180.485884  0.02039005
:BAN00289: 2890.4859270.489269  0.01128127
:BAN00290: 2900.4863180.490368  0.00721195
:BAN00291: 2910.4874310.490754  0.00403120

You use spin polarization (FM, AFM?). My setup was ferromagnetic. Maybe there 
is an AFM setup with the band gap?

My BerryPI run stops after LAPW2 in getNumberOfBands, which is logical since we 
cannot calculate the polarization of a metal.

File "/home/rubel/WIEN2k_21.1b/SRC_BerryPI/BerryPI/calculations.py", line 135, 
in getNumberOfBands
iHOMO = theList[-1][0] # highest occupied band index
IndexError: list index out of range

Also, I would consider setting the charge convergence (e.g., -cc 0.001) in 
addition to the energy convergence. Otherwise the calculation may be not well 
converged. In addition, your cell is quite big (-p option can be useful in 
WIEN2k and BerryPI).

I hope it will help
Oleg


From: Wien  on behalf of turchenko 

Sent: Saturday, October 2, 2021 10:15
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] Error in BerryPI   Ver. Mar 15, 2021

Dear WIEN2k Creators and Users,
I am running Wien2k v.21.1 on a machine
Z370/i7-8700K/32G2133/256G_M.2_PCIE/T2TB_W/8G_GTX1070/600W/ with
operating system Centos 7, fortran compiler INTEL
(parallel_studio_xe_2020), and Python 2.7.5
The purpose of my calculations is to get quantity of spontaneous
polarization in hexagonal cell of barium ferrites therefore I try to use
software BerryPI.
1) For initialization of calculation I have used follow parameters: XC
13 ; ecut -6.8 ; RKmax= 7 ; Gmax= 12 ; kgen= 25 ;

2) I am running from command line   runsp_lapw -ec 0.001

3) I am running from command line   berrypi -sp -k 2 2 2

This is the bottom part of the output file:
1st_BerryPI_SG186_z0_PBE.outputberry
…
[ BerryPI ] Calling command: x w2w -dn
[ BerryPI ] Finished Berry phase computation for
1st_BerryPI_SG186_z0_PBE
[ BerryPI ] Performing main calculation on 1st_BerryPI_SG186_z0_PBE
Reading case.struct file
   Lattice type: H
   Number of inequivalent atoms: 18
   a = 11.109794 bohr
   b = 11.109794 bohr
   c = 44.089276 bohr
   alpha = 90.0 deg
   beta  = 90.0 deg
   gamma = 20.0 deg
   Lattice type: H
   Reciprocal conventional lattice vectors br1_rec (2pi/bohr):
 [ 6.530452e-01,  0.00e+00,  0.00e+00]
 [ 3.265226e-01,  5.655537e-01,  0.00e+00]
 [ 0.00e+00,  0.00e+00,  1.425105e-01]
   Reciprocal primitive lattice vectors br2_rec (2pi/bohr):
 [ 6.530452e-01,  0.00e+00,  0.00e+00]
 [ 3.265226e-01,  5.655537e-01,  0.00e+00]
 [ 0.00e+00,  0.00e+00,  1.425105e-01]
   Real space conventional lattice vectors br1_dir (bohr):
 [ 9.621364e+00, -5.554897e+00,  0.00e+00]
 [ 0.00e+00,  1.110979e+01,  0.00e+00]
 [ 0.00e+00,  0.00e+00,  4.408928e+01]
   Real space primitive lattice vectors br2_dir (bohr):
 [ 9.621364e+00, -5.554897e+00,  0.00e+00]
 [ 0.00e+00,  1.110979e+01,  0.00e+00]
 [ 0.00e+00,  0.00e+00,  4.408928e+01]
   Unit cell volume: 4712.76312293 bohr3
Error in: {'Z-Coord': [0.0, 0.5], 'Y-Coord': [0.0, 0.0], 'X-Coord':
[0.0, 0.0], 'Znucl': 26.0, 'MULT': 2}
[ BerryPI ] ERROR: in automation of 1st_BerryPI_SG186_z0_PBE
[ BerryPI ] ERROR: Missing data in atom
[ BerryPI ] ERROR: missing tags: ('Element Name', 'Element Number')

Completed using BerryPI version: +++Version Mar 15, 2021
…

The program stops at this point:
Error in: {'Z-Coord': [0.0, 0.5], 'Y-Coord': [0.0, 0.0], 

Re: [Wien] Error in BerryPI Ver. Mar 15, 2021

[Rubel, Oleg]

Dear Vitalii,

thank you for reporting this issue and giving such a nice description (incl. 
the structure file). I will try to reproduce the error on my end and let you 
know.

Best regards 
Oleg

> On Oct 2, 2021, at 16:15, turchenko  wrote:
> 
> Dear WIEN2k Creators and Users,
> I am running Wien2k v.21.1 on a machine 
> Z370/i7-8700K/32G2133/256G_M.2_PCIE/T2TB_W/8G_GTX1070/600W/ with operating 
> system Centos 7, fortran compiler INTEL (parallel_studio_xe_2020), and Python 
> 2.7.5
> The purpose of my calculations is to get quantity of spontaneous polarization 
> in hexagonal cell of barium ferrites therefore I try to use software BerryPI.
> 1) For initialization of calculation I have used follow parameters: XC 13 ; 
> ecut -6.8 ; RKmax= 7 ; Gmax= 12 ; kgen= 25 ;
> 
> 2) I am running from command linerunsp_lapw -ec 0.001
> 
> 3) I am running from command lineberrypi -sp -k 2 2 2
> 
> This is the bottom part of the output file: 
> 1st_BerryPI_SG186_z0_PBE.outputberry
> …
> [ BerryPI ] Calling command: x w2w -dn
> [ BerryPI ] Finished Berry phase computation for 1st_BerryPI_SG186_z0_PBE
> [ BerryPI ] Performing main calculation on 1st_BerryPI_SG186_z0_PBE
> Reading case.struct file
>  Lattice type: H
>  Number of inequivalent atoms: 18
>  a = 11.109794 bohr
>  b = 11.109794 bohr
>  c = 44.089276 bohr
>  alpha = 90.0 deg
>  beta  = 90.0 deg
>  gamma = 20.0 deg
>  Lattice type: H
>  Reciprocal conventional lattice vectors br1_rec (2pi/bohr):
>[ 6.530452e-01,  0.00e+00,  0.00e+00]
>[ 3.265226e-01,  5.655537e-01,  0.00e+00]
>[ 0.00e+00,  0.00e+00,  1.425105e-01]
>  Reciprocal primitive lattice vectors br2_rec (2pi/bohr):
>[ 6.530452e-01,  0.00e+00,  0.00e+00]
>[ 3.265226e-01,  5.655537e-01,  0.00e+00]
>[ 0.00e+00,  0.00e+00,  1.425105e-01]
>  Real space conventional lattice vectors br1_dir (bohr):
>[ 9.621364e+00, -5.554897e+00,  0.00e+00]
>[ 0.00e+00,  1.110979e+01,  0.00e+00]
>[ 0.00e+00,  0.00e+00,  4.408928e+01]
>  Real space primitive lattice vectors br2_dir (bohr):
>[ 9.621364e+00, -5.554897e+00,  0.00e+00]
>[ 0.00e+00,  1.110979e+01,  0.00e+00]
>[ 0.00e+00,  0.00e+00,  4.408928e+01]
>  Unit cell volume: 4712.76312293 bohr3
> Error in: {'Z-Coord': [0.0, 0.5], 'Y-Coord': [0.0, 0.0], 'X-Coord': [0.0, 
> 0.0], 'Znucl': 26.0, 'MULT': 2}
> [ BerryPI ] ERROR: in automation of 1st_BerryPI_SG186_z0_PBE
> [ BerryPI ] ERROR: Missing data in atom
> [ BerryPI ] ERROR: missing tags: ('Element Name', 'Element Number')
> 
> Completed using BerryPI version: +++Version Mar 15, 2021
> …
> 
> The program stops at this point:
> Error in: {'Z-Coord': [0.0, 0.5], 'Y-Coord': [0.0, 0.0], 'X-Coord': [0.0, 
> 0.0], 'Znucl': 26.0, 'MULT': 2}
> 
> The same error was observed in the case of calculation GGA+U or in the case 
> of small variations of coordinate (0, 0, z) for ion Fe1.
> 
> Can somebody help me or explain the reason of such mistake?
> 
> The description for similar error was not found in the WIEN2k mailing list. I 
> am not sure about the reason of error, but I can suppose, that the reason is 
> linked with follow:   gamma= 120 degree in 1st_BerryPI_SG186_z0_PBE.struct, 
> whereas in 1st_BerryPI_SG186_z0_PBE.outputberry gamma is 20 degree…
> 
> 
> Thanks in advance for Your help,
> Vitalii Turchenko
> <1st_BerryPI_SG186_z0_PBE.outputberry>
> <1st_BerryPI_SG186_z0_PBE.struct>
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Re: [Wien] join_vectorfiles and fold2bloch mismatch

[Rubel, Oleg]

Dear Marcus,

I just locked into ${WIENROOT}/x script. Here is the relevant part:

case joinvec:
set exe=joinvec
set dopara=1 para=para
cat <$def
  4,'$file.klist', 'old','formatted',  0
  5,'$file.in1$cmplx1','old','formatted',  0
 20,'$file.struct','old','formatted',  0
 50,'$file.energy$hf$so$updn', 'old','formatted',  0
 51,'$file.energy$hf$so$updn', 'unknown','formatted',  0
 60,'$file.energy${hf}dum', 'old','formatted',  0
 61,'$file.energy${hf}dum', 'unknown','formatted',  0
EOF

It looks like case.klist is the input file (unit 4). It should probably be 
case.klist_band in your case. You can try to edit joinvec.def file manually 
(change case.klist to case.klist_band) and then run

${WIENROOT}/joinvec joinvec.def

Best regards
Oleg


From: Wien  on behalf of Marcus Ekholm 

Sent: Thursday, September 9, 2021 08:25
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] join_vectorfiles and fold2bloch mismatch

Dear all,

I have an issue with fold2bloch and join_vectorfiles (Wien2k 21.1)

I have 4 vectorfiles after lapw1 -band. I can run fold2bloch on each file 
individually:

fold2Bloch -c case.vectorup_X 2:2:2

where X=1..4, and the sum of the processed k-points equals the number of 
k-points in the case.klist(_band) file.

However, if I try to join the vectorfiles with

x joinvec -up
or
x join_vectorfiles -up

the resulting case.vectorup file seems to include too few points (120 points 
out of 338).
Am I using joinvec in the wrong way?

Best regards,
Marcus





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Re: [Wien] segmentation fault in lapwso

[Rubel, Oleg]

Dear Gerhard,

I did SOC calculations with v21.1 and they were OK. It would be interesting to 
try your case. Would it be possible to share the whole folder as tar.gz?

Thank you
Oleg


From: Wien  on behalf of Fecher, 
Gerhard 
Sent: Thursday, June 10, 2021 07:17
To: A Mailing list for WIEN2k users
Subject: [Wien] segmentation fault in lapwso

Dear all,
while running a -so calculation I hit a segmentation fault in lapwso (see 
below) with the latest version Wien2k21.1 that does NOT appear in 19.2.
(appeared for two different systems in fresh directories)

Did someone experience the same, or did I miss a report and may be not up to 
date?

I used all settings the same (mostly default values), and the same compilers 
and options (Intel OneAPI 2021 2.0 and Parallel Studio XE 2017.4.056) for both 
versions, 21.1 and 19.2

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLineSource
lapwso 0046CE0A  Unknown   Unknown  Unknown
libpthread-2.22.s  2AFBCC6DAB10  Unknown   Unknown  Unknown
libiomp5.so2AFBCCF2C8E8  Unknown   Unknown  Unknown
lapwso 0049F7A6  Unknown   Unknown  Unknown
lapwso 00421E9E  hmsec_926  hmsec.F

line 926 is;   deallocate(meigve)
indeed, if  this is the correct line at all.

indeed in 21.2 (I have seen that hmsec.F is different in 19.2)

Thanks for any suggestions that help

Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz
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Re: [Wien] wrap

[Rubel, Oleg]

Dear Sh. Rahim,


I would not worry about pi wrapping at this point and rather calculate a polarization
 difference between two structures. Polarization is similar to the total energy. Only difference matters. To assure proper calculation (eliminate pi wrapping artefacts), sometimes we need to explore intermediate structures (smooth evolution between two structures).
 Please check older posts in this list for more details.


Best regards 
Oleg


On May 29, 2021, at 04:00, shahrbano rahimi  wrote:







Dear Prof. Oleg Rubel,

Thank you very much for your
 valuable and complete reply. I found that the ionic and electronic polarizations are summed but, in my opinion, if the phases are near to pi, it is possible that the total polarization is bigger than half of the quantum of the polarization. Thus, maybe the
 total polarization also needs to be wrapped.
Sincerely,
Sh. Rahimi



On Sat, May 29, 2021 at 12:15 AM <sjal...@sci.ui.ac.ir> wrote:







-- Forwarded message --
From: "Rubel, Oleg" <rub...@mcmaster.ca>
To: A Mailing list for WIEN2k users <wien@zeus.theochem.tuwien.ac.at>
Cc: 
Bcc: 
Date: Fri, 28 May 2021 18:46:41 +
Subject: Re: [Wien] wrap
You refer to an older version of BerryPI, which I do not have in place. I am inclined to think that the total phase is _not_ wrapped, but it would help to see your output tables (as below) before giving the exact answer. (please post to the list)

As of WIEN2k v21, ionic and electronic phases are not added up, instead the corresponding polarizations are after converting into Cartesian coordinate. It is needed for generic (non-orthogonal) lattice vectors. This is how the new output (BaTiO3 tutorial) looks
 like:

CALCULATION OF ELECTRONIC POLARIZATION (primitive lattice coordinates)
===
Value                           |  spin   |    dir(1)    |    dir(2)    |    dir(3)
---
Berry phase wrapped (rad)          sp(1)  [-2.660094e-13,  3.450573e-13,  1.258913e+00]
Berry phase (rad)                  up+dn  [-5.320189e-13,  6.901146e-13,  2.517826e+00]
Berry phase wrapped (rad)          up+dn  [-5.320189e-13,  6.901146e-13,  2.517826e+00]
Electronic polarization (C/m2)     sp(1)  [-8.415856e-14,  1.091673e-13,  4.024760e-01]
===

The electronic polarization vector is presented in this coord. system:
     dir(1) = [ 7.547566e+00,  4.621551e-16,  4.621551e-16] bohr
     dir(2) = [ 0.00e+00,  7.547566e+00,  4.621551e-16] bohr
     dir(3) = [ 0.00e+00,  0.00e+00,  7.626934e+00] bohr
and will be transformed into Cartesian coordinates.


CALCULATION OF IONIC POLARIZATION (conventional lattice coordinates)
===
Elem.|  Fractional coord.  |  spin | Zion |    dir(1)    |    dir(2)    |    dir(3)
---
                                          + Ionic phase (rad) +
Ba  (0., 0., 0.)  sp(1) 10.00 [ 0.00e+00,  0.00e+00,  0.00e+00]
Ti  (0.5000, 0.5000, 0.5152)  sp(1) 12.00 [ 3.769911e+01,  3.769911e+01,  3.884323e+01]
 O  (0.5000, 0.5000, 0.9736)  sp(1)  6.00 [ 1.884956e+01,  1.884956e+01,  3.670240e+01]
 O  (0.5000, 0., 0.4834)  sp(1)  6.00 [ 1.884956e+01,  0.00e+00,  1.822516e+01]
 O  (0., 0.5000, 0.4834)  sp(1)  6.00 [ 0.00e+00,  1.884956e+01,  1.822516e+01]
---
Total ionic phase (rad)       sp(1)       [ 7.539822e+01,  7.539822e+01,  1.119960e+02]
Total ionic phase wrap. (rad) sp(1)       [ 3.552714e-15,  3.552714e-15, -1.101384e+00]
Ionic polarization (C/m2)     sp(1)       [ 5.619937e-16,  5.619937e-16, -1.760570e-01]
===
The ionic positions and associated polarization vector is presented in this coord. system:
     dir(1) = [ 7.547566e+00,  4.621551e-16,  4.621551e-16] bohr
     dir(2) = [ 0.00e+00,  7.547566e+00,  4.621551e-16] bohr
     dir(3) = [ 0.00e+00,  0.00e+00,  7.626934e+00] bohr


SUMMARY OF POLARIZATION CALCULATION IN CARTESIAN COORDINATES
===
Value                           |  spin   |       X      |       Y      |       Z
---
Electronic polarization (C/m2)     sp(1)  [-8.415856e-14,  1.091673e-13,  4.024760e-01]
Ionic polarization (C/m2)          sp(1)  [ 5.619937e-16,  5.619937e-16, -1.76

Re: [Wien] wrap

[Rubel, Oleg]

You refer to an older version of BerryPI, which I do not have in place. I am 
inclined to think that the total phase is _not_ wrapped, but it would help to 
see your output tables (as below) before giving the exact answer. (please post 
to the list)

As of WIEN2k v21, ionic and electronic phases are not added up, instead the 
corresponding polarizations are after converting into Cartesian coordinate. It 
is needed for generic (non-orthogonal) lattice vectors. This is how the new 
output (BaTiO3 tutorial) looks like:

CALCULATION OF ELECTRONIC POLARIZATION (primitive lattice coordinates)
===
Value   |  spin   |dir(1)|dir(2)|
dir(3)
---
Berry phase wrapped (rad)  sp(1)  [-2.660094e-13,  3.450573e-13,  
1.258913e+00]
Berry phase (rad)  up+dn  [-5.320189e-13,  6.901146e-13,  
2.517826e+00]
Berry phase wrapped (rad)  up+dn  [-5.320189e-13,  6.901146e-13,  
2.517826e+00]
Electronic polarization (C/m2) sp(1)  [-8.415856e-14,  1.091673e-13,  
4.024760e-01]
===

The electronic polarization vector is presented in this coord. system:
 dir(1) = [ 7.547566e+00,  4.621551e-16,  4.621551e-16] bohr
 dir(2) = [ 0.00e+00,  7.547566e+00,  4.621551e-16] bohr
 dir(3) = [ 0.00e+00,  0.00e+00,  7.626934e+00] bohr
and will be transformed into Cartesian coordinates.


CALCULATION OF IONIC POLARIZATION (conventional lattice coordinates)
===
Elem.|  Fractional coord.  |  spin | Zion |dir(1)|dir(2)|
dir(3)
---
  + Ionic phase (rad) 
+
Ba  (0., 0., 0.)  sp(1) 10.00 [ 0.00e+00,  0.00e+00,  
0.00e+00]
Ti  (0.5000, 0.5000, 0.5152)  sp(1) 12.00 [ 3.769911e+01,  3.769911e+01,  
3.884323e+01]
 O  (0.5000, 0.5000, 0.9736)  sp(1)  6.00 [ 1.884956e+01,  1.884956e+01,  
3.670240e+01]
 O  (0.5000, 0., 0.4834)  sp(1)  6.00 [ 1.884956e+01,  0.00e+00,  
1.822516e+01]
 O  (0., 0.5000, 0.4834)  sp(1)  6.00 [ 0.00e+00,  1.884956e+01,  
1.822516e+01]
---
Total ionic phase (rad)   sp(1)   [ 7.539822e+01,  7.539822e+01,  
1.119960e+02]
Total ionic phase wrap. (rad) sp(1)   [ 3.552714e-15,  3.552714e-15, 
-1.101384e+00]
Ionic polarization (C/m2) sp(1)   [ 5.619937e-16,  5.619937e-16, 
-1.760570e-01]
===
The ionic positions and associated polarization vector is presented in this 
coord. system:
 dir(1) = [ 7.547566e+00,  4.621551e-16,  4.621551e-16] bohr
 dir(2) = [ 0.00e+00,  7.547566e+00,  4.621551e-16] bohr
 dir(3) = [ 0.00e+00,  0.00e+00,  7.626934e+00] bohr


SUMMARY OF POLARIZATION CALCULATION IN CARTESIAN COORDINATES
===
Value   |  spin   |   X  |   Y  |   
Z
---
Electronic polarization (C/m2) sp(1)  [-8.415856e-14,  1.091673e-13,  
4.024760e-01]
Ionic polarization (C/m2)  sp(1)  [ 5.619937e-16,  5.619937e-16, 
-1.760570e-01]
Tot. spin polariz.=Pion+Pel (C/m2) sp(1)  [-8.359656e-14,  1.097293e-13,  
2.264190e-01]
---
TOTAL POLARIZATION (C/m2)  both   [-8.359656e-14,  1.097293e-13,  
2.264190e-01]
===

As one can see, there is no "Total phase" only "Tot. spin polariz.=Pion+Pel".

I hope it will help
Oleg


From: Wien  on behalf of shahrbano 
rahimi 
Sent: Friday, May 28, 2021 12:31
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] wrap

Dear Prof. Rubel Oleg and WIEN2k users,
I have a general question concerning Berry phase calculations.
Would you, please, let me know that in the BerryPI package whether only the 
ionic and electronic parts of the phase are wrapped into the [-pi, pi] or the 
total phase is also wrapped into this interval. By this I mean that if the 
total phase after summing the wrapped ionic and electronic parts became larger 
than pi or smaller than -pi, whether the BerryPI package also wraps the total 
phase into the interval [-pi, pi] or leaves it to be located outside of the 
interval?
The BerryPI version: 1.4.0 (May 25, 2018

Re: [Wien] WIEN2WANNIER

[Rubel, Oleg]

I would not expect any major problems. From the past experience: Compatibility 
issues (minor) usually arise when wannier90 developers change options in the 
input file case.win for wannier90.x This file is prepared by "write_win" and 
can be modified for compatibility. If you see any issues, please send it to 
this mailing list.

"x w2w" computes the overlaps Mmn and initial projections Amn, and writes them, 
together with
the eigenvalues En, to case.mmn, case.amn, and case.eig. These files should be 
fine for the new wannier90 version.

I hope it will help
Oleg


From: Wien  on behalf of shahrbano 
rahimi 
Sent: Friday, April 16, 2021 13:18
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] WIEN2WANNIER

Dear all,
Is the following version of the Wannier90 interfaced to the Wien2k by the 
WIEN2WANNIER?
https://iopscience.iop.org/article/10.1088/1361-648X/ab51ff/meta
Thank you for your kind attention to this matter.
Best Regards,
Shahrbano Rahimi
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Re: [Wien] Callen versus Born charge

[Rubel, Oleg]

Dear Laurence,


it could be related to sensitivity of Born charges to the orbital hybridization since a polarization change associated with a small displacement of an atom also captures a charge transfer resulted from this displacement (https://doi.org/10.1103/PhysRevB.58.6224 sec.
 IIIB). The charge transfer contribution is very large in perovskites with the exception of O_perpendicular. Perhaps the dielectric constant involved in evaluation of the Callen charge (eq. 9 in that paper) reduces sensitivity of the charge transfer term to
 the choice of functional? It would make sense to have a large charge transfer for a system with larger polarizability.


Best regards 
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton,
 Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On Apr 2, 2021, at 15:13, Laurence Marks  wrote:






One of my students recently calculated the Callen & Born charges for SrTiO3, finding that the Callen charge was almost independent of functional (LDA, PBE, PBEsol, PBEsol+onsite)
 whereas the Born charge was. For reference, the Bader charges are different.


I am perplexed by the invariance of the Callen charge -- any explanations?


-- 

Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Györgyi



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Re: [Wien] about the mstar program

[Rubel, Oleg]

Ramazan, it will help if you will make a table with data from the paper and 
your data. Otherwise it is unclear what does not agree? The expected output for 
the Si tutorial is also listed in
https://github.com/rubel75/mstar/wiki/Tutorial-Si-with-SOC-(WIEN2k)
"The effective masses in [100] direction are ... and well agree with results 
obtained from the band curvature ...". Can you reproduce that?

Thank you
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Wednesday, March 24, 2021 00:20
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] about the mstar program

Hii Ramazan
You can search my recent query about mstar.
Maybe you will find sufficient information there.

Regards
Bhamu


On Wed, Mar 24, 2021 at 9:47 AM Ramazan KATIRCI 
mailto:ramazankati...@sivas.edu.tr>> wrote:
Dear Wien2k users

I read the article of "Perturbation approach to ab initio effective mass 
calculations" completely and carefully. I implemented all the instructions in 
it to compare the results. But the data I acquired in minv-ij-up.data is 
different from the data presented in the article. Firstly I used default 
parameters in the bash file of mstar (E-max = 7  .inso file and Emax =10 in 
.in1 file). As I say the outputs in the minv_ij-up is completely different. 
Later, I changed the parameters of E-max=5 Ry .inso file and E-max=5  .in1 file 
as specified in the article. the outputs is  different again. Although I used 
the the same parameters as the article, why the results are so different. 
Actually I want this method to compare the effective mass with parabolic 
approximation method.

I have the other question. When I examined the minv_d-up.data and minv_c-up 
files, How can I understant which k points and band corresponding to the lowest 
conduction band and highest valance band.

The bash and minv-ij-up files were shared with this link above;

https://drive.google.com/drive/folders/1wkOCXyz__oLWz98cgrGUk3cLP2NCfzVB?usp=sharing


Thank you in advance for your help

Best regards
Ramazan Katırcı
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Re: [Wien] about effective mass

[Rubel, Oleg]

It can be related to "WIEN2k compatibility note" in README.md 
(https://github.com/rubel75/mstar)


From: Wien  on behalf of Ramazan 
KATIRCI 
Sent: Thursday, March 18, 2021 13:36
To: wien
Subject: Re: [Wien] about effective mass

Hello,

Thank you so much, your suggesions about the scratch solved my problem. But 
another problem emerged. I added the bash output error below. This problem 
emerged when the mstar program run. The other script (scf, optic etc.) 
completed normally. Thank you in advance for your help.

The bash output:
 The input file w2_3.mommat2up was found.
  number of lines in mommat file = 327804
 Entering the main loop...
 ERROR reading the line from mommat file containing
  1   1-0.129114E-16-0.348249E-10 0.671895E-17-0.174125E-10 
0.313031E-16-0.174125E-10   0.
line number 5
 while expecting something like this
  1  32 0.270604E-02 0.659085E-03 
0.555417E-03-0.308709E-02-0.132694E-11-0.600436E-11   2.35217055
(base) -bash-4.2$


Sincerely
Ramazan
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Re: [Wien] about effective mass

[Rubel, Oleg]

SCRATCH is a good point. The Si tutorail assumed that that vector files are in 
the same folder as the WIEN2k case. To make it error-proof I added in the 
begining

# SCRATCH setting will ensure that vector files are in the case folder
export SCRATCH=./

to the tutorial script at 
https://github.com/rubel75/mstar/wiki/Tutorial-Si-with-SOC-(WIEN2k)

Thank you
Oleg


From: Wien  on behalf of Peter Blaha 

Sent: Thursday, March 18, 2021 10:10
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] about effective mass

Another possibility:

You have a very funny   SCRATCH  variable:

/home/wien2k/jobs_w2/scratch/Si.vectorsoup

Maybe there is something wrong. ?

echo $SCRATCH
cat *lapwso.def
cat *optic.def

Compare the case.vectorso   lines.

After   lapwso the vector files should be where it says in the def file.

-
Is this from a batch job, and you are using some local SCRATCH ???
Then the vector files in $SCRATCH  are probably not available anymore
once the job has finished.
---

But all this are some hints, which can be totally wrong, since you are
not telling us any details.
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Re: [Wien] about effective mass

[Rubel, Oleg]

the error you mention in the latest email is (probably) caused by the way optic
deals with SOC. The section "8.19.1 Execution" of the UG mentions "In cases of
non-spinpolarized spin-orbit calculations WITHOUT inversion symmetry one must
do some tricks and “mimic” a spinpolarized calculation:". Si does have an
inversion symmetry but, to be on a safe side, I would do the trick.

~~ serial calculation ~~

Steps are described in
https://github.com/rubel75/mstar/wiki/Tutorial-Si-with-SOC-(WIEN2k) under "#
fake spin-polarized calculation for optic" section immediately before calling
optic.

...
# fake spin-polarized calculation for optic
rm ${case}.vspup
ln -s ${case}.vsp ${case}.vspup
rm ${case}.vspdn
ln -s ${case}.vsp ${case}.vspdn
ln -s ${case}.vectorso ${case}.vectorsoup
...

It relies on the ${case} variable. Maybe it was not set up?

case=${PWD##*/}

Please check the variable and all symbolic links.

~~ parallel calculation ~~

Now when you run optic in parallel (-p) after

run_lapw ... -so -p

the same "ln ..." has to be done to all case.vectorso_XX files. To deal with
this, I have a bash script:

# fake spin-polarized calculation for optic
echo "making symbolic link: ${case}.vspup -> ${case}.vsp"
rm ${case}.vspup
ln -s ${case}.vsp ${case}.vspup
echo "making symbolic link: ${case}.vspdn -> ${case}.vsp"
rm ${case}.vspdn
ln -s ${case}.vsp ${case}.vspdn
i="1" # init counter for parallel files
filevec=${case}.vectorso_${i} # name of vector file
while [ -f "$filevec" ] # while the vector file exists
do
  echo "$filevec exist"
  echo "making symbolic link: ${case}.vectorsoup_${i} -> $filevec"
  ln -s $filevec ${case}.vectorsoup_${i}
  i=$[$i+1] # increment the counter
  filevec=${case}.vectorso_${i} # next vector file
done

You need to verify that alter running the script you have pbe.vectorsoup_XX
files in place.


I hope it will help
Oleg


From: Wien  on behalf of Ramazan 
KATIRCI 
Sent: Thursday, March 18, 2021 09:39
To: wien
Subject: Re: [Wien] about effective mass

I am sorry, the page is always not available. I do not know the reason but I 
can not reach the links the from mail-archive.com web site

- Original Message -
From: "Rubel, Oleg" 
To: "wien" 
Sent: Thursday, March 18, 2021 3:41:17 PM
Subject: Re: [Wien] about effective mass

Please check the explanation here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20845.html
It might be relebant to this case too.

Oleg


From: Wien  on behalf of Lyudmila 
Dobysheva 
Sent: Thursday, March 18, 2021 06:51
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] about effective mass

18.03.2021 07:51, Ramazan KATIRCI wrote:
> upoptic.error file
> 'OPTIC' -  can't open unit: 10
>   'OPTIC' -  filename: /home/wien2k/jobs_w2/scratch/Si.vectorsoup
>   'OPTIC' -  status: OLD  form: UNFORMATTED

You can see that there is no file Si.vectorsoup. It should be formed by
the program lapwso -up.
Search here why it is absent.

Best wishes
Lyudmila Dobysheva
--
http://ftiudm.ru/content/view/25/103/lang,english/
Institute of Physics and Technology,
Udmurt Federal Research Center, Ural Br. of Rus.Ac.Sci.
426000 Izhevsk Kirov str. 132
Russia
---
Tel. +7 (34I2)43-24-59 (office), +7 (9I2)OI9-795O (home)
Skype: lyuka18 (office), lyuka17 (home)
E-mail: lyuk...@mail.ru (office), lyuk...@gmail.com (home)
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Re: [Wien] about effective mass

[Rubel, Oleg]

Please check the explanation here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20845.html
It might be relebant to this case too.

Oleg


From: Wien  on behalf of Lyudmila 
Dobysheva 
Sent: Thursday, March 18, 2021 06:51
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] about effective mass

18.03.2021 07:51, Ramazan KATIRCI wrote:
> upoptic.error file
> 'OPTIC' -  can't open unit: 10
>   'OPTIC' -  filename: /home/wien2k/jobs_w2/scratch/Si.vectorsoup
>   'OPTIC' -  status: OLD  form: UNFORMATTED

You can see that there is no file Si.vectorsoup. It should be formed by
the program lapwso -up.
Search here why it is absent.

Best wishes
Lyudmila Dobysheva
--
http://ftiudm.ru/content/view/25/103/lang,english/
Institute of Physics and Technology,
Udmurt Federal Research Center, Ural Br. of Rus.Ac.Sci.
426000 Izhevsk Kirov str. 132
Russia
---
Tel. +7 (34I2)43-24-59 (office), +7 (9I2)OI9-795O (home)
Skype: lyuka18 (office), lyuka17 (home)
E-mail: lyuk...@mail.ru (office), lyuk...@gmail.com (home)
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Re: [Wien] about effective mass

[Rubel, Oleg]

> I examined the mstar code you suggest. But I noticed that this code is not 
> compatible with gfortran. Actually, I installed wien2k code with gfortran. I 
> am not using ifort. Do you know any method to solve this problem.

I do not have personal experience with gfortran, but Dr. Blaha mentioned that 
it worked for him. There was a compilation issue related to dots in ".not." 
syntax, but it was later fixed. It should work.

Oleg
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[Wien] [SPAM?] Re: about effective mass

[Rubel, Oleg]

There is an alternative -- mstar code (https://github.com/rubel75/mstar) that 
work with WIEN2k. It outputs minv_d.dat - density of states inverse effective 
mass m0/m*_d = m0/(m_1 *m_2 *m_3)**(1/3)
Is this what you are looking for?

It will work if you want to get the DOS effective mass at the very top of a 
band parabola. However, if a material is heavily doped and the Fermi energy is 
far from band edges, it will not help.

Best regards
Oleg


From: Wien  on behalf of Tomas Kana  

Sent: Monday, March 15, 2021 16:51
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] about effective mass

In addition,
I suppose this link on ResearchGate:
https://www.researchgate.net/post/How-can-i-calculate-the-effective-mass-of-electron-and-hole-for-perovskite-materials-from-Wien2k-calculations-DFT
Tomas
wien2k mailing list
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/

In there you can ask for 'effective mass'
https://www.mail-archive.com/search?q=effective+mass=wien%40zeus.theochem.tuwien.ac.at
I suppose that this will give you some ideas.

De: Wien  en nombre de Ramazan KATIRCI 

Enviado: lunes, 15 de marzo de 2021 12:51 p. m.
Para: wien 
Asunto: Re: [Wien] [SPAM?] Re: about effective mass

sorry, I can not reach the older e-mails. I have a link of 
http://zeus.theochem.tuwien.ac.at/pipermail/wien/ to reach the older e-mails. 
But there is not a tool to search the topic

- Original Message -
From: "delamora" 
To: "wien" 
Sent: Monday, March 15, 2021 9:38:09 PM
Subject: [Wien] [SPAM?] Re: about effective mass

You could search in the mailing list...


Hello,

I want to find the effective mass for densitiy of state using wien2k code. I 
searched some information on the internet and found some knowledge. it says the 
spaghetti file should be used for the plot of E-k diagram. I examined the 
".spaghetti_ene" file. I tried to plot E-k diagram, but I couldn't make sure 
which data should be used.
Could you please let me know which file and which data in the file should be 
used to calculate effective mass for density of state.

Best regards
Ramazan Katırcı
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

It is overall useful to have a set of test cases (not only mstar) that can run 
without user's intervention for validation purposes. As far as I know we only 
have it in BerryPI 
(https://github.com/spichardo/BerryPI/blob/master/tutorials/run_tutor.sh). Now 
we are one step closer :)

Thank you
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Thursday, March 11, 2021 05:45
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Thank you for your patience for my query.
Here is my script to calculate mstar [1] from a successfully finished mstar 
calculation.

This is for Si only. For other systems, some parameters need to be tuned.
I am not a good programmer, so the script may not look in good format.

[1]. https://we.tl/t-SYldxNNner


Thank you
Bhamu


On Thu, Mar 11, 2021 at 4:26 AM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
I am glad Si worked out. Sorry, Bhamu. You need to figure it out even if it 
takes more time. When searching through eigenvalues, keep in mind the number of 
digits. For instance, 0.383706 from case.scf can appear as 0.3837058 in the 
eigenvalue file.

All the best
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Dr. K. C. Bhamu mailto:kcbham...@gmail.com>>
Sent: Wednesday, March 10, 2021 11:50
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
I tried to follow your advice and it worked for Si case. I found VBM at  #KP1 
and CBM at #KP15. The band index edges were matched with the particular KP in 
case.energyso.

But In my case, I could not find the VBM/CBM edges either in case.eneryso or in 
case.bands.agr/spagetti_ene.

I finished two different calculations (with shifted k-mesh and unshifted 
k-mesh) and both can be downloaded from [1].
[1] https://we.tl/t-Mhv6nv4Zlf

I would be grateful to you, if you can suggest me #KP's with respect to VBM/CBM.
CBM is not exactly on high-symmetry  k-point.


Thank you
Bhamu


On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca><mailto:rub...@mcmaster.ca<mailto:rub...@mcmaster.ca>>>
 wrote:
Dear Bhamu,

to get a VBM k-point index, you would need to look for "0.383706" in your 
case.energyso and see which k-point this eigenvalue belongs to. For CBE, look 
for "0.401998" (it can be a different k-point).

In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two 
different k-points. After some trials, I found that 7x7x7 unshifted k-mesh 
"hits" CBM of Si quite precisely.

Of course you need to be confident that the selected k-mesh "hits" the relevant 
extremum (extrema) of your band structure. For instance if you need Gamma, do 
not select a shifted mesh. When the extremum is away from the high-symmetry 
points and coordinates are known, it might be easier to use case.klist_band and 
target the point(s) of interest.

I hope it helps
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at><mailto:wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>>
 on behalf of Dr. K. C. Bhamu 
mailto:kcbham...@gmail.com><mailto:kcbham...@gmail.com<mailto:kcbham...@gmail.com>>>
Sent: Tuesday, March 9, 2021 08:15
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry for the late reply. As we have the opposite time zone so I am replying 
according to your office time.

My previous information was from pbe.spaghetti_ene.

Here is the relevant part from case.scf.

 Bandranges (emin - emax) and occupancy:
:BAN00066:  660.2189000.284902  1.
:BAN00067:  670.2817550.322256  1.
:BAN00068:  680.2817550.322256  1.
:BAN00069:  690.2879140.335582  1.
:BAN00070:  700.2879140.335582  1.
:BAN00071:  710.2941570.351734  1.
:BAN00072:  720.2941570.351734  1.
:BAN00073:  730.3010710.368987  1.
:BAN00074:  740.3010710.368987  1.
:BAN00075:  750.3400590.383706  1.
:BAN00076:  760.3400590.383706  1.  VBM
:BAN00077:  770.4019980.551266  0.  CBM
:BAN00078:  780.4019980.551266  0.
:BAN00079:  790.4728340.603663  0.
:BAN00080:  800.4728340.603663  0.
:BAN00081:  810.5567370.634231  0.
Energy to separate low and high energystates:   -0.57035

Just above this part, I see
:KPT   :  NUMBER OF K-POINTS: 40
   0.0   0.0 angle (M,z), angle (M,x) deg

SPIN-ORBIT EIGENVALUES:
 K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0 so 
you took KP =1?)
  MATRIX SIZE=  552   W

Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

I am glad Si worked out. Sorry, Bhamu. You need to figure it out even if it 
takes more time. When searching through eigenvalues, keep in mind the number of 
digits. For instance, 0.383706 from case.scf can appear as 0.3837058 in the 
eigenvalue file.

All the best
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Wednesday, March 10, 2021 11:50
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
I tried to follow your advice and it worked for Si case. I found VBM at  #KP1 
and CBM at #KP15. The band index edges were matched with the particular KP in 
case.energyso.

But In my case, I could not find the VBM/CBM edges either in case.eneryso or in 
case.bands.agr/spagetti_ene.

I finished two different calculations (with shifted k-mesh and unshifted 
k-mesh) and both can be downloaded from [1].
[1] https://we.tl/t-Mhv6nv4Zlf

I would be grateful to you, if you can suggest me #KP's with respect to VBM/CBM.
CBM is not exactly on high-symmetry  k-point.


Thank you
Bhamu


On Tue, Mar 9, 2021 at 11:13 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
Dear Bhamu,

to get a VBM k-point index, you would need to look for "0.383706" in your 
case.energyso and see which k-point this eigenvalue belongs to. For CBE, look 
for "0.401998" (it can be a different k-point).

In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two 
different k-points. After some trials, I found that 7x7x7 unshifted k-mesh 
"hits" CBM of Si quite precisely.

Of course you need to be confident that the selected k-mesh "hits" the relevant 
extremum (extrema) of your band structure. For instance if you need Gamma, do 
not select a shifted mesh. When the extremum is away from the high-symmetry 
points and coordinates are known, it might be easier to use case.klist_band and 
target the point(s) of interest.

I hope it helps
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Dr. K. C. Bhamu mailto:kcbham...@gmail.com>>
Sent: Tuesday, March 9, 2021 08:15
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry for the late reply. As we have the opposite time zone so I am replying 
according to your office time.

My previous information was from pbe.spaghetti_ene.

Here is the relevant part from case.scf.

 Bandranges (emin - emax) and occupancy:
:BAN00066:  660.2189000.284902  1.
:BAN00067:  670.2817550.322256  1.
:BAN00068:  680.2817550.322256  1.
:BAN00069:  690.2879140.335582  1.
:BAN00070:  700.2879140.335582  1.
:BAN00071:  710.2941570.351734  1.
:BAN00072:  720.2941570.351734  1.
:BAN00073:  730.3010710.368987  1.
:BAN00074:  740.3010710.368987  1.
:BAN00075:  750.3400590.383706  1.
:BAN00076:  760.3400590.383706  1.  VBM
:BAN00077:  770.4019980.551266  0.  CBM
:BAN00078:  780.4019980.551266  0.
:BAN00079:  790.4728340.603663  0.
:BAN00080:  800.4728340.603663  0.
:BAN00081:  810.5567370.634231  0.
Energy to separate low and high energystates:   -0.57035

Just above this part, I see
:KPT   :  NUMBER OF K-POINTS: 40
   0.0   0.0 angle (M,z), angle (M,x) deg

SPIN-ORBIT EIGENVALUES:
 K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0 so 
you took KP =1?)
  MATRIX SIZE=  552   WEIGHT= 8.00

Does it mean that I should look for #KP 1? and then of course, bandinxed 75,76 
for VBM and CBM, respectively.
But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
So now the band index is clear to me.

My next query is, how can I know #KP for VBM and CBM?

Sorry for the long conversation.

Thank you
Bhamu

On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca><mailto:rub...@mcmaster.ca<mailto:rub...@mcmaster.ca>>>
 wrote:
Dear Bhamu,

it seems you have k-point index=38, band index=653. To be on a safe side, I 
would look for band ranges (":BANXXX") in case.scf (last iteration). The 
occupancies are written down in the same table. If you have questions about 
interpretation of :BANXXX, it will be better if you list this section for your 
SCF file.

Thanks
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at><mailto:wien-boun...@zeus.theochem.tuwien.ac.at<mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>>
 on behalf of Dr. K. C. Bhamu 
mailto:kcbham...@gmail.com><mailto:kcbham...@gmail.com<mailto:kcbham...@gmail.com>>>
Sent: Sunday, March 7, 2021 08:09
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] op

Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

Dear Bhamu,

to get a VBM k-point index, you would need to look for "0.383706" in your 
case.energyso and see which k-point this eigenvalue belongs to. For CBE, look 
for "0.401998" (it can be a different k-point).

In Si VBM is at Gamma, and CBM is far away from Gamma. Thus we have two 
different k-points. After some trials, I found that 7x7x7 unshifted k-mesh 
"hits" CBM of Si quite precisely.

Of course you need to be confident that the selected k-mesh "hits" the relevant 
extremum (extrema) of your band structure. For instance if you need Gamma, do 
not select a shifted mesh. When the extremum is away from the high-symmetry 
points and coordinates are known, it might be easier to use case.klist_band and 
target the point(s) of interest.

I hope it helps
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Tuesday, March 9, 2021 08:15
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry for the late reply. As we have the opposite time zone so I am replying 
according to your office time.

My previous information was from pbe.spaghetti_ene.

Here is the relevant part from case.scf.

 Bandranges (emin - emax) and occupancy:
:BAN00066:  660.2189000.284902  1.
:BAN00067:  670.2817550.322256  1.
:BAN00068:  680.2817550.322256  1.
:BAN00069:  690.2879140.335582  1.
:BAN00070:  700.2879140.335582  1.
:BAN00071:  710.2941570.351734  1.
:BAN00072:  720.2941570.351734  1.
:BAN00073:  730.3010710.368987  1.
:BAN00074:  740.3010710.368987  1.
:BAN00075:  750.3400590.383706  1.
:BAN00076:  760.3400590.383706  1.  VBM
:BAN00077:  770.4019980.551266  0.  CBM
:BAN00078:  780.4019980.551266  0.
:BAN00079:  790.4728340.603663  0.
:BAN00080:  800.4728340.603663  0.
:BAN00081:  810.5567370.634231  0.
Energy to separate low and high energystates:   -0.57035

Just above this part, I see
:KPT   :  NUMBER OF K-POINTS: 40
   0.0   0.0 angle (M,z), angle (M,x) deg

SPIN-ORBIT EIGENVALUES:
 K=   0.14286   0.14286   0.14286 1  (In case of "Si" it is 0 0 0 so 
you took KP =1?)
  MATRIX SIZE=  552   WEIGHT= 8.00

Does it mean that I should look for #KP 1? and then of course, bandinxed 75,76 
for VBM and CBM, respectively.
But in case of Si, you took #KP =1 for VBM and #KP=15 for CBM.
So now the band index is clear to me.

My next query is, how can I know #KP for VBM and CBM?

Sorry for the long conversation.

Thank you
Bhamu

On Mon, Mar 8, 2021 at 8:48 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
Dear Bhamu,

it seems you have k-point index=38, band index=653. To be on a safe side, I 
would look for band ranges (":BANXXX") in case.scf (last iteration). The 
occupancies are written down in the same table. If you have questions about 
interpretation of :BANXXX, it will be better if you list this section for your 
SCF file.

Thanks
Oleg


From: Wien 
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>>
 on behalf of Dr. K. C. Bhamu mailto:kcbham...@gmail.com>>
Sent: Sunday, March 7, 2021 08:09
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry to interrupt you.
Earlier I was looking for the wrong file.
My case.klist has 40 k-points and thus #KP also varies upto 40.
>From my eigenvalue file, my VBM lies on band index=38 (XX)
row number   KP(YY)  ENE
6531.08800-0.04699
So according to your hint, I should look for #KP 653 and then index number 38.
But I have #KP upto 40.
You also mentioned occupancy, but I could not understand it.

Could you please correct me?

Thank you in advance.
Regards
Bhamu






On Thu, Mar 4, 2021 at 10:51 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca><mailto:rub...@mcmaster.ca<mailto:rub...@mcmaster.ca>>>
 wrote:
Oh, sorry about the misunderstanding. In your previous correspondence it 
sounded as you had a confusion about which klist file is used.

> In my case the CBM/CMB is at N-point which is located at 622 row number in 
> case.klist_band. But I have only 20 K-points in my case.klist and thus the 
> total KP in mstar output file is also 20.

To get band edges, I would check an eigenvalues file to identify band number 
XX, k point number YY, occupancy. Then look for a line "# KP: YY" and band XX 
below that in the output of mstar.

I hope it answers the question
Oleg
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

Dear Bhamu,

it seems you have k-point index=38, band index=653. To be on a safe side, I 
would look for band ranges (":BANXXX") in case.scf (last iteration). The 
occupancies are written down in the same table. If you have questions about 
interpretation of :BANXXX, it will be better if you list this section for your 
SCF file.

Thanks
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Sunday, March 7, 2021 08:09
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Oleg
Sorry to interrupt you.
Earlier I was looking for the wrong file.
My case.klist has 40 k-points and thus #KP also varies upto 40.
>From my eigenvalue file, my VBM lies on band index=38 (XX)
row number   KP(YY)  ENE
6531.08800-0.04699
So according to your hint, I should look for #KP 653 and then index number 38.
But I have #KP upto 40.
You also mentioned occupancy, but I could not understand it.

Could you please correct me?

Thank you in advance.
Regards
Bhamu






On Thu, Mar 4, 2021 at 10:51 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
Oh, sorry about the misunderstanding. In your previous correspondence it 
sounded as you had a confusion about which klist file is used.

> In my case the CBM/CMB is at N-point which is located at 622 row number in 
> case.klist_band. But I have only 20 K-points in my case.klist and thus the 
> total KP in mstar output file is also 20.

To get band edges, I would check an eigenvalues file to identify band number 
XX, k point number YY, occupancy. Then look for a line "# KP: YY" and band XX 
below that in the output of mstar.

I hope it answers the question
Oleg
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[Wien] PhD position at McMaster (Canada)

[Rubel, Oleg]

Dear Wien2k community:

I am looking for a PhD student to work on DFT modelling of energy materials 
(batteries). If you know anyone who will be interested, please feel free to 
pass this add around.

The project involves collaborative efforts of two experimental groups focused 
on material synthesis, characterization, and performance measurements, as well 
as an industry partner. Our role is to provide an atomistic insight into 
electrochemical mechanisms that govern the performance of cathode materials and 
help to interpret experimental observations.

The starting date will be either May 2021 or Sep 2021. A scholarship is 
available for 4 yrs. More details about the application process can be found at 
http://olegrubel.mcmaster.ca/jobs.html

Thank you
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

Oh, sorry about the misunderstanding. In your previous correspondence it 
sounded as you had a confusion about which klist file is used.

> In my case the CBM/CMB is at N-point which is located at 622 row number in 
> case.klist_band. But I have only 20 K-points in my case.klist and thus the 
> total KP in mstar output file is also 20.

To get band edges, I would check an eigenvalues file to identify band number 
XX, k point number YY, occupancy. Then look for a line "# KP: YY" and band XX 
below that in the output of mstar.

I hope it answers the question
Oleg
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

Dear Bhamu,

mstar gets k points from case.mommat2[up/dn] file. It is create by OPTIC. The 
OPTIC, in turn, gets k points from vector files. Thus you need to have right k 
points in the vector files.

The procedure described in 
https://github.com/rubel75/mstar/wiki/Tutorial-Si-with-SOC-(WIEN2k) has a part

# WFs and eigenvalues with increased band range
x lapw1
x lapwso

This will use case.klist (not case.klist_band) to generate vector files at 
LAPW1 step. Then it propagates to LAPWSO and OPTIC.
If you want k points from case.klist_band, we need to generate vector files 
with (-band) option in LAPW1

# WFs and eigenvalues with increased band range
x lapw1 -band
x lapwso

There are not other changes in the workflow. Then k points from case.klist_band 
propagate into LAPWSO, OPTIC, and mstar eventually.

Best regards
Oleg
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

You are right, it is not a universal line. It implies that the system is not 
magnetic (N at the end). Also, it avoids relativistic local orbitals (RLOs), 
which is default in init_so_lapw. I cannot point to a reference, but it seems 
that optic is not compatible with RLOs? (Maybe someone can comment.)

Thank you
Oleg
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Re: [Wien] opticcpara crashed for mstar

[Rubel, Oleg]

Dear Bhamu,

the error you mention in the latest email is (probably) caused by the way optic 
deals with SOC. The section "8.19.1 Execution" of the UG mentions "In cases of 
non-spinpolarized spin-orbit calculations WITHOUT inversion symmetry one must 
do some tricks and “mimic” a spinpolarized calculation:". Si does have an 
inversion symmetry but, to be on a safe side, I would do the trick.

~~ serial calculation ~~

Steps are described in 
https://github.com/rubel75/mstar/wiki/Tutorial-Si-with-SOC-(WIEN2k) under "# 
fake spin-polarized calculation for optic" section immediately before calling 
optic.

...
# fake spin-polarized calculation for optic
rm ${case}.vspup
ln -s ${case}.vsp ${case}.vspup
rm ${case}.vspdn
ln -s ${case}.vsp ${case}.vspdn
ln -s ${case}.vectorso ${case}.vectorsoup
...

It relies on the ${case} variable. Maybe it was not set up?

case=${PWD##*/}

Please check the variable and all symbolic links.

~~ parallel calculation ~~

Now when you run optic in parallel (-p) after

run_lapw ... -so -p

the same "ln ..." has to be done to all case.vectorso_XX files. To deal with 
this, I have a bash script:

# fake spin-polarized calculation for optic
echo "making symbolic link: ${case}.vspup -> ${case}.vsp"
rm ${case}.vspup
ln -s ${case}.vsp ${case}.vspup
echo "making symbolic link: ${case}.vspdn -> ${case}.vsp"
rm ${case}.vspdn
ln -s ${case}.vsp ${case}.vspdn
i="1" # init counter for parallel files
filevec=${case}.vectorso_${i} # name of vector file
while [ -f "$filevec" ] # while the vector file exists
do
  echo "$filevec exist"
  echo "making symbolic link: ${case}.vectorsoup_${i} -> $filevec"
  ln -s $filevec ${case}.vectorsoup_${i}
  i=$[$i+1] # increment the counter
  filevec=${case}.vectorso_${i} # next vector file
done

You need to verify that alter running the script you have pbe.vectorsoup_XX 
files in place.


I hope it will help
Oleg


From: Wien  on behalf of Dr. K. C. 
Bhamu 
Sent: Wednesday, March 3, 2021 14:04
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] opticcpara crashed for mstar

Dear Prof. Peter
I have tried with the new opticpara_lapw but still I am getting the same error:

x_lapw optic -so -up -p

[1] 13614
OPTIC - ERROR
[1]  + Done  ( cd $PWD; $t $exe ${def}_${loop}.def; rm 
-f .lock_$lockfile[$p] ) >> .timeop_$loop
[1] 13619
OPTIC - ERROR
[1]  + Done  ( cd $PWD; $t $exe ${def}_${loop}.def; rm 
-f .lock_$lockfile[$p] ) >> .timeop_$loop
[1] 13624
OPTIC - ERROR
[1]  + Done  ( cd $PWD; $t $exe ${def}_${loop}.def; rm 
-f .lock_$lockfile[$p] ) >> .timeop_$loop
**  OPTIC crashed!
0.151u 0.199s 0:04.15 8.1% 0+0k 6008+2104io 25pf+0w
error: command   /home/kcbhamu/soft/w2k192/opticcpara -up -c -so upoptic.def   
failed
 cat *error

 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_10
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_11
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_12
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_13
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_14
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_15
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_16
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_1
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_2
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_3
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_4
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_5
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_6
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_7
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_8
 'OPTIC' -  status: OLD  form: UNFORMATTED
 'OPTIC' -  can't open unit: 10
 'OPTIC' -  filename: ./pbe.vectorsoup_9
 'OPTIC' -  status: OLD  form: UNFORMATTED
**  Error in Parallel OPTIC
**  Error in Parallel OPTIC

On Wed, Mar 3, 2021 at 11:53 PM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> wrote:
Are you running in k-point 

Re: [Wien] write_inwf syntaxerror

[Rubel, Oleg]

You can also try a newer version with python 3 compatibility from
https://github.com/spichardo/BerryPI/tree/master/utils

It has some changes in the line with error.

Good luck 
Oleg 
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton,
 Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On Dec 28, 2020, at 11:01, Gavin Abo  wrote:





If your using WIEN2k_19.2, then only follow [3] (do not follow [1]).
Maybe you are not using your WIEN2k_19.2 installation directory but are still using your older WIEN2k version installation directory.
For example, in an older WIEN2k version, you might see write_inwf_lapw is version
1.0.0 and the same text as your 
error on line 58:

username@computername:~$ cd ~/WIEN2k17.1
username@computername:~/WIEN2k17.1$ sed -n 29p write_inwf_lapw
__version__ = "$version: v1.0.0-273-gaf9ce6b$"
username@computername:~/WIEN2k17.1$ sed -n
58p write_inwf_lapw
    return np.array([float (s) for s in l[12:22], l[25:35], l[38:48]])
In WIEN2k_19.2, you should see write_inwf_lapw is version 
2.0.0 and line 58 has different text:

username@computername:~/WIEN2k17.1$ cd ~/WIEN2k19.2
username@computername:~/WIEN2k19.2$ sed -n 28p write_inwf_lapw
__version__ = "$version: v2.0.0-7-g4c51be8$"
username@computername:~/WIEN2k19.2$ sed -n
58p write_inwf_lapw
    def readloro():
You may want to check that WIENROOT in your .bashrc file is set to your WIEN2k_19.2 installation directory:

username@computername:~/WIEN2k19.2$ grep WIENROOT= ~/.bashrc
export WIENROOT=/home/username/WIEN2k19.2

If it is set as intended, you might also check that it has been set in your environment:

username@computername:~/WIEN2k19.2$ echo $WIENROOT
/home/username/WIEN2k19.2

If the environment is not showing the change after you have saved the new WIEN2k installation directory path in .bashrc, you may need to execute "source ~/.bashrc", or restart the terminal or computer.

On 12/28/2020 4:05 AM, Abhijit B K wrote:


Dear Users,


I am using WIEN2k_19.2.


I am coming across the following error while running ''write_inwf"


  File "/./wien2k/write_inwf", line 58
    return np.array([float (s) for s in l[12:22], l[25:35], l[38:48]])
                                                ^
SyntaxError: invalid syntax



I would be grateful if someone could help me with this bug.




Best wishes,


Abhijit


PS: I followed the [1] and [3] in the following recommendation but the error persists.


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20308.html



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Re: [Wien] KP in mstar output files

[Rubel, Oleg]

Dear Majid,

In addition to Peter's comment, I would note that it might be easier to start 
with a non-shifted (Gamma centered) k mesh. Then the Gamma point is always the 
1st one.

Here is the case.klist_band used in the paper

   -10000 1520  2.0
-8000 1520  2.0
-6000 1520  2.0
-5000 1520  2.0
-4000 1520  2.0
-3000 1520  2.0
-2500 1520  2.0
-2000 1520  2.0
-1500 1520  2.0
-1000 1520  2.0
 -700 1520  2.0
 -400 1520  2.0
GAMMA 000 1520  2.0
  400 1520  2.0
  700 1520  2.0
 1000 1520  2.0
 1500 1520  2.0
 2000 1520  2.0
 2500 1520  2.0
 3000 1520  2.0
 4000 1520  2.0
 5000 1520  2.0
 6000 1520  2.0
 8000 1520  2.0
10000 1520  2.0
END

Its main purpose was to check our perturbation theory result vs band curvature 
fitting. It just happens to be that the Gamma point is #13 in that list.

Best regards
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster
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Re: [Wien] fold2bloch: problem with K - path in hexagonal lattice

[Rubel, Oleg]

Dear Weronika,

You suspected the fold.m script, but it worked fine. Your original coordinates

M = (1/2, 0, 0)
K = (1/3, 1/3, 0)

transform (with fold 2x2x2) into

M -> G(0, 0, 0)
K -> K'(-1/3, 2/3, 0)

as per the illustration you sent. Then fold.m (and also fold2Bloch) wraps up 
coordinate into a range [-0.5, +0.5], i.e., K'(-1/3,2/3,0) -> K'(-1/3,-1/3,0). 
The wrapping is applied to _all_ coordinates in the path (not just start and 
end), which results in the following case.klist_band

 1 0 0 0 1 1.00
 2-1 2 057 1.00
 3-2 4 057 1.00
 4-1 2 019 1.00
 5-4 8 057 1.00
 6-510 057 1.00
 7-2 4 019 1.00
 8-714 057 1.00
 9-816 057 1.00
10-3 6 019 1.00
11   -1020 057 1.00
12   -1122 057 1.00
13-4 8 019 1.00
14   -1326 057 1.00
15   -1428 057 1.00
16-5-9 019 1.00
17   -16   -25 057 1.00
18   -17   -23 057 1.00
19-6-7 019 1.00
20-1-1 0 3 1.00
END

The problem was in the plotting script (see GitHub for the updated version 
fold2Bloch-Wien2k/Utils/ubs_dots.m). The reason you had "gaps" in the plot has 
to do with rounding:

1/3 = 0.33 + err

The original ubs_dots.m script had a tolerable deviation from a path set = eps 
(machine precision), which is too small to work in all cases. It fails, for 
coordinates such as (1/3, 1/3) since it is stored in case.f2b file as 
(0.33, 0.33, 0).

Now the script contains a new variable

roundOffErrK = 0.01,

which is used to find the tolerable deviation from a desired path for an 
unfolded k point to be accepted and included in the plot.

As a test, I run hexagonal GaN supercell (2x2x2) and got folded (M-K) and 
unfolded band structures. (The Fermi energy was set at E_F=0 instead of a 
proper value, which puts it within the conductions band.) Band structures can 
be downloaded from this link (valid for 7 days):
https://wetransfer.com/downloads/609acabafc6a4d164a42701a84c0f86520201126200032/fb4badbb14116381c0391f963f367c6820201126200117/ccfa0c

Note that the folded (M-K) band structure has nothing in common with the 
unfolded one, since no point on the (M-K) path in the supercell unfolds to 
(M-K) path of the primitive cell.

Thank you for reporting a problem!


Best regards
Oleg

P.S. The ubs_dots_w2k_octave.m script is not updated yet

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster
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Re: [Wien] fold2bloch: problem with K - path in hexagonal lattice

[Rubel, Oleg]

Weronika, one more thing: Here are coordinates from Xcrysden

  0.0  0.0  0.0 GAMMA
  0.5  0.0  0.0 M
  0.3  0.3  0.0 K
  0.0  0.0  0.0 GAMMA
  0.0  0.0  0.5 A
  0.5  0.0  0.5 L
  0.3  0.3  0.5 H
  0.0  0.0  0.5 A

Here is your list: (GAMMA->M(1/2 0 0)->K(1/3 1/3 1/3)->GAMMA->A(0 0 1/2)->L(1/2 
0 1/2)->H(1/3 1/3 1/3)->A(0 0 1/2)

There are discrepancies. You need to use exactly the same path in "fold.m" and 
"ubs_dots_w2k_octave.m", otherwise you will get gaps in k-space. Maybe you can 
share the folded and unfolded band structures with the list?

> but it seems to me that fold.m doesn't work with a hexagonal lattice

I do not exclude such possibility in general, but the symmetry is not important 
for fold.m
There must be another reason.

> Shall I include a path which goes symmetrically around a* reciprocal lattice 
> vector or rather symmetrically around GAMMA (-K -> M -> K or -K -> -M)?

It will be a good exercise if you can make a 2D BZ from a piece of paper, 
locate points G, K, and M (connect them with a line). Then fold this piece of 
paper twice along each axis. Look at where your K and M point end up. You can 
assume 90 deg angle between a* and b* for simplicity.

I hope it will help.

Best regards
Oleg

________
From: Wien  on behalf of Rubel, Oleg 

Sent: Friday, November 20, 2020 16:28
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] fold2bloch: problem with K - path in hexagonal lattice

Dear Weronika,

thank you for the detailed email. I will try to address your questions.

The utility fold.m takes a desired path and _folds_ it according to folds = [2 
2 2]. So, if you set folds = [1 1 1], then your list of point will follow kpath 
= [1/2 0 0; 0 0 0;  1/3 1/3 0]. When folds /= [1 1 1], it becomes more 
complicated. The idea is to get a list of _folded_ k-points such that _after_ 
unfolding they will be on the desired path.

I will get back with more details after looking into your numbers, but there 
should be no "gaps" in k-space if folded k-points are generated correctly.

Thank you
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster



From: Wien  on behalf of Wolszczak, 
Weronika 
Sent: Thursday, November 19, 2020 19:54
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] fold2bloch: problem with K - path in hexagonal lattice

Dear Wien2k users,

I am trying to unfold a hexagonal 2x2x2 superlattice with fold2bloch tool, but 
I am having difficulty with getting the right k-path. As my path is rather 
complicated (GAMMA->M(1/2 0 0)->K(1/3 1/3 1/3)->GAMMA->A(0 0 1/2)->L(1/2 0 
1/2)->H(1/3 1/3 1/3)->A(0 0 1/2)), I tried to use the script which was 
previously advised here (fold.m)

https://github.com/rubel75/fold2Bloch-VASP/blob/master/utils/fold.m

in the following message:
https://www.mailarchive.com/wien@zeus.theochem.tuwien.ac.at/msg18482.html
However, this doesn't work properly (I'm having empty gaps in the unfolded 
diagram). I tried a much simpler path, like M->GAMMA->K, with the following 
input:

%% User input

kpath = [1/2 0 0; 0 0 0;  1/3 1/3 0]; % desired k-path after unfolding
npath = [16 16]; % # of points along each segment
folds = [2 2 2]; % multiplicity used to create a supercell

but this also results is a strange list of k-points:

 1 0 0 0 1 1.00
 2-1 0 015 1.00
 3-2 0 015 1.00
 4-1 0 0 5 1.00
 5-4 0 015 1.00
 6-1 0 0 3 1.00
 7-2 0 0 5 1.00
 8-7 0 015 1.00
 9 7 0 015 1.00
10 2 0 0 5 1.00
11 1 0 0 3 1.00
12 4 0 015 1.00
13 1 0 0 5 1.00
14 2 0 015 1.00
15 1 0 015 1.00
16 2 2 045 1.00
17 4 4 045 1.00
18 2 2 015 1.00
19 8 8 045 1.00
20 2 2 0 9 1.00
21 4 4 0  

Re: [Wien] fold2bloch: problem with K - path in hexagonal lattice

[Rubel, Oleg]

Dear Weronika,

thank you for the detailed email. I will try to address your questions.

The utility fold.m takes a desired path and _folds_ it according to folds = [2 
2 2]. So, if you set folds = [1 1 1], then your list of point will follow kpath 
= [1/2 0 0; 0 0 0;  1/3 1/3 0]. When folds /= [1 1 1], it becomes more 
complicated. The idea is to get a list of _folded_ k-points such that _after_ 
unfolding they will be on the desired path.

I will get back with more details after looking into your numbers, but there 
should be no "gaps" in k-space if folded k-points are generated correctly.

Thank you
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster



From: Wien  on behalf of Wolszczak, 
Weronika 
Sent: Thursday, November 19, 2020 19:54
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] fold2bloch: problem with K - path in hexagonal lattice

Dear Wien2k users,

I am trying to unfold a hexagonal 2x2x2 superlattice with fold2bloch tool, but 
I am having difficulty with getting the right k-path. As my path is rather 
complicated (GAMMA->M(1/2 0 0)->K(1/3 1/3 1/3)->GAMMA->A(0 0 1/2)->L(1/2 0 
1/2)->H(1/3 1/3 1/3)->A(0 0 1/2)), I tried to use the script which was 
previously advised here (fold.m)

https://github.com/rubel75/fold2Bloch-VASP/blob/master/utils/fold.m

in the following message:
https://www.mailarchive.com/wien@zeus.theochem.tuwien.ac.at/msg18482.html
However, this doesn't work properly (I'm having empty gaps in the unfolded 
diagram). I tried a much simpler path, like M->GAMMA->K, with the following 
input:

%% User input

kpath = [1/2 0 0; 0 0 0;  1/3 1/3 0]; % desired k-path after unfolding
npath = [16 16]; % # of points along each segment
folds = [2 2 2]; % multiplicity used to create a supercell

but this also results is a strange list of k-points:

 1 0 0 0 1 1.00
 2-1 0 015 1.00
 3-2 0 015 1.00
 4-1 0 0 5 1.00
 5-4 0 015 1.00
 6-1 0 0 3 1.00
 7-2 0 0 5 1.00
 8-7 0 015 1.00
 9 7 0 015 1.00
10 2 0 0 5 1.00
11 1 0 0 3 1.00
12 4 0 015 1.00
13 1 0 0 5 1.00
14 2 0 015 1.00
15 1 0 015 1.00
16 2 2 045 1.00
17 4 4 045 1.00
18 2 2 015 1.00
19 8 8 045 1.00
20 2 2 0 9 1.00
21 4 4 015 1.00
221414 045 1.00
231616 045 1.00
24 2 2 0 5 1.00
25 4 4 0 9 1.00
262222 045 1.00
27-7-7 015 1.00
28   -19   -19 045 1.00
29   -17   -17 045 1.00
30-1-1 0 3 1.00

First 15 points seem to be fine, it goes from GAMMA (0,0) to -M ( -7/15, 0, 0) 
and then from M(7/15, 0, 0) back to GAMMA (1/15, 0, 0). However, the next part 
it doesn' go to K point (1/3, 1/3, 0), but rather overshoots (22/45, 22/45, 0), 
and there are only 4 points on the negative side, while points between (-1/3 
-1/3 0) and (0 0 0) are missing. It seems to me that something is wrong here. 
Can someone comment if this is a correct output? I did the same part of the 
path -K -> GAMMA -> K with XCrysDen and it goes from (-1/3 -1/3 0) to (1/3 1/3 
0) without any gaps, and this seems to be reasonable but it doesn't agree well 
with the output of fold.m.

I'm not familiar with Matlab, but it seems to me that fold.m doesn't work with 
a hexagonal lattice nor with more complicated paths like (0 0 0 -> 1/2 0 0 -> 
1/3 1/3 0 -> 0 0 0). Can someone suggest how I can get the right path? I 
suppose I can manually split the whole path into segments in XCrysDen and 
stitch them all together  manually, but then how to treat points which are not 
going through GAMMA, but which are on the surface of BZ, like M->K? Shall I 
include a path which goes symmetrically around a* reciprocal lattice vector or 
rather symmetrically around GAMMA (-K -> M -> K or -K -> -M)? If I 

Re: [Wien] twisted angle

[Rubel, Oleg]

Sharing my experience: After playing in VESTA with graphene, I became skeptical 
about prospects of arranging two layers (miss-oriented and stress free!) with 
periodic boundary conditions and a reasonable (for DFT) number of atoms. But 
maybe others are more lucky :)

Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Gavin Abo 

Sent: Tuesday, November 10, 2020 01:19
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] twisted angle

Let's assume there are two sheets of graphene: sheet 1 and sheet 2.  If sheet 1 
is place at a fixed position but sheet 2 is placed directly above it in the z 
direction and then rotated around the z axis with an angle Theta. Perhaps this 
is one definition of a twisted angle (Theta).

In other words, similar to what is seen in Figure 1 of the article "Twisted 
Bilayer Graphene: Interlayer Configuration and Magnetotransport Signatures" at 
the link:

https://doi.org/10.1002/andp.201700025

And similar to FIG. 1b and FIG. 4b in the article "Gap Opening in Twisted 
Double Bilayer Graphene by Crystal fields" at the link:

https://arxiv.org/abs/1910.10524v2

If that is the case, it seems like it would be a matter of geometry on how you 
would have to define your structure in case.struct.

It looks like such a structure with two sheets would require 2D-slabs with 2 
layers separated by a vacuum.

WIEN2k has tools such as "x supercell" and "structeditor" that can help define 
2D-slabs.

There is information in the mailing list archive [ 
http://susi.theochem.tuwien.ac.at/reg_user/mailing_list/ ] and on the Internet 
for these tools.  A few examples are as follows.

Slides 5-8: 
http://susi.theochem.tuwien.ac.at/onlineworkshop/PB-getting_started3.pdf
Slides 11-14 (Exercise 4): 
http://susi.theochem.tuwien.ac.at/events/ws2015/Exercises_15.pdf
http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
http://wien2k-algerien1970.blogspot.com/2019/01/practising-supercell-tool.html
https://wien2k-algerien1970.blogspot.com/2017/12/how-to-create-slab-structure-2d-of.html

Section "9.29 structeditor" in the WIEN2k 19.1/19.2 usersguide 
[http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ] has "rotateatomlist" 
that you can read about that could of be interest for this.

Another tool that has been used by others is VESTA [ 
https://jp-minerals.org/vesta/en/ ]:

https://wien2k-algerien1970.blogspot.com/2017/12/how-to-construct-graphene-structure-and.html

However, slab calculation and vacuum are computationally expensive as you can 
read about in the following posts:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06138.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09158.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13625.html

So setting up such a calculation might be a waste of time if you don't have 
access to computer hardware that is capable of doing such a calculation.

A single personal desktop/laptop computer in my experience tends to be 
insufficient when going beyond about simple unit cells and small supercells 
with only a few atoms.

It may be that a group of GB networked computers is needed:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html
https://social.technet.microsoft.com/wiki/contents/articles/2539.diy-supercomputing-how-to-build-a-small-windows-hpc-cluster.aspx
https://diybigdata.net/personal-compute-cluster-2019-edition/
http://www.ssanalysis.co.uk/blog/spreading-the-load-an-abaqus-cluster-blog

If that is not enough, a small rack or small high computing cluster (HPC) may 
be needed:

https://www.admin-magazine.com/HPC/Articles/real_world_hpc_setting_up_an_hpc_cluster
http://techcenter.wikifoundrymobile.com/page/Dell+Life+Cycle+Controller+features+for+High+Performance+Computing+Cluster+Deployment

It is also possible that may not be enough and a larger HPC may be needed for 
such a calculation:

https://uwm.edu/hpc/specifications-3/
https://hpc.uni.lu/systems/gaia/
https://www.isip.piconepress.com/projects/neuronix/html/neuronix_overview.shtml
https://wiki.anunna.wur.nl/index.php/Architecture_of_the_HPC
https://www.delltechnologies.com/resources/en-us/asset/offering-overview-documents/ready-bundle-for-hpc-research-solution-overview.pdf

It is of course difficult to generalize what would be needed because computer 
hardware is very diverse as can be seen by looking at the systems at the above 
links and the structures (e.g., having different number of atoms) and 
calculation parameters used vary computer resources for computation, such that 
an attempt at running the calculation is sometimes the easiest why to determine 
if it will compute or not [ 

Re: [Wien] View structure in a remote machine

[Rubel, Oleg]

Hi Pablo,

of course it is up to you to select the software, but Zoom is great for video 
conferencing and is probably not an ideal solution for remote control. Here is 
a wiki quote: "Virtual Network Computing is a graphical desktop-sharing system 
that uses the Remote Frame Buffer protocol to remotely control another 
computer." There should be a plenty of info in internet on how to set it up. 
VNC is easier on network and gives a "smoother" control experience when it 
comes to xcrysden rendering. (At least this was my experience.)

Good luck
Oleg


From: Wien  on behalf of delamora 

Sent: Monday, October 5, 2020 21:22
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] View structure in a remote machine

I have used "zoom" and it works in my machine and the other people that are 
connected, but not in the remote computer.
Maybe there is a trick that I do not see.


Oleg, sorry for my late reply.
When I am working directly on one computer and I would like to see the crystal 
structure then I push the "view structure" button and the structure appears in 
the screen, but when I am in a remote computer working the WIEN2k and I push 
this button then the crystal structure is displayed in the other computer and 
non in mine.
Does VNC corrects or solves this problem?
Cheers

Pablo
____
De: Wien  en nombre de Rubel, Oleg 

Enviado: viernes, 2 de octubre de 2020 02:59 p. m.
Para: A Mailing list for WIEN2k users 
Asunto: Re: [Wien] View structure in a remote machine

I would suggest trying VNC (https://www.youtube.com/watch?v=EWkrqqnOgdo). It 
has a number of advantages over X11 display forwarding.

Oleg


From: Wien  on behalf of delamora 

Sent: Friday, October 2, 2020 15:39
To: A Mailing list for WIEN2k users
Subject: [Wien] View structure in a remote machine

Dear WIEN2k community,
I am doing calculations in a remote machine ("remote.machine")
I can connect with
remote.machine:7890
and with this I can do calculations in than machine
but when I try to see the crystal structure, xcrysden, the image appears in 
"remote.machine" so I cannot see it in my machine at home
Is there a way to visualize the crystal structure in my machine at home?
The same seems to happen with Electron Density Plots.

Cheers

Pablo
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Re: [Wien] View structure in a remote machine

[Rubel, Oleg]

I would suggest trying VNC (https://www.youtube.com/watch?v=EWkrqqnOgdo). It 
has a number of advantages over X11 display forwarding.

Oleg


From: Wien  on behalf of delamora 

Sent: Friday, October 2, 2020 15:39
To: A Mailing list for WIEN2k users
Subject: [Wien] View structure in a remote machine

Dear WIEN2k community,
I am doing calculations in a remote machine ("remote.machine")
I can connect with
remote.machine:7890
and with this I can do calculations in than machine
but when I try to see the crystal structure, xcrysden, the image appears in 
"remote.machine" so I cannot see it in my machine at home
Is there a way to visualize the crystal structure in my machine at home?
The same seems to happen with Electron Density Plots.

Cheers

Pablo
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Re: [Wien] Berrypi_GGA+U+SO

[Rubel, Oleg]

I can confirm that the latest version (WIEN2k + berrypi from GitHub) was 
recently tested for GGA+U+SOC and it works.

Oleg


From: Wien  on behalf of Gavin Abo 

Sent: Monday, September 14, 2020 21:48
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi_GGA+U+SO

The issue in your calculation case as given by the "(x) w2waddsp: neither mmn 
nor amn files present" message is probably due to the known WIEN2k 14.2 bug 
reported in the post:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15074.html

The WIEN2k version 19.2 has fixed code as Prof. Marks has stated, which is also 
shown on the WIEN2k updates page 
[http://susi.theochem.tuwien.ac.at/reg_user/updates/].  That is one of the bugs 
that WIEN2k 19.2 has fixed code for.

On 9/14/2020 7:01 PM, Laurence Marks wrote:
The most obvious statement: there have been numerous bug fixes since 14.2 which 
is ~ 5 years old and obsolete. Please update to 19.2. It is unlikely that 
anyone has a 14.2 version running and will be prepared to fix obsolete code.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu

On Mon, Sep 14, 2020, 19:50 tarek 
mailto:hammad_ta...@hotmail.com>> wrote:
Dear wien2k team/users

I managed to run Berrypi for GGA+U+SO case under OS ubuntu 14.4 and
wien2k_14.2.

I constructed 4X4x2 supercell of 48 atoms. However, I ran GGA+U+SO
successfully.

Therefore I applied Berrypi command as below:

 >berrypi -o -j -k3:2:2 -p  it failed .. then

 >berrypi -o -j -k2:2:2 -p  it failed .. then even with

 >berrypi -o -j -k1:1:1  No way,the calculations again crushed.

I attached the file containing my last results herein.

I hope if you can help me.

Thanks a lot for your help.

Yours sincerely

Tarek Hammad.
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Re: [Wien] Segmentation fault in w2w

[Rubel, Oleg]

Thank you for sharing that!

Would it be possible to share (maybe privately) the case.struct file and 
_exact_ sequence of commands (incl. initialization, scf run, etc.) with all 
options. Then it will be possible to reproduce and debug.

Thank you in advance
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Niraj Aryal 

Sent: Friday, September 11, 2020 14:02
To: A Mailing list for WIEN2k users
Subject: [Wien] Segmentation fault in w2w

Dear w2w experts and developers,

I am using Wien2k version 19.2 in scientific linux 7.5 using intel compilers 
(2018).

I am trying to wannierize f-electron system with antiferromagnetic magnetic 
ordering using w2w version 2.0 in the presence of SOC.

After self-consistent calculations, these are the steps I am following for the 
wannierisation:

init_w2w (to write case.klist, case.inwf, case.win etc)

 x lapw1 -up -p
 x lapw1 -dn -p
 x lapwso -up -orb -p

x w2w -so -up -p  --> segmentation fault here
x w2w -so -dn -p  --> segmentation fault here
..

Everything works perfectly if I use small kmesh (about 100 kpoints) for the 
wannierisation.
I have about 50 bands to wannierize.
When I increase the number of kpoints, w2w crashes giving segmentation fault.

I found that w2w can write case.mmn and case.eig with no problems but the seg 
fault occurred while writing case.amn.
I confirmed the following hoping that it could help in the debugging process:

1) If I decrease the number of bands to wannierize, the number of kpoints in 
the wannierisation can be slightly increased without seg fault.
2)The problem persists without -so and -p (i.e. without parallel calculation) 
flag.

In my opinion, there are some hard coded array size value(s) in the w2w program 
in amn/mmn subroutines which give segmentation fault when the number of 
projections*bands*kpoints exceeds that value.
This was confirmed by doing calculations in a simpler system like silicon with 
a large number of kpoints and bands.

I tried looking into the w2w source files and found few hard coded values.
However, I am hesitant to make changes because I am worried this could ruin 
other things.

This problem is similar to the one posted last year:
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18896.html
which was not solved.
I would greatly appreciate your suggestion/feedback regarding this problem.
You could also guide me to the right subroutines if you know the details of the 
code.

Thank you.

Sincerely,
Niraj Aryal
Research Associate
Brookhaven National Lab.
Upton, NY

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Re: [Wien] Exit code "0" for LAPW1 with an error

[Rubel, Oleg]

Thank you for the suggestions! Below is the end solution in python. The pattern 
search is "*lapw1*.error" or "*lapwso*.error", etc. I hope it will work with 
different spins or/and parallel error files. Also "*lapw1*.error" files get 
cleaned up before executing LAPW1. This prevents any leftovers from previous 
runs. Do you see any potentials problems with this implementation?

Thank you
Oleg

testerror('lapw1')

def testerror(corename):
pattern = '*'+corename+'*.error'
for errfilename in glob.glob(pattern):
errfilesize = os.path.getsize(errfilename)
if errfilesize != 0:
print("ERROR detected in", corename)
print("Please check the error file:",errfilename)
sys.exit(1)


From: Wien  on behalf of Peter Blaha 

Sent: Tuesday, September 8, 2020 16:01
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Exit code "0" for LAPW1 with an error

Exactly.
In run_lapw we define an alias (tcsh syntax, in bash it is slightly
different) like:

alias   testerror   'if (! -z \!:1.error) goto error'

and with
x lapw1
testerror lapw1

you can catch a problem.
Instead of "goto error" you could also do something else.

PS: Most of our shell scripts exit with an error code when a real error
came up. This can be catched with echo $status


Am 08.09.2020 um 20:38 schrieb Yundi Quan:
> The simplest way that I can think of is to check whether the lawp1.error
> file is empty or not after executing x lapw1. If it is empty after
> executing 'x lapw1', then lapw1 terminates without any errors. If it is
> not, then lapw1 terminates with error(s).
>
> On Tue, Sep 8, 2020 at 2:23 PM Rubel, Oleg  <mailto:rub...@mcmaster.ca>> wrote:
>
> Dear WIEN2k community,
>
> suppose we have a code that includes a sequence of commands. Before
> running the next command, I would like to check if the previous one
> completed successfully. It is convenient to use exit codes for that
> purpose. Here is a small example in bash (looking for a file that
> does not exist):
>
> [rubel@gra-login3 lambda1]$ ls oleg
> ls: cannot access 'oleg': No such file or directory
> [rubel@gra-login3 lambda1]$ echo $?
> 2
>
> Here "echo $?" returns the exit code of a previous command. If it is
> not "0", there is a problem (like in this case, there is no "oleg"
> file).
>
> Now I try to apply the same strategy to WIEN2k:
>
> [rubel@gra-login3 lambda1]$ x lapw1
> LAPW1 - Error
> 0.001u 0.018s 0:00.06 16.6% 0+0k 23592+16io 67pf+0w
> [rubel@gra-login3 lambda1]$ echo $?
> 0
>
> This is an unexpected result. The exist status is OK in spite of the
> fact that LAPW1 exited with an error. Of course, there are error
> files created for each program + spin up/dn (even process for
> parallel calculations). But it can be quite elaborate to search
> through them, and it depends on whether you run lapw1 or lapw2, etc.
>
> I wonder if there is a _simple_ alternative way for sensing an
> error? Also message is not always "X - Error". It can be
> different (e.g., segmentation fault).
>
> Thank you in advance
> Oleg
>
> --
> Oleg Rubel (PhD, PEng)
> Department of Materials Science and Engineering
> McMaster University
> JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
> Email: rub...@mcmaster.ca <mailto:rub...@mcmaster.ca>
> Tel: +1-905-525-9140, ext. 24094
> Web: http://olegrubel.mcmaster
>
>
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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:
http://www.imc.tuwien.ac.at/tc_blaha-

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Re: [Wien] Exit code "0" for LAPW1 with an error

[Rubel, Oleg]

It is a possibility. In case of LAPW1 it can be lapw1.error, but it can also be 
uplapw1.error, or uplapw1_1.error, or uplapw1_2.error, etc. Some error files 
could be in place from a previous run. Maybe there is a more elegant solution?


From: Wien  on behalf of Yundi Quan 

Sent: Tuesday, September 8, 2020 14:38
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Exit code "0" for LAPW1 with an error

The simplest way that I can think of is to check whether the lawp1.error file 
is empty or not after executing x lapw1. If it is empty after executing 'x 
lapw1', then lapw1 terminates without any errors. If it is not, then lapw1 
terminates with error(s).

On Tue, Sep 8, 2020 at 2:23 PM Rubel, Oleg 
mailto:rub...@mcmaster.ca>> wrote:
Dear WIEN2k community,

suppose we have a code that includes a sequence of commands. Before running the 
next command, I would like to check if the previous one completed successfully. 
It is convenient to use exit codes for that purpose. Here is a small example in 
bash (looking for a file that does not exist):

[rubel@gra-login3 lambda1]$ ls oleg
ls: cannot access 'oleg': No such file or directory
[rubel@gra-login3 lambda1]$ echo $?
2

Here "echo $?" returns the exit code of a previous command. If it is not "0", 
there is a problem (like in this case, there is no "oleg" file).

Now I try to apply the same strategy to WIEN2k:

[rubel@gra-login3 lambda1]$ x lapw1
LAPW1 - Error
0.001u 0.018s 0:00.06 16.6% 0+0k 23592+16io 67pf+0w
[rubel@gra-login3 lambda1]$ echo $?
0

This is an unexpected result. The exist status is OK in spite of the fact that 
LAPW1 exited with an error. Of course, there are error files created for each 
program + spin up/dn (even process for parallel calculations). But it can be 
quite elaborate to search through them, and it depends on whether you run lapw1 
or lapw2, etc.

I wonder if there is a _simple_ alternative way for sensing an error? Also 
message is not always "X - Error". It can be different (e.g., segmentation 
fault).

Thank you in advance
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca<mailto:rub...@mcmaster.ca>
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


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[Wien] Exit code "0" for LAPW1 with an error

[Rubel, Oleg]

Dear WIEN2k community,

suppose we have a code that includes a sequence of commands. Before running the 
next command, I would like to check if the previous one completed successfully. 
It is convenient to use exit codes for that purpose. Here is a small example in 
bash (looking for a file that does not exist):

[rubel@gra-login3 lambda1]$ ls oleg
ls: cannot access 'oleg': No such file or directory
[rubel@gra-login3 lambda1]$ echo $?
2

Here "echo $?" returns the exit code of a previous command. If it is not "0", 
there is a problem (like in this case, there is no "oleg" file).

Now I try to apply the same strategy to WIEN2k:

[rubel@gra-login3 lambda1]$ x lapw1
LAPW1 - Error
0.001u 0.018s 0:00.06 16.6% 0+0k 23592+16io 67pf+0w
[rubel@gra-login3 lambda1]$ echo $?
0

This is an unexpected result. The exist status is OK in spite of the fact that 
LAPW1 exited with an error. Of course, there are error files created for each 
program + spin up/dn (even process for parallel calculations). But it can be 
quite elaborate to search through them, and it depends on whether you run lapw1 
or lapw2, etc.

I wonder if there is a _simple_ alternative way for sensing an error? Also 
message is not always "X - Error". It can be different (e.g., segmentation 
fault).

Thank you in advance
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


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Re: [Wien] Born effective charge calculation

[Rubel, Oleg]

To add to the discussion, here is a tutorial "Born effective charge of GaN" 
from the last WIEN2k workshop 
(http://susi.theochem.tuwien.ac.at/events/ws2019/Exercises_19-tot.pdf). In this 
case LDA performs very well. One can try to do TBmBJ to see a difference.

Some systems with a small Eg (for example InN) have Eg = 0 at LDA/GGA level, 
which created a problem for Berry phase calculations that need a gap. In this 
case TBmBJ (or DFT+U) would be your best option.

I hope it will help
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Laurence 
Marks 
Sent: Saturday, September 5, 2020 22:39
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Born effective charge calculation

>From what I have found and my tests, either -eece or +U are better as GGA's 
>overestimate. MBJ does not appear to be better. However, values are often not 
>that well measured experimentally.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu

On Sat, Sep 5, 2020, 19:09 Wien2k User 
mailto:wien2k.u...@gmail.com>> wrote:
Dear Wien2k users,

Is it more precise to use mBJ for the calculation of born effective charge or 
gga is sufficient? (in a case where there is no comparison values)
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Re: [Wien] w2wc parallel

[Rubel, Oleg]

You are right. "x w2w -p" does not take advantage of parallelization (I am not 
sure about OMP?), but its main purpose is to properly reads files created at "x 
lapw1 -p" level.

[rubel@gra796 lambda1]$ cat .machines
1:localhost
1:localhost
[rubel@gra796 lambda1]$ x w2w  -p
W2W END
3.496u 0.110s 0:03.65 98.6% 0+0k 35720+5712io 113pf+0w

There is only one process at ~100%.

Here is what will happen if you run LAPW with -p and w2w not:

[rubel@gra796 lambda1]$ x w2w
forrtl: severe (24): end-of-file during read, unit 50, file 
/scratch/rubel/berrypi/tutorials/tutorial1/lambda1/lambda1.energy
Image  PCRoutineLineSource
w2wc   00448BBE  Unknown   Unknown  Unknown
w2wc   0047527A  Unknown   Unknown  Unknown
w2wc   0042DDEF  MAIN__ 99  main.f
w2wc   00402BEE  Unknown   Unknown  Unknown
libc.so.6  2B7FE008D2E0  Unknown   Unknown  Unknown
w2wc   00402AEA  Unknown   Unknown  Unknown
0.005u 0.028s 0:00.05 40.0% 0+0k 21672+16io 60pf+0w
error: command   /home/rubel/WIEN2k_19.2/w2wc w2w.def   failed

I hope it will help
Oleg


From: Wien  on behalf of karima 
Physique 
Sent: Thursday, September 3, 2020 16:16
To: A Mailing list for WIEN2k users
Subject: [Wien] w2wc parallel

Dear wien2k users,

When I run the x w2w -p command, I see that there is a one core occupied 
(non-parallel) despite the presence of the machine file

Any suggestions?
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Re: [Wien] Berrypi & w2w

[Rubel, Oleg]

P.S.: I tested spontaneous polarization in BaTiO3. With 1x1x1 k mesh we have Ps 
= 0.297 C/m2 vs the "good" result from 6x6x6 mesh of 0.305 C/m2. The difference 
is not that huge.

Oleg


From: Wien  on behalf of Rubel, Oleg 

Sent: Monday, August 24, 2020 16:17
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

Technically, it should work even with 1x1x1 mesh. The loop is closed in k space 
through periodic boundary conditions. For a surface, x1 mesh in the 
perpendicular direction should be sufficient.

Oleg


From: Wien  on behalf of Peter Blaha 

Sent: Monday, August 24, 2020 14:47
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

I'd guess that for an insulator this is not a problem.

It would be problematic for metals, but berrypi is not for metals anyway.

Am 24.08.2020 um 19:52 schrieb Laurence Marks:
> Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will
> happen with a surface calculation where along the long direction there
> is only one k-point?
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu <http://www.numis.northwestern.edu/>
> Corrosion in 4D: www.numis.northwestern.edu/MURI
> <http://www.numis.northwestern.edu/MURI>
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
>
> ___
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>

--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] Berrypi & w2w

[Rubel, Oleg]

Technically, it should work even with 1x1x1 mesh. The loop is closed in k space 
through periodic boundary conditions. For a surface, x1 mesh in the 
perpendicular direction should be sufficient.

Oleg


From: Wien  on behalf of Peter Blaha 

Sent: Monday, August 24, 2020 14:47
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Berrypi & w2w

I'd guess that for an insulator this is not a problem.

It would be problematic for metals, but berrypi is not for metals anyway.

Am 24.08.2020 um 19:52 schrieb Laurence Marks:
> Does anyone know if berrypi /w2w require a 3D k-mesh, e.g. what will
> happen with a surface calculation where along the long direction there
> is only one k-point?
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu 
> Corrosion in 4D: www.numis.northwestern.edu/MURI
> 
> Co-Editor, Acta Cryst A
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
>
> ___
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> SEARCH the MAILING-LIST at:  
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>

--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:
http://www.imc.tuwien.ac.at/tc_blaha-

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Re: [Wien] mBJ calculation for semimetallic system

[Rubel, Oleg]

Hi Fabien.

The paper (http://dx.doi.org/10.1021/acs.jpca.7b02882) does not mention SOC. I 
assume it is done without SOC? In SnTe SOC is important. It opens the gap, if I 
recall it correctly, which would also make sense for a topological insulator. 
SOC vs no-SOC could explain the difference between my results (PBE 0.24 eV and 
TB-mBJ 0.13 eV) and your results (0.07 and 0.15 eV, respectively).

Best regards
Oleg


From: Wien  on behalf of Tran, Fabien 

Sent: Friday, July 17, 2020 16:55
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mBJ calculation for semimetallic system

Hi,

Thanks for your comments. For which structure of SnTe did you get these gaps? In
http://dx.doi.org/10.1021/acs.jpca.7b02882
the PBE and mBJ gaps of SnTe (SG 225) are 0.07 and 0.15 eV, respectively?

FT


From: Wien  on behalf of Rubel, Oleg 

Sent: Friday, July 17, 2020 10:43 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mBJ calculation for semimetallic system

Hi Myung-Chul,

in addition to Fabien's comments, I had a very positive experience with TB-mBJ 
also for semimetals. For instance, (HgCd)Te alloy has a negative band gap on 
the HgTe-reach side. TB-mBJ predicts the negative gap correctly 
(https://doi.org/10.1103/PhysRevB.90.115202), while PBE makes it too negative. 
With TB-mBJ we were able to get correct zero-gap (HgCd)Te composition.

Regarding topological materials: SnTe is an interesting material system. It has 
the experimental band gap of 0.18 eV. PBE overestimates (!) the band gap and 
yields 0.24 eV, while TB-mBJ gives a smaller (!) gap of 0.13 eV. I would 
definitely trust more  TB-mBJ in this case.

I hope it will help
Oleg
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Tran, Fabien 

Sent: Thursday, July 16, 2020 03:36
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mBJ calculation for semimetallic system

Hi,

mBJ was proposed for the calculation of band gaps, which are more realistic 
than with LDA/PBE
for nonmagnetic semiconductors and insulators, as well as antiferromagnetic 
systems.

Concerning semimetals and topological insulators, I would recommend to search 
for results obtained with
mBJ for systems which are similar to the ones you want to study.

F. Tran



From: Wien  on behalf of Aaron Jung 

Sent: Thursday, July 16, 2020 8:15 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] mBJ calculation for semimetallic system

Dear users and developers,

Hello,

I performed the mBJ calculation in a semimetallic system, but it has a tiny gap 
already.
As considering SOC, the system becomes a semiconducting state.

I have two questions.
First, to investigate the Z2 indices on bulk system, I conduct the eigen parity 
for each TRIM points.
In the mBJ calculation, the eigen parity is reliable? That is, can I accept the 
result of parity eigen value from the irrep calculation?

Second,
For LDA+mBJ calculation,
Can I use the mBJ approach for semimatallic and nonmagnetic system?

Thank you,
Myung-Chul.

=
Myung-Chul Jung
Postdoctoral Researcher

Electronic Structure Theory Group (E6-2, 4310)

Department of Physics, Korea Advanced Institute of Science and Technology

291 Daehak-ro, Yuseong-gu, 34141, Korea
=
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Re: [Wien] mBJ calculation for semimetallic system

[Rubel, Oleg]

Hi Myung-Chul,

in addition to Fabien's comments, I had a very positive experience with TB-mBJ 
also for semimetals. For instance, (HgCd)Te alloy has a negative band gap on 
the HgTe-reach side. TB-mBJ predicts the negative gap correctly 
(https://doi.org/10.1103/PhysRevB.90.115202), while PBE makes it too negative. 
With TB-mBJ we were able to get correct zero-gap (HgCd)Te composition.

Regarding topological materials: SnTe is an interesting material system. It has 
the experimental band gap of 0.18 eV. PBE overestimates (!) the band gap and 
yields 0.24 eV, while TB-mBJ gives a smaller (!) gap of 0.13 eV. I would 
definitely trust more  TB-mBJ in this case.

I hope it will help
Oleg
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Tran, Fabien 

Sent: Thursday, July 16, 2020 03:36
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] mBJ calculation for semimetallic system

Hi,

mBJ was proposed for the calculation of band gaps, which are more realistic 
than with LDA/PBE
for nonmagnetic semiconductors and insulators, as well as antiferromagnetic 
systems.

Concerning semimetals and topological insulators, I would recommend to search 
for results obtained with
mBJ for systems which are similar to the ones you want to study.

F. Tran



From: Wien  on behalf of Aaron Jung 

Sent: Thursday, July 16, 2020 8:15 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] mBJ calculation for semimetallic system

Dear users and developers,

Hello,

I performed the mBJ calculation in a semimetallic system, but it has a tiny gap 
already.
As considering SOC, the system becomes a semiconducting state.

I have two questions.
First, to investigate the Z2 indices on bulk system, I conduct the eigen parity 
for each TRIM points.
In the mBJ calculation, the eigen parity is reliable? That is, can I accept the 
result of parity eigen value from the irrep calculation?

Second,
For LDA+mBJ calculation,
Can I use the mBJ approach for semimatallic and nonmagnetic system?

Thank you,
Myung-Chul.

=
Myung-Chul Jung
Postdoctoral Researcher

Electronic Structure Theory Group (E6-2, 4310)

Department of Physics, Korea Advanced Institute of Science and Technology

291 Daehak-ro, Yuseong-gu, 34141, Korea
=
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Re: [Wien] lapw7 with spin-orbit

[Rubel, Oleg]

Dear Mikhail,

I suggest setting up a different folder (to avoid mess), for instance "wfplot". 
Then you can copy (or better link) relevant files from your SCF calculation 
into this folder:
5 ,'wfplot.in7c',  'old','formatted',0
8 ,'wfplot.struct', 'old','formatted',0
10,'./wfplot.vector','old','unformatted',0
18,'wfplot.vsp',   'old','formatted',0

At this point you need to take SOC vector file case.vectorso and call it 
wfplot.vector within that folder to trick LAPW7. Then you can extract and plot 
WFs.

For degenerate states WFs can be extracted separately, then put as different 
blocks in one XSF file and added up in xcrysden. This is a delicate part, and I 
will not go into details, unless you really need it.

Best regards
Oleg
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien  on behalf of Mikhail 
Nestoklon 
Sent: Sunday, July 5, 2020 15:35
To: A Mailing list for WIEN2k users
Subject: [Wien] lapw7 with spin-orbit

Dear wien2k community,
I am trying to use lapw7 to plot a particular wave function for the case with 
spin-orbit switched on. In the manual it is mentioned that "It should be easy 
to run lapw7 in parallel mode, and/or to apply it to wave function data obtained
by a spin-orbit interaction calculation. None of these options have been 
implemented so far."
Does anyone has some recommendations how this can be done?
I have tried to change the lapw7.def to use SO results (replaced case.vector 
with case.vectorso[_n] file), this kind of worked, but the result is not what I 
expected. The energy mentioned in case.output7 file corresponds to the band 
number in the file without spin-orbit interaction. And the wave function looks 
like the one for the band numbered accordingly to the output of lapw1, not 
lapwso. I am pretty sure that lapw7 uses the "so" file: when I forgot to remove 
RLOs, the result was totally incorrect.
Of course, I will read the source code, but I don’t believe nobody tried to use 
lapw7 with SO before.

Thank you in advance.

Sincerely yours,
Mikhail Nestoklon





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Re: [Wien] polarisation of non magnetic compounds

[Rubel, Oleg]

It is due to partial occupancies of individual k points and bands. Also, it is not possible to disentangle crossings bands. This implies that we can only consider a “bundle” of bands separated by a gap. 


I hope it will help 
Oleg 

On Dec 27, 2019, at 19:07, Wien2k User <wien2k.u...@gmail.com> wrote:




dear dr.  Oleg  ;

Thank you for your answer
I have another question 

using BerryPI, I have read that we cannot study the spontaneous polarizations for metals, I want to know why?




thank you in advance




Le ven. 27 déc. 2019 à 23:07, Rubel, Oleg <rub...@mcmaster.ca> a écrit :




Any non-centrosymmetric material with a band gap should have some polarization.


Oleg 

On Dec 27, 2019, at 09:27, Wien2k User <wien2k.u...@gmail.com> wrote:





Dear Wien2k users;



how can we know if a non-magnetic material is polarized or not? or we have only to calculate its polarization (BerryPI)
 .




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Re: [Wien] polarisation of non magnetic compounds

[Rubel, Oleg]

Any non-centrosymmetric material with a band gap should have some polarization.


Oleg 

On Dec 27, 2019, at 09:27, Wien2k User  wrote:





Dear Wien2k users;



how can we know if a non-magnetic material is polarized or not? or we have only to calculate its polarization (BerryPI)
 .




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Re: [Wien] a query about fold2Bloch

[Rubel, Oleg]

In addition to Gavin's comment, I would suggest trying octave as a free alternative to Matlab.


Oleg

On Aug 28, 2018, at 23:27, Gavin Abo  wrote:




Regarding 2, fold2Bloch Guide [ 
https://github.com/rubel75/fold2Bloch-Wien2k/wiki/fold2Bloch-Guide ] and Tutorial 1 [

https://github.com/rubel75/fold2Bloch-Wien2k/wiki/Tutorial-1:-Lattice-of-Hydrogen-atoms ] show that eigenvalues are Ry in case.f2b.
Regarding 1, the ubs_dots.m [ 
https://github.com/rubel75/fold2Bloch-Wien2k/blob/master/Utils/ubs_dots.m ] in Tutorial 1 seems to use a scatter plot [

https://www.mathworks.com/help/matlab/ref/scatter.html ].  You might be able to use the plot function in gnuplot [

https://stackoverflow.com/questions/35075113/scatter-plot-with-different-size-for-each-point ,

http://gnuplot.sourceforge.net/docs_4.2/node100.html ] or Indexed Size (Bubble) and Color Map Graph in Origin [

https://www.originlab.com/doc/Origin-Help/2DSym-Graph ].

On 8/28/2018 11:40 AM, karima Physique wrote:


Dear dr. Oleg Rubel and Wien2k
 users:


1- do you have any idea to how to plot the band strcture using gnuplot or  Originlab (transform F2B file to dataplot file with X:Y columns).
2- the unit of energy is it eV or Ry in F2B file





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Re: [Wien] Spontaneous polarization of PbTiO3

[Rubel, Oleg]

Dear Gavin,


This is a very good point. I certainly agree that the symmetry of the cubic structure should be reduced to that of the tetragonal structure.


Thank you 
Oleg 

On May 8, 2018, at 04:05, Gavin Abo  wrote:




In the BaTiO3 tutorial, lambda1.struct and lambda0.struct both have spacegroup 99_P4mm and 8 symmetry operations [

https://github.com/spichardo/BerryPI/wiki/Tutorial-1:-Spontaneous-Polarization-in-BaTiO3 ].
I see a sentence in the tutorial:

The symmetry operations are identical (!) to the lambda1 case, in spite of a higher symmetry of the lambda0 structure.

Perhaps that is the sentence that another user got that the symmetry might need to remain the same [

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16112.html ].

The tet1.struct has spacegroup 99_P4mm, while cubic.struct has spacegroup 221_Pm3m.
According to the tutorial:

8. Spontaneous polarization is obtained by taking a difference in polarization between P(lambda1) and P(lambda0) -> Difference between tet1 and cubic for the PbTiO3 case?

For PbTiO3, is it okay that there are "8 NUMBER OF SYMMETRY OPERATIONS" in cubic.struct and "48 NUMBER OF SYMMETRY OPERATIONS" in tet1.struct for the spontaneous polarization calculation?

On 5/7/2018 4:36 AM, Lokanath Patra wrote:


Dear Oleg,


I am attaching the structure files which I have used for the calculation. I have used similar procedure as given for BaTiO3 tutorial (same parameters for initialising and same k-point mesh for Berrypi. The calculated polarisation for cubic phase is very
 low. So so spontaneous polarisation is still very low as given in my previous mail. I am unable to trace my mistakes.


Best regards
Lokanath


On Wed, May 2, 2018 at 7:25 PM, Oleg Rubel 
 wrote:

Dear Lokanath,

PbTiO3 was one of compounds used in the test of BerryPI (see Table 3 in
http://olegrubel.mcmaster.ca/publications/2013/Ahmed_CPC_184_2013.pdf). I think you should also compute polarization
 in the cubic structure of PbTiO3 even though they are deemed to have no polarization. If this does not help, I would suggest looking into the structure more carefully, tetragonal distortion, compare with experiment, etc.


I hope it will help
Oleg

-- 
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 
359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: 
rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: 
http://olegrubel.mcmaster.ca

On 2018-May-02 08:38, Lokanath Patra wrote:



Dear all,

I am using Berry phase tutorial to calculate the polarization of PbTiO3. I have followed the BaTiO3 tutorial. I have two structures, one is tetragonal (non-centrosymmetric) and the second one is cubic (centrosymmetric). I have calculated the (spontaneous) polarization
 as 1.189769e-01 C/m2 (as the cubic system doesn't posses any polarization) which is very low as the reported values are around 80 to 100 µC/cm2. Please help me.

Regards
Lokanath

-- 
Lokanath Patra
Ph.D Scholar
Dept. of Physics
School of Applied and Basic Sciences
Central University of Tamil Nadu
Thiruvarur
Tamil Nadu - 610004
Ph no - +91-8675834507





Central University of Tamil Nadu is in not responsible for the contents of this email. The sender takes responsibility for the content of this email. /This mail is also governed by the relevant disclaimer policies of Central University of Tamil Nadu.
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-- 

Lokanath Patra
Ph.D Scholar
Dept. of Physics
School of Applied and Basic Sciences
Central University of Tamil Nadu
Thiruvarur
Tamil Nadu - 610004
Ph no - +91-8675834507






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Re: [Wien] Spontaneous polarization of PbTiO3

[Rubel, Oleg]

Dear Lokanath,

I am traveling and will be able to look into this at the end of May. In the 
meanwhile would you please share a comparison of your PbTiO3 structure vs 
experiments through the list. 

Thank you 
Oleg

> On May 7, 2018, at 13:36, Lokanath Patra  wrote:
> 
> Lokanath
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Re: [Wien] NumPy-1.6.2 not found error occurs during Wien2k_17.1 installation

[Rubel, Oleg]

It depends on whether or not you are intended to use BerryPI. If not, then don't worry. If yes, then I suggest testing tutorials available on Github and see if they work or not with your version of numpy.


I hope it will help 
Oleg

On May 4, 2018, at 11:13, AJAY SINGH VERMA  wrote:





Dear Sir,

I have installed Wien2k 17.1 version on my PC having core i5 with ubuntu

17.10 operating system. All the software given in UG are installed (i.e. -libxc 3.0.0, fftw3, fortran compiler ifort and MKL libraries). During the
 installation process of wien2k_17.1, when i run ./expand_lapw command. following error occurred






NumPy-1.6.2 not found, instead you have: 1.14.3
BerryPI will not work with earlier versions  and has been tested only with 1.6.2 and 1.9.2


How to solve this?


Thanks


Ajay Singh Verma





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Re: [Wien] Fold2Bloch in parallel mode

[Rubel, Oleg]

The multiplicity 1:1:1 implies that the primitive cell and the supercell are 
the same. Thus, there is nothing to unfold. You should simply plot a classical 
band structure in this case.

Thank you
Oleg
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster


From: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] on behalf of Tristan de 
Boer [tristan.deb...@usask.ca]
Sent: October 18, 2017 17:31
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] Fold2Bloch in parallel mode

Thanks for the replies. Using join_vectorfiles is working well. I have a
follow up question. I've been able to replicate the tutorials, and a
supercell of my own, but when I use fold2bloch on a single unit cell
with folds of 1:1:1 the weights in the case.f2b file are all 1. Do you
have any comment on why this might be?
Best Regards,
Tristan

On 2017-10-18 9:12 AM, Rubel, Oleg wrote:
> Either solution (Peter’s or Maciej’s) should work. The user’s choice might 
> depend on the size of the vector files.
>
> If you process individual *.vector_X files with fold2Bloch, it will warn that 
> the number of k-points is less than in the klist-file. This warning can be 
> ignored since k-points are split between *.vector_X files.
>
> Thanks
> Oleg
>
> --
> Oleg Rubel (PhD, PEng)
> Department of Materials Science and Engineering
> McMaster University
> JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
> Email: rub...@mcmaster.ca
> Tel: +1-905-525-9140, ext. 24094
> Web: http://olegrubel.mcmaster.ca
>
>> On Oct 18, 2017, at 10:38, Peter Blaha <pbl...@theochem.tuwien.ac.at> wrote:
>>
>> There is a   join_vectorfile   utility which combines the parallel vector 
>> files into a single one.
>>
>> On 10/17/2017 07:21 PM, Tristan de Boer wrote:
>>> Dear WIEN2k Users,
>>> I'm trying to use Fold2Bloch for a calculation in which I've done
>>> 'x lapw1 -c -p -band'. In this case, the case.vector file is empty, and
>>> I have several case.vector_# files. If I simply execute fold2bloch using
>>> the case.vector_1 as an input it warns me that the case.klist file has
>>> more K-points than the vector file. Is there a way to provide as input
>>> multiple case.vector_# files, or can I only use this program having done
>>> 'x lapw1 -c -band' in a non-parallel mode?
>>> Best Regards,
>>> Tristan
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>>
>> --
>>
>>   P.Blaha
>> --
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
>> WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
>> --
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Re: [Wien] Fold2Bloch in parallel mode

[Rubel, Oleg]

Either solution (Peter’s or Maciej’s) should work. The user’s choice might 
depend on the size of the vector files.

If you process individual *.vector_X files with fold2Bloch, it will warn that 
the number of k-points is less than in the klist-file. This warning can be 
ignored since k-points are split between *.vector_X files.

Thanks
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

> On Oct 18, 2017, at 10:38, Peter Blaha  wrote:
> 
> There is a   join_vectorfile   utility which combines the parallel vector 
> files into a single one.
> 
> On 10/17/2017 07:21 PM, Tristan de Boer wrote:
>> Dear WIEN2k Users,
>> I'm trying to use Fold2Bloch for a calculation in which I've done
>> 'x lapw1 -c -p -band'. In this case, the case.vector file is empty, and
>> I have several case.vector_# files. If I simply execute fold2bloch using
>> the case.vector_1 as an input it warns me that the case.klist file has
>> more K-points than the vector file. Is there a way to provide as input
>> multiple case.vector_# files, or can I only use this program having done
>> 'x lapw1 -c -band' in a non-parallel mode?
>> Best Regards,
>> Tristan
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>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> 
> -- 
> 
>  P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/TC_Blaha
> --
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Re: [Wien] wien2wannier interfaced with wien2k 17.1

[Rubel, Oleg]

Hello Jianpeng,

> I don't understand why in GaAs including spin-orbit coupling would induce 
> such big changes in the MLWFs. But anyway, it is probably what it is.

I fully share your discomfort. During the Workshop last week, symmetry-adapted 
WFs were mentioned, but I do not have experience with that. Maybe other members 
of the List can point to a solution?

> My purpose is to extract some Kondo coupling  parameters between the Ce 4f 
> and 5d states. In my case, it may be important to generate atomic-orbital
> like WFs. I am not sure whether I should include 4f WFs or not. I am still 
> playing with it.

I agree that atomic orbitals-like WFs would be an ideal tool for that. To 
decide on which states to include in construction of WFs, I would plot a fat 
band structure to get an idea of hybridization.


Thank you
Oleg

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Re: [Wien] wien2wannier interfaced with wien2k 17.1

[Rubel, Oleg]

Hello Jianpeng,

> As to difference between the Wannier centers with and without SOC: did you 
> carry out maximal localization procedure in both cases (with and without SOC)?

Yes, I did optimization in both cases.

> What if you simply do a single-step projection, i.e., set num_iter=0 ?

I do not think you will get MLWF in this case since the purpose of iterations 
is to achieve a max localization.

> Then the projected localized functions will not hybridize with each other, 
> and should have the symmetry of atomic orbitals (as long as these initial 
> projections are well localized after some disentanglement procedure).

GaAs is easy since there is no need for disentanglement.

> As to the meaning of the tight-binding model: I think it is meaningful as 
> long as the low-energy bandstructure is the same as the DFT bandstructure and 
>  the Wannier functions are well localized. But I agree it may be more 
> convenient in some cases  if the Wannier functions are atomic-orbital like.

If you only need to fit the band structure, the it is OK to have WF shifted. 
But usually the objective is beyond that.  What would you like to do with WF 
after wannierization?


Thank you
Oleg

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Re: [Wien] wien2wannier interfaced with wien2k 17.1

[Rubel, Oleg]

Dear Jianpeng:

I applied your procedure to WF in zinc-blende GaAs. Your procedure works. I had 
to do two extra steps
$ cp wannier.inwf wannier.inwfup
$ cp wannier.inwf wannier.inwfdn
before running
$ x w2w -so -up
$ x w2w -so -dn

The projections are:
begin projections
  1:sp3(u,d)
  2:sp3(u,d)
end projections

At the end I got the following output with -so and -sp options:

 Final State
  WF centre and spread1  ( -0.457506,  0.457588,  0.457476 ) 4.36038947
  WF centre and spread2  (  0.457535,  0.457378, -0.457522 ) 4.36341214
  WF centre and spread3  ( -0.457477, -0.457464, -0.457434 ) 4.36424964
  WF centre and spread4  (  0.457409, -0.457465,  0.457515 ) 4.36405300
  WF centre and spread5  (  1.800179, -1.026445, -1.026433 ) 2.89020535
  WF centre and spread6  (  1.800146, -1.800199, -1.800158 ) 2.89044140
  WF centre and spread7  (  1.026459, -1.026417, -1.800189 ) 2.88989157
  WF centre and spread8  (  1.026408, -1.800139, -1.026430 ) 2.89026491
  WF centre and spread9  ( -0.457482,  0.457621,  0.457463 ) 4.36089512
  WF centre and spread   10  (  0.457601,  0.457520, -0.457595 ) 4.35805760
  WF centre and spread   11  ( -0.457628, -0.457579, -0.457578 ) 4.35685014
  WF centre and spread   12  (  0.457550, -0.457579,  0.457661 ) 4.35678662
  WF centre and spread   13  (  1.800180, -1.026454, -1.026421 ) 2.89005317
  WF centre and spread   14  (  1.800147, -1.800197, -1.800166 ) 2.88979441
  WF centre and spread   15  (  1.026464, -1.026412, -1.800185 ) 2.89031329
  WF centre and spread   16  (  1.026412, -1.800135, -1.026420 ) 2.88997190
  Sum of centres and spreads ( 11.306397,-11.306377,-11.306414 )58.00562975

It can be compared to the calculation without -so and -sp

 Final State
  WF centre and spread1  ( -0.00,  0.00, -0.00 ) 1.91775879
  WF centre and spread2  (  0.00, -0.00,  0.00 ) 5.85946098
  WF centre and spread3  ( -0.00, -0.00, -0.00 ) 5.85946098
  WF centre and spread4  (  0.00,  0.00,  0.00 ) 5.85946098
  WF centre and spread5  (  1.413300, -1.413300, -1.413300 ) 1.61203280
  WF centre and spread6  (  1.413300, -1.413300, -1.413300 ) 3.81968345
  WF centre and spread7  (  1.413300, -1.413300, -1.413300 ) 3.81968345
  WF centre and spread8  (  1.413300, -1.413300, -1.413300 ) 3.81968345
  Sum of centres and spreads (  5.653200, -5.653200, -5.653200 )32.56722487

It looks like Wannier centres with SOC are not centred at atomic positions, 
which implies that their interpretation as atomic orbitals will be a stretch. I 
am not sure how useful the Hamiltonian will be then.


Thank you
Oleg
--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

> On Sep 25, 2017, at 10:52, Jianpeng Liu  wrote:
> 
> Dear WIEN2k users and developers,
> 
> I am using wien2wannier to generate a tight-binding model for some rare-earth 
> compound including Ce.  Both spin-orbit coupling and spin-polarization have 
> been included in my calculation. The following is my workflow:
> 
> 1) Finish a scf calculation, then prepare_w2wdir wannier
> 
> 2) init_w2w -up
>   At this step, I have to specify the energy windows.
> 
> 3) write_inwf -f wannier
>   At this step, I have to input the minimal and maximal band indices  
> exported from the previous step, then specify the projections of the Wannier 
> functions. I want to project onto 5 Ce d orbitals, but I made two identical 
> copies of projections, i.e.: 
> Ce:d
> Ce:d
> One for spin-up, and the other for spin-dn, so in total there are 10 
> projections. I copied the generated file wannier.inwf to wannier.inwfup and 
> wannier.inwfdn. Now both wannier.inwfup and .inwfdn have 10 projections, but 
> actually there are only 5 orbitals without the spin degrees of freedom. Did I 
> do it correctly?
> 
> 4) Then I wrote a wannier.win file by myself, in which there 
> are 10 *spinor* Wannier-function projections, and I set spinors=.true. (is 
> this correct?).
> 
> 5)With all the inputs generated from the previous steps, I re-run the lapw1 
> calculation on the full BZ mesh, run wannier90 -pp to generate .nnkp file, 
> run w2w, and then finally wannier90:  
>   x lapw1 -up -p
>   x lapw1 -dn -p
>   x lapwso -up -p
>   x wannier90 -pp
>   x w2w -so -up -p
>   x w2w -so -dn -p
>   x wannier90 -so
> 
> The above is my workflow of wien2wannier.  The code seems to be running well, 
> but I am not sure if I did everything correctly. In particular I am worried 
> that there are 2 identical copies of the orbital projections in both 
> wannier.inwfup and .inwfdn. I would like to make sure that it is correct. I 
> 

Re: [Wien] Quick question about convergence criteria

[Rubel, Oleg]

Usually forces are most difficult to converge. I bet that by the time forces 
are converged within 1 mRy/Bohr your energy and charge are converged much 
better than your initial request.

Oleg

> On Sep 12, 2017, at 08:03, Luis Ogando  wrote:
> 
> Dear Wien2k community,
> 
>My system is a molecule (periodic along x and vacuum along y an z). 
>The structural optimization took a long time due to the small atoms soft 
> modes (N, C and H). In order to avoid that the optimization lasts for ever, I 
> used the following convergence criteria:
> 
> -ec 0.001 -cc 0.001 -fc 1.0
> 
>I would like to know if you consider that this convergence is acceptable.
>Thank you for your attention.
>All the best,
> Luis
> 
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Re: [Wien] problem when running berrypi

[Rubel, Oleg]

Wien2wannier evolved quite a bit since 2014. I am not sure if you can take the current version of w2w and put into the old wien2k. The best solution would be to invest time into compiling wien2k 2017, which already includes w2w.


Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton,
 Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

On Sep 8, 2017, at 23:05, halim said <halim_sai...@yahoo.fr> wrote:





Dear Professor   Gavin,


Thank you for your suggestion, but for my case I am working with wien2k14, also you said that I need to use wien2wannier, should I compiled and use it with BerryPi?


I appreciate for your answer.




Regards,


Halim






Le Vendredi 8 septembre 2017 11h45, Gavin Abo <gs...@crimson.ua.edu> a écrit :






I cannot recall if BerryPI works with Python 2.6.  You can try it, but maybe it doesn't work as section "8.2 BerryPI (Modern theory of polarization)" in the
 WIEN2k 17.1 usersguide on page 149 has:
"It consists of a set of Python scripts (requires
Python 2.7 and the NumPi library) and uses wien2wannier for the calculation of overlap integrals."

The current error, however, doesn't look like it is caused by 
Python 2.6.

In your config.py, there is:

#fix for location of python file locations when executing from the python commandline
DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH=/usr/bin/python

As Oleg mentioned, the current error will most likely be resolved if you edit it and add single quotes to those lines:

#fix for location of python file locations when executing from the python commandline
DEFAULT_BIN_PATH='/home/ha/SRC_BerryPI/BerryPI'

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/usr/bin/python'


On 9/7/2017 8:40 PM, halim said wrote:



Dear Prof Oleg,




Thank you for your suggestion, I don't work on personal computer and Python2.6 version is installed.
Is it ok? please find config.py as attached file.


Your suggestion is very much appreciated.


Looking forward for your answer.


All my best,


Halim 






Le Jeudi 7 septembre 2017 21h49, "Rubel, Oleg"

<rub...@mcmaster.ca> a écrit :




Ok. Can you reply with config.py file attached?

I remember python being picky about single quote signs for the text variable enclosures.

...
#fix for location of python file locations when executing from the python commandline
DEFAULT_BIN_PATH='/home/rubel/BerryPI'

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/software/CentOS-6/tools/python-2.7.3/bin/python’
…

Also check
[rubel@lg-1r14-n04 GaN-W]$ which berrypi

Here is what I have:
alias berrypi='/software/CentOS-6/tools/python-2.7.3/bin/python /home/rubel/BerryPI/berrypi'
    /software/CentOS-6/tools/python-2.7.3/bin/python

Thanks
Oleg

> On Sep 7, 2017, at 14:28, halim said <halim_sai...@yahoo.fr> wrote:
> 
> Dear Prof Oleg,
> 
> Thank you for your answer. I changed the path in config.py and set it  as in the mentioned folder, also the folder home/ha/SRC_BerryPI/BerryPI
> exists.
> 
> The same error occurs after changing the path, please what to do to solve the problem?
> 
> I appreciate your help.
> 
> Halim
> 
> 
> Le Jeudi 7 septembre 2017 19h23, "Rubel, Oleg" <rub...@mcmaster.ca> a écrit :
> 
> 
> Please check that the folder /home/ha/SRC_BerryPI/BerryPI
> really exists. Your error message suggests that it can be /home/ha/WIEN2k/SRC_BerryPI/BerryPI
> In this case you should edit DEFAULT_BIN_PATH in config.py
> 
> I hope it will fix your problem
> Oleg
> 
> > On Sep 7, 2017, at 12:11, halim said <halim_sai...@yahoo.fr> wrote:
> > 
> > Dear Wien2k  users community,
> > 
> > I am facing problem when running berrypi, i followed the example of GaN, but i am getting this error. How to solve it.
> > 
> > gan> berrypi -k6:6:6
> > Traceback (most recent call last):
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/berrypi", line 25, in 
> >    import submoduleProcess as b_PySubProcess
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/submoduleProcess.py", line 11, in 
> >    from config import BERRY_DEFAULT_CONSOLE_PREFIX as DEFAULT_PREFIX
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/config.py", line 14
> >    DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
> >                      ^
> > SyntaxError: invalid syntax
> > 
> > 
> > 
> > I would be thankful for your suggestion and answer to solve the problem.
> > 
> > Looking forward your answer.
> > 

Re: [Wien] problem when running berrypi

[Rubel, Oleg]

Ok. Can you reply with config.py file attached?

I remember python being picky about single quote signs for the text variable 
enclosures.

...
#fix for location of python file locations when executing from the python 
commandline
DEFAULT_BIN_PATH='/home/rubel/BerryPI'

#Fix for python path to make sure it grabs the latest version
DEFAULT_PYTHON_PATH='/software/CentOS-6/tools/python-2.7.3/bin/python’
…

Also check
[rubel@lg-1r14-n04 GaN-W]$ which berrypi

Here is what I have:
alias berrypi='/software/CentOS-6/tools/python-2.7.3/bin/python 
/home/rubel/BerryPI/berrypi'
/software/CentOS-6/tools/python-2.7.3/bin/python

Thanks
Oleg

> On Sep 7, 2017, at 14:28, halim said <halim_sai...@yahoo.fr> wrote:
> 
> Dear Prof Oleg,
> 
> Thank you for your answer. I changed the path in config.py and set it  as in 
> the mentioned folder, also the folder home/ha/SRC_BerryPI/BerryPI
> exists.
> 
> The same error occurs after changing the path, please what to do to solve the 
> problem?
> 
> I appreciate your help.
> 
> Halim
> 
> 
> Le Jeudi 7 septembre 2017 19h23, "Rubel, Oleg" <rub...@mcmaster.ca> a écrit :
> 
> 
> Please check that the folder /home/ha/SRC_BerryPI/BerryPI
> really exists. Your error message suggests that it can be 
> /home/ha/WIEN2k/SRC_BerryPI/BerryPI
> In this case you should edit DEFAULT_BIN_PATH in config.py
> 
> I hope it will fix your problem
> Oleg
> 
> > On Sep 7, 2017, at 12:11, halim said <halim_sai...@yahoo.fr> wrote:
> > 
> > Dear Wien2k  users community,
> > 
> > I am facing problem when running berrypi, i followed the example of GaN, 
> > but i am getting this error. How to solve it.
> > 
> > gan> berrypi -k6:6:6
> > Traceback (most recent call last):
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/berrypi", line 25, in 
> >import submoduleProcess as b_PySubProcess
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/submoduleProcess.py", line 11, 
> > in 
> >from config import BERRY_DEFAULT_CONSOLE_PREFIX as DEFAULT_PREFIX
> >  File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/config.py", line 14
> >DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
> >  ^
> > SyntaxError: invalid syntax
> > 
> > 
> > 
> > I would be thankful for your suggestion and answer to solve the problem.
> > 
> > Looking forward your answer.
> > 
> > Halim Said
> 
> > 
> > 
> > 
> > 
> > 
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Re: [Wien] problem when running berrypi

[Rubel, Oleg]

Please check that the folder /home/ha/SRC_BerryPI/BerryPI
really exists. Your error message suggests that it can be 
/home/ha/WIEN2k/SRC_BerryPI/BerryPI
In this case you should edit DEFAULT_BIN_PATH in config.py

I hope it will fix your problem
Oleg

> On Sep 7, 2017, at 12:11, halim said  wrote:
> 
> Dear Wien2k  users community,
> 
> I am facing problem when running berrypi, i followed the example of GaN, but 
> i am getting this error. How to solve it.
> 
> gan> berrypi -k6:6:6
> Traceback (most recent call last):
>   File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/berrypi", line 25, in 
> import submoduleProcess as b_PySubProcess
>   File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/submoduleProcess.py", line 11, in 
> 
> from config import BERRY_DEFAULT_CONSOLE_PREFIX as DEFAULT_PREFIX
>   File "/home/ha/WIEN2k/SRC_BerryPI/BerryPI/config.py", line 14
> DEFAULT_BIN_PATH=/home/ha/SRC_BerryPI/BerryPI
>  ^
> SyntaxError: invalid syntax
> 
> 
> 
> I would be thankful for your suggestion and answer to solve the problem.
> 
> Looking forward your answer.
> 
> Halim Said
> 
> 
> 
> 
> 
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Re: [Wien] Regarding spin-orbit calculations

[Rubel, Oleg]

Try youtube. There should be a couple of non-magnetic cases there.

Oleg

> On Aug 13, 2017, at 5:39 AM, mandeep hooda  wrote:
> 
> Dear Wien2k users,
>I was trying to do spin-orbit calculations as 
> mentioned in the manual. It starts well but after sometime it shows error, 
> type of error is  not known. I doubt that I am doing right steps. Please 
> suggest me the right steps for spin orbit calculations for magnetic and non- 
> magnetic cases. 
> 
> Thanking you in the advance
> Mandeep Kumar Hooda
> 
>
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Re: [Wien] Some Queries about Polarization and Strain

[Rubel, Oleg]

Definition of the spontaneous polarization is not always straightforward. It is determined with respect to a reference structure. The choice of the reference structure is a tricky part and depends on how the polarization manifests itself in an experimental
 situation. I would suggest checking those two tutorials to begin with:
https://github.com/spichardo/BerryPI/wiki/Tutorial-1:-Spontaneous-Polarization-in-BaTiO3
https://github.com/spichardo/BerryPI/wiki/Tutorial-4:-Polarization-in-GaN


Calculation of the response to strain (a piezoelectric coefficient) requires relaxation of atomic positions to be realistic. It also becomes not a trivial analysis, since the polarization changes due to two effects: the volume change as well as atomic
 displacements. It seems that the "raw" Berry phase is more suitable for this purpose. Please check the section "Calculation of piezoelectric coefficients" in http://olegrubel.mcmaster.ca/publications/2017/Rubel_SR_2017.pdf


I hope this will help 
Oleg

--
Oleg Rubel (PhD, PEng)
Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton,
 Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca


On Jul 28, 2017, at 2:39 AM, Jameela Fatheema  wrote:





Dear all,


I had a few questions regarding the calculation of spontaneous polarization.


First, for sponteous polarization, if the displacement are larger or smaller, the spontaneous polarization will remain same or it will change? if it changes how do we say that anyone of those is the spontaneous polarization of that specific material?


Second, for calculating the effect of strain i.e. we change any one lattice parameter by x%, would the atoms still need to be displaced as is done in non-centro-symmentric for spontaneous polarization or only the lattice parameter will be changed?


Third, if the atoms are to be displaced in non-centro-symmetric case, should it be along the axis in which strain has been introduced?


It would be very helpful to have answer to any of these questions.


Regards


Jameela Fatheema




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Re: [Wien] Inconsistency between case.inwf and case.win

[Rubel, Oleg]

I remember wandering about that too when requesting a “p” orbital and getting 
triple “s”. I tried both. In fact it doesn't matter as long as you have :s for 
every WF in your *.inwf file.

Oleg

--
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Department of Materials Science and Engineering
McMaster University
JHE 359, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
Email: rub...@mcmaster.ca
Tel: +1-905-525-9140, ext. 24094
Web: http://olegrubel.mcmaster.ca

> On Jul 22, 2017, at 3:54 PM, Gavin Abo  wrote:
> 
> There was a previous post about the orbital labels in case.win.  You should 
> able to view the post at the following link:
> 
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12320.html
> 
> In the NEWS file [1], I see that the latest Wien2Wannier included with WIEN2k 
> 17.1 contains several fixes to write_win.
> 
> However, I'm not seeing an entry about the orbital labels in case.win.  Maybe 
> the writing of the orbital labels has been corrected and just not documented 
> in the NEW file.  So, the new version would need to be tried to see.
> 
> [1] https://github.com/wien2wannier/wien2wannier/blob/v2.0.0/NEWS
> 
> On 7/22/2017 1:39 AM, Peng Bingrui wrote:
>> Dear wien2k commuity
>> 
>> I'm using wien2k of 14 version and now I'm working with the wien2kwannier 
>> interface. I find that there is inconsistency between the content in these 
>> two files: case.inwf and case.win. 
>> 
>> For the projections, I choose: 
>> Gd: d
>> Pt: s,d
>> Bi: p
>> 
>> My case.inwf seems to be OK, and it is like this:
>> ---
>> BOTH # AMN, MMN, or BOTH
>>  41  93  # min band, max band
>>   3  28  # LJMAX in exp(ibr) expansion, #WF
>> 2 # Gd:d -> 1:dxy
>>  1 2 -2   0.   0.70710678   
>>  1 2  2   0.  -0.70710678
>> 2 # Gd:d -> 1:dxz
>>  1 2 -1   0.70710678   0.
>>  1 2  1  -0.70710678   0.
>> 2 # Gd:d -> 1:dyz
>>  1 2 -1   0.   0.70710678
>>  1 2  1   0.   0.70710678
>> 2 # Gd:d -> 1:dx^2-y^2
>>  1 2 -2   0.70710678   0.
>>  1 2  2   0.70710678   0.
>> 1 # Gd:d -> 1:dz^2
>>  1 2  0   1.   0.
>> 1 # Pt:s,d -> 2:s
>>  2 0  0   1.   0.   
>> 2 # Pt:s,d -> 2:dxy
>>  2 2 -2   0.   0.70710678
>>  2 2  2   0.  -0.70710678
>> 2 # Pt:s,d -> 2:dxz
>>  2 2 -1   0.70710678   0.
>>  2 2  1  -0.70710678   0.
>> 2 # Pt:s,d -> 2:dyz
>>  2 2 -1   0.   0.70710678
>>  2 2  1   0.   0.70710678
>> 2 # Pt:s,d -> 2:dx^2-y^2
>>  2 2 -2   0.70710678   0.
>>  2 2  2   0.70710678   0.
>> 1 # Pt:s,d -> 2:dz^2
>>  2 2  0   1.   0.
>> 2 # Bi:p -> 3:px
>>  3 1 -1   0.70710678   0.  
>>  3 1  1  -0.70710678   0.
>> 2 # Bi:p -> 3:py
>>  3 1 -1   0.   0.70710678
>>  3 1  1   0.   0.70710678
>> 1 # Bi:p -> 3:pz
>>  3 1  0   1.   0.
>>  
>>  ( only show half of it )
>> 
>> -
>> 
>> However, the content about projections in my case.win is like this: 
>> -
>> begin projections
>>   1:s
>>   1:s
>>   1:s
>>   1:s
>>   1:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   3:s
>>   3:s
>>   3:s
>>   1:s
>>   1:s
>>   1:s
>>   1:s
>>   1:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   2:s
>>   3:s
>>   3:s
>>   3:s
>> end projections
>> -
>> 
>> It seems to be all s orbitals for projections, which is not what I want. 
>> 
>> Does this problem matter ?  As far as I'm concerned, if w2w reads 
>> information about projections from case.inwf, but not from case.win, to 
>> calculate the matrix Amn, then it doesn't matter, right ?
>> 
>> Thank you very much for your attention.
>> 
>> Sincerely Yours,
>> Bingrui Peng
>> from the Department of Physics, Nanjing University, China
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