Re: [Wien] Segmentation fault in w2w

[Gavin Abo]

Not sure if it is related, but are you using the w2w fix that Jindrich 
previously posted for WIEN2k 19.2 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19849.html 
] .  Or modules_rc.patch and modules_rc_wplot.patch related to w2web if 
you prefer to try them are at:


https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2

On 9/11/2020 12:02 PM, Niraj Aryal wrote:

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] Segmentation fault in w2w

[Laurence Marks]

Did you use -traceback in your compilation options? It may give line
information. Or add -g to the compilation of w2w.

_
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 Fri, Sep 11, 2020, 14:21 Rubel, Oleg  wrote:

> 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:
> https://urldefense.com/v3/__http://olegrubel.mcmaster__;!!Dq0X2DkFhyF93HkjWTBQKhk!D1PDZ4H4yGv1h-epxzlh30UnLvuZYsOSrQyNarRxqeZcD37uFXeXe9aC_XATsEa-hsiBYw$
>
> 
> 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://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18896.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!D1PDZ4H4yGv1h-epxzlh30UnLvuZYsOSrQyNarRxqeZcD37uFXeXe9aC_XATsEamPh9SGQ$
> 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
>
> ___
> Wien mailing list
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>
> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!D1PDZ4H4yGv1h-epxzlh30UnLvuZYsOSrQyNarRxqeZcD37uFXeXe9aC_XATsEZj553dpA$
> SEARCH the MAILING-LIST at:
> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!D1PDZ4H4yGv1h-epxzlh30UnLvuZYsOSrQyNarRxqeZcD37uFXeXe9aC_XATsEayRjIvkg$
>
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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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[Wien] Segmentation fault in w2w

[Niraj Aryal]

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] hyperfine field anisotropic of Li in battery materials

[Peter Blaha]

Hi,

As I mentioned before, I think you have to use the nmr package can 
calculate the orbital part of the NMR shift tensor.

This contribution is a full 3x3 tensor and you can get the anisotropy.

Regards

Am 11.09.2020 um 07:58 schrieb 林敏:

Dear Dr. Peter Blaha,

Thanks for your kind response.

I have run x lawpdm with following setup in case.indm:

-12.                      Emin cutoff energy
  6                       number of atoms for which density matrix is 
calculated

  1  3  0 1 2      index of 1st atom, number of L's, L1
  2  3  0 1 2      ditto for 2nd atom, repeat NATOM times
  3  3  0 1 2      index of 1st atom, number of L's, L1
  4  3  0 1 2      index of 1st atom, number of L's, L1
  5  3  0 1 2      ditto for 2nd atom, repeat NATOM times
  6  3  0 1 2      ditto for 2nd atom, repeat NATOM times
  3 5           r-index, (l,s)index

Getting the case.scfdmdn/up:

   Calculation of , X=c*Xr(r)*Xls(l,s)
   Xr(r)    =           (1/r**3)S (large component only)
   Xls(l,s) = *[-L*(L+1)*Sdzeta+(3/2){(L.S)Ldzeta+Ldzeta(L.S)}]
   c= 12.51690 Bhf(dip) in T
   atom   L        up          dn         total
  irtest           1           1   1.87
:XOP  1  0    0.00    0.00    0.00
:XOP  1  1    0.004304    0.00    0.004304
:XOP  1  2    0.001030    0.00    0.001030
:XOP  1  4    0.005334                                    total
  irtest           1           2   2.00
:XOP  2  0    0.00    0.00    0.00
:XOP  2  1   -0.492856    0.00   -0.492856
:XOP  2  2   -0.156715    0.00   -0.156715
:XOP  2  4   -0.649571                                    total
……
……
……

In my understanding, the total Bhf(dip) here contributes to a part of 
isotropic shift in NMR spectrum, according to the literature: 
https://pubs.acs.org/doi/10.1021/acs.jpcc.7b03494

This is not what I want.

I just want a symmetric 3x3 hyperfine tensor anisotropic matrix 
(neglecting the realistic effect) to simulate spectrum spin-sideband 
(MAS experiment), as the Figure 3 in 
http://pubs.acs.org/doi/10.1021/jacs.6b05747
I believe it has same mathematic form as EFG in case.scf. Only HFF in 
case.scf is considered for isotropic NMR shift in my calculations 
because of other terms (orbital, etc) have very small contribution.


Does the density matrix in case.outputdmdn/up associate with what I want 
? If Yes, how to transform the density matrix representation to 
hyperfine field anisotropic tensor? Is that available in lapwdm?


Thanks.

Best regards,

Min

———
Min Lin
2018 Ph. D student
Physical Chemistry
Chemistry Department Chemistry & College of Chemistry and 
Chemical Engineering

Xiamen University
China
e-mail: lin...@stu.xmu.edu.cn 

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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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