Re: [Wien] Band gap calculation

[Gavin Abo]

Difference might happen if it not converged [1].  Did you do a k-point 
convergence test [2]?


It might depend on the gap you talking about, refer to [3].  If indirect 
gap [4], I don't recall how the algorithm that gives the value for the 
:GAP for scf* works.  It might be that it is a limitation of the 
algorithm.  Someone else might know or remember the algorithm 
mechanism.  There is also the source code that you could study yourself 
to determine why.


It might also depend on whether you used a shifted or non-shifted k-mesh 
[5,6].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13466.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15599.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15445.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19404.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05699.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18040.html


On 12/22/2019 10:12 PM, Peeyush kumar kamlesh wrote:

Dear WIEN2k users!
Is it ok, if we get different values of band gap from scf2 file and 
spaghetti calculations?

Thank you!


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Re: [Wien] Band gap calculation

[Gavin Abo]

I don't recall seeing "test_conv-5.0.tar.gz" before.  I'm guessing that 
is the newer version of the full convergence tests package at [1] 
(unsupported at least by this group), which seems to not be accessible 
to the public (and likely only accessible to and perhaps supported by 
the private group [2]).


I'm guessing the algorithm that gets the gap value from the valence band 
maximum (VBM) and conduction band minimum (CBM) is not accurate for your 
calculation case.  Therefore, I would most likely go with the gap that 
you get yourself from the raw data (case.spaghetti_ene [3] or [4]) of 
the band structure plot from spaghetti.


If the differences are small like in [5], a percent difference [6] of 
about 2% [= (1.54 eV - 1.51 eV)/{(1.54 eV + 1.51 eV)/2}*100%] seems 
acceptable.  I believe greater than about 5% in when you should be 
concerned [7].


[1] 
http://wien2k-algerien1970.blogspot.com/2016/09/the-full-version-of-conversgence-tests.html

[2] https://www.facebook.com/groups/wien2k.Algeria/
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15255.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15258.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19405.html
[6] 
https://www.webassign.net/question_assets/ncsucalcphysmechl3/percent_error/manual.html

[7] https://socratic.org/questions/what-percent-error-is-too-high

On 12/22/2019 11:36 PM, Peeyush kumar kamlesh wrote:

Dear Gavin Sir,
Thank you for your response.
I did k-point convergence test by a test package 
"test_conv-5.0.tar.gz". I dont know whether it is gives completely 
satisfactory results or not. If you have any other package for kpt 
convergence kindly let me know, so that i can do the right 
calculations. Also I used non shifted k-mash in the calculations of 
the band gap.


Thank you so much!
Regards
Peeyush Kamlesh

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Re: [Wien] Band gap calculation

[Gavin Abo]

By the way, I suspect that the full convergence tests package might only 
do the k-point convergence test for a non-hf scf as adjusted by "x kgen".


If your doing an hf calculation, does the test_conv-5.0.tar.gz have an 
hf feature that uses the run_kgenhf_lapw for the k-point convergence 
test for the scf [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19131.html 
].


Also for the band structure k-point convergence test, is 
test_conv-5.0.tar.gz changing how fine the mesh is in case.klist_band 
(generated manually by hand, automatically by own script or XCrysDen?) 
before proceeding with run_bandplothf_lapw and "x spagehetti -hf" for an 
hf calculation [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18937.html 
, 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19403.html 
].


On 12/23/2019 1:33 AM, Gavin Abo wrote:
I don't recall seeing "test_conv-5.0.tar.gz" before.  I'm guessing 
that is the newer version of the full convergence tests package at [1] 
(unsupported at least by this group), which seems to not be accessible 
to the public (and likely only accessible to and perhaps supported by 
the private group [2]).


I'm guessing the algorithm that gets the gap value from the valence 
band maximum (VBM) and conduction band minimum (CBM) is not accurate 
for your calculation case.  Therefore, I would most likely go with the 
gap that you get yourself from the raw data (case.spaghetti_ene [3] or 
[4]) of the band structure plot from spaghetti.


If the differences are small like in [5], a percent difference [6] of 
about 2% [= (1.54 eV - 1.51 eV)/{(1.54 eV + 1.51 eV)/2}*100%] seems 
acceptable.  I believe greater than about 5% in when you should be 
concerned [7].


[1] 
http://wien2k-algerien1970.blogspot.com/2016/09/the-full-version-of-conversgence-tests.html

[2] https://www.facebook.com/groups/wien2k.Algeria/
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15255.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15258.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19405.html
[6] 
https://www.webassign.net/question_assets/ncsucalcphysmechl3/percent_error/manual.html

[7] https://socratic.org/questions/what-percent-error-is-too-high

On 12/22/2019 11:36 PM, Peeyush kumar kamlesh wrote:

Dear Gavin Sir,
Thank you for your response.
I did k-point convergence test by a test package 
"test_conv-5.0.tar.gz". I dont know whether it is gives completely 
satisfactory results or not. If you have any other package for kpt 
convergence kindly let me know, so that i can do the right 
calculations. Also I used non shifted k-mash in the calculations of 
the band gap.


Thank you so much!
Regards
Peeyush Kamlesh
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Re: [Wien] Kpoint unit in the wien2k band structure

[Gavin Abo]

The WIEN2k 19.1 usersguide [1] (page 11) states that a type of natural 
units [2] is used: "Rydberg atomic units are used except internally in 
the atomic-like programs (LSTART and LCORE) or in subroutine outwin 
(LAPW1, LAPW2), where Hartree units are used. The output is always given 
in Rydberg units."


The unit of k in case.spaghetti_ene is given in the post at:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05273.html

There k is 2*pi//a/, where /a/ is in unit of bohr. Thus, the answer to 
your question is 1/bohr.


Of course, if you are using the parabolic effective mass approximation, 
converting it to the SI system with unit of pi/m is recommended [3] but 
that approximation typical works best in simplistic cases [4].  As far 
as I know, the finite difference method that most likely would work 
better as a general approach for all structures has still not been 
implement yet for WIEN2k [5].


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] https://en.wikipedia.org/wiki/Natural_units#Atomic_units
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16786.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19411.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11446.html


On 12/24/2019 12:58 AM, Aamir Shafique wrote:

Hello,
Hope you are well. I want to calculate the effective mass at high 
symmetry point but I am unable to find the Kpoint unit in band 
structure whether it is 1/bohr or 1/ang.


*With Best Regards, *

*Aamir Shafique
*

*-*
*Postdoctoral fellow*

*Physical Sciences and Engineering*

*+King Abdullah University of Science and Technology *

Thuwal 23955, Saudia Arabia.

(*Direct*- +966  54  5351602

**Email* – aamir.shafi...@kaust.edu.sa 
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Re: [Wien] Kpoint unit in the wien2k band structure

[Gavin Abo]

Yes, the k numbers in case.spaghetti_ene should always be in 2*pi/bohr.

As was stated in [1], if Ang numbers are inputted (into StructGen of 
w2web), it is converted from Ang to bohr and stored always as a bohr 
number in case.struct and an Ang flag is set (if that unit type was 
selected in StructGen) in the file.  The Ang flag in case.struct is for 
StructGen, if the program sees the flag, then StructGen converts the 
bohr number before StructGen displays it to you.


The energy numbers in case.spaghetti_ene, however, might not always be 
in eV.  If you look at page 194 in section "8.23.2 Input" of the WIEN2k 
19.1 usersguide [2], there is "energy switch (1:Ry, 2:eV)" in 
case.insp.  So the energy might be in unit of Ry in case.spaghetti_ene 
if that switch was set to 1.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05273.html

[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

On 12/25/2019 12:06 AM, Aamir Shafique wrote:

Dear Govin and Oleg,
Thank for your reply. The k path will be still in 2pi/bohr if I used 
ang (for lattice parameter) as an input.


*With Best Regards, *

*Aamir Shafique
*



On Tue, Dec 24, 2019 at 8:37 PM Oleg Rubel > wrote:


I would recommend using the file 'case.spaghetti_ene'. It looks
like this

[rubel@gra-login1 case]$ head case.spaghetti_ene
   bandindex:           1
   -0.03869   0.0   0.0   0.0 -35.66092
   -0.03095   0.0   0.0   0.00774 -35.66093
   -0.02321   0.0   0.0   0.01548 -35.66094
   -0.01934   0.0   0.0   0.01935 -35.66094
   -0.01548   0.0   0.0   0.02321 -35.66094
   -0.01161   0.0   0.0   0.02708 -35.66095
   -0.00967   0.0   0.0   0.02902 -35.66095
   -0.00774   0.0   0.0   0.03095 -35.66095
   -0.00580   0.0   0.0   0.03289 -35.66095
...

The column 4 is k along the path (units 2pi/bohr). The 5th column
is the
energy (eV) relative to the Fermi energy.

For fitting, follow Gavin's instructions (see recent posts). In
addition
to that, I suggest fitting data only within 30-40 meV from the band
extremum, which is roughly kT at the room temperature. Higher
energies
will not be slumped by charge carriers and thus are irrelevant. Some
bands can be quite non-parabolic. It is always good to have at
least 7
point for fitting and check if the 2nd order coefficient in the
polynomial changes if you increase the polynomial order to 4th order.

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

-- 
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 2019-Dec.-24 02:58, Aamir Shafique wrote:
> Hello,
> Hope you are well. I want to calculate the effective mass at high
> symmetry point but I am unable to find the Kpoint unit in band
structure
> whether it is 1/bohr or 1/ang.
>
> *With Best Regards, *
>
> *Aamir Shafique
> *
>
> *-*
> *Postdoctoral fellow*
>
> *Physical Sciences and Engineering*
>
> *+King Abdullah University of Science and Technology *
>
> Thuwal 23955, Saudia Arabia.
>
> (*Direct*- +966  54  5351602
>
> **Email* – aamir.shafi...@kaust.edu.sa
 >
>

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Re: [Wien] Band gap calculation

[Gavin Abo]

Use the following information to check whether the Gamma point is 
included in the k-mesh or not.


For how k is defined in case.klist_band, refer to the following link and 
referenced links therein:


http://zeus.theochem.tuwien.ac.at/pipermail/wien/2015-June/022994.html

For how k is defined in case.spaghetti_ene:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05273.html
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00803.html
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2007-August/009659.html

Or for how k is defined in case.bands.agr:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15258.html

Gamma is a special point and is usually the k-vector (0,0,0) at the 
center of the cell [1,2].


In Bilbao Crystallographic Server, Gamma has the label GM and KVEC [3] 
can be helpful in that it should give what the special k points are for 
each space group.


[1] http://www.iue.tuwien.ac.at/phd/dhar/node18.html
[2] 
https://www.tf.uni-kiel.de/matwis/amat/semi_en/kap_2/backbone/r2_1_5.html

[3] https://www.cryst.ehu.es/cryst/get_kvec.html

On 12/23/2019 5:57 PM, Peeyush kumar kamlesh wrote:

Hello Gavin Sir and Blaha Sir,
Thank you so much for the valuable information.
Yes, I used full convergence tests package for kpt convergence. And i 
did not use run_kgenhf_lapw for scf calculations in this package. Also 
there is no feature to run hf calculations. For bandstructure I a 
using k-mash of (8x8x8) points.
Also I did not used shifted k-mash. i used the same to calculate 
bandstructure.
But I am unable to understand that how can we check whether gamma 
point is included in k-mesh or not?


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Re: [Wien] help detailed installation documentation for WIEN2k

[Gavin Abo]

The general installation steps between previous WIEN2k versions and the 
latest WIEN2k 19.1 has not changed.


1. You still go to the WIEN2k website: 
http://susi.theochem.tuwien.ac.at/reg_user/index.html


2. Click on the "Code download (after registration)" link followed by 
entering your User Name and Password


3. Download the new version (WIEN2k_19.1.tar) onto your Linux system (at 
the supercomputing center usually to home directory)


4. Extract the files:

?0?2?0?2?0?2 tar -xvf WIEN2k_19.1.tar
?0?2?0?2?0?2 gunzip *.gz

5. Set file execute permission and run the expand script:

?0?2?0?2?0?2 chmod +x ./expand_lapw
?0?2?0?2?0?2 ./expand_lapw

6. Execute the site configuration script to build WIEN2k:

./siteconfig_lapw

7. Execute the user configuration script to setup the environment (.bashrc):

./userconfig_lapw

For additional details, the scripts themselves are self documenting when 
you run them and there is information in the WIEN2k 19.1 usersguide 
(section "11 Installation and Dimensioning" starting on page 233) [ 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ].


In addition, there should be many posts in the mailing list archive 
describing installations of WIEN2k that are searchable, refer to:


http://www.wien2k.at/reg_user/mailing_list/

Three of the many posts as an example that I suggest as reading and 
follow as guidance are:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16627.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18663.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html

Since there have been several fixes given for WIEN2k 19.1 in the mailing 
list archive, I'm hoping a new release will be coming out soon.?0?2 I have 
fallen behind in maintaining my list, but until either a new release 
comes out or I'm get bring it up to date then some of them are listed at 
[ https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1 ].


Some of the other ones I believe I'm currently missing in my list are:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19005.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19088.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19103.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19246.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19244.html

On 12/30/2019 5:54 PM, ?? wrote:


We are installing Wien2k on the supercomputing center, Can you send us 
detailed installation documentation for WIEN2k?

We would be appreciated if you reply us.
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Re: [Wien] Error in OPTIC calculations

[Gavin Abo]

First, using a version other than the latest version (WIEN2k 19.1) might 
not be safe.  You mentioned you did the scf (lapw0, lapw1, lapw2) 
followed by a parallel optic calculation.  If you look at the WIEN2k 
updates page [1], you can see many improvements and fixes have been made 
to those packages (SRC_lapw0, SRC_lapw1, SRC_lapw2, opticpara_lapw, 
SRC_optic, etc.).


In addition, it may be necessary to patch bugs in WIEN2k 19.1 [2,3].

Second, I assume "Number of k-points: 0" is a typographical error.

If "forrtl: severe (24) : end-of-file during read, unit 5" really is 
from optic and not something else, unit 5 should be case.inop.  You 
likely should be able check if 5 is case.inop in the optic.def file.  If 
that is so, we might be able to provide further advice if the case.inop 
file is provided.


Also, it can sometimes help to have the full traceback.  For example in 
[4], you should see that there is usually 5 trackback columns (Image, 
PC, Routine, Line, and Source). However, I'm only seeing the Image 
column and rows may be missing as well in your post below.


[1] http://susi.theochem.tuwien.ac.at/reg_user/updates/
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19445.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19229.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14158.html


On 1/13/2020 3:34 PM, Victoria Maxwel wrote:

Good afternoon Wien2k experts,

I am running wien version 17 (and I tried it on version 13) on an HP 
Workstation unit with Ubuntu MATE 14.04.6 LTS, Desktop Environment 1.8.2.
The purpose of my calculation is to get the *Optical Properties of 
Palladium, *single atom, with plots (and later on will calculate the 
same with SrTiO3).
I am running the case, *StructGen:* Palladium scf, FCC crystal, 
Lattice Parameters: a, b, c= 3.90093495, alpha, beta, gamma= 90. 
Atom 1: Pd, Z=46.000, RMT: 2.5, Position: x, y, z=0.000.

R-MT*K-MAX...: 8.00      10     4     ELAP...,
K-VECTORS FROM UNIT: 4      -9.0        2.5        37  emin / de 
(emax=Ef+de) / nband,

Size of k-mesh: 8x8x8 ( and later on 16x16x16 and 32x32x32),
Initialize Calculation: I use the *Individual Mode (phase 16),* I 
select all individual options e.g. x nn, view outputnn, x sgroup, x 
symmetry, ..., instgen_lapw, x lstart, ..., In "prepare input file": I 
use Number of k-points: 0, Shift k-mesh: No, Number of k-points: 8x8x8 
(as mentioned above).

Spin polarized: No.
Then I continue with scf run, then save it under Pd_RKM7_1000k_exp-vol.
For Optic calculations, under Tasks: I run all Required Steps e.g.: x 
lapw2-fermi -p, ...

The Error that I get: Once I hit *x optic -p*, I get an error as follows:
[1] 7461
forrtl: severe (24) : end-of-file during read, unit 5, file 
/proc/7463/fd/0

Image ...
libifcore.so.5 ...
This gets repeated a few times, and at the very end I get:
OPTIC crashed!
error: command     /home/z403/wien2k_17/opticpara optic.def failed
The "edit pd.outputjoint" gives System Error, and is a blank page.
Also, no plot is produced (for obvious reasons).

I have also tried running this from scratch on different desktops with 
Ubuntu 14.04.5 but got the same error in OPTIC calculation :(


I'm a beginner at WIEN2K and I would love to know your input/advise on 
this.
Please forgive any lack of information provided above. Please do not 
hesitate to let me know of your questions.
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Re: [Wien] Error during scf calculation of PbI2

[Gavin Abo]

Yes, the SELECT error can be due to a bad struct file:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04617.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10860.html

You are correct to post the struct file as the problem is likely do to it.

I see 0.6667 in your struct file below instead of perhaps 
0.6667, did you check if you have the 2/3 and 1/3 problem with your 
struct file:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14955.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10094.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06287.html


On 1/13/2020 10:13 PM, Subhasis Panda wrote:

Dear wien2k users,
I'm trying to calculate the formation energy for RbPbI3. For that, I'm 
trying to estimate the energy of PbI2 and RbI. I've already calculated 
the energy for RbPbI3.


During the run_lapw step, the following error is encountered. Looking 
forward to your kind help.


"hup: Command not found.
  LAPW0 END
SELECT - Error
grep: lapw2*.error: No such file or directory

>   stop error"
I have searched the mailing list for a solution and also tried to run the same 
by changing RMT values. Still the error persists. I'm not performing any 
parallel calculations.
Following is the struct file.


pbi2-3
H   LATTICE,NONEQUIV.ATOMS:  2 164_P-3m1
MODE OF CALC=RELA unit=ang
   8.613375  8.613375 13.201632 90.00 90.00120.00
ATOM  -1: X=0. Y=0. Z=0.
           MULT= 1          ISPLIT= 4
Pb         NPT=  781  R0=0.0500 RMT=    2.5000   Z: 82.000
LOCAL ROT MATRIX:    1.000 0.000 0.000
                      0.000 1.000 0.000
                      0.000 0.000 1.000
ATOM  -2: X=0. Y=0.6667 Z=0.2675
           MULT= 6          ISPLIT= 8
       -2: X=0.6667 Y=0. Z=0.7325
       -2: X=0. Y=0. Z=0.2675
       -2: X=0.6667 Y=0.3334 Z=0.7325
       -2: X=0.3334 Y=0.6667 Z=0.2675
       -2: X=0. Y=0. Z=0.7325
I          NPT=  781  R0=0.1000 RMT=    2.5000   Z: 53.000
LOCAL ROT MATRIX:    0.000 0.500 0.8660254
                      0.000-0.8660254 0.500
                      1.000 0.000 0.000
   12      NUMBER OF SYMMETRY OPERATIONS
-1 0 0 0.
-1 1 0 0.
  0 0-1 0.
        1
-1 1 0 0.
-1 0 0 0.
  0 0 1 0.
        2
-1 0 0 0.
  0-1 0 0.
  0 0-1 0.
        3
-1 1 0 0.
  0 1 0 0.
  0 0 1 0.
        4
  0-1 0 0.
-1 0 0 0.
  0 0 1 0.
        5
  0 1 0 0.
-1 1 0 0.
  0 0-1 0.
        6
  0-1 0 0.
  1-1 0 0.
  0 0 1 0.
        7
  0 1 0 0.
  1 0 0 0.
  0 0-1 0.
        8
  1-1 0 0.
  0-1 0 0.
  0 0-1 0.
        9
  1 0 0 0.
  0 1 0 0.
  0 0 1 0.
       10
  1-1 0 0.
  1 0 0 0.
  0 0-1 0.
       11
  1 0 0 0.
  1-1 0 0.
  0 0 1 0.
       12

--



Best regards,

Subhasis Panda
Assistant Professor
Department of Physics
National Institute of Technology Silchar
Assam, India  - 788010.

-
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Re: [Wien] Raman Tensors

[Gavin Abo]

The phonopy interfaces with WIEN2k [1].

The phonopy mailing list might now more about whether the ramen tensor 
calculation is available or not to WIEN2k through phonopy, refer to [2].


[1] https://atztogo.github.io/phonopy/wien2k.html
[2] https://sourceforge.net/p/phonopy/mailman/message/33251244/


On 1/16/2020 3:42 AM, Wien2k User wrote:

Dear Wien2k users,

is there a method to calculate raman tensors using wien2k?

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Re: [Wien] plane wave exhausted error

[Gavin Abo]

Look at your "SnS2_Vopt_GGA_initial.struct" file (with text editor [1]).

I see:

...

H   LATTICE,NONEQUIV.ATOMS:  2164_P-3m1

...

ATOM  -2: X=0. Y=0.6667 Z=0.23026000

...

Refer to the previous mailing list post last week and links herein [2] 
about why 0. and 0.6667 cannot be used for 1/3 (e.g., needs 
to be 0.) and 2/3, respectively.


[1] https://en.wikipedia.org/wiki/List_of_text_editors
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19486.html


On 1/24/2020 4:54 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                                We are trying to simulate the 
properties of SnS2. We have created a struct file from cif file of 
SnS2 and then have modified the structure according to rietveld 
refinement. However we are getting error "plane wave exhausted" due to 
the wrong struct file created during initialization. I am sending both 
the cif file and the modified struct files herewith this mail for 
your reference.


We are getting this wrong struct file during "save structure".

Please convey us what we are supposed to do. Thanks in advance.

with regards,


--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] AFM type II

[Gavin Abo]

Space group 156 is part of the hexagonal crystal family [1].

It seems that AFM type I, II, and/or III typically are only defined for 
body centered cubic (bcc) and face centered cubic (fcc) lattices. That 
is based on books such as "Magnetism and Magnetic Materials" by J. M. D. 
Coey (Figure 6.9 and 6.10) [2] and Quantum Theory of Magnetism by R. M. 
White (Fig. 4.2) [3] defining AFM type I, II, and/or III for bcc and fcc 
lattices.  The bcc and fcc lattices are listed under the 14 Bravais 
Lattices in the table at [4].


The article titled "Ferromagnetic and antiferromagnetic spin 
fluctuations and superconductivity in the hcp-phase of Fe" [5] defines 
AFM type II as having opposite polarization on each layer perpendicular 
to the x-axis.


The article titled "Electronic origins of the magnetic phase transitions 
in zinc-blende Mn chalcogenides" [6] defines AFM type II as a 
super-lattice of period /p/ = 1 and layer orientation G = (111).


Since there seems to be varying definitions for the AFM types, it is 
unknown what your AFM type II and III are as you did not provide the 
definition for it using words or images like in those books and articles.


[1] https://en.wikipedia.org/wiki/Hexagonal_crystal_family
[2] https://doi.org/10.1017/CBO9780511845000
[3] https://www.springer.com/gp/book/9783540651161
[4] https://en.wikipedia.org/wiki/Crystal_structure#Lattice_systems
[5] https://arxiv.org/abs/cond-mat/0112382v1
[6] https://doi.org/10.1103/PhysRevB.48.6111

On 1/25/2020 4:41 AM, djamel slamnia wrote:

*dear wien2k user's *
*
*
*I got big problem to creat a structure for AFM type II  or type III*
*
*
*Compound :       H   LATTICE,NONEQUIV.ATOMS:  5 156_P3m1  4 atoms ??
*
*
*
*
*
*any solution ???*



*thanks in advance
*
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Re: [Wien] AFM type II

[Gavin Abo]

* the definition for the compound a=b = 3.74 A alpha = beta = 90 gamma 
= 120 *
*for AFM type I : i creat  superstructure  x super cell target lattice 
H  :  x =1,   y = 1 ,  Z =2  then x sgroup, program define 
automatically the space group the same of my original space group 156 
without warrning

*


As you have described above (for Z=2), your attempt at creating a 
supercell has failed as "x sgroup" collapsed the supercell structure 
back to the non-supercell structure.


As mentioned on the FAQ page for supercell construction, you need to 
displace an atom, change an atom, or use a special label:


http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html

In order to keep the supercell without "x sgroup" reducing it back to 
the original structure, refer to previous posts in the mailing list 
archive about breaking the symmetry.  A few of the many posts about that 
as examples are at the three links below:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18380.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01866.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15517.html


*but when try to do it for type II : x super cell  P :  x =1,   y = 1 
,  Z =1 x sgroup could not define the space group

*


In section "3.12 Setting up a new case" on page 29 in the WIEN2k 19.1 
usersguide [ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf ], 
there is the statement:


"Alternatively with the new StructGen you can specify the spacegroup and 
only the inequivalent positions. The equivalent ones will be generated 
automatically."


This means spacegroups in WIEN2k are defined according to the 
inequivalent positions and not by the equivalent positions.


For the case above (Z=1), it is likely that "x supercell" found some 
equivalent positions in the original structure and automatically added 
special labels to them changing them into inequivalent positions. Thus, 
a supercell structure was successfully created.  If you want the 
supercell structure to reduce back to the original structure, you would 
likely just need to remove all or some of the special labels in 
StructGen before running "x sgroup".


For understanding the inequivalent and equivalent positions with WIEN2k 
spacegroups, the example in the post at the following link might helpful:


http://zeus.theochem.tuwien.ac.at/pipermail/wien/2013-January/018171.html

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Re: [Wien] AFM type II

[Gavin Abo]

As previously mentioned [1], a short literature survey showed that AFM 
type II and III are terms used for /fcc/ and /bcc/ lattices.  Since 
spacegroup 156 is not one of those, it might be inappropriate to use 
those terms for spacegroup 156 having a /primitive/ lattice [2] of the 
hexagonal crystal family.  If you do a more extensive literature survey 
yourself and find a paper (article, book, etc.) that defines the AFM 
magnetic orders for spacegroup 156, then reference and use it for what 
the AFM order is.  If there is not any notations and terms for AFM 
magnetic orders for spacegroup 156, you might have to make your own 
figure or write in your own words what the definition is should any AFM 
magnetic orders exist for it.


Keep in mind that as mentioned before in the mailing list archive, the 
initial configuration can be set in case.inst with "instgen_lapw -ask" [3].


Though, you need to check the final magnetic order that comes out of the 
scf [4], because the configuration set in case.inst with instgen_lapw is 
just the initial one that could change [5,6].


It is also possible to try to force a magnetic order using dmatup/dn 
matrices but the final magnetic order is still what comes out of the scf 
and could be different [6-11].


Therefore, it likely not beneficial to name the AFM order before 
starting a calculation such that you would likely want to identify the 
name of the magnetic order after having finished the converged calculation.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19515.html

[2] https://en.wikipedia.org/wiki/Crystal_structure#Lattice_systems
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10044.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17516.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03243.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06739.html
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14259.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05054.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13124.html
[10] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16281.html
[11] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16286.html


On 1/26/2020 1:01 PM, djamel slamnia wrote:

*thanks again sir *
*
*
*i need to know what is the AFM orders for P3m1 (156) ??? type II or III *
**
**
*thanks in advance*
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Re: [Wien] Problem in x-optic

[Gavin Abo]

If you are not using the WIEN2k 19.1 patches to opticpara_lapw and 
joint.f, refer to the README at [1], you may want to try them to see if 
they improve the behavior.


Your optic.def file has:

./case.symmat

It looks like your w2web output has:

cat: .case.symmat_1: No such file or directory

The "/" missing in the second path above might point to a problem with 
the SCRATCH variable.  It might be how the variable is set in .bashrc.  
If you are using a queue system (such as qsub) and/or parallel program 
(such a mpirun) that most parallel calculations use, it might also be 
that the variables are not be propagated to the environment [2,3].  The 
"/" missing might also point to a bug in the opticpara_lapw script.


The "No such file or directory" might also point to a node or filesystem 
problem.


In addition, it might also be that a preceding step in your calculation 
failed earlier producing bad input file(s) to optic such that optic was 
unable to create the necessary case.symmat files [4].  The WIEN2k 19.1 
usersguide [5] has nice tables such as "Table 4.2: Input and output 
files of utility programs" on page 35 as what to expect for input and 
output files from the WIEN2k programs such as optic.


[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html
[3] 
https://software.intel.com/en-us/mpi-developer-reference-linux-global-options

[4] http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-August/015254.html
[5] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

On 2/14/2020 10:44 AM, Peeyush kumar kamlesh wrote:

Sir,
Greetings!
Problem still exists. Error is appearing during running JOINT. Details 
of optic.def file as follows:


4, './case.mommat2' , 'UNKNOWN', 'FORMATTED', 0

5, 'case.inop' , 'OLD', 'FORMATTED', 0

6, 'case.outputop' , 'UNKNOWN', 'FORMATTED', 0

3, './case.symmat' , 'UNKNOWN', 'FORMATTED', 0

13, './case.symma1' , 'UNKNOWN', 'FORMATTED', 0

14, './case.symma2' , 'UNKNOWN', 'FORMATTED', 0

9, './case.mat_diag' , 'UNKNOWN', 'FORMATTED', 0

10,'./case.vector' , 'OLD', 'UNFORMATTED', 0

11,'./case.vectordn' , 'UNKNOWN' , 'UNFORMATTED' ,0

18,'case.vsp' , 'OLD', 'FORMATTED', 0

19,'case.vspdn' , 'UNKNOWN' , 'FORMATTED', 0

20,'case.struct' , 'OLD', 'FORMATTED', 0

28,'case.inso' , 'UNKNOWN', 'FORMATTED' , 0

24,'./case.mme' , 'UNKNOWN', 'FORMATTED', 0

25,'case.symop' , 'UNKNOWN', 'FORMATTED', 0

30,'case.inc', 'UNKNOWN', 'formatted',0

35,'case.corewf', 'UNKNOWN','formatted',0

36,'case.corewfdn', 'UNKNOWN','formatted',0

40,'case.pmat', 'UNKNOWN', 'FORMATTED', 0


Kindly help me in solving this issue.
Best regards!

On Fri, Feb 14, 2020 at 5:41 PM Peeyush kumar kamlesh 
mailto:peeyush.physik@gmail.com>> 
wrote:


 Dear Blaha Sir,
When I run JOINT it is showing following error:

'JOINT' -  can't open unit:  3
 'JOINT' -  filename: ./KScC.symmat
 'JOINT' -  status: OLD          form: FORMATTED


Best Regards

On Fri, Feb 14, 2020 at 12:07 AM Peeyush kumar kamlesh
mailto:peeyush.physik@gmail.com>> wrote:

Dear Sir,
Thank you so much for you kind reply. I did not try joint. If
it looks OK then i can try for joint and kram.


On Thu, Feb 13, 2020 at 11:42 PM Peeyush kumar kamlesh
mailto:peeyush.physik@gmail.com>> wrote:

Dear Blaha Sir and Gavin Sir,
I am using WIEN2k_19.1. I read the previous problems. But
I am unable to find out the solution of my problem. Kindly
look into it

On Thu, Feb 13, 2020 at 1:16 AM Peeyush kumar kamlesh
mailto:peeyush.physik@gmail.com>> wrote:

Sir,
When I run the following command, I get error in its
execution. Error is as follows:

Commandline: *x optic -p *
Program input is: *""*

running OPTIC in parallel mode
[1] 5101
[2] 5108
[3] 5132
[4] 5137
  OPTIC END
  OPTIC END
  OPTIC END
  OPTIC END
[4]  + Done   ( cd $PWD; $t $exe ${def}_${loop}.def; 
rm -f .lock_$lockfile[$p] ) >>  ...
[3]  + Done   ( cd $PWD; $t $exe ${def}_${loop}.def; 
rm -f .lock_$lockfile[$p] ) >>  ...
[2]  + Done   ( cd $PWD; $t $exe ${def}_${loop}.def; 
rm -f .lock_$lockfile[$p] ) >>  ...
[1]  + Done   ( cd $PWD; $t $exe ${def}_${loop}.def; 
rm -f .lock_$lockfile[$p] ) >>  ...
Summary of opticpara:
localhost user=0  wallclock=40716
cat: .case.symmat_1: No such file or directory
cat: .case.symma1_1: No such file or directory
cat: .case.symma2_1: No such file or directory
ca

Re: [Wien] Problem in x-optic

[Gavin Abo]

There is an error in your opticpara_lapw script.

The "/" that should be at the end of about line 42 before the "#" is 
missing.


It should be:

set scratch=`echo $SCRATCH  | sed -e 's/\/$//'`/ # we are afraid

However, you have:


if ( $?SCRATCH && $SCRATCH != '') then
  set scratch=`echo $SCRATCH  | sed -e 's/\/$//'` # we are afraid 
<-Line 42

                                # different settings in different
                                # computing centers
                                #use global variable for scratch if set
endif



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Re: [Wien] Problem in x-optic

[Gavin Abo]

I'm using the WIEN2k 19.1 opticpara_lapw file that fixed the hf bug that 
Prof. Blaha sent to mailing list on November 14, 2019 [1].  The / is 
there in Prof. Blaha's fixed opticpara_lapw file.


Using the file you sent with / not there, I get the errors that you report.

cat: .case.symmat_1: No such file or directory
cat: .case.symma1_1: No such file or directory
cat: .case.symma2_1: No such file or directory
...

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19229.html


On 2/15/2020 12:03 PM, Peeyush kumar kamlesh wrote:

Dear Sir,
Last time when I was calculation optical properties using hf potential 
then i got some error. Then Peter Blaha sir suggested to remove that 
/. And problem was solved by doing this. Thats why this / is not here.


Best Regards


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Re: [Wien] Error in nlvdw

[Gavin Abo]

Perhaps it's just my system but the WIEN2k 19.1 nlvdw, which has been 
compiled with gfortran (gcc version 7.4.0 under Ubuntu 18.04.4 LTS), is 
behaving strangely.  It seems to get hung up trying to open 
$file.outputnlvdw in SCR_nlvdw/vdw.F.  In x_lapw, I see 
$file.outputnlvdw defined as unit 6.



It might be that use of unit 6 in the nlvdw package is problematic when 
compiled with gfortran similar to what we saw for SRC_symmetry:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16674.html


On 2/16/2020 9:18 AM, Tran, Fabien wrote:


The RAM of the computer was probably not sufficient and the job got 
killed. For such large systems you need to do MPI parallel 
calculations by adding a line "nlvdw:..." in the file .machines (see 
user's guide for detail) and using option -p (runsp_lapw -p ...). You 
should also run the other modules (lapw0, lapw1, lapw2) in parallel.


Beside this, I will very soon (probably tomorrow) send to the mailing 
list updated Fortran files for the nlvdw module. With these updates, 
MPI calculations should be much faster.


F. Tran



*From:* Wien  on behalf of 
shamik chakrabarti 

*Sent:* Sunday, February 16, 2020 4:50 PM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Error in nlvdw
Dear Sir,

          I am replying to each of queries as below;

On Sun, 16 Feb 2020 at 20:35, Laurence Marks > wrote:


It is probably impossible for anyone to help you with so little
information, beyond guesses which may be wrong.

1) What information (errors) are in *.error, *.outputnlvdw,
*.dayfile, :log ?

* in .error file;*
     Error in NLVDW

in *.outputnlvdw*
*
*
kernel type =  1 (M. Dion et al., PRL 92, 246401 (2004))
parameter Z_ab of kernel =    -1.8870
gmax =  25.0
density cutoff rhoc = 0.300E+00
the NL-vdW potential is calculated with gmax_pot =  10.0

n_max, m_max, p_max =    101    101    101
ifft1, ifft2, ifft3 (for proc myid     0) =    203  203    203
ifft1*ifft2*ifft3 (for proc myid     0) =    8365427
Number of G-vectors (for proc myid     0) =    3099627


%                %
% You are using vdW-DF, which was implemented by the Thonhauser group. %
% Please cite the following two papers that made this development      %
% possible and the two reviews that describe the various versions:     %
%                %
%   T. Thonhauser et al., PRL 115, 136402 (2015).                %
%   T. Thonhauser et al., PRB 76, 125112 (2007).               %
%   K. Berland et al., Rep. Prog. Phys. 78, 066501 (2015).             %
%   D.C. Langreth et al., J. Phys.: Condens. Matter 21, 084203 (2009). %
%                %
%                %
% If you are calculating the stress with vdW-DF, please also cite:     %
%                %
%   R. Sabatini et al., J. Phys.: Condens. Matter 24, 424209 (2012).   %
%                %


parameters of the kernel table:
Nq =  30, lambda = 0.111292E+01, q(1) = 0.10E-04, q_cut = 0.10E+02
Nr_points =   2000, r_max =   100.0
q_mesh =
     0.1000     0.05312929     0.11224701 0.17804050
     0.25126365     0.33275542     0.42344952 0.52438515
     0.63671875     0.76173753     0.90087384 1.05572188
     1.22805595     1.41985071     1.63330352 1.87086022
     2.13524270     2.42948008     2.75694394 3.12138629
     3.52698255     3.97838044     4.48075151 5.03985262
     5.66208887     6.35459089     7.12529230 7.98302412
     8.93761444    10.
* case.dayfile*:

 start (Sun Feb 16 20:49:03 IST 2020) with nlvdw (40/99 to go)
>   nlvdw (20:49:03) 111.6u 0.8s 2:47.73 67.0% 0+0k 95536+32io 24pf+0w
error: command   /usr/local/Wien2k/nlvdw nlvdw.def failed

>   stop error

in *.log file*.

Sun Feb 16 11:53:50 IST 2020>; (x_lapw) nn -f setrmt
Sun Feb 16 11:54:07 IST 2020>; (x) nn -up
Sun Feb 16 11:54:23 IST 2020>; (x) sgroup -up
Sun Feb 16 11:54:34 IST 2020>; (x) symmetry -up
Sun Feb 16 11:54:52 IST 2020>; (x) lstart -up
Sun Feb 16 11:55:32 IST 2020>; (x) kgen
Sun Feb 16 11:55:38 IST 2020>; (x) kgen -up
Sun Feb 16 11:55:47 IST 2020>; (x) dstart
Sun Feb 16 11:56:29 IST 2020>; (x) dstart -up
Sun Feb 16 11:56:58 IST 2020>; (x) dstart -dn
Sun Feb 16 12:00:37 IST 2020>; (x) optimize -up
Sun Feb 16 12:02:05 IST 2020>; (x) dstart -super -p
Sun Feb 16 12:02:24 IST 2020>; (x) dstart -super -up -p
Sun Feb 16 12:02:50 IST 2020>; (x) dstart -super -dn -p
Sun Feb 16 12:03:11 IST 2020>; (x) dstart -p -super
Sun Feb 16 12:03:31 IST 2020>; (x) clmaddsub
Sun Feb 16 12:03:33 IST 2020>; (x) dstart -up -p -super
Sun Feb 16 12:03:52 IST 2020>; (x) clmaddsub -up
Sun Feb 16 12:03:53 IST 2020>; (x) dstart -dn -p -super
Sun Feb 16 12:04:17 IST 2020>; (x) clmaddsub -dn
>;   (runsp_lapw) options: -nlvdw -ec 0.0001
Sun Feb 16 12:04:19 IST 2020>; (x) nlvdw
Sun Feb 16 20:44:14 IST 2020>; (x)

Re: [Wien] [Wien2K] help for EELS calculations in a spin-polarized system

[Gavin Abo]

I'm not an expert on telnes3, but some comments below.

The WIEN2k 19.1 usersguide [1] on page 202 has:

/case.vtotal (I). Total crystal potential (can be generated by lapw0). 
Read if EXTEND POTENTIAL is used./


From that statement, I suppose it means that after a spin-polarized 
calculation (runsp_lapw ...), NR2V needs changed to R2V in case.in0 [2] 
followed by executing "x lapw0" to output the two files case.vtotal 
(defined as unit 9 to lapw0 in x_lapw) and case.vtotaldn (written by 
SRC_lapw0/lapw0.F).


Your error message points to a possible interface code bug between lapw0 
and telnes3 as the program is looking for case.vtotalup instead of 
case.vtotal.


A workaround might be to copy case.vtotal to case.vtotalup before 
running "x telnes3 -up" while in the case directory (i.e., try2-omp in 
your case) with the command:


cp try2-omp.vtotal try2-omp.vtotalup

[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14623.html


On 1/4/2020 1:09 AM, sha haozhi wrote:


Dear Wien2k experts and users,

Recently, I’m calculating the EELS spectra of a spin-polarized system 
(LuFeO3 related material) using Wien2K 19.1. I followed the guide in 
the manual but some errors happened and I can’t figure out how to 
solve it.


(a)After invoking ‘x tenels3 -up’, there was a warning message in 
case.outputenls file like “:WARN : bad integral  E= La=   l=   i=  
0Typ=   I=  0.51E-07err =  0.64E-09 or   1% q=  0.20E+00”. However, 
the result seems right.


(b)When I added ‘EXTEND POTENTIAL’ term and set Rmax = 3 in 
case.innes, a fatal error happened and I didn’t know what cause it.


/rtl: severe (24): end-of-file during read, unit 19, file 
.../try2-omp.vtotalup/


/Image  PC Routine    Line    Source /

/telnes3    004DCD1B Unknown   Unknown  
Unknown/


/telnes3    004FA2E2 Unknown   Unknown  
Unknown/


/telnes3    00455065 ewp_init_ 291  
ewp_init.f/


/telnes3    004494A8 extend_wien2k_pot  79  
extend_wien2k_potential.f/


/telnes3    0041A7FE insld_    147  
insld.f/


/telnes3    0041758C hfsd_  52  
hfsd.f/


/telnes3    0040FADA corewavefunction_ 113  
corewavefunction.f/


/telnes3    00414285 MAIN__ 80  
elnes.f/


/telnes3    00404FA2 Unknown   Unknown  
Unknown/


/libc-2.17.so   2B869E9D53D5 __libc_start_main Unknown  
Unknown/


/telnes3    00404EA9 Unknown   Unknown  
Unknown/


/0.014u 0.013s 0:00.08 25.0%  0+0k 0+0io 0pf+0w/

/error: command   .../telnes3 uptelnes3.def failed/

(c)To get the spectrum of a spin-polarized atom like Fe, should I do 
the calculations for spin up and down and then add the spectra 
directly? When doing the spin up calculation, I invoked both ‘x qtl 
-telnes -up’ and ‘x qtl -telnes -dn’, do I need to do this again when 
doing the spin down calculation or I can directly run ‘x telnes3 -dn’?


(d)The experimental spectrum (from STEM) I get is an average signal of 
oxygen atoms located in a layer. To compare the simulated result with 
the experimental one, can I calculate the spectra of these oxygen 
atoms separately and then add them together?


My case.innes is as follows:

/“LuFeO-try2 O-K/

/33/

/1 0/

/528.00/

/300/

/-8. 32. 0.1000/

/26.00 25.00    # collection semi-angle and  convergence semi-angle/

/50 2   # NR NT/

/1.00/

/DETECTOR POSITION/

/0.000 0.000/

/MODUS/

/energy/

/SELECTION RULE/

/n/

/LSELECTION RULE/

/d/

/INITIALIZATION/

/y y/

/y y/

/RELATIVISTIC/

/1/

/ORIENTATION SENSITIVE/

/90.00 0.00 0.00/

/QGRID/

/U/

/END”/

Thanks a lot if there are some suggestions.

Best wishes.

Haozhi Sha

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Re: [Wien] Speedup for NL-vdW functionals in MPI (for WIEN2k_19)

[Gavin Abo]

Thanks, I have added that to my list of WIEN2k 19.1 patches in the 
README at [1] which seems to be becoming quite long now that I have 
brought it up to date.


I know there is at least one other fix that I don't have in my list, 
since there is not enough information available to patch for those.  
Though from the post at [2], it looks as if that fix can likely be 
expected in the next future version of WIEN2k.


[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19019.html


On 2/21/2020 2:25 AM, Tran, Fabien wrote:

Dear WIEN2k users,

If you are using the nonlocal van der Waals functionals in parallel MPI mode,
then you should copy the two attached Fortran files in $WIENROOT/SRC_nlvdw/
and recompile:
make all
cp nlvdw ..
cp nlvdw_mpi ..

The scaling with the number of processors was extremely inefficient, and
with these updates this problem is gone. Note that this will work only if you
are using WIEN2k_19.

F. Tran

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Re: [Wien] Error in nlvdw

[Gavin Abo]

   %
%   T. Thonhauser et al., PRB 76, 125112 (2007).   %
%   K. Berland et al., Rep. Prog. Phys. 78, 066501 (2015). %
%   D.C. Langreth et al., J. Phys.: Condens. Matter 21, 084203 (2009). %
%  %
%  %
% If you are calculating the stress with vdW-DF, please also cite: %
%  %
%   R. Sabatini et al., J. Phys.: Condens. Matter 24, 424209 (2012).   %
%  %


parameters of the kernel table:
Nq =  30, lambda = 0.111292E+01, q(1) = 0.10E-04, q_cut = 0.10E+02
Nr_points =   2000, r_max =   100.0
q_mesh =
 0.1000 0.05312929 0.11224701 0.17804050
 0.25126365 0.33275542 0.42344952 0.52438515
 0.63671875 0.76173753 0.90087384 1.05572188
 1.22805595 1.41985071 1.63330352 1.87086022
 2.13524270 2.42948008 2.75694394 3.12138629
 3.52698255 3.97838044 4.48075151 5.03985262
 5.66208887 6.35459089 7.12529230 7.98302412
 8.93761444    10.

*Al Calculation*

username@computername:~/wiendata/Al$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 18.04.4 LTS
Release:    18.04
Codename:    bionic
username@computername:~/wiendata/Al$ cat $WIENROOT/WIEN2k_VERSION
WIEN2k_19.1 (Release 25/6/2019)
username@computername:~/wiendata/Al$ dpkg -l gfortran
Desired=Unknown/Install/Remove/Purge/Hold
| 
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend

|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name   Version  Architecture Description
+++-==---=
ii  gfortran   4:7.4.0-1ubu amd64    GNU Fortran 95 compiler
username@computername:~/wiendata/Al$ ls
Al.struct
username@computername:~/wiendata/Al$ init_lapw -b
...
username@computername:~/wiendata/Al$ cp 
$WIENROOT/SRC_templates/case.innlvdw Al.innlvdw


For rev-vdW-DF2:

username@computername:~/wiendata/Al$ cat Al.innldvdw
1  kernel type
-1.887    parameters of the kernel
25 plane-wave expansion cutoff GMAX
0.3    density cutoff rhoc
T  calculation of the potential (T or F)
10 plane-wave expansion cutoff GMAXpot for the potential
username@computername:~/wiendata/Al$ cat Al.in0
TOT  XC_GGA_X_B86_R EC_LDA VC_LDA (XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN)
NR2V  IFFT  (R2V)
   30   30   30    2.00  1 NCON 9  # min IFFT-parameters, enhancement 
factor, iprint, NCON n

username@computername:~/wiendata/Al$ run_lapw -nlvdw
...
in cycle 6    ETEST: .00036186   CTEST: .0358926
hup: Command not found.
STOP  NLVDW END
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP  MIXER END
ec cc and fc_conv 1 1 1

>   stop

[1] http://mirrors.ocf.berkeley.edu/gnu/gcc/gcc-7.4.0/
[2] 
https://stackoverflow.com/questions/44867775/fortran-code-wont-write-to-file
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19663.html
[4] 
https://stackoverflow.com/questions/1533717/how-do-i-flush-output-to-file-after-each-write-with-a-gfortran-fortran-90-progra
[5] 
https://gcc.gnu.org/onlinedocs/gcc-7.4.0/gfortran/GFORTRAN_005fUNBUFFERED_005fALL.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19667.html



On 2/17/2020 3:16 AM, Peter Blaha wrote:
But in nlvdw we do NOT write to the screen (except in case of some 
errors).


In any case, please change nlvdw.def unit 6 to 66  and run nlvdw 
nlved.def to verify if this is the source of the problem.

It should print all output on the screen then.


On 2/16/20 6:39 PM, Gavin Abo wrote:
Perhaps it's just my system but the WIEN2k 19.1 nlvdw, which has been 
compiled with gfortran (gcc version 7.4.0 under Ubuntu 18.04.4 LTS), 
is behaving strangely.  It seems to get hung up trying to open 
$file.outputnlvdw in SCR_nlvdw/vdw.F.  In x_lapw, I see 
$file.outputnlvdw defined as unit 6.



It might be that use of unit 6 in the nlvdw package is problematic 
when compiled with gfortran similar to what we saw for SRC_symmetry:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16674.html
Al 
F   LATTICE,NONEQUIV.ATOMS:  1 225_Fm-3m   
MODE OF CALC=RELA unit=ang 
  7.660953  7.660953  7.660953 90.00 90.00 90.00   
ATOM   1: X=0. Y=0. Z=0.
  MULT= 1  ISPLIT= 2
Al NPT=  781  R0=0.0001 RMT=2.5000   Z: 13.000   

Re: [Wien] Error in nlvdw

[Gavin Abo]

Thanks for the hint about /var/log.  Indeed, you are correct as the OOM 
(Out of memory) error is there:


username@computername:~$ grep nlvdw /var/log/syslog
Feb 23 19:05:39 computername kernel: [105834.424171] [26474]  1000 
26474  2170623   645513 17096704   617348 0 nlvdw
Feb 23 19:05:39 computername kernel: [105834.424178] Out of memory: Kill 
process 26474 (nlvdw) score 713 or sacrifice child
Feb 23 19:05:39 computername kernel: [105834.424199] Killed process 
26474 (nlvdw) total-vm:8682492kB, anon-rss:2582048kB, file-rss:4kB, 
shmem-rss:0kB
Feb 23 19:05:39 computername kernel: [105835.094146] oom_reaper: reaped 
process 26474 (nlvdw), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB


On 2/23/2020 9:03 PM, Laurence Marks wrote:
Sounds like it was an OOM error [1]. There should be something in the 
system logs (e.g. /var/log). Since OOM handling is performed by the 
kernel it is not simple to trap this.


[1] e.g. https://en.m.wikipedia.org/wiki/Out_of_memory
_
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"Research is to see what everybody else has seen, and to think what 
nobody else has thought", Albert Szent-Gyorgi

www.numis.northwestern.edu 
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Re: [Wien] Ghost bands problem

[Gavin Abo]

To add to that:

a) Sometimes, but not always, such errors can be resolved by updating to 
the latest WIEN2k version and starting from a fresh directory (with only 
the case.struct in it).  You didn't mention, are you using the latest 
WIEN2k 19.1? If not, as the WIEN2k 19.1 updates page states, Version 
19.1 is a major update.  Are you also using any or all of the WIEN2k 
19.1 patches from the mailing list?  A list that I have assembled is at [1].


b) General tips for resolving a ghostbands error like the one you have 
below should be in section "12.1 Ghost bands" of the WIEN2k usersguide 
(starting on page 246) [2].


c)  I could be wrong, but I thought recalled calculations on structures 
with Nd possibly being more challenging.  You might have a look in the 
mailing list archive for past posts on Nd, such as [3] and [4].


d) For some other tips that might help with the "semicore band-ranges 
too large, ghostband" error, refer to [5].


[1] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1
[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18345.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18367.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10561.html


On 2/29/2020 6:44 AM, Laurence Marks wrote:

Without more information nobody can help you.

_
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 Sat, Feb 29, 2020, 06:14 姜若诗 > wrote:


Dear experts,

I got stuck on the problem when I do the supercell calculation of
heavy elements Nd.

The normal cell calculation is everything good, but it supercell
calculation, the ghost band showed up in lapw2.

---error
message---

'LAPW2' - semicore band-ranges too large, ghostbands ?


-

Do you know how to fix it ?

Looking forward to your reply. Thank you very much.

Best,

Jasmine

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Re: [Wien] number of plane waves

[Gavin Abo]

The article titled "Computation of Materials Properties at the Atomic 
Scale" by Dr. Schwarz states [1]:


/The size of the matrix is mainly given by the number of plane waves 
(PWs) but is increased slightly by the additional local orbitals that 
are used./


As mentioned at [2,3], while in the case directory for your structure 
after running the scf calculation [4], use the terminal command:


grep :RKM *.scf

The command should output a line(s), for example similar to [5]:

:RKM  : MATRIX SIZE 2241LOs: 42  RKM= 7.00  WEIGHT= 8.00  PGR:

From the above line, it seems that the number of PWs is 2199 (= MATRIX 
SIZE - LOs = 2241 - 42)


[1] http://dx.doi.org/10.5772/59108
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09912.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06111.html
[4] WIEN2k 19.1 User's Guide section "3.8 The SCF calculation" on page 
20: http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06114.html


On 3/3/2020 5:18 PM, Wahid Kamal wrote:

Dear wien2k users;

where I can find the number of plane waves.?
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Re: [Wien] compilation and run problems for 19.1

[Gavin Abo]

Most likely due to a WIEN2k 19.1 bug.  Did you apply the fix for that?

Refer to x_lapw.patch in the README at: 
https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1


On 3/7/2020 1:20 AM, Rania Afif wrote:

Dear Prof Blaha,
I am running wien version 19.1 on linux mint19.

I start with TiC example.

after I runc SCF, the program give this error :

stop error

STOP LAPW2 - Error. Check file lapw2.error
STOP  LAPW1 END
STOP  LAPW0 END
hup: Command not found.
when I check lapw2.error :

'LAPW2' - can't open unit: 15
 'LAPW2' -        filename: test5.tmp
 'LAPW2' -          status: scratch      form: unformatted

Sincerely yours,
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Re: [Wien] error in lapw1: 'INILPW' - Invalid k-point file on unit 0

[Gavin Abo]

In case.in1(c), the lapw1 program expects to read a line similar to:

K-VECTORS FROM UNIT:4 -9.0 1.5 187 emin / de (emax=Ef+de) / nband

With regards to the "Invalid k-point file on unit   0" error below, the 
important part is:


K-VECTORS FROM UNIT:4

The "K-VECTORS FROM UNIT:" must be there with no handmade changes to 
it.  For example, a space cannot be put in front of it:


(space)K-VECTORS FROM UNIT:

In the above where the "4" is, there must be a value greater than 1 but 
less than 100.  It must also read that line and not a blank line.


For example, if the ndiff value and number ENERGY PARAMETER lines does 
not match, it can lead to that error as seen in the post at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16452.html

If that doesn't help solve the problem, you probably need send the 
entire case.in1(c) file as an attachment (or a link to the file if it is 
too big for the mailing list, e.g., Google Drive).


On 3/7/2020 3:30 AM, pboulet wrote:

Dear all,

I am performing SCF calculations on rather big compounds and for two 
of them, containing 27 and 52 inequivalent atoms, I have the following 
error message in the lapw1.error files:

'INILPW' - Invalid k-point file on unit   0

I am using Wien2k 18.1.

I have set few k-points for these calculations: 25 (div:  10 10  1) 
and 10 (div:   8  8  1), respectively. The cells are tetragonal, with 
very large c compared with a and b (ratios of about 6 and 20).


I have set HDLOs, as suggested during the init_lapw process. Here are 
my settings in case.in1c (last line):
  0.30    6  0      (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global 
APW/LAPW)

 0    0.30     0. CONT 1
 0   -6.12     0.0001 STOP 1
 1    0.30     0. CONT 1
 1   -3.79     0.0001 STOP 1
 2    0.30     0.0005 CONT 1
 2   -1.20     0.0005 STOP 2

I have also set a broadening of the electrons, as the compounds should 
be semi-metals: TEMPS 0.010, in case.in2c.


Note that, I have set these features for other, similar  compounds, 
and got no problem, so I guess these are not the issue.


Of course, the jobs are running in parallel (MPI): 6 and 8 nodes for 
the smallest and biggest compound, respectively. Each node is composed 
of 24 CPUs.


The k-points are distributed this way:
- smallest compound: 5 k-pts on 1 node and 4 k-pts on 5 nodes
- biggest compound: 2k-pts on 2 nodes and 1 k-pts on 6 nodes
So clearly, there are CPUS with 0 k-pts.

Here is a piece of one of the log files I get from the queuing (SLURM) 
system:

LAPW0 END
[1]    Done                          srun -K1 
/scratch/cnt0022/pmc6881/paboulet/wien2k/.18.1/lapw0_mpi lapw0.def >> 
.time00
mv: impossible to evaluate « Mn7Si12.vector_1 »: No file or directory 
of this type
mv: impossible to evaluate « Mn7Si12.vector_2 »: No file or directory 
of this type
mv: impossible to evaluate « Mn7Si12.vector_3 »: No file or directory 
of this type
mv: impossible to evaluate « Mn7Si12.vector_4 »: No file or directory 
of this type
mv: impossible to evaluate « Mn7Si12.vector_5 »: No file or directory 
of this type
mv: impossible to evaluate « Mn7Si12.vector_6 »:No file or directory 
of this type


These files exist, but there are, as expected, empty.

What could be the problem?

Thank you for your help and time,
Best regards,
Pascal


Pascal Boulet
—
/Professor in computational materials - DEPARTMENT OF CHEMISTRY/
University of Aix-Marseille - Avenue Escadrille Normandie Niemen - 
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Email : pascal.bou...@univ-amu.fr 
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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

Disclaimer: I'm not an expert on qtl, but maybe the following can help.

Step 4 - What else did you put in case.inq besides 6 for QSPLIT on line 3?

1 for natom on line 2?

2 for iatom on line 3?

1 2 nL1 d on line 4 set for only d orbital?

Step 5 - case.cf_d_eg_t2g is labeled for eg.  It looks like you need to 
manually adjust the file for a1g. Currently, I cannot help you with that 
as I don't know what the unitary transformation matrix would be for 
that.  If someone else in the list knows, perhaps they will respond.  
Though, obtaining the appropriate unitary transformation matrix seemed 
to be left to the WIEN2k user (scientific researcher) to determine [2,3].


Step 6 - Is your Linux terminal command correct for "cp"?  I would 
expect it to be something similar to:


cp $WIENROOT/SRC_templates/case.cf_d_eg_t2g V2O3.cf1

For nL1 = 1 above, I think UG (User Guide of WIEN2k 19.1, section 
8.22.2, page 192 [1]) describes that you would need to use .cf1 file.


2 1 2 nL1 p d on line 4 instead as an example, I think UG describes need 
to have .cf1 file for p orbital and .cf2 file for d orbital.


Step 7 - What is the error message? Someone might have been able to 
suggest a solution if the error message had been provided.


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15958.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09768.html


On 3/25/2020 6:31 PM, Wasim Raja Mondal wrote:

Dear Wien2k experts,
                                  I am doing DOS calculation to 
reproduce some data for V2O3 corundum trigonal structure. In this 
distorted structure octahedra of oxygen atoms, d orbital should be 
split into single degenerate a1g and double degenerate eg. I have 
calculated projected density of states and I am not finding that. So, 
I have realized that I have to use rotation and for that I want to use 
QTL program. So far, I have done following steps:


      1. x cif2struct

      2. init_lapw

     3. run_lapw

    4.  edited   case.inq  and used the option qsplit=6

   5. copied templet for case_cf_eg_t2g in my directory.
   6. cp case_cf_eg_t2g to case_cf2 since my atom number V is assigned 
as 2


  7. Getting error.


Can you suggest any solution? Is this the way to project d to a1g and eg?

Thanks in advance
Wasim


On Wed, Mar 25, 2020 at 1:49 PM Wasim Raja Mondal 
mailto:wasimr.mon...@gmail.com>> wrote:


Dear expert,
                   I am trying to project out t2g and a1g states
of V d orbitals. For that I want to use qtl program for DOS
calculation. I am chosing QSPLIT=6 for unitary transformation. For
that I copied templet as case.cf_d_eg_t2g .

Can you please suggest me how can I proceed next?



Thanks

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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

Using WIEN2k 19.1, I expect it will output:

Select PDOS for V from: tot (give a comma-separated list).

In which case, I think you would need to do:

Select PDOS for V from: tot (give a comma-separated list).
tot

*** For finishing type 'end' ***

Enter the index of the atom for which you want to plot the DOS? 
(default:1) end


The "projected dos,user own unitary transformation" in your post below 
must have been a bug in older WIEN2k versions since it looks like the 
developers changed the program in 19.1 to have "tot" instead (i.e., 
qtlmain.f source code changed as seen next to SRC_qtl on the updates 
page [1]).


[1] http://www.wien2k.at/reg_user/updates/

On 3/25/2020 8:58 PM, Wasim Raja Mondal wrote:

Hi Gavin,
              Glad to hear from you. I am able to remove the error. 
Now it is asking as following:


 (C)2008 by Morteza Jamal



#                               #

 Configures and creates case3.int 

#                               #




atom 1 is O

atom 2 is V


*** For Total DOS type 'total' ***


*** For finishing type 'end' ***


Enter the index of the atom for which you want to plot the DOS? 
(default:total) 2


Select PDOS for V from: projected dos,user own unitary transformation 
(give a comma-separated list).






what should I give now?

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Re: [Wien] Bader

[Gavin Abo]

Not sure if it helps with your CRIT and SURF questions in your post 
below, but the WIEN2k 19.1 usersguide, section 8.2.3, starting on page 
153 [1] has:



CRIT Keyword to calculate critical points

SURF Keyword to calculate the Bader surface


Have you watched the "structure files, k-points, various input files, 
QTL and AIM" youtube video [2]?  I thought the video showed well what 
the critical points are.  There seemed to be less focus on what the 
Bader surface is but it looked like that was just the 3D surface or 
contour representation shown in the video or PB-getting_started slides 
[3].  The slide 17 in [3] also seemed to cite more AIM background 
information on the webpage [4].



[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

[2] http://susi.theochem.tuwien.ac.at/onlineworkshop/

[3] http://susi.theochem.tuwien.ac.at/onlineworkshop/PB-getting_started2.pdf

[4] https://www.chemistry.mcmaster.ca/aim/aim_0.html


On 3/25/2020 11:31 PM, delamora wrote:
As Professor Lawrence Marks suggested, I searched for exercises from a 
Workshop, so I found the 2019 Workshop where I took the exercises 
(Excercises_19.ppt) and I am still with problems;

First
Page 4; It shows the electron density of TiN where it can be seen 
'rho', 'Ti-d-band' and 'diference density'
I tried to reproduce it, so I went to the Electron Density of the 
WIEN2k interface, so I edited TiN.inst where I put 'P' in

Ti
Ar 2
3, 2,2.0  P ***
3, 2,0.0  P ***
4,-1,1.0  N
4,-1,1.0  N
...
after that I could not reproduce the figures shown in the Exercises

Second, the Bader analysis, AIM
Page 25 it says;
---
Calculate this in TiN and TiC (exercise 1 and 2)
cd ~/WIEN2k/TiN # we already have a scf density

  * x aim

# creates a default TiN.inaim (bond critical points)

  * x aim

# executes aim with the default input

so I do
" x aim"
where it should create the
"TiN.inaim" file
but it does not create it.
So, I still have the problem of how to create the "case.inaim" and 
what is the meaning of the different parameters in this file.

On the other hand; how to plot the electron density of Ti d-orbitals

Saludos

Pablo

*De:* delamora 
Thank you, I will

Pablo

Try looking in the lecture notes on the W2k page. I am sure you will 
find a Based exercise.


_
Professor Laurence Marks


On Sat, Mar 21, 2020, 20:26 delamora > wrote:


Dear WIEN2k community
I want to do bader analysis, but I find the usersguide difficult
to use for the case.inaim;
The usersguide gives two very different inputs, with "CRIT" or
"SURF" in the first line
Are these the only options? What do they mean?
The first case has 5 lines and the second has 8
These lines are not explaines.

There is supposedly ".../SRC aim/Notes.txt", but I did not find it
in last two WIEN2k versions, there is only "bader.ps
", but it does not deal in explaining the use of
"aim"

So I need help to find how to run the aim package and how to read
the results

Cheers

Pablo

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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

Sorry, my previous advice [1] about the .cf* files appears to be incorrect.

It looks like the number of .cf file will be set by the "number of 
selected atoms" and associated per iatom as shown in your case.inq file 
below.


So your step below of "cp $WIENROOT/SRC_templates/case.cf_d_eg_t2g 
case.cf2" looks fine.


Regarding the error, I believe with qsplit = 6, that might only work if 
nL = 1.


Have you tried nL2 = 1 with just l=2 for the d orbital to have the 
case.inq below:


-9.  3.  Emin Emax
 2   number of selected atoms
 1  -2  0  0  iatom1  qsplit1 symmetrize loro
 2  0  1 nL1 p  d
 2  6  0  0  iatom2  qsplit2 symmetrize loro
 1  2  nL2 d

[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19798.html


On 3/27/2020 6:11 PM, Wasim Raja Mondal wrote:

Dear Prof. Blaha,
                            Thank you for your reply. I understand now 
the space group and also no the unitary transformation for the V2O3 
which I am giving here:


                               a1g =  d3z2-1

                            eg\pi 1= \sqrt(2/3) dxy + 1/sqrt(3) dxz

                           eq\pi2 = -\sqrt(2/3) dx2-y2 -1/sqrt(3) dyz

I want to use this unitary transformation. For that My case.inq file 
is given below:



-9.  3.  Emin Emax
  2   number of selected atoms
  1  -2  0  0  iatom1  qsplit1 symmetrize loro
  2  0  1 nL1 p  d
  2  6  0  0  iatom2  qsplit2 symmetrize loro
  4  0  1  2  3   nL2 s  p  d  f
In the above file, iatom1 is oxygen and iatom2 is vanadium.

 From wien2kroot, I have copied case.cf_eg_t2g and renamed it as case.cf2. 
Next, when I run x qtl, I am getting this error:

forrtl: severe (59): list-directed I/O syntax error, unit -5, file 
Internal List-Directed Read



Image              PC                Routine            Line        
Source



qtl                0043A2BB  Unknown               Unknown  
Unknown



qtl                004577E1  Unknown               Unknown  
Unknown



qtl                0041D392  readc_                     44  
readc.f



qtl                0041969A  MAIN__                    330  
qtlmain.f



qtl                004046E2  Unknown               Unknown  
Unknown



libc-2.17.so        2B7E158E2505  
__libc_start_main     Unknown  Unknown



qtl                004045E9  Unknown               Unknown  
Unknown



0.011u 0.013s 0:00.02 100.0%0+0k 0+32io 0pf+0w


error: command   /usr/local/wien2k-19.1/qtl qtl.def   failed

Should I have to edit new2.cif file according to my unitary matrix as 
I described above my a1g,eg\pi,eg\sigma? I am using wien2k 19.1


Thanking you

Wasim

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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

In line 1 of case.cf2 below that you copied from 
$WIENROOT/SRC_templates/case.cf_d_eg_t2g case.cf2, first value (0.) goes 
in the "Real part of unitary matrix" and second value (0.) goes in the 
"Imaginary part of unitary matrix", then real and imaginary values keep 
repeating throughout the line.  Look under those same heading that 
should be printed in case.outputq, which seems to make it clearer what 
values are being read from case.cf2.


The $WIENROOT/SRC_qtl/comment file has:

/They [the *] mark which diagonal matrix elements should be summed over 
to obtain e.g. total j=1/2 density instead of the projection 1/2, -1/2, 
and 1/2,1/2./


The $WIENROOT/SRC_qtl/QTL-tehnical-report.pdf file has:

/For QSPLIT = 6 (unitary transformation prepared by user) the unitary 
matrices are read as in original Kune's QTL:  for atom type i they are 
stored in unit 50+i and ordered according to increasing //L//./


/Note that matrices in SRC_templates may be used, after replacing stars 
with spaces.

/

Looking a qtl.def, it seems the "50+i" would be "32+i" in WIEN2k 19.1.  
Is the error you are getting perhaps from deleting the * instead of 
replacing the star with a whitespace?


Since the unitary matrices are read as in the original Kune's QTL, I'm 
guessing the * still functions for giving the density instead of a 
projection.  In case.outputq with and without the * you'll probably see 
a difference under the BLOCKING SUMMARY.  Of note, SUMA keyword is no 
longer used as that was removed probably in WIEN2k 08.2 as seen by the 
"enhanced version with much more userfriendly input" statement next to 
SRC_qtl on the updates page at [1].  You may also be interested in 
reading the past thread of posts at [2].


[1] http://www.wien2k.at/reg_user/updates/
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18402.html


On 3/27/2020 8:57 PM, Wasim Raja Mondal wrote:
Thank you Gavin for your reply. You were right. At least qsplit=6 is 
working in wien2k. I am trying to understand the template is given for 
case.cf_t2g_eg. What are * here. If I remove *, it is giving error but 
with * it is not giving error. Below the templet I took for cf_t2g_eg:


0. 0. 0. 0.  1. 0.  0. 0.  0. 0.                  0. 0.  0. 0.  0. 0.  
0. 0.  0. 0.


*0.70710678 0.  0. 0.  0. 0.  0. 0.  0.70710678 0.  0. 0.  0. 0.  0. 
0.  0. 0.  0. 0.   Eg


 -0.70710678 0.  0. 0.  0. 0.  0. 0.  0.70710678 0. 0. 0.  0. 0.  0. 
0.  0. 0.  0. 0.


 0. 0.  0.70710678 0.  0. 0.  -.70710678 0.  0. 0.  0. 0. 0. 0.  0. 
0.  0. 0.  0. 0.


*0. 0.  0.70710678 0.  0. 0.  .70710678 0.  0. 0.   0. 0. 0. 0.  0. 
0.  0. 0.  0. 0.   T2g


 0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  1. 0.  0. 0.  0. 0.

*0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0.70710678 0.  0. 0.  0. 0.  0. 
0.  0.70710678 0.   Eg


 0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  -0.70710678 0.  0. 0. 0. 0.  0. 
0.  0.70710678 0.


 0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0.70710678 0.  0. 0.  
-.70710678 0.  0. 0.


*0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0. 0.  0.70710678 0.  0. 0.  
.70710678 0.  0. 0.   T2g


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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

I would suggest doing the "cp $WIENROOT/SRC_templates/case.cf_d_eg_t2g 
case.cf2" again as maybe the pr and ^@ characters got added to the file 
when you edited the case.cf2.  On the other hand, if you accidentally 
edited case.cf_d_eg_t2g, you would need to extract the original again 
from WIEN2k_19.1.tar.


I ran a quick test and looks like you should be able to change the 
labels in case.qtltext by changing the first line in case.cf* as shown 
below:


username@computername:~/wiendata/TiC$ cat TiC.inq
-9.0   3.0   Emin  Emax
   2 number of atoms
   1  6 0  0   iatom,qsplit,symmetrize,locrot
1 2 nL, l-values
   2  -2 0  0   iatom,qsplit,symmetrize,locrot
1 0 nL, l-values
username@computername:~/wiendata/TiC$ cp 
$WIENROOT/SRC_templates/template.cf_d_eg_t2g TiC.cf1

username@computername:~/wiendata/TiC$ head -1 TiC.cf1
# eg t2g
username@computername:~/wiendata/TiC$ x qtl
STOP  QTL END
0.2u 0.0s 0:00.32 100.0% 0+0k 0+648io 0pf+0w
username@computername:~/wiendata/TiC$ cat TiC.qtltext
 Ordering of DOS in QTL file for: TiC

 atom   1 ordering of projected DOS
d,eg,t2g user's splitting

 atom   2 ordering of projected DOS
s,

 Data for interstital DOS correspond to atom index    3
username@computername:~/wiendata/TiC$ gedit TiC.cf1
username@computername:~/wiendata/TiC$ head -1 TiC.cf1
# mylabel t2g
username@computername:~/wiendata/TiC$ x qtl
STOP  QTL END
0.2u 0.0s 0:00.32 96.8% 0+0k 0+648io 0pf+0w
username@computername:~/wiendata/TiC$ cat TiC.qtltext
 Ordering of DOS in QTL file for: TiC

 atom   1 ordering of projected DOS
d,mylabel,t2g user's splitting

 atom   2 ordering of projected DOS
s,

 Data for interstital DOS correspond to atom index    3

On 3/28/2020 12:50 AM, Wasim Raja Mondal wrote:


This is the output of my case.qtltext which is wrong with the *.



Ordering of DOS in QTL file for: blebleble

 atom   1 ordering of projected DOS

s,

p,px,py,pz, real basis


 atom   2 ordering of projected DOS

d,pr,pr, pr,pr, user's splitting

pr,pr, 
^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@


d,pr,pr, pr,pr, user's splitting


 Data for interstital DOS correspond to atom index    3

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Re: [Wien] Wien Installation

[Gavin Abo]

In your compile.msg, I see:

ifort -O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback 
-assume buffered_io 
-I/home-yw/compiler/intel2016/compilers_and_libraries_2016.3.210/linux/mkl/include 
-qopenmp -c modules_tmp_.F

./param.inc(16): error #5078: Unrecognized token '#27' skipped
?0?2?0?2?0?2?0?2?0?2 PARAMETER?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 
(NUME=?0?2?0?2 12000.)
---^

I suggest using a different version of ifort, the 2016.3.210 version of 
ifort I think was buggy such that even after a successful compile was 
giving runtime errors with WIEN2k [1].


The above error seems to be saying that the dot symbol (.) after the 
NUME value is not allowed.?0?2 Try removing the dot either directly in 
param.inc or more preferably by using ./siteconfig (D -> 1 -> NUME).?0?2 
Then, try recompiling (./siteconfig -> R -> A).


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16520.html



On 3/31/2020 6:00 AM,  wrote:


Dear Prof Blaha,

I am installing wien version 19.1 on Linux with intel compiler (ifort) 
and mkl.


I run ./sitecomfig_lapw. After I run ??R compiler/Recompile??, errors 
appear:


??Compile time errors (if any) were:

SRC_lapw1/compile.smg:./param.inc(16):error #5078: Unrecognized token 
??#27?? skipped?? etc.


More information is as an attachment.

Sincerely yours
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Re: [Wien] 3R crystal structure WS2 SCF problem

[Gavin Abo]

I entered the structure parameters that you provided in StructGen 
(Reduce RMTs by 0), which gave the attached WS.struct.  Using WIEN2k 
19.1 (compile with gfortran), a quick scf calculation converged such 
that I was unable to reproduce your error:



username@computername:~/wiendata/WS$ ls
WS.struct
username@computername:~/wiendata/WS$ init_lapw -b
...
  init_lapw finished ok
username@computername:~/wiendata/WS$ run_lapw
...
in cycle 10    ETEST: .000160785000   CTEST: .0025012
hup: Command not found.
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP  MIXER END
ec cc and fc_conv 1 1 1

>   stop


However, I'm using the R lattice fix [1] as well as other WIEN2k 19.1 
patches [2].  Have you applied the R lattice fix to the WIEN2k 19.1 
version that you are using?



[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19103.html


[2] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1


On 4/1/2020 9:10 AM, Luigi Maduro - TNW wrote:

 Dear WIEN2k users,

I am running WIEN2k version 19.1 with the 2017 version 4 intel fortran 
compiler. I am trying to run an SCF calculation of 3R WS2 unit cell.
The .struct file was created with the crystallographic information 
found in the american mineralogist crystal structure database:


Spacegroup 160
a = b = 3.158 Angstrom, c = 18.49 Angstrom, alpha = beta = 90, gamma = 120
W = 0 0 0
S =  0 0 0.2497
S = 0 0 0.4917

I used hex2rhomb to write down the atomic coordinates into 
rhombohedral coordinates, as is needed by WIEN2k, giving the atomic 
coordinates:


W = 0 0 0
S = 0.2497 0.2497 0.2497
S = 0.4190 0.4190 0.4190

However, when I try to run a regular SCF cycle the calculation crashes 
at the first SCF cycle when it reaches the lapw1 script.

The following error is found in lapw1.error:

Cholesky INFO =      274
'SECLR4' - POTRF (Scalapack/LAPACK) failed

In the past I noticed that when there are atoms at the borders of the 
unit cell the SCF calculation crashes, so I thought that maybe that 
this can be fixed by shifting the atoms a bit in the unit cell. The 
new atomic coordinates are, after using hex2rhomb:


W = 0.15 0.15 0.15
S =  0.3997 0.3997 0.3997
S = 0.5690 0.5690 0.5690

However, this gives the same error as before.
Any suggestions on how to go forward is highly appreciated.


Kind regards,
Luigi Maduro
Title  
R   LATTICE,NONEQUIV.ATOMS:  3 160_R3m 
MODE OF CALC=RELA unit=ang 
  5.967757  5.967757 34.941050 90.00 90.00120.00   
ATOM  -1: X=0. Y=0. Z=0.
  MULT= 1  ISPLIT= 4
W  NPT=  781  R0=0.0500 RMT=2.4700   Z: 74.000 
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0.2497 Y=0.2497 Z=0.2497
  MULT= 1  ISPLIT= 4
S  NPT=  781  R0=0.0001 RMT=2.0200   Z: 16.000 
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -3: X=0.4190 Y=0.4190 Z=0.4190
  MULT= 1  ISPLIT= 4
S  NPT=  781  R0=0.0001 RMT=2.0200   Z: 16.000 
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
   6  NUMBER OF SYMMETRY OPERATIONS
 0 0 1 0.
 0 1 0 0.
 1 0 0 0.
   1
 0 1 0 0.
 0 0 1 0.
 1 0 0 0.
   2
 0 0 1 0.
 1 0 0 0.
 0 1 0 0.
   3
 0 1 0 0.
 1 0 0 0.
 0 0 1 0.
   4
 1 0 0 0.
 0 0 1 0.
 0 1 0 0.
   5
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
   6
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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

According to [1], corundum has point group D3d in Schoenflies notation.

Character Tables at [2,3] have for D3d:

A1g with x2 + y2, z2 in quadratic notation

Eg with (x2 − y2, xy), (xz, yz) in quadratic notation

Prof. Blaha at [4] mentioned that with ISPLIT=4, the header of case.qtl 
is expected to give:

s,p,pz,pxy,d,d-z2,(d-xy,dx2-y2),(d-xz,dyz),f

Therefore, it looks like A1g is given as d-z2 and Eg is give as 
(d-xy,dx2-y2) and (d-xz,dyz).


At [3], if you click the "Click here to get more detailed information on 
they symmetry operations" link on the webpage, it gives another webpage 
with another table having a "Matrix form" column that seems to 
correspond to the transformation matrices (Identity, Inverse, Rotations, 
etc. [5]) used create the character table [8,9].


It is not clear to me what you mean by pi and sigma. Is pi for example 
when two d-xz orbitals overlap such as that in the image of [6,7]?


[1] https://en.wikipedia.org/wiki/Hexagonal_crystal_family
[2] 
https://en.wikipedia.org/wiki/List_of_character_tables_for_chemically_important_3D_point_groups#Antiprismatic_groups_(Dnd)

[3] https://www.cryst.ehu.es/cgi-bin/rep/programs/sam/point.py?sg=162&num=20
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19805.html
[5] 
http://w0.rz-berlin.mpg.de/imprs-cs/download/symmetry2011_1_K_Horn.pdf 
(slide 6)

[6] https://www.chemtube3d.com/salc-d-d-orbitaloverlap/
[7] 
https://commons.wikimedia.org/wiki/File:Quintuple_bond_orbital_diagram2.png


Informational video with PowerPoint slides on what a Character Table is:

[8] 
https://cosmolearning.org/video-lectures/character-tables-one-application-symmetry/

[9] https://www.chem.uci.edu/~lawm/10-2.pdf


On 4/4/2020 3:13 PM, Wasim Raja Mondal wrote:

Dear expert,
                     Can you anyone suggest what rotation matrix for 
V2O3 corundum structure with qsplit=4 should I take to decoupling the 
d orbital, a1g,eg\pi, eg\sigma?


Thanks
Wasim
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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

Ok, I think I understand now, in FIG. 1 of [1] the eg\sigma appears to 
be the high energy band while eg\pi the low energy band in the energy 
diagram.


In FIG. 5 of the reference [2] that you provided, I see eg\sigma peaks 
at high energy (i.e., at about 2 to 4 eV) while the eg\pi is at low 
energy (i.e., about -1 to 1 eV) in the DOS plot.


Thus, I think you will need to plot both (d-xy,dx2-y2) and (d-xz,dyz), 
then you can probably identify which is eg\pi and which is eg\sigma by 
looking at the DOS plot.


Based on Figure 4.2 in [3], (d-xy,dx2-y2) might be eg\sigma while 
(d-xz,dyz) the eg\pi.


[1] https://arxiv.org/abs/1502.04555v1
[2] https://arxiv.org/abs/cond-mat/0402133v1 , 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.70.205116

[3] http://ikee.lib.auth.gr/record/129214/files/GRI-2012-8671.pdf

On 4/4/2020 9:29 PM, Wasim Raja Mondal wrote:

Dear Gavin,
                   I am trying to reproduce simple LDA DOS as reported 
in Fig 5 of this paper.

https://journals.aps.org/prb/abstract/10.1103/PhysRevB.70.205116


I am really struggling. If you can do, please let me know.


Thanking you in advance
Wasim

On Sat, Apr 4, 2020 at 10:58 PM Gavin Abo <mailto:gs...@crimson.ua.edu>> wrote:


According to [1], corundum has point group D3d in Schoenflies
notation.

Character Tables at [2,3] have for D3d:

A1g with x2 + y2, z2 in quadratic notation

Eg with (x2 − y2, xy), (xz, yz) in quadratic notation

Prof. Blaha at [4] mentioned that with ISPLIT=4, the header of
case.qtl is expected to give:
s,p,pz,pxy,d,d-z2,(d-xy,dx2-y2),(d-xz,dyz),f

Therefore, it looks like A1g is given as d-z2 and Eg is give as
(d-xy,dx2-y2) and (d-xz,dyz).

At [3], if you click the "Click here to get more detailed
information on they symmetry operations" link on the webpage, it
gives another webpage with another table having a "Matrix form"
column that seems to correspond to the transformation matrices
(Identity, Inverse, Rotations, etc. [5]) used create the character
table [8,9].

It is not clear to me what you mean by pi and sigma. Is pi for
example when two d-xz orbitals overlap such as that in the image
of [6,7]?

[1] https://en.wikipedia.org/wiki/Hexagonal_crystal_family
[2]

https://en.wikipedia.org/wiki/List_of_character_tables_for_chemically_important_3D_point_groups#Antiprismatic_groups_(Dnd)
[3]
https://www.cryst.ehu.es/cgi-bin/rep/programs/sam/point.py?sg=162&num=20
[4]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19805.html
[5]
http://w0.rz-berlin.mpg.de/imprs-cs/download/symmetry2011_1_K_Horn.pdf
(slide 6)
[6] https://www.chemtube3d.com/salc-d-d-orbitaloverlap/
[7]
https://commons.wikimedia.org/wiki/File:Quintuple_bond_orbital_diagram2.png

Informational video with PowerPoint slides on what a Character
Table is:

[8]

https://cosmolearning.org/video-lectures/character-tables-one-application-symmetry/
[9] https://www.chem.uci.edu/~lawm/10-2.pdf


On 4/4/2020 3:13 PM, Wasim Raja Mondal wrote:

Dear expert,
                     Can you anyone suggest what rotation matrix
for V2O3 corundum structure with qsplit=4 should I take to
decoupling the d orbital, a1g,eg\pi, eg\sigma?

Thanks
Wasim


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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

If I interpret Prof. Blaha's post at [1] correctly, "x lapw2 -qtl" 
should automatically give what you need such that you would not have to 
use "x qtl" (thus, you would not need case.inq if that is the case).


Referring to the description for line 6 in section '4.3 The “master 
input“ file case.struct' of the WIEN2k 19.1 usersguide [2] on page 41, 
you will probably just want to check to insure that isplit was set to 4 
in case.struct after the "x symmetry" step during initialization with 
init_lapw.


You might recall the TiC getting started example of section "3.11.2 
Density of States (DOS)" on page 24 of the usersguide [2].  Your 
description below kind of sounds like you might have only plotted 'tot' 
for the total DOS rather than the PDOS for an individual atom.


For your V2O3 calculation, I think you will want to make sure you 
selected the d-z2, (d-xy,dx2-y2), and (d-xz,dyz) by setting case.int 
appropriately.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19805.html

[2] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

On 4/4/2020 11:26 PM, Wasim Raja Mondal wrote:

Gavin,
         Thank you for your reply. Now, I understand the group table. 
I am getting a1g, eg\pi and \eg \sigma as reported in literature for 
example in Fig5 of the paper I provided in the link. But, in my DOS 
a1g, eg\pi and eg\sigma are still mixed up.


For that, I tried in case.inq file different new z and x axis. But I 
am not getting the DOS as reported in the Fig 5 of the paper (link I 
provided.)


I know I should not ask this type of question here. But I am 
struggling bit for many days with this structure. My question is : 
starting with cif file , running LAPW, calculating DOS using qtl with 
option 4, what new z and x axis should I define in case.inq file to 
reproduce the LDA dos for this structure. It is just simple LDA 
calculation.



Please let me know if you find with just one look.


Thanks
Wasim

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Re: [Wien] phonon calculation

[Gavin Abo]

As I recall, the steps to install phonopy are at:

https://phonopy.github.io/phonopy/install.html

The steps to run a phonopy WIEN2k calculation are at:

https://phonopy.github.io/phonopy/wien2k.html#wien2k-interface

There are steps for older versions of phonopy in the mailing list 
archive that can perhaps be referenced as those instructions might not 
have to be change much:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14063.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13800.html

Also, as the WIEN2k updates page [ 
http://susi.theochem.tuwien.ac.at/reg_user/updates/ ] states: /Version 
19.1 is a major update/.  Thus, it is recommended to update from the 
WIEN2k 18.2 version you have to 19.1.  The WIEN2k 18.2 and 19.1 also 
have many bugs in common, but the fixes that can be found in the mailing 
list are only described and given for 19.1 (refer to mailing list links 
in the README list at [ 
https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1 ]).


On 4/3/2020 3:22 PM, Mesut KESEK wrote:


Dear Sir

I am running Wien2k version 18.2 on a machine of intercore i7-6700HQ 
2.60Hhz  8gb RAM  4 core 64 bit ,Virtualbox 
6 ,Linux ubuntu 20.4


The purpose of my calculation is to get phonon calculation of NaBr and 
NaI.


I couldn’t install Phonopy program I don’t know how to do it. There 
are some videos on internet but I have done step by step but I couldn’t.


Could you help me how to install Phonopy program step by step, and 
sent me the files needed to install this program.And also after 
installation the phonopy program, what I am going to do to calculate 
phonon calculation in wien2k. Could you inform me step by step what I 
am going to do.


Thank you so much.

Best wishes

Mesut KESEK


Windows 10 için Posta  
ile gönderildi


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Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

Using the V2O3.struct file from your previous email, are you saying you 
got the plot of dz2 (a1g), dx2y2+dxy (eg\pi), and dxz+dyz (eg\sigma) for 
the V atom doing steps similar to the quick and sloppy calculation below:


username@computername:~/wiendata/V2O3$ ls
V2O3.struct
username@computername:~/wiendata/V2O3$ init_lapw -b -vxc 5
...
  init_lapw finished ok
username@computername:~/wiendata/V2O3$ run_lapw
...
in cycle 12    ETEST: .000417425000   CTEST: .0013278
hup: Command not found.
STOP  LAPW0 END
STOP  LAPW1 END
STOP  LAPW2 END
STOP  CORE  END
STOP  MIXER END
ec cc and fc_conv 1 1 1

>   stop
username@computername:~/wiendata/V2O3$ x lapw2 -qtl
...
username@computername:~/wiendata/V2O3$ configure_int
...
atom 1 is O
atom 2 is V
...
Enter the index of the atom for which you want to plot the DOS? 
(default:total) 2
Select PDOS for V from: tot,s,p,pz,px+py,d,dz2,dx2y2+dxy,dxz+dyz,f (give 
a comma-separated list).

dz2,dx2y2+dxy,dxz+dyz
...
Enter the index of the atom for which you want to plot the DOS? 
(default:1) end

...
V2O3.int has been created and is ready for use in   x tetra.
username@computername:~/wiendata/V2O3$ x tetra
...

Then, used w2web to plot it.

Temporary Google Photos link to w2wb plot of V PDOS: 
https://photos.app.goo.gl/Cq6yT2krPkzUYTC57


On 4/6/2020 4:33 PM, Wasim Raja Mondal wrote:

Dear Prof Blaha,
                        Thank you for your reply. I have done the 
calculation with the structure file as you recommended. But in my 
density of states, a1g, eg1, eg2 are mixed up which is not the case as 
reported in this paper. May be I have to define new x and z axis in 
the case.inq file. But, I am not able to figure it out. Please find 
the structure file and  case.inq file that I have. I am not able to 
send my DOS because of the space limits.


blebleble

R LATTICE,NONEQUIV.ATOMS   2  167 R-3c

MODE OF CALC=RELA unit=bohr

  9.371341  9.371341 26.383222 90.00 90.00120.00

ATOM  -1: X=0.94382000 Y=0.55618000 Z=0.2500

          MULT= 6       ISPLIT= 8

      -1: X=0.05618000 Y=0.44382000 Z=0.7500

      -1: X=0.55618000 Y=0.2500 Z=0.94382000

      -1: X=0.44382000 Y=0.7500 Z=0.05618000

      -1: X=0.2500 Y=0.94382000 Z=0.55618000

      -1: X=0.7500 Y=0.05618000 Z=0.44382000

O          NPT=  781 R0=.00010 RMT= 1.74        Z:   8.0

LOCAL ROT MATRIX: 0.000 1.000 0.000

0.000 0.000 1.000

1.000 0.000 0.000

ATOM  -2: X=0.14783000 Y=0.14783000 Z=0.14783000

          MULT= 4       ISPLIT= 4

      -2: X=0.85217000 Y=0.85217000 Z=0.85217000

      -2: X=0.64783000 Y=0.64783000 Z=0.64783000

      -2: X=0.35217000 Y=0.35217000 Z=0.35217000

V          NPT=  781 R0=.5 RMT= 1.92        Z:  23.0

LOCAL ROT MATRIX: 1.000 0.000 0.000

0.000 1.000 0.000

0.000 0.000 1.000

  12      NUMBER OF SYMMETRY OPERATIONS

-1 0 0 0.

 0-1 0 0.

 0 0-1 0.

       1

 0 0-1 0.

-1 0 0 0.

 0-1 0 0.

       2

 0-1 0 0.

 0 0-1 0.

-1 0 0 0.

       3

 0 1 0 0.

 0 0 1 0.

 1 0 0 0.

       4

 0 0 1 0.

 1 0 0 0.

 0 1 0 0.

       5

 1 0 0 0.

 0 1 0 0.

 0 0 1 0.

       6

 0 0-1 0.5000

 0-1 0 0.5000

-1 0 0 0.5000

       7

 0 0 1 0.5000

 0 1 0 0.5000

 1 0 0 0.5000

       8

-1 0 0 0.5000

 0 0-1 0.5000

 0-1 0 0.5000




case.inq file



-9.0   3.0 Emin  Emax

   2 number of atoms

   1  -2  0  0 iatom,qsplit,symmetrize,locrot

2   0  1 nL, l-values

   2   -2  0  0 iatom,qsplit,symmetrize,locrot

3   0  1  2 nL, l-values



Thanks

Wasim



On Sun, Apr 5, 2020 at 7:00 AM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> 
wrote:


As expected, your struct file is the problem.  Why are you using P1
symmetry ??

In this paper they did a NON-SPINPOLARIZED calculation in LDA!!!

So when you want to reproduce their results, remove from your struct
file all the labels, i.e.

"V 1"  --> "V  "   and so on.

Please remember, the struct file is sensitive to the colums. So
you have
to overwrite the 1,2,.. by blanks, you must NOT delete the 1, because
then the rest of the line moves to the left!

Then follow the recommendations of nn and sgroup.

You should obtain a struct file with 2 non-equivalent positions
(one V,
one O)  and ISPLI=4 instead if ISPLIT=8



    Am 05.04.2020 um 08:05 schrieb Gavin Abo:
> If I interpret Prof. Blaha's post at [1] correctly, "x lapw2 -qtl"
> should automatically give what you need such that you would not
have to
> use "x qtl" (thus, you would not need case.inq if that is the case).
>
> Referring to the description for line 6 in section '4.3 The “master
> input“ file case.struct' of the WIE

Re: [Wien] Using option Qsplit=6 in qtl to rotate to get t2g and eg

[Gavin Abo]

See attached.

On 4/6/2020 9:41 PM, Wasim Raja Mondal wrote:
Gavin, Thank you for reply. I did not get the same plot. Can you 
please paste here the V2O3.struct file you have used for calculation?

I think I am doing some symmetry step wrong.


thanks
V2O3   
R   LATTICE,NONEQUIV.ATOMS:  2 167_R-3c
MODE OF CALC=RELA unit=ang 
  9.371341  9.371341 26.383222 90.00 90.00120.00   
ATOM  -1: X=0.94382002 Y=0.55618000 Z=0.2500
  MULT= 6  ISPLIT= 8
  -1: X=0.05617998 Y=0.44382000 Z=0.7500
  -1: X=0.55618000 Y=0.2500 Z=0.94382002
  -1: X=0.44382000 Y=0.7500 Z=0.05617998
  -1: X=0.2500 Y=0.94382002 Z=0.55618000
  -1: X=0.7500 Y=0.05617998 Z=0.44382000
O  NPT=  781  R0=0.0001 RMT=1.7400   Z:  8.000 
LOCAL ROT MATRIX:0.000 1.000 0.000
 0.000 0.000 1.000
 1.000 0.000 0.000
ATOM  -2: X=0.14782999 Y=0.14782999 Z=0.14782999
  MULT= 4  ISPLIT= 4
  -2: X=0.85217001 Y=0.85217001 Z=0.85217001
  -2: X=0.64782999 Y=0.64782999 Z=0.64782999
  -2: X=0.35217001 Y=0.35217001 Z=0.35217001
V  NPT=  781  R0=0.5000 RMT=1.9200   Z: 23.000 
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  12  NUMBER OF SYMMETRY OPERATIONS
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   1
 0 0-1-0.
-1 0 0 0.
 0-1 0 0.
   2
 0-1 0 0.
 0 0-1-0.
-1 0 0 0.
   3
 0 1 0 0.
 0 0 1 0.
 1 0 0-0.
   4
 0 0 1 0.
 1 0 0-0.
 0 1 0 0.
   5
 1 0 0-0.
 0 1 0 0.
 0 0 1 0.
   6
 0 0-1 0.5000
 0-1 0 0.5002
-1 0 0 0.5002
   7
 0 0 1 0.5000
 0 1 0 0.4998
 1 0 0 0.4998
   8
-1 0 0 0.5002
 0 0-1 0.5000
 0-1 0 0.5002
   9
 0-1 0 0.5002
-1 0 0 0.5002
 0 0-1 0.5000
  10
 0 1 0 0.4998
 1 0 0 0.4998
 0 0 1 0.5000
  11
 1 0 0 0.4998
 0 0 1 0.5000
 0 1 0 0.4998
  12
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Re: [Wien] Treating 4f states as core

[Gavin Abo]

You mention non-collinear spins, some links that might be of interest 
related to that:



http://susi.theochem.tuwien.ac.at/reg_user/ncm/

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07386.html

http://www.wien2k.at/events/ws2008/talks/Laskowski-SO-NCM.pdf

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10434.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16659.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17760.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16337.html


On 4/9/2020 11:56 AM, Ali Baghizhadeh wrote:
Thank you very much for your comments Prof. Laurence. Your paper is 
one of my references to do my set of calculations, and interprate my 
EELS data later on. Basically h-REFeO3 (RE: Lu, Yb, Sc ..) is AFM 
basal plane with non-collinear spins of Fe3+. Magnetism of Yb should 
contribute on c-axis weak FM component. and I wish to know if this is 
ground state of the system or not?

best regards
Ali
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Re: [Wien] init_orb_lapw -orb does not take atom parameters from command line

[Gavin Abo]

As I recall from the post at [1], the developers have on their computers 
for csh a symbolic link that uses tcsh.


I suspect it might because your system has csh (such that is not using 
tcsh).


You could trying changing the top of line of the init_orb_lapw script 
(in the $WIENROOT directory) from


#!/bin/csh -f

to

#!/bin/tcsh -f

Maybe you have also seen that a solution to the csh issues is expected 
in the next version to come after WIEN2k 19.1 that has not been released 
yet [2].


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16028.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18742.html


On 4/13/2020 11:42 AM, Luc Fruchter wrote:
With Wien2K 19.1 and Ubuntu : calling "init_orb_lapw -orb " from the 
terminal window does list the atoms of the unit cell, and then calls for:


"Enter the name, l, U(Ry) and J of the Atoms (eg. Fe 2 0.3 0.0; exit 
with RETURN)"


However, answering with a 4 data string separated with spaces as given 
in the example invariably loops to:


"You need to specify 4 values"

as if the 4 parameters were not recognized from the string sent. 
Probably a configuration problem, but which one ?


Thanks for your help.
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Re: [Wien] Lapw.2 error

[Gavin Abo]

Also, did compile with gfortran and not apply the bug fix to WIEN2k 19.1:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18771.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19741.html


On 4/17/2020 12:20 PM, Laurence Marks wrote:
This may have nothing to do with it, but why is your directory WIEN2k? 
The normal convention is, for instance, to have a directory TiC in 
which your structure file is TiC.struct etc. I hope you are not 
running in the installation directory, I suspect that could lead to chaos!


On Fri, Apr 17, 2020 at 1:02 PM Johnathon Street > wrote:


Prof. Blaha,

I am running Wien2k version 19.1 on Ubuntu. When running the SFC
cycle I am receiving the following error in Lapw2. error file.

 'LAPW2' - can't open unit: 15
 'LAPW2' -        filename: WIEN2k.tmp                          ​
 'LAPW2' -          status: scratch      form: unformatted

I have searched the mailing list and found a possible solution
would be to delete line 15 in the lapw2.def file which appears as
below:

 2,'WIEN2k.nsh',    'unknown','unformatted',0
 3,'WIEN2k.in1',   'unknown','formatted',0​
 4,'WIEN2k.inso',           'unknown','formatted',0​
 5,'WIEN2k.in2',   'old',    'formatted',0​
 6,'WIEN2k.output2','unknown','formatted',0​
 7,'WIEN2k.vorb','unknown','formatted',0​
 8,'WIEN2k.clmval','unknown','formatted',0​
10,'./WIEN2k.vector', 'unknown','unformatted',9000​
13,'WIEN2k.recprlist',  'unknown','unformatted',9000​
14,'WIEN2k.kgen',        'unknown','formatted',0​
16,'WIEN2k.qtl',       'unknown','formatted',0​
17,'WIEN2k.weightaver','unknown','formatted',0​
18,'WIEN2k.vsp',       'old',    'formatted',0​
19,'WIEN2k.vns',       'unknown','formatted',0​
20,'WIEN2k.struct',         'old',    'formatted',0​
21,'WIEN2k.scf2','unknown','formatted',0​
922,'WIEN2k.rotlm',   'unknown',    'formatted',0​
23,'WIEN2k.radwf',   'unknown',    'formatted',0​
26,'WIEN2k.weight',   'unknown','formatted',0​
27,'WIEN2k.weightdn',   'unknown','formatted',0​
29,'WIEN2k.energydn','unknown','formatted',0​
30,'WIEN2k.energy', 'unknown','formatted',0​
32,'WIEN2k.qdmft',   'unknown',    'formatted',0​
34,'WIEN2k.oubwin',   'unknown',    'formatted',0​
231,'WIEN2k.dmftsym',   'unknown',    'formatted',0

so that the lapw.def file looks like this.

line 15 prior to deletion is as follows:

15, 'WIEN2k.tmp', 'scratch', unformatted' ,0

I continue to get the same error following deleting line 15. Do
you have any suggestions

Thank you,
Johnathon Street


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www.numis.northwestern.edu 
Corrosion in 4D: www.numis.northwestern.edu/MURI 


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Re: [Wien] Spin densities in up and down cases

[Gavin Abo]

I read in the abstract [1] that GGA for the spin contamination was 
proposed and investigated.  I don't have access to the full paper.  Did 
they conclude if the result they obtained were valid or not?  As I saw a 
statement on Wikipedia [2] that spin contamination calculated with 
Kohn-Sham DFT codes may not necessarily be correct.


I know the WIEN2k webpage [3] talks about Kohn-Sham.  I'm not that 
familiar with the implementation(s) of hf in WIEN2k.  Is the calculation 
that is does or can it be set to do the unrestricted Hartree-Fock (UHF) 
that [1] and [2] mentions?


[1] https://doi.org/10.1063/1.2737773
[2] https://en.wikipedia.org/wiki/Spin_contamination
[3] http://susi.theochem.tuwien.ac.at/lapw/index.html

On 4/18/2020 10:40 AM, Tran, Fabien wrote:

I do not have experience with spin contamination, but without being sure it may 
not be that trivial to calculate for solids.​
https://www.mdpi.com/1420-3049/24/3/505


From: Wien  on behalf of pachineela rambabu 

Sent: Saturday, April 18, 2020 5:23 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Spin densities in up and down cases
   


Dear Sir, I want to calculate spin contamination from wien2k as suggested in the 
paper "The Journal of Chemical Physics 126, 214104 (2007).


Thanks,


On Sat, Apr 18, 2020, 20:08 Tran, Fabien  wrote:
  
If this is rho_up-rho_down​ that you want to integrate, then this is the spin magnetic moment.


When a calculation is finished, the integral of spin magnetic moment is printed 
in case.scf.

:MMTOT is for the unit cell

:MMI001, :MMI002, etc. are for the atomic spheres

:MMINT is in the interstitial region





From: Wien   on behalf of pachineela rambabu 

Sent: Saturday, April 18, 2020 3:21 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] Spin densities in up and down cases
   


Dear Tran, thank you very much for the reply. I want to find the spin densities 
difference and integrate the difference up to difference less than zero.


thanks,


On Sat, Apr 18, 2020, 18:47 Tran, Fabien  wrote:
  
The files case.clmup and case.clmdn ​contain the up and down electron densities.


But without knowing what you want to do, we can not help you more.





From: Wien   on behalf of pachineela rambabu 

Sent: Saturday, April 18, 2020 3:02 PM
To: A Mailing list for WIEN2k users
Subject: [Wien] Spin densities in up and down cases
   


Dear wien2k,
                        I want to get spin up and down density files from 
wien2k. How to get them.


Thanks,

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Re: [Wien] error in mixer

[Gavin Abo]

In your WIEN2k 19.1 options below, it looks like you are not using ELPA.

Are you using Thomas' patch from:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18777.html

Which is what my modules.patch is at:

https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1

As mentioned at the following two links, if want to apply all current 
patches you can install WIEN2k 19.2 unless you want to selectively apply 
19.1 patches to WIEN2k 19.1:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19925.html
http://susi.theochem.tuwien.ac.at/reg_user/updates/

On 4/24/2020 1:25 PM, Mohad Abbasnejad wrote:

Dear Pavel,

Actually not. The following is the content of WIEN2k options I have 
used for compilation.


current:FOPT:-O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML 
-traceback -assume buffered_io -I$(MKLROOT)/include
current:FPOPT:-O -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML 
-traceback -assume buffered_io -I$(MKLROOT)/include

current:OMP_SWITCH:-qopenmp
current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -lpthread 
-lm -ldl -liomp5

current:DPARALLEL:'-DParallel'
current:R_LIBS:-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
current:FFTWROOT:
current:FFTW_VERSION:
current:FFTW_LIB:
current:FFTW_LIBNAME:
current:LIBXCROOT:
current:LIBXC_FORTRAN:
current:LIBXC_LIBNAME:
current:LIBXC_LIBDNAME:
current:SCALAPACKROOT:
current:SCALAPACK_LIBNAME:
current:BLACSROOT:
current:BLACS_LIBNAME:
current:ELPAROOT:
current:ELPA_VERSION:
current:ELPA_LIB:
current:ELPA_LIBNAME:
current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
current:CORES_PER_NODE:1
current:MKL_TARGET_ARCH:intel64

Regards,
Mohaddeseh

On Fri, Apr 24, 2020 at 11:46 PM Pavel Ondračka 
mailto:pavel.ondra...@email.cz>> wrote:


> forrtl: severe (168): Program Exception - illegal instruction

Did you compile Wien2k on different machine than you run it now on?
What were your compilation options? This looks like your lapw1 binary
was compiled with some instructions which are not available on the
machine...

Best regards
Pavel

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Re: [Wien] case.in1c missing for a centrosymmetric case doing U+SO

[Gavin Abo]

To add a little to what Prof. Marks has said:

The -NI tells the WIEN2k program to continue an scf calculation with 
existing broyd files.


Perhaps, you have read the following post about save_lapw removing the 
broyd files:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01814.html

From that, you should see why there would be no need for the -NI flag 
in a run_* command just after a save_lapw.


Perhaps, you have read how -NI is useful if a run_* stops as it is still 
converging but has hit the default 40 cycle limit or a cluster 
performing the calculation has a scheduled power outage coming up where 
the calculation won't finish in time and you need to safely stop it 
using a .stop file so that it can be continued later with the -NI:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13945.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12648.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18171.html

Perhaps you have already read the WIEN2k usersguide [1] and posts about 
the importance of save_lapw between run_* commands such as between 
calculations without SO and with SO:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10350.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05130.html
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2009-April/012432.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02610.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12643.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12781.html

Posts that you might find to have very helpful information for SO and orb:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02807.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06449.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17735.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06561.html

If you have not read those and other related posts in the mailing list 
archive [2], a suggestion would be to read them.


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] http://susi.theochem.tuwien.ac.at/reg_user/mailing_list/

On 4/26/2020 5:38 AM, Laurence Marks wrote:
Definitely not. The -NI tells the mixer it can continue the same 
problem. However, when you add -orb, -so you have changed your problem.


This is different from running init_lapw again, which you don't want 
to do -- you are using the converged density from one phase as input 
to the next.


_
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 Sun, Apr 26, 2020, 05:07 Luc Fruchter > wrote:


># remember: the recommendation is to do this in steps in order to get
># more likely the groundstate for correlated compounds and usually you
># also want to see anyway what is the effect of SO and of U as compared
># to a plain PBE calculation
>runsp_lapw (-p)
>save_lapw PBE_no_so
>runsp_lapw -so (-p)
>save_lapw PBE_so
>runsp_lapw -orb -so (-p)
>save_lapw PBE_U_so



If one should process ORB and SO by steps to help converge to the
groundstate, then shouldn't one run the successive runsp_lapw with
-NI option, in order to initialize with the previous output ?

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Re: [Wien] compilation error - reg

[Gavin Abo]

If the problem is coming from the standard used, perhaps using the 
-std=f2003, for example, will resolve the problem, refer to:


https://gcc.gnu.org/onlinedocs/gcc-10.1.0/gfortran/Fortran-Dialect-Options.html#Fortran-Dialect-Options

Another possibility is that the .eq. in the if statement is 
problematic.  It's a little surprising that it even compiles as usually 
the .eq. works fine for ifort but does not work for gfortran.  For both 
ifort and gfortran to work, we have been having to change .eq. to .eqv.:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18770.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11545.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18762.html

The information at the following links might be of interest:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18767.html
https://gcc.gnu.org/onlinedocs/gcc-3.4.6/g77/Equivalence-Versus-Equality.html#Equivalence-Versus-Equality
https://gcc.gnu.org/onlinedocs/gcc-10.1.0/gfortran/Bitwise-logical-operators.html#Bitwise-logical-operators

On 5/9/2020 3:34 AM, Tran, Fabien wrote:

If the suggestion of P. Blaha does not help, remove "doit= .true." and rewrite 
it manually. Maybe there is some hidden character which perturbs the line.


From: Wien  on behalf of Peter Blaha 

Sent: Saturday, May 9, 2020 8:57 AM
To: wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] compilation error - reg

Which version of gfortran are you using ?

Maybe the newest gfortran is "buggy" or is using some newest fortran
standard which has eliminated the default types of fortran.

My gfortran-8 compiles this without problem.

The offending statement:

ados.f:79:48:

 79 |   if(kpp.eq.kselect.and.kselect.gt.0) doit= .true.
|1
Error: Cannot convert LOGICAL(4) to REAL(4) at (1)

looks innocent to me. kpp and kselect are by default integers.
Maybe you can switch-off the 2018 standard somewhere, or try to enclose
the 2 parts of the if with further brackets like:

   if((kpp.eq.kselect).and.(kselect.gt.0)) doit= .true.


Am 09.05.2020 um 04:50 schrieb Viswanathan Elumalai:

Dear Sir/Mam
Greetings
I had error while compiling the wien2k 19.2 version. I could not solve
it from my end. I searched in wien mail list, I did not see any report
in this regards. I copied the error message here and attached the
corresponding compile file.

SRC_tetra/compile.msg:Error: Cannot convert LOGICAL(4) to REAL(4) at (1)
SRC_tetra/compile.msg:make: *** [Makefile:108: ados.o] Error 1

I am looking forward your reply.
with best regards

Dr. Viswanathan Elumalai,
Assistant Professor in Physics



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Re: [Wien] compilation error - reg

[Gavin Abo]

Thanks, you are correct in this case about .eq. being the proper choice.

Today, I did an upgrade from Ubuntu 18.04 LTS to the April 2020 release 
of Ubuntu 20.04 LTS [1].


I was able to compile WIEN2k 19.2 using the stable gfortran 9.3.0 of 
Ubuntu 20.04 LTS successfully.


Since it is easy to install the developmental gfortran 10 [2] using 
"sudo apt install gfortran-10" in Ubuntu 20.04 LTS, I compiled the tetra 
program with that and it worked fine too as seen below.  Something that 
I have noticed is that in my compile.msg for SRC_tetra I have "76 
|   DO 30 K=1,KMAX" for a warning that does not affect the compile 
but in the compile.msg at [3] that Dr. Elumalai sent there is "73 
|   DO 30 K=1,KMAX" that seems to suggest the same warning occurred 
at different line numbers of 76 and 73, respectively.  Thus, 
SRC_tetra/ados.f file the Dr. Elumalai has is most likely different from 
the one I'm using.  I'm using the original file that is part of 
WIEN2k_19.2.tar that I got today from the Code download [4] area of the 
WIEN2k website.


Of note, the full WIEN2k 19.2 compiled successfully with gfortran 10, 
but the -fallow-invalid-boz and -fallow-argument-mismatch [5] compiler 
options [6] were needed to compile some of the modules.


[1] 
https://ubuntu.com/tutorials/tutorial-upgrading-ubuntu-desktop#1-before-you-start
[2] 
https://gcc.gnu.org/wiki/GFortran/News#gfortran_10_.28current_development_version.29
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20025.html

[4] http://www.wien2k.at/reg_user/index.html
[5] https://github.com/Unidata/netcdf-fortran/issues/212
[6] 
https://gcc.gnu.org/onlinedocs/gcc-10.1.0/gfortran/Fortran-Dialect-Options.html#Fortran-Dialect-Options 



username@computername:~/WIEN2k$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 20.04 LTS
Release:    20.04
Codename:    focal
username@computername:~/WIEN2k$ gfortran-10 -v
...
gcc version 10.0.1 20200411 (experimental) [master revision 
bb87d5cc77d:75961caccb7:f883c46b4877f637e0fa5025b4d6b5c9040ec566] 
(Ubuntu 10-20200411-0ubuntu1)

...
username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: R
...
 Selection: S
   Which program to recompile? tetra
...
SRC_tetra ...
...
gfortran-10  -ffree-form -O2 -ftree-vectorize -march=native 
-ffree-line-length-none -ffpe-summary=none -fallow-invalid-boz 
-fallow-argument-mismatch -c ados.f

ados.f:76:30:

76 |   DO 30 K=1,KMAX
  |  1
Warning: Fortran 2018 deleted feature: Shared DO termination label 30 at (1)
ados.f:86:72:

   86 |    10 F(I,KP)=FC(I,KPP,JJ)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is 
not END DO or CONTINUE with label 10 at (1)

ados.f:87:24:

   87 |    20 D(KP)=EBS(KPP,JJ)
  |    1
Warning: Fortran 2018 deleted feature: DO termination statement which is 
not END DO or CONTINUE with label 20 at (1)

...
Compile time errors (if any) were:


Check file   compile.msg   in the corresponding SRC_* directory for the
compilation log and more info on any compilation problem.

On 5/9/2020 9:18 AM, Peter Blaha wrote:
This is an if between 2 integers and for that   .eq.   is the proper 
choice.


Only for comparison of logical variables some "clever" informatic guys 
have invented  .eqv.  instead of the old f77 standard.


Another possibility is that the .eq. in the if statement is 
problematic.  It's a little surprising that it even compiles as 
usually the .eq. works fine for ifort but does not work for 
gfortran.  For both ifort and gfortran to work, we have been having 
to change .eq. to .eqv.:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18770.html 

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11545.html 

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18762.html 



The information at the following links might be of interest:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18767.html 

https://gcc.gnu.org/onlinedocs/gcc-3.4.6/g77/Equivalence-Versus-Equality.html#Equivalence-Versus-Equality 

https://gcc.gnu.org/onlinedocs/gcc-10.1.0/gfortran/Bitwise-logical-operators.html#Bitwise-logical-operators 



On 5/9/2020 3:34 AM, Tran, Fabien wrote:
If the suggestion of P. Blaha does not help, remove "doit= .true." 
and rewrite it manually. Maybe there is some hidden character which 
perturbs the line.



From: Wien  on behalf of 
Peter Blaha

Sent: Saturday, May 9, 2020 8:57 AM
To:wien@zeus.theochem.tuwien.ac.at
Subject: Re: [Wien] compilation error - reg

Which version of gfortran are you using ?

Maybe the newest gfortran is "buggy" or is using some newest fortran
standard which has eliminated the default types of fortran.

My gfortran-8 compiles this without problem.

The offending statement:

ados.f:79:48:

 79 |   if(kpp.eq.kselect.and.kselect.gt.0) doit= .true.
    |

Re: [Wien] Segmentation fault in Kgen

[Gavin Abo]

Currently, I'm using the source code package WIEN2k_19.2.tar from the 
Code download [1] area of the WIEN2k website but with the 
WIEN2k_VERSION.patch at [2] that adjusts the WIEN2k_VERSION file from 
having version 19.1 to match the version 19.2 information given on the 
WIEN2k website.  The Segmentation fault error seems to be particular to 
your system (Linux operating system, Fortran compiler, etc.) as I was 
NOT able to reproduce the error as seen below:


username@computername:~/wiendata/NiSbO4_V_14$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 20.04 LTS
Release:    20.04
Codename:    focal
username@computername:~/wiendata/NiSbO4_V_14$ gfortran -v
...
gcc version 9.3.0 (Ubuntu 9.3.0-10ubuntu2)
username@computername:~/wiendata/NiSbO4_V_14$ cat $WIENROOT/WIEN2k_VERSION
WIEN2k_19.2 (Release 21/4/2020)
username@computername:~/wiendata/NiSbO4_V_14$ ls
NiSbO4_V_14.struct
username@computername:~/wiendata/NiSbO4_V_14$ init_lapw -b
...
  init_lapw finished ok
username@computername:~/wiendata/NiSbO4_V_14$ x kgen
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
300
 length of reciprocal lattice vectors:   0.656   0.674   0.763 6.307   
6.479   7.342

  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
1
  45  k-points generated, ndiv=   6 6   6
STOP KGEN ENDS
0.0u 0.0s 0:04.27 0.4% 0+0k 0+136io 0pf+0w

[1] http://www.wien2k.at/reg_user/index.html
[2] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2

On 5/13/2020 9:28 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                               I have started simulation of NiSbO4 
(structure attached). During initialization I got the following error 
(during x kgen):


Segmentation fault
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /usr/local/Wien2k/kgen kgen.def   failed

I have given total k-point 300 which should give 14 k-points in irbz. 
I have also prepare a fresh directory & did all the initialization 
properly, but getting the same results always.


Looking forward to your reply eagerly.

with regards,

--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Segmentation fault in Kgen

[Gavin Abo]

If "morning" in your sentence below means that you shutdown your system 
at the end of the day and start it up in the morning, a possibility 
might be that your memory is being exhausted and was freed making it 
available again by the system reboot.


You could be read about memory exhaustion, insufficient RAM memory, and 
other segmentation fault causes at the following three links:


Possible Cause #2-prime: Stack Exhaustion Due to Heap or General Memory 
Exhaustion: 
https://software.intel.com/content/www/us/en/develop/articles/determining-root-cause-of-sigsegv-or-sigbus-errors.html


Check shell limits:https://kb.iu.edu/d/aqsj

Insufficient RAM memory: 
http://www.democritos.it/pipermail/pw_forum/2005-March/002272.html


On 5/14/2020 5:17 AM, shamik wrote:

Dear Gavin,

               The problem is solved, but, how I don't know. I have 
just re do the initilization in this morning, & it works.  I have 
encountered the similar problems before. Sometimes it is not working 
while sometimes it works...I have no clue why & how such thing 
happens..


with regards,

On Thu, 14 May 2020 at 06:48, Gavin wrote:

Currently, I'm using the source code package WIEN2k_19.2.tar from
the Code download [1] area of the WIEN2k website but with the
WIEN2k_VERSION.patch at [2] that adjusts the WIEN2k_VERSION file
from having version 19.1 to match the version 19.2 information
given on the WIEN2k website.  The Segmentation fault error seems
to be particular to your system (Linux operating system, Fortran
compiler, etc.) as I was NOT able to reproduce the error as seen
below:

username@computername:~/wiendata/NiSbO4_V_14$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 20.04 LTS
Release:    20.04
Codename:    focal
username@computername:~/wiendata/NiSbO4_V_14$ gfortran -v
...
gcc version 9.3.0 (Ubuntu 9.3.0-10ubuntu2)
username@computername:~/wiendata/NiSbO4_V_14$ cat
$WIENROOT/WIEN2k_VERSION
WIEN2k_19.2 (Release 21/4/2020)
username@computername:~/wiendata/NiSbO4_V_14$ ls
NiSbO4_V_14.struct
username@computername:~/wiendata/NiSbO4_V_14$ init_lapw -b
...
  init_lapw finished ok
username@computername:~/wiendata/NiSbO4_V_14$ x kgen
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3
divisions of G)
300
 length of reciprocal lattice vectors:   0.656   0.674 0.763  
6.307   6.479   7.342
  Shift of k-mesh allowed. Do you want to shift: (0=no, 1=shift)
1
  45  k-points generated, ndiv= 6   6   6
STOP KGEN ENDS
0.0u 0.0s 0:04.27 0.4% 0+0k 0+136io 0pf+0w

[1] http://www.wien2k.at/reg_user/index.html
[2] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2

On 5/13/2020 9:28 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                               I have started simulation of
NiSbO4 (structure attached). During initialization I got the
following error (during x kgen):

Segmentation fault
0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w
error: command   /usr/local/Wien2k/kgen kgen.def failed

I have given total k-point 300 which should give 14 k-points in
irbz. I have also prepare a fresh directory & did all the
initialization properly, but getting the same results always.

Looking forward to your reply eagerly.

with regards,

-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Alignment band

[Gavin Abo]

See WIEN2k 19.1 usersguide section "3.11.4 Bandstructure" [1] and [2].

[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf

[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19589.html


On 5/15/2020 9:21 AM, Brik Hamida wrote:

Dear

Im working on 2D semiconductor. I have calculated its electronic 
structure using Wien2k .


Actually , I need to plot the corresponding  alignment band means the 
band edge position which are usually named Homo and Lumo.


Please can you help me and tell me how  I can do that.
Thanks in advance .

 Best,
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Re: [Wien] Aligning magnetization direction along high symmetry crystallographic direction

[Gavin Abo]

If your referring to directions towards critical points like the "A - 
Center of a hexagonal face" at:


https://en.wikipedia.org/wiki/Brillouin_zone#Critical_points

The following two links might also be of interest to you:

http://lampx.tugraz.at/~hadley/ss1/bzones/hexagonal.php
https://www.cryst.ehu.es/cryst/get_kvec.html

On 5/19/2020 9:37 PM, Laurence Marks wrote:
I suggest that you read about what hexagonal symmetry is, e.g. 
https://en.m.wikipedia.org/wiki/Hexagonal_crystal_family. You will 
then be able to work out for yourself the answer to your question.


---
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 Tue, May 19, 2020, 22:31 Nileema Sharma > wrote:


Dear WIEN2k users and developers!!
I am working on a hexagonal system, I would like to know in which
direction(s) should I apply SOC so that it would represent high
symmetry crystallographic direction, for the calculation of the
energy in that particular direction?
Best regards.
Thank you!!
Nileema Sharma

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Re: [Wien] Aligning magnetization direction along high symmetry crystallographic direction

[Gavin Abo]

If your referring to themagnetocrystalline anisotropy (MCA) energy 
equation 2.77 on page 20 in:


https://www.ifw-dresden.de/userfiles/groups/itf_folder/Theses/carsten_neise_phd.pdf

I remember that there was this post on MAE:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09408.html

On 5/20/2020 12:21 AM, Xavier Rocquefelte wrote:
And another comment. Applying the magnetization along a high symmetry 
direction does not mean that you will apply SOC in the direction for 
which the effect will be maximum... It is why, people study the 
magnetocrystalline anisotropy energy (MAE).


Best regards

Xavier

Le 20/05/2020 à 08:07, Peter Blaha a écrit :

I think nobody really understands your question.

Obviously for a hexagonal system the c-axis is a very high symmetry 
direction. This corresponds to  0 0 1


Of course, the a (or b) direction is also a special direction, but it 
will break hexagonal symmetry as the a and b directions will no 
longer be equivalent. So when you choose 1 0 0, in many cases the 
symmetry will be automatically reduced by symmetso.



Am 20.05.2020 um 05:30 schrieb Nileema Sharma:

Dear WIEN2k users and developers!!
I am working on a hexagonal system, I would like to know in which 
direction(s) should I apply SOC so that it would represent high 
symmetry crystallographic direction, for the calculation of the 
energy in that particular direction?

Best regards.
Thank you!!
Nileema Sharma
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Re: [Wien] New installation of W2k

[Gavin Abo]

FYI, it looks like case.in1(c) and case.in2(c) is automatically created 
(in WIEN2k 19.2) around the "inputfiles prepared" when "c" is answered 
for the following question:


username@computername:~/wiendata/GaN_3db$ init_lapw
...
-> continue with kgen or edit the GaN_3db.inst file and rerun lstart 
(c/e)

c
File  is unavailable.
-> in  GaN_3db.in1_st  select   RKmax ( usually 5.0 - 9.0 ), LVNS 
and LOs

-> in  GaN_3db.in2_st  select   GMAX and Fermi-Energy method
>   inputfiles prepared    (05:41:45)
 inputfiles prepared
 inversion is NOT present
>   inputfiles for lapw1c/2c prepared, no inversion present    (05:41:45)
...
  init_lapw finished ok
username@computername:~/wiendata/GaN_3db$ ls -l *.in1* *.in2*
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1c
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1_st
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2c
-rw-rw-r-- 1 username username 171 May 25 05:41 GaN_3db.in2_ls
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2_st
-rw-rw-r-- 1 username username 126 May 25 05:40 GaN_3db.in2_sy

On 5/25/2020 12:37 AM, Peter Blaha wrote:
When you use   init_lapw in sequential mode, it asks many questions at 
each step. In one of the steps you were asked to copy the generated 
input files and you probably did not say yes at that point.


In any case, I recommend to run

x nn    (or setrmt case);  x sgroup; x symmetry
to check the symmetry and correctness of your struct file. Once this 
has passed without errors, initialize in batch mode:


init_lapw -h  (for options)
init -b -.

Check the output on the screen for problems.
If necessary you can repeat this command with different options.

Regards

Am 25.05.2020 um 08:05 schrieb Arthur H. Edwards:

Prof Blaha:

Thanks very much for such a quick response.l I was using the command 
line. Specifically, Iused init_lapw starting with the .struct file 
I'm attaching. I didn't modify any of the files that resulted from 
the various sub processes. I woild be glad to send anything else you 
might find useful.


Art Edwards
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[Wien] [SPAM?] Re: New installation of W2k

[Gavin Abo]

Are you getting during the "x symmetry" step of init_lapw that it "does 
not contain inversion"?


-> continue with symmetry (old case.struct) or use/edit 
GaN_3db.struct_sgroup ? (c/e)

c
 next is symmetry
>   symmetry    (14:50:47)  SPACE GROUP DOES NOT CONTAIN INVERSION
0.0u 0.0s 0:00.03 0.0% 0+0k 160+48io 1pf+0w

The init_lapw script does a check using grep, is grep working ok and 
showing after "x symmetry" that the output file "does not contain 
inversion"?


username@computername:~/wiendata/GaN_3db$ grep INVERSION *.outputs
 PGBSYM: SPACE GROUP DOES NOT CONTAIN INVERSION

The messages that you seem to be missing in the output on the screen in 
the terminal appear to be related to the echo command. Are you running 
init_lapw directly in the terminal, or are you perhaps running from 
within a job script, or do you know if you perhaps you have something 
set on your system that might be redirecting echo from the terminal to 
somewhere else like an output file?  You might check if the echo command 
is working for example with:


username@computername:~/wiendata/GaN_3db$ echo $WIENROOT
/home/username/WIEN2k


On 5/25/2020 2:07 PM, Arthur H. Edwards wrote:

Gavin:

Thanks for your response.

Fopr some reason, when I run this I don't get a message that there is 
no inversion. Here is the snippet.


-> continue with kgen or edit the GaN_3dc.inst file and rerun 
lstart (c/e)

c
-> in  GaN_3dc.in1_st  select   RKmax ( usually 5.0 - 9.0 ), LVNS 
and LOs

-> in  GaN_3dc.in2_st  select   GMAX and Fermi-Energy method
>   inputfiles prepared (12:23:21)
inputfiles prepared
next is kgen
>   kgen (12:23:21)   24  symmetry operations without inversion
inversion added (non-spinpolarized non-so calculation)
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)

I'm missing the line after inputfiles prepared, yet, in the kgen call, 
you see that no inversion is flagged.


Art Edwards

--
  Arthur H. Edwards
edwards...@fastmail.fm <mailto:edwards...@fastmail.fm>



On Mon, May 25, 2020, at 5:56 AM, Gavin Abo wrote:


FYI, it looks like case.in1(c) and case.in2(c) is automatically 
created (in WIEN2k 19.2) around the "inputfiles prepared" when "c" is 
answered for the following question:


username@computername:~/wiendata/GaN_3db$ init_lapw
...
-> continue with kgen or edit the GaN_3db.inst file and rerun 
lstart (c/e)

c
File  is unavailable.
-> in  GaN_3db.in1_st  select   RKmax ( usually 5.0 - 9.0 ), LVNS 
and LOs

-> in  GaN_3db.in2_st  select   GMAX and Fermi-Energy method
>  inputfiles prepared    (05:41:45)
 inputfiles prepared
 inversion is NOT present
>   inputfiles for lapw1c/2c prepared, no inversion present    (05:41:45)
...
  init_lapw finished ok
username@computername:~/wiendata/GaN_3db$ ls -l *.in1* *.in2*
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1c
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1_st
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2c
-rw-rw-r-- 1 username username 171 May 25 05:41 GaN_3db.in2_ls
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2_st
-rw-rw-r-- 1 username username 126 May 25 05:40 GaN_3db.in2_sy
On 5/25/2020 12:37 AM, Peter Blaha wrote:
When you use   init_lapw in sequential mode, it asks many questions 
at each step. In one of the steps you were asked to copy the 
generated input files and you probably did not say yes at that point.


In any case, I recommend to run

x nn    (or setrmt case);  x sgroup; x symmetry
to check the symmetry and correctness of your struct file. Once this 
has passed without errors, initialize in batch mode:


init_lapw -h  (for options)
init -b -.

Check the output on the screen for problems.
If necessary you can repeat this command with different options.

Regards

Am 25.05.2020 um 08:05 schrieb Arthur H. Edwards:


Prof Blaha:

Thanks very much for such a quick response.l I was using the 
command line. Specifically, Iused init_lapw starting with the 
.struct file I'm attaching. I didn't modify any of the files that 
resulted from the various sub processes. I woild be glad to send 
anything else you might find useful.


Art Edwards

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[Wien] [SPAM?] Re: New installation of W2k

[Gavin Abo]

What WIEN2k version are you using?

That looks similar to problems we had with older WIEN2k versions [1], 
which have been resolved with the latest version (WIEN2k 19.2), when 
compiled with gfortran.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18106.html


On 5/25/2020 7:21 PM, Arthur H. Edwards wrote:

Gavin:

This is what I'm getting:

  Names of point group: -43m  -43m    Td
Number and name of space group: 216 (F -4 3 m)
-> check in  GaN_3dc.outputsgroup  for proper symmetry, compare
   with your struct file and later with  GaN_3dc.outputs
   sgroup has also produced a new struct file based on your old one.
   If you see warnings above, consider to use the newly generated
   struct file, which you can view (edit) now.
-> continue with symmetry (old case.struct) or use/edit 
GaN_3dc.struct_sgroup ? (c/e)

c
next is symmery
>   symmetry (12:20:29) Note: The following floating-point exceptions 
are signalling: IEEE_DENORMAL

0.002u 0.000s 0:00.00 0.0% 0+0k 0+48io 0pf+0w
-> check in  GaN_3dc.outputs  the symmetry operations,
   the point symmetries and compare with results from sgroup
   if you find errors (often from rounding errors of positions), 
apply x patchsymm



--
  Arthur H. Edwards
edwards...@fastmail.fm <mailto:edwards...@fastmail.fm>



On Mon, May 25, 2020, at 3:14 PM, Gavin Abo wrote:


Are you getting during the "x symmetry" step of init_lapw that it 
"does not contain inversion"?


-> continue with symmetry (old case.struct) or use/edit 
GaN_3db.struct_sgroup ? (c/e)

c
 next is symmetry
>   symmetry    (14:50:47)  SPACE GROUP DOES NOT CONTAIN INVERSION
0.0u 0.0s 0:00.03 0.0% 0+0k 160+48io 1pf+0w

The init_lapw script does a check using grep, is grep working ok and 
showing after "x symmetry" that the output file "does not contain 
inversion"?


username@computername:~/wiendata/GaN_3db$ grep INVERSION *.outputs
 PGBSYM: SPACE GROUP DOES NOT CONTAIN INVERSION

The messages that you seem to be missing in the output on the screen 
in the terminal appear to be related to the echo command.  Are you 
running init_lapw directly in the terminal, or are you perhaps 
running from within a job script, or do you know if you perhaps you 
have something set on your system that might be redirecting echo from 
the terminal to somewhere else like an output file?  You might check 
if the echo command is working for example with:


username@computername:~/wiendata/GaN_3db$ echo $WIENROOT
/home/username/WIEN2k


On 5/25/2020 2:07 PM, Arthur H. Edwards wrote:

Gavin:

Thanks for your response.

Fopr some reason, when I run this I don't get a message that there 
is no inversion. Here is the snippet.


-> continue with kgen or edit the GaN_3dc.inst file and rerun 
lstart (c/e)

c
-> in  GaN_3dc.in1_st  select   RKmax ( usually 5.0 - 9.0 ), 
LVNS and LOs

-> in  GaN_3dc.in2_st  select   GMAX and Fermi-Energy method
>   inputfiles prepared (12:23:21)
inputfiles prepared
next is kgen
>   kgen (12:23:21)   24  symmetry operations without inversion
inversion added (non-spinpolarized non-so calculation)
  NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions 
of G)


I'm missing the line after inputfiles prepared, yet, in the kgen 
call, you see that no inversion is flagged.


Art Edwards

--
  Arthur H. Edwards
edwards...@fastmail.fm <mailto:edwards...@fastmail.fm>



On Mon, May 25, 2020, at 5:56 AM, Gavin Abo wrote:


FYI, it looks like case.in1(c) and case.in2(c) is automatically 
created (in WIEN2k 19.2) around the "inputfiles prepared" when "c" 
is answered for the following question:


username@computername:~/wiendata/GaN_3db$ init_lapw
...
-> continue with kgen or edit the GaN_3db.inst file and rerun 
lstart (c/e)

c
File  is unavailable.
-> in  GaN_3db.in1_st  select   RKmax ( usually 5.0 - 9.0 ), 
LVNS and LOs

-> in  GaN_3db.in2_st  select   GMAX and Fermi-Energy method
>  inputfiles prepared    (05:41:45)
 inputfiles prepared
 inversion is NOT present
>   inputfiles for lapw1c/2c prepared, no inversion present    
(05:41:45)

...
  init_lapw finished ok
username@computername:~/wiendata/GaN_3db$ ls -l *.in1* *.in2*
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1c
-rw-rw-r-- 1 username username 563 May 25 05:44 GaN_3db.in1_st
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2c
-rw-rw-r-- 1 username username 171 May 25 05:41 GaN_3db.in2_ls
-rw-rw-r-- 1 username username 297 May 25 05:41 GaN_3db.in2_st
-rw-rw-r-- 1 username username 126 May 25 05:40 GaN_3db.in2_sy
On 5/25/2020 12:37 AM, Peter Blaha wrote:
When you use   init_lapw in sequential mode, it asks many 
questions at each step. In one of the steps you were asked to copy 
the generated input files and you probably did not say yes at that 
point.


In any case, I recommend to run

x

Re: [Wien] Wien Installation

[Gavin Abo]

1. In a terminal, change into your WIEN2k directory: cd $WIENROOT

2. Run: ./siteconfig

3. Select Compiling Options: O

4. Check your R_LIBS line

Your SRC_aim-compile.msg looks like it probably used: 
/usr/lib64/libpthread.so


What works for me for R_LIBS is: -L/home/username/OpenBLAS-0.3.9 
-lopenblas -llapack_lapw -lpthread


In the above, "/home/username" has to be replaced by the path to your 
OpenBLAS.


The OpenBLAS I'm using is currently version 0.3.9 from:

https://www.openblas.net/


On 6/2/2020 4:14 AM,  wrote:


Dear W2k developers and users,

I am installing wien version 19.2 on Linux with gfortran and OpenBlas.

There were many warning messages in different compile.msg files of 
different directories after installing, so I attached some of them.


Sincerely yours Yu Chen



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Re: [Wien] Reagarding StructGen in Wien2K19.1

[Gavin Abo]

Are the lattice constants okay?


The webpage https://materialsproject.org/materials/mp-352/ has:


a = 5.142 Å, b = 5.195 Å, c = 5.326 Å (or a = 9.716976 bohr, b = 
9.817131 bohr, c = 10.064685 bohr)



In your struct file below, I see:


a = 0.523454 bohr, b = 0.648176 bohr, c = 0.633059 bohr


About struct file always being in bohr: 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01967.html



On 6/3/2020 5:19 AM, Tran, Fabien wrote:


Hi,


​What is the problem? Is the resulting struct file not the one you 
expected? How did you generate the struct file (e.g., from cif file)?





*From:* Wien  on behalf of 
Arvind Kumar 

*Sent:* Wednesday, June 3, 2020 12:52 PM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* [Wien] Reagarding StructGen in Wien2K19.1
Dear Sir,
I am running the Wien2K19.1 version on my laptop. I am trying to 
generate Monoclinic structure of HfO2 and La2NiMnO6 but facing 
problems to generate the correct struct file.


Struct file for reference as: {(Space Group 14 (P21/c)]

HfO2-m
P   LATTICE,NONEQUIV.ATOMS:  2 14_P21/c
MODE OF CALC=RELA unit=ang
0.523454  0.648176  0.633059 90.00 99.73 90.00
ATOM  -1: X=0.2770 Y=0.0420 Z=0.3350
          MULT= 4          ISPLIT= 8
ATOM  -1:X= 0.7230 Y=0.9580 Z=0.6650
ATOM  -1:X= 0.7230 Y=0.5420 Z=0.1650
ATOM  -1:X= 0.2770 Y=0.4580 Z=0.8350
Hf         NPT=  781  R0=0.0500 RMT=    0.1100   Z: 72.000
LOCAL ROT MATRIX:    1.000 0.000 0.000
                     0.000 1.000 0.000
                     0.000 0.000 1.000
ATOM   2: X=0.4470 Y=0.7590 Z=0.4830
          MULT= 4          ISPLIT= 8
ATOM   2:X= 0.5530 Y=0.2410 Z=0.5170
ATOM   2:X= 0.5530 Y=0.2590 Z=0.0170
ATOM   2:X= 0.4470 Y=0.7410 Z=0.9830
O          NPT=  781  R0=0.0001 RMT=    0.1000   Z:  8.000
LOCAL ROT MATRIX:    0.000 0.000 0.000
                     0.000 0.000 0.000
                     0.000 0.000 0.000
   0      NUMBER OF SYMMETRY OPERATIONS


Similar problems, I am facing for other monoclinic structures. Please 
guide me and suggest me, what I have to do to resolve this.




with regards,
Arvind


--
Dr. Arvind Kumar
Assistant Professor
Department of Physics
Atma Ram Sanatan Dharma College
(University of Delhi)
Dhaula Kuan, New Delhi-110021
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Re: [Wien] Xcrysden issues with w2web

[Gavin Abo]

Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html


On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, 
I am able to view directly from terminal when typing Xcrysden in 
command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set 
to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2


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Re: [Wien] How to add BoltzTrap2 in Wien2k 19.2

[Gavin Abo]

BoltzTraP2 is a separate program and it reads in files (*.scf, *.struct, 
*.energy*) from WIEN2k 19.2.  Thus, you do not need to add it to WIEN2k.


If you are using one of the latest Linux distributions that ships with 
Python 3, it is usually installed as given on the BoltzTraP2 website [1] 
with:


pip install BoltzTraP2

 or (depending on your installation)

pip3 install BoltzTraP2

If you are using an older Linux distribution or if you like the Anaconda 
environment, then conda [2] likely can be installed and BoltzTraP2 can 
be installed in the conda environment.


For BoltzTraP2, it is suggested to join the BoltzTraP mailing list given 
the BoltzTraP2 website [1] as question and answer posts in that Google 
group are searchable containing installation information and solutions 
to other commonly asked BoltzTraP2 questions.


[1] 
https://www.imc.tuwien.ac.at/forschungsbereich_theoretische_chemie/forschungsgruppen/prof_dr_gkh_madsen_theoretical_materials_chemistry/boltztrap2/


[2] https://www.anaconda.com/products/individual


On 6/7/2020 8:46 PM, Shahid Ramay wrote:

Dear Prof.

How to install properly BoltzTrap2 and then add it in Wien2k 19.2 version?

Thanks
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Re: [Wien] Wien Installation

[Gavin Abo]

In terms of OpenBLAS-0.3.9 libraries, in my OpenBLAS-0.3.9/lib, there 
are several files as the below: libopenblas_nehalemp-r0.3.9.a, 
libopenblas_nehalemp-r0.3.9.so, libopenblas.so, libopenblas.so.0, 
libopenblas.a. Are they as same as yours?
I have the following, but you have the same one named "libopenblas.so" 
that I use.


username@computername:~/WIEN2k$ ls ~/OpenBLAS-0.3.9/*.a 
~/OpenBLAS-0.3.9/*.so

/home/username/OpenBLAS-0.3.9/libopenblas.a
/home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.a
/home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.so
/home/username/OpenBLAS-0.3.9/libopenblas.so
In addition, are there commands such as lapw0_mpi, lapw1_mpi and 
lapw1c_mpi generated by installing with gfortran+OpenBLAS, just like 
by installing with ifort?
No, the Intel Parallel Studio XE 2020 Cluster Edition has the Intel MPI 
Library [1] that provides intelmpi making it easy to build the WIEN2k 
*_mpi files.?0?2 For gfortran, it can be done but it is extra work as one 
has to install scalapack [2] and MPI (such as OpenMPI [3]) separately 
and then include them in the parallel compiler settings of WIEN2k in 
order to build the files.


[1] 
https://software.intel.com/content/www/us/en/develop/tools/parallel-studio-xe.html

[2] http://www.netlib.org/scalapack/
[3] https://www.open-mpi.org/software/ompi/v4.0/


Then during ./siteconfig_lapw, I choose O to set libraries 
??R_LIBS(LAPACK+BLAS)??, then how to set the ??Real libraries??? Would you 
like to tell me how set the ??Real libraries?? parameter so that could 
obtain the result just like your path for R_LIBS as 
??-L/home/username/OpenBLAS-0.3.9 -lopenblas -llapack_lapw ?Clpthread???


In my setting, I did a couple of tries and obtain three kinds of 
results as below:


1.When I set the R_LIBS such as 
/home/username/OpenBLAS-0.3.9/lib/libopenblas.so (or libopenblas.so.0, 
or libopenblas_nehalemp-r0.3.9.so), then the massage is: /usr/bin/ld: 
warning: libgfortran.so.3, needed by 
/home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas.so, may conflict with 
libgfortran.so.5.


2.When I set the R_LIBS such as /home/username/OpenBLAS-0.3.9/lib or 
/home/username/OpenBLAS-0.3.9, then the massage is: file not 
recognized: Is a directory.


3.When I set he R_LIBS such as ?0?2/home/username/OpenBLAS-0.3.9/lib/ 
libopenblas_nehalemp-r0.3.9.a (or libopenblas.a), then the error 
massage is much, including: 
/home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas_nehalemp-r0.3.9.a(blas_server.o): 
In function `goto_set_num_threads': blas_server.c:(.text+0x7f3): 
undefined reference to `pthread_create'.


All above relating files were attached.
Attached is copy of my compile.msg from SRC_aim that you can compare to 
yours.
Below is what I used for a basic WIEN2k 19.2 install that should work 
for serial and k-point parallel calculations (but won't work for mpi 
calculations).?0?2 Of note, it looks like you will need to replace 
"/home/username/OpenBLAS-0.3.9" with "/home-yw/Soft/OpenBLAS-0.3.9/lib" 
on your system.?0?2 Also, you might notice below that the "-llapack_lapw" 
of WIEN2k is not needed since -lopenblas contains it own lapack library.



username@computername:~/WIEN2k$ ls WIEN2k_INSTALLDATE
WIEN2k_INSTALLDATE
username@computername:~/WIEN2k$ rm WIEN2k_INSTALLDATE
username@computername:~/WIEN2k$ ./siteconfig
...
continue or stop (c/s) c
...
?0?2 Selection: LG
...
?0?2?0?2?0?2?0?2 Press RETURN to continue
...
?0?2?0?2?0?2?0?2 Your compiler: gfortran
...
?0?2?0?2?0?2?0?2 Your compiler: gcc
...
?0?2Would you like to use LIBXC (that you have installed - usually not 
needed)? (y,N):

N
...
?0?2Do you want to use FFTW (recommended, but for sequential code not 
required)? (Y,n): n

...
Selection: R
?0?2?0?2?0?2?0?2 Real libraries=-L/home/username/OpenBLAS-0.3.9 -lopenblas 
-lpthread
...
?0?2Current settings:
?0?2 M?0?2?0?2 OpenMP switch:?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 -fopenmp
?0?2 O?0?2?0?2 Compiler options:?0?2?0?2?0?2?0?2?0?2?0?2?0?2 -ffree-form -O2 -ftree-vectorize 
-march=native -ffree-line-length-none -ffpe-summary=none

?0?2 L?0?2?0?2 Linker Flags:?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2 
$(FOPT) -L../SRC_lib
?0?2 P?0?2?0?2 Preprocessor flags?0?2?0?2?0?2?0?2?0?2?0?2 '-DParallel'
?0?2 R?0?2?0?2 R_LIBS (LAPACK+BLAS):?0?2?0?2?0?2 -L/home/username/OpenBLAS-0.3.9 
-lopenblas -lpthread

?0?2 F?0?2?0?2 FFTW options:
?0?2?0?2?0?2?0?2?0?2 FFTW-LIBS:
?0?2 X?0?2?0?2 LIBX options:
?0?2?0?2?0?2?0?2?0?2 LIBXC-LIBS:

?0?2 S?0?2?0?2 Save and Quit

?0?2?0?2?0?2?0?2?0?2 To change an item select option.
Selection: S
...
?0?2 Shared Memory Architecture? (y/N):y
?0?2 Do you know/need a command to bind your jobs to specific nodes?
?0?2 (like taskset -c). Enter N / your_specific_command: N
...
?0?2?0?2 (y/N) N
...
?0?2?0?2?0?2?0?2 Selection: Q
...
?0?2?0?2?0?2?0?2 Selection: A
...
Compile time errors (if any) were:


Check file?0?2?0?2 compile.msg?0?2?0?2 in the corresponding SRC_* directory for 
the
compilation log and more info on any compilation problem.
...
?0?2?0

Re: [Wien] Volume has changed during running optimization of c/a with constant volume & b/a

[Gavin Abo]

By volume on the w2web page, are you referring to the estimated actual 
optimized volume (or lattice constants) given by the Equation of State 
fit(s) such as by Birch-Murnaghan seen in the post at [1]? As you have 
probably read in the post [2] or noticed, the case.struct files from "x 
optimize" do not contain the structure parameters for the estimated 
actual optimized volume. Therefore, you have to take the fitted 
structure parameters and enter them in StructGen for example to create 
the optimized struct file unless you specified a very dense set of 
structure changes in "x optimize" around the energy minimum, usually 
pinpointed from a previous "x optimize" using a course set of structure 
changes, in which taking the struct file closest to the minimum 
approximately gives the same parameters as that from a fit.  There was a 
previous example given for one of the cases [3] that might help with 
other cases.  If you know Fortran, I think it was 
SRC_optimize/optimize.f that contained the code on how the input 
structure parameters are changed by "x optimize" to become the output 
struct files.  It your looking for fit results outside of w2web, those 
seem to be found in the case.outputeos* files [4-6]. Hopefully [1-12] 
will be helpful to you on the topic of structure optimization.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16043.html

[2] http://zeus.theochem.tuwien.ac.at/pipermail/wien/2011-June/014835.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10071.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15957.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08565.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14372.html
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02002.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06932.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg02859.html
[10] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09397.html
[11] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17074.html
[12] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17347.html


On 6/12/2020 11:14 PM, shamik chakrabarti wrote:

Dear All,
              I am sending the LiNiNbO4_ca_initial.struct file which 
is obtained after volume optimization with a:b:c =constant. Also I am 
sending LiNiNbO4_ba_initial.struct which is obtained after c/a 
optimization with constant volume and b/a. Both the structures are 
showing same unit cell volume as ~ 2144 bohr^3 as I have obtained in 
my calculation where as the printed volume in the w2web page obtained 
after c/a optimization is  2058.7690 bohr^3 which is different than 
the actual optimized volume we have obtained. Please comment on this.


with regards,


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[Wien] WIEN2k_19.2.tar Missing SRC_lapw1

[Gavin Abo]

Prof. Blaha,

When you have a chance, can you please fix the WIEN2k_19.2.tar in the 
download area of the website?  It seems that some change happened 
recently to it because the SRC_lapw1.tar.gz that used to be there when 
it was extracted from the downloaded file in the past is not there when 
you download it today.


Thanks,

Gavin

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[Wien] libxc 5.0.0

[Gavin Abo]

The libxc website [1] has a new version 5.0.0, but it doesn't compile 
with WIEN2k (version 19.2).  I have linked in libxc 4.3.4 from [2] 
instead.  Does anyone have a patch for using the version 5.0.0?


[1] https://www.tddft.org/programs/libxc/download/

[2] https://www.tddft.org/programs/libxc/download/previous/

Thanks,

Gavin

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Re: [Wien] Xcrysden issues with w2web

[Gavin Abo]

Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html

http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html


Regarding DISPLAY, maybe the following link to a xcrysden mailing list 
post can help:



http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html


On 6/11/2020 2:51 PM, Johnathon Street wrote:
Thank you for the response. That did resolve the issue. I am now 
seeing "Requires X-windows system..." in the view struct portion of 
w2web. I do have an xserver runner, as I am running on Ubuntu. Is 
there a place where I need to set DISPLAY?



*From:* Wien  on behalf of 
Gavin Abo 

*Sent:* Saturday, June 6, 2020 11:05 AM
*To:* wien@zeus.theochem.tuwien.ac.at 
*Subject:* Re: [Wien] Xcrysden issues with w2web

Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>



On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. However, 
I am able to view directly from terminal when typing Xcrysden in 
command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be 
set to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2
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Re: [Wien] Structure relaxation for WO3 with atomic insertion

[Gavin Abo]

In addition to the comments by the others, you might also check for the 
monoclinic if using beta as not equal 90 (where you have beta=90.881 
below) for optimization is okay or not by referring the following link:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html


On 6/14/2020 1:26 PM, Israel Omar Perez Lopez wrote:


Dear Wien2k experts

I am trying to do structure relaxation for WO3 with Li+ insertion for 
three different phases: cubic [SG Pm-3m (221)], hexagonal [SG P6/mmm 
(191)] and monoclinic [SG=P2_1 /n (14)] (no supercell in all cases).


For monoclinic I am working with

a=13.8066, b=14.2485 and c=14.5357, alpha=90, beta=90.881, gamma=90; 
with O1 x=0.284, y=0.2605, z=0.2848; O2 x=0.2827, y=0.0383, z=0.0046; 
O3 x=0.0025, y=0.035, z=0.2106; O4 x=0.2099, y=0.2568, z=0.7318; W1 
x=0.2538, y=0.0353, z=0.7807; W2 x=0.2465, y=0.0269, z=0.2859; O5 
x=0.2856, y=0.4840, z=0.9944; O6 x=0.9974, y=0.4636, z=0.2161; Li


x=y=z=0.5. With RMT for O=1.50, W=1.70 and Li=1.35.


For the initialization I used default parameters except RKmax=6 and a 
k-mesh of 4X4X4 (all atoms were set to nonmagnetic).



To do relaxation I ran optimize with option 7 .This asks for the 
number of structures which I set to 15 and 3% of difference for each 
structure. Then I set the otimize.job script to



min -I -j "run_lapw -I -ec 0.001 -cc 0.001 -fc 5.0 -i 40 -p"


as suggested by L. D. Marks in the optimization notes. The program 
stopped due to an error related to sphere overlapping between O and W. 
I guess this problem is related to a big percentage (3%) so I started 
over, also set 15 structures but 1% of difference with


min -I -j "run_lapw -I -ec 0.001 -cc 0.001 -fc 2.0 -i 40 -p"

This time the following errors showed up after a day of doing 
calculations:



Cholesky INFO = 4263

'SECLR4' - POTRF (Scalapack/LAPACK) failed.


And an error in mini.error

STOP in MINI, FORCES small


I don't know if the first error caused the second one or viceversa. 
What I am doing wrong?



For the hexagonal case I am using this:

a=b=13.7912 Bohr, c=7.3680 Bohr, alpha=beta=90, gamma=120, and 
positions W, x=0.5, y=z=0, O1 x=z=0.5 y=0 and O2 x=0.212, y=0.424 and 
z=0 with RMT values of W=1.7, O=1.5 and Li=1.35. Default initial 
parameters with a k-mesh 4X4X8.



To do relaxation I ran optimize with option 2 (for C/A ratio) and set 
the percentages to (15,7,0,-7,-15)% (before I also tried 12, 6, 0, -6, 
-12 no minimium either, linear distribution), then I set the script 
optimize.job to


min -I -j "run_lapw -I -ec 0.001 -cc 0.001 -fc 5.0 -i 40 -p"

The forces converged but no minimum point was observed in energy vs 
volume, the point distribution was not parabolic although the fitting 
was a parabola. Am I doing something wrong?



For the cubic case I am using a=7.056237 Bohr, W  x=x=z=0 and O x=0.5, 
0, 0. RMT for W=1.83 and O=1.57. Li is inserted at Li 
x=y=z=0.5withRMTLi=1.5. Initialization is with default parameters 
except a k-mesh 4X4X8. Then I run anscfcycle with fc=1.0 but the 
program immediately stops showing up an error reading this:



 LAPW0 END

Force-convergence not possible. Forces not present.
grep: lapw2*.error: No such file or directory

The same happens if I try to run minimization with either mode.


Could you please advice what is the right way to proceed for structure 
relaxation in these three cases? I would appreciate it.




Best regards


Israel



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Re: [Wien] Wien Installation

[Gavin Abo]

Those undefined references, such as _intel_fast_memcpy, are defined in 
an Intel compiler library [1].?0?2 When using Intel compilers 
(ifort/icc/mpiifort), typically mkl is used instead of OpenBLAS as well 
as the Intel MPI Library [2].?0?2 Since you have used the gnu compilers 
(gfortran/gcc) to compile OpenBLAS, WIEN2k, and your flavor of mpi 
(whether that be Open-MPI [3], MVAPICH [4], or another one [5]), most 
likely you need to recompile FFTW3 with your mpi compiler (e.g. [6]) 
based on gfortran/gcc too.



[1] https://software.intel.com/en-us/forums/intel-c-compiler/topic/815696
[2] 
https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html

[3] https://www.open-mpi.org/
[4] http://mvapich.cse.ohio-state.edu/
[5] https://en.wikipedia.org/wiki/MPICH#MPICH_derivatives
[6] https://www.open-mpi.org/faq/?category=mpi-apps#general-build

On 6/15/2020 7:36 PM,  wrote:


Thank you for your details.

Now, there is another problem. In order to generate the lapw0_mpi 
command, when I run ??make para?? in the SRC_lapw0, a part of the errors 
is shown as the following and the whole information is attached:


mpif90 -o ./lapw0_mpi cputim.o modules.o?0?2 W2kinit.o fft_modules.o 
reallocate.o acggac.o 


ylm.o -ffree-form -O2 -ftree-vectorize -march=native 
-ffree-line-length-none -ffpe-summary=none -DFFTW3 
-I/home-yw/Soft/fftw-3.3.8/include -fopenmp -L../SRC_lib -lfftw3_mpi 
-L/home-yw/Soft/fftw-3.3.8/lib -lfftw3 
/home-yw/soft/packagedir/Openblas-0.39/gcc820/lib/libopenblas.so


/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to 
`_intel_fast_memcpy'


/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to 
`_intel_fast_memset'


/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to 
`_intel_fast_memmove'


/home-yw/Soft/fftw-3.3.8/lib/libfftw3_mpi.so: undefined reference to 
`__intel_sse2_strlen'


collect2: error: ld returned 1 exit status

make[1]: *** [lapw0_mpi] Error 1

make[1]: Leaving directory `/home-yg/users/YG_cheny/Soft/19.2/SRC_lapw0'

make: *** [para] Error 2



--?0?2?0?2------
*??:*?0?2"Gavin Abo";
*:*?0?22020??6??8??(??) 8:18
*??:*?0?2"wien";
*:*?0?2Re: [Wien] Wien Installation

In terms of OpenBLAS-0.3.9 libraries, in my OpenBLAS-0.3.9/lib, there 
are several files as the below: libopenblas_nehalemp-r0.3.9.a, 
libopenblas_nehalemp-r0.3.9.so, libopenblas.so, libopenblas.so.0, 
libopenblas.a. Are they as same as yours?
I have the following, but you have the same one named "libopenblas.so" 
that I use.


username@computername:~/WIEN2k$ ls ~/OpenBLAS-0.3.9/*.a 
~/OpenBLAS-0.3.9/*.so

/home/username/OpenBLAS-0.3.9/libopenblas.a
/home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.a
/home/username/OpenBLAS-0.3.9/libopenblas_barcelonap-r0.3.9.so
/home/username/OpenBLAS-0.3.9/libopenblas.so
In addition, are there commands such as lapw0_mpi, lapw1_mpi and 
lapw1c_mpi generated by installing with gfortran+OpenBLAS, just like 
by installing with ifort?
No, the Intel Parallel Studio XE 2020 Cluster Edition has the Intel 
MPI Library [1] that provides intelmpi making it easy to build the 
WIEN2k *_mpi files.?0?2 For gfortran, it can be done but it is extra work 
as one has to install scalapack [2] and MPI (such as OpenMPI [3]) 
separately and then include them in the parallel compiler settings of 
WIEN2k in order to build the files.


[1] 
https://software.intel.com/content/www/us/en/develop/tools/parallel-studio-xe.html

[2] http://www.netlib.org/scalapack/
[3] https://www.open-mpi.org/software/ompi/v4.0/


Then during ./siteconfig_lapw, I choose O to set libraries 
??R_LIBS(LAPACK+BLAS)??, then how to set the ??Real libraries??? Would 
you like to tell me how set the ??Real libraries?? parameter so that 
could obtain the result just like your path for R_LIBS as 
??-L/home/username/OpenBLAS-0.3.9 -lopenblas -llapack_lapw ?Clpthread???


In my setting, I did a couple of tries and obtain three kinds of 
results as below:


1.When I set the R_LIBS such as 
/home/username/OpenBLAS-0.3.9/lib/libopenblas.so (or 
libopenblas.so.0, or libopenblas_nehalemp-r0.3.9.so), then the 
massage is: /usr/bin/ld: warning: libgfortran.so.3, needed by 
/home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas.so, may conflict with 
libgfortran.so.5.


2.When I set the R_LIBS such as /home/username/OpenBLAS-0.3.9/lib or 
/home/username/OpenBLAS-0.3.9, then the massage is: file not 
recognized: Is a directory.


3.When I set he R_LIBS such as ?0?2/home/username/OpenBLAS-0.3.9/lib/ 
libopenblas_nehalemp-r0.3.9.a (or libopenblas.a), then the error 
massage is much, including: 
/home-yw/Soft/OpenBLAS-0.3.9/lib/libopenblas_nehalemp-r0.3.9.a(blas_server.o): 
In function `goto_set_num_threads': blas_server.c:(.text+0x7f3): 
undefined reference to `pthread_create'.


All above relating files were attached.
Attached is copy of my compile.msg 

Re: [Wien] libxc 5.0.0

[Gavin Abo]

Thanks, I made the replacements as you described.


Then, when compiling libxc.F, I got several errors of:


Error: Type mismatch in argument ‘np’ at (1); passed INTEGER(4) to 
INTEGER(8)



The xc function calls such as


call xc_f90_lda_exc_vxc(xc_func,1,rho(1),exc(1),vrho(1))


were not compiling as the integer value 1 with the gfortran compiler was 
defaulting it to INTEGER(4) when it needed to be INTEGER(8).  Following 
https://stackoverflow.com/questions/24405760/fortran-passing-numbers-to-subroutines 
, I defined it to be integer 8:



integer*8 i1
i1 = 1

call xc_f90_lda_exc_vxc(xc_func,i1,rho(1),exc(1),vrho(1))


If your interested in the complete set of changes, they can be seen in a 
text editor by looking at inputpars.patch and libxc.patch files that 
should be at:



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


It is still experimental as I haven't ran any calculations yet (or tried 
compiling it with ifort) to see if there are any run-time errors or 
other problems, but WIEN2k 19.2 with libxc 5.0.0 did compile with 
gfortran successfully as shown below:



username@computername:~/Desktop$ cd ~
username@computername:~$ lsb_release -a
No LSB modules are available.
Distributor ID:    Ubuntu
Description:    Ubuntu 20.04 LTS
Release:    20.04
Codename:    focal
username@computername:~$ gfortran --version
GNU Fortran (Ubuntu 9.3.0-10ubuntu2) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
username@computername:~$ wget 
http://www.tddft.org/programs/libxc/down.php?file=5.0.0/libxc-5.0.0.tar.gz

...
username@computername:~$ tar xvf down.php\?file\=5.0.0%2Flibxc-5.0.0.tar.gz
...
username@computername:~$ cd libxc-5.0.0/
username@computername:~/libxc-5.0.0$ autoreconf -i --force
...
username@computername:~/libxc-5.0.0$ ./configure FC=gfortran CC=gcc 
--prefix=$HOME/libxc-5.0.0

...
username@computername:~/libxc-5.0.0$ make
...
username@computername:~/libxc-5.0.0$ make check
...
PASS: xc-run_testsuite

Testsuite summary for libxc 5.0.0

# TOTAL: 1
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0

...
username@computername:~/libxc-5.0.0$ make install
...
username@computername:~/libxc-5.0.0$ ls ~/libxc-5.0.0/lib
libxc.a  libxcf90.a  libxcf90.la  libxc.la  pkgconfig
username@computername:~/libxc-5.0.0$ cd ~/WIEN2k/SRC_lapw0
username@computername:~/WIEN2k/SRC_lapw0$ wget 
https://github.com/gsabo/WIEN2k-Patches/raw/master/19.2/inputpars.patch

...
username@computername:~/WIEN2k/SRC_lapw0$ patch -b inputpars.F 
inputpars.patch

patching file inputpars.F
username@computername:~/WIEN2k/SRC_lapw0$ wget 
https://github.com/gsabo/WIEN2k-Patches/raw/master/19.2/libxc.patch

...
username@computername:~/WIEN2k/SRC_lapw0$ patch -b libxc.F libxc.patch
patching file libxc.F
username@computername:~/WIEN2k/SRC_lapw0$ cd ..
username@computername:~/WIEN2k$ ./siteconfig
...
  Selection: O
...
Selection: X
...
Selection:RS
...
 Would you like to use LIBXC (that you have installed - usually not 
needed)? (y,N):

y
...
 Do you want to automatically search for LIBXC installations? (Y,n):
Y
 Please specify a comma separated list of directories to search! (If no 
list is entered, /usr/local and /opt will be searched as default):

/home/username/libxc-5.0.0
...
 Pick one of the following (enter the number of the line of your choice 
or 0 to manually specify a path)!:

/home/username/libxc-5.0.0/src/.libs/libxc.a
/home/username/libxc-5.0.0/lib/libxc.a
2
...
Selection:F
Enter the name of your LIBXC fortran interface!: xcf90
...
   Your current LIBXC options are:

   LIBXC_OPT: -DLIBXC -I/home/username/libxc-5.0.0/include
   LIBXC_LIBS:    -L/home/username/libxc-5.0.0/lib -lxcf90 -lxc
...
Selection:B
...
Selection: S
...
  Selection: R
...
 Selection: S
   Which program to recompile? lapw0
...
Compile time errors (if any) were:


Check file   compile.msg   in the corresponding SRC_* directory for the
compilation log and more info on any compilation problem.
...


On 6/13/2020 3:23 PM, Tran, Fabien wrote:


I think that it is enough to replace all "_f03_" by "_f90_" in libxc.F 
and inputpars.F of SRC_lapw0.​




*From:* Wien  on behalf of 
Gavin Abo 

*Sent:* Saturday, June 13, 2020 11:02 PM
*To:* wien@zeus.theochem.tuwien.ac.at
*Subject:* [Wien] libxc 5.0.0

The libxc website [1] has a new version 5.0.0, but it doesn't compile 
with WIEN2k (version 19.2).  I have linked in libxc 4.3.4 from [2] 
instead.  Does anyone have a patch for using the version 5.0.0?


[1] https://www.tddft.org/progr

Re: [Wien] Irrep output file

[Gavin Abo]

I'm not sure that I have the proper answers but given below is what I'm 
currently thinking they might be.
I am trying to extract irreducible representation of eigenvalues. I 
have obtained the case.outputirso and case.irrepso files. But I am not 
sure if I understood these files correctly. The Ci point group has two 
irreducible representations as listed in the file but many of the 
eigenstates are labelled by "??". Am I doing anything wrong?


The 3.99-0.00i  0.00+0.00i for band 109 for E and I values, 
respectively, look very close to 4.00+0.00i 0.00-0.00i for band 105. I 
wondering if perhaps there is some round off error where the ?? might 
indicate that the program was not able to identify a irreducible 
representation label corresponding to 3.99-0.00i  0.00+0.00i (since it 
would need to be 4.00+0.00i 0.00-0.00 to have G2+ + G2+ + G2- + G2- in 
this case).  I'm wondering if that would be effected by your k-mesh.  
Have you tried change it to see if the values change?  There is also a 
tolerance value (TOL variable) in SRC_irrep/wrtir.f that looks like it 
could be adjusted. Though, I would only fiddle with that as a last resort.


 The bands 105 -108 are four-fold degenerate with irrep of the double 
group G2+, G2+,G2-,G2-, respectively, right?


I believe you are right about that.

Also, can anyone please clarify what are the complex numbers under 
operators E and I?


Since in some point groups the characters can be complex [1], I guessing 
the developer for programming simplicity decided to output the results 
always in complex number notation even though in many cases it is only a 
real number.  For your calculation, it appears to be only be a real 
number as the imaginary part is zero (i.e., 0.00i).


[1] 
https://chem.libretexts.org/Courses/Pacific_Union_College/Quantum_Chemistry/12%3A_Group_Theory_-_The_Exploitation_of_Symmetry/12.06%3A_Character_Tables#Irreducible_representations_with_complex_characters



case. outputirso:

       The point group is Ci
       2 symmetry operations in  2 classes
       Table  6   on page  32 in Koster  et al [7]
       Table 11.4 on page 138 in Altmann et al [8]

                           E     I
       G1+   A1g    1     1
       G1-    A1u    1    -1
       
       G2+  A1/2g  1     1
       G2-   A1/2u  1    -1


class, symmetry ops, exp(-i*k*taui)
   E    2             (+1.00 0.00i)
    I    1             (+1.00 0.00i)

bnd ndg  eigval     E                   I
  1  2 -4.675588 1.99+0.00i -1.99-0.00i  ??
  3  2 -4.675572 1.99-0.00i   1.99-0.00i  ??
  5  2 -4.674606 1.98-0.00i  -1.98+0.00i ??
...
...
 97  4 -4.261267 3.97+0.00i -0.00-0.00i  ??
101  4 -4.261167 3.99-0.00i  0.01+0.00i  ??
105  4 -4.260795 4.00-0.00i  0.00+0.00i =G2+ + G2+ + G2- + G2-
109  4 -4.259344 3.99-0.00i  0.00+0.00i ??
113  4 -4.258747 4.00+0.00i  0.00-0.00i =G2+ + G2+ + G2- + G2-
117  4 -4.258715 4.00-0.00i  0.00+0.00i =G2+ + G2+ + G2- + G2-
121  4 -2.13 3.90-0.00i -0.01-0.00i ??
125  4 -2.333098 4.00+0.00i -0.00-0.00i =G2+ + G2+ + G2- + G2-
129  4 -2.332321 3.93+0.00i -0.02+0.00i ??

The corresponding bands in the case.irrepso file:

       104         4  -4.261165    0  0    0  0    0  0    0  0
       105         4  -4.260795    2  1    2  1   -2  1 -2  1
       106         4  -4.260795    2  1    2  1   -2  1 -2  1
       107         4  -4.260791    2  1    2  1   -2  1 -2  1
       108         4  -4.260791    2  1    2  1   -2  1 -2  1
       109         4  -4.259344    0  0    0  0    0  0  0  0
       110         4  -4.259344    0  0    0  0    0  0  0  0


What are the numbers in column 4-7?


In case. outputirso for band 105, there is:

G2+ + G2+ + G2- + G2-

In case.irrepso for band 105, there is:

2  1 2  1 -2  1 -2  1

The columns 4 & 5, 6 & 7, 8 & 9, and 10 & 11 might correspond to 
irreducible representation numbers that correspond with the labels 
(e.g., G2+ with 2 1 and G2- with -2 1).


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Re: [Wien] Wien Installation

[Gavin Abo]

Below it looks like the compiler shows you exactly what is wrong:

/usr/bin/ld: cannot find -llibscalapack.a

Most likely either the

SCALAPACK_LIBNAME: libscalapack.a

needs changed to use the dynamic scalapack library

SCALAPACK_LIBNAME: scalapack

to have -lscalapack or you might have to try to leave it blank to use 
the static scalapack library


/home/username/scalapack-2.1.0/libscalapack.a

seen in your output.


On 6/22/2020 3:43 AM,  wrote:


Thank you for your reply.

I am installing wien version 19.2 on Linux with gfortran and OpenBlas.

In the ??Specify ScaLAPACK settings??, I would like to know how to set 
the part of ??Please specify the target architecture of your ScaLAPACK 
libraries (e.g. intel64)!:??.


In addition, when the settings are as the following, there are some 
errors.


Settings:

SCALAPACKROOT:/home/username/scalapack-2.1.0/

SCALAPACK_LIBNAME: libscalapack.a

BLACSROOT: /home/username/BLACS/LIB

BLACS_LIBNAME: blacs_MPI-LINUX-0.a

MKL_TARGET_ARCH: /home/username/scalapack-2.1.0/libscalapack.a

Some errors:

-ftree-vectorize -march=native -ffree-line-length-none 
-ffpe-summary=none -DFFTW3 
-I/home-yg/users/YG_cheny/Soft/fftw-3.3.6-pl2/gcc820/include -fopenmp 
-L../SRC_lib -L/home-yg/users/YG_cheny/Soft/fftw-3.3.6-pl2/gcc820/lib 
-lfftw3?0?2?0?2/home-yw/soft/packagedir/Openblas-0.39/gcc820/lib/libopenblas.so 
-L/home-yg/users/YG_cheny/Soft/scalapack-2.1.0//home-yg/users/YG_cheny/Soft/scalapack-2.1.0/libscalapack.a 
-llibscalapack.a 
-L/home-yg/users/YG_cheny/Soft/BLACS/LIB//home-yg/users/YG_cheny/Soft/scalapack-2.1.0/libscalapack.a-lblacs_MPI-LINUX-0.a 


/usr/bin/ld: cannot find -llibscalapack.a
collect2: error: ld returned 1 exit status
make[1]: *** [hfc_mpi] Error 1
make[1]: Leaving directory `/home-yg/users/YG_cheny/Soft/19.2/SRC_hf'
make: *** [cp] Error 2

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Re: [Wien] Query regarding structure optimization

[Gavin Abo]

The WIEN2k 19.1 usersguide [1] on page 67 under section 5.1.4 has:

-dm   ->    calculate the density matrix (when -so is set, but -orb 
is not)


That seems to indicate that the -dm needs -so to work (e.g., runsp_lapw 
-dm -so).  If you use "runsp_lapw -dm -orb", the program will probably 
ignore the -dm switch and run fine. However, if you care about proper 
usage it would seem to be "runsp -orb" without the -dm based on that 
description in the usersguide.


On 21 June 2020, it looks like it was advised in the post [2] to use 
-min [3,4].  Based on that, you might want to reconsider your use of the 
min_lapw optimize.job line (min -I -j "run_lapw -I -fc 1.0 -i 40 ") in 
your email below.


It looks like it would be fine to use for -orb [5,6] and spin 
polarization, in optimize.job for simultaneous optimization of lattice 
parameters and atomic positions [7], the following line:


runsp_lapw -orb  -ec 0.0001 -cc 0.01 -fc 1 -min

However, if you encounter convergence problems, you might have to take 
the advice [8,9] to try a crude convergence followed by a more refined 
convergence such as:


runsp_lapw -orb -ec 0.1 -cc 0.01 -fc 4
save_lapw -d ${i}PreMin
runsp_lapw -orb -ec 0.0001 -cc 0.001 -fc 1 -min

[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20232.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13712.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18055.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18844.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19278.html
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18071.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17228.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18069.html


On 6/22/2020 7:40 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                              Whether this is the correct approach for 
editing optimize.job to run simultaneous force optimization with *-dm 
-orb and spin polarization* *on*;


                runsp_lapw -dm -orb -ec 0.0001

      min -I -j "run_lapw -I -fc 1.0 -i 40 "

 #    run_lapw -ec 0.0001   # -p -it -cc 0.01 -fc 1 -min

Looking forward to your response in this regard.

with regards,

On Sun, 21 Jun 2020 at 18:45, shamik chakrabarti 
mailto:shamik15041...@gmail.com>> wrote:


Should I edit the optimize.job file by the following way;

 runsp_lapw -dm -orb  -ec 0.0001 -cc 0.01 -fc 1 -min

to run simultaneous optimization of force with -dm -orb switch on

On Sun, 21 Jun 2020 at 13:16, shamik chakrabarti
mailto:shamik15041...@gmail.com>> wrote:

Thank you Sir. Your advice will be helpful.

With regards ,

On Sun, Jun 21, 2020, 12:50 Peter Blaha
mailto:pbl...@theochem.tuwien.ac.at>> wrote:

YES ! Force optimization is MUCH more important than
anything else.
Lattice parameters are usually well known from experiment
(and more
accurate than DFT), but atomic positions are often NOT
well known
experimentally.

Exception: Some structures like NaCl have "fixed positions
by symmetry".
So you have to find out yourself, if you have forces.

How to do:   Simply edit optimize.job and activate the
-min switch in
the run_lapw line.

ad 2): If your minimum is close enough to one of your
relaxed structures: no
However, whenever you change a,b or c, do a force
optimization.

On 6/21/20 9:01 AM, shamik chakrabarti wrote:
> Dear Wien2k users,
>
>         I have two queries;
>
> (1) Should we have to do force minimization
*simultaneously* for each
> step (a) V optimization, (b) c/a optimization, (c) b/a
optimization for
> a orthorhombic crystal?
>
> (2) After a, b, c optimization should we have to do
force minimization
> again? (I think yes!)
>
> with regards,
>
> --
> Dr. Shamik Chakrabarti
> Research Fellow
> Department of Physics
> Indian Institute of Technology Patna
> Bihta-801103
> Patna
> Bihar, 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
  

Re: [Wien] Xcrysden issues with w2web

[Gavin Abo]

As was already hinted at in [1], if you need more help, you probably 
need describe better what you system(s) configuration is like such as 
are you only using w2web and xcrysden in Ubuntu locally (physical Linux 
box or in a virtual machine) or are you connecting to them remotely?



If you have defined $DISPLAY, w2web might just pick that up.  If you 
know Perl, I suggest you have a look at 
$WIENROOT/SRC_w2web/htdocs/util/viewcrys.pl.



The xserver that you mentioned, is it setup for X11 forwarding?  If you 
are not using w2web locally with an offline setup [2], but are instead 
using an online setup were w2web is connected to the internet (or a 
local network) and is unable to get xcrysden to open in w2web, are you 
able to get it to open instead using an ssh connection with X11 
forwarding?  Refer to [3,4].



[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20243.html


[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01124.html


[3] 
http://sites.science.oregonstate.edu/~tatej/COURSES/ph575/doku.php?id=xcrysden


[4] https://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf


On 6/22/2020 2:21 PM, Johnathon Street wrote:
When typing echo $DISPLAY into the terminal I am seeing :0. I still 
continue to see "requires X-Windows System..." when I try to view the 
crystal in w2web. Is there a way to set the DISPLAY variable inside 
the w2web process so that it may work there as well. Where do you 
recommend I set DISPLAY?


Thank you

*From:* Wien  on behalf of 
Gavin Abo 

*Sent:* Saturday, June 13, 2020 4:55 PM
*To:* wien@zeus.theochem.tuwien.ac.at 
*Subject:* Re: [Wien] Xcrysden issues with w2web

Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEkzRTEgp$>


http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html 
[democritos.it] 
<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpElJMWCG9$>



Regarding DISPLAY, maybe the following link to a xcrysden mailing list 
post can help:



http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html 
[democritos.it] 
<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEmZACKf6$>



On 6/11/2020 2:51 PM, Johnathon Street wrote:
Thank you for the response. That did resolve the issue. I am now 
seeing "Requires X-windows system..." in the view struct portion of 
w2web. I do have an xserver runner, as I am running on Ubuntu. Is 
there a place where I need to set DISPLAY?



*From:* Wien  
<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Gavin 
Abo  <mailto:gs...@crimson.ua.edu>

*Sent:* Saturday, June 6, 2020 11:05 AM
*To:* wien@zeus.theochem.tuwien.ac.at 
<mailto:wien@zeus.theochem.tuwien.ac.at> 
 
<mailto:wien@zeus.theochem.tuwien.ac.at>

*Subject:* Re: [Wien] Xcrysden issues with w2web

Most likely you just need to kill and restart w2web.


Refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$>


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html 
[mail-archive.com] 
<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$>



On 6/6/2020 11:49 AM, Johnathon Street wrote:
I unable to view crystal with Xcrysden in w2web environment. 
However, I am able to view directly from terminal when typing 
Xcrysden in command line. I have found through the mailing list that 
XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be 
set to. Any help would be appreciated. I am running WIEN2k_19.2 and 
Xcrysden version 1.6.2.

Current Directory
 XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2
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Re: [Wien] Anti-ferromagnetism in FeO

[Gavin Abo]

If a struct file fails during initialization (init_lapw), it is very 
likely that it will fail and not work during the scf.  Your failed error 
during the scf seems to be proof of that as during init_lapw your struct 
file seems to fail right away during the nn step with errors "Mult not 
equal. PLEASE CHECK outputnn-file":


username@computername:~/wiendata/FeO_V$ ls -l FeO_V.struct
-rw-r--r-- 1 username username 6781 Jun 23 14:14 FeO_V.struct
username@computername:~/wiendata/FeO_V$ init_lapw -s nn
 next is nn
 next is nn
>   nn    (20:25:10)  specify nn-bondlength factor: (usually=2) [and 
optionally dlimit, dstmax (about 1.d-5, 20)]

2
 DSTMAX:   20.000
 iix,iiy,iiz   4   4   4 
31.6151201    31.6151201 31.6151201


    ATOM  1  Fe ATOM  8  O
 RMT(  1)=2.06000 AND RMT(  8)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  2  Fe ATOM  5  O
 RMT(  2)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  3  Fe ATOM  5  O
 RMT(  3)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  4  Fe ATOM  5  O
 RMT(  4)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  5  O  ATOM  2  Fe
 RMT(  5)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  6  O  ATOM  3  Fe
 RMT(  6)=1.77000 AND RMT(  3)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  7  O  ATOM  2  Fe
 RMT(  7)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  8  O  ATOM  2  Fe
 RMT(  8)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file

  NN created a new FeO_V.struct_nn file
STOP NN created a new CASE.STRUCT_NN FILE
0.0u 0.0s 0:01.72 1.1% 0+0k 0+72io 0pf+0w
-> check in  FeO_V.outputnn  for overlapping spheres,
   coordination and nearest neighbor distances
nn has created a new struct file with different multiplicities

On 6/23/2020 8:27 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                              I want to simulate antiferromagnetism in 
FeO. For that I have created a struct file (attached in the mail) in 
which the nearest neighbour Fe are presented as inequivalent atoms. I 
have edited the case.inst file and flip the spin of  nearest neighbour 
Fe atoms. I have also added U = 5eV for all the Fe (4 in numbers) 
atoms. During volume optimization I got the following error


 cycle 1 (Tue Jun 23 19:44:11 IST 2020) (40/99 to go)

>   lapw0   (19:44:11) 12.4u 0.1s 0:06.79 185.7% 0+0k 0+6072io 0pf+0w
>   lapw1  -up   -orb   (19:44:18) 42.8u 20.6s 0:24.38 260.2% 0+0k 
0+41480io 0pf+0w
>   lapw1  -dn   -orb   (19:44:42) 44.7u 19.3s 0:19.66 326.1% 0+0k 
0+41440io 0pf+0w
>   lapw2 -up       -orb (19:45:02) 0.0u 0.0s 0:00.02 300.0% 0+0k 
0+8io 0pf+0w

error: command   /usr/local/Wien2k/lapw2 uplapw2.def   failed

>   stop error

The case.output2up & case.scf2up are empty.

Thanks in advance.

with regards,
--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Anti-ferromagnetism in FeO

[Gavin Abo]

Probably you need to use special labels like that described on the 
webpage at:


http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html


On 6/24/2020 2:28 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                             If I accept the new struct file created 
by nn I am not able to model AFM order. what to do?


Looking forward to hearing from you.

with regards,

On Wed, 24 Jun 2020 at 08:01, Gavin Abo <mailto:gs...@crimson.ua.edu>> wrote:


If a struct file fails during initialization (init_lapw), it is
very likely that it will fail and not work during the scf.  Your
failed error during the scf seems to be proof of that as during
init_lapw your struct file seems to fail right away during the nn
step with errors "Mult not equal. PLEASE CHECK outputnn-file":

username@computername:~/wiendata/FeO_V$ ls -l FeO_V.struct
-rw-r--r-- 1 username username 6781 Jun 23 14:14 FeO_V.struct
username@computername:~/wiendata/FeO_V$ init_lapw -s nn
 next is nn
 next is nn
>   nn    (20:25:10)  specify nn-bondlength factor: (usually=2)
[and optionally dlimit, dstmax (about 1.d-5, 20)]
2
 DSTMAX:   20.000
 iix,iiy,iiz   4   4   4
31.6151201    31.6151201 31.6151201

    ATOM  1  Fe ATOM  8  O
 RMT(  1)=2.06000 AND RMT(  8)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  2  Fe ATOM  5  O
 RMT(  2)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  3  Fe ATOM  5  O
 RMT(  3)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  4  Fe ATOM  5  O
 RMT(  4)=2.06000 AND RMT(  5)=1.77000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  5  O  ATOM  2  Fe
 RMT(  5)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  6  O  ATOM  3  Fe
 RMT(  6)=1.77000 AND RMT(  3)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  7  O  ATOM  2  Fe
 RMT(  7)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189

    ATOM  8  O  ATOM  2  Fe
 RMT(  8)=1.77000 AND RMT(  2)=2.06000
 SUMS TO 3.83000  LT.  NN-DIST= 3.95189
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
 WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file

  NN created a new FeO_V.struct_nn file
STOP NN created a new CASE.STRUCT_NN FILE
0.0u 0.0s 0:01.72 1.1% 0+0k 0+72io 0pf+0w
-> check in  FeO_V.outputnn  for overlapping spheres,
   coordination and nearest neighbor distances
nn has created a new struct file with different multiplicities

On 6/23/2020 8:27 AM, shamik chakrabarti wrote:

Dear Wien2k users,
                              I want to simulate
antiferromagnetism in FeO. For that I have created a struct file
(attached in the mail) in which the nearest neighbour Fe are
presented as inequivalent atoms. I have edited the case.inst file
and flip the spin of  nearest neighbour Fe atoms. I have also
added U = 5eV for all the Fe (4 in numbers) atoms. During volume
optimization I got the following error

 cycle 1 (Tue Jun 23 19:44:11 IST 2020) (40/99 to go)

>   lapw0   (19:44:11) 12.4u 0.1s 0:06.79 185.7% 0+0k 0+6072io 0pf+0w
>   lapw1  -up   -orb   (19:44:18) 42.8u 20.6s 0:24.38 260.2%
0+0k 0+41480io 0pf+0w
>   lapw1  -dn   -orb   (19:44:42) 44.7u 19.3s 0:19.66 326.1%
0+0k 0+41440io 0pf+0w
>   lapw2 -up       -orb (19:45:02) 0.0u 0.0s 0:00.02 300.0% 0+0k
0+8io 0pf+0w
error: command   /usr/local/Wien2k/lapw2 uplapw2.def failed

>   stop error

The case.output2up & case.scf2up are empty.

Thanks in advance.

with regards,
-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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Re: [Wien] Mpirun Errors

[Gavin Abo]

Yu,

In addition to the usersguide [1] describing use of "run_lapw -p" along 
with an appropriately set up .machines file, don't forget about the 
WIEN2k-notes of the University of Texas [2], the workshop video on 
Parallelization [3], and mailing list archive for previous posts on the 
topic of mpi parallelization (for example [4-10] are just a few of the 
many posts existing in the archive).


[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html
[3] http://susi.theochem.tuwien.ac.at/onlineworkshop/
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08702.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg00985.html
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18967.html
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13632.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15984.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05622.html
[10] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html
[11] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17627.html


Kind Regards,

Gavin

On 7/5/2020 9:02 PM, Laurence Marks wrote:
Please carefully read the user guide -- "mpirun -np 4 run_lapw" is not 
how it works.


Also, to use mpi you need scalapack, which you did not mention. If you 
only have 4 cores you do not want to use mpi.

_
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 Sun, Jul 5, 2020, 21:57 晨晨 mailto:chin...@qq.com>> 
wrote:


Dear W2k developers and users,

  The wien2k version is 19.2 on Linux with gfortran, OpenBlas and
openmpi. Now executing parallel run_lapw occurs errors.

When I run the command “run_lapw”, there is not any error. When I
run the command “mpirun -np 4 run_lapw”, there are some errors. I
have tested the openmpi installed successfully.

1. The following error occurs when running run_LAPW in parallel on
four processors：

[YG_cheny@yg TiC]$ mpirun -np 4 run_lapw

STOP  LAPW0 END

STOP  LAPW0 END

mv: cannot move `.tmp' to `TiC.dayfile': No such file or directory

STOP  LAPW0 END

STOP  LAPW0 END

printf: write error: No such file or directory

>   stop error

---

Primary job terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

---

>   stop error

--

mpirun detected that one or more processes exited with non-zero
status, thus causing

the job to be terminated. The first process to do so was:

 Process name: [[45157,1],1]

   Exit code: 9

2. Since the file TiC. Dayfile exists, I ran the DOS2UNIX command
in order to solve the problem. Then, "No such File or Directory"
message disappeared.

3.However, run the command “mpirun -np 4 run_lapw”again and the
following error message still appears:

[YG_cheny@yg TiC]$ mpirun -np 4 run_lapw

STOP  LAPW0 END

STOP  LAPW0 END

STOP  LAPW0 END

>   stop error

---

Primary job terminated normally, but 1 process returned

a non-zero exit code. Per user-direction, the job has been aborted.

---

>   stop error

--

mpirun detected that one or more processes exited with non-zero
status, thus causing

the job to be terminated. The first process to do so was:

  Process name: [[46028,1],3]

  Exit code:    9

--

Sincerely yours Yu

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Re: [Wien] Ghost band error

[Gavin Abo]

Probably you need to mention how you handled the core leakage issue 
during initialization (init_lapw) of WIEN2k 19.2 since if that was not 
addressed it might lead to the QTL error later during the scf:


username@computername:~/wiendata/Li2NiPO4F_check$ ls
Li2NiPO4F_check.struct
username@computername:~/wiendata/Li2NiPO4F_check$ init_lapw -s lstart
 next is lstart
 next is lstart
 CREATE A NEW Li2NiPO4F_check.inst FILE with PROPER ATOMS
 If necessary specify switches for instgen_lapw (or press ENTER):
 -up (default)   -dn   -nm (non-magnetic)   -ask
-nm
 15 Atoms found:  with labels Li   Li   Li   Ni   Ni   P    P O    O    
O    O    O    O    F    F

generate atomic configuration for atom 1 : Li
generate atomic configuration for atom 2 : Li
generate atomic configuration for atom 3 : Li
generate atomic configuration for atom 4 : Ni
generate atomic configuration for atom 5 : Ni
generate atomic configuration for atom 6 : P
generate atomic configuration for atom 7 : P
generate atomic configuration for atom 8 : O
generate atomic configuration for atom 9 : O
generate atomic configuration for atom 10 : O
generate atomic configuration for atom 11 : O
generate atomic configuration for atom 12 : O
generate atomic configuration for atom 13 : O
generate atomic configuration for atom 14 : F
generate atomic configuration for atom 15 : F
>   lstart    (08:05:05)   SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
   LDA    [( 5)]
   WC [(11)  GGA of Wu-Cohen 2006]
   PBESOL [(19) GGA of Perdew etal. 2008]
13
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

-6.0
STOP LSTART ENDS
3.9u 0.0s 0:10.78 37.1% 0+0k 0+11808io 0pf+0w
WARNING:   0.038 P    CORE electrons leak out of MT-sphere 
:WARNING: 0.038  P    CORE electrons leak out of MT-sphere 
:WARNING: touch .lcore and run scf-cycle with core density superposition
:WARNING: Or: rerun lstart with lower E-core separation energy
:WARNING: ORBITAL:  2P*    -9.194    -9.194
:WARNING: ORBITAL:  2P -9.126    -9.126
WARNING:   0.038 P    CORE electrons leak out of MT-sphere 
   check Li2NiPO4F_check.outputst how much core charge leaks out
   if you continue, file .lcore will be created and the scf-cycle
   will be run with core-density superposition
   alternatively you can rerun lstart with a smaller ECORE
-> continue with kgen or edit the Li2NiPO4F_check.inst file and 
rerun lstart (c/e)


On 7/12/2020 7:38 AM, shamik chakrabarti wrote:

Dear Wien2k users,

                           I am trying to run a calculation of 72 
atomic unit cell & it shows Ghost band error at the first iteration.


In SCF2 file the following line indicates the error;

:WARN : QTL-B value eq.9283.65 in Band of energy  -3.30070  ATOM=    7 
 L=  0


:WARN : You should change the E-parameter for this atom and L-value in 
case.in1 (or try the -in1new switch)



I am attaching the struct file herewith this mail.

Looking forward to hearing from you.

with regards,
--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Ghost band error

[Gavin Abo]

It might only show that in a terminal.  Are you using w2web, are the 
warnings in the Li2NiPO4F_check.outputst file?


1. In w2web, click on "command line" under Execution in the left menu.

2. In the "Execute a command line" box, type: grep WARNING *.outputst

3. Click the Run button

Does it show any "CORE electron leak out of MT-sphere" warnings then?

Try referring to screenshots in temporary file 
at:https://drive.google.com/file/d/1CwHww6U2ChMU2QtxqtLga5lMpIJ6sGIB/view?usp=sharing


On 7/12/2020 9:07 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                      I am using  wien 2k 19.1 & surprisingly I am not 
getting any error regarding core-leakage. (I have kept initial 
reduction of RMT to 0%) The output is as given below.

Commandline: x lstart -up
Program input is: "13 -6.0 "

  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
               LDA    [( 5)]
               WC     [(11)  GGA of Wu-Cohen 2006]
               PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to 
select core state

STOP LSTART ENDS
1.4u 0.0s 0:01.45 100.0% 0+0k 0+11872io 0pf+0w

& during 1st iteration, it is showing the ghost band error

with regards,

On Sun, 12 Jul 2020 at 19:49, Gavin Abo <mailto:gs...@crimson.ua.edu>> wrote:


Probably you need to mention how you handled the core leakage
issue during initialization (init_lapw) of WIEN2k 19.2 since if
that was not addressed it might lead to the QTL error later during
the scf:

username@computername:~/wiendata/Li2NiPO4F_check$ ls
Li2NiPO4F_check.struct
username@computername:~/wiendata/Li2NiPO4F_check$ init_lapw -s lstart
 next is lstart
 next is lstart
 CREATE A NEW Li2NiPO4F_check.inst FILE with PROPER ATOMS
 If necessary specify switches for instgen_lapw (or press ENTER):
 -up (default)   -dn   -nm (non-magnetic)   -ask
-nm
 15 Atoms found:  with labels Li   Li   Li   Ni   Ni P    P   
O    O    O    O    O    O    F    F
generate atomic configuration for atom 1 : Li
generate atomic configuration for atom 2 : Li
generate atomic configuration for atom 3 : Li
generate atomic configuration for atom 4 : Ni
generate atomic configuration for atom 5 : Ni
generate atomic configuration for atom 6 : P
generate atomic configuration for atom 7 : P
generate atomic configuration for atom 8 : O
generate atomic configuration for atom 9 : O
generate atomic configuration for atom 10 : O
generate atomic configuration for atom 11 : O
generate atomic configuration for atom 12 : O
generate atomic configuration for atom 13 : O
generate atomic configuration for atom 14 : F
generate atomic configuration for atom 15 : F
>   lstart    (08:05:05)   SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
   LDA    [( 5)]
   WC [(11)  GGA of Wu-Cohen 2006]
   PBESOL [(19) GGA of Perdew etal. 2008]
13
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out of
MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97 and
1.0) to select core state
-6.0
STOP LSTART ENDS
3.9u 0.0s 0:10.78 37.1% 0+0k 0+11808io 0pf+0w
WARNING:   0.038 P    CORE electrons leak out of MT-sphere 
:WARNING: 0.038  P    CORE electrons leak out of MT-sphere 
:WARNING: touch .lcore and run scf-cycle with core density
superposition
:WARNING: Or: rerun lstart with lower E-core separation energy
:WARNING: ORBITAL:  2P*    -9.194    -9.194
:WARNING: ORBITAL:  2P -9.126    -9.126
WARNING:   0.038 P    CORE electrons leak out of MT-sphere 
   check Li2NiPO4F_check.outputst how much core charge leaks out
   if you continue, file .lcore will be created and the scf-cycle
   will be run with core-density superposition
   alternatively you can rerun lstart with a smaller ECORE
-> continue with kgen or edit the Li2NiPO4F_check.inst file
and rerun lstart (c/e)

On 7/12/2020 7:38 AM, shamik chakrabarti wrote:

Dear Wien2k users,

                           I am trying to run a calculation of 72
atomic unit cell & it shows Ghost band error at the first iteration.

In SCF2 file the following line indicates the error;

:WARN : QTL-B value eq.9283.65 in Band of energy  -3.30070  ATOM=
   7  L=  0

:WARN : You should change the E-parameter for this atom and
L-value in case.in1 (or try the -in1new switch)


I am attaching the struct file herewith this mail.

Looking forward to hearing from you.

wi

Re: [Wien] Ghost band error

[Gavin Abo]

I would suggest referring to previous advice given in the mailings list.

For example, there are different ways in which core leakage might need 
to be addressed:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19495.html

You might try swapping the RMT of O and P atoms:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18031.html

Li 1.56
Ni 2.05
P 1.36
O 1.52
F 1.88

Since your RMT of Li, Ni, P, O, and F are of various sizes and some are 
on the side of being small, you probably have one of those calculations 
that more difficult to setup and converge:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09842.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11853.html

This might be common problem [ 
http://susi.theochem.tuwien.ac.at/reg_user/faq/qtlb.html ] when working 
with structures having P with a small RMT:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01534.html

If I read correctly, -9.2 instead -6.0 as the separation energy in 
lstart and removal of a second l=0 line in case.in1 for handling P with 
a small RMT was used in the thread of posts at:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11933.html


On 7/12/2020 11:24 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                         I am sorry for the previous reply. Yes, 
after,  grep WARNING *.outputs the following warnings appeared


WARNING:   0.038 P    CORE electrons leak out of MT-sphere 
:WARNING:     0.038  P    CORE electrons leak out of MT-sphere 
:WARNING: touch .lcore and run scf-cycle with core density superposition
:WARNING: Or: rerun lstart with lower E-core separation energy
:WARNING:     ORBITAL:  2P*    -9.172    -9.141
:WARNING:     ORBITAL:  2P     -9.104    -9.074
WARNING:   0.038 P    CORE electrons leak out of MT-sphere 

Should I go for touch .lcore now...

with regards,

On Sun, 12 Jul 2020 at 21:48, shamik chakrabarti 
mailto:shamik15041...@gmail.com>> wrote:


I am using w2web. After following your suggestion, I got the
following message in w2web page.

 Commandline: : grep WARNING *.outputst
Program input is: ""


Execute another command line:


Type of execution:

Also, in case.outputst there is no warning message displayed.

with regards,

On Sun, 12 Jul 2020 at 21:30, Gavin Abo mailto:gs...@crimson.ua.edu>> wrote:

It might only show that in a terminal.  Are you using w2web,
are the warnings in the Li2NiPO4F_check.outputst file?

1. In w2web, click on "command line" under Execution in the
left menu.

2. In the "Execute a command line" box, type: grep WARNING
*.outputst

3. Click the Run button

Does it show any "CORE electron leak out of MT-sphere"
warnings then?

Try referring to screenshots in temporary file

at:https://drive.google.com/file/d/1CwHww6U2ChMU2QtxqtLga5lMpIJ6sGIB/view?usp=sharing

On 7/12/2020 9:07 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                      I am using  wien 2k 19.1 & surprisingly
I am not getting any error regarding core-leakage. (I have
kept initial reduction of RMT to 0%) The output is as given
below.
Commandline: x lstart -up
Program input is: "13 -6.0 "

  SELECT XCPOT:
  recommended: PBE    [(13) GGA of Perdew-Burke-Ernzerhof 96]
               LDA    [( 5)]
               WC     [(11)  GGA of Wu-Cohen 2006]
               PBESOL [(19) GGA of Perdew etal. 2008]
  SELECT ENERGY to separate core and valence states:
  recommended: -6.0 Ry (check how much core charge leaks out
of MT-sphere)
  ALTERNATIVELY: specify charge localization (between 0.97
and 1.0) to select core state
STOP LSTART ENDS
1.4u 0.0s 0:01.45 100.0% 0+0k 0+11872io 0pf+0w

& during 1st iteration, it is showing the ghost band error

with regards,

On Sun, 12 Jul 2020 at 19:49, Gavin Abo mailto:gs...@crimson.ua.edu>> wrote:

Probably you need to mention how you handled the core
leakage issue during initialization (init_lapw) of WIEN2k
19.2 since if that was not addressed it might lead to the
QTL error later during the scf:

username@computername:~/wiendata/Li2NiPO4F_check$ ls
Li2NiPO4F_check.struct
username@computername:~/wiendata/Li2NiPO4F_check$
init_lapw -s lstart
 next is lstart
 next is lstart
 CREATE A NEW Li2NiPO4F_check.inst FILE with PROPER ATOMS
 If necessary specify switches for instgen_lapw (or press
ENTER):
 -up (default)   -dn   -nm (non-magnetic) -ask
-nm
 15 Atoms found:  with labels Li

Re: [Wien] write_inwf syntaxerror

[Gavin Abo]

The write_inwf_lapw script was buggy in versions, such as WIEN2k 17.1 
[1], that came before WIEN2k 19.1 as shown on the WIEN2k updates page 
[2] by:


*VERSION_19.1: 17.6.2019*

*write_inwf_lapw**:* update for spinpolarization

It is recommended to use WIEN2k 19.2.  You may also want to apply the 
modules_rc.patch for WIEN2k 19.2 that should be available at [3] if you 
need more than 1000 bands with wien2wannier.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16099.html

[2] http://susi.theochem.tuwien.ac.at/reg_user/updates/
[3] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.2


On 7/22/2020 7:34 AM, Aaron Jung wrote:

Dear developer and users,


Hello,
I am performing the DFT calculation using wien2k v17.1.

For Wannierized calculation,
I have a problem.

When run write_inwf_lapw, there is an error message like below,

write_inwf_lapw

File "/home/Programs/wien2k/wien2k_v17.1/intel-18/write_inwf_lapw", 
line 58


return np.array([float (s) for s in l[12:22], l[25:35], l[38:48]])

^

SyntaxError: invalid syntax

How can I solve the problem?
Please give a comment.

Thanks,
Myung-Chul.
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Re: [Wien] Space group change during running x sgroup

[Gavin Abo]

View case.struct of the supercell in StructGen of w2web.  If the 
supercell has a space group, it will show what it is.  If it has no 
space group, it should instead have a general lattice highlighted such 
as "P".


The WIEN2k 19.1 usersguide [1] states on page 110 under section "6.2 
SGROUP":


/This program uses information from case.struct (lattice type, lattice 
constants, atomic positions)//

//and determines the spacegroup .../

From the above statement, you can probably derive that a purpose of the 
sgroup program is to take a case.struct as input having a structure 
defined in a general lattice having an unknown spacegroup and gives as 
output what space group fits the structure.  Therefore, the space group 
should be displayed after clicking "x sgroup" button in w2web or should 
be found in the case.outputsgroup file.


Since Phonopy can only parse space group 1_P1 as input [2], the output 
case.struct files from it are probably general P lattice that would also 
have space group 1_P1.  Phonopy might not add the space group or special 
labels in the output case.struct files.  If so, the special labels may 
need to be added manually (based on [3]) to all atoms so that "x sgroup" 
finds space group 1_P1 else it might reduce the cell to one with higher 
symmetry.


The triclinic space group P1 [4] has the lowest symmetry were there are 
no restrictions on the values of the cell parameters [5] in which it 
should have the advantage that any structure is definable in it.  The 
disadvantage that comes from that is it computationally extensive for 
WIEN2k calculations which is probably not surprising with a higher 
number of inequivalent positions compared to if you were able to group 
atomic positions into sets of equivalent position to make use of 
symmetry [6,7]. Typically WIEN2k users are interested in comparing a 
structure with slight parameter changes [9,10] in which a change in 
basis vectors of the structure [10] would be undesirable.


So, you would need to use your crystallographic knowledge to use "x 
sgroup" as to not have GIGO [11] that you may have learned such as be 
reading the Volumes on International Tables for Crystallography [12].


Bilbao Crystallographic Server's Subgroups might also be of interest 
because at [13] it mentions it can list other compatible space groups 
for a supercell.



[1] http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14219.html

[3] http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
[4] 
https://en.wikipedia.org/wiki/Space_group#Table_of_space_groups_in_3_dimensions

[5] http://xrayweb.chem.ou.edu/notes/symmetry.html
[6] http://chemistry.bd.psu.edu/jircitano/6symmetry.pdf
[7] 
https://www.mindat.org/article.php/2721/Determining+Symmetry+of+Crystals%3A+An+Introduction+
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20318.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14836.html
[10] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16765.html

[11] https://en.wikipedia.org/wiki/Garbage_in,_garbage_out
[12] https://it.iucr.org/
[13] https://www.cryst.ehu.es/cgi-bin/cryst/programs/subgrmag1_cell.pl

On 7/24/2020 6:55 PM, Peeyush Kumar Kamlesh wrote:

Sir,
One more question. How can I know the space group of the supercell? I 
searched but was unable to find it.

Thank you!
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Re: [Wien] Mailing List

[Gavin Abo]

If your case.struct file has one Mn atom corresponding to one 
inequivalent atomic position that has multiple equivalent atomic 
positions where you want to split the equivalent atomic positions into 
inequivalent ones, then you need to use the "set at least for one 
atom-name a special label" at [1].


There are different approaches that should work to split atoms: 1) Use 
WIEN2k's StructGen, select appropriate general lattice and use split, 2) 
Use WIEN2k's "x supercell", 3) Use WIEN2k's structeditor, or 4) Use 
another crystal maker program compatible with WIEN2k (e.g. Crystal Maker 
imports WIEN2k struct files and outputs cif according to their webpage 
at [2], and WIEN2k's cif2struct can likely be used to convert back to a 
struct file).


Some examples that might help are at [3-5].

If you are displacing Mn atomic position(s) such as to model a crystal 
defect [6], then most likely you need to do the special labels above 
first before doing that.  For the space group that you have for your 
supercell [7], the Mn atom you displace would need to have a free atomic 
position and not a fixed one if you are doing atomic position 
optimization [8,9].  Bilbao Crystallographic Server has tools such as 
Wyckoff Positions [10] that might help you determine in your atomic 
positions are free or fixed.


Displacing one Mn atom is not likely to give a realistic model for an 
experimental sample that probably would have a lot of dislocated Mn 
atoms.  Bigger supercells would be needed for calculations (e.g., refer 
to [11]).



[1] http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html
[2] http://crystalmaker.com/crystalmaker/index.html
[3] http://zeus.theochem.tuwien.ac.at/pipermail/wien/2009-April/012454.html
[4] http://susi.theochem.tuwien.ac.at/reg_user/faq/afm.html
[5] Exercise 4:  Creation of supercells (slide 11) 
http://susi.theochem.tuwien.ac.at/events/ws2017/notes/tutorial-Basic-exercises.pdf
[6] 
https://www.substech.com/dokuwiki/doku.php?id=imperfections_of_crystal_structure
[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20329.html
[8] Slide 39: 
http://susi.theochem.tuwien.ac.at/events/ws2015/WIEN2k-Blaha-lectures.pdf

[9] http://www.wien2k.at/reg_user/faq/minimization.html
[10] https://www.cryst.ehu.es/cryst/get_wp.html
[11] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06099.html


On 7/23/2020 1:47 PM, djamel slamnia wrote:

thanks for replay :
my compound has one Mn atom with one position , i'm trying to split it 
to get tow atoms of Mn in unit cell but i cant  because Mn has one 
position can i do for exemple : displace (at least one) atoms


Le jeudi 23 juillet 2020 à 17:49:26 UTC+2, Tran, Fabien 
 a écrit :



You need to construct a super cell which contains several Mn atoms (at 
least one for each orientation of the magnetic moment).
Then, you need to put labels (1, 2) in case.struct to avoid to 
reobtain the original cell after init_lapw.

See for instance discussion here
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19513.html

From: Wien > on behalf of djamel 
slamnia mailto:djamel4...@yahoo.fr>>

Sent: Thursday, July 23, 2020 5:25 PM
To: A. Mailing List for WIEN2k Users
Subject: [Wien] Mailing List

Dear wien2k user's

for antiferromagnetic calculation : i have to split the position of Mn 
atom to get 2 atoms in unit cell but

in my case.struct the Mn atom has only one position

so what i have to do ???

can i displace Mn atom ??

thanks in advance
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Re: [Wien] running wien2k as pure scripts

[Gavin Abo]

Also, if you prefer to use Python, you can make a wrapper around WIEN2k 
terminal commands.  For example, "init_lapw -b" could be used in an 
init_lapw.py file as shown in [1] by referencing [2].


[1] Temporary link: 
https://drive.google.com/file/d/1Kcw_aJHIVvuuX1Ld_UbP8WwlDkquCELx/view?usp=sharing


[2] https://janakiev.com/blog/python-shell-commands/

There are also other examples you could look at such as [3-8] below.

Examples using "init_lapw -b":

[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12122.html
[4] 
http://wien2k-algerien1970.blogspot.com/2016/09/hybrid-dft-calculation-using-ys-pbe0.html 



Example job scripts:

[5] http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html

Example of "x kgen" for a script:

[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14196.html


Example bash script (NiO.sh):

[7] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14460.html


Example awk scripts:

[8] https://github.com/aoterodelaroza/runwien

On 7/28/2020 2:07 PM, pboulet wrote:

Hello,

Have you tried the batch mode of init_lapw?

*init_lapw -h* 



PROGRAM:/zeus/WIEN2k/init_lapw
PURPOSE:initialisation of the l/apw-package WIEN2k
to be called within the case-directory
has to be located in WIEN-executable directory
needs case.struct  file
USAGE:  init_lapw [OPTIONS] [FLAGS]
FLAGS:
-h/-H   ->   help
-b  ->   batch (non-interactive) mode (see possible options below, SGROUP 
is always ignored)
-sp ->   in batch mode: select spin-polarized calculation
OPTIONS:
-red X ->in batch mode: RMT reduction by X % (default: RMT not 
changed)
-vxc X ->in batch mode: VXC option (default: 13 = PBE )
-ecut X->in batch mode: energy seperation between core/valence 
(default: -6.0 Ry)
-rkmax X   ->in batch mode: RKMAX  (default: 7.0, not changed)
-lvns L->   in batch mode: LVNS_max (default: 4)
-fermit X  ->in batch mode: use TEMP with smearing by X Ry (default: 
TETRA)
-fermits X ->in batch mode: use TEMPS with smearing by X Ry (default: 
TETRA)
-mix X ->in batch mode: set mixing to X  (default: 0.2, not changed)
-numk X->in batch mode: use X k-points in full BZ (default: 1000)
-s PROGRAM ->start with PROGRAM ($next)
-e PROGRAM ->exit after PROGRAM ($stopafter)
Best

Pascal Boulet
—
/Professor in computational materials - DEPARTMENT OF CHEMISTRY/
University of Aix-Marseille - Avenue Escadrille Normandie Niemen - 
F-13013 Marseille - FRANCE

Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
Email : pascal.bou...@univ-amu.fr 

Le 28 juil. 2020 à 21:25, Ilias Miroslav, doc. RNDr., PhD. 
mailto:miroslav.il...@umb.sk>> a écrit :


Hello,

I appreciate the web interface for wien2k.

However, I would like to use pure online commands, without manually 
entering any data into web interface.


I tried this sequence of commands below (extracted from web interface 
with the TiC example), but without success.


inp=TiC.struct
 instgen_lapw < $inp
 x -d nn
 x sgroup
 x symmetry
 instgen_lapw -s -up
 #kgen 30 1
 x -d kgen
 dstart
 run_lapw -ec 0.0001 -NI

Any help, please ?
Miro
#!/usr/bin/python3

import os
os.system('init_lapw -b')

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Re: [Wien] Python script

[Gavin Abo]

You might want to have a look at Spaghetti-prima.py and JPlot on the 
WIEN2k unsupported webpage:


http://susi.theochem.tuwien.ac.at/reg_user/unsupported/

Python based BoltzTraP2 plots bandstructure from WIEN2k:

https://gitlab.com/sousaw/BoltzTraP2/-/wikis/tutorial

BoltzTraP2 can be used as a Python library:

https://gitlab.com/sousaw/BoltzTraP2/-/wikis/library

Search the Internet, there may be others such as:

http://goh.physics.ucdavis.edu/wien2plot/wien2plot.html

On 7/28/2020 10:31 PM, Subhasis Panda wrote:

Dear Prof. Gavin and other experts,

Do you some information about Python script for plotting bandstructure 
using output of wien2k?

Thanks and regards
Subhasis

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Re: [Wien] optimization vs experiment

[Gavin Abo]

Perhaps some else in the list has a more direct answer or knows of 
better literature containing information for answering your question.


However, you might have a look at the reading material below that might 
contain some information on experiment and calculation that possibly can 
help you to answer your question:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17075.html
https://doi.org/10.1103/PhysRevB.79.085104 (Calculation of the lattice 
constant of solids with semilocal functionals)

https://molmod.ugent.be/deltacodesdft
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14004.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19382.html
https://doi.org/10.3390/computation5040049
https://www.bc.edu/content/dam/bc1/schools/mcas/physics/pdf/wien2k/DFT%20and%20APW.pdf 
(slide 6)

http://susi.theochem.tuwien.ac.at/onlineworkshop/KS-DFT-LAPW.pdf (slide 35)
https://arxiv.org/abs/1208.2057v2
https://doi.org/10.1515/9783110433920-003 (DFT calculations of solids in 
the ground state)

https://doi.org/10.1016/S0022-4596(03)00213-5
http://susi.theochem.tuwien.ac.at/papers/index.html

On 8/6/2020 2:43 PM, tarek wrote:

Dear Wien2k users/team

When optimizing some structure I sometimes find an observable 
differences between my computations and the published results in 
literature


As I know DFT calculations are carried out for the ground state which 
should be different from experimental  conditions.


Therefore, should I accept the computational results at all or within 
some range???


Thanks a lot for your help

Yours

Dr. Tarek Hammad.

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Re: [Wien] Calculating x kram with intra-band contribution

[Gavin Abo]

In addition, it 'might' be that you also need more than one plasma 
frequency.  However, it has been a long time since I ran spin polarized 
optical calculation, so I don't remember for sure.



I think there were plamsa frequencies from running both "x joint -up" 
and "x joint -dn" from a spin polarized calculation:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16552.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18325.html

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12116.html


I think it was possible to have multiple plasma frequencies from "x 
joint -up" (case.outputjointup) and "x joint -dn" (case.outputjointdn) 
based on:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16645.html


After using addjoint-updn, I think I might have had to combine all 
plasma frequencies from case.outputjointup and case.outputjointdn in 
case.inkram for "x kram" to run without error.



On 8/9/2020 5:05 AM, Tran, Fabien wrote:


According to the user's guide, at the 5th line of abc.inkram a value 
for each column in abc.injoint should be provided. Two values are 
probably not enough because the code fails when it reads this 5th line.




*From:* Wien  on behalf of 
Chukwuemeka Okoye 

*Sent:* Sunday, August 9, 2020 11:36 AM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Calculating x kram with intra-band contribution
Hi,
Please, here is abc.inkram:

0.1    Gamma: broadening of interband spectrum
0.0    energy shift (scissors operator)
1      add intraband contributions? yes/no: 1/0
4.149   plasma frequencies  (from joint, opt 6)
0.20 0.2   Gammas for Drude terms

CMI Okoye

/--
Chukwuemeka M I *Okoye*
/
/Department of Physics and Astronomy,
/
/University of Nigeria,
/
/Nsukka, Enugu State,
/
/Nigeria/
Telephone: +234 7038766990
E-mail: cmi.ok...@unn.edu.ng 


On Sun, Aug 9, 2020 at 10:21 AM Tran, Fabien > wrote:


The error message indicates that there is a problem with your
input file ​abc.inkram​. Show us this file.




*From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of
Chukwuemeka Okoye mailto:cmi.ok...@unn.edu.ng>>
*Sent:* Sunday, August 9, 2020 11:05 AM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Calculating x kram with intra-band contribution
Hi,
Please find the error on the screen:

xx
  zz
   Energy units:  [eV]
   Lorentzian broadening with gamma:   0.100   [eV]
 3501  data points
   ENERGY INCREMENT:   1.361E-002
forrtl: severe (59): list-directed I/O syntax error, unit 5, file 
/home/cmi/abc.inkram
Image  PCRoutineLineSource
kram   0040A2AB  Unknown   Unknown  Unknown
kram   0042894B  Unknown   Unknown  Unknown
kram   004271B5  Unknown   Unknown  Unknown
kram   0040453C  MAIN__179  kram.f
kram   00403822  Unknown   Unknown  Unknown
libc-2.31.so  152C6750E0B3  
__libc_start_main Unknown  Unknown
kram   0040372E  Unknown   Unknown  Unknown
0.017u 0.005s 0:00.21 4.7%  0+0k 5328+0io 20pf+0w
error: command   /home/cmi/wien2k/2k18v2/kram kram.def   failed

Thanks.

CMI Okoye

/--
Chukwuemeka M I *Okoye*
/
/Department of Physics and Astronomy,
/
/University of Nigeria,
/
/Nsukka, Enugu State,
/
/Nigeria/
Telephone: +234 7038766990
E-mail: cmi.ok...@unn.edu.ng 


On Sun, Aug 9, 2020 at 10:02 AM Tran, Fabien
mailto:fabien.t...@tuwien.ac.at>> wrote:

Hi,

What is the error message (either on the screen or in
kram.error)?​




*From:* Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> on behalf of
Chukwuemeka Okoye mailto:cmi.ok...@unn.edu.ng>>
*Sent:* Sunday, August 9, 2020 10:59 AM
*To:* A Mailing list for WIEN2k users
*Subject:* [Wien] Calculating x kram with intra-band contribution

Dear all,
I am trying to calculate optical properties for a
spin-polarized half-metal. x optic, x joint ( with both
options 6 & 4 as specified) all ran smoothly. Without
intra-band i.e 0 in line 3 of inkram, x kram executed smoothly
also. However, when intra-band contribution is added by using
'1' as input in line  3 of inkram, x kram 

Re: [Wien] Calculating x kram with intra-band contribution

[Gavin Abo]

It is recommended to use WIEN2k 19.2 rather than the 18.2 that you are 
using.  As you should see on the WIEN2k updates page [ 
http://susi.theochem.tuwien.ac.at/reg_user/updates/ ], there was a bug 
(possibly a very important one) found in the joint program for optical 
calculations for WIEN2k versions prior to WIEN2k 19.1.  For which you 
see the problem was corrected under WIEN2k 19.1:


/SRC_joint: joint.f (fix for wrong sign of Re-xy,Re_xz,Re_yz components. 
Thanks to Jaroslav Hamrle for reporting the problem./


You have to run your own test cases to see what the program accepts, but 
it might be that you have to run switch 6 for both "x joint -up" and "x 
joint -dn" for kram for it to work correctly after previously having ran 
addjoint-updn.


The number of drude terms you have is important:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01102.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01671.html
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/optic_handout.pdf

The problems might be that you have three drude terms "0.1  0.1  0.3" 
with NUMBER OF COLUMNS set to 2 instead of 3 for each of your drude 
terms in case.injoint but only have two of them in kram "0.20 0.2" when 
it likely needs to be six (three from running "x joint -up" and another 
three from "x joint -dn") if the same case.injoint files were used for 
both -up an -dn.


Also, I see only one plasma frequency, 4.149, in case.kram.  However, 
there likely needs to be two in your calculation case (one plamsa 
frequency from running "x joint -up" and the second from running "x 
joint -dn").



On 8/9/2020 10:17 AM, Chukwuemeka Okoye wrote:

Please, find the abc.injoint:
This is a half-metallic compound. It is metallic in the 
majority(up-spin) channel.
I think there is only one plasma frequency which is obtained when x 
joint -up is run with switch 6.
x joint -dn is run only with switch 4( my understanding of the 
Usersguide). I am using Wien2kv18.2.

Thanks

1 88               : LOWER,UPPER and (optional) UPPER-VAL BANDINDEX
0.    0.00100   3.5000 : EMIN DE EMAX FOR ENERGYGRID IN ryd
eV                            : output units  eV / ryd  / cm-1
4                        : SWITCH
2                        : NUMBER OF COLUMNS
0.1  0.1  0.3              : BROADENING (FOR DRUDE MODEL - switch 6,7 -
ONLY)

SWITCH:

   0...JOINTDOS FOR EACH BAND COMBINATION
   1...JOINTDOS AS SUM OVER ALL BAND COMBINATIONS
   2...DOS FOR EACH BAND
   3...DOS AS SUM OVER ALL BANDS
   4...Im(EPSILON)
   5...Im(EPSILON) for each band combination
   6...INTRABAND contributions
   7...INTRABAND contributions including band analysis
/--
Chukwuemeka M I *Okoye*
/
/Department of Physics and Astronomy,
/
/University of Nigeria,
/
/Nsukka, Enugu State,
/
/Nigeria/
Telephone: +234 7038766990
E-mail: cmi.ok...@unn.edu.ng <mailto:cmi.ok...@unn.edu.ng>


On Sun, Aug 9, 2020 at 4:28 PM Gavin Abo <mailto:gs...@crimson.ua.edu>> wrote:


In addition, it 'might' be that you also need more than one plasma
frequency.  However, it has been a long time since I ran spin
polarized optical calculation, so I don't remember for sure.


I think there were plamsa frequencies from running both "x joint
-up" and "x joint -dn" from a spin polarized calculation:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16552.html
<https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16552.html>

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18325.html
<https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18325.html>

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12116.html
<https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12116.html>


I think it was possible to have multiple plasma frequencies from
"x joint -up" (case.outputjointup) and "x joint -dn"
(case.outputjointdn) based on:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16645.html
<https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16645.html>


After using addjoint-updn, I think I might have had to combine all
plasma frequencies from case.outputjointup and case.outputjointdn
in case.inkram for "x kram" to run without error.


On 8/9/2020 5:05 AM, Tran, Fabien wrote:


According to the user's guide, at the 5th line of abc.inkram a
value for each column in abc.injoint should be provided. Two
values are probably not enough because the code fails when it
reads this 5th line.



*From:* Wien 
<mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of
Chuk

Re: [Wien] Lattice thermal conductivity

[Gavin Abo]

As far as I currently know, no one has implemented a lattice thermal 
conductivity calculation for WIEN2k and made software for it available 
in the public domain yet.


Though, it has been done with other DFT software such as VASP [1] and 
Quantum Espresso (QE) [2,3] by interfacing it with software such as 
phono3py [4].  Unfortunately, it likely is not implemented in phono3py 
as mentioned at [5-7]. As given in [8], there is ALAMODE, PhonTS, and 
ShengBTE. ShengBTE lists VASP and QE but not WIEN2k at [9]. PhonTS also 
lists VASP and QE but not WIEN2k at [10].  The ALAMODE 1.0.2 
documentation [11] has on page 3:


/In addition to the above requirements, users have to get and install a 
first-principles package (such as VASP, Wien2k,QUANTUM-ESPRESSO, or 
xTAPP) or another force field package (such as LAMMPS) by themselves in 
order to compute harmonic and anharmonic force constants./


However, if you look at the latest documentation [12] (for currently 
version 1.1.0) it no longer lists WIEN2k, just:


/Interface to VASP, Quantum-ESPRESSO, xTAPP, and LAMMPS codes/

[1] https://www.vasp.at/
[2] https://www.quantum-espresso.org/
[3] https://doi.org/10.1016/j.rinp.2018.06.053 


[4] https://phonopy.github.io/phono3py/interfaces.html
[5] https://sourceforge.net/p/phonopy/mailman/message/35680830/
[6] https://sourceforge.net/p/phonopy/mailman/message/35579734/
[7] https://sourceforge.net/p/phonopy/mailman/message/37091926/
[8] https://arxiv.org/abs/1704.04142v1
[9] http://www.shengbte.org/
[10] https://phonts.mse.ufl.edu/
[11] https://alamode.readthedocs.io/_/downloads/en/v.1.0.2/pdf/
[12] https://alamode.readthedocs.io/en/latest/intro.html#features

On 8/23/2020 11:03 AM, Peeyush Kumar Kamlesh wrote:

Hello everyone!
Greetings of the day!
Please suggest any package by which I can calculate lattice thermal 
conductivity using WIEN2k.


best regards
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Re: [Wien] Error during abc & gamma (4D) optimization of a monoclinic system

[Gavin Abo]

The 4D is option 7 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html 
, 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html 
]:


[7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice)

I think that only worked correctly when the gamma angle was the one that 
was greater than 90 (e.g., in your case it would likely need to be 
alpha=90 degrees, beta = 90 degrees, Gamma=104.15 degrees), refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html


On 8/23/2020 11:42 AM, shamik chakrabarti wrote:

Dear wien2k users,

                        During 4D optimization of a monoclinic system 
(file attached) I have obtained an error as described below;


'FERMI' - EFERMI OUT OF ENERGY RANGE
 'FERMI' - STOP IN EFI
 'FERMI' - ENERGY OF LOWER BOUND                 :  -4.50517
 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND   :   0.0
 'FERMI' - ENERGY OF UPPER BOUND                 :3003.00451
 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND   : 112.0
 'FERMI' - ADD  112.0
 'FERMI' - SOS 0.........0003.156
 'FERMI' - NOS **

 What is the meaning of this error & how to get out of it?

I have two more queries:
(1) During 4D optimization, I am also expecting the change in the 
value of Gamma, but it remains the same along with all structures 
produced by x optimize & also in the case_default.struct the Gamma is 
not changing. why so?


(2) In my structure, I have alpha=90 degree, beta = 104.15 degrees, 
Gamma=90 degree. Whether the code will change the beta of my structure 
or I have to change the lattice parameter a to b, b to c & c to a to 
produce alpha to beta, beta to gamma & gamma to alpha?


Looking forward to your reply in this regard. Thanks in advance.

with regards,
--
Dr. Shamik Chakrabarti
Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India
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Re: [Wien] Error during abc & gamma (4D) optimization of a monoclinic system

[Gavin Abo]

;Research is to see what everybody else has seen, and to think
what nobody else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu <http://www.numis.northwestern.edu>

On Mon, Aug 24, 2020, 07:29 shamik chakrabarti
mailto:shamik15041...@gmail.com>> wrote:

Dear Prof. Gavin,

                       If I change a to b, b to c & c to a to
make alpha to beta, beta to gamma & gamma to alpha the
produced structure shows unphysical RMTs for all the atoms.: 1
for Nb & 0.51 for Se. What to do?

with regards,

On Mon, 24 Aug 2020 at 16:07, Gavin Abo mailto:gs...@crimson.ua.edu>> wrote:

The 4D is option 7 [

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html

<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04931.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvLE6WOCw$>
,

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html

<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6btgMniYYw$>
]:

[7] VARY A, B, C and Gamma (4D-case) (monoclinic lattice)

I think that only worked correctly when the gamma angle
was the one that was greater than 90 (e.g., in your case
it would likely need to be alpha=90 degrees, beta = 90
degrees, Gamma=104.15 degrees), refer to:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html

<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12124.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!FEEtwhA5ust8qZ33lpDr8XYIkrrX9Q-5dJZwtsegrpZeCBDX0vBodglHQ7hv6bvcYwvi9Q$>


On 8/23/2020 11:42 AM, shamik chakrabarti wrote:

Dear wien2k users,

                        During 4D optimization of a
monoclinic system (file attached) I have obtained an
error as described below;

'FERMI' - EFERMI OUT OF ENERGY RANGE
 'FERMI' - STOP IN EFI
 'FERMI' - ENERGY OF LOWER BOUND   :  -4.50517
 'FERMI' - NUMBER OF STATES AT THE LOWER BOUND   :   0.0
 'FERMI' - ENERGY OF UPPER BOUND   :3003.00451
 'FERMI' - NUMBER OF STATES AT THE UPPER BOUND   : 112.0
 'FERMI' - ADD  112.0
 'FERMI' - SOS
0.........0003.156
 'FERMI' - NOS
**

 What is the meaning of this error & how to get out of it?

I have two more queries:
(1) During 4D optimization, I am also expecting the
change in the value of Gamma, but it remains the same
along with all structures produced by x optimize & also
in the case_default.struct the Gamma is not changing. why so?

(2) In my structure, I have alpha=90 degree, beta =
104.15 degrees, Gamma=90 degree. Whether the code will
change the beta of my structure or I have to change the
lattice parameter a to b, b to c & c to a to produce
alpha to beta, beta to gamma & gamma to alpha?

Looking forward to your reply in this regard. Thanks in
advance.

with regards,
-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103
Patna
Bihar, India

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-- 
Dr. Shamik Chakrabarti

Research Fellow
Department of Physics
Indian Institute of Technology Patna
Bihta-801103

Re: [Wien] Error during abc & gamma (4D) optimization of a monoclinic system

[Gavin Abo]

I recommend the following readings:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg12150.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01512.html

On 8/25/2020 1:05 AM, shamik chakrabarti wrote:

Dear Prof. Gavin,

                           Thanks a lot for your help. It is 
working now. However, I have another query. After x optimize with the 
struct file a message comes as: SPACE GROUP CONTAINS INVERSION
* alpha(3) .gt. 91.0; reset to 90.1. *However, the struct file remains 
the same after this message. Hence, should we ignore the message?


with regards,
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Re: [Wien] unexpected error in SOC calculations for non spin-polarized case

[Gavin Abo]

Also, consider using the latest WIEN2k version (19.2) because many spin 
orbit (SO) bugs can be seen to have been fixed since the 14.2 version 
that you are using:


http://susi.theochem.tuwien.ac.at/reg_user/updates/

The WIEN2k 19.2 version also has a user friendly init_so_lapw script 
that can be ran to automatically generate the case.inso making it less 
error prone then manually editing the case.inso by hand.


There is a bug fix [1] (or init_so_lapw.patch [2]) needed for WIEN2k 
19.2 that fixes cases WITH inversion symmetry when for when init_so_lapw 
is ran several times.


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18801.html


[2] https://github.com/gsabo/WIEN2k-Patches/tree/master/19.1

On 9/5/2020 11:28 AM, Laurence Marks wrote:

Does 001 (no spaces) work - I thought it should be 0 0 1

_
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 Sat, Sep 5, 2020, 12:23 Peter Blaha > wrote:


Your TiC.inso file has 2 errors:

WFFIL
4  0  0                 llmax,ipr,kpot
-10  1.5                Emin, Emax
     001                           h,k,l (direction of magnetization)
  2                       number of atoms with RLO
1 -2.58 0.002 CONT             atom-number, E-param for RLO
2 0.30 0.000 CONT             atom-number, E-param for RLO
0 0      number of atoms without SO, atomnumbers

The line for the RLO of the second atom is missing a blank and
should read:
2  0.30 0.000 CONT             atom-number, E-param for RLO

In addition: It does not make sense to add a RLO for C-p states.
C is a very light element, has no semicore states and the C-2p
valence
states are not really "relativistic".
I've never tried it, but it may even lead to a crash.


 Weitergeleitete Nachricht 
Betreff: Re: [Wien] unexpected error in SOC calculations for non
spin-polarized case
Datum: Sat, 5 Sep 2020 19:06:40 +0200
Von: Peter Blaha mailto:pbl...@theochem.tuwien.ac.at>>
An: wien@zeus.theochem.tuwien.ac.at


The error is exactly what it tells you:

The file /home/tarek/TiC/TiC.inso is not correct.

We cannot know what the error is without looking into the file.

Am 05.09.2020 um 18:46 schrieb tarek:
> Dear Wien2k useres / team
>
> I ran scf calculations for non spin-polarized case using
wien2k_14.2
> under linux.
>
> I followed exactly the steps predicted on youtube for Prof. Oleg
Rubel
> but for unclear reason the scf with -so switch were crushed and
>
> give me this message:
>
> /usr/local/mpich-1.2.7/bin/mpichversion/hup: Not a directory.
>   LAPW0 END
>   LAPW1 END
> forrtl: severe (59): list-directed I/O syntax error, unit 5, file
> /home/tarek/TiC/TiC.inso
> Image  PC    Routine Line    Source
> lapwso 00454FE8  Unknown Unknown Unknown
> lapwso 00479641  Unknown Unknown Unknown
> lapwso 0041E9C1  init_ 75  init.F
> lapwso 00424392  MAIN__ 185 lapwso.F
> lapwso 00403CDE  Unknown Unknown Unknown
> libc.so.6  2B5857A82F45  Unknown Unknown Unknown
> lapwso 00403BE9  Unknown Unknown Unknown
>
>  >   stop error
> I have tried to solve this problem by all means but no way.
>
> Would you please help me.
>
> Thanks in advance
>
> Yours sincerely
>
> Tarek Hammad.
>
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> Wien@zeus.theochem.tuwien.ac.at

>

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-- 
--

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Phone: +43-1-58801-165300      

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] ssh command in Wien2k scripts

[Gavin Abo]

A good IT admin should know the ins and outs their own particular 
computer system such that they should be able to better advise you on a 
solution for environmental variable passing for their specific system.



You may want to have that IT admin work for their paycheck.  At least 
according to [1], an IT admin on average is compensated $110k per year.



I don't see a lot of information provided about the computer system such 
as its configuration and policy for usage.  If you can provide in-depth 
knowledge about your computer system that your IT admin would already 
now about or could gather from the system, we might be able to provide 
more specific advice.  For example, it can be quite typical for cluster 
computer systems to disallow running commands directly on the main node 
and running such commands there can sometimes even lead to getting 
banned from using the computer system.  Instead, the commands are 
committed to compute nodes with a schedule (queue) system which may be 
tasked with propagating the environmental variables to the computation 
nodes.  Some queue systems can require a special flag in the job script 
to get the environmental variables to the compute node(s). For 
additional details on such a case, see the post:



https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17562.html


So it may be possible for a command to fail when executed on the main 
node that may run fine when submitted to queue system (such as PBS, 
slurm, etc. [3]) with a script such as your command:



ssh vsli2 'echo $WIENROOT'


[1] https://www.theladders.com/salary/it-systems-administrator-salary

[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17562.html


[3] https://slurm.schedmd.com/rosetta.pdf


On 9/12/2020 2:34 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

I have similar problem as decribed here 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19049.html 
 .


ssh vsli2 'echo $WIENROOT'

The ssh connection does not preserve the WIENROOT envirovariable.

IT admin does not want the variable ""PermitUserEnvironment"  in 
.sshd_config to be set .


Therefore, I have to change Wien2k scripts to incorporate enviromental 
variable passing.


Any hints, howtos ?

Miro
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Re: [Wien] parallel instalation of Wien2k: elpa, fftw

[Gavin Abo]

See that "./configure --enable-mpi" was used.


Of note, sometimes -gcc-sys is needed:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18664.html


On 9/13/2020 2:53 AM, Ilias Miroslav, doc. RNDr., PhD. wrote:

Hello,

to profit from parallelization, one has to install ELPA and the 
parallel version fftw library.


For fftw library I used ./configure --enable-mpi, but Wien2k 
installator says "!!!  WARNING:  No MPI version of the FFTW library 
found!" But my installed * fftw-3.3.8/lib contains *also libfftw3_mpi.a .


Any clues what is wrong ? Maybe it would be better to have defined 
environmental variables from ELPA, fftw ?


Miro
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Re: [Wien] Berrypi_GGA+U+SO

[Gavin Abo]

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 > 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] Optimization of orthorhombic and monoclinic structure.

[Gavin Abo]

Suggested reading:

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08820.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20406.html

On 9/16/2020 12:18 AM, Ramsewak Kashyap wrote:

Dear Wien2k team/users,
Which method is best for optimizing orthorhombic structure: i) option 
(6) "Vary A,B,C (3-D case)" or ii) optimization by volume > then> b/a 
> then > c/a . and for monoclinic also, is this method applicable or 
not? If not then which one is most appropriate?


With regards,
Ramsewak
Applied Nuclear Physics Division
Saha Institute of Nuclear Physics
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Re: [Wien] monoclinic optimization

[Gavin Abo]

Most likely the data resulting from parabolfit_lapw has to be analyzed 
to determine that.  I suggest reading of previous posts about 
parabolfit_lapw, for example:


https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg14255.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17381.html

On 9/16/2020 9:22 AM, karima Physique wrote:

Dear WIEN2k users,

How to find the optimized structure after an optimization using option 
7 (a b c and gamma) for monoclinic case?

Thank you in advance


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Re: [Wien] Problem faced during elastic constant calculation using Elast package.

[Gavin Abo]

It is likely that you have to follow the previous advice in the mailing 
list archive regarding those WARNING by running (for example, see [1-3]):


x nn
cp case.struct_nn case.struct


[1] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05509.html
[2] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05513.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07769.html


On 9/19/2020 8:02 AM, upasana Rani wrote:

Dear Users,
Greetings!
I am working on the calculation of elastic constants by using  Elast 
(for cubic) package.
The  eos.job and rhomb.job runs smoothly but as I enter parameters to 
set rmt for tetra, I have faced an error.



-
WARNING: Mult not equal. PLEASE CHECK outputnn-file
 WARNING: ityp not equal. PLEASE CHECK outputnn-file
--


Kindly tell the solution.
Thanks!

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Re: [Wien] BoltzTrap

[Gavin Abo]

If you are using Ubuntu (currently 20.04.1 LTS) [1], the download and 
install can be done with one terminal command, which is:


pip3 install BoltzTraP2

If you are using another operating system distribution and the above 
command does not work, then you may need to use instead:


pip install BoltzTraP2

That is also shown on the BoltzTraP website at [2].

[1] https://ubuntu.com/download/desktop
[2] 
https://www.imc.tuwien.ac.at/forschungsbereich_theoretische_chemie/forschungsgruppen/prof_dr_gkh_madsen_theoretical_materials_chemistry/boltztrap2/ 




On 9/25/2020 8:23 AM, Karima Karim wrote:

Dear user wien2k ,I want to calculated BoltzTrap transport properties  in code 
wien2k ,tell me  how  To download and install of BoltzTrap

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Re: [Wien] AFM structure for double perovskite oxide

[Gavin Abo]

If you look at the AFM Cr example of Exercise 7 on slide 17 of [1], the 
struct file has Cr1 atom with a multiplicity of 1 at a non-equivalent 
atomic position of (0,0,0) and it also has Cr2 atom with a multiplicity 
of 1 at an non-equivalent atomic position of (0.5, 0.5, 0.5).  Since 
multiplicity is 1, there are no equivalent atomic positions in this example.


At [2], you can see during the "instgen_lapw -ask" step during execution 
of "init_lapw" that "u" was entered for Cr1 and "d" was entered for 
Cr2.  After the scf calculation, the Cr1 moment from the calculation was 
1.13184 for MMI001 and the Cr2 moment was -1.13184 for MMI002.  The Cr1 
and Cr2 are antiferromagnetic [3] with their moments having equal 
magnitude and opposite sign resulting zero total moment (MMTOT).


Similar for your case, I think you need to ask and answer yourself the 
same questions as you would for the above example. In other words:  What 
are the non-equivalent atomic positions for Cr (but for Fe and Ni in 
your case)?  What is the multiplicity of each non-equivalent atomic 
position?  What are the equivalent atomic position for Cr (i.e, Fe and 
Ni in your case), if any? What atoms at the non-equivalent and 
equivalent [4] atomic positions give the AFM configuration(s) of 
interest and are expected to cancel to give a zero total moment?  Of 
note, if you not familiar with what the multiplicity is in the struct 
file, refer to section "4.3. THE CASE.STRUCT.FILE" on page 40 in the 
usersguide for WIEN2k 19.1 and 19.2 [5].


I realize the use of runafm_lapw in the above Cr example might be 
misleading as runsp_lapw typically has to be used in most cases as 
explained in previous posts in the mailing list archive such as [6-8].


Also, since the configuration set in case.inst with instgen_lapw is just 
the initial one that could change during the scf as explained in [9,10], 
don't forget to check the final magnetic order that comes out of the scf 
to see if you have AFM or not [11].


Though, in some cases when the scf does not result in the expected spin 
state, it might be possible to force a particular state as described in 
previous posts in the mailing list archive such as [12-14].


There used to be a presentation online that I think illustrated WIEN2k 
calculations on a structure for different AFM configurations like Type 
G, Type A, and Type C that might been of interest to you, but 
unfortunately I could not find it again in a Google search.  So 
something might have happened to the website that was hosting it.  It 
might have been the presentation "P. Blaha: “Magnetic and charge order 
phase transition in YBaFe2O5" seen in [15].


[1] http://susi.theochem.tuwien.ac.at/events/ws2015/Exercises_15.pdf
[2] 
http://wien2k-algerien1970.blogspot.com/2016/02/how-to-do-antiferromagnetic-calculation.html
[3] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13159.html
[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17879.html

[5] http://www.wien2k.at/reg_user/textbooks/usersguide.pdf
[6] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16805.html

[7] http://susi.theochem.tuwien.ac.at/reg_user/faq/afm.html
[8] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17307.html
[9] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03243.html
[10] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg06739.html
[11] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17516.html
[12] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18051.html
[13] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18895.html
[14] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19462.html

[15] https://publik.tuwien.ac.at/files/PubDat_175934.pdf

On 10/13/2020 4:29 PM, BUSHRA SABIR wrote:

Hi Wien2k users,

I want to perform AFM calculations for double perovskite oxide La2FeNiO6
For this, I have a cubic 225-Fm3m structure.
My question is ..Do I need to flip the spin of Ni only during 
instgen_lapw -ask?
or should I make a supercell with two Fe and then choose spin up for 
one Fe and spin dn for second Fe.


Need help for this

Bushra
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