Re: [Wien] Which Error (?) in W2Web

[Fecher, Gerhard]

Dear Gavin,
thanks for the answer, was helpful on a rainy sunday afternoon.
It was the most stupid mistake, I guess you know which one (I wanted to do only 
one scf cycle for test purpose).

The "bug" was sitting 20 cm in front of my monitor. 

Ciao
Gerhard

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


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Gavin Abo 
[gs...@crimson.ua.edu]
Gesendet: Sonntag, 13. November 2016 17:40
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Which Error (?) in W2Web

grep "making" $WIENROOT/makescratch

The above terminal command should return in the output:

echo making $scratch directory

I looks like $scratch might have somehow got set to: -i

Since the mkdir command does not have a -i option, it returns that
"invalid option" error.

I would first try checking the contents of scratch variable in the
terminal/script environment and also the "Scratch Directory" box in
w2web under run_SCF.

Second, I would try adding -x to makescratch_lapw to see if the long
output could give a better idea were the problem might be coming
(similar to what was mentioned for troubleshooting csh scripts like
x_lapw [
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07734.html
]).

On 11/13/2016 8:58 AM, Fecher, Gerhard wrote:
> On one, and only on one, of my computers I receive:
>
> making -i directory
> mkdir: invalid option -- 'i'
> Try `mkdir --help' for more information.
> ERROR: option 1 does not exist!
>
> when I try to start the scf from w2web, has anyone an idea what that might be 
> ?
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Inorganic and Analytical Chemistry
> Johannes Gutenberg - University
> 55099 Mainz
> and
> Max Planck Institute for Chemical Physics of Solids
> 01187 Dresden
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Re: [Wien] What's the correct procedure for mBJ calculation

[Maciej Polak]

You shouldn't modify case.in0abp unless you really know what you're 
doing. Default parametrization usually works very well, and if you want 
to change it, try the options that are given to you during second 
init_mbj_lapw.


A difference that big means that there is probably something wrong 
earlier, especially if you don't have a very complicated case, you 
shouldn't get a difference bigger than 20-30% (usually less, e.g. GaAs 
is nearly perfect). Or if you have a very difficult material, read the 
mbjlda paper because maybe it doesn't work perfectly for your compound.


I would try getting either a confident crystallographic data or doing a 
proper geometry optimization once again. Both lattice constants and 
atomic positions greatly influence the band gap and overall band structure.


Or if you really want to change the "c" parameter (which I wouldn't do 
to solve a problem of 1.2eV difference), do it as it says in the 
userguide by modifying the grr file.


Best regards

Maciej Polak


On 11/14/2016 12:26 AM, Abderrahmane Reggad wrote:

Thank you Mr Polak for your answer
Yes, you are about the userguide as a unique reference.

I have followed the procedure of the first reference and I got results.

Another question:

I have got a gap value of 1.3 ev for my compound which is bigger than the 
experimental
value (0.1 ev) with the default value of  -1.200E-002
for the c-parameter in the case.in0abp file.

Which value of c , I got a gap value of 0.1 ev?

Best regards
--
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie




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Re: [Wien] lapwso_mpi error

[Gavin Abo]

Ok, I agree that it is likely not due to the set up of the scratch 
directory.


What version of ifort was used?  If you happened to use 16.0.3.210, 
maybe it is caused by an ifort bug [ 
https://software.intel.com/en-us/articles/read-failure-unformatted-file-io-psxe-16-update-3 
].


Perhaps you can use the linux "od" command to try to troubleshot and 
identify what the data mismatch is between the writing and reading of 
the 3Mn.vectordn_1 file, similar to what is described on the web pages at:


https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/269993
https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/270436
https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/268503

Though, it might be harder to diagnose with the large 3Mn.vectordn_1, 
which looks to be about 12 GB.  So you may want to create a mpi SO 
calculation that creates a smaller case.vectordn_1 for that.


On 11/13/2016 7:30 AM, Md. Fhokrul Islam wrote:


Hi Gavin,


   In my .bashrc scratch is defined as $SCRATCH = ./ so if I use the 
command


echo $SCRATCH, it always returns ./


For large jobs, I use local temporary directory that is associated 
with each node


in our system and is given by $SNIC_TMP.  This temporary directory is 
created


on fly, so I set $SCRATCH = $SNIC_TMP in my job submission script. As 
I said


this set up works fine if I do MPI calculations without spin-orbit and 
I get converged


results. But if I submit the job after initializing with spin-orbit, 
it crashes at lapwso.


SO I think problem is probably not due to the set up with scratch 
directory, it is


something to do with MPI version of LAPWSO.



Thanks for your comment.


Fhokrul

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Re: [Wien] What's the correct procedure for mBJ calculation

[Abderrahmane Reggad]

Thank you Mr Polak for your answer


Yes, you are about the userguide as a unique reference.

I have followed the procedure of the first reference and I got results.

Another question:

I have got a gap value of 1.3 ev for my compound which is bigger than
the experimental

value (0.1 ev) with the default value of  -1.200E-002

for the c-parameter in the case.in0abp file.

Which value of c , I got a gap value of 0.1 ev?

Best regards
-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie
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Re: [Wien] What's the correct procedure for mBJ calculation

[Maciej Polak]

Dear A. Reggad,

I think it doesn't really matter when you save, you may not save at all 
if you don't want to, it's just good practice so you don't have to redo 
everything when you mess something up.


Also, I would advice always reading the Userguide first, follow what you 
find there, and you will never be dissapointed, it tells you everything 
you need to know. Only if you really don't understand something, go to 
other places. And if you run init_mbj_lapw it tells you to save in the 
same way as the userguide.


Best regards

Maciej Polak

On 11/13/2016 11:53 PM, Abderrahmane Reggad wrote:

Dear Prof Tran

In the page 14 of WIEN2k_lecture-notes_2013 , It's mentionned that the 
saving of the PBE calculation precedes the first mBJ initialization ( 
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/Exercises_13.pdf) 
while in the userguide ( 
http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ) it's 
mentionned the inverse order .


What's the correct procedure or It doesn't matter

Best regards
--
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie




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[Wien] What's the correct procedure for mBJ calculation

[Abderrahmane Reggad]

Dear Prof Tran

In the page 14 of WIEN2k_lecture-notes_2013 , It's mentionned that the
saving of the PBE calculation precedes the first mBJ initialization (
http://www.wien2k.at/reg_user/textbooks/WIEN2k_lecture-notes_2013/Exercises_13.pdf)
while in the userguide (
http://www.wien2k.at/reg_user/textbooks/usersguide.pdf ) it's mentionned
the inverse order .

What's the correct procedure or It doesn't matter

Best regards
-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie
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Re: [Wien] vacancy

[Peter Blaha]

a) If one want to have some low symmetry (eg. P1) you should "label" the 
atoms. This means, in your supercell, call the atoms like

"U 1" or
"Si1",  (any number in 3rd place will make this atom nonequivalent 
to non-labeled atoms (or to other labelled atoms).

So just label enough atoms until you get P1.

b) Is your error always coming with this message:

 _nb in zhcgst.F 640 128
???
Are you using a very old wien2k-version ??? I could see that such 
problems were fixed in Version 12

(see http://www.wien2k.at/reg_user/updates/)

and I guess in versions 12 and 13 this message was still printed (but 
without giving an error), while in 14 the print was removed.


PS:  I expect that we will release a new wien2k version in the next few 
weeks 


Am 13.11.2016 um 16:06 schrieb Viktor Zano:

Dear Peter
Of course I repeated that calculation few times, every time with a new
session name  and new directory
Still without success."
The reason I didn't want to use that higher symmetry was to do
relaxation of the atoms (and vacancy) without enforcing symmetry
considerations.
Best regards, Victor



2016-11-10 16:12 GMT+02:00 Peter Blaha >:

a) You must not ignore warnings of nn (and of sgroup).

b) If you do and continue the initialization until it stops, it has
created a wrong   case.inst   file, and thus this file must be
removed again before you make a new trial (or make a new directory
and copy just the case.struct file. So this explains the first two
problems you report.

c) I do not understand what you did to obtain multiple vacancies.

I'm trying to introduce a vacancy into a tetragonal lattice
(U4Al7Si5;
original space group : /I4///mmm)/ with 64 atoms.

I did it manually putting only 63 atoms in a P1 space group

when I used 'nn' it gave mean error:

WARNING: Mult not equal. PLEASE CHECK outputnn-file

First I didn't change it (and also didn't change space group
into higher
symmetry, as I planned to relax the atoms) and got an stop 'error ':

error: command /home/refelov/WIEN2k_13/lapw1c lapw1.def failed

with lots of raws:

_nb in zhcgst.F 640 128


I have to mention that I used "complex calculation (no inversion)"



The next time I used the suggested file made by nn:
case.struc_nn as the
case.struc

Now I had 63 atoms in 23 wykocf positions in primitive space
group (P).

sgroup found: 99 (P 4 m m).

I didn't change the space group and got “lstart lstart.def failed”


also:

error: U4Al7Si5_Si_vacancy5.inst not consistent with Z
edit U4Al7Si5_Si_vacancy5.inst and rerun lstart afterwards or
change Z
in StructGen!


Now I went back and agreed to change the space groupand I
saw that
more atoms are missing (I only wanted to 1 vacancy!)

Any idea how to proceed?

Victor



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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 
 FAX: +43-1-58801-165982 
Email: bl...@theochem.tuwien.ac.at
WIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php

--
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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, 

Re: [Wien] No convergence during Volume Optimization

[Abderrahmane Reggad]

Thank you Dr Pieper for your interesting to my questions.

I have optimized the atomic positions before doing calculation.

Tha thing that I didn't understand is that the convergence is reached for
some points but not for others.

For the "optimization notes " , there is no mention on the difference
betwwen the energy and force approaches.

Best regards


-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie
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Re: [Wien] degeneracy problem in dipole matrix elements

[Xavier Rocquefelte]

Dear Mengxi Wu

If I clearly understand you, you are considering the GAMMA point where 
the bands are degenerate.


At the GAMMA point these bands have the same symmetry to my point of 
view, explaining why the dipole matrix is non-zero. Thus your result is 
expected to my point of view.


Best Regards

Xavier


Le 13/11/2016 à 17:29, Little Grass a écrit :

Dear WIEN2k users,

I'm trying to study the dipole matrix elements of MgO at Gamma point, 
but the dipole matrix elements between the degenerated bands seem to 
have been mixed together. Are there any ways to sort out the 
degeneracy, so that the dipole matrix elements are non-zero only for 
bands with the same symmetry?



The band structure can be generated from the spaghetti program. In 
addition, bands with different symmetries are colored differently with 
irrep.  For example, Fig1 shows the band structure from X to Gamma to 
X. According to symmetry, only the bands with the same color will be 
dipole allowed in px. So we expect that the dipole matrix elements (in 
file mommat2) for px is zero between bands with different colors. For 
example, the dipole matrix elements between band 6 and band 9 is 
non-zero, but the dipole matrix elements between band 7 and 9 or 8 and 
9 are zero. But if one looks at the px component of the dipole matrix 
element from the optic program, we see that at Gamma point, the dipole 
matrix elements between the degenerated bands are mixed together. For 
example, dipole matrix elements between band 6 and 9, between 7 and 9, 
and between 8 and 9 are all non-zero. In other words, the dipole 
matrix is much denser than it should be.
So is there a way to fix the dipole matrix so that the dipole matrix 
become very sparse and only bands with the same symmetry have non-zero 
dipole matrix elements?


Fig1:http://imgur.com/a/c7p0u

Thanks in advance for the help.
Best,
Mengxi Wu


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Re: [Wien] Which Error (?) in W2Web

[Gavin Abo]

grep "making" $WIENROOT/makescratch

The above terminal command should return in the output:

echo making $scratch directory

I looks like $scratch might have somehow got set to: -i

Since the mkdir command does not have a -i option, it returns that 
"invalid option" error.


I would first try checking the contents of scratch variable in the 
terminal/script environment and also the "Scratch Directory" box in 
w2web under run_SCF.


Second, I would try adding -x to makescratch_lapw to see if the long 
output could give a better idea were the problem might be coming 
(similar to what was mentioned for troubleshooting csh scripts like 
x_lapw [ 
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07734.html 
]).


On 11/13/2016 8:58 AM, Fecher, Gerhard wrote:

On one, and only on one, of my computers I receive:

making -i directory
mkdir: invalid option -- 'i'
Try `mkdir --help' for more information.
ERROR: option 1 does not exist!

when I try to start the scf from w2web, has anyone an idea what that might be ?

Ciao
Gerhard

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


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden

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[Wien] degeneracy problem in dipole matrix elements

[Little Grass]

Dear WIEN2k users,

I'm trying to study the dipole matrix elements of MgO at Gamma point, but
the dipole matrix elements between the degenerated bands seem to have been
mixed together. Are there any ways to sort out the degeneracy, so that the
dipole matrix elements are non-zero only for bands with the same symmetry?


The band structure can be generated from the spaghetti program. In
addition, bands with different symmetries are colored differently with
irrep.  For example, Fig1 shows the band structure from X to Gamma to X.
According to symmetry, only the bands with the same color will be dipole
allowed in px. So we expect that the dipole matrix elements (in file
mommat2) for px is zero between bands with different colors. For example,
the dipole matrix elements between band 6 and band 9 is non-zero, but the
dipole matrix elements between band 7 and 9 or 8 and 9 are zero. But if one
looks at the px component of the dipole matrix element from the optic
program, we see that at Gamma point, the dipole matrix elements between the
degenerated bands are mixed together. For example, dipole matrix elements
between band 6 and 9, between 7 and 9, and between 8 and 9 are all
non-zero. In other words, the dipole matrix is much denser than it should
be.
So is there a way to fix the dipole matrix so that the dipole matrix become
very sparse and only bands with the same symmetry have non-zero dipole
matrix elements?

Fig1:http://imgur.com/a/c7p0u

Thanks in advance for the help.
Best,
Mengxi Wu
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Re: [Wien] charge density

[Xavier Rocquefelte]

Could you clarify your question. What do you mean by "each range"?

- Energy range

- Density value



Le 13/11/2016 à 16:54, boudiaf khadidja a écrit :

Dear Wien2k user
I use VIETA to plot the charge density ;But I need to know a way to 
plot or get the values of each range for the charge density; What can 
i do ?

Best regardes.


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[Wien] Which Error (?) in W2Web

[Fecher, Gerhard]

On one, and only on one, of my computers I receive:

making -i directory
mkdir: invalid option -- 'i'
Try `mkdir --help' for more information.
ERROR: option 1 does not exist!

when I try to start the scf from w2web, has anyone an idea what that might be ? 

Ciao
Gerhard

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


Dr. Gerhard H. Fecher
Institut of Inorganic and Analytical Chemistry
Johannes Gutenberg - University
55099 Mainz
and
Max Planck Institute for Chemical Physics of Solids
01187 Dresden
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[Wien] charge density

[boudiaf khadidja]

Dear Wien2k user
I use VIETA to plot the charge density ;But I need to know a way to plot or
get the values of each range for the charge density; What can i do ?
Best regardes.
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Re: [Wien] vacancy

[Viktor Zano]

Dear Peter
Of course I repeated that calculation few times, every time with a new
session name  and new directory
Still without success.
The reason I didn't want to use that higher symmetry was to do relaxation
of the atoms (and vacancy) without enforcing symmetry considerations.
Best regards, Victor



2016-11-10 16:12 GMT+02:00 Peter Blaha :

> a) You must not ignore warnings of nn (and of sgroup).
>
> b) If you do and continue the initialization until it stops, it has
> created a wrong   case.inst   file, and thus this file must be removed
> again before you make a new trial (or make a new directory and copy just
> the case.struct file. So this explains the first two problems you report.
>
> c) I do not understand what you did to obtain multiple vacancies.
>
> I'm trying to introduce a vacancy into a tetragonal lattice (U4Al7Si5;
>> original space group : /I4///mmm)/ with 64 atoms.
>>
>> I did it manually putting only 63 atoms in a P1 space group
>>
>> when I used 'nn' it gave mean error:
>>
>> WARNING: Mult not equal. PLEASE CHECK outputnn-file
>>
>> First I didn't change it (and also didn't change space group into higher
>> symmetry, as I planned to relax the atoms) and got an stop 'error ':
>>
>> error: command /home/refelov/WIEN2k_13/lapw1c lapw1.def failed
>>
>> with lots of raws:
>>
>> _nb in zhcgst.F 640 128
>>
>>
>> I have to mention that I used "complex calculation (no inversion)"
>>
>>
>>
>> The next time I used the suggested file made by nn: case.struc_nn as the
>> case.struc
>>
>> Now I had 63 atoms in 23 wykocf positions in primitive space group (P).
>>
>> sgroup found: 99 (P 4 m m).
>>
>> I didn't change the space group and got “lstart lstart.def failed”
>>
>>
>> also:
>>
>> error: U4Al7Si5_Si_vacancy5.inst not consistent with Z
>> edit U4Al7Si5_Si_vacancy5.inst and rerun lstart afterwards or change Z
>> in StructGen!
>>
>>
>> Now I went back and agreed to change the space groupand I saw that
>> more atoms are missing (I only wanted to 1 vacancy!)
>>
>> Any idea how to proceed?
>>
>> Victor
>>
>>
>>
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>>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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