subject:"\[Wien\] dstart.error"

Re: [Wien] dstart.error

2020-09-09 Thread Peter Blaha

As was mentioned, such simulations are possible on a bigger cluster with 
infiniband connection and at least 64 (better more) cores in total.


However, unless you already have sufficient experience with WIEN2k, I 
would STRONGLY suggest to "learn" how to run such big calculations on 
eg. a 2x2 supercell first.
I'm pretty sure, you can reproduce their results (and experiment) also 
with a smaller cell. Next step would be to do a 3x3 cell and compare to 
your previous results. If nothing changes, you are ok.


Regards
On 9/8/20 10:46 PM, Ilias Miroslav, doc. RNDr., PhD. wrote:
Ad: 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20439.html


Dear Professor Blaha,

thanks for your answer.

I took this Quartz structure from the work of Pershina, 
https://pubs.rsc.org/en/content/articlepdf/2016/cp/c6cp02253g , where 
the 4x4 supercell is the best choice for comparison with experiments.


What could be done to make such 4x4 supercell  feasible with Wien2k ? 
This is slightly more than 300 atoms, no symmetry (H-passivation is only 
from the top side).  Clearly, I would reduce the vacuum to 40 Bohr, as 
you suggest, but  would it be sufficient ? If there is a hope to 
simulate such system with Wien2k on 256GB RAM equipped nodes, I would 
try it...


Best, Miro


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  P.Blaha
--
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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
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Re: [Wien] dstart.error

2020-09-08 Thread Laurence Marks

I doubt that P1 symmetry is correct, and forced H-passivation is probably
ineffecient and/or wrong. However, since he did not provide atomic
positions it is impossible to know, and in fact it is technically
impossible to reproduce this work. This is why I will urge all reviewers to
reject DFT papers where there is not complete information about atomic
positions.

With care 300 atoms is not a critical issue, assuming that you have fast
nodes with infiniband or similar.

On Tue, Sep 8, 2020 at 3:47 PM Ilias Miroslav, doc. RNDr., PhD. <
miroslav.il...@umb.sk> wrote:

> Ad:
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20439.html
> 
>
> Dear Professor Blaha,
>
> thanks for your answer.
>
> I took this Quartz structure from the work of Pershina,
> https://pubs.rsc.org/en/content/articlepdf/2016/cp/c6cp02253g
> 
>  ,
> where the 4x4 supercell is the best choice for comparison with experiments.
>
> What could be done to make such 4x4 supercell  feasible with Wien2k ? This
> is slightly more than 300 atoms, no symmetry (H-passivation is only from
> the top side).  Clearly, I would reduce the vacuum to 40 Bohr, as you
> suggest, but  would it be sufficient ?  If there is a hope to simulate such
> system with Wien2k on 256GB RAM equipped nodes, I would try it...
>
> Best, Miro
>
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
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>


-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: www.numis.northwestern.edu/MURI
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
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Re: [Wien] dstart.error

2020-09-08 Thread Ilias Miroslav, doc. RNDr., PhD.

Ad: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20439.html

Dear Professor Blaha,

thanks for your answer.

I took this Quartz structure from the work of Pershina, 
https://pubs.rsc.org/en/content/articlepdf/2016/cp/c6cp02253g , where the 4x4 
supercell is the best choice for comparison with experiments.

What could be done to make such 4x4 supercell  feasible with Wien2k ? This is 
slightly more than 300 atoms, no symmetry (H-passivation is only from the top 
side).  Clearly, I would reduce the vacuum to 40 Bohr, as you suggest, but  
would it be sufficient ?  If there is a hope to simulate such system with 
Wien2k on 256GB RAM equipped nodes, I would try it...

Best, Miro

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Re: [Wien] dstart.error

2020-08-28 Thread Peter Blaha


I cannot reproduce this error. init -b ...  runs fine.

The struct file you included has no symmetry operation. With this struct 
file, dstart would fail.
However, during initialization the identity is written to the file and 
this one must be used later on.

---

However, this structure is completely ridiculous and Wien2k calculation 
for it would take weeks and would probably need a computer with at least 
1000 cores + memory !!!


Why ?   What counts for cpu time is only partially the number of atoms, 
but the size of the cell. You have 38x38x190 bohr !


You have a vacuum of about 160 bohr !!!  and also the x-y supercell for 
ONE Tl-OH molecule is MUCH too large (they are separated by 40 bohr !!).
In addtion, your distances (some of the O-H) are ridiculous small, 
forcing very small RMTs.
You passivate only one of the SiO2 surfaces by H, but then put the Tl-OH 
on the passivated surface ???


I don't know from where the structure is (except from ASE) ?? but this 
one would be very expensive in WIEN2k (and I'm pretty sure with any code 
this is very hard). Have you ever visualized it ???



Wien2k offers very powerful tools to generate a "good" model of SiO2/Tl-OH.
- Start with the bulk SiO2, relax the volume and positions. Use optimal 
lattice parameters.
- Create the corresponding surface. For simple surfaces use   x 
supercell, for complicated ones use the structeditor (you need octave !) 
- A typical vacuum is 30 bohr, maybe if you later plan to add Tl-OH, use 
40 bohr.
- Decide whether you want to passivate the surface with H and add them 
"manually" for each surface O-atom). In WIEN2k it is usually much more 
efficient to have inversion symmetry, so I would passivate either both 
or none of the surfaces.

- Relax the surface.
- Now decide on the xy-supercell to isolate the Tl-OH molecule. 
Typically, very often even a 2x2 supercell is sufficient. (x supercell)

- Now add the Tl-OH "manually" and relax it.

PS: How to add atoms manually ???
open the structure in xcrysden. Select the site where you want to add 
the atoms. Identify their coordinates using xcrysden (use eg "distances" 
and click on two atoms - select fractional coordinates). With this you 
can easily get a good guess about the coordinates of our "add-atoms".


Adding this atom can be done in w2web (for beginners) or directly 
editing the struct file:
Copy an "atom-block" and paste it at the end. Modify coordinates, name, 
ZZ, and eventually R0.
Don't forget to increase the number of atoms at the top of the struct 
file and to set the number of symm.ops to zero.


Start with a "small" model and fully relax it.
Later on you can check your results by increasing the model (with x 
supercell you can add vacuum, or make another 2x2 supercell and remove 3 
of the Tl-OH molecules to have a smaller coverage.


Best regards
Peter Blaha


---
Betreff:
dstart.error
Von:
"Ilias Miroslav, doc. RNDr., PhD." 
Datum:
28.08.2020, 13:23
An:
"wien@zeus.theochem.tuwien.ac.at" 

Hello,

I prepared this structure (307 atoms)- from xyz via ase,  and it passed 
until dstart , giving:


 'ROTDEF' - no symmetry operation found.
 'ROTDEF' - for jatom, index   1   1 

 'ROTDEF' - atomposition of jatom   0.9979360   0.0003974   0.462 


 'ROTDEF' - atomposition of index   0.9979360   0.0003974   0.462

Any help, please ?

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


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[Wien] dstart.error

2014-12-01 Thread Sayah Jamal

Dear Peter Blaha
https://www.mail-archive.com/search?l=wien%40zeus.theochem.tuwien.ac.atq=from:%22Peter+Blaha%22

 I mad SUPERCELL Li0,5TiO2 and When I
try to run the x dstart appears the error:
ROTDEF – Error
0.0u 0.0s 0:00.05 0.0% 0+0k 1728+16io 8pf+0w
and dstart.error
ROTDEF' - no symmetry operation found.
'ROTDEF' - for jatom, index 1 2

'ROTDEF' - atomposition of jatom
0.000 0.000 0.000

'ROTDEF' - atomposition of index
0.250 0.500 0.500

and  case.struct
tio2 tio2
P LATTICE,NONEQUIV.ATOMS: 5
MODE OF CALC=RELA unit=ang
17.453518 8.726759 5.597371 90.00 90.00 90.00
ATOM -1: X=0. Y=0. Z=0.
MULT= 2 ISPLIT= 8
-1: X=0.2500 Y=0.5000 Z=0.5000
Ti NPT= 781 R0=0.5000 RMT= 1.0800 Z: 22.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -2: X=0.5000 Y=0. Z=0.
MULT= 2 ISPLIT= 8
-2: X=0.7500 Y=0.5000 Z=0.
Ti NPT= 781 R0=0.5000 RMT= 1.0800 Z: 22.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -3: X=0.3475 Y=0.6950 Z=0.
MULT= 4 ISPLIT= 8
-3: X=0.1525 Y=0.3050 Z=0.
-3: X=0.4025 Y=0.1950 Z=0.5000
-3: X=0.0975 Y=0.8050 Z=0.5000
O NPT= 781 R0=0.0001 RMT= 0.9600 Z: 8.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -4: X=0.8475 Y=0.6950 Z=0.
MULT= 4 ISPLIT= 8
-4: X=0.6525 Y=0.3050 Z=0.
-4: X=0.9025 Y=0.1950 Z=0.5000
-4: X=0.5975 Y=0.8050 Z=0.5000
O NPT= 781 R0=0.0001 RMT= 0.9600 Z: 8.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -5: X=0.5000 Y=0. Z=0.5000
MULT= 1 ISPLIT= 8
Li NPT= 781 R0=0.0001 RMT= 1.0200 Z: 3.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
2 NUMBER OF SYMMETRY OPERATIONS
1 0 0 0.
0 1 0 0.
0 0-1 0.
1
1 0 0 0.
0 1 0 0.
0 0 1 0.
2
help me thank you
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Re: [Wien] dstart.error

2014-12-01 Thread Gavin Abo


Are there any WARNING messages when you run 'x nn' on the supercell?

On 12/1/2014 3:58 PM, Sayah Jamal wrote:


Dear Peter Blaha 
https://www.mail-archive.com/search?l=wien%40zeus.theochem.tuwien.ac.atq=from:%22Peter+Blaha%22


  I mad SUPERCELL Li0,5TiO2 and When I
try to run the x dstart appears the error:
ROTDEF -- Error
0.0u 0.0s 0:00.05 0.0% 0+0k 1728+16io 8pf+0w
and dstart.error
ROTDEF' - no symmetry operation found.
'ROTDEF' - for jatom, index 1 2

'ROTDEF' - atomposition of jatom
0.000 0.000 0.000

'ROTDEF' - atomposition of index
0.250 0.500 0.500

and  case.struct
tio2 tio2
P LATTICE,NONEQUIV.ATOMS: 5
MODE OF CALC=RELA unit=ang
17.453518 8.726759 5.597371 90.00 90.00 90.00
ATOM -1: X=0. Y=0. Z=0.
MULT= 2 ISPLIT= 8
-1: X=0.2500 Y=0.5000 Z=0.5000
Ti NPT= 781 R0=0.5000 RMT= 1.0800 Z: 22.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -2: X=0.5000 Y=0. Z=0.
MULT= 2 ISPLIT= 8
-2: X=0.7500 Y=0.5000 Z=0.
Ti NPT= 781 R0=0.5000 RMT= 1.0800 Z: 22.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -3: X=0.3475 Y=0.6950 Z=0.
MULT= 4 ISPLIT= 8
-3: X=0.1525 Y=0.3050 Z=0.
-3: X=0.4025 Y=0.1950 Z=0.5000
-3: X=0.0975 Y=0.8050 Z=0.5000
O NPT= 781 R0=0.0001 RMT= 0.9600 Z: 8.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -4: X=0.8475 Y=0.6950 Z=0.
MULT= 4 ISPLIT= 8
-4: X=0.6525 Y=0.3050 Z=0.
-4: X=0.9025 Y=0.1950 Z=0.5000
-4: X=0.5975 Y=0.8050 Z=0.5000
O NPT= 781 R0=0.0001 RMT= 0.9600 Z: 8.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -5: X=0.5000 Y=0. Z=0.5000
MULT= 1 ISPLIT= 8
Li NPT= 781 R0=0.0001 RMT= 1.0200 Z: 3.0
LOCAL ROT MATRIX: 1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
2 NUMBER OF SYMMETRY OPERATIONS
1 0 0 0.
0 1 0 0.
0 0-1 0.
1
1 0 0 0.
0 1 0 0.
0 0 1 0.
2
help me thank you
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Re: [Wien] dstart.error

Re: [Wien] dstart.error

Re: [Wien] dstart.error

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[Wien] dstart.error

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