Re: [Wien] error in symmetry step (not seen by sgroup)

[Bartek Wiendlocha]

Indeed, there is a small distortion, which lowers the symmetry.  a change in 
the 'tol' value fixed the problem.   Thanks for the quick response!  
best  Bartek Wiendlocha  Dnia 15 maja 2018 19:44 Peter Blaha 
 napisał(a):  Of course the error occurs 
always, also when running   x symmetry.  In init_lapw in batch mode, the error 
is catched automatically and init  stops, while in the step-by-step 
initialization you are supposed to  examine case.outputs by yourself and find 
the problem on your own.   Just check the case.outputs file.   The problem is 
that this site has "almost"  C3v symmetry and not only  C3i. The mirror 
planes and C2 operations are only slightly invalid and  the test in symmetry 
was not accurate enough.   Edit symmetry.f in SRC_symmetry and search for 
"tol".   Change the value of tol from 1.d-3 to 1.d-4:    tol=1.e-3  
  -->    tol=1.e-4   and recompile.   Thanks for reporting the problem.   Am 
15.05.2018 um 18:55 schrieb Laurence Marks:  Actually I found it when doing it 
step by step, although the error was  only in the output. Peter is the expert 
on this   On Tue, May 15, 2018 at 11:32 AM, Fecher, Gerhard 
>; wrote:      
Strange, just as a diagnostic     it seems the error appears only when running 
batch initialisation     I do not see it when using step by step initialisation 
in w2web     or running x symmetry directly from the command line      also 
strange, when converting the structure to P1 then sgroup finds     space group 
146 instead of 148     but the batch initialisation has the same problem 
(indeed after     accepting the structure from sgroup)     again, no error from 
x symmetry only from batch initialisation      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.tu     ;]     Gesendet: Dienstag, 15. Mai 2018 15:20  
   An:   w...@zeus.theochem.tuwien.ac.a      www.numis.northwestern.edu>  ;  
Corrosion in 4D: MURI4D.numis.northwestern.edu  

Re: [Wien] error in symmetry step (not seen by sgroup)

[Peter Blaha]

Of course the error occurs always, also when running   x symmetry.
In init_lapw in batch mode, the error is catched automatically and init 
stops, while in the step-by-step initialization you are supposed to 
examine case.outputs by yourself and find the problem on your own.


Just check the case.outputs file.

The problem is that this site has "almost"  C3v symmetry and not only 
C3i. The mirror planes and C2 operations are only slightly invalid and 
the test in symmetry was not accurate enough.


Edit symmetry.f in SRC_symmetry and search for "tol".

Change the value of tol from 1.d-3 to 1.d-4:

  tol=1.e-3-->tol=1.e-4

and recompile.

Thanks for reporting the problem.

Am 15.05.2018 um 18:55 schrieb Laurence Marks:
Actually I found it when doing it step by step, although the error was 
only in the output. Peter is the expert on this


On Tue, May 15, 2018 at 11:32 AM, Fecher, Gerhard > wrote:


Strange, just as a diagnostic
it seems the error appears only when running batch initialisation
I do not see it when using step by step initialisation in w2web
or running x symmetry directly from the command line

also strange, when converting the structure to P1 then sgroup finds
space group 146 instead of 148
but the batch initialisation has the same problem (indeed after
accepting the structure from sgroup)
again, no error from x symmetry only from batch initialisation

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
Bartek Wiendlocha [bwiendlo...@tlen.pl ]
Gesendet: Dienstag, 15. Mai 2018 15:20
An: wien@zeus.theochem.tuwien.ac.at

Betreff: [Wien] error in symmetry step (not seen by sgroup)

Dear Wien2k Users & Developers,

I have a strange problem with the symmetry step (during the
initialization procedure), seems not to be reported to the mailing
list before.
My original system was rather a big one, so I created a smaller
struct file to track the error (attached).
Struct file was checked with sgroup before initialization, there are
no problems with rounding of positions as well.

During the initialization, symmetry reports the error:
-- ERROR --
ERROR: (multiplicity of atom           2 )*(number of
pointgroup-operations)
ERROR: is NOT = (number of spacegroup-operations)
ERROR: MULT:           1  ISYM:          12  NSYM           6
ERROR: Check your struct file with    x sgroup
-- ERROR --

Space group is #148 R-3 with 6 symmetry operations. In the attached
struct file there are 2 inequivalent positions: (6f) and (1a)
=(0,0,0). If you remove the 1a atom, symmetry has no problems, but
when (1a) is present, error pops up. It looks like symmetry wants to
have 12 symm operations, instead of 6 (?).
Is there an error in the symmetry program or how can I deal with
such a structure?

best,

Bartek Wiendlocha
Department of Condensed Matter Physics
AGH University of Science and Technology
Krakow, Poland

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Re: [Wien] error in symmetry step (not seen by sgroup)

[Laurence Marks]

Actually I found it when doing it step by step, although the error was only
in the output. Peter is the expert on this

On Tue, May 15, 2018 at 11:32 AM, Fecher, Gerhard 
wrote:

> Strange, just as a diagnostic
> it seems the error appears only when running batch initialisation
> I do not see it when using step by step initialisation in w2web
> or running x symmetry directly from the command line
>
> also strange, when converting the structure to P1 then sgroup finds space
> group 146 instead of 148
> but the batch initialisation has the same problem (indeed after accepting
> the structure from sgroup)
> again, no error from x symmetry only from batch initialisation
>
> 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 Bartek
> Wiendlocha [bwiendlo...@tlen.pl]
> Gesendet: Dienstag, 15. Mai 2018 15:20
> An: wien@zeus.theochem.tuwien.ac.at
> Betreff: [Wien] error in symmetry step (not seen by sgroup)
>
> Dear Wien2k Users & Developers,
>
> I have a strange problem with the symmetry step (during the initialization
> procedure), seems not to be reported to the mailing list before.
> My original system was rather a big one, so I created a smaller struct
> file to track the error (attached).
> Struct file was checked with sgroup before initialization, there are no
> problems with rounding of positions as well.
>
> During the initialization, symmetry reports the error:
> -- ERROR --
> ERROR: (multiplicity of atom   2 )*(number of
> pointgroup-operations)
> ERROR: is NOT = (number of spacegroup-operations)
> ERROR: MULT:   1  ISYM:  12  NSYM   6
> ERROR: Check your struct file withx sgroup
> -- ERROR --
>
> Space group is #148 R-3 with 6 symmetry operations. In the attached struct
> file there are 2 inequivalent positions: (6f) and (1a) =(0,0,0). If you
> remove the 1a atom, symmetry has no problems, but when (1a) is present,
> error pops up. It looks like symmetry wants to have 12 symm operations,
> instead of 6 (?).
> Is there an error in the symmetry program or how can I deal with such a
> structure?
>
> best,
>
> Bartek Wiendlocha
> Department of Condensed Matter Physics
> AGH University of Science and Technology
> Krakow, Poland
>
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-- 
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 ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
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Re: [Wien] error in symmetry step (not seen by sgroup)

[Fecher, Gerhard]

Strange, just as a diagnostic
it seems the error appears only when running batch initialisation
I do not see it when using step by step initialisation in w2web
or running x symmetry directly from the command line

also strange, when converting the structure to P1 then sgroup finds space group 
146 instead of 148
but the batch initialisation has the same problem (indeed after accepting the 
structure from sgroup)
again, no error from x symmetry only from batch initialisation

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 Bartek 
Wiendlocha [bwiendlo...@tlen.pl]
Gesendet: Dienstag, 15. Mai 2018 15:20
An: wien@zeus.theochem.tuwien.ac.at
Betreff: [Wien] error in symmetry step (not seen by sgroup)

Dear Wien2k Users & Developers,

I have a strange problem with the symmetry step (during the initialization 
procedure), seems not to be reported to the mailing list before.
My original system was rather a big one, so I created a smaller struct file to 
track the error (attached).
Struct file was checked with sgroup before initialization, there are no 
problems with rounding of positions as well.

During the initialization, symmetry reports the error:
-- ERROR --
ERROR: (multiplicity of atom   2 )*(number of pointgroup-operations)
ERROR: is NOT = (number of spacegroup-operations)
ERROR: MULT:   1  ISYM:  12  NSYM   6
ERROR: Check your struct file withx sgroup
-- ERROR --

Space group is #148 R-3 with 6 symmetry operations. In the attached struct file 
there are 2 inequivalent positions: (6f) and (1a) =(0,0,0). If you remove the 
1a atom, symmetry has no problems, but when (1a) is present, error pops up. It 
looks like symmetry wants to have 12 symm operations, instead of 6 (?).
Is there an error in the symmetry program or how can I deal with such a 
structure?

best,

Bartek Wiendlocha
Department of Condensed Matter Physics
AGH University of Science and Technology
Krakow, Poland

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[Wien] error in symmetry step (not seen by sgroup)

[Bartek Wiendlocha]

Dear Wien2k Users & Developers,   I have a strange problem with the 
symmetry step (during the initialization procedure), seems not to be reported 
to the mailing list before.  My original system was rather a big one, so I 
created a smaller struct file to track the error (attached).  Struct file was 
checked with sgroup before initialization, there are no problems with rounding 
of positions as well.   During the initialization, symmetry reports the error:  
-- ERROR --  ERROR: (multiplicity of atom   2 
)*(number of pointgroup-operations)  ERROR: is NOT = (number of 
spacegroup-operations)  ERROR: MULT:   1  ISYM:  12  NSYM   
    6  ERROR: Check your struct file with    x sgroup  -- ERROR 
--   Space group is #148 R-3 with 6 symmetry operations. In the 
attached struct file there are 2 inequivalent positions: (6f) and (1a) 
=(0,0,0). If you remove the 1a atom, symmetry has no problems, but when (1a) is 
present, error pops up. It looks like symmetry wants to have 12 symm 
operations, instead of 6 (?).  Is there an error in the symmetry program or how 
can I deal with such a structure?   best,   Bartek Wiendlocha  Department of 
Condensed Matter Physics  AGH University of Science and Technology  Krakow, 
Poland


sg-148.struct-sgroup
Description: Binary data
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Re: [Wien] (no subject)

[Laurence Marks]

That is due to overlapping spheres. You need to use smaller spheres (in
setrmt) when initializing, as explained in the user guide.

_
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 Tue, May 15, 2018, 12:34 AM Arvind Kumar 
wrote:

> Dear Prof. Blaha and Wien2k users,
>  I am trying to run volume optimization calculation on
> Gd2Cu2In and other related compounds but it shows error during run scf
>
> *ERROR status in Gd2Cu2In_vol_ -10.0*
>
> *> stop error  *
>
> *NN Error*
> *LAPW0 END*
> *hup: Command not found*
>
>
> I am running these calculation by Wien2k 16.1 version compiled in HP
> laptop having 8GB RAM and 1 TB harddisk with mkl library with ifort+ icc
> compiler.
>
>
> thanks & regards,
>
> Dr. Arvind Kumar
>
>
> --
> 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] Dense mesh calculation

[Peter Blaha]

You can avoid the vector file by an option in case.in1. See UG

On 05/15/2018 09:58 AM, Lukasz Plucinski wrote:

Dear All,

Could you let me know how to avoid saving huge vector files during dense 
mesh calculations? I am trying to do this for spin-polarized+SOC 
calculations. Perhaps someone could share a script that would only save 
eigenvalues?


Best,
Lukasz
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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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[Wien] Dense mesh calculation

[Lukasz Plucinski]

Dear All,

Could you let me know how to avoid saving huge vector files during dense 
mesh calculations? I am trying to do this for spin-polarized+SOC 
calculations. Perhaps someone could share a script that would only save 
eigenvalues?


Best,
Lukasz
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Re: [Wien] Finite temperature DFT: electronic free energy

[Peter Blaha]

Thanks for the bug report in init_lapw.

Please note: when the temperature (broadening) is set to zero, it will 
use automatically "room temperature" (0.0018 Ry).


On 05/15/2018 06:40 AM, Gavin Abo wrote:
I think you found a bug in init_lapw.  The fix seems like it should be 
simple though.  On line 498 in the init_lapw script in the sed command, 
it looks like $fermit just needs changed to $fermits.


I made a patch file called init_lapw.patch [ 
https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1 ], which you 
should be able to apply and try simply using:


username@computername:~/Desktop$ cd $WIENROOT
username@computername:~/WIEN2k$ wget 
https://raw.githubusercontent.com/gsabo/WIEN2k-Patches/master/17.1/init_lapw.patch

username@computername:~/WIEN2k$ patch -b init_lapw init_lapw.patch
patching file init_lapw

Maybe F is the :ENE (TOTAL ENERGY) in case.scf.

I tried following what a previous user did [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html 
] but with a quick TiC calculation using run_lapw in WIEN2k 17.1:


T = 1000 K = 0.00633 Ry
init_lapw -b -fermits 0.00633
TiC.scf::ENE  : ** TOTAL ENERGY IN Ry = -1783.95041939
TiC.output2:  Kb * T    =   0.00633000
TiC.output2:  -T*Entr   =  -0.00054181

T = 0 K = 0.0 Ry
init_lapw -b -fermits 0.0
TiC.scf::ENE  : ** TOTAL ENERGY IN Ry = -1783.94928338
TiC.output2:  Kb * T    =   0.0018
TiC.output2:  -T*Entr   =  -0.5329

F_1000K - F_0K = (E - T*S) - (E - 0) = -T*S = -1783.95041939 - 
(-1783.94928338) = -0.001136 => -T*S = -0.001136


If -T*S divided by 2:

-T*S = -0.001136/2 = - 0.000568 <- This seems reasonably close to the 
above -0.00054181 for T = 1000 K.


As I recall, the -T*S term was doubled in WIEN2k versions after 2014 [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg10319.html 
].


Though, there may be a flaw in my above calculation.

On 5/14/2018 5:35 PM, Sabry Moustafa wrote:


Hi;

I am interested in the electronic free energy (F=E-TS) using the 
finite temperature DFT using Fermi-Dirac statistics (i.e., Mermin's 
extension to 0 K DFT) -- i.e., I am not just looking for Fermi-Dirac 
as a broadening/smearing technique. So,how this can be done in WIEN2k?


It looks like I have to define "-fermits X" in the init_lapw command 
(where X= kT, in Ry). But when I did (T=1000K in my case):


init_lapw -b -fermits 0.00633

I got "fermit: Undefined variable." at the end. This is fixed though 
when defined fermit as well:


init_lapw -b -fermit 0.00633 -fermits 0.00633

So, do I have to define both?


Also, where can I find this "free energy F". It does not seem to be 
the "TOTAL ENERGY" in case.scf. Seems like I need to add this "TOTAL 
ENERGY" (E) to "-T*Entr" (-TS) in case.output2 file to get F?



Thanks ;

Sabry


:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:-:

Sabry G. Moustafa, Ph.D.
Department of Chemical and Biological Engineering,
University at Buffalo, The State University of New York.
511 Furnas Hall
Buffalo, NY 14260-4200
716-645-1186 (office)
716-239-8543 (cell)

E-mail: sabry...@buffalo.edu 



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--

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--
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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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