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

2018-05-17 Thread Peter Blaha 

Probably the same change should be made there.

One problem: It could be that for some weired structures this lower tol 
value leads to other problems 


On 05/17/2018 10:59 AM, Gavin Abo wrote:
In WIEN2k 17.1, is tol=1.e-3 in SRC_symmetso/symmetso.f on line 110 okay 
or does the same change need to be made too?  Thanks in advance.


On 5/15/2018 11:43 AM, Peter Blaha wrote:

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.


___
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


--

  P.Blaha
--
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
--
___
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] error in symmetry step (not seen by sgroup)

2018-05-17 Thread Gavin Abo 
In WIEN2k 17.1, is tol=1.e-3 in SRC_symmetso/symmetso.f on line 110 okay 
or does the same change need to be made too?  Thanks in advance.


On 5/15/2018 11:43 AM, Peter Blaha wrote:

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.


___
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] error in symmetry step (not seen by sgroup)

2018-05-15 Thread 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 
pbl...@theochem.tuwien.ac.at 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 
fec...@uni-mainz.de  mailto:fec...@uni-mainz.de; 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     mailto:wien-bounces@zeu im 
Auftrag von     Bartek Wiendlocha [bwiendlo...@tlen.pl 
mailto:bwiendlo...@tlen.pl;]     Gesendet: Dienstag, 15. Mai 2018 15:20  
   An:   w...@zeus.theochem.tuwien.ac.a     mailto:wien@zeus.theoch     
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      
     Wien mailing list     Wien@zeus.theochem.tuwie 
mailto:w...@zeus.theochem.tuw      urldefense.proofpoint.com 
urldefense.proofpoint.com      urldefense.proofpoint.com 
urldefense.proofpoint.com     SEARCH the MAILING-LIST at:      
urldefense.proofpoint.com urldefense.proofpoint.com      
urldefense.proofpoint.com urldefense.proofpoint.com  --  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 
 www.numis.northwestern.edu www.numis.northwestern.edu  ;  
Corrosion in 4D: MURI4D.numis.northwestern.edu  
http://MURI4D.numis.northwest  Partner of the CFW 100% program for gender 
equity,  www.cfw.org/100-percent  www.cfw.org www.cfw.org  Co-Editor, Acta 
Cryst A__  Wien mailing list   
w...@zeus.theochem.tuwien.ac.a  zeus.theochem.tuwien.ac.at 
zeus.theochem.tuwien.ac.at  SEARCH the MAILING-LIST at:  

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

2018-05-15 Thread 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

___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at 

https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=9sFYvMHWQPxxlBbFjX6aqVekcH0IspjZ-VNidVjyZqI=SH-n4bK9eJe_2DkJ0sJ0bgi58SoJp2VKU-Cd9ytGQgQ=


SEARCH the MAILING-LIST at:

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html=DwICAg=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=9sFYvMHWQPxxlBbFjX6aqVekcH0IspjZ-VNidVjyZqI=n6NCHyy6hmQyqWUCeF9VzdK104aqjmSqxgxVO_Ip_5M=

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

2018-05-15 Thread 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
>
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.
> theochem.tuwien.ac.at_mailman_listinfo_wien=DwICAg=
> yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=9sFYvMHWQPxxlBbFjX6aqVekcH0Isp
> jZ-VNidVjyZqI=SH-n4bK9eJe_2DkJ0sJ0bgi58SoJp2VKU-Cd9ytGQgQ=
> SEARCH the MAILING-LIST at:  https://urldefense.proofpoint.
> com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-
> 40zeus.theochem.tuwien.ac.at_index.html=DwICAg=
> yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_
> T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=9sFYvMHWQPxxlBbFjX6aqVekcH0Isp
> jZ-VNidVjyZqI=n6NCHyy6hmQyqWUCeF9VzdK104aqjmSqxgxVO_Ip_5M=
>



-- 
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
___
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] error in symmetry step (not seen by sgroup)

2018-05-15 Thread 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

___
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