date:20161011

Re: [Wien] Change of structure symmetry

2016-10-11 Thread delamora

Thank you,

No, I do not think that it is crystallographically wrong, it is just the way 
that sgroup chooses to put the lines

This way

.   .   .

  /  /

.   .   .

connecting diagonally

or this way

.   .   .

|  |

.   .   .
connecting vertically

both are correct


De: Wien  en nombre de Laurence Marks 


I agree with you -- it would be nice if 90 was kept although formally I believe 
it is crystallographically wrong. I have never tried to tweak the code as it is 
in C which I don't like much. Maybe someone who likes C can look.

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, 
www.cfw.org/100-percent
Co-Editor, Acta Cryst A


On Oct 11, 2016 21:51, "delamora" > 
wrote:
I want to see how Cu interacts with the TiO2 surface, so I construct with 
'supercell' an enlarged cell, with
SG 35 (C m m 2)
then I attach Cu and O on the surface in a way that I break the symmetry in the 
b direction
The cell is orthorhombic

CXY LATTICE,NONEQUIV.ATOMS: 21
MODE OF CALC=RELA unit=bohr
 11.187184 23.838706 23.838290 90.0 90.0 90.0

if I run initialize calculation and then sgroup the new cell changes to

CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm
MODE OF CALC=RELA unit=bohr
 23.838706 33.712727 11.187184 90.0 90.0 135.000500

which is correct, but it is no longer orthogonal which is awkward, one angle 
changes from
90 to 135.0005
also the a, b, c => c, a, b

Also I cannot see the structure with XCrySDen, unless I change the 135.0005 
angle by little.

With the new structure and the old one I managed to make a new TiO2.struct with 
orthorhombic and can be seen with XCrySDen

It would be nice that sgroup would generate a structure with the orthorhombic 
symmetry

  Saludos

  Pablo de la Mora

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Re: [Wien] Change of structure symmetry

2016-10-11 Thread delamora

Thank you,

I have encountered this problem before and I was able to use the orthorhombic 
cell, but in this case the task was much harder, and if sgroup had this ability 
to choose the most "compact" cell it would be nice.

For example a square cell is correct (in 2D), but if one puts lines at 45 
degrees it is also correct in certain cases. Which is what is happening here, 
the program chooses 90+45 degrees instead of 90

I hope to make myself clear



De: Wien  en nombre de Peter Blaha 

Enviado: miércoles, 12 de octubre de 2016 12:32:03 a. m.
Para: A Mailing list for WIEN2k users
Asunto: Re: [Wien] Change of structure symmetry

It is not always mandatory to take the changes suggested by sgroup into
account. (This is the reason why it is not made automatically). For low
symmetry structures (monoclinic) there are many possible settings and
even the construction of the unit cell is not unique, but arbitrary
equivalent choices exists.

The following "rules" exist: Run

x nn   #  and accept all changes to get the proper multiplicity of the
atoms.
x sgroup   #  and check if sgroup has reduced the unit cell (or changed
the multiplicity). Only in this case you have to accept the changes by
sgroup. ("Reduced" means: the total number of atoms in the cell got
smaller). If sgroup just changed the lattice type or a,b,c,angles; there
is no need to accept the scgroup changes.
To be sure that you can neglect the changes, just  remember the number
of symmetry operations which sgroup has found.

x symmetry  # compare the number of symmetry operations from symmetry
and sgroup. If this is the same (of course, the individual operations
may be different) and symmetry also found identical site symmetry of all
positions, you are save and can simply neglect sgroup.


Am 12.10.2016 um 04:50 schrieb delamora:
> I want to see how Cu interacts with the TiO2 surface, so I construct
> with 'supercell' an enlarged cell, with
> SG 35 (C m m 2)
> then I attach Cu and O on the surface in a way that I break the symmetry
> in the b direction
> The cell is orthorhombic
>
> CXY LATTICE,NONEQUIV.ATOMS: 21
> MODE OF CALC=RELA unit=bohr
>  11.187184 23.838706 23.838290 90.0 90.0 90.0
>
> if I run initialize calculation and then sgroup the new cell changes to
>
> CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm
> MODE OF CALC=RELA unit=bohr
>  23.838706 33.712727 11.187184 90.0 90.0 135.000500
>
> which is correct, but it is no longer orthogonal which is awkward, one
> angle changes from
> 90 to 135.0005
> also the a, b, c => c, a, b
>
> Also I cannot see the structure with XCrySDen, unless I change the
> 135.0005 angle by little.
>
> With the new structure and the old one I managed to make a new
> TiO2.struct with orthorhombic and can be seen with XCrySDen
>
> It would be nice that sgroup would generate a structure with the
> orthorhombic symmetry
>
>   Saludos
>
>   Pablo de la Mora
>
>
>
> ___
> Wien mailing list
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> 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
>

--
--
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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/staff/tc_group_e.php
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Re: [Wien] Change of structure symmetry

2016-10-11 Thread Peter Blaha

It is not always mandatory to take the changes suggested by sgroup into 
account. (This is the reason why it is not made automatically). For low 
symmetry structures (monoclinic) there are many possible settings and 
even the construction of the unit cell is not unique, but arbitrary 
equivalent choices exists.


The following "rules" exist: Run

x nn   #  and accept all changes to get the proper multiplicity of the 
atoms.
x sgroup   #  and check if sgroup has reduced the unit cell (or changed 
the multiplicity). Only in this case you have to accept the changes by 
sgroup. ("Reduced" means: the total number of atoms in the cell got 
smaller). If sgroup just changed the lattice type or a,b,c,angles; there 
is no need to accept the scgroup changes.
To be sure that you can neglect the changes, just  remember the number 
of symmetry operations which sgroup has found.


x symmetry  # compare the number of symmetry operations from symmetry 
and sgroup. If this is the same (of course, the individual operations 
may be different) and symmetry also found identical site symmetry of all 
positions, you are save and can simply neglect sgroup.



Am 12.10.2016 um 04:50 schrieb delamora:

I want to see how Cu interacts with the TiO2 surface, so I construct
with 'supercell' an enlarged cell, with
SG 35 (C m m 2)
then I attach Cu and O on the surface in a way that I break the symmetry
in the b direction
The cell is orthorhombic

CXY LATTICE,NONEQUIV.ATOMS: 21
MODE OF CALC=RELA unit=bohr
 11.187184 23.838706 23.838290 90.0 90.0 90.0

if I run initialize calculation and then sgroup the new cell changes to

CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm
MODE OF CALC=RELA unit=bohr
 23.838706 33.712727 11.187184 90.0 90.0 135.000500

which is correct, but it is no longer orthogonal which is awkward, one
angle changes from
90 to 135.0005
also the a, b, c => c, a, b

Also I cannot see the structure with XCrySDen, unless I change the
135.0005 angle by little.

With the new structure and the old one I managed to make a new
TiO2.struct with orthorhombic and can be seen with XCrySDen

It would be nice that sgroup would generate a structure with the
orthorhombic symmetry

  Saludos

  Pablo de la Mora



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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
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
--
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Re: [Wien] Change of structure symmetry

2016-10-11 Thread Laurence Marks

I agree with you -- it would be nice if 90 was kept although formally I
believe it is crystallographically wrong. I have never tried to tweak the
code as it is in C which I don't like much. Maybe someone who likes C can
look.

---
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
http://www.numis.northwestern.edu
Corrosion in 4D http://MURI4D.numis.northwestern.edu
Partner of the CFW 100% gender equity project, www.cfw.org/100-percent
Co-Editor, Acta Cryst A


On Oct 11, 2016 21:51, "delamora"  wrote:

> I want to see how Cu interacts with the TiO2 surface, so I construct with
> 'supercell' an enlarged cell, with
> SG 35 (C m m 2)
> then I attach Cu and O on the surface in a way that I break the symmetry
> in the b direction
> The cell is orthorhombic
>
> CXY LATTICE,NONEQUIV.ATOMS: 21
> MODE OF CALC=RELA unit=bohr
>  11.187184 23.838706 23.838290 90.0 90.0 90.0
>
> if I run initialize calculation and then sgroup the new cell changes to
>
> CXZ LATTICE,NONEQUIV.ATOMS: 28 8 Cm
> MODE OF CALC=RELA unit=bohr
>  23.838706 33.712727 11.187184 90.0 90.0 135.000500
>
> which is correct, but it is no longer orthogonal which is awkward, one
> angle changes from
> 90 to 135.0005
> also the a, b, c => c, a, b
>
> Also I cannot see the structure with XCrySDen, unless I change the
> 135.0005 angle by little.
>
> With the new structure and the old one I managed to make a new TiO2.struct
> with orthorhombic and can be seen with XCrySDen
>
> It would be nice that sgroup would generate a structure with the
> orthorhombic symmetry
>
>   Saludos
>
>   Pablo de la Mora
>
>
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[Wien] Wannier90 and the case_hr.dat file

2016-10-11 Thread Tim Hackett

Greetings,

I am working with the new Wannier90 program (v2.0.1) and the program bkq in
the crystal field parameters.  I have done the following steps in step 3:

x kgen -fbz
x lapw1 -orb (-p)
x  joinvec
write_inwf
write_win
x wannier90 -pp
made the case.fermi with one line containing the fermi number
x w2w (-p)
x wannier90

Wannier90 gives a case_hr.dat file that is used in step 4 to make the
output file case.outbkq, which is later copied.  The output from my system
starts as:

 written on 10Oct2016 at 17:27:56
   7
 195
211124222421112
211124222421112
211122111221112
211122111221112
211122111221112
211124222421112
211122111221112
211124222421112
211122111221112
211122111221112
211122111221112
211124222421112
211124222421112
   -4   -2   -2110.002444   -0.005910
   -4   -2   -2210.002181   -0.005484
   -4   -2   -2310.0026960.007591
   -4   -2   -241   -0.0026510.006366
   -4   -2   -251   -0.0008320.003992
   -4   -2   -2610.0020110.003671

and continues for a total of 9571 lines.  In the example provided with
RECFP package, this file is completely different.

Can you tell me where I might have made a mistake?

Cheers,

-- 

Timothy A. Hackett

Research Associate I-X

Division of Materials Science & Engineering

Ames Laboratory, Iowa State University, Ames, IA 50011
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Re: [Wien] Which notation for the spin direction in hexagonal structure

2016-10-11 Thread Laurence Marks

3 index notation is used everywhere in Wien2k.

On Tue, Oct 11, 2016 at 9:40 AM, Zhu, Jianxin  wrote:

> Dear Xavier,
>
> It means it is not defined with respect to the primitive lattice vectors.
> The lattice parameters given in case.struct file are sometimes for the
> conventional unit cell.
>
> I appreciate if you can confirm.
>
> Thanks,
>
> Jianxin
>
>
> From: Wien  on behalf of Xavier
> Rocquefelte 
> Reply-To: A Mailing list for WIEN2k users  >
> Date: Sunday, October 9, 2016 at 5:00 AM
> To: "wien@zeus.theochem.tuwien.ac.at" 
> Subject: Re: [Wien] Which notation for the spin direction in hexagonal
> structure
>
> Dear Colleague
>
> The notation is with three indices.
>
> It will be along the directions defined in your case.struct file.
>
> In other words, if you put 0 0 1, it will be along the c-axis of your
> case.struct file.
>
> Best Regards
>
> Xavier
>
>
>
> Le 09/10/2016 à 12:52, Abderrahmane Reggad a écrit :
>
> Dear Wien2k users
>
> I want to introduce the spin-orbit coupling in my calculation for a
> hexagonal structure.
>
> Would you inform me which notation should we use to introduce the spin
> direction : that of 3 indicesor that of 4 indices.
>
> NB: The spin direction for my case is the z direction
>
> Best regards
>
> --
> Mr: A.Reggad
> Laboratoire de Génie Physique
> Université Ibn Khaldoun - Tiaret
> Algerie
>
>
>
>
> ___
> Wien mailing 
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>  
> 
> SEARCH the MAILING-LIST at:  
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html 
> 
>
>
>


-- 
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] Which notation for the spin direction in hexagonal structure

2016-10-11 Thread Abderrahmane Reggad

Hello again

I have resolved the problem.

Now I ovserved that as in the case of NiO , the spin-orbit coupling doesn't
improve the gap for my compound.

My question is:

Which quantities are influenced by the spin-orbit coupling?

Best regards

-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Algerie
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Re: [Wien] Change of structure symmetry

Re: [Wien] Change of structure symmetry

Re: [Wien] Change of structure symmetry

Re: [Wien] Change of structure symmetry

[Wien] Wannier90 and the case_hr.dat file

Re: [Wien] Which notation for the spin direction in hexagonal structure

Re: [Wien] Which notation for the spin direction in hexagonal structure

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