[Wien] Question about Bismuth structure file generated by wien2k
Gerhard Fecher
fecher at uni-mainz.de
Sun Oct 28 12:14:10 CET 2007
sgroup is supposed to find always the correct symmetry (at least if a structure is not that complicated that any roundoff error
prevents to find the correct symmetry).
Try to convert youre structure to P1 (all symmetry operations removed, but indeed you will probably have more atoms)
You will see that sgroup finds the correct space group.
-----Ursprüngliche Nachricht-----
Von: wien-bounces at zeus.theochem.tuwien.ac.at im Auftrag von Bo Qiu
Gesendet: So 28.10.2007 04:05
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] Question about Bismuth structure file generated by wien2k
Thanks a lot for your reply!
I've tried for another day, I know it sounds stupid, but I still have
something unclear, could you please still help me with that? Sorry for
keeping asking such entrance level questions for such a long time, but I
really want to know more, thanks a lot for your help again!!!
First, I checked ICSD, yes the bismuth space group is 166 R-3m, however, on
American Mineralogist Crystal Structure Database (AMD
http://rruff.geo.arizona.edu/AMS/amcsd.php ) if I search "bismuth", then I
can see some papers show its space group is 166 R-3m, while others show its
space group is 160 R3m (h axes).
Then I downloaded the CIF file from ICSD, it is exactly that one showed in
Dr Blaha' last email (6 equivalent atoms, h axes). And I used CIF2STRUCT on
this CIF file, it generated a struct file almost the same as in Dr Blaha's
last email, but GAMMA angle is 120 instead of 90. I don't know if there is
any problem with that.
Second, I downloaded CIF file from AMD which says the space group of Bismuth
is 160 R3m , I examined that CIF file and find that it is in Hex axes which
complies with the required input of CIF2STRUCT, so I run CIF2STRUCT, and a
struct like below was generated:
==============================
blebleble
H LATTICE,NONEQUIV.ATOMS 1 160 R3m
MODE OF CALC=RELA unit=bohr
8.590695 8.590695 22.415931 90.000000 90.000000120.000000
ATOM -1: X=0.00000000 Y=0.00000000 Z=0.23389000
MULT= 3 ISPLIT=15
-1: X=0.66666667 Y=0.33333333 Z=0.56722333
-1: X=0.33333333 Y=0.66666667 Z=0.90055667
Bi NPT= 781 R0=.000005000 RMT= 2.00000 Z: 83.00000
LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
0 NUMBER OF SYMMETRY OPERATIONS
=================================
Then I continued with Init_lapw, (NN distance is 8.59070 in this case ) when
I run sgroup, it told me 166 R-3m symmetry was found and the Bravais lattice
has changed. I got a question here: according to the CIF file, the atomic
positions in this case is due to the symmetry of 160 R3m space group (in hex
settings), but why after "sgroup" it told me 166 R-3m symmetry was found?
Last question:
A CIF file which contains the file like below can still work with CIF2STRUCT
directly, although it is in rhombohedral axes, am I right? Thanks a lot!
======================
Bismuth
Wyckoff R W G
Crystal Structures 1 (1963) 7-83
Second edition. Interscience Publishers, New York, New York
4.7459 4.7459 4.7459 57.237 57.237 57.237 R-3m
atom x y z
Bi .237 .237 .237
==========================
Thanks and Best Wishes
Sincerely yours,
Bo Qiu
On 10/25/07, Peter Blaha <pblaha at theochem.tuwien.ac.at> wrote:
>
> First: You need to learn some basic crystallography.
> Some spacegroups have more than one setting. Click on the link in the
> STRUCTEDITOR.
>
> Second: Bi is R-3m (number 166) and not 160 R3m !!!
>
> When you take a cif file which gives the structure in hex
> cit2struct converts it into a hex lattice:
>
> blebleble
>
> H LATTICE,NONEQUIV.ATOMS 1 166 R-3m
> MODE OF CALC=RELA unit=bohr
> 8.569908 8.569908 22.325225 90.000000 90.000000120.000000
> ATOM -1: X=0.00000000 Y=0.00000000 Z=0.76600000
> MULT= 6 ISPLIT=15
> -1: X=0.00000000 Y=0.00000000 Z=0.23400000
> -1: X=0.66666667 Y=0.33333333 Z=0.09933333
> -1: X=0.66666667 Y=0.33333333 Z=0.56733333
> -1: X=0.33333333 Y=0.66666667 Z=0.43266667
> -1: X=0.33333333 Y=0.66666667 Z=0.90066667
> Bi 0+ NPT= 781 R0=.000005000 RMT= 2.00000 Z: 83.00000
>
> So there are 6 equivalent positions, not 3 !
>
> This struct file does not obey the WIEN2k rules for R lattices, so you
> MUST NOT save it in STRUCTEDITOR.
>
> When you run init_lapw with this struct file, sgroup will convert it to
> a WIEN2k conform structure and create a file like:
>
> Bismut
> R LATTICE,NONEQUIV. ATOMS 1
> MODE OF CALC=RELA
> 8.590000 8.590000 22.415000 90.000000 90.000000 90.000000
> ATOM -1: X=0.23400000 Y=0.23400000 Z=0.23400000
> MULT= 2 ISPLIT= 4
> ATOM -1: X=0.76600000 Y=0.76600000 Z=0.76600000
> Bi NPT= 781 R0=0.00001000 RMT= 2.8000 Z: 83.0
>
> You can also find this file in $WIENROOT/example_struct_files.
>
>
> Bo Qiu schrieb:
> > Thanks for your instructions!
> >
> > However, I did have specified the space group to be R3m. Actually what I
> > have done is to use hex2rhomb to give this transformation
> > (0,0,0.23407)-->(0.23407,0.23407,0.23407), once I get this internal
> > parameters, I go back to w2web and use STRUCTGEN to make the structure
> > file, and I specified the space group to be 160_R3m, however I just get
> > one atom, and the successive initializations failed...
> >
> > Then I try to download the CIF file from American Mineralogist Crystal
> > Structure database, then use cif2struct to generate the file. Then I go
> > back to w2web and take a look at the structure file, the internal
> > parameters are:
> >
> > ATOM -1: X=0.00000000 Y=0.00000000 Z=0.23407000
> > MULT= 3 ISPLIT=15
> > -1: X=0.66666667 Y=0.33333333 Z=0.56740333
> > -1: X=0.33333333 Y=0.66666667 Z=0.90073667
> >
> > they looked good. However, once I pressed "edit struct file" then "save
> > structure" without any change, I found the structure file has been
> > modified, again, to be:
> >
> > ATOM -1: X=0.99999999 Y=0.00000000 Z=0.23407000
> > MULT= 3 ISPLIT= 5
> > ATOM -1:X= 0.00000000 Y=0.23407000 Z=0.99999999
> > ATOM -1:X= 0.23407000 Y=0.99999999 Z=0.00000000
> >
> > And I run init_lapw, it still failed... I don't really know why.
> >
> > So later I tried just use the structure file generated by cif2struct and
> > run init_lapw, but when it gets to sgroup, it told me that the space
> > group found was R-3m instead of R3m (while R3m is the specified one in
> > that cif file). I accepted that and afterwards there is core electron
> > leakage when setting separation energy to be -6Ry, then I changed it to
> > -10Ry. Seemed it worked. And SCF seemed to be working. Then I proceeded
> > to generate the band structure plotting, and compare it with
> > literature... but it seems to have not much similarity...
> >
> > Could you please help me with that? I really don't know what's wrong
> > with my setup... could you please tell me how to do that? Thank you very
> > very much!!!!
> >
> > Sincerely yours,
> >
> > Bo Qiu
> >
> >
> >
> > On 10/25/07, *Peter Blaha* <pblaha at theochem.tuwien.ac.at
> > <mailto:pblaha at theochem.tuwien.ac.at>> wrote:
> >
> > But you still need to specify the space group.
> > Only by knowing the spacegroup, STRUCTGEN can put the second
> position
> > into your struct file.
> >
> > Bo Qiu schrieb:
> > > Thank you very much for your reply!!! It really helps me a lot!
> > >
> > > However, I still have some problem with that...
> > >
> > > Due to your instructions, I use hex2rhomb to convert the
> > coordinates:
> > > (0,0,0.23407)-->(0.23407,0.23407,0.23407)
> > >
> > > Then I modified the input:
> > >
> > > lattice parameters:
> > > a=b=4.5330 A, c=11.797 A, alpha=belta=90 degree, gamma=120
> degree.
> > > Atom 1: Bi , Z=83, RMT= 0.99
> > > x=0.23407, y=0.23407, z=0.23407.
> > >
> > > After I "save and clean up", I only got one atom... and when I
> > continued
> > > with initialization, when it reached the step "sgroup", it
> reported
> > > inconsistency between the space group found and the struct
> > file... and
> > > more errors to come...
> > >
> > > Could you please tell me what is still wrong in my setup? Thanks
> > a lot!
> > >
> > > Best Wishes,
> > >
> > > Sincerely yours,
> > > Bo Qiu
> > >
> > >
> > >
> > > On 10/24/07, *Rocquefelte* <Xavier.Rocquefelte at cnrs-imn.fr
> > <mailto:Xavier.Rocquefelte at cnrs-imn.fr>
> > > <mailto: Xavier.Rocquefelte at cnrs-imn.fr
> > <mailto:Xavier.Rocquefelte at cnrs-imn.fr>>> wrote:
> > >
> > > Dear Bo Qiu,
> > >
> > > In the particular case of rhombohedral structures the
> > initialization of
> > > the Wien2k calculation should be done by specifying the
> > hexagonal
> > > lattice parameters and the rhombohedral coordinates in the
> > structure
> > > file. An auxiliary program can be used to convert your
> > coordinates from
> > > hexagonal to rhombohedral (hex2rhomb). You will find more
> > details about
> > > this question in the userguide (p. 40).
> > >
> > > Have a nice day
> > >
> > > Regards
> > >
> > > Xavier
> > >
> > >
> > > Bo Qiu a écrit :
> > > > Dear Wien2k users and developers,
> > > >
> > > > Recently I'm trying to calculate Bismuth, using the data
> > got from
> > > > American Mineralogist Crystal Structure database, however,
> > I'm not
> > > > sure about the structrue generated by wien2k, and what's
> > more, based
> > > > on that structure generated, calculation failed even at
> the
> > > > initialization step. Could you please help me with that?
> > Thanks a
> > > lot!!!
> > > >
> > > > Below is the data from American Mineralogist Crystal
> > Structure
> > > database
> > > > ===============================================
> > > > Bismuth
> > > >
> > > > Schiferl D, Barrett CS
> > > > Journal of Applied Crystallography 2 (1969) 30-36
> > > > The crystal structure of arsenic at 4.2, 78 and 299 K
> > > > Sample: T = 4.2 K
> > > >
> > > > 4.5330 4.5330 11.797 90 90 120 R3m
> > > > atom x y z
> > > > Bi 0 0 .23407
> > > > ==============================================
> > > >
> > > > Then based on this data, I start a session with 1
> > inequivalent atom,
> > > > space group R3m,
> > > > lattice parameters:
> > > > a=b=4.5330 A, c=11.797 A, alpha=belta=90 degree, gamma=120
> > degree.
> > > > Atom 1: Bi , Z=83, RMT=0.99
> > > > x=0, y=0, z=0.23407.
> > > >
> > > > However after I saved the structure, I got this structrue
> > file:
> > > >
> > > > ==================================================
> > > > bi
> > > > R LATTICE,NONEQUIV.ATOMS: 1160_R3m
> > > > MODE OF CALC=RELA unit=ang
> > > > 8.566510 8.566510 22.293108 90.000000
> 90.000000120.000000
> > > > ATOM -1: X=0.99999999 Y=0.00000000 Z=0.23407000
> > > > MULT= 3 ISPLIT= 8
> > > > ATOM -1:X= 0.00000000 Y=0.23407000 Z=0.99999999
> > > > ATOM -1:X= 0.23407000 Y=0.99999999 Z=0.00000000
> > > > Bi NPT= 781 R0= 0.00000500 RMT= 1.1000 Z:
> 83.0
> > > > LOCAL ROT MATRIX: 0.0000000 1.0000000 0.0000000
> > > > 0.0000000 0.0000000 1.0000000
> > > > 1.0000000 0.0000000 0.0000000
> > > > 6 NUMBER OF SYMMETRY OPERATIONS
> > > > ......
> > > >
> > > > ==================================================
> > > > I'm not quite sure, but I think the coordinates for atom
> 1,2,3
> > > might be:
> > > > (0,0,0.23407 ),
> > (2/3,1/3,1/3+0.23407),(1/3,2/3,2/3+0.23407) due to
> > > > space group symmetry which is different from that one in
> the
> > > structure
> > > > file. So why is the difference? Thanks a lot!
> > > >
> > > > Though I don't understand the structure file, I still
> > proceeded to
> > > > initialization. At the first step it seemed to be ok,
> however,
> > > when it
> > > > reached "x lstart", there is warning about core electron
> > leakage.
> > > So I
> > > > go back to increase RMT, however, after that, NN error
> > showed up
> > > > during initialization... then I tried to keep RMT but to
> > reduce
> > > > separation energy, it failed when this energy is set to be
> > less than
> > > > -10 Ry...
> > > >
> > > > That's the problem I met. Could you please help me with
> that?
> > > Thanks a
> > > > lot!
> > > >
> > > > The system I'm using is
> > > > Ifort, mkl 9.0, bash shell, wien2k_07
> > > >
> > > > --
> > > > Thanks and Best Wishes.
> > > >
> > > > Sincerely yours,
> > > > Bo Qiu
> > > > http://web.ics.purdue.edu/~qiub/
> > <http://web.ics.purdue.edu/%7Eqiub/>
> > > >
> > >
> >
> ------------------------------------------------------------------------
> >
> > > >
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> > >
> > >
> > >
> > >
> > > --
> > > Thanks and Best Wishes.
> > >
> > > Sincerely yours,
> > > Bo Qiu
> > > http://web.ics.purdue.edu/~qiub/
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> > >
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> >
> >
> >
> >
> > --
> > Thanks and Best Wishes.
> >
> > Sincerely yours,
> > Bo Qiu
> > http://web.ics.purdue.edu/~qiub/
> >
> >
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--
Thanks and Best Wishes.
Sincerely yours,
Bo Qiu
http://web.ics.purdue.edu/~qiub/
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