# [Wien] Question about Bismuth structure file generated by wien2k

Peter Blaha pblaha at theochem.tuwien.ac.at
Thu Oct 25 22:18:12 CEST 2007

```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:
>
> 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...
>
> 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
>
>     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
>      >     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
>     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...
>      >      >
>      >     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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