[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:
> 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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