[Wien] Question about Bismuth structure file generated by wien2k
Bo Qiu
200210qb at gmail.com
Thu Oct 25 19:35:01 CEST 2007
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> 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>> 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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> > >
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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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