The ABINIT Users Mailing List ( CLOSED )

["Razvan Caracas" <r.caracas@gl.ciw.edu>]

Dear Stephen,

One way is:

rprim 1 0 0  0 1 0  0 0 1
acell 5.627 5.575 12.425 Angstrom
xred
... the xred from icsd

then

chkprim 0
spgroup 63
spgaxor 1..9

You should check the orientation of your Bmmb setting with respect to the
standard orientation of group 63. Some trial and error should give you the
proper answer fast enough. In the end you must have 20 atoms. Once you
have this you can try to figure out the primitive cell.

Good luck
Razvan


> Gian-Marco and any other interested experts in crystallography
>
> When I set chkprim 0, abinis 4.4.3 insists on a primitive unit cell
> of 8 atoms. This is not possible, since there are 5 atoms in the
> formula Pb Bi Cl O2.
>
> Unfortunately, ICSD does not give the atomic positions of the
> primitive unit cell, only the irreducible unit cell and the space
> group information. I hoped that ABINIT could figure out the primitive
> unit cell. Here is what I have from the ICSD:
>
> Unit Cell   5.627(50) 5.575(20) 12.425(90) 90. 90. 90.
> Vol         389.78
> Z           4
> Space Group B m m b
> SG Number   63
> Cryst Sys   orthorhombic
> Pearson     oS20
> Wyckoff     e c3
> Red Cell    B  5.575 5.627 6.819 114.364 90 89.999 194.889
> Trans Red   0.000 1.000 0.000 / -1.000 0.000 0.000 / 0.500 0.000 0.500
> Comments    PDF 13-352, nadorite is Sb-analogue
>              Compound with mineral name: Perite
>              The structure has been assigned a PDF number: 13-352
>              X-ray diffraction (powder)
>              No R value given in the paper.
>              At least one temperature factor missing in the paper.
> Atom  #   OX   SITE      x           y           z           SOF      H
> Pb   1  +2    4 c   0           0.25        0.385          1.         0
> Bi   1  +3    4 c   0           0.25        0.09           1.         0
> Cl   1  -1    4 c   0           0.25        0.75           1.         0
> O    1  -2    8 e   0.25        0           0              1.         0
> *end for    ICSD #31860
>
> The ICSD information should be sufficient to construct the primitive
> unit cell that ABINIT wants. How do I put the ICSD information into
> the ABINIT input file?
>
> Thanks
>
> Stephen
>
>
> On Nov 15, 2005, at 10:10 PM, Gian-Marco Rignanese wrote:
>
>> Dear Ste[jem
>>
>>> The job crashes as follows:
>>>
>>> gensymspgr : WARNING -
>>>    The assigned brvltt        4 is not equal
>>>    to the input value        6
>>>    Assume experienced user. Execution will continue.
>>>    the choosen orientation corresponds to:  acb
>>>
>>> chkprimit : ERROR -
>>>    According to the symmetry finder, the unit cell is
>>>    NOT primitive. The multiplicity is  2 .
>>>    The use of non-primitive unit cells is allowed
>>>    only when the input variable chkprim is 0.
>>>    Action : either change your unit cell (rprim or angdeg),
>>>    or set chkprim to 0.
>>>
>>> leave_new : decision taken to exit ...
>>> STOP 1
>>
>> You can see that there is an ERROR and WARNING... You focused on
>> the WARNING not on the ERROR!
>>
>> Just put "chkprim 0" in your input file... The program will
>> generate the conventional unit cell for that
>> space group. This cell has a multiplicity of 2. Now, if you
>> reallywant the primitive cell, you need to
>> introduce all the atomic positions by hand and change the
>> description of the cell accordingly (acell and
>> rprim). My guess (since you only provided a part of the input file)
>> is that your input (acell and rprim)
>> corresponds to the conventional cell, otherwise ABINIT would have
>> complained even more...
>>
>> Finally, regarding the WARNING, for group 63, the bravais lattice
>> is somewhat arbitrary depending on
>> the choice of the origin and the orientation of the cell. The
>> ABINIT space groups table is intended for
>> the cases where you specify the atomic positions by hand (you
>> choose the origin and the orientation
>> and the code finds them). When you decide to work with spgroup, the
>> origin and the orientation are
>> defined by default. Hence, you should not use (spgaxor, spgorig,
>> brvltt).
>>
>> I hope this helps...
>>
>> Best regards,
>>
>> Gian-Marco.
>>
>> -------------------------------------------------
>> This mail sent through IMP: atlas.pcpm.ucl.ac.be
>
>
>
> _______________
> Stephen E. Derenzo
>
> Senior Scientist
> Lawrence Berkeley National Laboratory
> Mail Stop 55-121
> Berkeley, CA 94720
> (510) 486-4097 (fax 486-4768)
> sederenzo@lbl.gov
> http://CFI.LBL.Gov
>
>


-- 
===============================================
Dr. Razvan Caracas
PostDoctoral Fellow
Carnegie Institution of Washington,
Geophysical Laboratory,
5251 Broad Branch Rd. N.W.,
Washington DC 20015, USA
tel: 1-202-478-8945; fax: 1-202-478-8901
http://www.gl.ciw.edu/~r.caracas