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[Stephen Derenzo <sederenzo@lbl.gov>]

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.

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Stephen E. Derenzo

Senior Scientist

Lawrence Berkeley National Laboratory

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