The ABINIT Users Mailing List ( CLOSED )

[mmikami@rc.m-kagaku.co.jp]

Hello, Christoph:

About a week passed. So I expect that you might find a right solution.
Still, I would like to follow my previous e-mail (as cited below),
just in case that you (and followers) might be led in a wrong direction 
....

I attach a sample input for MgZn2, based on the data
"Komura & Tokunaga 1980" available on "EMS on line".
(Kindly remember the previous e-mail)
I set up two dataset for you; the dataset1 assign all the atoms
in the unit cell, and the dataset2 assign only the inequivalent atoms
in the unit cell. In the both case, natom should be assigned as 12.
In the second case, number of the inequivalent atoms should be
assigned (i.e. natrd 3). <-- Please be aware this hint was given in my 
mail.

Now you will see the both dataset will give the same crystal structure.

Here, it may be noteworthy that we should use 1/3 etc, not 0.33333.
This way to set fractional numbers (e.g. in xred ) is well described in
the "abinis (main)" help file.

If one set the xred2 in the original input as the below :
 typat2 1 2*2
 xred 2
 0.33333  0.66667  0.06299
-0.16947 -0.33894  0.25000
0.00000  0.00000  0.00000
the abinis will complain, "natom should be 20".
Then, if you set natom2 20, you will find 8 (fake-)Mg atoms
almost overlap the right Mg atoms. (You can confirm by yourself.)

In passing, you can test this in the dataset1, i.e. limited few digits
for xred without assigning "spgroup 194".
Abinit will say,"Pm m a (# 51); Bravais oP (primitive ortho.)"

Thus, 1/3 (2/3) will be preferred to 0.33333 (0.66667) in xred.

Hmm ... it took about an lunch time break to prepare this e-mail ...
If I would be in Germany, you might want to buy me a jug
of Beck's (or better). ;-)

Hope this helps,
Masayoshi

--------------------------------------------------
Here is the input file I tested, please be aware that parameters
related to convergence etc. (ecut, k-point, nstep, occopt, tsmear ...)
should be carefully tested. And also, the pseudopotentials, LDA/GGA
might be checked to see if results are physically meaningful or not...
(These are beyond my scope. I just wanted to test the crystal
structure assignment.)

Attachment: MgZn2.in
Description: Binary data

--------------------------------------------------

On 2003.7.22, at 23:26 Asia/Tokyo, Masayoshi Mikami wrote:

> Hello,
>
> The input for your crystal structure may have problems.
> Please take a look the table:
>  http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=194
> At least, the multiplicity of the site (0, 0, 0) is two,
> so the keywords "natom 3" "typat 1 2 2" seems strange ...
>
> (The above table is obtained from the Bilbao Crystallographic Server:
>    http://www.cryst.ehu.es/
>  Kindly try "WYCKPOS -- Wyckoff Positions of Space Groups"
>  This site is cited in ~ABINIT/Infos/Miscellaneous/Crystals )
>
> I do not know MgZn2 ... So that I consulted with "EMS on line".
>   http://cimesg1.epfl.ch/CIOLS/crystal1.pl
> (This site will be mentioned in the above file.)
> "MgZn2 - Komura & Tokunaga 1980" can be found in the right list.
> The crystal view of the MgZn2 can be confirmed on the WEB page...
> (Hereafter... could you please check your input file ?
>  "abinis help" file and "input variables" file may also help you ...
>  e.g. natrd ...)
>
> Hope this helps,
> Masayoshi
>
>
>
> From: c.gross@physik.uni-frankfurt.de
> Subject: [abinit-forum] Definition of hexagonal cell / MgZn2
> Date: Tue, 22 Jul 2003 14:54:15 +0200
> Message-ID: <sympa.1058877662.10212.14@abinit.org>
>
> > Hello everybody,
> >
> > this is (probably) a newbie question...
> >
> > I am trying to define the unit cell of MgZn2 (primitive hexagonal) by 
> > the following lines in my input file:
> >
> > ------------
> >
> > #Definition of the unit cell
> > acell 5.223 5.223 8.5666 angstrom
> > angdeg 90 90 120     # hexagonal cell
> > spgroup 194          # space group no 194, P63/mmc
> >
> > #Definition of the atom types
> > ntypat 2             # Two types of atoms (Mg, Zn)
> > znucl 12 30          # The keyword "znucl" refers...
> >
> > #Definition of the atoms
> > natom 3              # There are three atoms
> > typat 1 2 2          # First atom: type 1, second: type 2, third: 
> > type 2
> > xred                 # This keyword indicate that the location of the 
> > atoms
> >                      # will follow, one triplet of number for each 
> > atom
> > 1/3 2/3 0.06286      # Triplet giving the REDUCED coordinate of atom 
> > 1 (Mg).
> > 0.83048 0.66096 1/4  # Triplet giving the REDUCED coordinate of atom 
> > 2 (Zn2).
> > 0 0 0                # Triplet giving the REDUCED coordinate of atom 
> > 3 (Zn1).
> >
> > (...)
> > ------------
> >
> > But, ABINIT sends lots of warnings of the following type to the log 
> > file (and finally stops):
> >
> > ------------
> >
> >  symatm : WARNING -
> >   Trouble finding symmetrically equivalent atoms
> >   Applying inv of symm number  2 to atom number   1  of typat  1
> >   gives tratom=  6.6667E-01  3.3333E-01 -4.3714E-01.
> >   This is further away from every atom in crystal than the allowed 
> > tolerance.
> >   The inverse symmetry matrix is  0 -1  0
> >                                   1  1  0
> >                                   0  0  1
> >   and the nonsymmorphic transl. tnons =    0.0000000    0.0000000    
> > 0.5000000
> >   The nearest coordinate differs by  3.333E-01 -3.333E-01  5.000E-01
> >   for indsym(nearest atom)=    1
> >
> >   This indicates that when symatm attempts to find atoms symmetrically
> >   related to a given atom, the nearest candidate is further away than 
> > some
> >   tolerance.  Should check atomic coordinates and symmetry group 
> > input data.
> >
> > ------------
> >
> > Is this a problem with my input file ? Am I using the SPGROUP command 
> > correctly, or am I supposed to provide the positions of all atoms in 
> > the unit cell, not just the asymmetric unit ?
> >
> > I would be thankful for a hint,
> > Christoph