ABINIT Discussion Forums

Dear Abinit users.

I have some xred values from experimental data for systems with free parameters. In crystallography tables Wyckoff positions for this space group are considerably different.

When I prepare .in file the normal way (xred and rprim or angdeg) Abinit chooses automatically the other space group.

when I add spgroup X to .in file I obtain this:
...
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.
...

for spgroup X and chkprim 0:
...
symatm : WARNING -
Trouble finding symmetrically equivalent atoms
...
symatm : ERROR -
Largest error (above) is so large that either input atomic coordinat es (xred)
are wrong or space group symmetry data is wrong.
Action : correct your input file.
...

I can use other software (e.g. FPLO) but I think ABINIT can do it much faster (PAW).

How can I force my ABINIT (5.8.3) to do it without symmetry problems?

With Regards,

Maciej Winiarski

maciek wrote:Dear Abinit users.

I have some xred values from experimental data for systems with free parameters. In crystallography tables Wyckoff positions for this space group are considerably different.

When I prepare .in file the normal way (xred and rprim or angdeg) Abinit chooses automatically the other space group.

Make sure you are using the correct primitive cell, not the conventional one, and that your xred are correct wrt the lattice abinit is actually using. What do you mean "the other space group"?

when I add spgroup X to .in file I obtain this:
...
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.
...

If you set spgroup, abinit will symmetrize all the positions you give, eventually adding atoms. Normally you should set only the irreducible atoms with natrd < natom, and let abinit find the symmetric positions. If you give all positions, and they are not perfectly symmetrized, abinit will duplicate atoms which are not perfectly (to within tolsym which defaults to 1e-10) on the high symmetry points.

for spgroup X and chkprim 0:

This is not the way to go - you want a primitive cell. With your full input file it would be easier to see your problem.


Matthieu

...
symatm : WARNING -
Trouble finding symmetrically equivalent atoms
...
symatm : ERROR -
Largest error (above) is so large that either input atomic coordinat es (xred)
are wrong or space group symmetry data is wrong.
Action : correct your input file.
...

I can use other software (e.g. FPLO) but I think ABINIT can do it much faster (PAW).

How can I force my ABINIT (5.8.3) to do it without symmetry problems?

With Regards,

Maciej Winiarski

Hello,
I'm sorry for my first post. It was too chaotic.
The problem is: I don't know how to set up calculations for any structure with free parameters.

My input file is following:
...
natom 3 # number of atoms
ntypat 3 # number of atom types
typat 1 2 3 # list of atom types
acell 5.0 5.0 10.0 angstrom # unit cell parameters
spgroup 139 # this space group is needed
xred 0 0 0
0 0.5 0.25
0 0 0.36
...

and then output:
...
symlatt : the Bravais lattice is tP (primitive tetragonal)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is tP (primitive tetragonal)

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.
...

How can I do basic calculations on primitive cell generated by abinit?
I'm going to investigate magnetism (AFM) and using non-primitive unit cells.
How should I give the xred manually for all atoms in unit cell (needed for other magnetic moments on the same site)?

with regards,
Maciek

If you want an AFM system, you need to specify spinat - this will make spin up and down atoms inequivalent by normal symmetries, and the chkprim will not be an issue any more (the space group is magnetic with more operations)

From your snippets I can't tell whether this would be enough: no idea what the full set of positions and cell look like once the spgroup has been used. Send full input and log information if you want a proper answer.

Matthieu

Hello once again,
I think my problem is a little knowledge about ABINIT. I have studied on simple systems like fcc, hcp, or bcc, but now I don't know how to prepare input for any larger unit cells. Let's forget my earlier posts and take an example:

I would like to do some calculations for BaFe2As2 compound which forms structure in space group Fmmm (# 69). I found in papers wykoff positions of Ba (0,0,0), Fe (1/4,1/4,1/4) and As (0,0,036). All my attempts to prepare input failed. Other software takes only wykoffs and primitive or unit cell is built automatically, but copies of that xreds and rprims are useless in ABINIT. Primitive cell is formed by 5 atoms, unit cell has 10 atoms.

I found rprims and site symmetries at http://cst-www.nrl.navy.mil/lattice/struk/b24.html and Bilbao Crystallographic Server, and prepared the input for hypothetical compound SrNi2Si2 in the same structure:
........
# SrNi2Si2 in space group 69
natom 5
ntypat 3
znucl 38 28 14
typat 1 2 2 3 3
acell 20.5 20.7 34.0
rprim 0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
xred 0.0 0.0 0.0
0.25 0.25 0.25
0.75 0.75 0.75
0.0 0.0 0.3538
0.0 0.0 -0.3538

(the rest of input is unimportant)
.........

but output is then:
.........
inpspheads : deduce mpsang = 3, n1xccc = 1.

invars1m : enter jdtset= 0
invars1 : treat image number 1

symlatt : the Bravais lattice is aP (primitive triclinic)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is aP (primitive triclinic)

symlatt : the Bravais lattice is aP (primitive triclinic)
symspgr : the symmetry operation no. 1 is the identity
symspgr : the symmetry operation no. 2 is an inversion
symspgr : spgroup= 2 P-1 (=Ci^1)
getkgrid : length of smallest supercell vector (bohr)= 2.899138E+01
Simple Lattice Grid
symkpt : found identity, with number 1
inkpts : after getkgrid, nkpt= 0
invars1: mkmem undefined in the input file. Use default mkmem = nkpt
invars1: With nkpt_me= 4 and mkmem = 4, ground state wf handled in core.
invars1: mkqmem undefined in the input file. Use default mkqmem = nkpt
invars1: With nkpt_me= 4 and mkqmem = 4, ground state wf handled in core.
invars1: mk1mem undefined in the input file. Use default mk1mem = nkpt
invars1: With nkpt_me= 4 and mk1mem = 4, ground state wf handled in core.

Symmetries : space group P-1 (# 2); Bravais aP (primitive triclinic)
getkgrid : length of smallest supercell vector (bohr)= 2.899138E+01
Simple Lattice Grid
symkpt : found identity, with number 1
inkpts : after getkgrid, nkpt= 4
chkneu : initialized the occupation numbers for occopt= 3
spin-unpolarized case :

(and so on)
........

ABINIT found only 2 symrels, but Fmmm has 8 symrels. Is it good for final results of calculations? Every other combinations (non-primitive unit cell and so on) lead to space group 2 or 1, but how can I attain the proper space group? I think I missed the point.

with regards,
Maciek

acell are the lengths of the lattice vectors you give with rprim

they are not the conventional lattice constants, unless you set things up that way. In your case the cell is tetragonal (not cubic) so you should either
1) set acell 1 1 1 and put the rprim properly by hand (simplest)
2) use a different unit cell, e.g. with c along the z axis (so acell(3) = c) and then adjust the fractional coordinates of the first 2 lattice vectors along z to fit the c/a ratio you want

and in any case make sure that the xred are correctly represented wrt the unit cell you chose.

Matthieu

Ok. Thanks for replies,
I will rather use non-primitive cells to bypass all my symmetries problems.

Maciek