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- From: Xenophon Krokidis <Xenophon.Krokidis@scienomics.com>
- To: forum@abinit.org
- Subject: Re: [abinit-forum] Symmetry problem in hexagonal supercells
- Date: Tue, 22 Sep 2009 09:35:13 +0200
- Organization: Scienomics
Title: Signature text
Dear Marc,
simply comment the line : spgroup 186 and your calculation will run
fine.
Regards,
Xenophon
Marc Sämann wrote:
4AB7BBCE.3040709@ipe.uni-stuttgart.de" type="cite">
Dear Matthieu,
thank you for your fast reply.
I set chkprim = 0 and removed the statements to fix atoms. Then I tried
and again, but it didn't work.
Abinit complains right at the beginning and stops.
If I do not explicitly set a spgroup, it does not recognize a symmetry
and the logfile says "the unit cell is not primitive".
How can I check, which symmetry is sending the atom to the specified
position?
Attached you find the input / output & log file.
Thank you very much for your time.
Marc
matthieu verstraete schrieb:
Normally chkprim 1 should complain about your supercell, as it
replicates the irreducible primitive one.
Your coordinates look ok: does abinit complain from the beginning, or
only after some cycles of relaxation?
Normally you do not need to fix the atoms, as they are fixed by
symmetry (try without the iatfix etc)
You may be constraining things too much by specifying the spgroup
explicitly. Try without it, and see if abinit finds the correct one by
itself. You could check which symmetry is sending the atom to the
specified position, and whether it is correct...
We also need the output/log to say more.
cheers,
Matthieu
On Mon, Sep 21, 2009 at 10:44 AM, Marc Sämann
<marc.saemann@ipe.uni-stuttgart.de> wrote:
Dear abinit users and developers,
I am trying to do a structural optimization of a 3x3x2 zinc oxide
supercell with 72 atoms.
The optimization works fine with a 4 atom unit cell and a 2x2x1 supercell.
But with larger cells I get a lot of the following warnings:
symatm : WARNING -
Trouble finding symmetrically equivalent atoms
Applying inv of symm number 2 to atom number 19 of typat 1
gives tratom= 2.2222E-01 1.1111E-01 -5.5511E-17.
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 1.111E-01 -1.111E-01 -5.551E-17
for indsym(nearest atom)= 1
My input file is the following:
#ZnO wurzite (hexagonal) structure
#Structural optimization run
#Datasets: convergence on ecut
ndtset 2
# Set 1 : Internal coordinate optimization
ionmov1 2 # Use BFGS algorithm for structural optimization
ntime1 20 # Maximum number of optimization steps
tolmxf1 1.0e-6 # Optimization is converged when maximum force
# (Hartree/Bohr) is less than this maximum
natfix1 3 6 # Fix the position of two symmetry-equivalent atoms
# in doing the structural optimization
iatfix1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
# Set 2 : Lattice parameter relaxation (including re-optimization of
# internal coordinates)
dilatmx2 1.20 # Maximum scaling allowed for lattice parameters
getxred2 -1 # Start with relaxed coordinates from dataset 1
getwfk2 -1 # Start with wave functions from dataset 1
ionmov2 2 # Use BFGS algorithm
ntime2 24 # Maximum number of optimization steps
optcell2 2 # Fully optimize unit cell geometry, keeping symmetry
tolmxf2 1.0e-6 # Convergence limit for forces as above
strfact2 100 # Test convergence of stresses (Hartree/bohr^3) by
# multiplying by this factor and applying force
# convergence test
natfix2 36 # Fix the position of two symmetry-equivalent atoms
# in doing the structural optimization
iatfix2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
#Common input data
#Starting approximation for the unit cell
acell 2*18.72 20.24 #3x3x2 unit cell
angdeg 90 90 120
spgroup 186
brvltt -1
chkprim 1
#Definition of the atom types and atoms
ntypat 2
znucl 30 8
natom 72
typat 36*1 36*2
xred 1/9 2/9 0
4/9 2/9 0
7/9 2/9 0
1/9 5/9 0
4/9 5/9 0
7/9 5/9 0
1/9 8/9 0
4/9 8/9 0
7/9 8/9 0
2/9 1/9 1/4
5/9 1/9 1/4
8/9 1/9 1/4
2/9 4/9 1/4
5/9 4/9 1/4
8/9 4/9 1/4
2/9 7/9 1/4
5/9 7/9 1/4
8/9 7/9 1/4
1/9 2/9 1/2
4/9 2/9 1/2
7/9 2/9 1/2
1/9 5/9 1/2
4/9 5/9 1/2
7/9 5/9 1/2
1/9 8/9 1/2
4/9 8/9 1/2
7/9 8/9 1/2
2/9 1/9 3/4
5/9 1/9 3/4
8/9 1/9 3/4
2/9 4/9 3/4
5/9 4/9 3/4
8/9 4/9 3/4
2/9 7/9 3/4
5/9 7/9 3/4
8/9 7/9 3/4
1/9 2/9 0.189
4/9 2/9 0.189
7/9 2/9 0.189
1/9 5/9 0.189
4/9 5/9 0.189
7/9 5/9 0.189
1/9 8/9 0.189
4/9 8/9 0.189
7/9 8/9 0.189
1/9 2/9 0.689
4/9 2/9 0.689
7/9 2/9 0.689
1/9 5/9 0.689
4/9 5/9 0.689
7/9 5/9 0.689
1/9 8/9 0.689
4/9 8/9 0.689
7/9 8/9 0.689
2/9 1/9 0.439
5/9 1/9 0.439
8/9 1/9 0.439
2/9 4/9 0.439
5/9 4/9 0.439
8/9 4/9 0.439
2/9 7/9 0.439
5/9 7/9 0.439
8/9 7/9 0.439
2/9 1/9 0.939
5/9 1/9 0.939
8/9 1/9 0.939
2/9 4/9 0.939
5/9 4/9 0.939
8/9 4/9 0.939
2/9 7/9 0.939
5/9 7/9 0.939
8/9 7/9 0.939
#Definition of the plane wave basis set
ecut 20.0 # Maximum kinetic energy cutoff (Hartree)
ecutsm 1/2 # Smoothing energy needed for lattice paramete
pawecutdg 40 # optimization. This will be retained for
# consistency throughout.
#Definition of the k-point grid
ngkpt 4 4 4 # 4x4x4 Monkhorst-Pack grid
nshiftk 1 # Use one copy of grid only (default)
shiftk 0.0 0.0 1/2 # This choice of origin for the k point grid
# preserves the hexagonal symmetry of the grid,
# which would be broken by the default choice.
#Definition of the self-consistency procedure
diemac 9.0 # Model dielectric preconditioner
nstep 40 # Maxiumum number of SCF iterations
tolvrs 1.0d-18 # Strict tolerance on (squared) residual of the
# SCF potential needed for accurate forces and
# stresses in the structural optimization, and
# accurate wave functions in the RF calculations
Any help or comments are very appreciated.
Kind regards,
Marc Saemann
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