The ABINIT Users Mailing List ( CLOSED )

[matthieu verstraete <matthieu.jean.verstraete@gmail.com>]

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
>
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Prof. Matthieu Verstraete

Universite de Liège
Institut de Physique, Bat. B5
Allée du 6 aout, 17
B- 4000 Sart Tilman, Liège
Belgium

Phone : +32 4 366 37 50
Fax   : +32 4 366 36 29

Mail : matthieu.jean.verstraete@gmail.com