The ABINIT Users Mailing List ( CLOSED )

[Marc Sämann <marc.saemann@ipe.uni-stuttgart.de>]

Dear Xenophon,

thanks, the calculation is running now.
I was expecting a lot more memory and time consumption without setting a
spgroup, but it doesn't seem so.

Kind regards,
Marc


Xenophon Krokidis schrieb:
> Dear Marc,
>
> simply comment  the line :   spgroup 186 and your calculation will run
> fine.
>
> Regards,
>
> Xenophon
>
> www.scienomics.com
>
>
> Marc Sämann wrote:
>> 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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