The ABINIT Users Mailing List ( CLOSED )

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

the increase in memory consumption has already happened, when you
chose "chkprim 0". It basically can't get much worse.

On Wed, Sep 23, 2009 at 9:29 AM, Marc Sämann
<marc.saemann@ipe.uni-stuttgart.de> wrote:
> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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