Problem with CIF import of hexagonal structures

Michael Fischer domm... at gmx.de
Fri Feb 17 15:21:08 CET 2012


Hello everyone,

I am a newbie to CP2K trying to perform standard DFT calculations on a
variety of different structures. To do so, I usually use the import of
CIF files, e.g.:
    &TOPOLOGY
      CONNECTIVITY OFF
      COORD_FILE_FORMAT CIF
      COORD_FILE_NAME MWW.cif
    &END TOPOLOGY
This worked fine for several structures for orthogonal cells. However,
when I use a CIF file of a hexagonal cell that has atoms located on
one of the cell planes (i.e. one of x,y,y = 0), the calculation
crashes. After some time, I found out that this is caused by the
generation of additional atoms that should not be there.
I have attached the input and the CIF file of MWW zeolite, one
structure where the problem arises. The number of atoms in the cell
should be 216. However, the output of the calculation tells me that
there are more atoms recognised by CP2K:
Total number of
- Atomic kinds:                                   2
- Atoms:                                        282

Obviously, the calculation is doomed to crash (and so it does!). There
are possible work-arounds, either using a rhombohedral setting when
possible, or exporting the structure as XYZ file (ATEN works nicely,
VESTA seems to generate additional atoms, too). However, I wanted to
bring this observation to your attention.

Best wishes
Michael

INP****************************************************

&FORCE_EVAL
  METHOD Quickstep
  &DFT
    &PRINT
        &V_HARTREE_CUBE
         STRIDE 1 1 2
	&END
    &END
    BASIS_SET_FILE_NAME ../BASIS_MOLOPT
    POTENTIAL_FILE_NAME ../POTENTIAL
    &MGRID
      CUTOFF 400
    &END MGRID
    &QS
      EPS_DEFAULT 1.0E-12
    &END QS
    &SCF
      EPS_SCF 1.0E-6
      SCF_GUESS ATOMIC
      MAX_SCF 25
      &OUTER_SCF
         EPS_SCF 1.0E-6
         MAX_SCF 4
      &END
      &OT
         MINIMIZER DIIS
         PRECONDITIONER FULL_ALL ! or FULL_SINGLE_INVERSE
         ENERGY_GAP 0.001
      &END
    &END SCF
    &XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC
  &END DFT
  &SUBSYS
    &CELL
      ABC 14.390 14.390 25.198
      ANGLES 90.0 90.0 120.0
    &END CELL
    &TOPOLOGY
      CONNECTIVITY OFF
      COORD_FILE_FORMAT CIF
      COORD_FILE_NAME MWW.cif
    &END TOPOLOGY
    &KIND Si
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND
    &KIND O
      BASIS_SET DZVP-MOLOPT-SR-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL

&GLOBAL
  PROJECT MWW
  PRINT_LEVEL MEDIUM
  RUN_TYPE ENERGY_FORCE
&END GLOBAL

CIF****************************************************

data_MWW
#**************************************************************************
#
# CIF taken from the IZA-SC Database of Zeolite Structures
# Ch. Baerlocher and L.B. McCusker
# Database of Zeolite Structures: http://www.iza-structure.org/databases/
#
# The atom coordinates and the cell parameters were optimized with
DLS76
# assuming a pure SiO2 composition.
#
#**************************************************************************

_cell_length_a                  14.3900(0)
_cell_length_b                  14.3900(0)
_cell_length_c                  25.1980(0)
_cell_angle_alpha               90.0000(0)
_cell_angle_beta                90.0000(0)
_cell_angle_gamma              120.0000(0)

_symmetry_space_group_name_H-M     'P 6/m m m'
_symmetry_Int_Tables_number         191
_symmetry_cell_setting             hexagonal

loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'-y,+x-y,+z'
'-x+y,-x,+z'
'-x,-y,+z'
'+y,-x+y,+z'
'+x-y,+x,+z'
'-y,-x,+z'
'-x+y,+y,+z'
'+x,+x-y,+z'
'+y,+x,+z'
'+x-y,-y,+z'
'-x,-x+y,+z'
'-x,-y,-z'
'+y,-x+y,-z'
'+x-y,+x,-z'
'+x,+y,-z'
'-y,+x-y,-z'
'-x+y,-x,-z'
'+y,+x,-z'
'+x-y,-y,-z'
'-x,-x+y,-z'
'-y,-x,-z'
'-x+y,+y,-z'
'+x,+x-y,-z'

loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
    O1    O     0.6667    0.3333    0.0000
    O2    O     0.5448    0.2724    0.0850
    O3    O     0.3953    0.1060    0.1374
    O4    O     0.5447    0.2724    0.1890
    O5    O     0.6667    0.3333    0.2739
    O6    O     0.3869    0.0000    0.2238
    O7    O     0.5000    0.0000    0.1419
    O8    O     0.5000    0.0000    0.3058
    O9    O     0.3935    0.1052    0.3101
   O10    O     0.5453    0.2726    0.3593
   O11    O     0.3520    0.1760    0.3986
   O12    O     0.1821    0.0000    0.4302
   O13    O     0.2989    0.1495    0.5000
    Si1   Si    0.4696    0.2348    0.1370
    Si2   Si    0.4198    0.2099    0.3443
    Si3   Si    0.2540    0.1270    0.4401
    Si4   Si    0.3927    0.0000    0.1601
    Si5   Si    0.3927    0.0000    0.2876
    Si6   Si    0.6667    0.3333    0.0637
    Si7   Si    0.6667    0.3333    0.2101
    Si8   Si    0.6667    0.3333    0.3377




More information about the CP2K-user mailing list