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Avagadro crashes on save


#1

Hello All

Whenever i attempt to save a cif file (either through save or save as) the program hard crashes. The program does manage to write out some information about the crystal, but dies once it begins writing atoms. I am using Avagadro version 1.2.0 and OpenBabel version 2.4.1 on windows.

Cif that i started with:
#======================================================================

CRYSTAL DATA

#----------------------------------------------------------------------

data_VESTA_phase_1

_chemical_name_common ‘’
_cell_length_a 22.77000
_cell_length_b 38.25000
_cell_length_c 23.21200
_cell_angle_alpha 90
_cell_angle_beta 115.68400
_cell_angle_gamma 90
_space_group_name_H-M_alt ‘P 1’
_space_group_IT_number 1

loop_
_space_group_symop_operation_xyz
’x, y, z’

loop_
_atom_site_label
_atom_site_occupancy
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_type_symbol
O1 1.0 0.470450 0.454580 0.357350 O
Ni2 1.0 0.413250 0.497530 0.335420 Ni
C3 1.0 0.354500 0.485400 0.400700 C
O4 1.0 0.336300 0.470170 0.348100 O
C5 1.0 0.311450 0.485400 0.435250 C
O6 1.0 0.396950 0.487990 0.247230 O
C7 1.0 0.557900 0.415400 0.410150 C
O8 1.0 0.526000 0.457460 0.464650 O
C9 1.0 0.513700 0.445050 0.410200 C
O10 1.0 0.407150 0.503500 0.422550 O
O11 1.0 0.488450 0.529620 0.349600 O
O12 1.0 0.357630 0.538700 0.306120 O
C13 1.0 0.529200 0.541850 0.402500 C
O14 1.0 0.536050 0.533740 0.457300 O
C15 1.0 0.573500 0.570800 0.399600 C
C16 1.0 0.470800 0.458150 0.597500 C
O17 1.0 0.463950 0.466260 0.542700 O
C18 1.0 0.426500 0.429200 0.600400 C
O19 1.0 0.592850 0.496500 0.577450 O
O20 1.0 0.511550 0.470380 0.650400 O
O21 1.0 0.644230 0.462030 0.694500 O
C22 1.0 0.442100 0.584600 0.589850 C
O23 1.0 0.474000 0.542540 0.535350 O
C24 1.0 0.486300 0.554950 0.589800 C
O25 1.0 0.529550 0.545420 0.642650 O
Ni26 1.0 0.586750 0.502470 0.664580 Ni
C27 1.0 0.645500 0.514600 0.599300 C
O28 1.0 0.663700 0.529830 0.651900 O
C29 1.0 0.688550 0.514600 0.564750 C
O30 1.0 0.610330 0.513080 0.754090 O
Ni31 1.0 0.500000 0.500000 0.500000 Ni
H32 1.0 0.388530 0.562420 0.316490 H
H33 1.0 0.300850 0.457300 0.444170 H
H34 1.0 0.263710 0.499320 0.404730 H
H35 1.0 0.337330 0.499580 0.482900 H
H36 1.0 0.443530 0.489350 0.242850 H
H37 1.0 0.558000 0.413630 0.361170 H
H38 1.0 0.539370 0.389750 0.421150 H
H39 1.0 0.609550 0.420530 0.448090 H
H40 1.0 0.564880 0.574940 0.347900 H
H41 1.0 0.626520 0.563160 0.429660 H
H42 1.0 0.562350 0.596030 0.419060 H
H43 1.0 0.457350 0.407070 0.631910 H
H44 1.0 0.395720 0.418860 0.550150 H
H45 1.0 0.393180 0.439950 0.621320 H
H46 1.0 0.695610 0.470970 0.715130 H
H47 1.0 0.401420 0.573800 0.600880 H
H48 1.0 0.420050 0.597690 0.540890 H
H49 1.0 0.471600 0.604590 0.627820 H
H50 1.0 0.662450 0.528520 0.516870 H
H51 1.0 0.699590 0.486500 0.556300 H
H52 1.0 0.736070 0.528780 0.595030 H
H53 1.0 0.661240 0.522850 0.777230 H
H54 1.0 0.606220 0.489030 0.778870 H
H55 1.0 0.375590 0.461480 0.233450 H
H19 1.0 0.644230 0.440000 0.694500 H
H20 1.0 0.320000 0.538700 0.306120 H

Partial Cif

CIF file generated by openbabel 2.3.90, see http://openbabel.sf.net

data_I
_chemical_name_common ‘’
_cell_length_a 22.77
_cell_length_b 38.25
_cell_length_c 23.212
_cell_angle_alpha 90
_cell_angle_beta 115.684
cell_angle_gamma 90
loop

_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy


#2

Since the file is getting re-formatted by the discussion board, can you please post a link to the CIF?

Thanks


#3

Sorry about the delay. Here is a link to the two cifs:
https://drive.google.com/file/d/0B9jpH7slazdNZXFhVFNBVklvTGM/view?usp=sharing
https://drive.google.com/file/d/0B9jpH7slazdNVm52d2Q5T29NQjA/view?usp=sharing
VEXTUO2 is the original file and VEXTUO3 is what Avogadro outputs before the crash.

Thanks!