search

stefsmeets / topas_tools

Set of scripts for working with Topas
MIT License
14 stars 4 forks source link

error in topasdiff #2

Closed MehmetTopsakal closed 6 years ago

MehmetTopsakal commented 6 years ago

Hi there

I am getting the error below. Any thoughts ?

I am also adding my structure.cif and

image

structure.cif

data_topas_cif_out
_chemical_name_mineral ??
_cell_length_a 10.008(16)
_cell_length_b 10.008(16)
_cell_length_c 10.008(16)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 1003(5)
_symmetry_space_group_name_H-M Fm3m
loop_
    _symmetry_equiv_pos_as_xyz
     'x, y, z '
     '-x, -y, z '
     '-x, -z, -y '
     '-x, -z, y '
     '-x, z, -y '
     '-x, z, y '
     '-x, y, -z '
     '-x, y, z '
     '-y, -x, -z '
     '-y, -x, z '
     '-y, -z, -x '
     '-y, -z, x '
     '-y, z, -x '
     '-y, z, x '
     '-y, x, -z '
     '-y, x, z '
     '-z, -x, -y '
     '-z, -x, y '
     '-z, -y, -x '
     '-z, -y, x '
     '-z, y, -x '
     '-z, y, x '
     '-z, x, -y '
     '-z, x, y '
     'z, -x, -y '
     'z, -x, y '
     'z, -y, -x '
     'z, -y, x '
     'z, y, -x '
     'z, y, x '
     'z, x, -y '
     'z, x, y '
     'y, -x, -z '
     'y, -x, z '
     'y, -z, -x '
     'y, -z, x '
     'y, z, -x '
     'y, z, x '
     'y, x, -z '
     'y, x, z '
     'x, -y, -z '
     'x, -y, z '
     'x, -z, -y '
     'x, -z, y '
     'x, z, -y '
     'x, z, y '
     'x, y, -z '
     '-x, -y, -z '
     'x+1/2, y+1/2, z '
     '-x+1/2, -y+1/2, z '
     '-x+1/2, -z+1/2, -y '
     '-x+1/2, -z+1/2, y '
     '-x+1/2, z+1/2, -y '
     '-x+1/2, z+1/2, y '
     '-x+1/2, y+1/2, -z '
     '-x+1/2, y+1/2, z '
     '-y+1/2, -x+1/2, -z '
     '-y+1/2, -x+1/2, z '
     '-y+1/2, -z+1/2, -x '
     '-y+1/2, -z+1/2, x '
     '-y+1/2, z+1/2, -x '
     '-y+1/2, z+1/2, x '
     '-y+1/2, x+1/2, -z '
     '-y+1/2, x+1/2, z '
     '-z+1/2, -x+1/2, -y '
     '-z+1/2, -x+1/2, y '
     '-z+1/2, -y+1/2, -x '
     '-z+1/2, -y+1/2, x '
     '-z+1/2, y+1/2, -x '
     '-z+1/2, y+1/2, x '
     '-z+1/2, x+1/2, -y '
     '-z+1/2, x+1/2, y '
     'z+1/2, -x+1/2, -y '
     'z+1/2, -x+1/2, y '
     'z+1/2, -y+1/2, -x '
     'z+1/2, -y+1/2, x '
     'z+1/2, y+1/2, -x '
     'z+1/2, y+1/2, x '
     'z+1/2, x+1/2, -y '
     'z+1/2, x+1/2, y '
     'y+1/2, -x+1/2, -z '
     'y+1/2, -x+1/2, z '
     'y+1/2, -z+1/2, -x '
     'y+1/2, -z+1/2, x '
     'y+1/2, z+1/2, -x '
     'y+1/2, z+1/2, x '
     'y+1/2, x+1/2, -z '
     'y+1/2, x+1/2, z '
     'x+1/2, -y+1/2, -z '
     'x+1/2, -y+1/2, z '
     'x+1/2, -z+1/2, -y '
     'x+1/2, -z+1/2, y '
     'x+1/2, z+1/2, -y '
     'x+1/2, z+1/2, y '
     'x+1/2, y+1/2, -z '
     '-x+1/2, -y+1/2, -z '
     'x+1/2, y, z+1/2 '
     '-x+1/2, -y, z+1/2 '
     '-x+1/2, -z, -y+1/2 '
     '-x+1/2, -z, y+1/2 '
     '-x+1/2, z, -y+1/2 '
     '-x+1/2, z, y+1/2 '
     '-x+1/2, y, -z+1/2 '
     '-x+1/2, y, z+1/2 '
     '-y+1/2, -x, -z+1/2 '
     '-y+1/2, -x, z+1/2 '
     '-y+1/2, -z, -x+1/2 '
     '-y+1/2, -z, x+1/2 '
     '-y+1/2, z, -x+1/2 '
     '-y+1/2, z, x+1/2 '
     '-y+1/2, x, -z+1/2 '
     '-y+1/2, x, z+1/2 '
     '-z+1/2, -x, -y+1/2 '
     '-z+1/2, -x, y+1/2 '
     '-z+1/2, -y, -x+1/2 '
     '-z+1/2, -y, x+1/2 '
     '-z+1/2, y, -x+1/2 '
     '-z+1/2, y, x+1/2 '
     '-z+1/2, x, -y+1/2 '
     '-z+1/2, x, y+1/2 '
     'z+1/2, -x, -y+1/2 '
     'z+1/2, -x, y+1/2 '
     'z+1/2, -y, -x+1/2 '
     'z+1/2, -y, x+1/2 '
     'z+1/2, y, -x+1/2 '
     'z+1/2, y, x+1/2 '
     'z+1/2, x, -y+1/2 '
     'z+1/2, x, y+1/2 '
     'y+1/2, -x, -z+1/2 '
     'y+1/2, -x, z+1/2 '
     'y+1/2, -z, -x+1/2 '
     'y+1/2, -z, x+1/2 '
     'y+1/2, z, -x+1/2 '
     'y+1/2, z, x+1/2 '
     'y+1/2, x, -z+1/2 '
     'y+1/2, x, z+1/2 '
     'x+1/2, -y, -z+1/2 '
     'x+1/2, -y, z+1/2 '
     'x+1/2, -z, -y+1/2 '
     'x+1/2, -z, y+1/2 '
     'x+1/2, z, -y+1/2 '
     'x+1/2, z, y+1/2 '
     'x+1/2, y, -z+1/2 '
     '-x+1/2, -y, -z+1/2 '
     'x, y+1/2, z+1/2 '
     '-x, -y+1/2, z+1/2 '
     '-x, -z+1/2, -y+1/2 '
     '-x, -z+1/2, y+1/2 '
     '-x, z+1/2, -y+1/2 '
     '-x, z+1/2, y+1/2 '
     '-x, y+1/2, -z+1/2 '
     '-x, y+1/2, z+1/2 '
     '-y, -x+1/2, -z+1/2 '
     '-y, -x+1/2, z+1/2 '
     '-y, -z+1/2, -x+1/2 '
     '-y, -z+1/2, x+1/2 '
     '-y, z+1/2, -x+1/2 '
     '-y, z+1/2, x+1/2 '
     '-y, x+1/2, -z+1/2 '
     '-y, x+1/2, z+1/2 '
     '-z, -x+1/2, -y+1/2 '
     '-z, -x+1/2, y+1/2 '
     '-z, -y+1/2, -x+1/2 '
     '-z, -y+1/2, x+1/2 '
     '-z, y+1/2, -x+1/2 '
     '-z, y+1/2, x+1/2 '
     '-z, x+1/2, -y+1/2 '
     '-z, x+1/2, y+1/2 '
     'z, -x+1/2, -y+1/2 '
     'z, -x+1/2, y+1/2 '
     'z, -y+1/2, -x+1/2 '
     'z, -y+1/2, x+1/2 '
     'z, y+1/2, -x+1/2 '
     'z, y+1/2, x+1/2 '
     'z, x+1/2, -y+1/2 '
     'z, x+1/2, y+1/2 '
     'y, -x+1/2, -z+1/2 '
     'y, -x+1/2, z+1/2 '
     'y, -z+1/2, -x+1/2 '
     'y, -z+1/2, x+1/2 '
     'y, z+1/2, -x+1/2 '
     'y, z+1/2, x+1/2 '
     'y, x+1/2, -z+1/2 '
     'y, x+1/2, z+1/2 '
     'x, -y+1/2, -z+1/2 '
     'x, -y+1/2, z+1/2 '
     'x, -z+1/2, -y+1/2 '
     'x, -z+1/2, y+1/2 '
     'x, z+1/2, -y+1/2 '
     'x, z+1/2, y+1/2 '
     'x, y+1/2, -z+1/2 '
     '-x, -y+1/2, -z+1/2 '
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
_atom_site_B_iso_or_equiv
Cu Cu   4 0.5 0.5 0.5 1 0.6
Fe Fe   4 0 0 0 1 3.2
N N  24 0.30612 0 0 1 2.6
C C  24 0.19168 0 0 1 2.6

fobs.hkl

   1   1   1      0.0034
   2   0   0      0.0479
   2   2   0      0.0236
   2   2   2      0.0037
   3   1   1      0.0029
   3   3   1      0.0021
   3   3   3      0.0016
   4   0   0      0.0456
   4   2   0      0.0271
   4   2   2      0.0130
   4   4   0      0.0289
   4   4   2      0.0171
   4   4   4      0.0190
   5   1   1      0.0052
   5   3   1      0.0043
   5   3   3      0.0037
   5   5   1      0.0053
   5   5   3      0.0047
   5   5   5      0.0052
   6   0   0      0.0345
   6   2   0      0.0233
   6   2   2      0.0132
   6   4   0      0.0240
   6   4   2      0.0158
   6   4   4      0.0170
   6   6   0      0.0205
   6   6   2      0.0142
   6   6   4      0.0152
   6   6   6      0.0138
   7   1   1      0.0040
   7   3   1      0.0036
   7   3   3      0.0033
   7   5   1      0.0043
   7   5   3      0.0040
   7   5   5      0.0044
   7   7   1      0.0038
   7   7   3      0.0037
   7   7   5      0.0039
   7   7   7      0.0036
   8   0   0      0.0183
   8   2   0      0.0117
   8   2   2      0.0056
   8   4   0      0.0131
   8   4   2      0.0078
   8   4   4      0.0093
   8   6   0      0.0122
   8   6   2      0.0077
   8   6   4      0.0089
   8   6   6      0.0085
   8   8   0      0.0069
   8   8   2      0.0037
   8   8   4      0.0049
   8   8   6      0.0050
   8   8   8      0.0027
   9   1   1      0.0045
   9   3   1      0.0042
   9   3   3      0.0041
   9   5   1      0.0045
   9   5   3      0.0043
   9   5   5      0.0043
   9   7   1      0.0040
   9   7   3      0.0039
   9   7   5      0.0039
   9   7   7      0.0036
   9   9   1      0.0039
   9   9   3      0.0038
   9   9   5      0.0038
   9   9   7      0.0035
   9   9   9      0.0033
  10   0   0      0.0177
  10   2   0      0.0131
  10   2   2      0.0088
  10   4   0      0.0137
  10   4   2      0.0097
  10   4   4      0.0105
  10   6   0      0.0124
  10   6   2      0.0092
  10   6   4      0.0098
  10   6   6      0.0091
  10   8   0      0.0082
  10   8   2      0.0057
  10   8   4      0.0064
  10   8   6      0.0061
  10   8   8      0.0041
  10  10   0      0.0085
  10  10   2      0.0066
  10  10   4      0.0069
  10  10   6      0.0065
  11   1   1      0.0040
  11   3   1      0.0039
  11   3   3      0.0038
  11   5   1      0.0040
  11   5   3      0.0038
  11   5   5      0.0038
  11   7   1      0.0036
  11   7   3      0.0035
  11   7   5      0.0035
  11   7   7      0.0032
  11   9   1      0.0035
  11   9   3      0.0034
  11   9   5      0.0034
  11   9   7      0.0031
  11  11   1      0.0032
  11  11   3      0.0031
  12   0   0      0.0104
  12   2   0      0.0074
  12   2   2      0.0046
  12   4   0      0.0081
  12   4   2      0.0055
  12   4   4      0.0063
  12   6   0      0.0077
  12   6   2      0.0054
  12   6   4      0.0061
  12   6   6      0.0058
  12   8   0      0.0051
  12   8   2      0.0033
  12   8   4      0.0040
  12   8   6      0.0040
  12  10   0      0.0057
  12  10   2      0.0043
  13   1   1      0.0037
  13   3   1      0.0036
  13   3   3      0.0035
  13   5   1      0.0035
  13   5   3      0.0034
  13   5   5      0.0034
  13   7   1      0.0033
  13   7   3      0.0032
  13   7   5      0.0031
  13   9   1      0.0031
  14   0   0      0.0075
  14   2   0      0.0056
  14   2   2      0.0037
  14   4   0      0.0061
  14   4   2      0.0044
  14   4   4      0.0049
  14   6   0      0.0058
  14   6   2      0.0043
  14   6   4      0.0047
  15   1   1      0.0034
  15   3   1      0.0033
  15   3   3      0.0032
  15   5   1      0.0032
stefsmeets commented 6 years ago

Thanks for the report. I am away from the office until next week, so I don't have the opportunity to properly test it, but I think f3d6f594575cd6e9e724820467e73947b85e4ef3 fixes it. Can you have a look and see if it works for you?

stefsmeets commented 6 years ago

Seems to be a bug introduced by using the latest version of pandas 0.23, which apparently no longer takes iterators to initialize DataFrames. f3d6f594575cd6e9e724820467e73947b85e4ef3 fixes it.

MehmetTopsakal commented 6 years ago

Thanks