I used: atkpython match_au_mose2.py | grep '0 0 1'
With the files:
match_au_mose2.py
configuration_1 = nlread('au.cif',BulkConfiguration)[-1]
configuration_2 = nlread('MoSe2.cif',BulkConfiguration)[-1]
generalized_lattice_match = GeneralizedLatticeMatch(
configuration_1,
configuration_2,
max_strain=0.02,
maximum_miller_index=1,
longest_surface_lattice_vector=100*Angstrom,
max_surface_area=10000.0*Angstrom**2,
user_given_miller_index=(1,1,1)
)
With au.cif:
data_global
_cell_length_a 2.97513963
_cell_length_b 2.97513963
_cell_length_c 2.97513963
_cell_angle_alpha 60.00000000
_cell_angle_beta 60.00000000
_cell_angle_gamma 60.00000000
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Au 0.00000000 0.00000000 0.00000000
and MoSe2.cif
data_global
_cell_length_a 3.32910723
_cell_length_b 3.32910723
_cell_length_c 13.06127836
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 120.00000000
_symmetry_space_group_name_H-M 'P -1'
loop_
_symmetry_equiv_pos_as_xyz
'x,y,z'
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Mo 0.33333300 0.66666700 0.25000000
Se 0.66666700 0.33333300 0.12100000
Se 0.66666700 0.33333300 0.37900000
I disagree, your log-file shows exactly the same numbers. The first three matchings are:
+----------------------------------------------------------------------------------------+
| A B Strain Atoms Area Aspect Angle Rotation |
+----------------------------------------------------------------------------------------+
[ 1 1 1] >-< [ 0 0 1] 0.000050 1750 69.0 1.0 60.0 19.1
[ 1 1 1] >-< [ 0 0 1] 0.000070 1705 69.0 1.0 60.0 19.1
[ 1 1 1] >-< [ 0 0 1] 0.000110 232 69.0 1.0 60.0 19.1
Which have differing numbers of atoms (1750, 1705 and 232) but apparently the same Area (69.0).
I would assume that collumn "Area" shows the area of the cross-section. Is that wrong, what does "Area" refer to?
EDIT:
Is there an easy way of actually assemble this interface? I have not managed to get the same interfaces through the Interface Builder in VNL and the output of GeneralizedLatticeMatch is not sufficient to create it manually.