Value error on Wulff for AFT zeolite
I encountered an error while using the Single Crystal function.
Here is an excerpt from my code:
surf_energies = {(0, 0, 1): 1.0, (1, 0, 0): 2.48, (1, 0, 1): 2.68, (1, 0, 2): 3.19, (1, 0, 3): 3.89, (2, -1, 0): 4.3, (2, -1, 1): 4.42, (1, 0, 4): 4.71, (2, -1, 2): 4.74, (2, 0, 1): 5.07}
particle = SingleCrystal(surface_energies=surf_energies, primitive_structure=prim)
Output:
/home/solid2/PycharmProjects/venv/lib/python3.11/site-packages/wulffpack/core/base_particle.py:68: RuntimeWarning: divide by zero encountered in scalar divide
normal *= facets[i].energy / np.dot(normal, facets[i].normal) /home/solid2/PycharmProjects/venv/lib/python3.11/site-packages/wulffpack/core/base_particle.py:68: RuntimeWarning: invalid value encountered in multiply
normal *= facets[i].energy / np.dot(normal, facets[i].normal)
Traceback (most recent call last):
File "/home/solid2/PycharmProjects/Testes/Test005_zeoliteAFT.py", line 36, in
particle = SingleCrystal(surface_energies=surf_energies, primitive_structure=prim)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/solid2/PycharmProjects/venv/lib/python3.11/site-packages/wulffpack/single_crystal.py", line 60, in init super().init(forms=forms,
File "/home/solid2/PycharmProjects/venv/lib/python3.11/site-packages/wulffpack/core/base_particle.py", line 75, in init facet.remove_redundant_vertices()
File "/home/solid2/PycharmProjects/venv/lib/python3.11/site-packages/wulffpack/core/facet.py", line 95, in remove_redundant_vertices
if abs(angleish - round(angleish)) > self.tol / 100:
^^^^^^^^^^^^^^^
ValueError: cannot convert float NaN to integer
CIF file of the material:
data_AFT
#**************************************************************************
CIF taken from the IZA-SC Database of Zeolite Structures
Ch. Baerlocher and L.B. McCusker
http://www.iza-structure.org/databases/
Database of Zeolite Structures:The atom coordinates and the cell parameters were optimized with DLS76
assuming a pure SiO2 composition.
#**************************************************************************
_cell_length_a 13.6910(0) _cell_length_b 13.6910(0) _cell_length_c 29.4490(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 63/m m c' _symmetry_Int_Tables_number 194 _symmetry_cell_setting hexagonal
loop_ _symmetry_equiv_pos_as_xyz '+x,+y,+z' '-y,+x-y,+z' '-x+y,-x,+z' '-x,-y,1/2+z' '+y,-x+y,1/2+z' '+x-y,+x,1/2+z' '-y,-x,+z' '-x+y,+y,+z' '+x,+x-y,+z' '+y,+x,1/2+z' '+x-y,-y,1/2+z' '-x,-x+y,1/2+z' '-x,-y,-z' '+y,-x+y,-z' '+x-y,+x,-z' '+x,+y,1/2-z' '-y,+x-y,1/2-z' '-x+y,-x,1/2-z' '+y,+x,-z' '+x-y,-y,-z' '-x,-x+y,-z' '-y,-x,1/2-z' '-x+y,+y,1/2-z' '+x,+x-y,1/2-z'
loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z O1 O 0.2582 0.0012 0.2500 O2 O 0.2415 0.1207 0.1837 O3 O 0.3070 0.9741 0.1664 O4 O 0.0965 0.9035 0.1893 O5 O 0.3347 0.4121 0.4168 O6 O 0.2132 0.4263 0.4828 O7 O 0.3559 0.3559 0.5000 O8 O 0.4313 0.5687 0.4795 O9 O 0.4742 0.2371 0.6446 O10 O 0.5458 0.4542 0.6501 T1 Si 0.2257 0.9998 0.1974 T2 Si 0.3339 0.4409 0.4697 T3 Si 0.4413 0.3332 0.6361