hackingmaterials
describer.py line 247 en.join(orientations): ValidationError Input should be a valid string
Hi,
When calling:
from pymatgen.core import Structure
from robocrys import StructureCondenser
from robocrys import StructureDescriber
structure = Structure.from_file("C.cif")
sc = StructureCondenser()
describer = StructureDescriber()
condensed_structure = sc.condense_structure(structure)
description = describer.describe(condensed_structure)
I was having this error:
File ".../robocrys/describe/describer.py", line 247, in get_component_makeup_summary
en.join(orientations), s_direction
File ".../pydantic/_internal/_validate_call.py", line 100, in __call__
res = self.__pydantic_validator__.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
pydantic_core._pydantic_core.ValidationError: 1 validation error for join
0.0
Input should be a valid string [type=string_type, input_value=(0, 0, 1), input_type=tuple]
For further information visit https://errors.pydantic.dev/2.4/v/string_type
Fix that helped in describer.py lines 241-249 is adding orientations_str:
if component_group.dimensionality in [1, 2]:
orientations = list(
{c.orientation for c in component_group.components}
)
orientations_str = [str(o) for o in orientations]
s_direction = en.plural("direction", len(orientations))
comp_desc += " oriented in the {} {}".format(
en.join(orientations_str), s_direction
)
I am using Python 3.10.13 and the following package versions: matminer 0.9.1.dev5 monty 2023.11.3 pydantic 2.4.2 pydantic_core 2.10.1 pydantic-settings 2.1.0 pymatgen 2023.3.23 robocrys 0.2.8 ruamel.yaml 0.17.40 ruamel.yaml.clib 0.2.7
And that is my "C.cif" file:
# generated using pymatgen
data_C
_symmetry_space_group_name_H-M P6/mmm
_cell_length_a 2.46803014
_cell_length_b 2.46803014
_cell_length_c 19.99829300
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 120.00000000
_symmetry_Int_Tables_number 191
_chemical_formula_structural C
_chemical_formula_sum C2
_cell_volume 105.49320255
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 'x-y, x, z'
4 '-x+y, -x, -z'
5 '-y, x-y, z'
6 'y, -x+y, -z'
7 '-x, -y, z'
8 'x, y, -z'
9 '-x+y, -x, z'
10 'x-y, x, -z'
11 'y, -x+y, z'
12 '-y, x-y, -z'
13 '-y, -x, -z'
14 'y, x, z'
15 '-x, -x+y, -z'
16 'x, x-y, z'
17 '-x+y, y, -z'
18 'x-y, -y, z'
19 'y, x, -z'
20 '-y, -x, z'
21 'x, x-y, -z'
22 '-x, -x+y, z'
23 'x-y, -y, -z'
24 '-x+y, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
C C0 2 0.33333333 0.66666667 0.00000000 1
Could you look into this please?
This error also occurs in
pydantic==2.6.1 pydantic-settings==2.1.0
all other versions are the same as above.
This is because variable "orientations_str" is None and the en module need the "orientations_str" has a value.
For example,
condenser = StructureCondenser().
describer = StructureDescriber()
structure = Structure.from_file("DyBi2IO4.cif")
condensed_structure = condenser.condense_structure(structure)
for k,v in condensed_structure.items():
print(k, v)
You will get:
components {0: {'formula': 'Dy(BiO2)2', 'dimensionality': 2, 'orientation': (0, 0, 1), 'molecule_name': None, 'sites': [0, 1, 1, 4, 4, 4, 4]}, 1: {'formula': 'I', 'dimensionality': 0, 'orientation': None, 'molecule_name': 'hydriodic acid', 'sites': [3]}}.
Notice: orientation of I is None. And if you use description = describer.describe(condensed_structure), you will get this error.
To avoid it, a simple method is
describer = StructureDescriber(describe_component_makeup=False)
Or you can dive into the source code describer.py, and change the code from line 240 to 249:
if component_group.dimensionality in [1, 2]:
orientations = list(
{c.orientation for c in component_group.components}
)
s_direction = en.plural("direction", len(orientations))
# comp_desc += " oriented in the {} {}".format(
# en.join(orientations), s_direction
# )
comp_desc += f" oriented in the {orientations} {s_direction}"
