`mpr.materials.grain_boundaries` throws: `ModuleNotFoundError: No module named 'pymatgen.analysis.gb'`

[DanielYang59]

Env:

• Python 3.13.5, mp_api 0.45.7, MacOS 15.5

---

The following code:

from mp_api.client import MPRester

with MPRester() as mpr:
    gb_docs = mpr.materials.grain_boundaries.search(
        chemsys="Fe",
        sigma=5,
        rotation_axis=["0 0 1"]
    )

Gives:

Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/test_gb_download.py", line 4, in <module>
    gb_docs = mpr.materials.grain_boundaries.search(
        chemsys="Fe",
        sigma=5,
        rotation_axis=["0 0 1"]
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/routes/materials/grain_boundaries.py", line 109, in search
    return super()._search(
           ~~~~~~~~~~~~~~~^
        num_chunks=num_chunks,
        ^^^^^^^^^^^^^^^^^^^^^^
    ...<3 lines>...
        **query_params,
        ^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1191, in _search
    return self._get_all_documents(
           ~~~~~~~~~~~~~~~~~~~~~~~^
        kwargs,
        ^^^^^^^
    ...<3 lines>...
        num_chunks=num_chunks,
        ^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1264, in _get_all_documents
    results = self._query_resource(
        query_params,
    ...<3 lines>...
        num_chunks=num_chunks,
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 570, in _query_resource
    data = self._submit_requests(
        url=url,
    ...<5 lines>...
        timeout=timeout,
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 717, in _submit_requests
    initial_data_tuples = self._multi_thread(
        self._submit_request_and_process, initial_params_list
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 939, in _multi_thread
    data, subtotal = future.result()
                     ~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ~~~~~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1038, in _submit_request_and_process
    raise MPRestError(
    ...<2 lines>...
    )
mp_api.client.core.client.MPRestError: REST query returned with error status code 500 on URL https://api.materialsproject.org/materials/grain_boundaries/?rotation_axis=0+0+1&sigma=5&_all_fields=True&chemsys=Fe&_limit=1000 with message:
Response Internal Server Error

[esoteric-ephemera]

Hey @DanielYang59 I think your query needs to be adjusted for rotation_axis:

mpr.materials.grain_boundaries.search(chemsys="Fe",sigma=5,rotation_axis=["1","0", "1"])

works but returns no results. We only have 3 grain boundary docs for Fe with sigma = 5:

mpr.materials.grain_boundaries.count({"chemsys": "Fe", "sigma": 5})
>>> 3

Probably worth changing the docstr for this

Also, we're aware of a monty deserialization bug that was introduced by renaming pymatgen.analysis.gb. You can get around this by using MPRester(monty_decode=False) for now

[DanielYang59]

Thanks a lot (was trying to redirect materialsproject/pymatgen#4439 (comment) to api repo), sorry I misunderstood the docstring (which is missing the quotes for str):

api/mp_api/client/routes/materials/grain_boundaries.py

Line 43 in 766c0eb

rotation_axis(List[str]): The Miller index of rotation axis. e.g., [1, 0, 0], [1, 1, 0], and [1, 1, 1]

And thanks for the head up on monty deserialization bug, I also see this if query returns anything, say:

with MPRester() as mpr:
    gb_docs = mpr.materials.grain_boundaries.search(
        chemsys="Fe",
    )

>>> ModuleNotFoundError: No module named 'pymatgen.analysis.gb'

But with monty_decode=False I'm still getting the same error from pydantic model validation:

api/mp_api/client/core/client.py

Line 1053 in 766c0eb

raw_doc_list = [self.document_model.model_validate(d) for d in data] # type: ignore

Full log:

Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/debug/test_gb_api.py", line 4, in <module>
    gb_docs = mpr.materials.grain_boundaries.search(
        chemsys="Fe",
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/routes/materials/grain_boundaries.py", line 109, in search
    return super()._search(
           ~~~~~~~~~~~~~~~^
        num_chunks=num_chunks,
        ^^^^^^^^^^^^^^^^^^^^^^
    ...<3 lines>...
        **query_params,
        ^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1191, in _search
    return self._get_all_documents(
           ~~~~~~~~~~~~~~~~~~~~~~~^
        kwargs,
        ^^^^^^^
    ...<3 lines>...
        num_chunks=num_chunks,
        ^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1264, in _get_all_documents
    results = self._query_resource(
        query_params,
    ...<3 lines>...
        num_chunks=num_chunks,
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 570, in _query_resource
    data = self._submit_requests(
        url=url,
    ...<5 lines>...
        timeout=timeout,
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 717, in _submit_requests
    initial_data_tuples = self._multi_thread(
        self._submit_request_and_process, initial_params_list
    )
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 939, in _multi_thread
    data, subtotal = future.result()
                     ~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ~~~~~~~~~~~~~~~~~^^
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/lib/python3.13/concurrent/futures/thread.py", line 59, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1017, in _submit_request_and_process
    data["data"] = self._convert_to_model(data["data"])
                   ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/mp_api/client/core/client.py", line 1053, in _convert_to_model
    raw_doc_list = [self.document_model.model_validate(d) for d in data]  # type: ignore
                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/pydantic/main.py", line 705, in model_validate
    return cls.__pydantic_validator__.validate_python(
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
        obj, strict=strict, from_attributes=from_attributes, context=context, by_alias=by_alias, by_name=by_name
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
pydantic_core._pydantic_core.ValidationError: 2 validation errors for GrainBoundaryDoc
initial_structure
  Value error, Error while deserializing GrainBoundary object: Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/monty/json.py", line 287, in _validate_monty
    new_obj = MontyDecoder().process_decoded(__input_value)
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/monty/json.py", line 796, in process_decoded
    mod = __import__(modname, globals(), locals(), [classname], 0)
ModuleNotFoundError: No module named 'pymatgen.analysis.gb'
 [type=value_error, input_value={'@module': 'pymatgen.ana...': {'magmom': 2.215}}]}}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.11/v/value_error
final_structure
  Value error, Error while deserializing GrainBoundary object: Traceback (most recent call last):
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/monty/json.py", line 287, in _validate_monty
    new_obj = MontyDecoder().process_decoded(__input_value)
  File "/Users/yang/developer/pymatgen/.venv/lib/python3.13/site-packages/monty/json.py", line 796, in process_decoded
    mod = __import__(modname, globals(), locals(), [classname], 0)
ModuleNotFoundError: No module named 'pymatgen.analysis.gb'
 [type=value_error, input_value={'@module': 'pymatgen.ana...': {'magmom': 2.215}}]}}, input_type=dict]
    For further information visit https://errors.pydantic.dev/2.11/v/value_error

[esoteric-ephemera]

My bad, then you need: MPRester(use_document_model=False, monty_decode=False). Just checked that should work

[DanielYang59]

Yep could confirm this works ;) thanks a lot

Free feel to close this if you could commit the docstring cleanup somewhere I guess we should leave this open until GB API is fixed

[esoteric-ephemera]

Sure thing! Will add the docstr; we'll close this after migrating the grain boundary data

[esoteric-ephemera]

The data should now correctly deserialize with the default kwargs. Thanks to @tsmathis!

The following should work - will close once #992 is merged or settled on:

from mp_api.client import MPRester

with MPRester() as mpr:
   grain_bdy = mpr.materials.grain_boundaries.search()

[DanielYang59]

Great I could confirm it's working now ;) thanks!