[WIP] Fix the issue in big system

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Original prompt

fix the issue in big system:

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[CCSun21]

A ValueError in the big input system (120 atoms), but small system (20 atoms) works.

❯ python ORB_GSM.py
/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/pyGSM/coordinate_systems/topology.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  from pkg_resources import parse_version
/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/orb_models/utils.py:30: UserWarning: Setting global torch default dtype to torch.float32.
  warnings.warn(f"Setting global torch default dtype to {torch_dtype}.")
#========================================================#
#|                   Building the LOT                   |#
#========================================================#
 Assuming gradient states are  [(1, 0)]
 initializing LOT from geom
 making folder scratch/000/0
#========================================================#
#|                   Building the PES                   |#
#========================================================#
#========================================================#
#|                    building bonds                    |#
#========================================================#
None
 In build bonds
2025-10-14 11:01:03 | INFO     | himatcal.recipes.gsm.SE_GSM:build_topology:95 -  Adding bond (127, 129) to top1
#========================================================#
#|       Building Primitive Internal Coordinates        |#
#========================================================#
127
<class 'int'>
Traceback (most recent call last):
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/pyGSM/coordinate_systems/primitive_internals.py", line 1339, in get_hybrid_indices
    new_hybrid_indices.remove(elem)
ValueError: list.remove(x): x not in list

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/inbox/251014_10.Build_IM1/01.half_cover/ORB_GSM.py", line 43, in <module>
    gsm.run()
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/himatcal/recipes/gsm/SE_GSM.py", line 178, in run
    self.build_primitives()
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/himatcal/recipes/gsm/SE_GSM.py", line 101, in build_primitives
    self.p1 = PrimitiveInternalCoordinates.from_options(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/pyGSM/coordinate_systems/internal_coordinates.py", line 112, in from_options
    return cls(cls.default_options().set_values(kwargs))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/pyGSM/coordinate_systems/primitive_internals.py", line 86, in __init__
    self.get_hybrid_indices(xyz)
  File "/media/suncc/data/TAT/02.Mat/12.2509LFP_EC/.venv/lib/python3.11/site-packages/pyGSM/coordinate_systems/primitive_internals.py", line 1343, in get_hybrid_indices
    raise RuntimeError
RuntimeError

@copilot please fix this.