oqp.library.neb_utils
=====================

.. py:module:: oqp.library.neb_utils

.. autoapi-nested-parse::

   .. code-block:: text

      Dependency-light helpers for geomeTRIC NEB endpoint paths.



Attributes
----------

.. autoapisummary::

   oqp.library.neb_utils.BOHR_TO_ANGSTROM


Classes
-------

.. autoapisummary::

   oqp.library.neb_utils.NEBImage


Functions
---------

.. autoapisummary::

   oqp.library.neb_utils.kabsch_align
   oqp.library.neb_utils.interpolate_xyz_endpoints
   oqp.library.neb_utils.write_neb_xyz


Module Contents
---------------

.. py:data:: BOHR_TO_ANGSTROM
   :value: 0.52917721092


.. py:class:: NEBImage

   .. code-block:: text

      One NEB path image in user-facing Angstrom coordinates.


   .. py:attribute:: symbols
      :type:  list[str]


   .. py:attribute:: coordinates_angstrom
      :type:  list[list[float]]


.. py:function:: kabsch_align(reference: Iterable[Iterable[float]], mobile: Iterable[Iterable[float]]) -> list[list[float]]

   .. code-block:: text

      Rigidly align ``mobile`` coordinates onto ``reference``.

      Coordinates may use any common unit.  The returned coordinates retain the
      reference centroid, and the fitted transform is constrained to a proper
      rotation so a reflection cannot change molecular handedness.


.. py:function:: interpolate_xyz_endpoints(reactant_xyz: str | pathlib.Path, product_xyz: str | pathlib.Path, nimage: int, align: bool = False) -> list[NEBImage]

   .. code-block:: text

      Return linearly interpolated NEB images including both endpoints.

      Input and output coordinates are Angstrom, matching OpenQP XYZ/system input
      conventions. Atom symbols/count/order must match exactly so each image can
      be evaluated on the same state-specific surface.  With ``align=True``, the
      product endpoint is first rigidly superimposed on the reactant, removing
      overall translation and rotation before interpolation.


.. py:function:: write_neb_xyz(path: str | pathlib.Path, symbols: Iterable[str], images_bohr: Iterable[Iterable[float]], energies: Iterable[float] | None = None) -> pathlib.Path

   .. code-block:: text

      Write a final NEB path as a standard multi-frame XYZ file.

      ``images_bohr`` accepts flat ``3*natom`` arrays or ``(natom, 3)`` arrays.
      Optional energies are written in Hartree in each frame's comment line.