oqp.library.qmmm_md
===================

.. py:module:: oqp.library.qmmm_md


Attributes
----------

.. autoapisummary::

   oqp.library.qmmm_md.md


Classes
-------

.. autoapisummary::

   oqp.library.qmmm_md.QMMM_MD


Functions
---------

.. autoapisummary::

   oqp.library.qmmm_md.parse_ini_to_config


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

.. py:function:: parse_ini_to_config(filepath)

   .. code-block:: text

      Parse an INI-style configuration file into a flat dictionary
      with ``section.key`` keys.

      Numeric values are auto-converted to int or float.
      Entries with empty values are skipped.


.. py:class:: QMMM_MD(oqp_cfg=None, mol=None)

   .. code-block:: text

      QM/MM Molecular Dynamics with NVE / NVT / NPT support.

      All parameters are read from the configuration. Provide **exactly one** of:

      *   ``oqp_cfg``  - a ``dict`` with flat ``"section.key"`` entries
          **or** a path to an INI file. QM/MM settings live under the
          ``[qmmm]`` section / ``"qmmm.*"`` keys.

      *   ``mol`` - a pre-built OpenQP mol object whose
          ``mol.config["qmmm"]`` contains the same keys.

      Recognised ``[qmmm]`` keys
      --------------------------
      pdb_file           : str            (required)
      forcefield_files   : str            comma-separated list
      qm_atoms           : str or list    ``"0,1,2"`` or ``"0-2"``
      cutoff             : str            PME | NoCutoff | Ewald | ...
      embedding          : str            mechanical | electrostatic
      n_steps            : int            default 1000
      timestep           : float (fs)     default 1.0
      temperature        : float (K)      default 300.0
      ensemble           : str            nve | nvt | npt   (default nve)
      friction           : float (ps^-1)  default 1.0      (NVT/NPT only)
      pressure           : float (bar)    default 1.0      (NPT only)
      barostat_interval  : int            default 25       (NPT only)
      trajectory_format  : str            pdb | dcd        (default pdb)
      trajectory_file    : str            default qmmm_trajectory.<format>
      log_file           : str            default qmmm_trajectory.dat
      report_interval    : int            default 1
      energy_file        : str            default total_energy.npz
      qm_atoms_xyz       : str            optional XYZ file
      qm_list            : str or list    optional index mapping

      Saved observables (in ``energy_file`` as ``.npz``)
      --------------------------------------------------
      step          : MD step index
      time_ps       : simulation time (ps)
      E_pot         : potential energy (kJ/mol)
      E_kin         : kinetic energy (kJ/mol)
      E_tot         : total energy (kJ/mol)
      temperature   : instantaneous T from kinetic energy (K)
      volume_nm3    : box volume (nm^3), only populated for NPT


   .. py:attribute:: pdb


   .. py:attribute:: forcefield


   .. py:attribute:: qm_atoms


   .. py:attribute:: cutoff


   .. py:attribute:: embedding
      :value: ''



   .. py:attribute:: frontier_scheme
      :value: ''



   .. py:attribute:: n_steps


   .. py:attribute:: timestep


   .. py:attribute:: temperature


   .. py:attribute:: ensemble
      :value: ''



   .. py:attribute:: friction


   .. py:attribute:: pressure


   .. py:attribute:: barostat_interval


   .. py:attribute:: trajectory_format
      :value: ''



   .. py:attribute:: trajectory_file
      :value: ''



   .. py:attribute:: log_file
      :value: ''



   .. py:attribute:: report_interval


   .. py:attribute:: energy_file
      :value: ''



   .. py:attribute:: oqp_cfg
      :value: None



   .. py:attribute:: mol
      :value: None



   .. py:attribute:: oqp_driver
      :value: None



   .. py:attribute:: mm_systems
      :value: None



   .. py:attribute:: simulation_md
      :value: None



   .. py:attribute:: system_md
      :value: None



   .. py:attribute:: qmmm_ext
      :value: None



   .. py:method:: setup()

      .. code-block:: text

         Full setup: build driver, MD system, and simulation context.



   .. py:method:: step()

      .. code-block:: text

         Perform one QM/MM MD step.

         :returns: **E_tot**
         :rtype: float   Total energy (kJ/mol).



   .. py:method:: run()

      .. code-block:: text

         Run the full simulation in the configured ensemble.

         :returns: Keys: step, time_ps, E_pot, E_kin, E_tot, temperature, volume_nm3.
         :rtype: dict of np.ndarray



.. py:data:: md