IMLCV.implementations.energy
============================

.. py:module:: IMLCV.implementations.energy


Classes
-------

.. autoapisummary::

   IMLCV.implementations.energy.OpenMmEnergy
   IMLCV.implementations.energy.AseEnergy
   IMLCV.implementations.energy.Cp2kEnergy
   IMLCV.implementations.energy.MACEASE


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

.. py:class:: OpenMmEnergy

   Bases: :py:obj:`IMLCV.base.bias.Energy`


   .. py:attribute:: pdb
      :type:  pathlib.Path


   .. py:attribute:: forcefield_name
      :type:  str
      :value: 'amber14-all.xml'



   .. py:attribute:: _simul
      :type:  openmm.app.Simulation | None
      :value: None



   .. py:method:: to_jax_vec(thing)
      :staticmethod:



   .. py:method:: get_info()


   .. py:method:: _compute_coor(sp: IMLCV.base.CV.SystemParams, nl: IMLCV.base.CV.NeighbourList, gpos=False, vir=False) -> IMLCV.base.bias.EnergyResult


   .. py:method:: _get_simul()


   .. py:method:: __getstate__()


   .. py:method:: __setstate__(state)


.. py:class:: AseEnergy(atoms: ase.Atoms, calculator=None)

   Bases: :py:obj:`IMLCV.base.bias.Energy`


   Conversion to ASE energy


   .. py:attribute:: atoms


   .. py:property:: cell


   .. py:property:: coordinates


   .. py:method:: _compute_coor(sp, nl, gpos=False, vir=False) -> IMLCV.base.bias.EnergyResult

      use unit conventions of ASE



   .. py:method:: _calculator()
      :abstractmethod:



   .. py:method:: _handle_exception(e=None)


   .. py:method:: __getstate__()


   .. py:method:: __setstate__(state)


.. py:class:: Cp2kEnergy(atoms, input_file, input_kwargs: dict, cp2k_path: pathlib.Path | None = None, **kwargs)

   Bases: :py:obj:`AseEnergy`


   Conversion to ASE energy


   .. py:attribute:: default_parameters


   .. py:attribute:: atoms


   .. py:attribute:: cp2k_inp


   .. py:attribute:: input_kwargs


   .. py:attribute:: kwargs


   .. py:attribute:: rp
      :value: None



   .. py:method:: _relative(target: pathlib.Path, origin: pathlib.Path)
      :staticmethod:


      return path of target relative to origin



   .. py:method:: _calculator()


   .. py:method:: _handle_exception(e=None)


   .. py:method:: __getstate__()


   .. py:method:: __setstate__(state)


.. py:class:: MACEASE(atoms: ase.Atoms, calculator=None)

   Bases: :py:obj:`AseEnergy`


   Conversion to ASE energy


   .. py:method:: _calculator()


   .. py:method:: __getstate__()


   .. py:method:: __setstate__(state)