tqchem.ttconf.electronic_structure_interfaces
=============================================

.. py:module:: tqchem.ttconf.electronic_structure_interfaces


Attributes
----------

.. autoapisummary::

   tqchem.ttconf.electronic_structure_interfaces.DielectricConstant


Classes
-------

.. autoapisummary::

   tqchem.ttconf.electronic_structure_interfaces.ElectronicStructureInterface
   tqchem.ttconf.electronic_structure_interfaces.TBliteInterface
   tqchem.ttconf.electronic_structure_interfaces.OpenFFInterface
   tqchem.ttconf.electronic_structure_interfaces.CrestEnsembleInterface


Functions
---------

.. autoapisummary::

   tqchem.ttconf.electronic_structure_interfaces.sageFF_interface
   tqchem.ttconf.electronic_structure_interfaces.amberFF_interface


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

.. py:data:: DielectricConstant
   :type:  _typeshed.Incomplete

.. py:class:: ElectronicStructureInterface

   Bases: :py:obj:`abc.ABC`


   Interface to electronic structure codes

   Needs to implement a single point calculation and a gradient optimization

   .. method:: __call__:

      Calculate energy for ase.Atoms object (i.e. the molecule)

   .. method:: _single_point_calculation:

      Calculate energy for the current structure of the ase.Atoms object

   .. method:: _local_optimization:

      Perform gradient optimization for ase.Atoms object
      and return energy for the optimized structure

   .. method:: _morse_energy:

      Calculate energy based on a simple morse potential



   .. py:method:: __call__(molecule: ase.Atoms) -> float

      Calculate energy for molecule

      :param molecule: Molecule object containing atom types and positions
      :type molecule: ase.Atoms

      :returns: **energy** -- Single point energy in eV
      :rtype: float



.. py:class:: TBliteInterface(method: str, ref_mol: ase.Atoms, charge: int = 0, accuracy: float = 1.0, solvent: str = None, local_optimization: bool = True)

   Bases: :py:obj:`ElectronicStructureInterface`


   Interface/Wrapper for ASE/TBLite library to calculate energies

   https://tblite.readthedocs.io/en/latest/users/ase.html

   .. attribute:: calculator

      TBLite calculator to perform single point calculations.

   .. method:: __call__:

      Calculate energy for ase.Atoms object (i.e. the molecule)

   .. method:: _single_point_calculation:

      Calculate energy for the current structure of the ase.Atoms object

   .. method:: _local_optimization:

      Perform gradient optimization for ase.Atoms object
      and return energy for the optimized structure



   .. py:attribute:: calculator
      :type:  _typeshed.Incomplete


   .. py:attribute:: local_optimization
      :type:  _typeshed.Incomplete


   .. py:attribute:: adjacency
      :type:  _typeshed.Incomplete


.. py:class:: OpenFFInterface(simulation: openmm.app.Simulation, ref_mol: ase.Atoms, local_optimization: bool = True)

   Bases: :py:obj:`ElectronicStructureInterface`


   Interface to OpenFF

   Different Force Fields are supported by changing the OpenMM simulation
   object from which this interface is constructed

   Implementing functions for single point calculations, optimization
   and extracting of coordinates from the openMM system

   .. attribute:: simulation

      OpenMM simulation class for calculating energies and optimized structures

      :type: Simulation

   .. attribute:: adjacency

      Adjacency matrix of the molecular system

      :type: np.array


   .. py:attribute:: local_optimization
      :type:  _typeshed.Incomplete


   .. py:attribute:: simulation
      :type:  _typeshed.Incomplete


   .. py:attribute:: adjacency
      :type:  _typeshed.Incomplete


.. py:function:: sageFF_interface(molecule: ase.Atoms, local_optimization: bool = True, charge: int = 0, solvent: str = None) -> OpenFFInterface

   Set up OpenMM simulation environment for the Sage OpenFF forcefield

   :param molecule: Molecule to create openMM simulation object from
   :type molecule: ase.Atoms
   :param local_optimization: Enable gradient optimziation
   :type local_optimization: bool, default=True
   :param charge: Formal charge of the molecule
   :type charge: int, default=0
   :param solvent: Add implicit solvation using solvent specified by name
   :type solvent: str, default=None


.. py:function:: amberFF_interface(molecule: ase.Atoms, local_optimization: bool = True, charge: int = 0, solvent: str = None) -> OpenFFInterface

   Set up OpenMM Simulation environment for Amber Forcefield

   :param molecule: Molecule to create openMM simulation object
   :type molecule: ase.Atoms
   :param local_optimization: Enable gradient optimziation
   :type local_optimization: bool, default=True
   :param charge: Formal charge of the molecule
   :type charge: int, default=0
   :param solvent: Add implicit solvation using solvent specified by name
   :type solvent: str, default=None


.. py:class:: CrestEnsembleInterface(method: str, ref_mol: ase.Atoms, charge: int = 0, solvent: str = None, threads: int = 4)

   .. py:attribute:: optlevel
      :type:  str


   .. py:attribute:: threads
      :type:  _typeshed.Incomplete


   .. py:attribute:: charge
      :type:  _typeshed.Incomplete


   .. py:attribute:: solvent
      :type:  _typeshed.Incomplete


   .. py:attribute:: adjacency
      :type:  _typeshed.Incomplete


   .. py:attribute:: method
      :type:  _typeshed.Incomplete


   .. py:method:: __call__(molecules: list[ase.Atoms]) -> numpy.ndarray

      Prepare ensemble of molecules whithout collided atoms and optimize with CREST