polymerist.mdtools.openmmtools.thermo
=====================================

.. py:module:: polymerist.mdtools.openmmtools.thermo

.. autoapi-nested-parse::

   API for selecting thermostat and barostat actions which realize particular thermodynamic ensembles



Attributes
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.thermo.LOGGER
   polymerist.mdtools.openmmtools.thermo.ThermostatSerializer
   polymerist.mdtools.openmmtools.thermo.BarostatSerializer


Exceptions
----------

.. autoapisummary::

   polymerist.mdtools.openmmtools.thermo.NPHEnsembleUnsupported


Classes
-------

.. autoapisummary::

   polymerist.mdtools.openmmtools.thermo.Thermostat
   polymerist.mdtools.openmmtools.thermo.ThermostatParameters
   polymerist.mdtools.openmmtools.thermo.Barostat
   polymerist.mdtools.openmmtools.thermo.BarostatParameters
   polymerist.mdtools.openmmtools.thermo.Ensemble
   polymerist.mdtools.openmmtools.thermo.ThermoParameters


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

.. py:data:: LOGGER

.. py:class:: Thermostat(*args, **kwds)

   Bases: :py:obj:`enum.Enum`


   Common thermostats which OpenMM implements and which adhere to the interface defined here


   .. py:attribute:: ANDERSEN


   .. py:attribute:: BROWNIAN


   .. py:attribute:: LANGEVIN


   .. py:attribute:: LANGEVIN_MIDDLE


   .. py:attribute:: NOSE_HOOVER


   .. py:attribute:: LANGEVINMIDDLE


   .. py:attribute:: NOSEHOOVER


.. py:data:: ThermostatSerializer

.. py:class:: ThermostatParameters

   Interface for initializing a constant-temperature simulation


   .. py:attribute:: temperature
      :type:  openmm.unit.Quantity


   .. py:attribute:: timescale
      :type:  openmm.unit.Quantity


   .. py:attribute:: thermostat
      :type:  Union[str, Thermostat]


   .. py:method:: forces() -> Iterable[openmm.Force]

      The forces required to realized the desired thermostat



   .. py:method:: integrator(time_step: openmm.unit.Quantity) -> openmm.Integrator

      The integrator required to realized the desired thermostat



.. py:class:: Barostat(*args, **kwds)

   Bases: :py:obj:`enum.Enum`


   Common barostats which OpenMM implements and which adhere to the interface defined here


   .. py:attribute:: MONTE_CARLO


   .. py:attribute:: MONTE_CARLO_FLEXIBLE


   .. py:attribute:: MC


   .. py:attribute:: MONTECARLO


   .. py:attribute:: FLEXIBLE


.. py:data:: BarostatSerializer

.. py:class:: BarostatParameters

   Interface for initializing a constant-pressure simulation


   .. py:attribute:: pressure
      :type:  openmm.unit.Quantity


   .. py:attribute:: temperature
      :type:  Optional[openmm.unit.Quantity]
      :value: None



   .. py:attribute:: update_frequency
      :type:  int
      :value: 25



   .. py:attribute:: barostat
      :type:  Union[str, Barostat]


   .. py:method:: forces() -> Iterable[openmm.Force]

      The forces required to realized the desired barostat



   .. py:method:: integrator(time_step: openmm.unit.Quantity) -> openmm.Integrator

      The integrator required to realized the desired barostat



.. py:exception:: NPHEnsembleUnsupported(msg: str = f'NPH ensemble not supported; either add a thermostat or remove a barostat from thermodynamic parameters', *args, **kwargs)

   Bases: :py:obj:`ValueError`


   Raised when a user attempts to initialize ThermoParameters with a barostat but not thermostat
   Would cause OpenMM to produce incorrect results (https://docs.openmm.org/latest/userguide/application/02_running_sims.html#pressure-coupling)


.. py:class:: Ensemble

   Bases: :py:obj:`enum.StrEnum`


   Common thermodynamic ensembles which are realizable with the interfaces provided here


   .. py:attribute:: NVE
      :value: 'microcanonical'



   .. py:attribute:: NVT
      :value: 'canonical'



   .. py:attribute:: NPT
      :value: 'isothermal-isobaric'



.. py:class:: ThermoParameters

   Encapsulation for initializing the OpenMM forces and integrator which realize a particular thermodynamic ensemble


   .. py:attribute:: thermostat_params
      :type:  Optional[ThermostatParameters]
      :value: None



   .. py:attribute:: barostat_params
      :type:  Optional[BarostatParameters]
      :value: None



   .. py:property:: ensemble
      :type: Ensemble


      The standard name of the thermodynamic ensemble being implemented here


   .. py:method:: describe_ensemble() -> str

      Verbal description of ensemble



   .. py:method:: integrator(time_step: openmm.unit.Quantity) -> openmm.Integrator

      Specify how to integrate forces in each timestep



   .. py:method:: forces() -> Optional[Iterable[openmm.Force]]

      Specify any additional force contributions to position/velocity updates