polymerist.mdtools.openmmtools.thermo

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

Attributes

`LOGGER`
`ThermostatSerializer`
`BarostatSerializer`

Exceptions

NPHEnsembleUnsupported

Raised when a user attempts to initialize ThermoParameters with a barostat but not thermostat

Classes

`Thermostat`	Common thermostats which OpenMM implements and which adhere to the interface defined here
`ThermostatParameters`	Interface for initializing a constant-temperature simulation
`Barostat`	Common barostats which OpenMM implements and which adhere to the interface defined here
`BarostatParameters`	Interface for initializing a constant-pressure simulation
`Ensemble`	Common thermodynamic ensembles which are realizable with the interfaces provided here
`ThermoParameters`	Encapsulation for initializing the OpenMM forces and integrator which realize a particular thermodynamic ensemble

Module Contents

polymerist.mdtools.openmmtools.thermo.LOGGER

class polymerist.mdtools.openmmtools.thermo.Thermostat(*args, **kwds)[source]

Bases: enum.Enum

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

ANDERSEN

BROWNIAN

LANGEVIN

LANGEVIN_MIDDLE

NOSE_HOOVER

LANGEVINMIDDLE

NOSEHOOVER

polymerist.mdtools.openmmtools.thermo.ThermostatSerializer

class polymerist.mdtools.openmmtools.thermo.ThermostatParameters[source]

Interface for initializing a constant-temperature simulation

temperature: openmm.unit.Quantity

timescale: openmm.unit.Quantity

thermostat: str | Thermostat

forces() → Iterable[openmm.Force][source]: The forces required to realized the desired thermostat

integrator(time_step: openmm.unit.Quantity) → openmm.Integrator[source]: The integrator required to realized the desired thermostat

class polymerist.mdtools.openmmtools.thermo.Barostat(*args, **kwds)[source]

Bases: enum.Enum

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

MONTE_CARLO

MONTE_CARLO_FLEXIBLE

MC

MONTECARLO

FLEXIBLE

polymerist.mdtools.openmmtools.thermo.BarostatSerializer

class polymerist.mdtools.openmmtools.thermo.BarostatParameters[source]

Interface for initializing a constant-pressure simulation

pressure: openmm.unit.Quantity

temperature: openmm.unit.Quantity | None = None

update_frequency: int = 25

barostat: str | Barostat

forces() → Iterable[openmm.Force][source]: The forces required to realized the desired barostat

integrator(time_step: openmm.unit.Quantity) → openmm.Integrator[source]: The integrator required to realized the desired barostat

exception polymerist.mdtools.openmmtools.thermo.NPHEnsembleUnsupported(msg: str = f'NPH ensemble not supported; either add a thermostat or remove a barostat from thermodynamic parameters', *args, **kwargs)[source]

Bases: 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)

class polymerist.mdtools.openmmtools.thermo.Ensemble[source]

Bases: enum.StrEnum

Common thermodynamic ensembles which are realizable with the interfaces provided here

NVE = 'microcanonical'

NVT = 'canonical'

NPT = 'isothermal-isobaric'

class polymerist.mdtools.openmmtools.thermo.ThermoParameters[source]

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

thermostat_params: ThermostatParameters | None = None

barostat_params: BarostatParameters | None = None

property ensemble: Ensemble: The standard name of the thermodynamic ensemble being implemented here

describe_ensemble() → str[source]: Verbal description of ensemble

integrator(time_step: openmm.unit.Quantity) → openmm.Integrator[source]: Specify how to integrate forces in each timestep

forces() → Iterable[openmm.Force] | None[source]: Specify any additional force contributions to position/velocity updates