BioSimSpace.Protocol.Production¶

class BioSimSpace.Protocol.Production(timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=100, restart_interval=100, first_step=0, restart=False)¶

A class for storing production protocols.

__init__(timestep=2.0000 fs, runtime=1.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=100, restart_interval=100, first_step=0, restart=False)¶

Constructor.

Parameters

timestep (Time) – The integration timestep.
runtime (Time) – The running time.
temperature (Temperature) – The temperature.
pressure (Pressure) – The pressure. Pass pressure=None to use the NVT ensemble.
report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)
restart_interval (int) – The frequency at which restart configurations and trajectory
first_step (int) – The initial time step (for restart simulations).
restart (bool) – Whether this is a continuation of a previous simulation.

Methods

`__init__`([timestep, runtime, temperature, …])	Constructor.
`getFirstStep`()	Return the first time step.
`getPressure`()	Return the pressure.
`getReportInterval`()	Return the interval between reporting statistics.
`getRestartInterval`()	Return the interval between saving restart confiugrations, and/or trajectory frames.
`getRunTime`()	Return the running time.
`getTemperature`()	Return temperature.
`getTimeStep`()	Return the time step.
`isRestart`()	Return whether this restart simulation.
`setFirstStep`(first_step)	Set the initial time step.
`setPressure`(pressure)	Set the pressure.
`setReportInterval`(report_interval)	Set the interval at which statistics are reported.
`setRestart`(restart)	Set the restart flag.
`setRestartInterval`(restart_interval)	Set the interval between saving restart confiugrations, and/or trajectory frames.
`setRunTime`(runtime)	Set the running time.
`setTemperature`(temperature)	Set the temperature.
`setTimeStep`(timestep)	Set the time step.

getFirstStep()¶

Return the first time step.

Returns: step – The first time step.
Return type: int

getPressure()¶

Return the pressure.

Returns: pressure – The pressure.
Return type: Pressure

getReportInterval()¶

Return the interval between reporting statistics. (In integration steps.).

Returns: report_interval – The number of integration steps between reporting statistics.
Return type: int

getRestartInterval()¶

Return the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Returns: restart_interval – The number of integration steps between saving restart configurations and/or trajectory frames.
Return type: int

getRunTime()¶

Return the running time.

Returns: runtime – The simulation run time.
Return type: Time

getTemperature()¶

Return temperature.

Returns: temperature – The simulation temperature.
Return type: Temperature

getTimeStep()¶

Return the time step.

Returns: timestep – The integration time step.
Return type: Time

isRestart()¶

Return whether this restart simulation.

Returns: is_restart – Whether this is a restart simulation.
Return type: bool

setFirstStep(first_step)¶

Set the initial time step.

Parameters: step (int) – The first time step.

setPressure(pressure)¶

Set the pressure.

Parameters: pressure (Pressure) – The pressure.

setReportInterval(report_interval)¶

Set the interval at which statistics are reported. (In integration steps.).

Parameters: report_interval (int) – The number of integration steps between reporting statistics.

setRestart(restart)¶

Set the restart flag.

Parameters: restart (bool) – Whether this is a restart simulation.

setRestartInterval(restart_interval)¶

Set the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Parameters: restart_interval (int) – The number of integration steps between saving restart configurations and/or trajectory frames.

setRunTime(runtime)¶

Set the running time.

Parameters: runtime (Time) – The simulation run time.

setTemperature(temperature)¶

Set the temperature.

Parameters: temperature (Temperature) – The simulation temperature.

setTimeStep(timestep)¶

Set the time step.

Parameters: timestep (Time) – The integration time step.