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.