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)[source]#

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)[source]#

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()[source]#

Return the first time step.

Returns:

step – The first time step.

Return type:

int

getPressure()[source]#

Return the pressure.

Returns:

pressure – The pressure.

Return type:

Pressure

getReportInterval()[source]#

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

Returns:

report_interval – The number of integration steps between reporting statistics.

Return type:

int

getRestartInterval()[source]#

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()[source]#

Return the running time.

Returns:

runtime – The simulation run time.

Return type:

Time

getTemperature()[source]#

Return temperature.

Returns:

temperature – The simulation temperature.

Return type:

Temperature

getTimeStep()[source]#

Return the time step.

Returns:

timestep – The integration time step.

Return type:

Time

isRestart()[source]#

Return whether this restart simulation.

Returns:

is_restart – Whether this is a restart simulation.

Return type:

bool

setFirstStep(first_step)[source]#

Set the initial time step.

Parameters:

step (int) – The first time step.

setPressure(pressure)[source]#

Set the pressure.

Parameters:

pressure (Pressure) – The pressure.

setReportInterval(report_interval)[source]#

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)[source]#

Set the restart flag.

Parameters:

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

setRestartInterval(restart_interval)[source]#

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)[source]#

Set the running time.

Parameters:

runtime (Time) – The simulation run time.

setTemperature(temperature)[source]#

Set the temperature.

Parameters:

temperature (Temperature) – The simulation temperature.

setTimeStep(timestep)[source]#

Set the time step.

Parameters:

timestep (Time) – The integration time step.