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.