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.
Return the first time step.
Return the pressure.
Return the interval between reporting statistics.
Return the interval between saving restart confiugrations, and/or trajectory frames.
Return the running time.
Return temperature.
Return the time step.
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
- 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:
- getTemperature()[source]#
Return temperature.
- Returns:
temperature – The simulation temperature.
- Return type:
- getTimeStep()[source]#
Return the time step.
- Returns:
timestep – The integration time step.
- Return type:
- 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.
- 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.