def _validate(self, value):
"""Validate that the value is of the correct type."""
if type(value) is _Types.Time:
return value._convert_to(self._unit)
else:
# Extract the value and unit from the argument string.
value, unit = _validate_unit_requirement(value, "time")
if unit is None:
return _Types.Time(value, self._unit)
else:
return _Types.Time(value, unit)._convert_to(self._unit)
def __init__(self,
help=None,
default=None,
unit=None,
minimum=None,
maximum=None,
allowed=None):
"""Constructor.
Parameters
----------
help : str
The help string.
default : :class:`Time <BioSimSpace.Types.Time>`
The default value.
unit : str
The unit.
minimum : :class:`Time <BioSimSpace.Types.Time>`
The minimum allowed value.
maximum : :class:`Time <BioSimSpace.Types.Time>`
The maximum allowed value.
allowed : [:class:`Time <BioSimSpace.Types.Time>`]
The list of allowed values.
"""
# Validate the unit.
if unit is not None:
time = _Types.Time("1 %s" % unit)
self._unit = time.unit()
self._print_unit = time._print_format[time.unit()]
else:
try:
self._unit = default.unit()
except:
raise ValueError(
"No unit or default value has been specified!")
# Call the base class constructor.
super().__init__(help=help,
default=default,
unit=self._unit,
minimum=minimum,
maximum=maximum,
allowed=allowed)
def __init__(self,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(0.2, "nanoseconds"),
temperature_start=_Types.Temperature(300, "kelvin"),
temperature_end=_Types.Temperature(300, "kelvin"),
temperature=None,
pressure=None,
frames=20,
restrain_backbone=False):
"""Constructor.
Parameters
----------
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature_start : :class:`Temperature <BioSimSpace.Types.Temperature>`
The starting temperature.
temperature_end : :class:`Temperature <BioSimSpace.Types.Temperature>`
The final temperature.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The equilibration temperature. This takes precedence of over
the other temperatures, i.e. to run at fixed temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. If this argument is omitted then the simulation
is run using the NVT ensemble.
frames : int
The number of trajectory frames to record.
restrain_backbone : bool
Whether the atoms in the backbone are fixed.
"""
# Call the base class constructor.
super().__init__()
# Set the time step.
self.setTimeStep(timestep)
# Set the running time.
self.setRunTime(runtime)
# Constant temperature equilibration.
if temperature is not None:
self.setStartTemperature(temperature)
self.setEndTemperature(temperature)
self._is_const_temp = True
# Heating / cooling simulation.
else:
self._is_const_temp = False
# Set the start temperature.
self.setStartTemperature(temperature_start)
# Set the final temperature.
self.setEndTemperature(temperature_end)
# Constant temperature simulation.
if self._temperature_start == self._temperature_end:
self._is_const_temp = True
# Constant pressure simulation.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
# Set the number of trajectory frames.
self.setFrames(frames)
# Set the backbone restraint.
self.setRestraint(restrain_backbone)
def __init__(self,
collective_variable,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(1, "nanosecond"),
temperature=_Types.Temperature(300, "kelvin"),
pressure=_Types.Pressure(1, "atmosphere"),
hill_height=_Types.Energy(1, "kj per mol"),
hill_frequency=1000,
bias_factor=None,
hills_file=None,
grid_file=None,
colvar_file=None
):
"""Constructor.
Parameters
----------
collective_variable : :class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`, \
[:class:`CollectiveVariable <BioSimSpace.Metadynamics.CollectiveVariable>`]
The collective variable (or variables) for the simulation.
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. Pass pressure=None to use the NVT ensemble.
hill_height : :class:`Energy <BioSimSpace.Types.Energy>`
The height of the Gaussian hills.
hill_frequency : int
The frequency at which hills are deposited.
bias_factor : float
The bias factor for well tempered metadynamics.
hills_file : str
The path to a HILLS file from a previous simulation. This can
be used to restart in order to contiune sampling. The information
in the file must be consistent with the 'collective_variable'
argument.
grid_file : str
The path to a GRID file from a previous simulation. This can
be used to restart in order to continue sampling. The information
in the file must be consistent with the 'collective_variable'
argument.
colvar_file : str
The path to a COLVAR file from a previous simulation. The
information in the file must be consistent with the
'collective_variable' argument.
"""
# Call the base class constructor.
super().__init__()
# Whether this is a newly created object.
self._is_new_object = True
# Set the collective variable.
self.setCollectiveVariable(collective_variable)
# Set the time step.
self.setTimeStep(timestep)
# Set the runtime.
self.setRunTime(runtime)
# Set the system temperature.
self.setTemperature(temperature)
# Set the system pressure.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
# Set the hill parameters: height, frequency.
self.setHillHeight(hill_height)
self.setHillFrequency(hill_frequency)
# Set the bias factor for well tempered metadynamics.
if bias_factor is not None:
self.setBiasFactor(bias_factor)
else:
self._bias_factor = None
# Set the restart files.
if hills_file is not None:
self.setHillsFile(hills_file)
else:
self._hills_file = None
if grid_file is not None:
self.setGridFile(grid_file)
else:
self._grid_file = None
if colvar_file is not None:
self.setColvarFile(colvar_file)
else:
self._colvar_file = None
# Flag that the object has been created.
self._is_new_object = False
def __init__(self,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(1, "nanosecond"),
temperature=_Types.Temperature(300, "kelvin"),
pressure=_Types.Pressure(1, "atmosphere"),
frames=20,
first_step=0,
restart=False
):
"""Constructor.
Parameters
----------
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. Pass pressure=None to use the NVT ensemble.
frames : int
The number of trajectory frames to record.
first_step : int
The initial time step (for restart simulations).
restart : bool
Whether this is a continuation of a previous simulation.
"""
# Call the base class constructor.
super().__init__()
# Set the time step.
self.setTimeStep(timestep)
# Set the runtime.
self.setRunTime(runtime)
# Set the system temperature.
self.setTemperature(temperature)
# Set the system pressure.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
# Set the number of trajectory frames.
self.setFrames(frames)
# Set the restart flag.
self.setRestart(restart)
# Set the first time step.
self.setFirstStep(first_step)
def __init__(self,
lam=0.0,
lam_vals=None,
min_lam=0.0,
max_lam=1.0,
num_lam=11,
timestep=_Types.Time(2, "femtosecond"),
runtime=_Types.Time(1, "nanosecond"),
temperature=_Types.Temperature(300, "kelvin"),
pressure=_Types.Pressure(1, "atmosphere")):
"""Constructor.
Parameters
----------
lam : float
The perturbation parameter: [0.0, 1.0]
lam_vals : [float]
The list of lambda parameters.
min_lam : float
The minimum lambda value.
max_lam : float
The maximum lambda value.
num_lam : int
The number of lambda values.
timestep : :class:`Time <BioSimSpace.Types.Time>`
The integration timestep.
runtime : :class:`Time <BioSimSpace.Types.Time>`
The running time.
temperature : :class:`Temperature <BioSimSpace.Types.Temperature>`
The temperature.
pressure : :class:`Pressure <BioSimSpace.Types.Pressure>`
The pressure. Pass pressure=None to use the NVT ensemble.
"""
# Call the base class constructor.
super().__init__()
# Validate and set the lambda values.
self.setLambdaValues(lam, lam_vals, min_lam, max_lam, num_lam)
# Set the time step.
self.setTimeStep(timestep)
# Set the runtime.
self.setRunTime(runtime)
# Set the system temperature.
self.setTemperature(temperature)
# Set the system pressure.
if pressure is not None:
self.setPressure(pressure)
else:
self._pressure = None
