"""
Clocks for the simulator.
"""
__docformat__ = "restructuredtext en"
from abc import ABC, abstractmethod
import numpy as np
from brian2.core.names import Nameable
from brian2.core.variables import Variables
from brian2.groups.group import VariableOwner
from brian2.units.allunits import second
from brian2.units.fundamentalunits import Quantity, check_units
from brian2.units.stdunits import ms
from brian2.utils.logger import get_logger
__all__ = ["BaseClock", "Clock", "defaultclock", "EventClock"]
logger = get_logger(__name__)
[docs]
def check_dt(new_dt, old_dt, target_t):
"""
Check that the target time can be represented equally well with the new
dt.
Parameters
----------
new_dt : float
The new dt value
old_dt : float
The old dt value
target_t : float
The target time
Raises
------
ValueError
If using the new dt value would lead to a difference in the target
time of more than `Clock.epsilon_dt` times ``new_dt`` (by default,
0.01% of the new dt).
Examples
--------
>>> from brian2 import *
>>> check_dt(float(17*ms), float(0.1*ms), float(0*ms)) # For t=0s, every dt is fine
>>> check_dt(float(0.05*ms), float(0.1*ms), float(10*ms)) # t=10*ms can be represented with the new dt
>>> check_dt(float(0.2*ms), float(0.1*ms), float(10.1*ms)) # t=10.1ms cannot be represented with dt=0.2ms # doctest: +ELLIPSIS
Traceback (most recent call last):
...
ValueError: Cannot set dt from 100. us to 200. us, the time 10.1 ms is not a multiple of 200. us.
"""
old_t = np.int64(np.round(target_t / old_dt)) * old_dt
new_t = np.int64(np.round(target_t / new_dt)) * new_dt
error_t = target_t
if abs(new_t - old_t) / new_dt > Clock.epsilon_dt:
old = str(old_dt * second)
new = str(new_dt * second)
t = str(error_t * second)
raise ValueError(
f"Cannot set dt from {old} to {new}, the "
f"time {t} is not a multiple of {new}."
)
[docs]
class BaseClock(VariableOwner, ABC):
"""
Abstract base class for all clocks in the simulator.
This class should never be instantiated directly, use one of the subclasses
like Clock or EventClock instead.
Parameters
----------
name : str, optional
An explicit name, if not specified gives an automatically generated name
"""
epsilon = 1e-14
def __init__(self, name):
# We need a name right away because some devices (e.g. cpp_standalone)
# need a name for the object when creating the variables
Nameable.__init__(self, name=name)
self.variables = Variables(self)
self.variables.add_array(
"timestep", size=1, dtype=np.int64, read_only=True, scalar=True
)
self.variables.add_array(
"t",
dimensions=second.dim,
size=1,
dtype=np.float64,
read_only=True,
scalar=True,
)
self.variables["timestep"].set_value(0)
self.variables.add_constant("N", value=1)
self._enable_group_attributes()
self._i_end = None
logger.diagnostic(f"Created clock {self.name}")
[docs]
@abstractmethod
def advance(self):
"""
Advance the clock to the next time step.
Must be implemented by subclasses.
"""
pass
[docs]
@abstractmethod
@check_units(start=second, end=second)
def set_interval(self, start, end):
"""
Set the start and end time of the simulation.
Must be implemented by subclasses.
"""
pass
[docs]
@abstractmethod
def same_time(self, other):
"""
Check if two clocks are at the same time (within epsilon).
Parameters
----------
other : BaseClock
The other clock to compare with
Returns
-------
bool
True if both clocks are at the same time
"""
pass
[docs]
class EventClock(BaseClock):
"""
A clock that advances through a predefined sequence of times.
Parameters
----------
times : array-like
The sequence of times for the clock to advance through
name : str, optional
An explicit name, if not specified gives an automatically generated name
"""
def __init__(self, times, name="eventclock*"):
super().__init__(name=name)
times = Quantity(times)
from brian2.units.fundamentalunits import fail_for_dimension_mismatch
fail_for_dimension_mismatch(
times,
second.dim,
error_message="'times' must have dimensions of time",
dim=times,
)
times_array = np.asarray(times, dtype=float)
unique_times = np.unique(times_array)
if len(unique_times) != len(times_array):
raise ValueError(
"The times provided to EventClock must not contain duplicates."
)
self._times = sorted(times)
self._times.append(np.inf * ms)
self.variables.add_array(
"times",
dimensions=second.dim,
size=len(self._times),
values=self._times,
dtype=np.float64,
read_only=True,
)
self.variables["t"].set_value(self._times[0])
logger.diagnostic(f"Created event clock {self.name}")
[docs]
def advance(self):
"""
Advance to the next time in the sequence.
"""
new_ts = self.variables["timestep"].get_value().item()
if self._i_end is not None and new_ts + 1 > self._i_end:
raise StopIteration(
"EventClock has reached the end of its available times."
)
new_ts += 1
self.variables["timestep"].set_value(new_ts)
self.variables["t"].set_value(self._times[new_ts])
[docs]
@check_units(start=second, end=second)
def set_interval(self, start, end):
"""
Set the start and end time of the simulation.
Parameters
----------
start : second
The start time of the simulation
end : second
The end time of the simulation
"""
start = float(start)
end = float(end)
start_idx = np.searchsorted(self._times, start)
end_idx = np.searchsorted(self._times, end)
self.variables["timestep"].set_value(start_idx)
self.variables["t"].set_value(self._times[start_idx])
self._i_end = end_idx
def __getitem__(self, timestep):
"""
Get the time at a specific timestep.
Parameters
----------
timestep : int
The timestep to get the time for
Returns
-------
float
The time at the specified timestep
"""
return self._times[timestep]
[docs]
def same_time(self, other):
"""
Check if two clocks are at the same time.
For comparisons with `Clock` objects, uses the Clock's dt and epsilon_dt.
For comparisons with other `EventClock` or `BaseClock` objects, uses the base
epsilon value.
Parameters
----------
other : BaseClock
The other clock to compare with
Returns
-------
bool
True if both clocks are at the same time
"""
t1 = self.variables["t"].get_value().item()
t2 = other.variables["t"].get_value().item()
if isinstance(other, Clock):
return abs(t1 - t2) / other.dt_ < other.epsilon_dt
else:
# Both are pure EventClocks without dt.
return abs(t1 - t2) < self.epsilon
[docs]
class Clock(BaseClock):
"""
An object that holds the simulation time and the time step.
Parameters
----------
dt : float
The time step of the simulation as a float
name : str, optional
An explicit name, if not specified gives an automatically generated name
Notes
-----
Clocks are run in the same `Network.run` iteration if `~Clock.t` is the
same. The condition for two
clocks to be considered as having the same time is
``abs(t1-t2)<epsilon*abs(t1)``, a standard test for equality of floating
point values. The value of ``epsilon`` is ``1e-14``.
"""
#: The relative difference for times (in terms of dt) so that they are
#: considered identical.
epsilon_dt = 1e-4
def __init__(self, dt, name="clock*"):
super().__init__(name=name)
self._old_dt = None
self.variables.add_array(
"dt",
dimensions=second.dim,
size=1,
values=float(dt),
dtype=np.float64,
read_only=True,
constant=True,
scalar=True,
)
self.dt = dt
logger.diagnostic(f"Created clock {self.name} with dt={self.dt}")
def __repr__(self):
return f"Clock(dt={self.dt!r}, name={self.name!r})"
[docs]
def advance(self):
"""
Advance to the next time step.
"""
new_ts = self.variables["timestep"].get_value().item() + 1
if self._i_end is not None and new_ts > self._i_end:
raise StopIteration("Clock has reached the end of its available times.")
self.variables["timestep"].set_value(new_ts)
new_t = new_ts * self.dt_
self.variables["t"].set_value(new_t)
def _get_dt_(self):
return self.variables["dt"].get_value().item()
@check_units(dt_=1)
def _set_dt_(self, dt_):
self._old_dt = self._get_dt_()
self.variables["dt"].set_value(dt_)
@check_units(dt=second)
def _set_dt(self, dt):
self._set_dt_(float(dt))
dt = property(
fget=lambda self: Quantity(self.dt_, dim=second.dim),
fset=_set_dt,
doc="""The time step of the simulation in seconds.""",
)
dt_ = property(
fget=_get_dt_,
fset=_set_dt_,
doc="""The time step of the simulation as a float (in seconds)""",
)
def _calc_timestep(self, target_t):
"""
Calculate the integer time step for the target time. If it cannot be
exactly represented (up to epsilon_dt of dt), round up.
Parameters
----------
target_t : float
The target time in seconds
Returns
-------
timestep : int
The target time in integers (based on dt)
"""
new_i = np.int64(np.round(target_t / self.dt_))
new_t = new_i * self.dt_
if new_t == target_t or np.abs(new_t - target_t) / self.dt_ <= Clock.epsilon_dt:
new_timestep = new_i
else:
new_timestep = np.int64(np.ceil(target_t / self.dt_))
return new_timestep
@check_units(target_t=second)
def _set_t_update_dt(self, target_t=0 * second):
"""
Set the time to a specific value, checking if dt has changed.
Parameters
----------
target_t : second
The target time to set
"""
new_dt = self.dt_
old_dt = self._old_dt
target_t = float(target_t)
if old_dt is not None and new_dt != old_dt:
self._old_dt = None
check_dt(new_dt, old_dt, target_t)
new_timestep = self._calc_timestep(target_t)
self.variables["timestep"].set_value(new_timestep)
self.variables["t"].set_value(new_timestep * self.dt_)
set_t = self.variables["t"].get_value().item()
logger.diagnostic(f"Setting Clock {self.name} to t={set_t}, dt={new_dt}")
[docs]
@check_units(start=second, end=second)
def set_interval(self, start, end):
"""
Set the start and end time of the simulation.
Sets the start and end value of the clock precisely if
possible (using epsilon_dt) or rounding up if not. This assures that
multiple calls to `Network.run` will not re-run the same time step.
Parameters
----------
start : second
The start time of the simulation
end : second
The end time of the simulation
"""
self._set_t_update_dt(target_t=start)
end = float(end)
self._i_end = self._calc_timestep(end)
if self._i_end > 2**40:
logger.warn(
"The end time of the simulation has been set to "
f"{str(end * second)}, which based on the dt value of "
f"{str(self.dt)} means that {self._i_end} "
"time steps will be simulated. This can lead to "
"numerical problems, e.g. the times t will not "
"correspond to exact multiples of "
"dt.",
"many_timesteps",
)
[docs]
def same_time(self, other):
"""
Check if two clocks are at the same time (within epsilon_dt * dt).
Parameters
----------
other : BaseClock
The other clock to compare with
Returns
-------
bool
True if both clocks are at the same time
"""
t1 = self.variables["t"].get_value().item()
t2 = other.variables["t"].get_value().item()
if isinstance(other, Clock):
# Both are pure Clocks with dt so we take the min.
dt = min(self.dt_, other.dt_)
return abs(t1 - t2) / dt < self.epsilon_dt
else:
return abs(t1 - t2) / self.dt_ < self.epsilon_dt
def __le__(self, other):
return self.__lt__(other) or self.same_time(other)
def __ge__(self, other):
return self.__gt__(other) or self.same_time(other)
[docs]
class DefaultClockProxy:
"""
Method proxy to access the defaultclock of the currently active device
"""
def __getattr__(self, name):
if name == "_is_proxy":
return True
from brian2.devices.device import active_device
return getattr(active_device.defaultclock, name)
def __setattr__(self, key, value):
from brian2.devices.device import active_device
setattr(active_device.defaultclock, key, value)
#: The standard clock, used for objects that do not specify any clock or dt
defaultclock = DefaultClockProxy()
