brainpy.integrators.ode.exponential.ExponentialEuler

class brainpy.integrators.ode.exponential.ExponentialEuler(f, var_type=None, dt=None, name=None, show_code=False, dyn_vars=None, state_delays=None, neutral_delays=None)

Exponential Euler method using automatic differentiation.

This method uses brainpy.math.vector_grad to automatically infer the linear part of the given function. Therefore, it has minimal constraints on your derivative function. Arbitrary complex functions can be numerically integrated with this method.

Examples

Here is an example uses ExponentialEuler to implement HH neuron model.

>>> import brainpy as bp
>>> import brainpy.math as bm
>>>
>>> class HH(bp.dyn.NeuGroup):
>>>   def __init__(self, size, ENa=55., EK=-90., EL=-65, C=1.0, gNa=35., gK=9.,
>>>                gL=0.1, V_th=20., phi=5.0, name=None):
>>>     super(HH, self).__init__(size=size, name=name)
>>>
>>>     # parameters
>>>     self.ENa = ENa
>>>     self.EK = EK
>>>     self.EL = EL
>>>     self.C = C
>>>     self.gNa = gNa
>>>     self.gK = gK
>>>     self.gL = gL
>>>     self.V_th = V_th
>>>     self.phi = phi
>>>
>>>     # variables
>>>     self.V = bm.Variable(bm.ones(size) * -65.)
>>>     self.h = bm.Variable(bm.ones(size) * 0.6)
>>>     self.n = bm.Variable(bm.ones(size) * 0.32)
>>>     self.spike = bm.Variable(bm.zeros(size, dtype=bool))
>>>     self.input = bm.Variable(bm.zeros(size))
>>>
>>>     # functions
>>>     self.int_h = bp.ode.ExponentialEuler(self.dh)
>>>     self.int_n = bp.ode.ExponentialEuler(self.dn)
>>>     self.int_V = bp.ode.ExponentialEuler(self.dV)
>>>
>>>   def dh(self, h, t, V):
>>>     alpha = 0.07 * bm.exp(-(V + 58) / 20)
>>>     beta = 1 / (bm.exp(-0.1 * (V + 28)) + 1)
>>>     dhdt = self.phi * (alpha * (1 - h) - beta * h)
>>>     return dhdt
>>>
>>>   def dn(self, n, t, V):
>>>     alpha = -0.01 * (V + 34) / (bm.exp(-0.1 * (V + 34)) - 1)
>>>     beta = 0.125 * bm.exp(-(V + 44) / 80)
>>>     dndt = self.phi * (alpha * (1 - n) - beta * n)
>>>     return dndt
>>>
>>>   def dV(self, V, t, h, n, Iext):
>>>     m_alpha = -0.1 * (V + 35) / (bm.exp(-0.1 * (V + 35)) - 1)
>>>     m_beta = 4 * bm.exp(-(V + 60) / 18)
>>>     m = m_alpha / (m_alpha + m_beta)
>>>     INa = self.gNa * m ** 3 * h * (V - self.ENa)
>>>     IK = self.gK * n ** 4 * (V - self.EK)
>>>     IL = self.gL * (V - self.EL)
>>>     dVdt = (- INa - IK - IL + Iext) / self.C
>>>
>>>     return dVdt
>>>
>>>   def update(self, _t, _dt):
>>>     h = self.int_h(self.h, _t, self.V, dt=_dt)
>>>     n = self.int_n(self.n, _t, self.V, dt=_dt)
>>>     V = self.int_V(self.V, _t,  self.h, self.n, self.input, dt=_dt)
>>>     self.spike.value = bm.logical_and(self.V < self.V_th, V >= self.V_th)
>>>     self.V.value = V
>>>     self.h.value = h
>>>     self.n.value = n
>>>     self.input[:] = 0.
>>>
>>> run = bp.dyn.DSRunner(HH(1), inputs=('input', 2.), monitors=['V'], dt=0.05)
>>> run(100)
>>> bp.visualize.line_plot(run.mon.ts, run.mon.V, legend='V', show=True)

(Source code, png, hires.png, pdf)

The above example can also be defined with brainpy.JointEq.

>>> import brainpy as bp
>>> import brainpy.math as bm
>>>
>>> class HH(bp.dyn.NeuGroup):
>>>   def __init__(self, size, ENa=55., EK=-90., EL=-65, C=1.0, gNa=35., gK=9.,
>>>                gL=0.1, V_th=20., phi=5.0, name=None):
>>>     super(HH, self).__init__(size=size, name=name)
>>>
>>>     # parameters
>>>     self.ENa = ENa
>>>     self.EK = EK
>>>     self.EL = EL
>>>     self.C = C
>>>     self.gNa = gNa
>>>     self.gK = gK
>>>     self.gL = gL
>>>     self.V_th = V_th
>>>     self.phi = phi
>>>
>>>     # variables
>>>     self.V = bm.Variable(bm.ones(size) * -65.)
>>>     self.h = bm.Variable(bm.ones(size) * 0.6)
>>>     self.n = bm.Variable(bm.ones(size) * 0.32)
>>>     self.spike = bm.Variable(bm.zeros(size, dtype=bool))
>>>     self.input = bm.Variable(bm.zeros(size))
>>>
>>>     # functions
>>>     derivative = bp.JointEq([self.dh, self.dn, self.dV])
>>>     self.integral = bp.ode.ExponentialEuler(derivative)
>>>
>>>   def dh(self, h, t, V):
>>>     alpha = 0.07 * bm.exp(-(V + 58) / 20)
>>>     beta = 1 / (bm.exp(-0.1 * (V + 28)) + 1)
>>>     dhdt = self.phi * (alpha * (1 - h) - beta * h)
>>>     return dhdt
>>>
>>>   def dn(self, n, t, V):
>>>     alpha = -0.01 * (V + 34) / (bm.exp(-0.1 * (V + 34)) - 1)
>>>     beta = 0.125 * bm.exp(-(V + 44) / 80)
>>>     dndt = self.phi * (alpha * (1 - n) - beta * n)
>>>     return dndt
>>>
>>>   def dV(self, V, t, h, n, Iext):
>>>     m_alpha = -0.1 * (V + 35) / (bm.exp(-0.1 * (V + 35)) - 1)
>>>     m_beta = 4 * bm.exp(-(V + 60) / 18)
>>>     m = m_alpha / (m_alpha + m_beta)
>>>     INa = self.gNa * m ** 3 * h * (V - self.ENa)
>>>     IK = self.gK * n ** 4 * (V - self.EK)
>>>     IL = self.gL * (V - self.EL)
>>>     dVdt = (- INa - IK - IL + Iext) / self.C
>>>
>>>     return dVdt
>>>
>>>   def update(self, t, dt):
>>>     h, n, V = self.integral(self.h, self.n, self.V, _t, self.input, dt=_dt)
>>>     self.spike.value = bm.logical_and(self.V < self.V_th, V >= self.V_th)
>>>     self.V.value = V
>>>     self.h.value = h
>>>     self.n.value = n
>>>     self.input[:] = 0.
>>>
>>> run = bp.dyn.DSRunner(HH(1), inputs=('input', 2.), monitors=['V'], dt=0.05)
>>> run(100)
>>> bp.visualize.line_plot(run.mon.ts, run.mon.V, legend='V', show=True)

(Source code)

Parameters

• f (function, joint_eq.JointEq) – The derivative function.

• var_type (optional, str) – The variable type.

• dt (optional, float) – The default numerical integration step.

• name (optional, str) – The integrator name.

• dyn_vars (optional, dict, sequence of JaxArray, JaxArray) –

__init__(f, var_type=None, dt=None, name=None, show_code=False, dyn_vars=None, state_delays=None, neutral_delays=None)

Methods

__init__(f[, var_type, dt, name, show_code, ...])
build()
load_states(filename[, verbose])	Load the model states.
nodes([method, level, include_self])	Collect all children nodes.
register_implicit_nodes(nodes)
register_implicit_vars(variables)
save_states(filename[, variables])	Save the model states.
set_integral(f)	Set the integral function.
train_vars([method, level, include_self])	The shortcut for retrieving all trainable variables.
unique_name([name, type_])	Get the unique name for this object.
vars([method, level, include_self])	Collect all variables in this node and the children nodes.

Attributes

arg_names
arguments	All arguments when calling the numer integrator of the differential equation.
dt	The numerical integration precision.
integral	The integral function.
name
neutral_delays	neutral delays.
parameters	The parameters defined in the differential equation.
state_delays	State delays.
variables	The variables defined in the differential equation.