2.21 Custom Class for coupled PDEs

This example shows how to solve a set of coupled PDEs, the spatially coupled FitzHugh–Nagumo model, which is a simple model for the excitable dynamics of coupled Neurons:

\[\begin{split}\partial_t u &= \nabla^2 u + u (u - \alpha) (1 - u) + w \\ \partial_t w &= \epsilon u\end{split}\]

Here, \(\alpha\) denotes the external stimulus and \(\epsilon\) defines the recovery time scale. We implement this as a custom PDE class below.

pde coupled
  0%|          | 0/100.0 [00:00<?, ?it/s]
Initializing:   0%|          | 0/100.0 [00:00<?, ?it/s]
  0%|          | 0/100.0 [00:00<?, ?it/s]
  0%|          | 0.25/100.0 [00:00<01:18,  1.27it/s]
  1%|          | 0.81/100.0 [00:00<00:29,  3.37it/s]
  3%|▎         | 3.49/100.0 [00:00<00:12,  7.84it/s]
  9%|▉         | 9.41/100.0 [00:00<00:08, 10.31it/s]
 18%|█▊        | 18.08/100.0 [00:01<00:07, 10.37it/s]
 28%|██▊       | 27.58/100.0 [00:02<00:06, 10.74it/s]
 38%|███▊      | 38.04/100.0 [00:03<00:05, 11.30it/s]
 50%|████▉     | 49.75/100.0 [00:04<00:04, 11.09it/s]
 61%|██████    | 60.82/100.0 [00:05<00:03, 11.32it/s]
 73%|███████▎  | 72.58/100.0 [00:06<00:02, 11.38it/s]
 84%|████████▍ | 84.29/100.0 [00:07<00:01, 11.34it/s]
 96%|█████████▌| 95.7/100.0 [00:08<00:00, 11.52it/s]
 96%|█████████▌| 95.7/100.0 [00:08<00:00, 10.97it/s]
100%|██████████| 100.0/100.0 [00:08<00:00, 11.47it/s]
100%|██████████| 100.0/100.0 [00:08<00:00, 11.47it/s]

from pde import FieldCollection, PDEBase, UnitGrid


class FitzhughNagumoPDE(PDEBase):
    """FitzHugh–Nagumo model with diffusive coupling"""

    def __init__(self, stimulus=0.5, τ=10, a=0, b=0, bc="auto_periodic_neumann"):
        super().__init__()
        self.bc = bc
        self.stimulus = stimulus
        self.τ = τ
        self.a = a
        self.b = b

    def evolution_rate(self, state, t=0):
        v, w = state  # membrane potential and recovery variable

        v_t = v.laplace(bc=self.bc) + v - v**3 / 3 - w + self.stimulus
        w_t = (v + self.a - self.b * w) / self.τ

        return FieldCollection([v_t, w_t])


grid = UnitGrid([32, 32])
state = FieldCollection.scalar_random_uniform(2, grid)

eq = FitzhughNagumoPDE()
result = eq.solve(state, t_range=100, dt=0.01)
result.plot()

Total running time of the script: (0 minutes 9.056 seconds)