Bulk-boundary coupling

Demonstrates coupling of bulk and boundary fields.

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import numpy as np

import pde

import emulsim

# set up a 2d cytosol with a 1d boundary membrane
grid = pde.UnitGrid([32, 8], periodic=[True, False])
cytosol = emulsim.ScalarFieldElement.from_field(pde.ScalarField(grid, 0.001))
membrane = emulsim.ScalarBoundaryFieldElement.from_bulk_grid(
    grid, axis=1, upper=True, data=np.random.uniform(-1, 1, 32)
)
state = emulsim.State({"cytosol": cytosol, "membrane": membrane})

# set up simulation of phase separation in membrane and diffusion in cytosol
simulation = emulsim.Simulation(state)
simulation.add_actor("cytosol", emulsim.DiffusionActor())
simulation.add_actor("membrane", emulsim.ScalarPDEActor(pde.CahnHilliardPDE()))
# couple both domains using an exchange flux
boundary_coupling = emulsim.FieldBoundaryExchangeActor(
    {"exchange_flux": "0.1 * (bulk - boundary)"}
)
simulation.add_actor(("cytosol", "membrane"), boundary_coupling)

# run the simulation
result = simulation.run(t_range=100)
result.plot(vmin=-0.2, vmax=0.2)