https://github.com/finsberg/fenicsx-beat
https://github.com/finsberg/fenicsx-beat
cardiac ecg electrophysiology fenicsx finite-element-analysis monodomain-model
Last synced: 6 months ago
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- Host: GitHub
- URL: https://github.com/finsberg/fenicsx-beat
- Owner: finsberg
- License: mit
- Created: 2024-04-09T08:12:48.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-12-18T18:12:06.000Z (6 months ago)
- Last Synced: 2024-12-18T19:26:00.331Z (6 months ago)
- Topics: cardiac, ecg, electrophysiology, fenicsx, finite-element-analysis, monodomain-model
- Language: Python
- Homepage: https://finsberg.github.io/fenicsx-beat/
- Size: 9.2 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# fenicsx-beat
Cardiac electrophysiology simulator in FEniCSx
- Source code: https://github.com/finsberg/fenicsx-beat
- Documentation: https://finsberg.github.io/fenicsx-beat
## Install
You can install the library with pip
```
python3 -m pip install fenicsx-beat
```
## Getting started
```python
from mpi4py import MPI
import dolfinx
import ufl
import beat
import numpy as np
comm = MPI.COMM_WORLD
mesh = dolfinx.mesh.create_unit_square(comm, 10, 10, dolfinx.cpp.mesh.CellType.triangle)
time = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(0.0))
# Create stimulus
stim_expr = ufl.conditional(ufl.And(ufl.ge(time, 0.0), ufl.le(time, 0.5)), 200.0, 0.0)
stim_marker = 1
cells = dolfinx.mesh.locate_entities(
mesh, mesh.topology.dim, lambda x: np.logical_and(x[0] <= 0.5, x[1] <= 0.5)
)
stim_tags = dolfinx.mesh.meshtags(
mesh,
mesh.topology.dim,
cells,
np.full(len(cells), stim_marker, dtype=np.int32),
)
dx = ufl.Measure("dx", domain=mesh, subdomain_data=stim_tags)
I_s = beat.Stimulus(expr=stim_expr, dZ=dx, marker=stim_marker)
# Create PDE model
pde = beat.MonodomainModel(time=time, mesh=mesh, M=0.01, I_s=I_s, dx=dx)
# Define scheme to solve ODE
def fun(t, states, parameters, dt):
v, s = states
a, b = parameters
values = np.zeros_like(states)
values[0] = v - a * s * dt
values[1] = s + b * v * dt
return values
# Define ODE solver
ode_space = dolfinx.fem.functionspace(mesh, ("P", 1))
parameters = np.array([1.0, 1.0])
init_states = np.array([0.0, 0.0])
ode = beat.odesolver.DolfinODESolver(
v_ode=dolfinx.fem.Function(ode_space),
v_pde=pde.state,
fun=fun,
init_states=init_states,
parameters=parameters,
num_states=2,
v_index=1,
)
# Combine PDE and ODE solver
solver = beat.MonodomainSplittingSolver(pde=pde, ode=ode)
# Solve
T = 5.0
t = 0.0
dt = 0.01
while t < T:
v = solver.pde.state.x.array
solver.step((t, t + dt))
t += dt
```
See more examples in the [documentation](https://finsberg.github.io/fenicsx-beat)
## License
MIT
## Need help or having issues
Please submit an [issue](https://github.com/finsberg/fenicsx-beat/issues)