finsberg / fenicsx-pulse

Next generation cardiac mechanics solver based on FEniCSx

fenicsx-pulse

fenicsx-pulse is a cardiac mechanics solver based on FEniCSx. It is a successor of pulse which is a cardiac mechanics solver based on FEniCS.

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Notice

This repo is a complete rewrite of pulse to work with FEniCSx. The package is not yet ready for release.

If you are using FEniCS please check out pulse instead

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• Documentation: https://finsberg.github.io/fenicsx-pulse/
• Source code: https://github.com/finsberg/fenicsx-pulse

Install

To install fenicsx_pulse you need to first install FEniCSx. Next you can install fenicsx_pulse via pip

python3 -m pip install fenicsx-pulse

We also provide a pre-built docker image with FEniCSx and fenicsx_pulse installed. You pull this image using the command

docker pull ghcr.io/finsberg/fenicsx-pulse:v0.1.5

Simple Example

import dolfinx
import numpy as np
import fenicsx_pulse
from mpi4py import MPI
from petsc4py import PETSc

# Create unit cube mesh
mesh = dolfinx.mesh.create_unit_cube(MPI.COMM_WORLD, 3, 3, 3)

# Specific list of boundary markers
boundaries = [
    fenicsx_pulse.Marker(marker=1, dim=2, locator=lambda x: np.isclose(x[0], 0)),
    fenicsx_pulse.Marker(marker=2, dim=2, locator=lambda x: np.isclose(x[0], 1)),
]
# Create geometry
geo = fenicsx_pulse.Geometry(
    mesh=mesh,
    boundaries=boundaries,
    metadata={"quadrature_degree": 4},
)

# Create passive material model
material_params = fenicsx_pulse.HolzapfelOgden.transversely_isotropic_parameters()
f0 = dolfinx.fem.Constant(mesh, PETSc.ScalarType((1.0, 0.0, 0.0)))
s0 = dolfinx.fem.Constant(mesh, PETSc.ScalarType((0.0, 1.0, 0.0)))
material = fenicsx_pulse.HolzapfelOgden(f0=f0, s0=s0, **material_params)

# Create model for active contraction
Ta = dolfinx.fem.Constant(mesh, PETSc.ScalarType(0.0))
active_model = fenicsx_pulse.ActiveStress(f0, activation=Ta)

# Create model for compressibility
comp_model = fenicsx_pulse.Incompressible()

# Create Cardiac Model
model = fenicsx_pulse.CardiacModel(
    material=material,
    active=active_model,
    compressibility=comp_model,
)

# Specific dirichlet boundary conditions on the boundary
def dirichlet_bc(
    state_space: dolfinx.fem.FunctionSpace,
) -> list[dolfinx.fem.bcs.DirichletBCMetaClass]:
    V, _ = state_space.sub(0).collapse()
    facets = geo.facet_tags.find(1)  # Specify the marker used on the boundary
    dofs = dolfinx.fem.locate_dofs_topological((state_space.sub(0), V), 2, facets)
    u_fixed = dolfinx.fem.Function(V)
    u_fixed.x.set(0.0)
    return [dolfinx.fem.dirichletbc(u_fixed, dofs, state_space.sub(0))]

# Use a traction on the opposite boundary
traction = dolfinx.fem.Constant(mesh, PETSc.ScalarType(-1.0))
neumann = fenicsx_pulse.NeumannBC(traction=traction, marker=2)

# Collect all boundary conditions
bcs = fenicsx_pulse.BoundaryConditions(dirichlet=(dirichlet_bc,), neumann=(neumann,))

# Create mechanics problem
problem = fenicsx_pulse.MechanicsProblem(model=model, geometry=geo, bcs=bcs)

# Set a value for the active stress
Ta.value = 2.0

# Solve the problem
problem.solve()

# Get the solution
u, p = problem.state.split()

# And save to XDMF
xdmf = dolfinx.io.XDMFFile(mesh.comm, "results.xdmf", "w")
xdmf.write_mesh(mesh)
xdmf.write_function(u, 0.0)
xdmf.write_function(p, 0.0)

Contributing

See https://finsberg.github.io/fenicsx-pulse/CONTRIBUTING.html

fenicsx-pulse's Issues

Navier Stokes steady implementation

Description

Hi @finsberg

How to implement the below problem in Fenics?

The given expression will be interpreted at run-time so that vx = 6(y − 1)(2 − y). As y ∈ [1, 2] thereby creating a parabolic velocity profile with a mean velocity of unity.