ambit-fe 1.1.3

A FEniCS-based cardiovascular physics solver

README

• Ambit - A FEniCS-based cardiovascular physics solver

3D nonlinear solid and fluid mechanics finite element Python code using FEniCS and PETSc libraries, supporting

Heart cycle simulation of a generic bi-ventricular heart model coupled to a closed-loop circulation model.

Heart cycle simulation of a generic bi-ventricular heart model coupled to a closed-loop circulation model.

• Solid mechanics
  • Finite strain elastodynamics, implementing a range of hyperelastic isotropic and anisotropic as well as viscous constitutive laws
  • Active stress for modeling of cardiac contraction mechanics
  • Quasi-static, generalized-alpha, or one-step theta time integration
  • Nearly incompressible as well as fully incompressible formulations (latter using pressure dofs)
  • Prestressing using MULF method in displacement formulation
  • Volumetric growth & remodeling
• Fluid dynamics
  • Incompressible Navier-Stokes/Stokes equations, either in nonconservative or conservative formulation
  • Navier-Stokes/Stokes flow in an Arbitrary Lagrangian Eulerian (ALE) reference frame
  • One-step theta, or generalized-alpha time integration
  • SUPG/PSPG stabilization for equal-order approximations of velocity and pressure
• Lumped (0D) models
  • Systemic and pulmonary circulation flow models
  • 2-element as well as 4-element Windkessel models
  • Signalling network model
• Coupling of different physics:
  • Monolithic coupling of ALE and fluid, 3D solid/fluid/ALE-fluid with lumped 0D flow models
  • Multiscale-in-time analysis of growth & remodeling (staggered solution of 3D-0D coupled solid-flow0d and G&R solid problem)
• Fluid-reduced-solid interaction (FrSI)
  • Boundary subspace-projected physics-reduced solid model (incl. hyperelastic, viscous, and active parts) in an ALE fluid reference frame
• POD-based model order reduction (MOR)
  • Projection-based model order reduction applicable to main fluid or solid field (also in a coupled problem), by either projecting the full problem or a boundary to a lower dimensional subspace spanned by POD modes

• author: Dr.-Ing. Marc Hirschvogel, [e-mail]

Still experimental / to-do:

• Fluid-solid interaction (FSI) (started)
• Finite strain plasticity
• Electrophysiology/scalar transport
• ... whatever might be wanted in some future ...

Documentation

Documentation can be viewed at https://ambit.readthedocs.io

Installation

In order to use Ambit, you need to install FEniCSx (latest Ambit-compatible dolfinx development version dates to 19 Aug 2023)

Ambit can then be installed using pip, either the current release

python3 -m pip install ambit-fe

or latest development version:

python3 -m pip install git+https://github.com/marchirschvogel/ambit.git

Alternatively, you can pull a pre-built Docker image with FEniCSx and Ambit installed:

docker pull ghcr.io/marchirschvogel/ambit:latest

If a Docker image for development is desired, the following image contains all dependencies needed to install and run Ambit (including the dolfinx mixed branch):

docker pull ghcr.io/marchirschvogel/ambit:devenv

Usage

Check out the examples for the basic problem types in demos to quickly get started running solid, fluid, or 0D model problems. Further, you can have a look at input files in ambit/tests and the file ambit_template.py in the main folder as example of all available input options.

Best, check if all testcases run and pass, by navigating to ambit/tests and executing

./runtests.py

Build your input file and run it with the command

mpiexec -n <NUMBER_OF_CORES> python3 your_file.py