| Name | ambit-fe JSON |
| Version |
1.2.9
JSON |
| download |
| home_page | None |
| Summary | A FEniCS-based cardiovascular multi-physics solver |
| upload_time | 2024-08-28 11:36:48 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | None |
| license | MIT License Copyright (c) 2024 Marc Hirschvogel Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
finite elements
solid mechanics
fluid mechanics
fluid-solid interaction
fsi
0d models
3d-0d coupling
monolithic
lumped-parameter models
model reduction
heart
circulation
cardiac
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# README #
[](https://doi.org/10.21105/joss.05744)
Ambit is an open-source multi-physics finite element solver written in Python, supporting solid and fluid mechanics, fluid-structure interaction (FSI), and lumped-parameter models.
It is tailored towards solving problems in cardiac mechanics, but may also be used for more general nonlinear finite element analysis. It uses the finite element backend FEniCSx and
linear algebra library PETSc.
https://github.com/marchirschvogel/ambit/assets/52761273/a438ff55-9b37-4572-a1c5-499dd3cfba73
**Heart cycle simulation of a generic bi-ventricular heart model coupled to a closed-loop circulation model.**
https://github.com/marchirschvogel/ambit/assets/52761273/8e681cb6-7a4f-4d1f-b34a-cefb642f44b7
**FSI simulation (Turek benchmark, FSI2 case) of an elastic flag in incompressible channel flow.**
The following is supported:
* 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:
- Fluid-solid interaction (FSI): Monolithic FSI in ALE formulation using Lagrange multiplier
- Monolithic coupling of 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, marc.hirschvogel@ambit.net
Still experimental / to-do:
- 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](https://github.com/FEniCS/dolfinx#installation)
Latest Ambit-compatible dolfinx release version: v0.8.0\
Latest tested Ambit-compatible dolfinx development version dating to 28 Aug 2024
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
```
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"description": "# README #\n\n[](https://doi.org/10.21105/joss.05744)\n\nAmbit is an open-source multi-physics finite element solver written in Python, supporting solid and fluid mechanics, fluid-structure interaction (FSI), and lumped-parameter models.\nIt is tailored towards solving problems in cardiac mechanics, but may also be used for more general nonlinear finite element analysis. It uses the finite element backend FEniCSx and\nlinear algebra library PETSc.\n\nhttps://github.com/marchirschvogel/ambit/assets/52761273/a438ff55-9b37-4572-a1c5-499dd3cfba73\n\n**Heart cycle simulation of a generic bi-ventricular heart model coupled to a closed-loop circulation model.**\n\nhttps://github.com/marchirschvogel/ambit/assets/52761273/8e681cb6-7a4f-4d1f-b34a-cefb642f44b7\n\n**FSI simulation (Turek benchmark, FSI2 case) of an elastic flag in incompressible channel flow.**\n\nThe following is supported:\n\n* Solid mechanics\n - Finite strain elastodynamics, implementing a range of hyperelastic isotropic and anisotropic as well as viscous constitutive laws\n - Active stress for modeling of cardiac contraction mechanics\n - Quasi-static, generalized-alpha, or one-step theta time integration\n - Nearly incompressible as well as fully incompressible formulations (latter using pressure dofs)\n - Prestressing using MULF method in displacement formulation\n - Volumetric growth & remodeling\n* Fluid dynamics\n - Incompressible Navier-Stokes/Stokes equations, either in nonconservative or conservative formulation\n - Navier-Stokes/Stokes flow in an Arbitrary Lagrangian Eulerian (ALE) reference frame\n - One-step theta, or generalized-alpha time integration\n - SUPG/PSPG stabilization for equal-order approximations of velocity and pressure\n* Lumped (0D) models\n - Systemic and pulmonary circulation flow models\n - 2-element as well as 4-element Windkessel models\n - Signalling network model\n* Coupling of different physics:\n - Fluid-solid interaction (FSI): Monolithic FSI in ALE formulation using Lagrange multiplier\n - Monolithic coupling of 3D solid/fluid/ALE-fluid with lumped 0D flow models\n - Multiscale-in-time analysis of growth & remodeling (staggered solution of 3D-0D coupled solid-flow0d and G&R solid problem)\n* Fluid-reduced-solid interaction (FrSI)\n - Boundary subspace-projected physics-reduced solid model (incl. hyperelastic, viscous, and active parts) in an ALE fluid reference frame\n* POD-based model order reduction (MOR)\n - Projection-based model order reduction applicable to main fluid or solid field (also in a coupled problem), by either projecting\n the full problem or a boundary to a lower dimensional subspace spanned by POD modes\n\n- author: Dr.-Ing. Marc Hirschvogel, marc.hirschvogel@ambit.net\n\nStill experimental / to-do:\n\n- Finite strain plasticity\n- Electrophysiology/scalar transport\n- ... whatever might be wanted in some future ...\n\n### Documentation ###\n\nDocumentation can be viewed at https://ambit.readthedocs.io\n\n### Installation ###\n\nIn order to use Ambit, you need to [install FEniCSx](https://github.com/FEniCS/dolfinx#installation)\n\nLatest Ambit-compatible dolfinx release version: v0.8.0\\\nLatest tested Ambit-compatible dolfinx development version dating to 28 Aug 2024\n\nAmbit can then be installed using pip, either the current release\n```\npython3 -m pip install ambit-fe\n```\n\nor latest development version:\n```\npython3 -m pip install git+https://github.com/marchirschvogel/ambit.git\n```\n\nAlternatively, you can pull a pre-built Docker image with FEniCSx and Ambit installed:\n```\ndocker pull ghcr.io/marchirschvogel/ambit:latest\n```\n\nIf a Docker image for development is desired, the following image contains all dependencies needed to install and run Ambit (including the dolfinx mixed branch):\n```\ndocker pull ghcr.io/marchirschvogel/ambit:devenv\n```\n\n### Usage ###\n\nCheck 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\nat input files in ambit/tests and the file ambit_template.py in the main folder as example of all available input options.\n\n\nBest, check if all testcases run and pass, by navigating to ambit/tests and executing\n```\n./runtests.py\n```\n\nBuild your input file and run it with the command\n```\nmpiexec -n <NUMBER_OF_CORES> python3 your_file.py\n```\n",
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