معرفی شرکت ها
fenicsx-pulse-0.1.2
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مشاهده بیشتر
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مشاهده بیشتر
تبلیغات ما
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مشاهده بیشترتوضیحات
Next generation cardiac mechanics solver based on FEniCSx
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | fenicsx-pulse-0.1.2 |
| نام | fenicsx-pulse |
| نسخه کتابخانه | 0.1.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | Henrik Finsberg <henriknf@simula.no> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/fenicsx-pulse/ |
| مجوز | Copyright 2022 Henrik Finsberg 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. |
[](https://github.com/finsberg/fenicsx-pulse/blob/main/LICENSE)
[](https://pypi.org/project/fenicsx_pulse/)
[](https://github.com/finsberg/fenicsx-pulse/actions/workflows/test_package_coverage.yml)
[](https://github.com/finsberg/fenicsx-pulse/actions/workflows/pre-commit.yml)
[](https://github.com/finsberg/fenicsx-pulse/actions/workflows/build_docs.yml)
[](https://github.com/psf/black)
[](https://github.com/finsberg/fenicsx-pulse/pkgs/container/fenicsx_pulse)
# fenicsx-pulse
`fenicsx-pulse` is a cardiac mechanics solver based on FEniCSx. It is a successor of [`pulse`](https://github.com/finsberg/pulse) which is a cardiac mechanics solver based on FEniCS.
---
## 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`](https://github.com/finsberg/pulse) instead
---
* 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](https://github.com/FEniCS/dolfinx#installation). 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:v0.1.2
```
## Simple Example
```python
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
TBW
نیازمندی
| مقدار | نام |
|---|---|
| - | fenics-dolfinx |
| - | fenicsx-pulse[test] |
| - | fenicsx-pulse[docs] |
| - | fenicsx-pulse[dev] |
| - | pdbpp |
| - | ipython |
| - | bump2version |
| - | pre-commit |
| - | jupyter-book |
| - | jupytext |
| <8.7.0 | ipython |
| - | pytest |
| - | pytest-cov |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.10.0 | Python |
نحوه نصب
نصب پکیج whl fenicsx-pulse-0.1.2:
pip install fenicsx-pulse-0.1.2.whl
نصب پکیج tar.gz fenicsx-pulse-0.1.2:
pip install fenicsx-pulse-0.1.2.tar.gz