scifem

Scientific finite element toolbox

https://github.com/scientificcomputing/scifem

Science Score: 44.0%

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Low similarity (13.9%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Scientific finite element toolbox

Basic Info

Host: GitHub
Owner: scientificcomputing
License: mit
Language: Python
Default Branch: main
Homepage: https://scientificcomputing.github.io/scifem/
Size: 2.09 MB

Statistics

Stars: 29
Watchers: 7
Forks: 4
Open Issues: 25
Releases: 22

Created over 1 year ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

Scientific Computing Tools for Finite Element Methods

This package contains a collection of tools for scientific computing with a focus on finite element methods. The tools are written in Python and are intended to be used in conjunction with the dolfinx.

Many users that are transitioning from legacy FEniCS to FEniCSx may find the transition difficult due to the lack of some functionalities in FEniCSx. This package aims to provide some of the functionalities that are missing in FEniCSx. The package is still in its early stages and many functionalities are still missing.

Features

Real-space implementation for usage in DOLFINx (>=v0.8.0)
Save quadrature functions as point clouds
Save any function that can tabulate dof coordinates as point clouds.
Point sources for usage in DOLFINx (>=v0.8.0)
- Point sources in vector spaces are only supported on v0.9.0, post DOLFINx PR 3429. For older versions, apply one point source in each sub space.
Simplified wrapper to create MeshTags based on a list of tags and corresponding locator functions.
Maps between degrees of freedom and vertices: vertex_to_dofmap and dof_to_vertex
Blocked Newton Solver
Function evaluation at specified points

Installation

The package is partly written in C++ and relies on dolfinx. User are encouraged to install scifem with pip in an environment where dolfinx is already installed or with conda.

`pip`

To install the package with pip run

bash python3 -m pip install scifem --no-build-isolation

To install the development version you can run

bash python3 -m pip install --no-build-isolation git+https://github.com/scientificcomputing/scifem.git

Note that you should pass the flag --no-build-isolation to pip to avoid issues with the build environment, such as incompatible versions of nanobind.

`spack`

The spack package manager is the recommended way to install scifem, and especially on HPC systems. For information about the package see: spack-package: py-scifem First, clone the spack repository and enable spack

```bash git clone --depth=2 https://github.com/spack/spack.git

For bash/zsh/sh

. spack/share/spack/setup-env.sh

For tcsh/csh

source spack/share/spack/setup-env.csh

For fish

. spack/share/spack/setup-env.fish ```

Next create an environment:

bash spack env create scifem_env spack env activate scifem_env Find the compilers on the system bash spack compiler find

and install the relevant packages bash spack add py-scifem+petsc+hdf5+biomed+adios2 ^mpich ^petsc+mumps+hypre ^py-fenics-dolfinx+petsc4py spack concretize spack install Finally, note that spack needs some packages already installed on your system. On a clean ubuntu container for example one need to install the following packages before running spack bash apt update && apt install gcc unzip git python3-dev g++ gfortran xz-utils -y

`conda`

To install the package with conda run

bash conda install -c conda-forge scifem

Having issues or want to contribute?

If you are having issues, feature request or would like to contribute, please let us know. You can do so by opening an issue on the issue tracker.

Owner

Name: Scientific Computing at Simula Research Laboratory
Login: scientificcomputing
Kind: organization

Repositories: 7
Profile: https://github.com/scientificcomputing

Citation (CITATION.cff)

abstract: '<p>Testing bump my version, no significant changes.</p>

  <p><strong>Full Changelog</strong>: https://github.com/scientificcomputing/scifem/compare/v0.2.0...v0.2.2</p>'
authors:
- affiliation: Simula Research Laboratoy
  family-names: Henrik Finsberg
- affiliation: Simula Research Laboratory
  family-names: "Jørgen Schartum Dokken"
cff-version: 1.2.0
date-released: '2024-09-18'
doi: 10.5281/zenodo.13784791
license:
- cc-by-4.0
repository-code: https://github.com/scientificcomputing/scifem/tree/v0.2.2
title: 'scientificcomputing/scifem: v0.2.2'
type: software
version: v0.2.2

GitHub Events

Total

Create event: 39
Commit comment event: 1
Release event: 12
Issues event: 22
Watch event: 15
Delete event: 18
Issue comment event: 46
Push event: 170
Pull request review comment event: 63
Pull request review event: 66
Pull request event: 95
Fork event: 2

Last Year

Create event: 39
Commit comment event: 1
Release event: 12
Issues event: 22
Watch event: 15
Delete event: 18
Issue comment event: 46
Push event: 170
Pull request review comment event: 63
Pull request review event: 66
Pull request event: 95
Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 10
Total pull requests: 32
Average time to close issues: 5 days
Average time to close pull requests: 7 days
Total issue authors: 5
Total pull request authors: 5
Average comments per issue: 1.1
Average comments per pull request: 0.28
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 17

Past Year

Issues: 10
Pull requests: 32
Average time to close issues: 5 days
Average time to close pull requests: 7 days
Issue authors: 5
Pull request authors: 5
Average comments per issue: 1.1
Average comments per pull request: 0.28
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 17

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Top Authors

Issue Authors

jorgensd (17)
ottarph (3)
finsberg (3)
RemDelaporteMathurin (3)
peterrjohnston (2)
bleyerj (1)
rsn766 (1)
tdoerff (1)
dhalatsis (1)
bagla0 (1)

Pull Request Authors

finsberg (24)
pre-commit-ci[bot] (24)
jorgensd (19)
minrk (4)
dependabot[bot] (3)
cdaversin (1)
RemDelaporteMathurin (1)

Top Labels

Issue Labels

Pull Request Labels

dependencies (3) github_actions (3)

Packages

Total packages: 1
Total downloads:
- pypi 5,044 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 22
Total maintainers: 2

pypi.org: scifem

Scientific tools for finite element methods

Documentation: https://scifem.readthedocs.io/
License: MIT License Copyright (c) 2024 Scientific Computing at Simula Research Laboratory 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.
Latest release: 0.7.0
published 6 months ago

Versions: 22
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 5,044 Last month

Rankings

Dependent packages count: 10.3%

Average: 34.2%

Dependent repos count: 58.1%

Maintainers (2)

finsberg dokken