The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation.

DOLFINx is the computational environment of FEniCSx and implements the FEniCS Problem Solving Environment in C++ and Python.

This package provides the C++ interface.

Basix is a finite element definition and tabulation runtime library.

Basix allows users to:

• evaluate finite element basis functions and their derivatives at a set of points;

• access geometric and topological information about reference cells;

• apply push forward and pull back operations to map data between a reference cell and a physical cell;

• permute and transform DOFs to allow higher-order elements to be use on arbitrary meshes;

• interpolate into and between finite element spaces.

Basix includes a range of built-in elements, and also allows the user to define their own custom elements.

This package provides the Python wrapper for Basix.

Library implementing Block-GMres with Inexact Breakdown and Deflated Restarting, Breakdown Free Block Conjudate Gradiant, Block General Conjugate Residual and Block General Conjugate Residual with Inner Orthogonalization and with inexact breakdown and deflated restarting.

FFCx is a compiler for finite element variational forms.

From a high-level description of the form in the UFL, it generates efficient low-level C code that can be used to assemble the corresponding discrete operator (tensor). In particular, a bilinear form may be assembled into a matrix and a linear form may be assembled into a vector.

This package provides the UFCx interface header.

The Basic Linear Algebra Subprograms (BLAS) have been around for many decades and serve as the de facto standard for performance-portable and numerically robust implementation of essential linear algebra functionality. The objective of BLAS++ is to provide a convenient, performance oriented API for development in the C++ language, that, for the most part, preserves established conventions, while, at the same time, takes advantages of modern C++ features, such as: namespaces, templates, exceptions, etc.

FFCx is a compiler for finite element variational forms.

From a high-level description of the form in the UFL, it generates efficient low-level C code that can be used to assemble the corresponding discrete operator (tensor). In particular, a bilinear form may be assembled into a matrix and a linear form may be assembled into a vector.

This package provides the CLI and Python library.

The Linear Algebra PACKage (LAPACK) is a standard software library for numerical linear algebra. The objective of LAPACK++ is to provide a convenient, performance oriented API for development in the C++ language, that, for the most part, preserves established conventions, while, at the same time, takes advantages of modern C++ features, such as: namespaces, templates, exceptions, etc.

CDT is a C++ library for generating constraint or conforming Delaunay triangulations.

DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations. It is MPI and OpenMP parallel and can exploit Nvidia and AMD GPUs via CUDA and HIP.

DOLFINx is the computational environment of FEniCSx and implements the FEniCS Problem Solving Environment in C++ and Python.

This package provides the Python interface.

This package provides a Python library for manipulating data saved as ISMRMRD.

Plastimatch is a computer software application which has been designed for volumetric (usually medical) image processing and radiation therapy applications. It can be used for the following purposes:

• Deformable registration

• Atlas-based segmentation

• Image conversion and manipulation

• Vector field conversion and manipulation

• Gamma analysis

• Dose calculation

• Registration analysis (Jacobian)

• Segmentation analysis (Dice, Hausdorff)

A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. The ISMRMRD project describes such a common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. This package provides a C/C++ library for working with the format.

The siemens_to_ismrmrd converter is used to convert data from Siemens raw data format into ISMRMRD raw data format.

STIR is an object-oriented framework for tomographic image reconstruction, with an emphasis on iterative reconstruction in PET and SPECT. This package includes the C++ core and Python bindings.

Approximate convex decomposition enables efficient geometry processing algorithms specifically designed for convex shapes (e.g., collision detection). We propose a method that is better to preserve collision conditions of the input shape with fewer components. It thus supports delicate and efficient object interaction in downstream applications.

libsupermesh is a Fortran 2008 library to intersect two overlapping meshes element by element. Pairs of overlapping elements are identified and a local mesh of their intersection is generated.

The Gamma Mesh Format (GMF) and the associated library libMeshb provide programers of simulation and meshing software with an easy way to store their meshes and physical solutions. The GMF features more than 200 kinds of data types, like vertex, polyhedron, normal vector or vector solution field. The libMeshb provides a convenient way to move data between those files, via keyword tags, and the user's own structures.

The libOL first store a mesh made of vertices, edges and triangles in an octree structure with a very small memory footprint. Subsequently, you can perform geometrical queries very quickly on this mesh:

• retrieve the closest entity from a given set of coordinates

• build the list of mesh entities than are include in a given bounding box

• project a vertex on any kind of geometrical entity

• launch a ray and get the first intersected entity

• all query operations can be performed in parallel as the library is thread safe

The purpose of the LPlib is to provide programmers of solvers or automated meshers in the field of scientific computing with an easy, fast and transparent way to parallelize their codes. This library is based on posix standard threads, also known as pthreads, thus taking advantage of multi-core chips and shared memory architectures supported by most platforms (Linux, macOS, Windows).

Version 4 provides an early implementation of colored grains scheduling for better scaling and memory localization with high core count systems.

libspatialindex provides spatial indexing utilities, with support for sophisticated spatial queries and interfaces for updating information and customizing the storage management of indices. The library is written in C++, with a C API.

The purpose of the GMlib is to provide programmers of solvers or automated meshers in the field of scientific computing with an easy, fast and transparent way to port their codes on GPUs (Graphic Processing Units).

This library is based on the OpenCL language standard, thus taking advantage of almost every architectures supported by most platforms (Linux, macOS, Windows).

It is a simple loop parallelization scheme (known as kernels in the realm of GPU computing), provides the programer with pre defined mesh data structures, automatically vectorizes unstructured data like the ball of points or the edge shells, and handles transparently the transfer and vectorization of mesh data structures.