v2.3.1.alpha.1

Fixes to multicell meshing function, temporary solver fix for returning nan.

v2.3.0.alpha

Updates to multicellular meshing function and introduction of advective transport and associated tests.

v2.3.0.beta.1

Introduce new meshing function create_multicell to generate a multicellular mesh with two different types of cells embedded in a larger cube, including both extracellular and intracellular environments. New example 7 demonstrates its use.

Full Changelog: v2.3.0.beta...v2.3.0.beta.1

v2.3.0.beta

Introduce new meshing function create_multicell to generate a multicellular mesh with two different types of cells embedded in a larger cube, including both extracellular and intracellular environments. New example 7 demonstrates its use.

Full Changelog: v2.3.0-alpha.1...v2.3.0.beta

v2.3.0-alpha.1

Bump version number from alpha version, minor edits to example 5 with SOCE.

v2.3.0-alpha

Testing new mesh features and SOCE-relevant example. This involves defining parameters that can be assigned custom values in different regions of the mesh, as illustrated in example5_withSOCE.ipynb.

Full Changelog: v2.2.3...v2.3.0-alpha

v2.2.3

What's Changed

• Add upper bound on numpy since v2.0 breaks petsc4py by @finsberg in #173
• Fix type for sym_expr in parameter (allow Any for now) by @emmetfrancis in #174
• Update implicit curve function and fix diffusion units check by @emmetfrancis in #178
• Load spatial parameters from XDMF by @emmetfrancis in #176

Full Changelog: v2.2.2...v2.2.3

v2.2.2

What's Changed

• Bump version of base image and change pyvista backend by @finsberg in #172
• Update README with system requirements by @emmetfrancis in #171

Full Changelog: v2.2.1...v2.2.2

v2.2.1

New release for SMART scientific computing manuscript. See 2.2.0 for updates from version 2.1

v2.2.0

Major changes

• SMART is now compatible with recent changes to MeshView in FEniCS. All cases of dolfin.MeshView.create() are now dolfin.create_meshview() and cases of dolfin.assemble() are dolfin.assemble_mixed()
• Axisymmetric feature by @emmetfrancis in #146 - allows user to define an axisymmetric 3D problem over a 2D mesh.
• Add dolfin timers by @finsberg in #151
• Compute curvature on mesh boundary and use in model specifications by @emmetfrancis in #152 - allows user to compute curvature over a mesh and use in reaction terms or initial condition for species.
• Load curvature from file by @finsberg in #154 - allows user to load curvature (computed in GAMer2) and use in reaction terms or initial condition for species.
• Restrict species and/or reactions to subdomains by @emmetfrancis in #164 - restrict initial condition or reaction to an annotated subregion within a compartment.
• Fix formatting of Latex tables by @emmetfrancis in #162
• Spatial parameters @emmetfrancis in #160 - SMART parameters can now be functions of both space and time.

Other changes

• Changes and additions to mesh_tools for smart-comp-sci examples by @emmetfrancis in #145
• Make compatible with python3.8 by @finsberg in #148
• Set loglevel in UFL_LEGACY by @finsberg in #149
• Add function to load mesh and a test by @finsberg in #150
• Remove dataclasses and termplotlib as dependencies by @finsberg in #155
• Load initial conditions from file by @emmetfrancis in #156
• Add petsc logging for snes solve by @finsberg in #166
• Remove duplicate code and slightly tweak assembly logic by @jorgensd in #168