[Unreleased] (git-diff)

[2.0.1] (git-diff) - 2024-04-22

Fixed

Fix memory errors on Blocked Jacobi !197
Remove Muparser invalid assertions !196

[2.0.0] (git-diff) - 2024-03-26

Note: This version is a complete re-write of the library based on a custom version of PDELab tailored for this module. Thus, this changelog does not make much sense in comparison to version 1.1.0. Instead, the following entries are written with respect to the first refactor from 1.1.0 made on !83.

Refactor

Allows different parser backends: muparser, exprtk, and SymEngine !83
Adds constants, (lambda) function, and random fields definitions within the parsers !83
Re-implementation of local operator: huge performance improvements !83
Adds tensor cross-diffusion, storage, velocity, and external boundary terms !83
Allows for volume coupling between compartments !83
Splits the subdomain and the compartment concepts. Now compartments with no entities or no components are perfectly possible !83
Uses new basis functions from dune-pdelab that allows native usage of multi-domains (branch: features/dune-assembler/main) !83
Extends compatibility of tiff images to different bit sizes !83
Adds monitoring (info, warning and error) of variables with new generic reduce operators !83
Switches logging from dune-logging to spdlog !83
Designed to be thread-safe, although is not entirely yet implemented !83
Adds tracing capabilities with perfetto !83
Allows Selection of between direct and sparse solvers, and matrix free operators !83
Allows to print matrix layout in a SVG file !83
Unifies the executable for different dimensions and different degrees of freedom layouts !83
Improves command line interface !83

Added

Docusaurus now upgrades latest canary wasm binary automatically !186
Hierarchical ISTL solvers and preconditioners in a dynamic registry !156
Initial web interface for Wasm executable !170
Deploy NPM packages to GitLab registry !179
Tutorial and test on Cardiac Electrophysiology simulations !157
Grid cell data !175
Push CI artifacts to the GitLab registry !169 !173
Test more complicated cases !158
Job to build Wasm binaries in the CI !150
Math expressions with only numbers as scientific notation don't need a parser !154
Allow underscores in parser function arguments !152
Make multi-threading optional !149
Compile 2D and 3D in GitHub Actions !141
Customization point on grid axis names !139
Diagnostic information on SymEngine compilation failure !134
Test on pattern generation !132
Multi-threaded assembly !98
Allow arbitrary number of functions in ExprTk !148
Codequality check on the CI !123
LLVM visitor for SymEngine !121
Throw meaningful error message when config file is empty !119
Diagnostic information on ExprTk compilation failure !115
Command line help information !107 !120 !138
Interpolation for 1D functions !102
Initial value to reuction operations !100
Code spelling to the CI !88
Helper constraints for function spaces !87
Support libc++ and reduce minimum required standard from C++23 to C++20 !84
Show error when config file does not exist !86
~~Doxygen documentation is now deployed to Netlify !73~~ (reverted on !176)

Changed

Update docusaurus documentation to latest changes !176 !178 !88
Math parsers now can only take move only functions !187
Reduce operations now receive one less argument !184
Reorganize files and add DiffusionReaction namespace !183
Use grid leaf view instead of level 0 grid view for grid cell data !177
Author email address !181
Improve support for Wasm binaries !170 !182
Move configuration options to a JSON file and use schema validator on it !174
Use Debian Bookworm in the CI !171
Conditinally test possion config if ExprTk is available !168
Use (faster) integer based multi-domain grid !165
Simplify CMake usage !161 !162 !163
Improve version handler !159
Improve local basis cache to also handle intersections !145
Improve log error on failure !136
How to use constraints !135
Update docusaurus to version 3.0.0 !124
Cleanup of the build system files !118
Cleanup the CI installation scripts !110
Make options consistent with respect to file inputs --*.path=/path/to/file !109
Use PDELab::Execution to express (possible) concurrency !108
Use newer commit on parafields-core !105
Improve implementation of muParser and ExprTk parsers !96
Update docusaurus to version 2.0.0-alpha.75 !72

Fixed

Missing CMake installation of Hierarchical ISTL solvers (from !156) !183
Boundary constraints were handled incorrectly !167
Coloring option for multi-threading was swapped with micro-locks !166
Remove wrong definition of maximum number of ExpTk functions !130
Wrong definition for SuiteSparse library !144
Missing user in Dockerfile !153 !155
~~Freeze dune-grid dependency !147~~ (reverted by !164)
Use the keyword no_value to identify special values in the parsers !140
Inheritance of parser_context.parser_type !133
Entries per row estimate for pattern creation !127
Use NDEBUG compiler definition on release build !131
Compatibility issue with {fmt} 10.2 !125
Duplicated output on reduction algorithms !117
Testing in the CI !114
Correct construction on parser contexts !116
Compatibility with XCode and Msys !111
Consistent use of struct across different headers !104
Unused function keywords on SymEngine where throwing unnecessary errors !101
Deprecation warning on SVG writer !97
Compile final executable with different parsers !95
CMake problems on target installation !94
Support for {fmt} >= 9.0.0 !90 !91 !93 !129
Docker image now uses dune-copas executable instead of dune-copasi-[sd|md] !91
CI jobs now passes since the re-write !89
Solver on linear problems was wrongly reused !85

Removed

Unused header files from version 1.1.0 !183
Dependency on dune-testtools !122
Inherited parafield-core tests !112
Fallback for std::filesystem !94

Security

Update follow-redirects in web documentation !126

[1.1.0] (git-diff) - 2021-04-29

Added

Dune options file receives CMAKE_OPTIONS and MAKE_OPTIONS !60
Parameter to use max norm on newton steps !65
Parameter to accept best solution in linear search on newton steps !65
Event timestepper !64
Preprocessor macros containing version information !67

Changed

TIFF helper is compiled in the dunecopasi library !62
Use NewtonMethod instead of Newton class from PDELab !65

Fixed

Executables can be compiled without the library !60
All dune cmake flags are now transitively passed to dune-copasi targets !60
System tests on main executables were ignored !66
Snap to final time now avoids very small timesteps !61
CMake config file was installed on the wrong path !68

[1.0.0] (git-diff) - 2021-02-11

Added

Custom membrane flux !30
Skip intersection methods in local operators !36
Parameters to control Newton's method !30
Stepper interface to snap solution to a specific time !45
Provide help message when executables are not used correctly !49
Produce Debian Packages on the CI !49
Installation is now divided on three components: Runtime|Library|Development !49
Define a recommended dune options file dune-copasi.opts !49
Versioned documentation !49
Dependency on pkg-config !52

Changed

TIFF images are clamped instead of zeroed when evaluated outside its domain !47
Produce versioned documentation !49
Travis and Appveyor are replaced for GitHub Actions on Linux|MacOS|Windows !49
Increment CMake required version to 3.13 !49
Installed CMake project is now consumable by other CMake projects !49
Vendor GHC with CMake instead of git submodules !49
Increase vendored GHC version to 10.5 !49 & !51
Force GHC usage whenever c++ filesystem cannot be found, else, optional !49
CI scripts are improved to simplify usage !49
Simplify build and usage on docker containers !49
Drastically reduce size of final docker container !49
Improve performance on cases with no interaction between all species !43
dune-logging and dune-multidomaingrid no longer require a COPASI namespace fork !53

Removed

Automatic flux between compartment components with same name !30
Jacobian operator is managed by the stepper instead of the model !39
Jacobian tests are improved and extended to cover more cases !39
CMake module to find muparser, use pkg-config instead !52

Fixed

Finished and documented Installation procedure !49
Wrong rounding on y pixels on TIFF file reads !47
Improper vector allocation in multidomain intersections !39
Final timestep reduction to reach end_time failed in adaptive stepper !43
Infinite loop when final adaptive step failed !45
Binary executables are now installed !49
Support for shared libraries !54

[0.3.0] (git-diff) - 2020-10-07

Added

User documentation !28
Scape VTK write by omitting [writer] section !24
Added Explicit and Diagonally Runge-Kutta time solvers !25
3D simulations are now possible !27

Changed

Improved errors when a config file is incorrect !25
Update meaningful logging values on the test ini file !25
Clean up logger output !25
Time stepping is now done outside the model class !25
Writer might write on different files on request !25
Move read/write responsibility to model state !25
States are now independent from models !25
Output files changed its name scheme !25
Configuration file changed its structure (see git diff on tests) !25

Removed

Coefficient mapper and its use on local operators !25
Remove the operator map of objects within the model class !25

Fixed

Violation of the One-Definition-Rule due to external linkage of LocalOperatorApply lambdas !23
Error on the gaussian equation used on comparisons !23

[0.2.0] (git-diff) - 2020-02-20

Added

Code documentation
Data Context concept for factories
Factory concept for arbitrary object instantiation
Add factories for finite element and finite element map
Brief installation instructions
Models can interpolate grid functions
Grid utilities to recognize and mark tripes of entities
A finite volume loca operator
Grid function getters for external use
Single domain executable

Changed

Move and rename header files
Multidomain finite element was split into a multidomain and a dynamic power finite element
Code DUNE dependencies are set to release 2.7 (See README.md)
Other DUNE dependencies are set to COPASI/support/dune-copasi (See README.md)
Executable is an optional build
Library is optional and is split into smaller libraries
Bump version utility updated to python3

Fixed

Dirichlet-Dirichlet condition at interfaces was being computed twice

0.1.0 - 2019-10-11

Added

Semantic Versioning
Solver for reaction-diffusion systems in multiple compartments.