Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, openCARP uses a vMAJOR.PATCH versioning scheme. We increase the

• MAJOR version when we add functionality, and the
• PATCH version when we make backwards compatible bug fixes

Unreleased

Changed

• The documentation of bench commands in the PDF manual is now autogenerated from bench --help
• Improved documentation for MLIR builds (thanks @vincent.loechner)
• Major rewrite of LIMPET moving from C to C++ (thanks @Raphael)
• Deprecated -buildinfo argument, now the build info is printed by default
• igbapd: linear interpolation of AP start
• State structure data layout optimization of ionic models (thanks @Raphael)

Fixed

• ISAC_Hu model was missing some parentheses
• Missing initialization of pointers to parameter structures in ION_IF.h
• Include units in PDF and online parameter help
• make_dynamic_model.sh works with CMake based compilation for CVODE and DEBUG (#330)
• Compatibility with SUNDIALS v6
• Checkpointing when data layout optimization (DLO) was enabled (thanks @Raphael)
• Dynamic models (#310)
• Incorrect memory copies and memory initialization on GPU when using multiple regions

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)
• State vector access can fail when building with data layout optimization (#330)

[13.0] - 2023-05-25

Added

• Elec matrix integration: Added output of element and region info in case of NaN matrix entries. This help with spotting errors in the tissue parametrization (e.g zero fibers or conductivities, deteriorated elements).
• Ionic models: Added support for AMD code generation with MLIR. Ionic models can now be compiled and ran on AMD GPUs.
• Compilation of multiple versions of a given ionic model in the same build (see docs/BUILD_WITH_MLIR.md)
• --target option to select execution platform in bench (see docs/BUILD_WITH_MLIR.md)
• User manual: Cite carphelp and give an example of usage
• CI job building openCARP using the provided Makefile

Changed

• Elec matrix integration: Optimized choice of integration order.
• CMake process in physics/limpet refactored for readability
• GPU models can now access data correctly with -DENABLE_MLIR_CODEGEN=DATA_LAYOUT_OPTIMIZATION
• Use overlay2 as DOCKER_DRIVER in CI pipelines

Fixed

• Fixed a number of compiler warnings. Now builds clean with clang15.
• Build process based on plain Makefile.

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)

[12.0] - 2022-12-19

Added

• New macOS package, compatible with Apple Silicon Macs.
• Tomek ionic model.
• Pre-commit hook to generate CITATION.cff from codemeta.json
• Added Ginkgo numerical backend (use CMake option ENABLE_GINKGO)
• Added the printout of all parameters with --output-setup option
• Optimized CPU and GPU code generation for ionic models using MLIR compiler infrastructure (use CMake option ENABLE_MLIR_CODEGEN, see docs/BUILD_WITH_MLIR).

Changed

• macOS precompiled packages now contain MPICH, shipped with PETSc, like the Linux packages.
• Continuous Benchmarking can now be run on any branch (commit hash passed to Continuous Benchmarking trigger)
• Abstraction of interface to numerical backend (vectors etc.)
• Release step consists of two steps (manual tag pre-vX.Y and automatic tag vX.Y) now to include specific DOI in metadata in repo
• Steward model renamed to Stewart (fixing a typo in the name)

Fixed

• cleaned up stim.crct.type and stimulus.stimtype to only contain available stimulus types.
• --initial flag in example 01/02B

Known issues

• Some regression tests are failing when using Ginkgo as the numerical backend (#151)

[11.0] - 2022-07-18

Added

• Control over output domain for (phie, phie_i, and vm) via -dataout_i and -dataout_e.
• Dedicated, asynchronous IO processes via -num_io_nodes.
• Support for arctan, atan, sin, floor functions in .model and CellML files
• CI pipeline extended by Continuous Benchmarking via Megware's framework
• Modify package generation and include paths in make_dynamic_model.sh to make it usable in precompiled packages (rpm, deb, pkg and AppImage).

Fixed

• When using cmake to build openCARP with external tools, openMP is disabled in meshtool if it is disabled for openCARP
• Right-handed coordinate system also for 2D elements in SF::get_transformed_pts() (thanks @jk)
• Maintenance on tutorials (thanks @joshuasteyer, @jk)
• CMake aborted when libgfortran wasn't found (thanks @teo.puig)
• Fix include path hints in make_dynamic_model.sh for the case where openCARP is compiled from sources

[10.0] - 2022-05-30

Added

• EasyML2mmt.py to faciliatate conversion from .model to .cellml via .mmt, see example 01/11 for detailed instructions
• Documentation on monodmain and bidomain boundary conditions (sections 3.2 and 3.3 of the manual)
• Performance stats output for ionics (ODE_stats.dat) and IO (IO_stats.dat) in sim output dir

Changed

• The AppImage package now contains some helper scripts: one to extract openCARP binaries from the AppImage, the other one to install carputils.
• In the postinstall phase of cmake, symbolic links created for MPI executables in /usr/local/bin could potentially interfer with an existing installation. These symbolic links were removed and the path to the MPI executable is now configured in carputils settings.
• openCARP Docker image is now based on Ubuntu 20.04
• bench --imp-info now also shows plugin metadata
• Metadata lines in .model files do not need to end with a semicolon anymore
• Added _build/physics/limpet to make_dynamic_model.sh include directories to be compatible with CMake-based installations

Fixed

• square(X) and cube(X) in .model files were causing error during code generation when using the Rosenbrock method
• make_dynamic_model.sh: Skip tests on contents of my_switches.def if it does not exist in install directory
• Fix the inclusion of MPI executables in Linux precompiled packages
• Fix documentation pipeline to include Stim structure.
• Fix error when trying to recompile openCARP after adding a new ionic model
• Ionic model metadata fields were cut if they contained a colon
• Made ionic model metadata fields consistent
• Compilation on macOS with M1 processor
• Changed xmltree.etree.getchildren() to list(xmltree.etree) for Python3.9 compatibility
• Better support for exponential notation in CellML files

[9.0] - 2022-02-22

Added

• Implementation for --stim-species and --stim-ratios parameters in bench
• Option for OpenMP support in CMake (-DUSE_OPENMP=ON)

Changed

• Names of ionic models and plugins. See physics/limpet/models/README.md for details of the naming scheme and a mapping from old to new names. Additionally, variables were named consistenly across all available ionic models and plugins.
• bench: consistently no output of progress to terminal if using --fout irrespective of wheter --validate is being used or not.
• model files: changed pow(x,2) and pow(x,3) to square(X) and cube(X), respectively.
• Ensure fibre vectors have unit length (https://git.opencarp.org/openCARP/openCARP/-/merge_requests/73)
• Courtemanche.model now considers dynamically changing intracellular potassium concentration as in the original publication

Fixed

• Add missing link to hydra_pmi_proxy in /usr/local/bin in postinstall phase for MPICH
• Kurata et al. ionic model
• mesher fiber generation for off-center meshes (https://git.opencarp.org/openCARP/openCARP/-/issues/132)
• Loading of external IMPs when openCARP is built with -DNDEBUG flag

[8.2] - 2021-12-18

Added

• Add CI jobs for testing (on schedule) and releasing openCARP Spack package when a new version is released.
• Added libjpeg as a dependency in CPack for being able to install pillow python package
• Documentation for the installation of openCARP via Spack.
• Optional building igbdft, required FFTW3 library
• --buildinfo flag for bench
• Added autotester pipeline
• Added AppImage building and release

[8.1] - 2021-10-01

Fixed

• Fixed bench not starting when tracing is used.
• Fixed trace output granularity.

[8.0] - 2021-09-23

Added

• Added trace functionality.
• Added human readable interpretations of PETSc solver divergence errors.
• Automatically add dropdown entries on webpage (parameters, doxygen, test reports) for release versions.

Fixed

• Many fixes and improvements.

[7.0] - 2021-06-29

Added

• Pathmanathan & Gray cell model for test cases with analytical solution
• Loewe-Lutz-Fabbri-Severi cell model (human sinus node)
• Extended documentation on gvec[] parameters
• A filename given as parameter can now be given with its extension
• Warning in header to not change auto-generated files in simulator
• Numerical schemes as chapter 29 of the user manual

Changed

• Default PETSc linear solver options set more sensibly.
• limpet/common.py module renamed to limpet/limpetcommon.py for better compatibility with other common modules
• Ionic model code is only re-generated in the CMake compilation when changes are present (determined per model)
• Types of some parameters of type string but corresponding to file names to RFile/WFile
• carp.prm was renamed to openCARP.prm as well as the auto-generated files in simulator

Fixed

• Adjustments per node were only applied to the first node of the mesh.

[6.0] - 2021-05-17

Added

• illumination ionics interface and IchR2 model supporting it
• Bench parameter --start-out to control first output time step
• dump_vtx option for stimuli

Fixed

• Archiving of releases in the RADAR repository
• mesher fix for 2D mesh lon files.
• many fixes throughout the codebase.
• CI fixes.

[5.0] - 2021-01-20

Fixed

• CVODE related fixes.

Added

• Added EasyML function rand01(): random number in range [0,1]
• Header to restitution*.dat files generated by bench (starting with '# ')
• Added stim[].ptcl.stimlist to specify list of stimulation times.
• Documentation on units for currents on the single cell level.

[4.0] - 2020-09-29

Fixed

• Several fixes to FEM integration.

Added

• External projects (carputils, examples, and meshtool) in the packages.
• Added support for Prism and Pyramid element types.
• Added support for per-element conductivity scaling.
• Added support for element renumbering and element-based input data.

Changed

• Restructured docker files, merged user-version and developer-version docker images.

[3.2] - 2020-07-13

Added

• mMS ionic model.
• Increased robustness of im_param option by applying whitespace removal to option string.
• CI improvements.

Fixed

• Fixed write_statef option not working.
• Fixed dynamic model building workflow.

[3.1] - 2020-06-18

Added

• MacOS installer.

[3.0] - 2020-06-17

Added

• Support for heterogenous electrode strength scaling via stimulus[].vtx_fcn (legacy stim) and stim[].elec.vtx_fcn (new stim format).

Fixed

• Fixes to igbapd. It is now more consistent in its output handling.

Changed

• Exposed more state vars in COURTEMANCHE model.
• CI updates.
• Reworked index and indexed data reading.

[2.0] - 2020-05-09

Added

• Python3 support complete.
• Added support for different (i.e. non-PETSc) matrix and solver implementations.
• KDtree partitioner is faster and requires less memory.

Fixed

• Fixed MacCannell_Fb_plug and I_KATP models.
• Laplace solver only requires extracellular mesh.
• Many fixes and optimizations to the cmake building and packaging workflow.

Changed

• CONTRIBUTORS.md is now CONTRIBUTORS.yml, which will also be used to generate the metadata for archives of the releases.
• Exposed TT2.Gto limpet variable.
• Build-time code generation now uses python3.

[1.2] - 2020-03-17

Fixed

• adjust_MIIF_variable now tells the user what adjustment went wrong.

Added

• Added gridout_p for partitioning output.

Removed

• Removed some unsupported simulator parameters.

Changed

• Further improved python3 compatibility.
• Improved message output for gridout.

[1.1] - 2020-03-05

Fixed

• Dynamic ionic model loading was fixed.

Changed

• Many python scripts are now python3 compatible. The transition is not complete yet.

[1.0] - 2020-03-03

• Initial public release