Tags

- Bug fix on #938: PseudoNormalManager::Destroy() should not be called if it is not instantiated in the first place.

- Feature #938: Implement first draft of pseudo-normals (to be continued in #946...)
- Feature #943: Implement distance function.

Ongoing tickets:

- #9 Add missing Doxygen comments.

- Feature #922: Hyperelastic laws might now be used outside pof hyperelastic operator (and so are invariants and Cauchy-Green tensors).
- Feature #919: PostProcessing: create a new executable that enable visualization by Ensight for high order for quadragular meshes (we mimic the case of a Q1 modal on a much finer mesh). It's likely this works only for a Model in sequential at the moment.
- Support #936: Provide a convertor for matrices from HappyHeart to Freefem. This convertor is quite crude and not very user-friendly, but
nonetheless very handy to debug the code. It works properly for 2D case with P1 and P1b element so far; additional case will be added when the need
arises.
- Support #932: Clean-up of Assembling().
- Support #929: Add a new compile mode (alongside 'debug' and 'release') for callgrind which provides debug symbols on a release compilation.
- Support #923: Add in Filesystem a function File::Copy() than handles correctly autocopy.
- Support #920: GeometricMeshManager: new unique id might now be called out of Create() method.
- Support #939: Replace the Lua files used for acoustic wave model in integration tests.
- Bug #937: In post-processing, only the dofs located on vertex were correctly loaded.
- Bug #934: Coefficients of ScalarDivVectorial were inverted.
- Bug #925: In post-processing, if a Model was used the output directory was deleted in the call to InputParameterFile.
- Bug #924: GeometricMeshRegion::GetGeometricEltPtr() was not functional (it wasn't used anywhere anyway...); it has been replaced by GetGeometricEltFromIndex(),
with a comment saying it should be avoided when performances are at stake (it is used currently in PostProcessing only).
- Bug #921: A change from v16.18.2 made models with Ensight mesh fail.

Ongoing tickets:

- #820 Implicit fluid step: the variational formulation involving matrix ((m, v, p), (m, v, p)) now yields the correct result.
- #9 Update Doxygen comments.

- Bug #911: Fix an important bug in SubsetOrSuperset that could lead to wrong results when several numbering subsets were defined in the same FEltSpace.
- Support #914: Add a more direct constructor in GeometricMeshRegion, for the need of Federica and Sebastien I. This constructor takes directly the list of Coords and GeomElt rather than assuming it's provided in a file. GeometricMeshRegion object must be created through the GeometricMeshRegionManager dedicated Create() method.
- Support #915: QuadratureRulePerTopology is now given by copy value rather than by move assignment.
- Support #916 Rename more accurately RefFEltSpace into RefLocalFEltSpace.
- Bug #917: Fix a bug introduced in #909 (poorly written assert in Gauss formula computation).

Ongoing tickets:

- Feature #820: Fix parallel code in Poromechanics (UpdateGhosts() was missing in several locations, and #911 was found as well).

- Support #907: Minor fixes to issues found during the test phase of the ta, during which I ran the integration test for the first time in a while. Running thse tests will now be part of the standard procedure before releasing any tag.
- Support #909: Gauss formula for quadrature points were lifted from Ondomatic (which itself took them from another code) and therefore lacked the usual debug safeties provided by HappyHeart. This led to a bug tricky to identify while using new quadrature rules for hexahedra; so asserts have been added to avoid such a time loss should another bug be hidden there.
- Feature #904: Extend time dependancy of Parameter so that it now may be given from an input file rather than by a functor. Currently the input file must give time-dependant values for eacjh time step considered; in the future extrapolation shall be introduced (probably as an policy).
- Feature #900: Refactor quadrature rules so that they are now stored at FEltSpace level. Each GlobalVariationalOperator may supersede them with its own through an optional constructor argument.
- Support #902: Secure the use of AXPY for matrices: previously default argument assumed X and Y follows the same pattern, which could lead to bugs if that is not the case. So now it is an explicit template argument not defaulted.
- Bug #903: Fix a computation that overestimated in parallel the number of processor-wise interfaces (to put in a nutshell ghosted were counted as processor-wise).

Ongoing tickets:

- Feature #820: Poromechanics: implicit step fluid a bit further (and AXPY bug corrected - see #902).

- Bug #899: Wrappers/Petsc: the options to reuse matrices in MatMatMult type operations were poorly implemented.
- Feature #898: Finite elements given by Spectral should use different quadrature rules (expands what was begun in #896).
- Support #897: In Geometry, Local2Global has been rewritten to avoid copy by value.
- Bug #896 - bug #335: Fix the shape functions for Spectral finite elements.

Ongoing tickets:

- Design #887: Files in Geometry have been reorganized deeply; however the work is still in progress concerning the renaming of namespaces following Advanced/Internal convention.

- Bug #894 - #891: NodeBearerList was not correctly computed during reduction in parallel. This bug was there for a long time but impacted only models with certain kinds of interpolators (so only poromechanics was concerned...)
- Feature #885: Expand Scalar div Vectorial to handle more cases.
- Support #888 Petsc: introduce a wrapper over MatMatMultNumeric and MatMatMultSymbolic.
- Support #890: Write a function that checks a matrix really respect its expected pattern.
- Support #892: Add SNESConvergenceTestFunction in SNES.
- Bug #893: Coords: an assert for operator== was completely off
- Support #886: Interpolator: FromVertexMatching interface has been simplified.
- Feature #885: Expand ScalarDivVectorial to handle more cases in both Operators library and Poromechanics model (which defines its own version of the operator).

Ongoing tickets:

- Documentation #9 - Design #882: FormulationSolver, Core and Domain in Geometry have been cleant-up a bit.
- Feature #820: Implement poromechanics model - part T11 of the implicit fluid matrix has been computed (with difficulty due to #891).

- Feature #860: Cardiac law implemented, no longer in UnderDevelopment directory.
- Support #850: Add Matlab scripts.
- Bug #880: Poromechanics code was not working in parallel.
- Bug #879: In Poromechanics, porosity was evaluated on the wrong god of dof. It is now properly evaluated on the solid one and only then interpolated to the fluid one.

Ongoing tickets:

- Documentation #9: Finite element and Model Doxygen documentation is cleant-up.
- Design #882: Clean-up use of namespace for FiniteElement and Model modules.
- Feature #820: Implement poromechanics model.

- Feature #873: Add the possibility of a decoupled time dependency in Parameter (and hence in TransientSource).
- Feature #875: Extend ParameterAtDof so it might encompass several finite element spaces (one per dimension at most).
- Documentation #9: Fix all Doxygen warnings in FElt library.
- Bug #870: Fix huge bug in GeometricMeshRegion::GetSubsetGeometricEltList(), which produced ill-defined range of subset of geometric elements of a given dimension.
- Support #869: Make all tests work again and add them in the integration tests procedure.
- Support #872: VariationalFormulation: Rename the AllocateGlobalMatrix() and AllocateGlobalVector() methods to avoid ambiguity with namesake functions.

- Feature #867: Write P1 -> P1b interpolator (and its opposite one for the sake of tests...)
- Documentation #9: Improve Doxygen documentation (still in progress...)
- Feature #866: New operator for Parameters.

- Feature #820: Still in progress: Poromechanics.
- Bug #862: In XCode project, Ops and Seldon were poorly located if HappyHeart was installed in an unusual place.
- Feature #861: Integration of a sibling git repository that deals with development internal to M3DISIM team. Main repository provides utilities to set it up immediately, but may also work finely without this other repository.
- Support #858: Replace method ExtractFEltValuesFrom() by free function ExtractLocalDofValues(), which also works in cases the former didn't (for instance when dealing with a different unknown than the one considered in the current operator).

- Feature #782: Add fiber contribution in the stresses.
- Feature #802: Acoustic wave model.
- Support #857: Main programs should return EXIT_FAILURE if they stop through an exception.
- Bug #856: EnsightOutput has been rewritten to work with environment variable HAPPY_HEART_RESULT_DIR.
- Bug #855: Safeties in FiberList were not trapping some cases (such as fiber list too big for the mesh).

- Bug #853: Geometry: add a new index to Coords. This was required to make Fiber work properly in parallel.
- Bug #852 - #854: Fix a race condition on the creation of output directory by several ranks acting on the same filesystem. Crtp mpi has been moved into Utilities and applied to InputParameterList.
- Bug #851: An assert could be unduly activated if a small mesh was splitted on too many processors.
- Support #849: Create a script that performs a very basic check of the output of the executables.
- Bug #848: ParameterAtDof template parameter was actually ignored, as scalar was hardcoded.

- Support #847: Cauchy Green and invariants are now independent objects outside of Hyperelastic operator.
- Support #846: Update the version of the Perl script that counts the number of lines; put it in Sources/ThirdParty folder to make its origin crystal clear.
- Bug #844: Fix gcc compilation errors.
- Support #843: Refactor CauchyGreen tensor for SecondPiolaKirchhoffStressTensor operator.
- Feature #841: Introduce a Solid class which encompass all the solid-related parameters. Consistency between them is now thoroughly checked.
- Support #840: SVenantKirchhoff: rewrite it so that input parameters are directly Lame parameters.
- Support #839: Tone down the use of Yuni library in HappyHeart.
- Documentation #832: Clarify in Parameter::Policy::OpsFunction the meaning of second template parameter.

- Feature #831: Generalize InitializeVectorSystemSolution to a vectorial unknown; improve its encapsulation.
- Feature #838: Add an input parameter that enables to print outputs only every few iterations.
- Support #836: Introduce as an experimentation libmesh6 in place of libmesh5. The latter has been kept at hand to allow a quick reversal should an issue arise.
- Support #835: Geometry: make much more obvious the fact that single precision is used when a version 1 of a Medit mesh is used. Upgrade all current mesh files to version 2.
- Bug #830: Default values in InputParameter for Petsc not up-to-date.
- Support #829: Add wrappers for norm for Petsc Vector and Matrix.
- Support #826: Adjust the demo lua files for hyperelasticity.
- Feature #822: Broaden movemesh so that a displacement may be applied on initial position rather on current one.
- Bug #824: Correct small bugs related to FSI (Lua file and XCode project.)

- Feature #813: Space unit has been added for meshes and coords.
- Feature #818: FSI is finally done; dev code has therefore been cleant-up. A legacy folder has been introduced in ModelInstances for Models that are not completely reliable (the FSI with one mesh has been put there).
- Bug #808: In ALE operator, two indexes were inverted.
- Bug #801: In header guards, some path were related to a specific user.

- Profile #809: Refactor the call to LocalVariationalOperator::ComputeEltArray() to make it both simpler and more efficient.
- Bug #816: Demo lua file for reaction/diffusion 2D CRN was not up-to-date.
- Bug #814: Documentation had two identical folders, manual and Manual.

- Support #811: Fix compilation for Linux.
- Bug #807: Fix SCons compilation for post processing.
- Support #806: Introduce a global diagonal matrix.
- Feature #805: Use properly the Ale enum to toggle on/off the use of ALE in FSI.
- Feature #779: New ALE operator for FSI model.
- Feature #800: provide two new tools:
    . One allow to find the dofs in a numbering subset that share the same node bearer than dofs of another numbering subset (put more plainly, it answers question as: which velocity dofs is at the same location than my pressure dof?).
    . Another that returns the Coords for each Dof of a GlobalVector (i.e. where are the dofs covered in the GlobalVector?)
- Documentation #618: Write a documentation about SCons build of HappyHeart. Said build has at this occasion beem thoroughly refactored so that most of the customized functions have been put in a dedicated file; SConstruct is much less bulky that it used to be.
- Bug #803: Elastic model: there were undue references to path specific to my own machine.

- Feature #795: Refactor GradientOnGradientBasedHyperelasticity operator so that it may be extended for also manage visco-elasticity and active stress.

- Bug #788: Clean-up XCode project to remove obsolete targets and put back those removed unduly in some git operations.
- Support #787: Add SConscript for RivlinCube.
- Bug #791: A list of numbering subset was incorrectly sort, which led to undefined behaviour in parallel.
- Feature #778 - Support #793: Introduce the possibility to move a mesh and use it in FSI model.
- Support #789: FSI: ALE could use two boundary conditions rather than four with a cleverer domain definition.
- Feature #783: Fix parallel for FSI. In the process, two new fields have been added to EssentialBoundaryCondition in the input parameter file: one to tell whether there might be an overlap with another and the other to specify whether thr values may vary over time.
- Feature #780: Model FSI: introduce new variational formulation for ALE.