Santiago Ospina De Los Ríos authored May 23, 2024 and Santiago Ospina De Los Ríos committed May 24, 2024

Implement a forward euler on the residual between the degrees of freedom of a local basis and store the result in the local jacobian matrix

Santiago Ospina De Los Ríos authored Jun 11, 2024 and Santiago Ospina De Los Ríos committed Jun 27, 2024

See discussion in https://github.com/oneapi-src/oneTBB/pull/1395#issuecomment-2160713912

With recent changes in dune-common, super builds are now feasible. This simplifies the instructions to install from source.

Previously, if finding muParser failed, the target is still defined with wrong properties. Moreover, the library recognized muParser because of the header even if it was not working properly. This commit fixes those problems by guarding with a preprocessor macro and by defining the target if it's properly working.

The common headers are using {fmt}, if their headers are placed somewhere
else than the system headers, the current set up would fail to find the headers.

* Use an extra config to pass domain deformation to the local equations
* The finite element cache has to be passed by reference, so we change this and numerical jacobian cache to be a thread_local right a way.

The main offender is TBB whose parallel sort has memory leaks
https://github.com/oneapi-src/oneDPL/pull/1589
so now, the parallel sorts need to be explictely enabled.

Arash Partow authored Jan 01, 2024 and Santiago Ospina De Los Ríos committed Nov 21, 2024

Signed-off-by: Santiago Ospina De Los Ríos <sospinar@gmail.com>

Santiago Ospina De Los Ríos authored May 10, 2024 and Santiago Ospina De Los Ríos committed Nov 25, 2024

Fix JOSS DOIs
* Update electrophysiology figure
* Why does the package have "COPASI" in its name? This could cause confusion to new users who've used (arguably, the more well known) computational biology GUI and package, also called Copasi before (https://copasi.org/).
* Summary does not align with JOSS instructions: The summary should have "a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience". In my opinion, the language right now is a bit dense for a non-specialist to follow.
* A section or summary of background is better to include before presenting the "Model problem".
* In the model problem, what are the compartments and "the problem". I think these need to be defined before giving the mathematical formulation.
* Capitalize D in *dirichlet?
* The Spatial Model Editor is referred in Line 35 without reference or description of what it might be or how it relates to dune-copasi.
* In caption of Figure 1, towards the end, is the experimental data from Wehling et al. 2022? Worth mentioning if that's the case.
* The statement of need could probably be moved before the previous two sections because it sets up the motivation.
* Fix acronyms
* Move pipeline figure earlier in the paper
* Change citation style