Datatype `DAEMesh` for DAEs #384

lisawim · 2023-11-30T13:38:34Z

Together with @brownbaerchen I implemented a datatype for DAEs that allows to distinguish between the differential part and the algebraic part of the problem. fully_implicit_DAE does not change, but solve_system needs to be adapted, since it also has to be distinguish between these different parts. Since the scipy root solver don't know such a mesh type, a separate function implSysAsNumpy is defined to convert the current mesh into a numpy array of appropriate shape. The DAE hook class also have a new hook logging the error in the algebraic variable, which is more clean with the new datatype now.

I guess a pretty nice advantage is that the IMEX-SDC-DAE sweeper (that will come in another PR sometime) can also be used for the same problems as fully_implicit_DAE can be used. Thus, no IMEX DAE versions of the problems are necessary here.

For this, all files and all tests of the DAE projects needs to be adapted. Yesterday, we noticed that the tests for the problems and also for the sweeper could be way more strict, however.. The PinTSimE project needs to be adapted as well since it contains this folder for the paper including more DAE stuff. But this is moved to future, where more time is available to do that.

If you have some further comments, improvements, etc. I'm happy when you let me know that.

codecov · 2023-11-30T14:13:29Z

Codecov Report

Attention: Patch coverage is 95.97315% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 75.62%. Comparing base (05adc5a) to head (5921aff).

Files	Patch %	Lines
pySDC/projects/DAE/problems/simple_DAE.py	86.36%	3 Missing ⚠️
pySDC/projects/DAE/problems/synchronous_machine.py	81.25%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #384      +/-   ##
==========================================
+ Coverage   75.61%   75.62%   +0.01%     
==========================================
  Files         309      310       +1     
  Lines       24953    24980      +27     
==========================================
+ Hits        18869    18892      +23     
- Misses       6084     6088       +4

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pySDC/projects/DAE/misc/HookClass_DAE.py

pySDC/projects/DAE/problems/simple_DAE.py

pySDC/projects/DAE/problems/synchronous_machine.py

pySDC/projects/DAE/problems/transistor_amplifier.py

pySDC/tests/test_projects/test_DAE/test_misc.py

…lemDAE.py

lisawim · 2024-01-12T09:49:47Z

Corrections to be continued.

lisawim · 2024-01-12T13:18:39Z

Corrections are finished now. Feel free to merge (or to comment).

brownbaerchen · 2024-01-12T13:31:56Z

We certainly added some mess while reducing the mess. Since it's all contained within the DAE project, I am fine with merging this and cleaning it up later. Whichever you prefer @lisawim, @pancetta.

lisawim · 2024-01-12T13:43:32Z

Using fully-implicit DAEs with mesh type and semi-explicit DAEs with DAEMesh type with FI-SDC still causes some inconvenient handlings that I have fixed but it's kind of some mess as @brownbaerchen mentioned. At this time, I had no reasonable idea to make it as clean as possible. But I've arranged to meet @brownbaerchen in Bruges to clean it up. I'm also fine with both. But the SISDC sweeper will follow anyway. 😈

lisawim · 2024-01-12T13:55:18Z

pySDC/projects/DAE/misc/HookClass_DAE.py

+        # compute and save errors
+        # Note that the component from which the error is measured is specified here
+        upde = P.u_exact(step.time + step.dt)
+        err = abs(upde.diff - L.uend.diff)


But here @pancetta and @brownbaerchen the error is computed over the differential variables. When I would use the generic error hook classes I got the maximum error over both the differential and the algebraic variables. I can rename it such that it is clear what this hook class does. So, I still would like to keep this class at least for the semi-explicit DAEs. For the fully-implicit DAEs the generic error hook classes does make sense to use!

…able(s)

pancetta · 2024-01-12T15:34:55Z

So, do you want to leave it open until Bruges or should I merge?

lisawim · 2024-01-15T06:35:58Z

I'd like to leave it open until Bruges. When the new data type will be merged into pySDC, then it should be implemented in a clean way.

… ugit add pySDC/implementations/datatype_classes/MultiComponentMesh.py

brownbaerchen · 2024-02-14T14:00:41Z

Can you extend the test of DAE mesh different shapes, i.e. PDAEs? Also, you only add a number to the entire array, but we should check what happens when you do ufuncs with the components of the mesh as well.

lisawim · 2024-02-14T15:56:57Z

Ah, cool! I did not see your commit.. Indeed, it can deal with that. I adapted the first test for the mesh for initialization. Adaption of the other test will follow!

brownbaerchen · 2024-02-14T16:23:05Z

pySDC/tests/test_projects/test_DAE/test_DAEMesh.py

@@ -10,17 +10,26 @@ def testInitialization():
    import numpy as np
    from pySDC.projects.DAE.misc.DAEMesh import DAEMesh

-    init = (6, None, np.dtype('float64'))
+    nvars_1d = 6


you can just give the shape as an argument to the function and call the function multiple times with the decorator scipy.mark.parametrize(shape, [(6,), (4, 6)]). You can just assign random values.

pancetta · 2024-02-20T14:13:27Z

Are we good to go now?

lisawim · 2024-02-20T14:21:09Z

Yes, Mr. @pancetta!

brownbaerchen · 2024-02-20T14:19:47Z

pySDC/projects/DAE/misc/ProblemDAE.py

+            sys = impl_sys(me, **kwargs)
+            return np.append(sys.diff.flatten(), sys.alg.flatten())  # TODO: more efficient way?
+
+        if type(me) == DAEMesh:


We don't need this anymore, right? We should be able to plug this into scipy solvers directly.

brownbaerchen · 2024-02-20T14:25:34Z

pySDC/projects/DAE/sweepers/fully_implicit_DAE.py

@@ -118,11 +107,14 @@ def implSystem(params):
                    System to be solved as implicit function.
                """

-                params_mesh = P.dtype_f(P.init)
-                params_mesh[:] = params
+                if type(params) == DAEMesh:


I think we also don't need this anymore...? Maybe we need to do sth like params_mesh[...] = params?

@caklovicka

) * first working SDC version (M and Minv) * Update playground.py * cleaning up * Added some hyphens in plots (#389) * Removed seperate file for GPU Dahlquist implementation (#391) Co-authored-by: Thomas <[email protected]> * Review (#388) * Bug is fixed and added new code * new code for the table * Edits in markdown file * some edits in test * Bugs fix * Codecov * I cleaned up my code and separated classes to make it easier to work with. It is not ready yet; if Codecov fails, I will include more tests. * forgot black * flake8 * bug fix * Edits codes according to the comments * Edited codes according to the comments in the GitHub * Defined new function in stability_simulation.py to check stability for given points and excluded codecov function that generates a table. * small edits for codecov * removed no cover * NCCL communicators (#392) * Added wrapper for MPI communicator to use NCCL under the hood * Small fix * Moved NCCL communicator wrapper to helpers --------- Co-authored-by: Thomas <[email protected]> * Version bump for new release * proper readme and link * Started playground for machine learning generated initial guesses for (#394) SDC * playing with FEniCS * blackening * Bug fix (#395) * readme file changes * fixed bugs for stability plots and some edits in README file * some edits * typo in citation * Bump version * Bug fix (#396) * Clear documentation and some edits in the code * forgot black * some changes * bump version * Cosmetic changes (#398) * Parallel SDC (Reloaded) project (#397) TL: Added efficient diagonal preconditioners and associated project. Coauthored by @caklovicka * Generic multi-component mesh (#400) * Generic multicomponent mesh * new try * Added a test for MultiComponentMesh * Test that the type is conserved also after numpy operations * Added documentation for how to use `MultiComponentMesh` * Changed formatting of the documentation * Update ci_pipeline.yml * version freak show * version freak show II * version freak show III * version freak show IV * Update ci_pipeline.yml * version freak show V * 2D Brusselator problem (#401) * Added 2D Brusselator problem from Hairer-Wanner II. Thanks @grosilho for the suggestion! * Added forgotten pytest marker * Fix brain afk error * Added work counter for right hand side evaluations * Removed file for running Brusselator from project * Retry at removing the file * I need to go to git school * Datatype `DAEMesh` for DAEs (#384) * Added DAE mesh * Updated all DAE problems and the SDC-DAE sweeper * Updated playgrounds with new DAE datatype * Adapted tests * Minor changes * Black.. :o * Added DAEMesh only to semi-explicit DAEs + update for FI-SDC and ProblemDAE.py * Black :D * Removed unnecessary approx_solution hook + replaced by LogSolution hook * Update WSCC9 problem class * Removed unnecessary comments * Removed test_misc.py * Removed registering of newton_tol from child classes * Update test_problems.py * Rename error hook class for logging global error in differential variable(s) * Added MultiComponentMesh - @brownbaerchen + @tlunet + @pancetta Thank ugit add pySDC/implementations/datatype_classes/MultiComponentMesh.py * Updated stuff with new version of DAE data type * (Hopefully) faster test for WSCC9 * Test for DAEMesh * Renaming * ..for DAEMesh.py * Bug fix * Another bug fix.. * Preparation for PDAE stuff (?) * Changes + adapted first test for PDAE stuff * Commented out test_WSCC9_SDC_detection() - too long runtime * Minor changes for test_DAEMesh.py * Extended test for DAEMesh - credits for @brownbaerchen * Test for HookClass_DAE.py * Update for DAEMesh + tests * 🎉 - speed up test a bit (at least locally..) * Forgot to enable other tests again * Removed if-else-statements for mesh type * View for unknowns in implSysFlatten * Fix for RK sweeper - changed nodes in BackwardEuler class (#403) * Made aborting the step at growing residual optional (#405) * `pySDC`-build-in `LagrangeApproximation` class in `SwitchEstimator` (#406) * SE now uses LagrangeApproximation class + removed Lagrange class in SE * Removed log message again (not corresponding to PR) * version bump * Added hook for logging to file (#410) * Monodomain project (#407) * addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems * added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen) * added exponential imex and mES, added parabolic_system in vec format * added new stabilized integrators using multirate, splitting and exponential approaches * before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods * added first order exponential runge kutta as underlying collocation method. To be generalized to higher order * generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly * fixed a few things * optimized a few things * renamed project ExplicitStabilized to Monodomain * removed deprecated problems * fixed some renaming issues * did refactoring of code and put in Monodomain_NEW * removed old code and renamed new code * added finite difference discretization * added many things, cant remember * old convergence_controller * addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems * added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen) * added exponential imex and mES, added parabolic_system in vec format * added new stabilized integrators using multirate, splitting and exponential approaches * before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods * added first order exponential runge kutta as underlying collocation method. To be generalized to higher order * generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly * fixed a few things * optimized a few things * renamed project ExplicitStabilized to Monodomain * removed deprecated problems * fixed some renaming issues * did refactoring of code and put in Monodomain_NEW * removed old code and renamed new code * added finite difference discretization * added many things, cant remember * added smooth TTP model for conv test, added DCT for 2D and 3D problems * added plot stuff and run scripts * fixed controller to original * removed explicit stabilized files * fixed other files * removed obsolete splittings from ionic models * removed old sbatch scripts * removed mass transfer and sweeper * fixed something * removed my base transfer * removed hook class pde * removed FD files * fixed some calls to FD stuff * removed FEM FEniCSx files * renamed FD_Vector to DCT_Vector * added hook for output and visualization script * removed plot scripts * removed run scripts, except convergence * removed convergence experiments script * fixed TestODE * added stability test in run_TestODE * added stability test in run_TestODE * added stability test in run_TestODE * removed obsolete stuff in TestODE * removed unneeded stuff from run_MonodomainODE * cleaned a bit run_MonodomainODE * removed utils/ * added few comments, cleaned a bit * removed schedule from workflow * restored tutorial step 7 A which I has modified time ago * run black on monodomain project * fixed a formatting thing * reformatted everything with black * Revert "revert formatted with black" This reverts commit 82c82e9. * added environment file for monodomain project, started to add stuff in workflow * added first test * added package tqdm to monodomain environment * added new TestODE using DCT_vectors instead of myfloat, moved phi_eval_lists from MonodomainODE to the sweeper * deleted old TestODE and myfloat stuff * renamed TestODEnew to TestODE * cleaned a bit * added stability, convergence and iterations tests. Changed a bit other scripts as needed * reactivated other tests in workflow * removed my tests temporarly * added monodomain marker to project pyproject.toml * changed files and function names for tests * fixed convergence test * made one test a bit shorter * added test for SDC on HH and fixed missing feature in SDC imex sweeper for monodomain * reformatted with correct black options * fixed a lint error * another lint error * adding tests with plot * modified convergence test * added test iterations in parallel * removed plot from tests * added plots without writing to file * added write to file * simplified plot * new plot * fixed plot in iterations parallel * added back all tests and plots * cleaned a bit * added README * fixed readme * modified comments in controllers * try to compute phi every step * removed my controllers, check u changed before comuting phis * enabled postprocessing in pipeline * added comments to data_type classes, removed unnecessary methods * added comments to hooks * added comments to the problem classes * added comments to the run scripts * added comments to sweepers and transfer classes * fixed the readme * decommented if in pipeline * removed recv_mprobe option * changed back some stuff outiside of monodomain project * same * again * fixed Thomas hints * removed old unneeded move coverage folders * fixed previously missed Thomas comments * begin change datatype * changed run_Monodomain * added prints * fixed prints * mod print * mod print * mod print * mod print * rading init val * rading init val * removed prints * removed prints * checking longer time * checking longer time * fixed call phi eval * trying 2D * trying 2D * new_data type passing tests * removed coverage folders * optmized phi eval lists * before changing phi type * changed eval phi lists * polished a bit * before switch indeces * reformatted phi computaiton to its traspose * before changing Q * optimized integral of exp terms * changed interfate to c++ code * moved definition of dtype u f * tests passed after code refactoring * Generic MPI FFT class (#408) * Added generic MPIFFT problem class * Fixes * Generalized to `xp` in preparation for GPUs * Fixes * Ported Allen-Cahn to generic MPI FFT implementation * Ported Gray-Scott to generic MPI FFT (#412) * Ported Gray-Scott to generic MPI FFT class * `np` -> `xp` * Reverted poor changes * Update README.md (#413) Added the ExaOcean grant identified and the "Supported by the European Union - NextGenerationEU." clause that they would like us to display. * TIME-X Test Hackathon @ TUD: Test for `SwitchEstimator` (#404) * Added piecewise linear interpolation to SwitchEstimator * Started with test for SwitchEstimator [WIP] * Test to proof sum_restarts when event occuring at boundary * Started with test to check adapt_interpolation_info [WIP] * Added test for SE.adapt_interpolation_info() * Update linear interpolation + logging + changing tolerances * Test for linear interpolation + update of other test * Correction for finite difference + adaption tolerance * Added test for DAE case for SE * Choice of FD seems to be important for performance of SE * Removed attributes from dummy probs (since the parent classes have it) * Test for dummy problems + using functions from battery_model.py * Moved standard params for test to function * Updated hardcoded solutions for battery models * Updated hardcoded solutions for DiscontinuousTestODE * Updated docu in SE for FDs * Lagrange Interpolation works better with baclward FD and alpha=0.9 * Added test for state function + global error * Updated LogEvent hooks * Updated hardcoded solutions again * Adapted test_problems.py * Minor changes * Updated tests * Speed-up test for buck converter * Black.. * Use msg about convergence info in Newton in SE * Moved dummy problem to file * Speed up loop using mask * Removed loop * SDC-DAE sweeper for semi-explicit DAEs (#414) * Added SI-SDC-DAE sweeper * Starte with test for SemiImplicitDAE * Test for SI-SDC sweeper * Clean-up * Removed parameter from function * Removed test + changed range of loop in SI-sweeper --------- Co-authored-by: Robert Speck <[email protected]> Co-authored-by: Thomas Baumann <[email protected]> Co-authored-by: Thomas <[email protected]> Co-authored-by: Ikrom Akramov <[email protected]> Co-authored-by: Thibaut Lunet <[email protected]> Co-authored-by: Lisa Wimmer <[email protected]> Co-authored-by: Giacomo Rosilho de Souza <[email protected]> Co-authored-by: Daniel Ruprecht <[email protected]>

@caklovicka

commit cbaae05 Author: jakob-fritz <[email protected]> Date: Wed Apr 24 10:34:09 2024 +0200 Make create_gitlab_ci branch up-to-date before merging into master (Parallel-in-Time#418) * first working SDC version (M and Minv) * Update playground.py * cleaning up * Added some hyphens in plots (Parallel-in-Time#389) * Removed seperate file for GPU Dahlquist implementation (Parallel-in-Time#391) Co-authored-by: Thomas <[email protected]> * Review (Parallel-in-Time#388) * Bug is fixed and added new code * new code for the table * Edits in markdown file * some edits in test * Bugs fix * Codecov * I cleaned up my code and separated classes to make it easier to work with. It is not ready yet; if Codecov fails, I will include more tests. * forgot black * flake8 * bug fix * Edits codes according to the comments * Edited codes according to the comments in the GitHub * Defined new function in stability_simulation.py to check stability for given points and excluded codecov function that generates a table. * small edits for codecov * removed no cover * NCCL communicators (Parallel-in-Time#392) * Added wrapper for MPI communicator to use NCCL under the hood * Small fix * Moved NCCL communicator wrapper to helpers --------- Co-authored-by: Thomas <[email protected]> * Version bump for new release * proper readme and link * Started playground for machine learning generated initial guesses for (Parallel-in-Time#394) SDC * playing with FEniCS * blackening * Bug fix (Parallel-in-Time#395) * readme file changes * fixed bugs for stability plots and some edits in README file * some edits * typo in citation * Bump version * Bug fix (Parallel-in-Time#396) * Clear documentation and some edits in the code * forgot black * some changes * bump version * Cosmetic changes (Parallel-in-Time#398) * Parallel SDC (Reloaded) project (Parallel-in-Time#397) TL: Added efficient diagonal preconditioners and associated project. Coauthored by @caklovicka * Generic multi-component mesh (Parallel-in-Time#400) * Generic multicomponent mesh * new try * Added a test for MultiComponentMesh * Test that the type is conserved also after numpy operations * Added documentation for how to use `MultiComponentMesh` * Changed formatting of the documentation * Update ci_pipeline.yml * version freak show * version freak show II * version freak show III * version freak show IV * Update ci_pipeline.yml * version freak show V * 2D Brusselator problem (Parallel-in-Time#401) * Added 2D Brusselator problem from Hairer-Wanner II. Thanks @grosilho for the suggestion! * Added forgotten pytest marker * Fix brain afk error * Added work counter for right hand side evaluations * Removed file for running Brusselator from project * Retry at removing the file * I need to go to git school * Datatype `DAEMesh` for DAEs (Parallel-in-Time#384) * Added DAE mesh * Updated all DAE problems and the SDC-DAE sweeper * Updated playgrounds with new DAE datatype * Adapted tests * Minor changes * Black.. :o * Added DAEMesh only to semi-explicit DAEs + update for FI-SDC and ProblemDAE.py * Black :D * Removed unnecessary approx_solution hook + replaced by LogSolution hook * Update WSCC9 problem class * Removed unnecessary comments * Removed test_misc.py * Removed registering of newton_tol from child classes * Update test_problems.py * Rename error hook class for logging global error in differential variable(s) * Added MultiComponentMesh - @brownbaerchen + @tlunet + @pancetta Thank ugit add pySDC/implementations/datatype_classes/MultiComponentMesh.py * Updated stuff with new version of DAE data type * (Hopefully) faster test for WSCC9 * Test for DAEMesh * Renaming * ..for DAEMesh.py * Bug fix * Another bug fix.. * Preparation for PDAE stuff (?) * Changes + adapted first test for PDAE stuff * Commented out test_WSCC9_SDC_detection() - too long runtime * Minor changes for test_DAEMesh.py * Extended test for DAEMesh - credits for @brownbaerchen * Test for HookClass_DAE.py * Update for DAEMesh + tests * 🎉 - speed up test a bit (at least locally..) * Forgot to enable other tests again * Removed if-else-statements for mesh type * View for unknowns in implSysFlatten * Fix for RK sweeper - changed nodes in BackwardEuler class (Parallel-in-Time#403) * Made aborting the step at growing residual optional (Parallel-in-Time#405) * `pySDC`-build-in `LagrangeApproximation` class in `SwitchEstimator` (Parallel-in-Time#406) * SE now uses LagrangeApproximation class + removed Lagrange class in SE * Removed log message again (not corresponding to PR) * version bump * Added hook for logging to file (Parallel-in-Time#410) * Monodomain project (Parallel-in-Time#407) * addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems * added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen) * added exponential imex and mES, added parabolic_system in vec format * added new stabilized integrators using multirate, splitting and exponential approaches * before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods * added first order exponential runge kutta as underlying collocation method. To be generalized to higher order * generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly * fixed a few things * optimized a few things * renamed project ExplicitStabilized to Monodomain * removed deprecated problems * fixed some renaming issues * did refactoring of code and put in Monodomain_NEW * removed old code and renamed new code * added finite difference discretization * added many things, cant remember * old convergence_controller * addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems * added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen) * added exponential imex and mES, added parabolic_system in vec format * added new stabilized integrators using multirate, splitting and exponential approaches * before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods * added first order exponential runge kutta as underlying collocation method. To be generalized to higher order * generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly * fixed a few things * optimized a few things * renamed project ExplicitStabilized to Monodomain * removed deprecated problems * fixed some renaming issues * did refactoring of code and put in Monodomain_NEW * removed old code and renamed new code * added finite difference discretization * added many things, cant remember * added smooth TTP model for conv test, added DCT for 2D and 3D problems * added plot stuff and run scripts * fixed controller to original * removed explicit stabilized files * fixed other files * removed obsolete splittings from ionic models * removed old sbatch scripts * removed mass transfer and sweeper * fixed something * removed my base transfer * removed hook class pde * removed FD files * fixed some calls to FD stuff * removed FEM FEniCSx files * renamed FD_Vector to DCT_Vector * added hook for output and visualization script * removed plot scripts * removed run scripts, except convergence * removed convergence experiments script * fixed TestODE * added stability test in run_TestODE * added stability test in run_TestODE * added stability test in run_TestODE * removed obsolete stuff in TestODE * removed unneeded stuff from run_MonodomainODE * cleaned a bit run_MonodomainODE * removed utils/ * added few comments, cleaned a bit * removed schedule from workflow * restored tutorial step 7 A which I has modified time ago * run black on monodomain project * fixed a formatting thing * reformatted everything with black * Revert "revert formatted with black" This reverts commit 82c82e9. * added environment file for monodomain project, started to add stuff in workflow * added first test * added package tqdm to monodomain environment * added new TestODE using DCT_vectors instead of myfloat, moved phi_eval_lists from MonodomainODE to the sweeper * deleted old TestODE and myfloat stuff * renamed TestODEnew to TestODE * cleaned a bit * added stability, convergence and iterations tests. Changed a bit other scripts as needed * reactivated other tests in workflow * removed my tests temporarly * added monodomain marker to project pyproject.toml * changed files and function names for tests * fixed convergence test * made one test a bit shorter * added test for SDC on HH and fixed missing feature in SDC imex sweeper for monodomain * reformatted with correct black options * fixed a lint error * another lint error * adding tests with plot * modified convergence test * added test iterations in parallel * removed plot from tests * added plots without writing to file * added write to file * simplified plot * new plot * fixed plot in iterations parallel * added back all tests and plots * cleaned a bit * added README * fixed readme * modified comments in controllers * try to compute phi every step * removed my controllers, check u changed before comuting phis * enabled postprocessing in pipeline * added comments to data_type classes, removed unnecessary methods * added comments to hooks * added comments to the problem classes * added comments to the run scripts * added comments to sweepers and transfer classes * fixed the readme * decommented if in pipeline * removed recv_mprobe option * changed back some stuff outiside of monodomain project * same * again * fixed Thomas hints * removed old unneeded move coverage folders * fixed previously missed Thomas comments * begin change datatype * changed run_Monodomain * added prints * fixed prints * mod print * mod print * mod print * mod print * rading init val * rading init val * removed prints * removed prints * checking longer time * checking longer time * fixed call phi eval * trying 2D * trying 2D * new_data type passing tests * removed coverage folders * optmized phi eval lists * before changing phi type * changed eval phi lists * polished a bit * before switch indeces * reformatted phi computaiton to its traspose * before changing Q * optimized integral of exp terms * changed interfate to c++ code * moved definition of dtype u f * tests passed after code refactoring * Generic MPI FFT class (Parallel-in-Time#408) * Added generic MPIFFT problem class * Fixes * Generalized to `xp` in preparation for GPUs * Fixes * Ported Allen-Cahn to generic MPI FFT implementation * Ported Gray-Scott to generic MPI FFT (Parallel-in-Time#412) * Ported Gray-Scott to generic MPI FFT class * `np` -> `xp` * Reverted poor changes * Update README.md (Parallel-in-Time#413) Added the ExaOcean grant identified and the "Supported by the European Union - NextGenerationEU." clause that they would like us to display. * TIME-X Test Hackathon @ TUD: Test for `SwitchEstimator` (Parallel-in-Time#404) * Added piecewise linear interpolation to SwitchEstimator * Started with test for SwitchEstimator [WIP] * Test to proof sum_restarts when event occuring at boundary * Started with test to check adapt_interpolation_info [WIP] * Added test for SE.adapt_interpolation_info() * Update linear interpolation + logging + changing tolerances * Test for linear interpolation + update of other test * Correction for finite difference + adaption tolerance * Added test for DAE case for SE * Choice of FD seems to be important for performance of SE * Removed attributes from dummy probs (since the parent classes have it) * Test for dummy problems + using functions from battery_model.py * Moved standard params for test to function * Updated hardcoded solutions for battery models * Updated hardcoded solutions for DiscontinuousTestODE * Updated docu in SE for FDs * Lagrange Interpolation works better with baclward FD and alpha=0.9 * Added test for state function + global error * Updated LogEvent hooks * Updated hardcoded solutions again * Adapted test_problems.py * Minor changes * Updated tests * Speed-up test for buck converter * Black.. * Use msg about convergence info in Newton in SE * Moved dummy problem to file * Speed up loop using mask * Removed loop * SDC-DAE sweeper for semi-explicit DAEs (Parallel-in-Time#414) * Added SI-SDC-DAE sweeper * Starte with test for SemiImplicitDAE * Test for SI-SDC sweeper * Clean-up * Removed parameter from function * Removed test + changed range of loop in SI-sweeper --------- Co-authored-by: Robert Speck <[email protected]> Co-authored-by: Thomas Baumann <[email protected]> Co-authored-by: Thomas <[email protected]> Co-authored-by: Ikrom Akramov <[email protected]> Co-authored-by: Thibaut Lunet <[email protected]> Co-authored-by: Lisa Wimmer <[email protected]> Co-authored-by: Giacomo Rosilho de Souza <[email protected]> Co-authored-by: Daniel Ruprecht <[email protected]> commit 24cdf05 Author: Jakob Fritz <[email protected]> Date: Wed Apr 24 09:11:38 2024 +0200 Split installation and running into two jobs As one of the two jobs often failed during installation, while the other one succeeded. So it might be a race condition. Therefore, splitting installation and usage into separate jobs commit 488e7a4 Author: Jakob Fritz <[email protected]> Date: Wed Apr 24 08:34:59 2024 +0200 ci_pipeline.yml now more similar to upstream commit 9ab9b63 Author: Jakob Fritz <[email protected]> Date: Tue Apr 23 15:36:39 2024 +0200 Reduced diff to master commit cdb77d4 Author: jakob-fritz <[email protected]> Date: Mon Apr 22 16:46:44 2024 +0200 WIP: Use HPC for CI (Parallel-in-Time#386) Works on Parallel-in-Time#415 Added sync with Gitlab, now also for pull requests --------- Co-authored-by: Robert Speck <[email protected]> and Thomas Baumann <[email protected]> commit fb4b745 Author: Jakob Fritz <[email protected]> Date: Mon Apr 22 16:02:49 2024 +0200 Moved development of action into main branch and added version-tag commit 7de7187 Author: Jakob Fritz <[email protected]> Date: Mon Apr 22 11:19:53 2024 +0200 Added triggers for workflows again commit 5f45785 Author: Jakob Fritz <[email protected]> Date: Thu Apr 18 14:22:13 2024 +0900 Updated name of step, as merge is not ff-only anymore commit 2e9930f Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 13:36:44 2024 +0900 Wrong syntax for if else commit e33a611 Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 13:33:40 2024 +0900 Unshallow repo if needed commit c7db47a Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 13:18:26 2024 +0900 Add name and email for merge-commit commit f34de9c Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 12:09:20 2024 +0900 Also allow non-fast-forward merges commit 82d9233 Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 11:49:56 2024 +0900 Don't run mirror on push now (as gitlab-file is incorrect in this branch) commit d1b7250 Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 11:49:02 2024 +0900 Make unshallow before merging to properly compare history commit 9cfeea3 Author: Jakob Fritz <[email protected]> Date: Wed Apr 17 11:17:48 2024 +0900 Changed way to use variables (set locally and later in github_env) commit 6961ef3 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 16:31:51 2024 +0900 Reverted and changed way to store variable commit d906604 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 16:21:54 2024 +0900 Redone storing of var again commit faec097 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 14:50:56 2024 +0900 Corrected querying of a variable commit cbf0b5d Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 13:57:31 2024 +0900 Added more reporting for better debugging commit efdaa05 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 13:23:08 2024 +0900 Don't run main CI during development commit ccd646a Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 13:22:44 2024 +0900 First fetch, to be able to checkout branch commit 2712998 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 12:15:13 2024 +0900 Don't rerun CI on every push during this development commit 8a316e2 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 12:14:31 2024 +0900 Moved the check of condition from shell to yaml commit d347bd3 Author: Jakob Fritz <[email protected]> Date: Tue Apr 16 11:52:02 2024 +0900 Try to merge code (from PR) first So that merged state is tested in Gitlab-CI commit bcd64a5 Author: Jakob Fritz <[email protected]> Date: Mon Feb 5 11:25:43 2024 +0100 Use specific version of github2lab action commit 28472dc Author: Jakob Fritz <[email protected]> Date: Mon Jan 29 15:10:38 2024 +0100 Uses newer checkout-action to use new node-version (20) Version 16 is deprecated commit fefe88b Author: Jakob Fritz <[email protected]> Date: Mon Jan 29 14:53:18 2024 +0100 Minor formatting updates in README to trigger CI commit 3de1b56 Author: Jakob Fritz <[email protected]> Date: Fri Jan 26 16:13:53 2024 +0100 Formatted md-file to trigger CI commit ef6a866 Author: Jakob Fritz <[email protected]> Date: Thu Jan 18 15:48:25 2024 +0100 Set sha for checkout properly commit be3aef7 Author: Jakob Fritz <[email protected]> Date: Mon Jan 15 16:14:41 2024 +0100 Using default shallow checkout Otherwise, other own action complains commit f38f0e5 Author: Jakob Fritz <[email protected]> Date: Mon Jan 15 16:11:05 2024 +0100 Updated ref to use lastest code from PR; not merge Previously, a version of the code was used that was how a merge could look like. Now, the code is used as it is in the PR commit 249741b Author: Jakob Fritz <[email protected]> Date: Mon Jan 15 08:47:45 2024 +0100 Updated workflow for mirroring commit d8604b7 Author: Jakob Fritz <[email protected]> Date: Mon Jan 8 16:39:49 2024 +0100 Try exapnding the predefined variable commit c49accd Author: Jakob Fritz <[email protected]> Date: Mon Jan 8 16:37:10 2024 +0100 Another attempt to get the action to work commit 5e0118a Author: Jakob Fritz <[email protected]> Date: Mon Jan 8 16:28:51 2024 +0100 Hopefully now, variable is expanded instead using the name commit 832e7e5 Author: Jakob Fritz <[email protected]> Date: Mon Jan 8 16:07:29 2024 +0100 Exit instead of return needed Because exiting the shell instead of a function commit 5a5de4a Author: Jakob Fritz <[email protected]> Date: Mon Jan 8 12:00:55 2024 +0100 First version of CI to mirror pull_requests to Gitlab If someone with write-permissions triggered the workflow

lisawim added 6 commits November 30, 2023 13:34

Added DAE mesh

901e3e4

Updated all DAE problems and the SDC-DAE sweeper

18806f3

Updated playgrounds with new DAE datatype

2ca0d5c

Adapted tests

64dbb94

Minor changes

c7f4cfd

Black.. :o

eaf4448

brownbaerchen reviewed Dec 1, 2023

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lisawim added 4 commits January 9, 2024 14:57

Merge remote-tracking branch 'upstream/master' into dae_meshtype

20b8f40

Merge remote-tracking branch 'upstream/master' into dae_meshtype

b001b7c

Added DAEMesh only to semi-explicit DAEs + update for FI-SDC and Prob…

0fd9525

…lemDAE.py

Black :D

49de7ef

lisawim added 4 commits January 12, 2024 13:54

Removed unnecessary approx_solution hook + replaced by LogSolution hook

bbb605a

Update WSCC9 problem class

9594e1d

Removed unnecessary comments

68cc407

Removed test_misc.py

6315781

lisawim commented Jan 12, 2024

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lisawim added 4 commits January 12, 2024 15:39

Removed registering of newton_tol from child classes

88e8175

Update test_problems.py

af1848e

Rename error hook class for logging global error in differential vari…

87d6d56

…able(s)

Merge remote-tracking branch 'upstream/master' into dae_meshtype

ad0ca26

lisawim added 3 commits February 14, 2024 13:03

Merge remote-tracking branch 'upstream/master' into dae_meshtype

bda5014

Added MultiComponentMesh - @brownbaerchen + @tlunet + @pancetta Thank…

c68305b

… ugit add pySDC/implementations/datatype_classes/MultiComponentMesh.py

Updated stuff with new version of DAE data type

1555ee9

lisawim added 6 commits February 14, 2024 15:05

Renaming

da5e663

..for DAEMesh.py

a45900d

Bug fix

82b692d

Another bug fix..

be4f248

Preparation for PDAE stuff (?)

04fdedc

Changes + adapted first test for PDAE stuff

58101ea

brownbaerchen reviewed Feb 14, 2024

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lisawim added 10 commits February 15, 2024 11:43

Commented out test_WSCC9_SDC_detection() - too long runtime

522d80c

Minor changes for test_DAEMesh.py

3af100f

Extended test for DAEMesh - credits for @brownbaerchen

bdc548c

Merge remote-tracking branch 'upstream/master' into dae_meshtype

9540354

Test for HookClass_DAE.py

40bf6c6

Merge remote-tracking branch 'upstream/master' into dae_meshtype

70ef02e

Update for DAEMesh + tests

75d1d8b

Merge remote-tracking branch 'upstream/master' into dae_meshtype

27ea264

🎉 - speed up test a bit (at least locally..)

d44e2a2

Forgot to enable other tests again

e24ff2b

brownbaerchen requested changes Feb 20, 2024

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brownbaerchen reviewed Feb 20, 2024

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lisawim added 3 commits February 23, 2024 11:31

Removed if-else-statements for mesh type

486cfbb

Merge remote-tracking branch 'upstream/master' into dae_meshtype

c359d22

View for unknowns in implSysFlatten

5921aff

brownbaerchen approved these changes Feb 23, 2024

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pancetta merged commit b059c62 into Parallel-in-Time:master Feb 27, 2024
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Datatype `DAEMesh` for DAEs #384

Datatype `DAEMesh` for DAEs #384

lisawim commented Nov 30, 2023

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Datatype DAEMesh for DAEs #384

Datatype DAEMesh for DAEs #384

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Datatype `DAEMesh` for DAEs #384

Datatype `DAEMesh` for DAEs #384

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