Merge branch 'jeremy/cov-xml' into 'main'

Fix CI coverage reporting

See merge request phypid/honee!7

make - make all by default

Merge branch 'jrwrigh/make_docs' into 'main'

Enable documenatation building

See merge request phypid/honee!5

doc: Get documentation running

Merge branch 'jeremy/ci' into 'main'

ci - add initial ci yml

See merge request phypid/honee!1

make - capture j correctly

make - add info, info-basic

make - add format

chore: Get tests back up and running

Merge pull request #1581 from CEED/jrwrigh/pytorch_external_sgs

fluids: Add PyTorch external DD SGS evaluation

fluids: Force recompilation if Makefile changes

fluids: Add PyTorch external DD SGS evaluation

- Rename sequential_internal -> *_ceed

Merge pull request #1510 from CEED/jrwrigh/fluids_matceed

fluids: Add MatCeed

fluids: Make MatShell functions static

This is done primarily to allow MatCeed to coexist with the context
operators for right now.

This has the nasty side-effect of forcing `Mat` objects to be NUL

fluids: Make MatShell functions static

This is done primarily to allow MatCeed to coexist with the context
operators for right now.

This has the nasty side-effect of forcing `Mat` objects to be NULL when
they're passed into CreateMatShell_Ceed, but that will soon be replaced
with MatCeed, so it is only temporary for the transition in this PR

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fluids: Include config.mk from top level

Now `SMARTREDIS_DIR` can be added to the config.mk and it passed into
the fluids Makefile

Merge pull request #1203 from CEED/jrwrigh/smartsim

fluids: SmartSim Online Data-Driven SGS training

fluids: Add SmartSim build to Makefile

Merge pull request #1345 from CEED/jrwrigh/fluids-asan

fluids: Add ASAN, Correct memory out-of-bounds error

fluids: Add ASAN, Correct memory out-of-bounds error

fluids: Fix time label for strong STG #1057

fluids: Add STATIC and print-% to makefile

Merge pull request #962 from CEED/jed/fluids-jacobian

examples/fluids: add analytic Jacobian

examples/fluids: add IJacobian for SUPG

I think this is exact for Galerkin on channel.yaml and blasius.yaml.
Specifically, SNES converges almost perfectly in this test than when
-snes_mf_operator is

examples/fluids: add IJacobian for SUPG

I think this is exact for Galerkin on channel.yaml and blasius.yaml.
Specifically, SNES converges almost perfectly in this test than when
-snes_mf_operator is added.

-options_file examples/fluids/channel.yaml -snes_monitor -ksp_converged_reason -stab none -ts_max_steps 3 -newtonian_unit_tests -ksp_rtol 1e-10 -order 2 -ts_dt 3e-6 -pc_type lu

I say "think" because something is fishy with the viscous energy term
velocity*stress. If I disable that term, then convergence is clearly
better with the analytic Jacobian (makes sense because it's accuracy is
machine epsilon) than with -snes_mf_operator. This is unexpected, but
the difference is near the limit of numerical stability so I'm not
confident it's wrong. Also, the term itself is so simple.

The Jacobian is inexact for SUPG in that Tau_d is frozen.

WIP: examples/fluids: support MatShell and Blasius_Inflow_Jacobian

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minor - update copyright headers

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memor

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memory for context problem

* freed allocated memory

* WIP: fluids: split density current into new compilation unit
I have dropped last changes before this commit so there might be some
bugs

* Fixed bugs after dropping the commit containing unnecessary changes

* NS: dropped unused variable from User struct

* WIP: factored out DMAddBoundary() for density_current

* split advection and advection2d into separate compilation units as well

* fluids: added *.o to make clean

* removed bc from problemData

* style

* commented the error handlers and moved petsc options regarding the boundary conditions to each compilation unit

* call bc functions inside SetUpDM()

* Moved all bc related statements from SetUpDM() to each compilation unit

* examples/fluids/advection.h: style

* WIP: modified CeedQFunctionContexts

* FFR: By creating a struct for DC context, one of the last test crushed so I had to reverse it. This should be investigated later.

* style

* examples/navierstokes: Use heap memory for ctxSetup

* examples/fluids: WIP - reading arrays through cl options for DC is enabled by using double pointers but there is still a problem with unit conversions and also need to fix other structs

* style

* WIP: Trying to assign values to context data in each problem function

* bug: there is a problem in pointer to struct

* WIP: Everything seems to be working but it breaks and I haven't figured out the reason ...

* fixed typo

* comment out stuff that have been moved to densitycurrent.c

* WIP: The first two regression test pass. There is a problem with stabilization.

* style

* Fluids: QFContext -> Physics

* WIP: passing StabilizationType to Physics (but PETSc is not happy and it diverges for SU and SUPG)

* Initial commit for refactoring advection(2d)

* WIP: Advection is set up except for wind_type

* WIP: refactored advection2d; need to fix the BCs for translation and also passing implicit to advection correctly

* WIP: pass wind_type to all functions correctly but there is still a problem with BCs in the case of translation (changes are not applied to advection yet)

* Apply the same fixes for BCs in advection

* Fluids - Refactor: Moved warnings to advection(2d)

* Fluids - Refactor: remove dead code

* Fluids - Refactor: Move *.h to /qfunctions and *.c to /src

* style

* Fluids - Refactor: drop the supg regression test for now

We need to debug SU/SUPG for density_current. The test does not work.

* Fluids - Refactor: Fixed the double-pointer issue

* Fluids - Refactor: Assign ctxSetup->time = 0 inside each problem's *.c

* Fluids - Refactor: make implicit a member of Physics

* Fluids - Refactor: Add warning for the usage of explicit and supg

* Some comments and naming

* Merge main after v0.8 (#723)

* Fluids - Five regression tests added for euler_vortex

* Fluids - Drop some of the regression tests for now (Needs to get fixed)

* Fluids - Moved all functions to their corresponding source files

* Fluids - move problem source files to /problems

* Fluids - drop dead regression test reference files

* Fluids - more consistent file names

* Fluids - drop dead code and comments

* Fluids - removed CreateVectorFromPetscVec() since it was only used once

* Fluids - created AppCtx for cl option variables and moved cl options to a cloption.c

* Fluids: change style of AppCtx

* style

* Fluids: /src -> /utils

* Created CreateDistributedDM() and some style

* Fluids - create RegisterProblem()

* style - minor

* style - minor

* Fluids - some more C style

* Fluids - /utils -> /src

* Fluids - create VizRefineDM() for viz_refine

* Fluids: some style and name change

* Fluids - style

* Fluids - remove the second ceed initialization

* Fluids - Created CeedData and SetupLibCEED()

* Fluids - create SetupContextForProblems()

* Fluids - Assign structs after they are created

* Fluids - style, minor

* Fluids - created RegressionTests_NS

* Fluids - created GetError_NS()

* Fluids - created PrintOutput_NS()

This processes bash output except for the problem summary which will be
included after mem_type is managed properly.

* Fluids - remove unused variables

* Fluids - created TSSolve_NS() which creates, sets up, and solves ts

* Fluids: Fixed a bug caused by merging#714

* Fluids - style

* Fluids - created SetupICsFromBinary() for case of -continue

* Fluids - create SetBCsFromICs_NS()

* Fluids - default degree had is 1 not 2

* Fluids: clean-up

* Fluids: style - minor

* Fluids - drop redundant operation

* Fluids: clean-up SetupLibCEED()

* Fluids: style - minor

* Fluids: WIP - C style

* Fluids: style - minor

* Fluids: move ceed vector creation to SetupLibCEED()

* Fluids: WIP - clean-up CreateOperatorForDomain()

* Fluids: major clean-up in CreateOperatorForDomain()

* Fluids: style - minor

* Fluids: drop VectorPlacePetscVec()

* Fluids: move ICs_FixMultiplicity() to misc.c

* Fluids: WIP - C style

* Fluids: fix merge conflict after 7b616370c27647626988b5d34b0f4eaa81450ad4

* Fluids: drop unused function call DMLocalizeCoordinates()

* Fluids: replace user requested memType with MemTypeP2C()

* Fluids: C style

* Fluids: Q->num_Q (Q (# qpts) and Q (global state vector) were confusing my fresh petsc config)

* Fluids: WIP - add GPU vectors

* Fluids: Fixed the memory leak caused by Physics struct

* Fluids: style -minor

* Fluids: no need for casting

* Fluids: Fix mem leak (q0_ceed had to be destroyed at the end of navierstokes.c)

* Fluids: Fixed all mem leaks

* Fluids: Set VecType for dm_hierarchy

* Fluids/doc: fix style

* Fluids: fix missing VecRestoreArray()

* Fluids: clean-up ComputeLumpedMassMatrix()

* Fluids: Cleanup ICs_FixMultiplicity()

* Fluids: WIP - cleanup setupts.c

* Fluids: style - minor

* Fluids: Create element coord ceed vector locally and drop it from CeedData

* Fluids: fix some todos

* Fluids: drop unused code for EULER BCs

* Fluids: PetscMalloc1 -> PetscCalloc1

* Fluids - Define BCs for ADVECTION(2D) for all cases without having the user specify them and change the regressions accordingly

ToDo: For some reason I can't create new regression tests for explicit scheme.

* Fluids - Define problem->print_info() for each problem

* Fluids: Shorten some problem specific command line variables & style

* Fluids - Cleanup BCs in the translation mode

* Fluids - cleanup

* Fluids - more cleanup in BCs

* Fluids - Updated doc, README, and cleanup in the code and cl options

* Fluids - add more regression tests

* Fluids - Define tolerance for the convergence test

* Fluids: include x_coord in CeedData

* wip - gpu

Revert "Fluids: include x_coord in CeedData"

I had to revert this commit since it crashes DC

* style

* Fluids - remove unused variables

* Fluids - fix unused function warnings

* Fluids - fix the remaining warnings

* Fluids - style

* Fluids - add missing licence

* Fluids - bring back contexts to the QFunction header files

* Fluids - transfer QFunctions for boundary integral to their corresponding setupgeo(2d).h header files and add description for Setup2d

* fluids - fix context data sizes

* GPU - add helper function macro

* ex - use consistent MPI info output

* GPU - improve CEED_QFUNCTION_HELPER macro, more flexible

* Fluids - turn on some gpu tests

* Fluids - bring back element coordinate to CeedData

* Fluids - cleanup

* qfunction - clean up helper function macro

* Fixed the remaining conflicts from #769 (helped-by: @rezgarshakeri)

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>

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