Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning u

Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* WIP: Notes on using finite differencing for dS

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* remove extra print statement

* added coulped MR FSInitial-MRc qfunction

* MR coupled version doc update

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* fixed some typo

* rerunning plot files

* Mooney-Rivlin coupled model

* some minor changes

* Mooney-Rivlin coupled model

* some clean-up and update

* clean-up, rebased

* examples/solids: revise docs/derivation and fix Newton

The (fixed) Newton linearization yields an indefinite operator causing
Newton to fail (so output/MR-strain1.csv is broken). This can be handled
by switching to minres, but a better solution would be nice.

* format: added newlines and removed unused/commented code blocks

* doc: removed GP model dropdown.

* examples/solids: Mooney-Rivlin docs/notation

* examples/solids: Mooney-Rivlin notation and experimental configuration

* examples/solids: process -dm_plex_box_faces with PETSc main

* make style

* examples/solids: syntax fix and minor cleanup

* make style

* doc: fixing Holzapfel ref in Mooney-Rivlin

* added TESTARGS for Mooney-Rivlin

* fixed TESTARGS for MR

* tests/tap.sh: make test for solids examples with names

* WIP: adding test option. added -expect_final_strain_energy and RegressionTests_solids function but not sure how to actually pull the reference strain energy from the reference file

* examples/solids: add regression tests using expected strain energy

* examples/solids: error on MMS with model that does not provide manufactured solutions

* examples/solids: fix HIP via CEED_QFUNCTION_HELPER

* update in-line comments

* changed as Jeremy suggested

* examples/solids: make style

Co-authored-by: Rezgar Shakeri <Rezgar.Shakeri@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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ex - fix vla/fixed length mismatches

git - add *.a to petsc gitignore

examples/fluids/README.md: fixed the link (from #754)

Merge pull request #766 from CEED/jed/rust-crates

rust: split crates into libceed-sys and libceed

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 d63eecaab22a26d3072677a1b66c0cf77aa9009d

* 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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Merge pull request #770 from CEED/jed/cuda-ci

gitlab-ci: add lv-cuda

make: consolidate examples/petsc utilities into library to avoid races

Parallel recursive make races itself building the utilities when
creating multiple executables, so consolidate so invocations n

make: consolidate examples/petsc utilities into library to avoid races

Parallel recursive make races itself building the utilities when
creating multiple executables, so consolidate so invocations never build
overlapping targets.

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examples/solids: rewrite Cauchy-Green (b-I) in terms of grad(u)/Green-Euler strain for better stability (#769)

* FSCurrent-NH1.h: rewrite (b-I3) in terms of Grad(u)

* fixed the error

* rewrite

examples/solids: rewrite Cauchy-Green (b-I) in terms of grad(u)/Green-Euler strain for better stability (#769)

* FSCurrent-NH1.h: rewrite (b-I3) in terms of Grad(u)

* fixed the error

* rewrite (b-I3) in terms of Grad(u) in FSCurrent-NH2.h

* update documentation

* doc: defined Green_Euler strain tensor

* Update examples/solids/index.rst

Co-authored-by: Jed Brown <jed@jedbrown.org>

* added eq numbers in tip

* Update examples/solids/index.rst

Co-authored-by: Jed Brown <jed@jedbrown.org>

Co-authored-by: Jed Brown <jed@jedbrown.org>

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petsc - fix deps for parallel build of petsc example

Merge pull request #764 from CEED/jeremy/ci-exit

junit - set CEED_ERROR_HANDLER to exit

doc - rename tutorials folder to match use of language name

rust - clean up workspace split

Update examples/solids/index.rst

Co-authored-by: Jed Brown <jed@jedbrown.org>

update documentation

added computeJM1 function instead of computeDetCM1 function

petsc - clean up some header inclusions

examples: fix DMAddBoundary for petsc-3.16 (next release) API change

petsc - new compatibility macro for DMAddBoundary

style - minor

petsc - drop mesh dir in petsc examples

style - use one sentence per line in docs for petsc examples

style - update to new style for petsc examples

petsc - move Kershaw transformation to petscutils

petsc - rename header guards for consistency