petsc - use DMPlexGetLocalOffsets for building restrictions

petsc - use PetscFECreateLagrange

Solids: fixed duplicate definitions in structs.h

qf - drop unneeded guards on math.h

examples/solids: fix typo

Solids - Fix default number of faces in the box mesh

solids - refactor to separate problem formulations

minor - folder name consistency

Merge pull request #703 from CEED/jed/doc-myst-nb

doc: replace recommonmark with MyST

doc: fix Altair plots by finding source files from DOCUTILSCONFIG

The current directory is different in ReadTheDocs builds than in local
builds. This environment variable specifies where conf.py liv

doc: fix Altair plots by finding source files from DOCUTILSCONFIG

The current directory is different in ReadTheDocs builds than in local
builds. This environment variable specifies where conf.py lives in both
cases, and thus allows finding inputs relative to this directory.

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doc: move from {math:numref} to {eq} (no visual change)

doc: replace ReST tables/list-table with MyST

added Matinverse function

clean-up

doc: replace recommonmark with MyST and migrate ReST to MyST

This offers more familiar syntax for most writing, as well as natural
$\pi$ math (versus :math:`\pi`) and markdown syntax for all ReST
fe

doc: replace recommonmark with MyST and migrate ReST to MyST

This offers more familiar syntax for most writing, as well as natural
$\pi$ math (versus :math:`\pi`) and markdown syntax for all ReST
features.

The API doc stubs remain in ReST as recommended for autodoc.

https://myst-parser.readthedocs.io/en/latest/sphinx/use.html#use-sphinx-ext-autodoc-in-markdown-files

The change was largely implemented using
https://github.com/executablebooks/rst-to-myst/ with some manual
fix-ups. Tables (both ReST built-in tables and list-table) remain under
eval-rst until they can be manually updated.

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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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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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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>

show more ...

Update examples/solids/index.rst

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

update documentation

added computeJM1 function instead of computeDetCM1 function

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

petsc - new compatibility macro for DMAddBoundary

style - minor

style - updating C variable style