Merge MR !153, 'jrwrigh/checkbadSource', into 'main'

style: Add checkbadSource

See merge request phypid/honee!153

style: Add checkbadSource

Modified from PETSc's checkbadSource

Merge branch 'jrwrigh/fix_compiler_warnings' into 'main'

fix: Address GCC compiler warnings

See merge request phypid/honee!14

chore: Add *.json, others to .gitignore

Mostly for ignoring `compile_commands.json`, but presumably useful for
other things too

Merge branch 'jrwrigh/make_docs' into 'main'

Enable documenatation building

See merge request phypid/honee!5

doc: Get documentation running

chore: Get tests back up and running

Fluids - Minor Refactor (#995)

* Fluids - remove *.bin* since it exists in libCEED/.gitignore

* cleanup

* WIP: Fluids - use FluxInviscid_fwd() for computing the flux jacobean

strong_conv is

Fluids - Minor Refactor (#995)

* Fluids - remove *.bin* since it exists in libCEED/.gitignore

* cleanup

* WIP: Fluids - use FluxInviscid_fwd() for computing the flux jacobean

strong_conv is not reproduced and stab is not computed correctly

* WIP: working on variational notation for stabilization

* Fluids - fix missing parts after rebasing onto main

* Fluids - fix SU in the IFunction

* Fluids - refactor stabilization

* Fluids - move stab helper functions to stabilization.h

* Fluids - minor style

* Fluids - minor refactor

* Fluids - add regression test for primitive variables

* Fluids - use UnpackState_*()

* Fluids - more refactoring of stabilization

* Fluids - DC: use utility functions

* Fluids - refactor total flux

* Fluids - minor cleanup

* Fluids - set x[0] = 0 for channel to exclude gravitational potential

* Fluids - updated stabilization.h

* Fluids - zero strong_conv before pass it to FluxInviscidStrong() to be safe

* Fluids - move switch-case for STAB to a helper function

* Fluids - rename Y -> R in Stabilization*()

* Fluids - fix stab sign in RHS

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

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examples/fluids: added *.csv to gitignore

gitignore: adding *.png for ignoring convergence plots

examples/fluids: added a bash file to get verification test results in .log files. TODO: add test flags to be able to change the test setup through run time arguments.

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-au

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>


* Solids - initial commit of elasticity example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - add VLA macro

* Solids - fix test for mesh file output string

* Solids - update documentation

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - update README

* Solids - update ctx struct and casting for CUDA

* Tests - clean up test conditions for GPU backends

* GPU - fix falbacks identified

* CUDA - whitelist FDM Inverse

* make style

* doc: solids editing/correctness

* Solids - separate FE boilerplate into its own function

* Solids - clean up double includes

* doc: add more complete explanation of hyperelasticity and formulation

* Solids - Use ISGetSize for global number of face sets (had no effect on PETSc bug in MR 2615)

* edited docs for hyperFS

* Improve doc of solids example with some constitent notation and fonts

* HyperSS docs modified

* edited typo

* linearization added

* fixed a typo

* Improved doc

* doc: more writing on hyperelasticity and implementation tradeoffs

* Solids - fix typo

* Solids - compute and store C, Cinv, and S as symmetric

* Solids - use new Newton linearization, but its not converging

* Solids - update BC handling

* Solids - update README with new BC options

* removed old notation

* Solids - whitespace changes only in documentation

* doc: adjust differential notation and derive dP(dF)

* Solids - small documentation flow edits

* Solids - simplify setting BCs

* Solids - Symmetritize e in SS

* Solids - set more reasonable default number of steps for nonlinear

* Solids - fix documentation typo

* Solids - clean up computation of deltaS

* Solids - fix sample runs

* Solids - fix hyperSS jacobian

* Solids - fix hyperSS documentation

* Solids - clean up code for hyperSS

* Solids - add file and function docstrings

* doc: commutative diagram of linearization and stable stress expression

* Solids - update hyperSS documentation with linearization

* doc: further tips on stable computation

* Solids - fix typo with trace in hyperSS

* Solids - intro and hyperSS documentation updates

* Solids - update hyperFS for numerical stability with small E and nearly incompressible

* examples/solids: simpler C = I + 2E

* Solids - more compact/readable E computation

* Solids - minor style consistency change

* Solids - replace log1p with series approximation, log1p is not vectorized in libc

* Solids - refactor common components between hyperFSF and hyperFSdF

* examples/solids: use PETSc dependency flags for incremental rebuild

* examples/solids: extend range of log1p_series via shift/scale

* Solids - add bc_clamp_max option to specify maximum displacement for clamped boundary

* make style

* Solids - update with sample run informantion and spellchecking

* Doc - typo fixes

* Solids - homogonize presentation of command line options

* examples/solids: fix -Wmisleading-indentation

* examples/fluids: PETSc 3.13 compatibility

* examples/solids: use log1p for numerical stability in hyperSS

* doc: copy editing in examples/solids

* Solids - update documentation on running the code

* Solids - convert README to rst and include in documentation

* Solids - clean dependency file

* Solids - use log1p approximation in hyperSS as well

* Solids - update README to explain mms

* Solids - switch range on hyperSS log1p series approximation

* Solids - update README to clarify mandatory options

* Solids - add link to sample meshes

* Solids - simplify listing of mesh options

* Travis - use newer PETSc

* Solids - update sample run to list [.exo file] instead of name of sample mesh

* Solids - update make clean to remove src/*.d

* examples/solids: makefile cleanup

* make style

* doc examples/solids: clean up and explain nondimensionalization

* examples/solids: document algebraic solver

* examples/solids: use CG for Chebyshev eig estimation

* doc: fix references to examples/fluids

* Solids - remove mesh folder

* Solids - drop expicit ExodusII requirement, PETSc supports many types of meshes

* doc: mention PETSc --download-exodusii for Exodus

* doc: fix latexpdf

* Fix \longrightarrow rendering in PDF

* Solids - fix toctree link to README for pdflatex

* Examples and BPs Docs: Homogenize math with dS and dV and other tiny esthetics

* Solids - fix unshifted series for hyperSS log1p

* Improve doc of bpssphere: Add differential for consistency with all other examples and explain domain for clarity

* Solids - include sample mesh image

* Move mesh figure after note and slightly rename inclusion marker

Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: valeriabarra <valeriabarra21@gmail.com>

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