ex - update example folder Readmes

Merge pull request #1829 from CEED/jeremy/documentation-markers

Use HTML comments as doc inclusion markers

doc - use HTML comments as inclusion markers

doc - hide inclusion markers in md

Merge pull request #1008 from CEED/jeremy/doc-fixes

Small Doc Fixes

doc - update style since I'm touching the file

Merge pull request #915 from CEED/jed/libceed.org

Update links to https://libceed.org

Update links to https://libceed.org

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

doc: replace recommonmark with MyST

doc: replace ReST tables/list-table with MyST

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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Merge branch 'master' into valeria/jupyter-notebook-tutorials

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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Merge pull request #469 from CEED/jed/doc-examples

Jed/doc examples

Update examples/README

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update READ

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update README: remove density_current_primitive problem option for now
Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive
Remove a bunch of unused or double-declared variables
Update README
NS: use const in VLA casts to suppress icc warning
NS: add command-line support for specifying DC center/axis
NS: return to insulated no-slip walls instead of full-Dirichlet
NS: remove dead code for scaling VTK output back to dimensional units
NS: add support for free slip wall boundary conditions
NS density_current: remove redundant initial/boundary condition and trailing whitespace
Some changes in documentation
Update top-level README
Update examples/README
Update examples/navier-stokes/README
Update .gitignore
Update documentation
Initialize *problem pointer as NULL
NS: move nsplex.c to navierstokes.c
...

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Update examples/README

Rename ceed examples and minor doc changes (#442)

* Rename ex-1 -> ex1-volume, ex2 -> ex2-surface and add ex2-surface.okl

* Update READMEs

* Update doc

PETSc example: Areasphere (#439)

* Initial development of area sphere

* Update examples/ceed/.gitignore with ex2

* Fix file path for OKL files

Add PETSc example areaplex (#394)


Update bps files with new subfolders structure

* Add header h and okl files

* Update REAMDE.md

QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

* Gallery - add initial QFunctions

* Add a test for using the QF gallery

* Modify ex1 to use gallery

* Add multiple test configs to tap

* Move output to test directory

* Update junit

* Add OCCA galley exception

* Add ex2

* Update ex2 for dim->ncompx

* Gallery - modify to work for CUDA as is

* Update Documentation

* Gallery - typo fix

* Gallery - convention change, postappend qfunction family variant

* Gallery - update template with new name checking convention

* Gallery - condense diff3DBuild QFunction

* Gallery - rename diff -> poisson

* Gallery - clarify poisson3DBuild comment

* Gallery - use Pragma SIMD, store Qdata in Voigt convention

* Examples - Convert BP3-6 to Voigt convention

* Examples - add cl option to switch between header and gallery qfs in CEED examples

* Examples - clean up construction of QF name

* Gallery - Switch to PascalCase for gallery names

* Doc - fix function type page

* Interface - Make sure strncpy result is null terminated

* Gallery - Update Poisson 2/3D Apply to new QF body

* make style

* make style - fix worst style problems

* make style - add gallery to make style

* Doc - update documentation errors and inconsistencies

* Examples - test ex1 ex2 with and without gallary

* Examples - reduce testing of ex1/ex2 without gallery, clean up non-gallery qfunctions

* MFEM - revert another make style mistake

* Manual make style updates

* Doc - update function documentation page

* Style updates, document test numbering conventions

* doc: resolve ambiguous image location warning, allow more Dot nodes

* Tests - style and cast cleanup

* Tests - fix README indentation

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Merge pull request #300 from CEED/jeremy/doc-fix

README: Update corectness for examples

README: Update corectness for examples

Update nek5000 example scripts (#241)

* Update nek5000 examples to use NEKTOOLS_DIR

* Remove +x

* Nek: Fix a bug in generate-boxes.sh script

* Use one script for nek exaamples

* Update m

Update nek5000 example scripts (#241)

* Update nek5000 examples to use NEKTOOLS_DIR

* Remove +x

* Nek: Fix a bug in generate-boxes.sh script

* Use one script for nek exaamples

* Update make-nek-tests.sh

* Update nek-examples.sh

* Change permissions of make-nek-tests.sh

* Update examples Makefile to use new nek script

* Update nek5000 examples build process

* Trying to make travis happy

* Polishing the script

* This should make Travis happy

* Polish nek-examples.sh

* Update examples/Makefile

* Update top-level makefile

* Delete make-nek-tests.sh & update nek-examples.sh

* Update Makefile and examples/Makefile

* Update nek-examples.sh

* Update TESTARGS in bp .usr files

* Update Makefile

* Update .travis.yml

* Update nek-examples.sh

* Add CEED_DIR to tap.sh

* Uncomment OCCA_DIR in Makefile

* Fix make prove and update tap.sh

* Pass NEK5K_DIR and CEED_DIR in prove-all

* Set MPI=0 default for Nek examples/tests

* Nek5K make updates

* Make prove update

* Update make-prove to make all ex except Nek5K in parallel

* Set Nek5K examples to use MPI by default

* Makefile: Improved Nek5k handling

* Makefile: build Nek bps in separate directories

* Nek: rename dir for f77 file length

* debugging

* Nek: use single source

* Makefile: fix Nek mpif.h issue

* Nek: Clean up build proces, improve documentation

* Makefile: enable building single Nek example in parallel with other examples

* Nek: Fix CC/FC and TESTARGS

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Merge branch 'master' into yohann/cuda-restr-opt

Conflicts:
backends/cuda-reg/ceed-cuda-reg-restriction.c
backends/cuda-shared/ceed-cuda-shared-basis.c