doc: provide altair-plot.css for ReadTheDocs

doc: skip CeedPragmaOptimizeOn/Off at Doxygen level

Sphinx does not understand the push/pop model, and this leads to
warnings. It's an idiosyncrasy that I don't think needs to be part of
the Sphinx

doc: skip CeedPragmaOptimizeOn/Off at Doxygen level

Sphinx does not understand the push/pop model, and this leads to
warnings. It's an idiosyncrasy that I don't think needs to be part of
the Sphinx site.

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README: update badge and table style

bib: add DOI

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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Merge pull request #798 from CEED/jeremy/fix-codecov

Add missing codecov exclusions

style - add missing codecov exclusion

Merge pull request #797 from CEED/jeremy/less-output

Refactor tests to reduce use of output

py - refactor tests needing output

tests - refactor t301,302 to not use output

tests - refactor t202,203,208,213 to not use output

Refactor Preconditioning Ingredients (#795)

* op - split preconditioning into separate file

* pc - move FDM to interface level

* pc - initial move of diagonal assembly to interface

* interf

Refactor Preconditioning Ingredients (#795)

* op - split preconditioning into separate file

* pc - move FDM to interface level

* pc - initial move of diagonal assembly to interface

* interface - only return error code or error

* doc - improve preconditioning helper function documentation

* pc - use qdata layout for interface diagonal assembly

* pc - update for consistency in naming, use of CeedChk, and static

* doc - spelling

* style - minor

* doc - add doc for CeedBuildMassLaplace

* doc - update release notes

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

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

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doc - add citing yaml (#796)

* doc - add citing yaml

* doc - add CITATION.cff to release procedures

* doc - add scope to python citation

* docs: revise title/intro of README and CITATION

doc - add citing yaml (#796)

* doc - add citing yaml

* doc - add CITATION.cff to release procedures

* doc - add scope to python citation

* docs: revise title/intro of README and CITATION

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

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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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Merge pull request #793 from CEED/jeremy/vla-ex1-ex2

ex - remove recast of fixed length array as vla

ex - fix vla/fixed length mismatches

Merge branch 'release'

Makefile CC_VENDOR: support cross-compilation strings like aarch64-linux-gnu-gcc-10

Add JOSS paper citation (#790)

* Add JOSS paper link to README and update How-to-cite

* Add JOSS paper to User Manual and references

* Docs: bib format

Co-authored-by: Jed Brown <jed@jedbro

Add JOSS paper citation (#790)

* Add JOSS paper link to README and update How-to-cite

* Add JOSS paper to User Manual and references

* Docs: bib format

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

* Bib: Remove url field

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

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Merge branch 'release'

* release:
Joss paper (#530)

Joss paper (#530)

* [JOSS paper] Initial commit

* Remove double colon in authors field leading to formatting error

* Remove double colon in date field leading to format error

* WIP: Update

Joss paper (#530)

* [JOSS paper] Initial commit

* Remove double colon in authors field leading to formatting error

* Remove double colon in date field leading to format error

* WIP: Update affiliation of other authors

* Remove displaymath mode around align environment

* JOSS: move images in img subdirectory and make some edits

* JOSS: Use pdf image instead of svg

* Update doc/papers/joss/paper.md

Co-authored-by: Valeria Barra <39932030+valeriabarra@users.noreply.github.com>

* JOSS: Mention F77 & Python interfaces - Describe briefly the Python interface

* Add Orszag's citation

* Insert ; between multiple citations

* Update Authors according to user-manual authorship

* Use "University of Colorado at Boulder" as affiliation

* add ORCID for Natalie

* add Jeremy orcid

* Leila orcid

* Update paper.md

Stan orcid

* Add information for Ahmad. I assumed that the names are alphabetically ordered by last names.

* In doc/papers/joss/paper.md, add my orcid id.

* Tzanio

* Orcid update

* Put @jedbrown frist author :)

* Change @dmed256 affiliation

* update orcid for Yohann Dudouit.

* Add some citations

* Typo fix. Thanks-to @tzanio

Co-authored-by: Tzanio Kolev <tzanio@llnl.gov>

* Mention Numba for the Python interface and add related references

* Review feedback: Add CEED website and BP paper citations

* Acknowledgements: Add the full ECP disclaimer

* Update CEED BP paper info now that it's available online

* Use BP1 & BP3 results from Noether

* Update BP figure captions

* Update BP figures with new data

These were run by @jedbrown after he updated Noether's NPS4 BIOS setting

* Add libCEED's SciPy reference

* Add HIP backend

* Add HIP backend

* Update backends image and resize

* [JOSS paper] Initial commit

* Remove double colon in authors field leading to formatting error

* Remove double colon in date field leading to format error

* WIP: Update affiliation of other authors

* Remove displaymath mode around align environment

* JOSS: move images in img subdirectory and make some edits

* JOSS: Use pdf image instead of svg

* Update doc/papers/joss/paper.md

Co-authored-by: Valeria Barra <39932030+valeriabarra@users.noreply.github.com>

* JOSS: Mention F77 & Python interfaces - Describe briefly the Python interface

* Add Orszag's citation

* Insert ; between multiple citations

* Update Authors according to user-manual authorship

* Use "University of Colorado at Boulder" as affiliation

* add ORCID for Natalie

* add Jeremy orcid

* Leila orcid

* Update paper.md

Stan orcid

* Add information for Ahmad. I assumed that the names are alphabetically ordered by last names.

* In doc/papers/joss/paper.md, add my orcid id.

* Tzanio

* Orcid update

* Put @jedbrown frist author :)

* Change @dmed256 affiliation

* update orcid for Yohann Dudouit.

* Add some citations

* Typo fix. Thanks-to @tzanio

Co-authored-by: Tzanio Kolev <tzanio@llnl.gov>

* Mention Numba for the Python interface and add related references

* Review feedback: Add CEED website and BP paper citations

* Acknowledgements: Add the full ECP disclaimer

* Update CEED BP paper info now that it's available online

* Use BP1 & BP3 results from Noether

* Update BP figure captions

* Update BP figures with new data

These were run by @jedbrown after he updated Noether's NPS4 BIOS setting

* Add libCEED's SciPy reference

* Add HIP backend

* Add HIP backend

* Update backends image and resize

* Undo resize because it does not render on their Markdown parser

* Add application examples

* Update latest pubs

* JOSS: Mention Julia interface. Add Will to authors.

* JOSS - add brief description of Rust interface

* JOSS - unify language references

* JOSS - fix bad copy-paste

* joss: fix Numba citation

https://numba.readthedocs.io/en/stable/user/faq.html?highlight=citing#how-do-i-reference-cite-acknowledge-numba-in-other-work

* joss: fix NumPy cite

https://numpy.org/citing-numpy/

* Update bib reference with user manual in place of dev site

* JOSS paper: substantial editing and figure adjustments

* JOSS paper: minor edits

* JOSS paper: fix DOI in bib

* joss - address some review comments

* joss - small wording improvement

* joss - add some preconditioner notes

* Fix Yohann's last name!

Co-authored-by: Yohann <dudouit1@llnl.gov>

* joss - minor updates

* Update libCEED User Manual citation

* joss: fix Thilina's name and add ORCID

* joss: copy edits and citation updates

* joss: fix bib entry

* joss: describe benchmark configuration

* joss: bib capitalization

* joss: adjust heading

Co-authored-by: Jeremy L Thompson <25011573+jeremylt@users.noreply.github.com>
Co-authored-by: nbeams <246972+nbeams@users.noreply.github.com>
Co-authored-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Co-authored-by: Stan Tomov <tomov@eecs.utk.edu>
Co-authored-by: Ahmad Abdelfattah <ahmad@icl.utk.edu>
Co-authored-by: Veselin Dobrev <dobrev@llnl.gov>
Co-authored-by: Tzanio Kolev <tzanio@llnl.gov>
Co-authored-by: camierjs <camier1@llnl.gov>
Co-authored-by: Yohann Dudouit <dudouit1@llnl.gov>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>
Co-authored-by: Will Pazner <will.e.p@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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