Merge pull request #1920 from CEED/jeremy/hoverxref

Doc - remove hoverxref

doc - remove hovverxref; its deprecated

doc - remove sphinx warning

Merge pull request #1226 from CEED/jed/fix-doc-math

doc: fix math in headers

doc: fix math in headers

There is a bad hyperref/unicode-math interaction apparently resulting
from how PDF bookmarks work. This replaces math in headers (section
titles) with unicode Greek letters

doc: fix math in headers

There is a bad hyperref/unicode-math interaction apparently resulting
from how PDF bookmarks work. This replaces math in headers (section
titles) with unicode Greek letters to fix doc-latexpdf.

https://tex.stackexchange.com/questions/570000/improper-alphabetic-constant-error-in-title-with-greek-bug-with-unicode-math-an

show more ...

Merge pull request #1215 from CEED/jed/altair-sphinxext

doc: update to altair-5.0 and sphinext-altair

doc: update to altair-5.0 and sphinext-altair

https://github.com/altair-viz/altair/issues/3051#issuecomment-1546730887

Merge pull request #1162 from CEED/jed/doc-update-packages

doc: update packages

doc: remove unnecessary breathe path hack

https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/283#issuecomment-1028446347

doc: switch from sphinx-panels (deprecated) to sphinx-design (#1161)

Merge pull request #1124 from CEED/jed/release-0.11

Release 0.11

doc: use lualatex and unicode-math for font consistency in pdf manual

Due to a mix of older packages, our math rendered with Computer Modern
rather than the intended TeX Gyre Pagella Math (a font ma

doc: use lualatex and unicode-math for font consistency in pdf manual

Due to a mix of older packages, our math rendered with Computer Modern
rather than the intended TeX Gyre Pagella Math (a font made to go with
our main text). The bm package does not work with unicode-math so we
provide a replacement for consistency with KaTeX.

show more ...

Merge pull request #1104 from CEED/jeremy/formatting

Minor Formatting Fixes

doc - fix myst_url_schemes type

Merge pull request #1046 from CEED/jeremy/doc-warning

doc - fix ref warning for hoverxref_role_types

doc - fix ref warning for hoverxref_role_types

Merge pull request #1045 from CEED/jed/fix-docs

fix docs

doc: fix warnings and malformed hyperlink target

Merge pull request #962 from CEED/jed/fluids-jacobian

examples/fluids: add analytic Jacobian

doc: support Sphinx-5 and fix man page

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

doc: replace recommonmark with MyST

doc: provide altair-plot.css for ReadTheDocs

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.

show more ...

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>

show more ...

Merge pull request #748 from CEED/jed/doc-linking

Improve documentation linking