doc: update intersphinx link for Python to squash warning

Merge pull request #708 from CEED/Add_ftr_cur_config

examples/solids: add current configuration for residual and Jacobian

* Add_ftr_cur_config:
examples/solids: Add residual and Jacobian in curre

Merge pull request #708 from CEED/Add_ftr_cur_config

examples/solids: add current configuration for residual and Jacobian

* Add_ftr_cur_config:
examples/solids: Add residual and Jacobian in current configuration
Stricter field checking and better error messages

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examples/solids: Add residual and Jacobian in current configuration

There are some benefits to evaluating residuals and/or Jacobians in
current configuration. This includes simpler representation of

examples/solids: Add residual and Jacobian in current configuration

There are some benefits to evaluating residuals and/or Jacobians in
current configuration. This includes simpler representation of body
forces and contact, as well as lower storage and lower arithmetic in the
Jacobian action. We add these implementations as well documentation to
derive their representations via linearize-then-pushforward and
pushforward-then-linearize.

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

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Merge pull request #681 from CEED/jed/doc-fixes

doc fixes

doc: use pre-release KaTeX with amscd (commutative diagrams)

This (newly-merged feature) gets us nicer formatting for the commutative
diagram in examples/solids and will likely come in handy elsewhe

doc: use pre-release KaTeX with amscd (commutative diagrams)

This (newly-merged feature) gets us nicer formatting for the commutative
diagram in examples/solids and will likely come in handy elsewhere.

https://github.com/KaTeX/KaTeX/pull/2396

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doc: use KaTeX recommended way to consolidate macros

https://github.com/hagenw/sphinxcontrib-katex#latex-macros

Merge pull request #671 from CEED/origin/jed/ci-github-ubuntu-20.04

CI: move GitHub Actions to ubuntu 20.04

sphinx: prepare for sphinxcontrib-bibtex 2.0, but pin to <2.0

The new sphinxcontrib-bibtex supports parallel building and requires the
listing of all *.bib sources in bibtex_bibfiles, but it also re

sphinx: prepare for sphinxcontrib-bibtex 2.0, but pin to <2.0

The new sphinxcontrib-bibtex supports parallel building and requires the
listing of all *.bib sources in bibtex_bibfiles, but it also requires
that sphinx be run twice, first to generate a bibtex.json file and then
again to insert the references. I don't know a clean way to do this on
ReadTheDocs so let's stick with 1.x until this issue is resolved or we
need new features.

https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/215

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Merge branch 'master' into valeria/NSfixes

Merge pull request #533 from CEED/jed/activate-hoverxref

Jed/activate hoverxref

doc: activate hoverxref after RTD update

Merge pull request #523 from CEED/jed/breathe-4.17

Jed/breathe 4.17

doc: switch to Breathe 4.17 and C domain

Solids - Add Twist BCs and Strain Energy (#504)

* Solids - add strain energy computations

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

Co-authored-by: Arash Mehraban <arashm81@gmail.com>

*

Solids - Add Twist BCs and Strain Energy (#504)

* Solids - add strain energy computations

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

Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - add multi-direction clamp translation

* Solids - add clamped boundary rotation

* Solids - use KSPCG, not KSPPREONLY for degree=1 to get correct convergence

* Solids - add strain energy density to documentation
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - wJ->wdetJ

* Solids - specify direction of constant forcing function

* Solids - error on hyperFS and constant forcing

* Solids - fix PCMG printing

* Solids - fix translation boundary condition cl option

* Solids - refactor bcs to allow translation and rotation, set bc_zero as default for bc_clamp

* Solids - update documentation discussion of energy density

* make style

* Solids - update sample runs at top of file

Co-authored-by: Arash Mehraban <arashm81@gmail.com>

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make style

doc: disable hoverxref until upgrade + sphinx-3.0 support is ready

Merge pull request #502 from CEED/jed/python-autopep8

Python: apply autopep8 and add to CI

Small doc fixes (#499)

* A small shift in notation

* Docs: Clarify ex2-surface mathematical description

* Refactor \boldsymbol -> \bm

* Refactor \mathbf -> \bm

* Sphinx: clear html_stati

Small doc fixes (#499)

* A small shift in notation

* Docs: Clarify ex2-surface mathematical description

* Refactor \boldsymbol -> \bm

* Refactor \mathbf -> \bm

* Sphinx: clear html_static_path

This is needed to avoid the 'html_static_path entry '_static' does not exist' warning

https://github.com/readthedocs/readthedocs.org/issues/1776

* Fix some incosistencies

* Invert inner products (u,v) -> (v,u)

* Add SVG figure for coordinates on the sphere

* doc: use dirhtml on readthedocs

* Improve caption of sphere coords figure

* Add reference to figure in the bps on the cubed-sphere section

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

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Python: apply autopep8 and add to CI

Merge pull request #496 from CEED/v0.6changelog

v0.6: Release notes

libCEED-0.6

Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>

Merge pull request #494 from CEED/valeria/update-README

Update READMEs

Doc: exclude examples/README.rst

This is needed otherwise sphinx launches a warning about the examples/README.rst file not being included in any toctree

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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