Merge pull request #510 from CEED/jed/sphinx-3.0

doc: upgrade to sphinx-3.0

doc: add Sphinx build to make distclean

Suggested-by: Jeremy L. Thompson <jeremy.thompson@colorado.edu>

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

Python: apply autopep8 and add to CI

Python: apply autopep8 and add to CI

Merge branch 'jed/fix-CC_VENDOR-ubuntu' [PR #501]

* jed/fix-CC_VENDOR-ubuntu:
make: another fix for CC_VENDOR on Ubuntu
make: fix CC_VENDOR identification on Ubuntu

make: another fix for CC_VENDOR on Ubuntu

make: fix CC_VENDOR identification on Ubuntu

ubuntu$ gcc --version
gcc-9 (Ubuntu 9.2.1-9ubuntu2) 9.2.1 20191008
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the sourc

make: fix CC_VENDOR identification on Ubuntu

ubuntu$ gcc --version
gcc-9 (Ubuntu 9.2.1-9ubuntu2) 9.2.1 20191008
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

versus

arch$ gcc --version
gcc (Arch Linux 9.3.0-1) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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Merge pull request #491 from CEED/jed/intel-compiler

Jed/intel compiler

make: cc_check_flag -Werror because clang only warns for wrong flag

make: support CEED_LDFLAGS for things like -dynamic on Cray

make: better default flags by vendor

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 #487 from CEED/jed/python-packaging

Jed/python packaging

python: switch from manylinux2014 to manylinux2010 (for older pip/machines)

python: use default MARCHFLAG for build; set -march=generic for wheels

Suggested-by: Lisandro Dalcin <dalcinl@gmail.com>

python: install libceed.so and headers with Python; make wheels

* Install libceed.so and obtain at run-time via $ORIGIN
* Updates some nonconforming package metadata
* Use Docker with cache for buil

python: install libceed.so and headers with Python; make wheels

* Install libceed.so and obtain at run-time via $ORIGIN
* Updates some nonconforming package metadata
* Use Docker with cache for building manylinux2014 wheels
* qfunction extensions don't call libceed.so directly; can get include
path from libceed module

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Merge pull request #484 from CEED/valeria/doc-fixes

Doc fixes

Merge branch 'valeria/doc-fixes' of github.com:CEED/libCEED into valeria/doc-fixes

AUTHORS: trim by significance and explain rationale

Merge pull request #477 from CEED/jed/mtune-native

make: MARCHFLAG: try -march=native, -mcpu=native, then skip (fix #467)

make: MARCHFLAG: try -march=native, -mcpu=native, then skip (fix #467)

Pass OPT from top-level to examples/* that need OPT set.

Reported-by: Yohann Dudouit <dudouit1@llnl.gov>

Merge pull request #475 from CEED/jeremy/make-style-fix

Fix Make Style (....Again)

Merge pull request #472 from CEED/jed/config

Jed/config

make: detect vendor, -fopenmp-simd, and AVX for clang (previously only gcc)

Co-authored-by: Veselin Dobrev <dobrev@llnl.gov>