Composite Operator support for AssembleLinearDiag/PBDiag (#552)

* ref - add composite operator support for building diagonal/pb diagonal

* ref - add error for non-composite mult-field operator di

Composite Operator support for AssembleLinearDiag/PBDiag (#552)

* ref - add composite operator support for building diagonal/pb diagonal

* ref - add error for non-composite mult-field operator diagonal/pb diagonal assembly

* tap - add t538 exclusion because OCCA does not support galleries

* tests - adjust test cases for ceed examples for test coverage

* Op - fix documentation

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Restriction - convert restiction to use offsets instead of interlace mode. CPU and Python impl only, CUDA and MAGMA left to do.

Remove inclusion of ceed.h in examples/ header files

Jupyter-notebook tutorials and docs: Update mathematical description of standalone libCEED examples

Add double inclusion guard in examples/ceed header files

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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ex2-surface: fix documentation

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

Jed/intel compiler

make: support CEED_LDFLAGS for things like -dynamic on Cray

Fix doc conflicts after updates in PR #474

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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Jupyter-notebooks and User Manual: Use consistent notation for the linear and bilinear forms in ceed/ex2 math formulation

doc: split examples into separate files in the source tree

* Copy examples/**.rst into the source directory so they can be picked
up by Sphinx.
* Some minor corrections/clarifications to docs that

doc: split examples into separate files in the source tree

* Copy examples/**.rst into the source directory so they can be picked
up by Sphinx.
* Some minor corrections/clarifications to docs that I noticed while
splitting them apart (shame on me for bundling in this commit).

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PETSc BPs on the cubed-sphere (#463)

* Add setupsphere.c and bpssphere.c and improve doc of area problems

* Improve doc of area.c

* Areasphere: improve doc

* Update Makefile for bpssphere

PETSc BPs on the cubed-sphere (#463)

* Add setupsphere.c and bpssphere.c and improve doc of area problems

* Improve doc of area.c

* Areasphere: improve doc

* Update Makefile for bpssphere

* Use Sqr define in area/areasphere.okl

* BPs on the sphere: Add BP1 and BP2

* Update ./gitignore for bpssphere

* BPs on the sphere: Use MatSetNullSpace for Laplace operator

* BPs on the sphere: Add BP3

* Style fix in navierstokes.c

* ceed/ex2-surface: remove ununsed M_PI_2 define

* BP3: Use different rhs and true_soln functions

* bpssphere: normalize quadrature point coordinates to sphere

* Remove extra DMSetFromOptions() call in SetupDMByDegree function

* Add bp3sphere.okl

* Update bpssphere problems after interface change in PR #447

* Make style

* Update TESTARGS

* Fix make style change

* Slightly increase the tolerance for test_mode

* Update bp2sphere.h and bp2sphere.okl with asymmetric formulation consistent with PR #464

* Add BP4

* Enable BP5/BP6

* Add bp4sphere.okl and style

* Update after Strided Restrictions and latest updates in PETSc

* change booleans to PetscBooleans

Not to be pedantic, but this change was suggested by my IDE ^_^

* examples: s,pysical,physical, and small comment

* Simplify unnecessary bidimensional matrices

Co-authored-by: jeremylt <jeremy.thompson@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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ElemRestriction - add CEED_ELEMRESTRICTION_NONE so we can stop making dummy restrictions for CEED_EVAL_WEIGHT fields

Restriction - add CEED_STRIDES_BACKEND

Restriction - replace identity restrictions with strided restrictions

ElemRestriction - make lmode a separate enum

Examples - initalize variable to silence compiler warning

ElemRestriction - move lmode to constructor over apply

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

Examples - fix missing free in ex2

Operator - add QFUNCTION_NONE