Multigrid - simplify diagonal computation logic

PETSc - simplify calls to gather/scatter

PETSc - convert multigrid example to use GAMG on coarse solve

User manual: Add description of PETSc BPs on the cubed-sphere

Update examples/README

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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Merge pull request #466 from CEED/leila/test-on-DC

Add component names (needs current PETSc) and include gravitational potential
energy in energy density state variable.

doc: convert to Sphinx documentation at libceed.readthedocs.io

Some technical notes about the expanded docs/process:

* Doxygen is now restricted to API documentation. Sphinx docs are
incomplete

doc: convert to Sphinx documentation at libceed.readthedocs.io

Some technical notes about the expanded docs/process:

* Doxygen is now restricted to API documentation. Sphinx docs are
incomplete surrogates due to not hyperlinking code listings, though
we hope the Doxygen site can be removed eventually.

* PDF output uses XeTeX (unicode and OTF fonts) with TeX Gyre Pagella
and DejaVu Sans Mono. You may need to install these fonts in order
to build the PDF users manual.

* Obtaining the author list from Git has not worked on
ReadTheDocs (`git shortlog` is empty even though `git log` is not),
so we automatically generate it on developer machines with `make
doc`. If the author information is incorrect/mangled, edit .mailmap
to fix the mapping.

* Math semantics are based on the description here
https://github.com/sphinx-doc/sphinx/issues/3785

Sphinx chooses one of two setups for the maths.

* If there is a single equation, then we wrap the maths in
\begin{equation*} (or equation).

* If there are multiple equations (as determined by the presence of
an empty line), then we wrap the maths first in \begin{aligned}
and then in \begin{align*} (or align).

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

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Make style

NS: update stabilization to avoid dividing by zero

update documentation

Add support for Plex field names

NS: E = internal energy + kinetic energy + potential energy

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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examples/petsc: update for PETSc master

PETSc recently merged a change that replaced the (incorrectly named)
PetscDTGaussJacobiQuadrature() with PetscDTStroudConicalQuadrature().

https://gitlab.com

examples/petsc: update for PETSc master

PETSc recently merged a change that replaced the (incorrectly named)
PetscDTGaussJacobiQuadrature() with PetscDTStroudConicalQuadrature().

https://gitlab.com/petsc/petsc/-/merge_requests/2574

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Style - fix style error

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

Make style

Restriction - add CEED_STRIDES_BACKEND

CPU - fix CPU backend stridiniding for CEED_BACKENDSTRIDE

Restriction - add CEED_STRIDES_BACKEND

Restriction - replace identity restrictions with strided restrictions

PETSc - remove some symmetries in the BP test cases

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update READ

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update README: remove density_current_primitive problem option for now
Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive
Remove a bunch of unused or double-declared variables
Update README
NS: use const in VLA casts to suppress icc warning
NS: add command-line support for specifying DC center/axis
NS: return to insulated no-slip walls instead of full-Dirichlet
NS: remove dead code for scaling VTK output back to dimensional units
NS: add support for free slip wall boundary conditions
NS density_current: remove redundant initial/boundary condition and trailing whitespace
Some changes in documentation
Update top-level README
Update examples/README
Update examples/navier-stokes/README
Update .gitignore
Update documentation
Initialize *problem pointer as NULL
NS: move nsplex.c to navierstokes.c
...

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NS: remove density_current_primitive (still work in progress)

Suggested-by: Valeria Barra <valeriabarra21@gmail.com>
Acked-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>