make: move -DUNDERSCORE to CPPFLAGS (it is semantically not a CFLAG)

make: support different MKL install schema

Merge pull request #471 from CEED/jeremy/revert-restrict

Interface - use __restrict__ for C++ compatibility

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

Update examples/README

change restrict to __restrict__ for t

Interface - use __restrict__ instead of restrict for C++ compatability

Merge pull request #470 from CEED/jeremy/readme-doc-link

README - update link to API example

README - update link to API example

doc: use latest Sphinx (2.4.4) instead of legacy RTD default

doc: minor reorganization

* Rename Implementation to Interface Concepts
* Move Theoretical Framework into Interface Concepts
* Drop top-level toctree depth from 5 to 4

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.

Merge pull request #446 from CEED/user-manual

Sphinx user manual published at libceed.readthedocs.io

doc: process restrict qualifier as predefined

Breathe and/or Sphinx lacks support for restrict qualifiers, so use
the workaround suggested here to hide the restrict qualifier from
Breathe/Sphinx.

h

doc: process restrict qualifier as predefined

Breathe and/or Sphinx lacks support for restrict qualifiers, so use
the workaround suggested here to hide the restrict qualifier from
Breathe/Sphinx.

https://github.com/michaeljones/breathe/issues/477#issuecomment-593145041

An alternative is to use the C domain for *.c and *.h files. This
handles restrict, but reduces enum names to their numeric value. Once
that Breathe/Sphinx bug is fixed, we could skip the restrict elision
in favor of using the C domain.

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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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doc: separate Doxygen groups by Public API/Backend API/Internal Functions

Helped-by: Valeria Barra <valeriabarra21@gmail.com>
Squashed-by: Jed Brown <jed@jedbrown.org>

python: join lines with '\n' so we don't need to ignore comment lines

The parser handles line comments fine. This also avoids malfunction
in case // comments appear in ceed.h (the former rule exclu

python: join lines with '\n' so we don't need to ignore comment lines

The parser handles line comments fine. This also avoids malfunction
in case // comments appear in ceed.h (the former rule excluded all
lines containing '///' and ignored '//' lines, resulting in all
subsequent lines being ignored).

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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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