updated ICs and comments, still need to figure out BCs

Initial commit for adding euler traveling vortex test; ICs and BCs to be added

Fluids - More Regression Tests (#687)

* examples/fluids: Regression tests: Changed the reference files' names and
the flags to associate with the corresponding example (so far
density_current only

Fluids - More Regression Tests (#687)

* examples/fluids: Regression tests: Changed the reference files' names and
the flags to associate with the corresponding example (so far
density_current only)

Changed the files' names

Changed the flags

* examples/fluids: added new regression tests for advection(2d)

* examples/fluids: regression tests: removed the enums and passed defined command-line options for filepath and test tolerance.
Removed solver controls and assigned testtol=1E-11 for explicit cases.

style

examples/fluids: regression tests: fixed the pathfile issue (it needs to be relative)

examples/fluids: Specified a name for each test

examples/fluids: TESTARGS - trying absolute path for the test files

* tests/tap.sh: Print out test names for fluids examples

inspired-by: @jeremylt

tests/tap.sh: drop quotation marks from the printed test names

* tests: specify test name for ceed and nek examples and print the names when there are multiple test arguments

* examples/fluids: remove test_ from test names

* style

* tests/junit.py: Add name for tests with multiple test cases

* examples/ceed/ex1-volume.c: make the naming of the tests consistent

* tests/junit.py: a more compact if statement

helped-by: @jeremylt

* examples/fluids: drop the broken supg test of density_current for now

The stabilization enum is not passed to density_current QFunction hence
the test doesn't work. We need to create a new test when the code is
debugged.

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Merge pull request #714 from CEED/leila/ex-output-dir

Fluids & Solids | add/modify cl options for viz output folder

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz outpu

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz output

change: output folder -> output directory

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

examples: change variable name outputfolder -> outputdir

examples: update the README files

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headers - clearify includes to not rely on transitive includes (#701)

* headers - clearify includes to not rely on transitive includes

* style - add header recommendations from 'include-what-you-

headers - clearify includes to not rely on transitive includes (#701)

* headers - clearify includes to not rely on transitive includes

* style - add header recommendations from 'include-what-you-use'

* style - apply 'include-what-you-use' changes to CUDA backends

* style - 'include-what-you-use' for hip backends

* style - drop ceed.h includes in gallery qf source

* docs - add dev notes for header files

* style - header style and alphabetize

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Merge pull request #685 from CEED/jed/fluids-squash-warnings

examples/fluids: squash -Wmaybe-uninitialized

examples/fluids: squash -Wmaybe-uninitialized

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

OCCA - update backend resource names to match conventions

QFunction Context Data Object (#596)

* Ctx - create context object for QFunction context data

* Context - rename UserContext -> QFunctionContext

* Ctx - add lcov markers

* Ctx - fix leak in

QFunction Context Data Object (#596)

* Ctx - create context object for QFunction context data

* Context - rename UserContext -> QFunctionContext

* Ctx - add lcov markers

* Ctx - fix leak in identity QFunctions

* Hip/Cuda - rename sync functions for vector/context

* Tests - lcov marker update

* QFunction - drop unused function

* Python - fix copy-paste errors

* Ctx - update notes for Fortran usage

* Fortran - drop unneeded cast

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

* Interface - use void* for SetData interfaces

* Make - use call quiet for NVCC

* Interface - use void* for GetData interfaces

* Make - add quiet call option for examples

* Makefile - create common makefile to reduce duplication/complexity in example makefiles

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

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PETSc examples: Update DMPlexCreateSphereMesh() and DMAddBoundary() calls after changes in PETSc's API (#600)

* PETSc examples: Update DMPlexCreateSphereMesh call after change in API

* PETSc bps:

PETSc examples: Update DMPlexCreateSphereMesh() and DMAddBoundary() calls after changes in PETSc's API (#600)

* PETSc examples: Update DMPlexCreateSphereMesh call after change in API

* PETSc bps: Update DMAddBoundary() call after change in API

* Add compatibility macros

* solids/ and fluids/ : Update DMAddBoundary() call and add compatibility macros

* Travis: Update PETSc ref with latest hash from master

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Merge branch 'leila/bc' [PR #540]

* leila/bc: (57 commits)
examples/fluids: fix doc
examples/fluids: comments on ICs and BCs & style
NS: style
examples/fluids: CreateRestrictionFromPlex: han

Merge branch 'leila/bc' [PR #540]

* leila/bc: (57 commits)
examples/fluids: fix doc
examples/fluids: comments on ICs and BCs & style
NS: style
examples/fluids: CreateRestrictionFromPlex: handle empty domainIS
examples/fluids: style
examples/fluids/advection.h: spherical bubble is the default IC
examples/fluids: style
examples/fluids/advection.h: fixed in/outflow signs for implicit scheme
examples/fluids: comments
examples/fluids: PetscBool -> bool in QFunctions
examples/fluids: removed periodicity from the setup struct
examples/fluids: clear DS and fields in -viz_refine
examples/fluids/setup-boundary.h: comment
examples/fluids/advection2d.h: removed unused variables
doc/NS: update
examples/fluids/advection.h: spherical bubble is the default IC
examples/fluids: fix sign and simplify advection2d inflow/outflow for implicit/explicit
examples/fluids: u_* = u_R on inflow boundaries
doc: added representative runs for TRANSLATION mode
examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind
...

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examples/fluids: fix doc

examples/fluids: comments on ICs and BCs & style

NS: style

examples/fluids: CreateRestrictionFromPlex: handle empty domainIS

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

examples/fluids: style

examples/fluids/advection.h: spherical bubble is the default IC

examples/fluids: style

examples/fluids/setup-boundary.h: fix style

examples/fluids/advection.h: fixed in/outflow signs for implicit scheme

examples/fluids: comments

examples/fluids: fixed the comments on outflow BCs

examples/fluids/setup-boundary.h: fix comments

examples/fluids: updated comments on ICs and BCs

examples/fluids: PetscBool -> bool in QFunctions

examples/fluids: removed periodicity from the setup struct

examples/fluids: clear DS and fields in -viz_refine

Reported-by: Leila Ghaffari <leila.ghaffari@colorado.edu>

examples/fluids/setup-boundary.h: comment