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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resolve merge conflicts for v0.7 release

Merge pull request #634 from CEED/jeremy/occa-order

OCCA - update backend resource names to match other GPU backends

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 'main' into natalie/hip-ref-v2

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

NS: style

examples/fluids: CreateRestrictionFromPlex: handle empty domainIS

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

examples/fluids: style

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

examples/fluids: clear DS and fields in -viz_refine

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

examples/fluids: u_* = u_R on inflow boundaries

examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind

initial commit for specifying total energy instead of pressure and density for inflow BCs

update navi

examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind

initial commit for specifying total energy instead of pressure and density for inflow BCs

update navierstokes.c

update README

update doc

comments updated

prescribe E_wind = 1.e6

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examples/fluids: some corrections

examples/fluids: qf_Sur -> qf_applySur

examples/fluids: removed unused variable

style

examples/fluids/advection(2d).h: implementing a more readable conditional

examples/fluids: some corrections

examples/fluids: qf_Sur -> qf_applySur

examples/fluids: removed unused variable

style

examples/fluids/advection(2d).h: implementing a more readable conditional statement for in/outflow BCs

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examples/fluids: error handling when TRANSLATION is chosen for density_current

examples/fluids: WIP - in/outflow for explicit/implicit schemes are implemented in a single QFunction

WIP - changing the setup for inflow and outflow BCs - a new struct defined

changed the problem

examples/fluids: WIP - in/outflow for explicit/implicit schemes are implemented in a single QFunction

WIP - changing the setup for inflow and outflow BCs - a new struct defined

changed the problem options and typedef struct for having single in/outflow QFunction

added surface struct to QFunctions

temporarily commenting out QFunctions that won't be needed

in/outflow + implicit/explicit are all included in a single QFunction & comments

primary setup for single in/outflow QFunction

fixed a bug caused by floating point arithmetic

fixed a bug

Some clean-up

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examples/fluids: updated command line options, doc, README and, comments

examples/fluids: updated command line options and README

doc updated

examples/fluids: updated README & ~_left -> ~_wi

examples/fluids: updated command line options, doc, README and, comments

examples/fluids: updated command line options and README

doc updated

examples/fluids: updated README & ~_left -> ~_wind & ~_right -> ~ & comments

update doc

examples/fluids/advection(2d).h: update comments

examples/fluids: fix doc

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examples/fluids: added a warning for using -problem_advection_wind_translation with -problem_advection_wind rotation

examples/fluids: some corrections

examples/fluids: remove -bc_outflow and -bc_inflow from command line options

examples/fluids/advection(2d).h: added original blobs to the translation mode

example

examples/fluids: some corrections

examples/fluids: remove -bc_outflow and -bc_inflow from command line options

examples/fluids/advection(2d).h: added original blobs to the translation mode

examples/fluids: Implemented diagonal wind on advection 2D

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fluids/examples: Refactored Advection(2d) to ROTATION and TRANSLATION & some clean-up

fluids/examples: Refactored Advection(2d) to ROTATION and UNIFORM wind type

examples/fluids: removed the suppor

fluids/examples: Refactored Advection(2d) to ROTATION and TRANSLATION & some clean-up

fluids/examples: Refactored Advection(2d) to ROTATION and UNIFORM wind type

examples/fluids: removed the support for in/out-flow of density_current

style

examples/fluids: uniform -> translation & some comments

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examples/fluids: added inflow BCs

examples/fluids: inflow BCs added (only implemented for advection2d)

fluids/advection2d: brought back the original ICs

examples/fluids: add support for inflow BCs

examples/fluids: added inflow BCs

examples/fluids: inflow BCs added (only implemented for advection2d)

fluids/advection2d: brought back the original ICs

examples/fluids: add support for inflow BCs

examples/fluids: added inflow QFunction to Advection2d

examples/fluids: WIP - fixed a bug & comment

removed unused variable

examples/fluids/navierstokes.c: fixed a bug caused by refactoring

examples/fluids: fixed some bugs

examples/fluids/advection2d.h: fixed the implementation of inflow BCs

examples/fluids: Inflow BCs added for implicit Advection 2d and 3d

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fluids: changed the suffixes Sur -> Out to be able to add Inflow BCs