Make style

Assemble Linear Operator Diagonal (#375)

* Operator - Interface for CeedOperatorAssembleyLinearDiagonal

* Operator - Initial AssembleLinearDiagonal

* Tests - Add t533, t534, t535 assemble diag

Assemble Linear Operator Diagonal (#375)

* Operator - Interface for CeedOperatorAssembleyLinearDiagonal

* Operator - Initial AssembleLinearDiagonal

* Tests - Add t533, t534, t535 assemble diag

* Tests - add t536, nontensor operator diag

* AssembleDiag - small changes

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LCOV - minor updates

Assemble Linear QFunction (#306)

* Operator - add interface for AssembleLinearQF

* Operator - Refactor Ref/Blocked/Opt basis apply

* Operator - Add AssembleLinearQF impl for Ref/Blocked/Opt, n

Assemble Linear QFunction (#306)

* Operator - add interface for AssembleLinearQF

* Operator - Refactor Ref/Blocked/Opt basis apply

* Operator - Add AssembleLinearQF impl for Ref/Blocked/Opt, not impl message for OCCA/CUDA

* AssembleQF - Add grad test and clean up code

* CPU - Add operator eval mode error, remove opt inlineing

* Operator - clarify QF assemble documentation, style updates

* Interface - style and consistency updates

* Tests - add more complex assembled qfunction test

* Tests - add fortran test for assemble linear qfunction

* Tests - Update t53* tests for new Fortran source macro

* Merge - small fixes

* Operator - convert to backend creating assembled qdata vector

* Operator - zero qvecs before using in assembly of qf

* Operator - expand assemble QF documentation

* CPU - minor fix in AssembleLineaorQF to prevent uninitalized memory

* Tests - fix wording in t531, t532

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Operator - add refcounts for Operator field components

Improve ceed-elemrestriction interface doc (#370)

* Improve ceed-elemrestriction interface doc

QFunction - Fix identity qfunction field size

Style - minor typo fix

Merge pull request #360 from CEED/jed/config-flags

Jed/config flags and string processing

Clean up string processing code smells; -Wstringop-truncation

This pattern is detected by gcc-9 at high optimization:

warning: ‘strncpy’ output truncated before terminating nul copying as many byte

Clean up string processing code smells; -Wstringop-truncation

This pattern is detected by gcc-9 at high optimization:

warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
87 | strncpy(source_copy, source, strlen(source));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Tests - add t210, restriction view

Tests - add identity with size>1 test

Codecov Exceptions (#356)

* Tests - Add lcov exceptions to t304-f/t305-f

* Backends - add lcov exceptions for error messages intentionally not tested

* Interface - add lcov exceptions for erro

Codecov Exceptions (#356)

* Tests - Add lcov exceptions to t304-f/t305-f

* Backends - add lcov exceptions for error messages intentionally not tested

* Interface - add lcov exceptions for error messages intentionally not tested

* Tests - additional lcov exceptions

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Add Identity QFunctions (#279)

* QFunction - add initial identity qfunction

* Identity - preformance optimization and add ctx memory free

* QFunction - Improve documentation and clean up destr

Add Identity QFunctions (#279)

* QFunction - add initial identity qfunction

* Identity - preformance optimization and add ctx memory free

* QFunction - Improve documentation and clean up destroy

* Doc - Improve identity QF and Operator documentation

* Gallery - doc and typo fixes

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CeedOperatorSetField: validate that each input is non-NULL

It's easy to accidentally pass uninitialized objects and leads to far
more confusing errors later.

QFunction - document absolute path requirement (#343)

Symmetric Schur and Simultaneous Diagonalization (#299)

This PR adds simultaneous diagonalization and reorders the t3* tests.

* Interface: add Schur Decomp and interface for Simultaneous Diagonal

Symmetric Schur and Simultaneous Diagonalization (#299)

This PR adds simultaneous diagonalization and reorders the t3* tests.

* Interface: add Schur Decomp and interface for Simultaneous Diagonalization, implement Schur Decomp

* Tests: add Symmetric Schur Fortran test

* Interface: implement Simult Diag

* Tighten Givens tolerance in symmetric Schur

* Tests: Reorder t3* tests

* Basis - Check bounds for symmetric Schur

* Simult Diag - Add LAPACK function reference

* Typo fix

* Basis - 'static' CeedMatrixMultiply

* Merge - fix small issues

* Basis - typo fix

* Basis - Documentation fixes

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QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

QFunction Create by Name (#311)

This PR adds a QFunction gallery to libCEED with 1D, 2D, and 3D mass and Poisson operators.

Closes issue #37, issue #340

* Add QFunction gallery, rename focca

* Gallery - add initial QFunctions

* Add a test for using the QF gallery

* Modify ex1 to use gallery

* Add multiple test configs to tap

* Move output to test directory

* Update junit

* Add OCCA galley exception

* Add ex2

* Update ex2 for dim->ncompx

* Gallery - modify to work for CUDA as is

* Update Documentation

* Gallery - typo fix

* Gallery - convention change, postappend qfunction family variant

* Gallery - update template with new name checking convention

* Gallery - condense diff3DBuild QFunction

* Gallery - rename diff -> poisson

* Gallery - clarify poisson3DBuild comment

* Gallery - use Pragma SIMD, store Qdata in Voigt convention

* Examples - Convert BP3-6 to Voigt convention

* Examples - add cl option to switch between header and gallery qfs in CEED examples

* Examples - clean up construction of QF name

* Gallery - Switch to PascalCase for gallery names

* Doc - fix function type page

* Interface - Make sure strncpy result is null terminated

* Gallery - Update Poisson 2/3D Apply to new QF body

* make style

* make style - fix worst style problems

* make style - add gallery to make style

* Doc - update documentation errors and inconsistencies

* Examples - test ex1 ex2 with and without gallary

* Examples - reduce testing of ex1/ex2 without gallery, clean up non-gallery qfunctions

* MFEM - revert another make style mistake

* Manual make style updates

* Doc - update function documentation page

* Style updates, document test numbering conventions

* doc: resolve ambiguous image location warning, allow more Dot nodes

* Tests - style and cast cleanup

* Tests - fix README indentation

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Single Source QFunction (#304)

Introduce a new macro CEED_QFUNCTION that allows to define qFunctions in a single source code independently of the targeted backend.

Thanks-to: Jeremy Thompson
Tha

Single Source QFunction (#304)

Introduce a new macro CEED_QFUNCTION that allows to define qFunctions in a single source code independently of the targeted backend.

Thanks-to: Jeremy Thompson
Thanks-to: Jed Brown
This work is the result of a fruitful discussion between Jed Brown, Jeremy Thompson and Yohann Dudouit. Jeremy Thompson also implemented important features in this commit and was very active and helpful all along the progress of this work.

[NEWS] Breaking change: QFunctionField parameter 'ncomp' changed to 'size'. This change requires setting the previous value of 'ncomp' to 'ncomp*dim' when adding a QFunctionField with eval mode 'CEED_EVAL_GRAD'.

* First steps toward cuda-gen backend!

* Closer to real code generation.

* Generated code should be ready for nvrtc.

* The code generation skeleton is ready.

* Hack with the qfunction to make the operator kernel compile.

* Some tweaks in the makefile + Input fields structure change.

* Remove using cout.

* 1d interp and grad device functions.

* 1d readDofs, readQuads, writeDofs, writeQuads.

* Remove dead code.

* readDofs, readQuads, writeDofs, writeQuads for 2d and 3d

* 2d interp and grad

* 3d interp and grad

* - weight functions for 1d,2d,3d
- link the indices to the kernel
- link the fields to the kernel
- link the basis to the kernel

* Add the qFunction reader + inlining

* Add qf files for the tests.

* Add qf file for ceed/ex1

* Add qf file for mfem/bp1

* All tests pass.

* Add qFunction for mfem/bp3, petsc/bp1, and petsc/bp3.

* mfem/bp1 passes + remove dead code

* Fix a bug in n_quads_out for writeQuads

* mfem/bp3 passes.

* All tests all examples pass.

* Temporary tweaks for mfem benchmarking

* Add Context management.

* Modify .qf files to take into account the context.

* Enable optimizations.

* First set of optimization for 2D and 3D.

* double pointer format for the qFunction.

* Change the .qf files to have the same code as the C functions.

* Make previous Cuda backends use .qf files.

* Add a return value to qFunctions.

* Make cpu backends use .qf files.

* Minor: clean commented code.

* Add guarded math.h for petsc examples.

* Remove previous nek qf files.

* Remove .cu files.

* Remove .qf files.

* Remove dead code in the tests.

* make style

* Make style fix.

* more make style fixes.

* CEED_QFUNCTION - improve macro for CPU filenames

* Add CEED_QFUNCTION macro to navierstokes.c

* Fix PETSc gitignore

* Change default NS problemtype to density_current (#307) in navierstokes.c

* Fix petsc bp1.h

* Real Fix for petsc bp1.h...

* fix

* README - Add /gpu/cuda/gen

* PETSc - Update dmplex example to use *_loc

* cuda/reg - fix typo

* Revert a couple of small changes

* Fix a bug in mfem bp3 similar to the previous bug in petsc bp3.

* Make PETSc qfunctions look closer to master, and minor style for debugging.

* More uniformity changes

* Fix a strange CUDA_OUT_OF_RESSOURCE bug.

* NS - fix fname variables

* Use a different convention for qFunction ncomp.

* update cuda-gen backend and bpsdmplex.

* PETSc - style update

* update mfem bp1 and bp3.

* Interface - Use size instead of ncomp for QFunction fields

* update ceed example and tests.

* Tests - Update ncomp to size

* CPU Backends - Update ncomp to size

* CPU Backends - style

* Nek - Update ncomp to size

* Opt - fix style

* CUDA - update ncomp to size

* Doc - Update API documentation for QFunction \ncomp->size

* OCCA - Patch QFunction ncomp -> size, work but revamp will be better

* OCCA - assert dim>0 for clang-tidy

* CUDA - Change GetNumComp to GetSize

* Basis - Shift check for dim > 0 to interface

* Doc update

* Update NS field size

* NS - Fix problem options

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Make style

Rename NDoF to NNodes and style updates

Documentation Typo Fixes (#321)

* Basis - fix typo in doc

* Ceed - fix typo in doc

* Operator - fix typo in doc

* QFunction - fix typo in doc

* Ceed.h - fix typos in doc

* Ref - fix t

Documentation Typo Fixes (#321)

* Basis - fix typo in doc

* Ceed - fix typo in doc

* Operator - fix typo in doc

* QFunction - fix typo in doc

* Ceed.h - fix typos in doc

* Ref - fix typos in doc

* Blocked - fix typos in doc

* READMEs - typo fixes

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Refine PETSc DMPlex BPs

This currently only views shape, but could some day learn to view
values. Adding to public interface because it's a useful tool for
debugging user code.

Add ElemRestrGetMult and tests

Fix underinterpolation mode for /cpu/self backends