Merge pull request #1414 from CEED/zach/bps-swarm

Add support for running BPs with integration at particle points

Add BPs with integration at arbitrary points

DMSwarm Example with Interpolation and Projection (#1284)

* petsc - initial DMSwarm example

* swarm - links and runs

* swarm - fixed default box dims

* swarm - clearer error messages

* s

DMSwarm Example with Interpolation and Projection (#1284)

* petsc - initial DMSwarm example

* swarm - links and runs

* swarm - fixed default box dims

* swarm - clearer error messages

* swarm - clearer background mesh setup requirements

* swarm - Tensor bad :(

* Fix inequality direction for verification

* swarm - add viewing command

* swarm - DMSwarmPICField_coor

* swarm - DMSwarmGetCellDM

* swarm - dm_plex_hash_location true

* fix coordinate ordering

* "working" two-way projection

* libceed mostly correct, off by a permutation or something

* add tolerance parameter and make test succeed

* Use DMProjectFunction to support high-order bases

* minor clarity change

* prefer PetscPrintf over printf

* consistency

* minor - make uniform vs sin distributed points cl option

* fix VLA declaration

* minor reorganizing

* swarm value check in separate fn

* minor reorg and rename

* style

* separate interpolate logic into its own fns

* consistency

* fix error message

* woops, use field name arg

* improve indexing, switch to uniform for test

* fix multiple comp

* drop unused function

* draft documentation

* style

* Update PETSc style documentation

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* Update examples/petsc/dmswarm.c

* add create/destroy for ceed ctx object

* use libCEED rstr

* add P2C/C2P utils

* minor simplifications

* add projection swarm to mesh

* minor

* update gitignore

* add gauss point locations, lumped comparison

* simplify uniform/gauss coords logic

* fix segfault

* drop comparison - can replicate with CL options

* add polynomial target option

* minor tidying

* revert accidental change

* lumped test

* update tolerance option description

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* add points_per_cell option

* Fix siliness by Jeremy

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

* fix scoping and logic

* style

* discontinuous sphere target

* add cellwise random swarm

---------

Co-authored-by: Zach Atkins <zach.atkins@colorado.edu>

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Merge pull request #780 from CEED/jeremy/bps-gitignore

git - add *.a to petsc gitignore

git - add *.a to petsc gitignore

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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Add directory separator to examples/petsc/.gitignore (#404)

Some cleaning (#400)

* Some cleaning

* PETSc - update gitignore

Add PETSc example areaplex (#394)


Update bps files with new subfolders structure

* Add header h and okl files

* Update REAMDE.md

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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Merge pull request #302 from CEED/jeremy/dmplex

Create DMPlex PETSc BPs

PETSc - Update example output and DMPlex boundary conditions

PETSc DMPlex BP1-6 working in unified code

Add PETSc BP2, BP4, BP5, BP6 (#243)

* Add PETSc BP2, BP4, BP5, BP6

* Documentation update

* Update make benchmark

* Minor changes

* Add PETSc bpData structure

* Update make benchmarks

Add PETSc BP2, BP4, BP5, BP6 (#243)

* Add PETSc BP2, BP4, BP5, BP6

* Documentation update

* Update make benchmark

* Minor changes

* Add PETSc bpData structure

* Update make benchmarks

* Benchmark - use default qextra

* Documentation fix

* Clean up PETSc bps.c, add benchmarking first run

* Drop -ksp_max_it from benchmarkscript

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Ns fix alignment (#226)

* Fix alignment

* remove #include <ceed-impl.h> from tests/t306-basis.c

* Update examples/pets/Makefile

Merge branch 'master' into fortran_interface

.gitignore for examples