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* add clang-tidy workflow
* fix missing newline
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* make clang.14.sh executable
* remove non explicitly selected checks
* complete list of dependencies
* fix bug
* specify path of clang-tidy file
* fix bug
* add new check
* remove one check
* add magic numbers check
* removed one check
* keep only one check
* Docs: Conda Dev w/ Boost (#3911)
Add the `boost` package to the conda developer environment.
Used for QED table generation.
* Fix typo in Adastra cluster documentation (#3918)
* add back three checks
* prepare clang-tidy wrapper
* actually use clang-tidy in the script
* test
* fix bug
* actually use clang-tidy
* fixed bug
* fixed bug
* fixed bug
* fixed bug
* remove all checks except the selected 3
* fixed bug
* fixed bug
* fixed bug
* enforce const correctness using clang-tidy
* remove one check
* Fix Concurrency Issue
* BLAS++/LAPACK++ for RZ+PSATD
* Build all 4 WarpX DIMS
* add few echo for test purposes
* try to debug mysterious error
* don't test RZ with clang-tidy
* add back RZ test
* add some const
* fix bug
* check also header files
* remove header filter since it does not work as expected
* fixed bug
* check also WarpX headers
* fix bugs
* continue enforcing const correctness
* continue enforcing const correctness
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* fixed bug
* fix bugs and add new const
* clean .clang-tidy
* make regex more precise according to Weiqun's suggestion
* add more const
* fix bugs
* fix bug
* silence warning on float comparison
* fixed bug
* fixed bugs
* fix bug and add const
* fixed bugs
* fix bug
* fix bug
* fix bug
* fixed bug
* fix bug
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* replace amrex::Abort with WarpX macros
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* adding back missing include
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* bump precision
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* Interpolate on GPU
* another fix in Diagnostics
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* Correct particle positions outside refined injection
* Improve test
* Update benchmark
* Modifications for vector refinement ratio
* Update getPosition function
* Update code for anisotropic injection
* Correct compilation
* Correct code for RZ and 1D
* Correct indentation
* Correct integer overflow, as suggested by Weiqun
* Generalize interpolation routines in diagnostics for anisotropic ref ratio
* Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Utils/Interpolate.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Utils/Interpolate.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Utils/Interpolate_K.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Utils/Interpolate.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* apply review suggestion
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* initial tests with IWYU
* added a couple of forward declarations
* used iwyu on more files
* progress
* used iwyu on more files
* progress with iwyu
* progress with iwyu
* fixed bug
* progress with iwyu
* progress with IWYU
* progress with IWYU
* fixed bug
* fixed bug
* progress with IWYU
* progress with IWYU + use forward declarations in WarpX.H
* first try with .def files
* fix bugs
* progress with IWYU
* progress with IWYU
* progress with iwyu
* correct copyright
* fixed bug
* fixed bugs
* fix missing include
* fixed bug
* fix bug
* fix bug introduced during last bugfix
* use iwyu on newly added files
* add space
* fix bug
* fix missing include
* fix missing include
* fix missing include
* fixed bugs
* fixed bug
* attempt at fixing issue with math functions
* added missing include
* fixed missing include
* using _fwd.H
* fixed bug
* progress with iwyu
* update AMReX branch
* enforce alphabetic order
* progress with iwyu
* use right version of amrex
* use right version of amrex for tests
* fixed bug
* fix another bug
* fix missing include
* fix missing include
* fix missing include
* updated amrex
* initial work to document new include strategy
* updated documentation
* Fix rst & private includes
* Remove accidentially added files
* Fix rst code blocks
* one more rst block
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Define: _OPENMP -> AMREX_USE_OMP
Replace the define check of `_OPENMP` with the explicit
backend control of `AMREX_USE_OMP` for parallel constructs.
Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency
pulls it in for linear algebra, I/O, etc. This can led to confusion if the
user explicitly requested a serial build. Also, we might want to use OpenMP
functionality here and there for auxiliary functions w/o having to use the
AMReX OpenMP backend, i.e. because we compile for GPUs.
* Add missing amrex::Gpu::notInLaunchRegion
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* CI Lamor MR: Cover raw fields
Reproduce and cover raw field plots in CI.
* fix staggering of box indices in Interpolate
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* replace wherever possible .reset(new with = make_unique
* fixed bug
* fixed bug
* revert WarpXOpenPMD.cpp to the original version
* removed another .reset(new
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This PR fixes the source of several compilation warnings.
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* remove obsolete functions in FieldIO
* * Remimplement interpolation of coarse patch onto fine grids without div cleaning in C++.
* No longer need to have a Fortran compiler.
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* Start implementation of new averaging with staggering:
- face-to-cell-center and edge-to-cell-center replaced so far;
- TODO: node-to-cell-center and 1D behavior (AMREX_SPACEDIM=1).
* first implementation of Diags base classes
* add example, temporarily
* Continue implementation of new averaging with staggering:
- new function takes reference to single MultiFab (no vector);
- TODO: node-to-cell-center still in progress.
* Fix small bug and clean up
* Fix bug in loop over n=0,...,ncomp-1 and clean up
* add more functions
* Add Doxygen documentation and clean up
* Small clean-up in Doxygen documentation
* Compile in single precision: add _rt suffix to avoid unnecessary conversions
* Avoid accessing staggering index directly from IntVect in innermost loops
* Replace do-while loop with for loop (default ncomp=1)
* Remove temporary pointer and pass reference to MultiFab (instead of MultiFab*)
* Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor
* cleaning and initialize output mf
* use general average routine
* move flush in new class, and implemented the Plotfile derived class
* add comments
* eol
* free memory in destructor
* typo
* typo
* no need to clear MF pointers there
* though shalt not break existing tests
* FlushRaw doesnt have to be virtual for now
* The importance of being constant
* Capability to select fields in output files
* EOL
* revert to old inputs
* const in right place
* avoid brace initializer there
* oops, fix logic error in is_in
* user can choose flush interval, same behavior as plot_int
* Add option to plot raw fields
* eol
* replace ter flush with dump to avoid confusion
* add options
* Diagnostics stores a vector of functors to compute diags on the fly
* eol
* Field gather from diags to sync particle quantities
* New diagnostics handle RZ with same behavior as old ones
* cleaning and doc
* const ref for string
* smarter for loop from Axel and typo fix from Reva
* Functors to compute some fields
* simplify code following Dave's comments
* Create subfolders and add more output options (divE etc.)
* eol
* rename mode_avg to convertRZmodes2cartesian
* Update CellCenterFunctor.H
* fill varnames and vector of functors at the same time
* output rho_new, not rho_old
* WarpX instance not needed here
* add const
* little bit more of reorganization
* Apply suggestions from code review
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* add a bunch of const
* make derived classes final
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Luca Fedeli
Prabhat Kumar
David Grote
Axel Huebl
Revathi Jambunathan
WeiqunZhang
NeilZaim
MaxThevenet
