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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
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* 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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amrex::Abort(Utils::TextMsg::Err("msg")) (#3879)
* use WARPX_ABORT_WITH_MSG instead of amrex::Abort(Utils::TextMsg::Err(msg)) [WIP]
* use WARPX_ABORT_WITH_MESSAGE
* fix typo
* fix missing parenthesis
* remove spaces to prevent automatic text wrapping
* remove wrong parenthesis
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* Introduce `warpx.grid_type` parameter
* Replace `or` with `||`
* Update examples with new user input syntax
* Fix `if` condition
* Improve error message
* Fix `if` condition
* Fix bugs
* Fix warning
* Fix RZ
* Debugging
* Fix RZ
* Fix bug
* Clean up
* More changes:
- set default algo parameters with hybrid grid
- all hybrid input parameters under warpx name
* Set default field gathering algo for hybrid grids
* Update documentation
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* Add "None" as an option for the Maxwell solver
* fixed some of the reasons for failing CI tests
* no longer pass `do_electrostatic` to `GuardCellManager`
* renamed `MaxwellSolverAlgo` to `ElectromagneticSolverAlgo`
* rename `do_electrostatic` to `electrostatic_solver_id`
* rename `maxwell_solver_id` to `electromagnetic_solver_id`
* changes requested during PR review
* remove `do_no_deposit` from tests without field evolution
* Fix doc-string in `GuardCellManager.H`
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Fix stair-case solver in 2D Cartesian
* Generalization for the macroscropic solver
* Update automated test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Update benchmark
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort()
* fix bug
* Update Source/WarpX.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* use more uniform text formatting
* fixed bug
* fixed bug
* using Utils::TextMsg in more files
* fixed bug
* use Utils::TextMsg in more files
* fixed bug
* use Utils::TextMsg in more files
* fixed last merge conflict
* fixed bug
* fix indentation
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Fixed computation of ECT Rho
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Adding a missing preprocessor directive
* Updated contributors list
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixed an abort message
* Fix in Source/Initialization/WarpXInitData.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Added some comments
* Made EvolveRhoCartesianECT not static
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: lgiacome <lorenzo.giacome@cern.ch>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Build System: Add 1D Geometry
* test PR
* test PR
* 1D cartesian yee algorithm
* fixed typo
* Fixes for PML
* 1D support related multiple changes
* Fix compilation
* change 1D to 1D_Z
* 1D Field Gather and typo fix
* 1D Charge Deposition
* Particle Pusher
* multiple changes related to 1D
* 1D diagnostics and initialization
* PlasmaInjector and PEC fixes for 1D
* clean-up delete diags file
* mobility 1D laser particle and bilinear filter
* deleted diags files
* update laser particle weight formula
* delete diags files
* Azure: Add 1D Cartesian Runner
* 1D fixes for FieldProbe
* Update Docs/source/developers/dimensionality.rst
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* 1d laser injection and langmuir test input files
* 1d tests
* clean up : delete print statements
* analyse simulation result for laser injection and Langmuir tests
* EOL
* delete input files for which there are no automated tests
* delete input files for which there are no automated tests
* add ignore_unused to remove warnings
* remove space
* Fix compilation issues
* fix error : macro name must be an identifier
* Small bug fix
* cleanup Python script for analysis
* bug fix
* bug fix
* Update ParticleProbe: Check 1D in-domain
* Update Source/Make.WarpX
* Update .azure-pipelines.yml
* Add USE_OPENPMD=FALSE to .azure-pipeline.yml
* resolve conflict
* resolve conflict
* fix typo
* Correct out-of-bound access
* Fix Particle BC in WarpXParticleContainer and correct path to checksumAPI in python analysis scripts
* EOL
* Fix bug : accessing out of bound index of cell in 1D
* remove 1d test for cartesian3d
* Fix CI check
* Slight style change
* Address review comments
* Fix GPU compilation Filter.cpp
* Fix CI
* Fix Indentation
* Address review comments
* More consistent ifdef for dimension bigger than 1
* Update Examples/Tests/Langmuir/analysis_langmuir_multi_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update GNUmakefile
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Regression/prepare_file_ci.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/CartesianCKCAlgorithm.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/CartesianNodalAlgorithm.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Filter/Filter.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Filter/Filter.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Filter/Filter.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Filter/Filter.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Initialization/PlasmaInjector.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Initialization/PlasmaInjector.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add comment inline to explain twice push_back
* Add amrex::Abort for NCIGodfreyFilter
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Remi Lehe <rlehe@lbl.gov>
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* adding base implementation of the conformal solver
* adding some preprocessor directives
* qualifying the isnan's correctly
* getting rid of some unused fields
* computing S_stab on the fly
* using empty in length check
* Source/FieldSolver/FiniteDifferenceSolver/EvolveB.cpp
* replaced a looponcpu with a parallelfor
* trying to not pass lending/borrowing info by reference in evolveB
* passing data using dataPtr
* converting inds into a device vector
* simplifying some +=
* extracting the inds BaseFabs as DataPtr
* Revert "extracting the inds BaseFabs as DataPtr"
This reverts commit bc709d2fcaa347c119514de79a3f57169a05af65.
* implementing new way ogf handling cell extensions (gpu compatible)
* fixing some white spaces
* removed a typo
* made a function static
* tidying up
* tidying up
* getting rid of the rho vector
* moving the rho update to evolveE
* refectoring the cell extension
* small chenge in input parameters
* updating WarpX.H
* bug fix
* fixing another bug
* rotating the cube
* updated gitignore
* using the conformal soler in the cube test
* fixing the signature of a function
* trying to fix the setVal problem
* Revert "trying to fix the setVal problem"
This reverts commit c7d0e5e3709b730ff570183b2a6df5f587ca4640.
* trying to fix the setVal problem
* cleaning some comments
* removing an abort in device code
* Including geometric information in the external field initializer
* cleaned up the test
* moving the geometric data initialization before the external fields initialization
* changing way of saving info about intruded cells
* fixed some white spaces
* Using S_mod instead of S_red and S_enl
* substituting a std::vector with amrex::Array1D
* bug fix in the uint8_t -> coords maps
* Condensed ect cell info into one single MultiFab
* fixing some includes
* fixing some more includes
* fixed a typo
* making some functions available in gpu code
* using tilebox instead of validbox for the geometry initialization
* communicating the geometric info in the guard cells
* fixing the guard cells initialization for ect
* fixing an unused parameter
* fixing an unused parameter
* ignored some unused variables when EB is not supported
* cleaning up
* cleaning up
* ignored some unused variables when EB is not supported
* evolving rho just for ect
* handling some more unused variables
* removing some white spaces
* adding the rotated cube test
* removed some white spaces
* change cells into faces
* small fix in unused parameters
* fixed a comment
* for safety for now just initialize the geometric data when lev==maxLevel
* adding some preprocessor directives to isolate EB code
* updating Makefile stuff
* Improving the rotated cube test
* bug fix in mesh refinement
* fixing boundary conditions in rotated cube test
* deactivating MPI in rotated cube test
* activating mpi in test
* improving outputs of cells extension
* improved the documentation
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Removed some obsolete isnan's
* undone change to gitignore
* adding some missing AMREX_GPU_DEVICEs
* Changing some amrex::Real(0) into 0.
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Adding amrex:: to some ignore_unused
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Enhancing readability of some parallelfor's
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Removed some unecessary includes
* Fixing some tags
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixing the function CountExtFaces
* added a comment for Rhofield
* Fixed a typo in CountExtCells
* trying to remove accesses to private members in ComputeEdgeLengths
* making some functions public
* undoing some useless changes
* undoing some useless changes
* adding some AMREX_GPU_DEVICEs
* adding some unused variables
* adding some AMREX_GPU_DEVICEs to fix warnings
* fixing relative error
* Making several variables const
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixed a comment
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* changing some double to amrex::Real
* removing commented lines
* changing some double to amrex::Real
* removing commented lines
* inizialing nelems_x,y,z to avoid a warning
* Fixing number of cells
* Adding missing analysis routine in rotated cube test
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Making some variables constexpr
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Improving some reduce operations
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* reading time directly from the output
* fixed a few data types
* fixing another int
* Replacing or->||, and->&&, not->!
* Adding license info
* Adding a white space
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* removed some unused imports
* Moving the doxygen documentation
* Including AMReX_LayoutData.H
* removing some useless parameters
* adding ect solver to the doc
* Removing some useless reductions
* Small change for consistency
* Handling the resizing of arrays
* Handling correctly the resing of arrays
* Fixing some whitespaces
* Fixing an indentation
* Improving a comment
* Removed a useless initialization
* Renamed Rhofield to ECTRhofield
* Renamed Rhofield to ECTRhofield
* Added some if conditions to isolate some EB related code
* Improved some comments
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Made some functions not member of WarpX anymore
* Isolated some EB-only code
* Isolated some EB-only code
* Using the square brackets to access vectors
* Ignoring some unused variables
* Bug fix in initialization
* Removed a redundant if
* Using enumeration for connectivity and improved names
* Added a comment
* added a few comments
* Removed some useless template parameters
* Printing some info only in verbose mode
* Revert "Removed some useless template parameters"
This reverts commit 2c527980e6872c0212767c27f00e2b53ecbcfd0a.
* Fixed a bug with the neighbours enumeration
* Initializing geom data alsoo in the ghost cells
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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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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* Added staircased embedded boundaris to the YEE solver
* adding spherical resonating cavity test
* adding functions for fields initialization
* style adjustments
* fixing tabs
* fixed name of analysis script
* fixed name of analysis script
* fixed a few wrong preprocessor directives
* workaround for missing boost
* Revert "workaround for missing boost"
This reverts commit 601f9eb2ec6f8c2100304379b2bea1c6cf9d1851.
* another workaround for missing boost
* getting rid of boost by depending on c++17
* Removed a few unused variables
* adding USE_EB to addToCompileString for EB testing
* removed tabs
* fixing the inputs name for EB sphere test
* shortened the test
* zero padding the names of the images
* adjusted two for loops
* removed some unused variables
* improving the fields initialization
* removed the sphere test and implemented the cube test
* fixed edges lengths computation and added comments
* Fixed the case of all_regular geometries
* fixing a bug that was breaking some tests
* adding test folder
* fixed the default values for the EB cube test
* simplified the analysis script
* fixed cubic resonator default results
* inputting the plot file name from command line
* fixing the diag name
* Fixed a bug in edges initialization
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Adding comments to the staircased yee solver (thanks Remi)
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* fixed the cube resonator test
* removed an unused import
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Add timers
* eol
* AtomicAdd
* lev argument for getCosts
* style
* style
* wip
* eol
* .ipynb
* passing down lev
* eol
* passing lev
* eol
* Update Source/Particles/Collision/PairWiseCoulombCollision.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add for QED and ionization routines
* eol
* remove unneeded
* mfi-->pti
* move cost
* eol
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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* Docs: PSATD Runtime Option
* Tests: PSATD Runtime Option
Add new runtime option to PSATD regression test matrix.
* PICMI: PSATD runtime option
* Source: PSATD Runtime Option
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Generalize includes to base path.
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* Prepare EvolveE
* Cartesian equations without current
* Implement Cartesian EvolveE
* Progress towards cylindrical solver
* Correct typo
* Implement cylindrical solver (without on-axis condition)
* Fix compilation errors
* Add regularization for RZ solver
* Added correction term for F
* Remove file for nodal stencil
* Apply stylistic changes to EvolveE
* Fix compilation errors
* Correction to avoid out of bound
* Remove references to old file
* Correct bug in EvolveB
* Implement correction on axis for Et
* Remove previous field update functions
* Remove unused code
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Luca Fedeli
Edoardo Zoni
Roelof Groenewald
Remi Lehe
Lorenzo Giacomel
Prabhat Kumar
Michael E Rowan
Axel Huebl
MaxThevenet
David Grote
