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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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* 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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* Fix SyncCurrent and SyncRho for multi-levels
Previously these two function did not work when max_level > 1. For example,
when max_level = 2, the coarse patch data from level 2 were coarsened and
added to the fine patch on level 1. However, the coarse patch on level 1 did
not have any contribution from level 2 as it should have, because the
coarsening was performed before the fine patch on level 1 received the level
2 contribution. The order has been fixed in this commit.
* Improve inline comment
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Improve inline comments
* Reset CI benchmark
* Add comments
* Update Source/Parallelization/WarpXComm.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Parallelization/WarpXComm.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Parallelization/WarpXComm.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
---------
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* `SyncRho`: Pass References To Charge MultiFabs
* Keep a function SyncRho for the Python interface
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---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* ABLASTR: Coarsen Functions
Move coarsen functions to ABLASTR.
Rename by property of the coarsening function.
* Remove unused imports
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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* 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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* ABLASTR: Always Sync Option
Add an option to ABLASTR/WarpX to always sync nodal cells that are
owned by multiple blocks. This can be used for debugging.
* Fix typo
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Use New Option in One CI Test
* Fix Logic: Force only to be `true`, not `false`
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* initial work to clean WarpX Utils
* remove AMRCore from Ionization tables
* progress
* refactoring of a part of the utils directory
* fix bug
* fixed bug
* fixed bug
* remove debug line accidentally slipped into the code
* remove debug line accidentally slipped into the code
* remove debug line accidentally slipped into the code
* cleaning
* fixed bug
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* Split ApplyFilterandSumBoundaryJ
* Fix Bug
* Fix Bug
* Fix CI
* Pass Correct Periodicity to SumBoundaryJ
* Use ApplyFilterJ and SumBoundaryJ w/ MR
* Fix Bug (duplicate loops over dimensions)
* Use ApplyFilterJ and SumBoundaryJ w/ MR
* Clean up Variable Names in ApplyFilterJ
* Increase Guard Cells of All MultiFabs, Not Only J
* Reset CI Checksums
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* `SyncCurrent`: Pass References To Current MultiFabs
* Add Doxygen for `SyncCurrent`
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* Merge `FillBoundary` and `NodalSync` (`OneStep_multiJ`)
* `NodalSync` Not Needed Anymore
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* Move: WarpXCommUtils to ABLASTR
* Update Usage Locations
* Refactor: `WarpX::do_single_precision_comms`
Do not use a global from WarpX in ABLASTR routines.
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* Add argument for synchronizing nodal points
* Add the option to overridesync in FillBoundaryE / FillBoundaryB
* Remove explicit synchronization
* Cleanup calls to nodal synchronization
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Improve const Correctness
* Cleaning
* Merge NodalSync and FillBoundary First
Restarting the implementation from scratch.
To-do: remove redundant FillBoundary calls.
* Merge Only for OneStep_nosub and OneStep_sub1
* Fix Checksums of Python_wrappers
* Define sync_nodal_points as WarpX Private Member Variable
* Keep Calls to NodalSync for B
* Keep Calls to NodalSync for F
* Reset Benchmark of reduced_diags_single_precision
* OneStep_sub1: Remove All Calls to NodalSync
* OneStep_nosub: Remove All Calls to NodalSync
* Reset Benchmark of divb_cleaning_3d
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* Remove Nodal Sync of J and Rho
* Reset Benchmark of reduced_diags_single_precision
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* Refactoring: More General Interfaces (J, rho)
* Refactoring: More General Interfaces (E, B)
* Refactoring: More General Interfaces (rho)
* Fix const Correctness
* Fix const Correctness (continued)
* Fix Bugs
* Refactoring: More General Interfaces (averaged E, averaged B)
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* Refactoring
* Separate Arrays (Fine Patch)
* Add Aborts w/ Current Centering, MR
* Cleaning
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Hybrid Algorithms: Add FDTD Support for Centering
* Current Centering Incompatible with Esirkepov Deposition
* Remove FDTD v. PSATD Runtime Conditions
* Add CI Test
* Rename coefs as coeffs in getFornbergStencilCoefficients
* amrex::Vector: Use at() Instead of Operator []
* Reset Benchmark
* Reset Benchmark
* Cleaning
* Reduce Size of New CI Test
* Reset Benchmark
* Fix Bug
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* initial work to add msg formatter
* wip
* replace AMREX_ALWAYS_ASSERT_WITH_MESSAGE with WarpX equivalent
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Make sure we update the right costs multifab when apply the filter in the presence of mesh refinement.
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Similarly to #2375, I'm trying to see if we can reduce the amount of duplicate code, in this case for the functions `Exchange<E,B>` of the PML class. Open for discussion.
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* Initial version of RZ PSATD PML BCs
* Cleaned up some bugs
* Add support of do_pml_in_domain option
* Cleaned up stuff for building
* Fix PMLPsatdAlgorithm macro
* Removed unneeded variable from SpectralSolverRZ
* Change length 3 arrays to length 2 (for 2D)
* Cleanup around DampPML
* Added more checks of pml[lev]
* Added CI test for RZ PML
* Added code to update the corner guard cells
* Further updates
* Added CI test
* Fixed EOL space
* Updated CI benchmarks, removing round off fields
* Changes to CI missed on previous commit
* Various fixes for clean up
* More fixes for clean up
* Further cleanup
* Updated benchmark
* Fixed benchmarks file
* Minor cleanup
* Added round off benchmark values
* Fixed testname in analysis_pml_psatd_rz.py
* Update comment in analysis file
* Put pml_rz code in RZ and PSATD macro blocks
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Add geometry.dims input to CI test input file, inputs_rz
* Cleanup to match recent changes
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* AMREX_SPACEDIM : Boundary Conditions
* AMREX_SPACEDIM : Parallelization
* Fix compilation
* Update Source/Parallelization/WarpXComm_K.H
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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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* WarpXComm.cpp: Use Explicit Types, not `auto`
* Use MultiFab* const instead of MultiFab* const&
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* option to use single precision guard cell exhanges
* add missing files
* fix namespace issue
* change precision of comms to float
* ParmParse the single_precision_comms flag
* set back to real
* test
* make sure dst is filled
* nGrow -> nGrowVect
* restore float
* don't override valid cells
* single precision mesh
* whitespace
* wrap SumBoundary
* Wrap additional uses of FillBoundary.
* catch missing copies of ParallelCopy
* missing OverrideSyncs
* add wrapper for iMultifab
* fix typo
* moar typos
* typo
* strip single_precision_mesh option
* fix original copy
* update fusible syntax
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* Fix: Single Precision Builds
Should not copy around data for `do_single_precision_comms`
* Docs: warpx.do_single_precision_comms
* initialize this tmp multifab to 0.0
* fix tiny profile label
* remove orig copies, they are only correct for FillBoundary
* loosen tolerance for space charge tests for single precision
* missing some setVal
* another missing setVal
* missing setVal
* add wrapper for new version of sumboundary
* add explicit cast to silence compiler warning
* add a test for single precision comms
* revert change to test precision
* add benchmark for single precision comms test
* restore tolerance I removed by mistake
* tolerance
* copyright headers
* drop tolerance for single precision tests in default analysis script
* missing python module
* bump tol again
* fix bad merge
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
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* Fix PML Behavior in FillBoundary for F,G
* Update Benchmark of Test pml_psatd_dive_divb_cleaning
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* SumBoundary: Use Fewer Guard Cells for J/rho
* Account for Stencil of Bilinear Filter
* Revert Last Commit, Replace SumBoundary/Copy With ParallelAdd
* Account for Stencil of Bilinear Filter
* Reset Benchmarks of Averaged Galilean Hybrid Tests
* Revert Last Commit
This reverts commit 7963176b46708eb08e7c41e67a3b0a6fe6cb2147.
* Account for Stencil of Current Centering
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* Allow more work for OpenMP threads in AuxilaryData
* Better parallelization in stagger-to-nodal current interpolation
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(#2144)
* Use less guard cells in ParallelCopy of refined level's UpdateAuxilaryData
* Update Source/Parallelization/WarpXComm.cpp
* Add inline comments and use explicit type for ng_src
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Add Cost Calculations to ApplyFilter
* Add Cost Calculations to ApplyStencil
* Update Doxygen
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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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* Implement div(B) Cleaning With FDTD
* Add CI Test
* Clean Up
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* Add div(E)/div(B) cleaning options for PSATD in PMLs
* Pass missing flags to spectral solver in PML
* Duplicate MPI exchange and communication functions for G
* Use separate parameters for div cleaning in PMLs
* Add asserts for features that are not implemented
* Do not need to duplicate MPI exchange functions for G
* Add short documentation for new input parameters
* Set new parameters true by default with PSATD solver
* Add CI test for PML div cleaning with PSATD
* Use new syntax <diag_name>.intervals in new input file
* Reset benchmark of new CI test
* Always synchronize nodal points of G MultiFab
* Fix few warnings in 2D build
* Update Benchmark of pml_psatd_dive_divb_cleaning
* Improve Documentation of warpx.do_pml_dive_cleaning
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Improve Documentation of warpx.do_pml_divb_cleaning
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Improve Abort Message
* Clean Up
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
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* Add nodal synchronization of E and B fields in the main grid
* Update benchmarks
* Update value in pml analysis file and put synchronization between PSATD push and FillBoundary
* Update PML benchmarks and put the synchronization back in its original position
* Bogus change in benchmark to trigger CI again
* Update benchmarks
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* Start adding centering of current
* Implement arbitrary order centering and split inputs
* No need to define a brand new interpolation function
* Update input file of hybrid CI tests
* Clean up
* Clean up more
* Fix bug and clean up
* Use current centering in two existing CI tests
* Update documentation
* Move Calls To UpdateCurrentNodalToStag Into SyncCurrent
* Add Doxygen For New Function UpdateCurrentNodalToStag
* Add Doxygen For New Functions Used For Stencil Coefficients
* Finite-Order Centering of Currents Not Implemented With MR
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* Refactor and clean up some spectral classes
* Abort when current correction or Vay deposition are not implemented
* Implement general equations for averaged Galilean
* Allocate averaged MultiFabs also when aux_is_nodal=1 and do_nodal=0
* Allocate +ngextra guard cells also for averaged MultiFabs
* Make alias MultiFabs for averaged aux data
* With averaging, interpolate from avg_fp (not fp) to aux
* Fix some limits of the coefficients
* Fix bug causing NaNs in spectral coefficients
* Add 2D CI test with same analysis as nodal test
* Add 3D CI test with same analysis as nodal test
* Add limit that was not covered (knorm=0 && knorm_c!=0 && nu=0)
* Allocate T2_coef only if Galilean algorithm is used
* Allocate X4_coef only if Galilean algorithm is used
* Remove extra ghost cell from 'avg_fp' MultiFabs
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* CI: Always with FFTW/PSATD
Reduce build time by always building with FFTW and unifying
PSATD tests.
This also adds coverage for the case that we forget to make
`#ifdef WARPX_USE_PSATD` runtime blocks, which can
potentially be seen in FDTD runs now.
* Remove worker with environment USE_WARPX_PSATD
* Fix warpx_interp: Unconditional PSATD
Fix the `warpx_interp` function to properly enable/disable PSATD
logic based on runtime logic.
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Clarify loop over boxes in WarpX::UpdateAuxilaryDataStagToNodal
* Loop over fabbox instead and pad with zeros beyond ghost cells
* Clean up names of source and destination arrays
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gathering (#1653)
* Unify high-order Fornberg interpolation functions
* Add Doxygen documentation for new function
* Unify also FDTD linear interpolation functions
* Improve new implementation
* Compute stencil coefficients only at initialization
* Small clean-up and optimization
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* Always synchronize nodal points of PML MultiFabs
* Reset benchmark for CI test pml_x_psatd
* Use new separate functions NodalSyncPML
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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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Edoardo Zoni
Luca Fedeli
Weiqun Zhang
Remi Lehe
Axel Huebl
Roelof Groenewald
Andrew Myers
David Grote
Prabhat Kumar
Andrew Myers
Neïl Zaim
