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* Fill Guard Cells of Fields and Currents Independently
* Fill Guard Cells of Averaged Fields as Regular Fields
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* Refactor Vay Deposition Functions
* Use rho Index Type for FFT of D
* Improve Doxygen Strings
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* Refactor Current Correction Functions
* Clean Up, Reset Benchmark
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* Doxygen: Fix Diags, FieldSolver, Parallelization & Particles
* Apply suggestions: Remi
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Apply suggestions: Roelof
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
* Apply suggestions: Luca
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
* Apply suggestions: Edoardo
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Apply suggestions: Andrew
* Apply suggestions: Edoardo
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Apply suggestions: Neil
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Apply suggestions: Roelof
* Apply suggestions: Weiqun
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
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* AMREX_SPACEDIM : Boundary Conditions
* AMREX_SPACEDIM : Parallelization
* Fix compilation
* AMREX_SPACEDIM : Initialization
* Fix Typo
* space
* AMREX_SPACEDIM : Particles
* AMREX_SPACEDIM : Evolve and FieldSolver
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* Add New Spectral Index Class
* Cleaning
* Use New Spectral Index Class in PML
* Cleaning
* Reuse Available Data for divE
* Allocate Rho Data Only when Necessary
* Cleaning
* Fix Bug in RZ Geometry
* Revert Commits for Allocation of Rho Data
* Cleaning
* Update Forward Declaration Header
* Do Not Include Unnecessary Header Files
* Doxygen
* Do Not Use Separate div() Cleaning Flags
* SpectralFieldIndex: Add Missing param to Doxygen
* Remove Unused getRequiredNumberOfFields
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* Do Not Always Fill Guard Cells with Inverse FFTs
* Query psatd.fill_guards from Inputs
* Clean Up and Reduce Style Changes
* Fix Bug for Periodic Single Box
* Clean Up and Reduce Style Changes
* Fix Bug for RZ PSATD
* Remove Input Parameter, Default 0 Unless Damping
* Fix CI Tests (2D)
* Fix CI Tests (3D)
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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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* 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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This PR fixes the source of several compilation warnings.
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Introduce option to update E with/without rho
* Clean up
* Implement current correction for Galilean PSATD (needs bug fix)
* Include equations in docs
* Fix EOL whitespaces error
* Small clean-up
* Implement Galilean PSATD update without rho
* Clean up
* Fix bug in current correction
* Fix EOL whitespaces
* Clean up
* Fix unused import
* Remove unused variable
* [skip CI] Improve docs
* Clean up style
* Fix EOL whitespaces
* Fix EOL whitespaces
* Clean up style
* Revert analysis script to old status
* [skip CI] Clean up style
* Make equations more human-readable and improve comments
* 2D test with current correction works
* Temporary build fix as in #1197
* 3D test with current correction works
* Rename th and th_star as theta and theta_star
* Fix a couple of wrong comments
* Add vertical spaces to improve readability
* Improve documentation
* Function CurrentCorrection is now pure
* 2D benchmark fields data are now correct
* Add limits of coefficients for nu=-1
* Change default of update_with_rho for Galilean PSATD
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* Added stub for current correction in RZ spectral solver
* Start implementation of Vay deposition
* Continue implementation of Vay deposition
* Correct deposition of D
* Add phase shift for staggered currents
* Small clean-up
* Fix units in deposition of D
* Implement average of cumulative sum (needs bug fix)
* Start fixing bug in average of cumulative sum
* Still debugging
* Cumulative sums should be correct now
* Subtract averages of cumulative sums:
- current implementation: cumulative sums, inverse Fourier transform, subtraction of averages
- needs to be tested (including units of D after Vay deposition)
- needs to be shortened (too many loops over boxes and ParallelFors)
* [skip CI] Clean up and fix units
* Still fixing units
* [skip CI] Remove temporarily averages of cumulative sums
* [skip CI] Remove distinction between staggered and nodal
* Vay and Esirkepov similar results on periodic single box:
TODO:
- debug (charge not conserved);
- try using compute_shifted_shape_factor as in Esirkepov deposition;
- clean up;
- try on multiple boxes and with correction of mode at 0 frequency.
* [skip CI] Clean up
* Fix bug in 3D deposition
* [skip CI] Clean up
* Fix 2D and 3D implementation:
- simulation results agree between direct and Vay deposition in both 2D and 3D
- Travis CI tests should pass except for check of charge conservation (debug)
* Small clean-up
* Fix bug when compiling in RZ geometry
* Add benchmark json files (will be reset later)
* Do not set zero current at zero frequency
* [skip CI] Revert last commit and clean up
* Fix small bug after reverting commit
* Set nodal test first on Travis
* Fix benchmark for nodal test in 3D
* Fix particle output for nodal test in 3D
* Fix bugs due to staggering
* Rename current nodal Travis tests
* Add Travis tests staggered in 2D and 3D
* Further clean-up after bug fix
* Abort when using Vay deposition with domain decomposition
* Add optional argument of index type to forward FFT
* Fourier shifts can be private members as before
* Small clean-up
* Clean up and improve Doxygen documentation
* Fix small bug in analysis script for 2D tests
* Fix tests (remove E and B fields from particle diags)
* Add option to fill guard cells and docs
* Fix value of last guard cell by enforcing periodicity
* Revert changes merged from #1121
* Clean up style
* Improve docs
* Fix forgotten alignment
* Improve docs
* Make base class functions VayDeposition pure
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
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* Start implementing PSATD push without rho.
TODO: 1) fix unit test pml_x_psatd;
2) try new PSATD push in PML;
3) avoid intro of new derived class?
* Correct PSATD push to fix PML test.
* Few improvements on new PSATD push:
- new class name is 'PsatdAlgorithmMixed' (both rho and J are used);
- new algorithm parameter to choose between available implementations:
parameter name is 'psatd_push', possible values are 'standard' for
old implementation using rho via Gauss law and continuity equation
and 'mixed' for new implementation using rho via Gauss law and J for
all remaining terms.
* Fix style error (tabs vs four white spaces).
* Improve comments for available PSATD algorithms.
* Correct few typos in latest comments.
* Implement first current correction:
- new member function 'CurrentCorrection' in class SpectralSolver;
- correction applied only without subcycling (in function 'OneStep_nosub');
- TODO: add correction when subcycling is used (in function 'OneStep_sub1');
- back to old implementation of PSATD push of E and B (class 'PsatdAlgorithmMixed' removed);
- TODO: PML unit test 'pml_x_psatd' does not pass.
* Small cleanup:
- remove residual option for choice of PSATD push algorithm (only one choice now);
- improve comments.
* Implement div(E) diagnostics for spectral case.
* split travis tests in bigger matrix
* split more TravisCI tests, add electrostatic, use defaults values
* typo
* Move computation of div(E) to base class SpectralBaseAlgorithm.
* need to split psatd too
* consistent variable names and use function to avoid duplication
* fix typo for qed tests
* typo
* also need to update run_tests.sg
* Update copyright tags.
* change matrix
* Add test of div(E) vs rho/epsilon_0 in PML test.
* Small clean-up.
* Small clean-up
* Remove option for current correction from input files of two new tests (not used)
* Small clean-up: remove unnecessary references
* More clean-up (minimize style changes to keep PR simple).
* Add specific 2D/3D tests for current correction:
- 'Langmuir_multi_2d_psatd_cc': same input file as 'Langmuir_multi_2d_psatd',
except for current correction and output of divE;
- 'Langmuir_multi_psatd_cc': same input file (3D) as 'Langmuir_multi_psatd',
except for current correction and output of divE;
- add corresponding Python scripts for analysis: same as previous ones,
except for check on L-infinity spatial norm of rho/epsilon_0 vs div(E);
- revert changes on old tests: do not use current correction in old tests
(benchmarks on Battra do not need to be updated).
* Improve comments.
* 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).
* Remove unrelated style changes (cleaner PR).
* Avoid duplication of input files and analysis scripts for new tests
* Improve comments for Doxygen documentation.
* Improve comments for Doxygen documentation.
* Small clean-up
* first implementation of Diags base classes
* Small clean-up
* Small clean-up
* Fix erroneous non-ASCII character
* Small clean-up
* Auxiliary function for current correction in class WarpX to keep OneStep_nosub clean
* Remove unrelated style changes (cleaner PR)
* Improve comments
* Instrument virtual function 'CurrentCorrection'
* Trying to fix build error detected by LGTM analysis only
* 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
* Implement periodic-single box option for spectral
* Fix out-of-bound in the periodic, single-box case
* 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
* Use old name for output image of new 2D test
* user can choose flush interval, same behavior as plot_int
* Small clean-up in Doxygen documentation
* 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
* Add documentation for periodic_single_box_fft
* For periodic, single-box, apply current correction after guard cell exchange
* 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
* Travis CI: force 2 MPI processes only for numprocs > 2
* Use special FFT (PR #834) and new diagnostics (PR #844) in new tests
* Improve Doxygen documentation
* Move option do_current_correction from warpx to psatd
* Fix path to output files for tests using new diagnostics
* Fix additional paths to output files for new diagnostics
* Add input paramter do_current_correction to documentation
* Fix test Langmuir_multi_psatd_hybrid: do not plot divE
* Remove input parameter amr.plot_int in tests using new diagnostics
* Trigger failing source/style checks on Travis CI
* Fix build error due to public include
* Add missing const keywords
* Change test names and corresponding analysis scripts
* Improve Python script for analysis
* Do not rename output files in old CI tests (without current correction)
* Fix output file name prefix for some tests
* Trigger Travis CI build after AMReX bug fix
* Void commit: trigger Travis CI build
* Fix some tests failing due to recent changes in master
* Use new diagnostics for particle output correctly
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Print tolerance and error in Python analysis
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Print tolerance and error in Python analysis
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Improve documentation
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Fix EOL white spaces
* Fix name of particle output variables
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Fix compiler warnings with DIM=2
* Fix compiler warnings with USE_RZ=TRUE
* Fix compiler warnings with USE_PSATD=TRUE and DIM=2
* Fix compiler warnings with USE_PSATD=TRUE and DIM=3
* Fix bug: discard only return value when calling DefineAndReturnParticleTile
* Remove unused variables not triggering warnings
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* Implement div(E) diagnostics for spectral case.
* split travis tests in bigger matrix
* split more TravisCI tests, add electrostatic, use defaults values
* typo
* Move computation of div(E) to base class SpectralBaseAlgorithm.
* need to split psatd too
* consistent variable names and use function to avoid duplication
* fix typo for qed tests
* typo
* also need to update run_tests.sg
* Update copyright tags.
* change matrix
* Add test of div(E) vs rho/epsilon_0 in PML test.
* SpectralFieldIndex: reuse memory slot for Bx when computing divE.
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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- Use `""` for WarpX-local includes
- Order: WarpX `""`, AMReX `<>`, other third party includes `<>`
- Add dir prefixes for WarpX
Add order to includes by including from `Source/` onward and keeping
directory prefixes of non-local includes for clarity.
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* Read Galilean velocity
* Prepare structures for Galilean solver
* Started implementing Galilean equations
* Analytical limits for X1, X2, X3, X4 coefficients added
* Slight changes added
* Added Galilean position pusher
* Scale galilean velocity
* Remove unneeded Abort
* Fix Galilean pusher
* Allocate Theta2 array
* Fix definition of coefficients
* Increase guard cells for Galilean
* Add guard cell in particle exchange
* Type corrected
* v_gal added to warpx_current_deposition
* v_gal added to WarpXParticleContainer.H
* Bug fixed - update particle x-position over one time step
* Fix issues with merge from dev
* Preparation for merging dev into galilean.
* Adding galilean shift
* Implemented galilean shift
* Changed method's name from GalileanShift to ShiftGalileanBoundary
* Added doxygen string for ShiftGalileanBoundary
* Removed never used method LowerCornerWithCentering
* Removed temporary comments
* Removed dt as a variable from DepositCharge method and its dependencies
* Converted tab to spaces
* Removed EOL white space
* Add documentation and automated tests
* Fix compilation error
* Add automated test
* Update automated test
* Removed temporary used galilean shift
* Removed temporary used particle's push for Galilean PSATD
* Removed unused statement
* Remove EOL white space.
* Added zero shift for LowerCorner in RZ geometry
* Minor changes to Galilean implementation
* Modifications for GPU
* Fix typo
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Edoardo Zoni
Axel Huebl
Prabhat Kumar
Luca Fedeli
Michael E Rowan
Olga Shapoval
Tools
Remi Lehe
