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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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* Introduce new option skip_deposition
* Properly implement the option to skip deposition
* Skip deposition for electrostatic solver
* Correct typo
* Add Index Enumerator and Equations for F/G Without Averaging
* Define new functions for current deposition and charge deposition
* Disable interpolation between levels
* Correct compilation error in RZ mode
* Add argument for relative time
* Add Index Enumerator and Equations for F/G With Averaging
* [skip ci] Add new OneStep function
* Fix compilation errors
* Correct more compilation errors
* [skip ci] Fix compilation
* Split the PSATD push into separate functions
* Add guards for rho field
* [skip ci] Use new functions in OneStep
* [skip ci] Separate the inverse transform of E_avg, B_avg
* Add deposition of rho
* [skip ci] Prevent deposition of rho if unallocated
* Fix error in deposition function
* Add subcycling of current deposition
* [skip ci] Add inverse transform of averaged fields
* [skip ci] Move component of rho
* Add function to copy J
* Temporarily deactivate contribution from F
* [skip ci] Implement call to linear in J
* Add psatd time averaging for multiJ
* [skip ci] Fix implementation of averaging
* [skip ci] Implement divE cleaning
* Fix Bug for RZ Builds
* Fix Bug for RZ Builds
* Fix Bug in Init of PML Spectral Solvers
* Cleaning
* Cleaning
* Add div(B) Cleaning (G Equation)
* Multi-J Not Implemented with Galilean PSATD or PMLs
* Add 2D CI Test Using Multi-J Scheme
* Add More Inline Comments
* Add More Inline Comments & Doxygen
* Add Doxygen for Constructor of SpectralSolver
* More Doxygen in Class SpectralSolver
* Add Doxygen for New Functions in WarpXPushFieldsEM.cpp
* Add Doxygen for New Functions in WarpX/MultiParticleContainer
* do_dive/b_cleaning Must Be True With linear_in_J Option
* Cast multij_n_depose to Real in Divisions
* New Input Syntax
* Add const where Possible, Fix Warnings
* Docs for New Input Syntax, Fix Abort Messages
* Consistent Use of Idx, IdxAvg, IdxLin
* Improve Documentation of psatd.J_linear_in_time
* Use const Type Qualifier whenever Possible
* Simplify Initialization of Pointer ion_lev
* Improve Doxygen
* Update documentation
* Add Note on NCI to Docs
* Make warpx.do_multi_J_n_depositions Not Optional
* Simplify Logic in getRequiredNumberOfFields
* Use More const Type Qualifiers
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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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 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 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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* 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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* Implement Galilean PSATD equations on staggered grids
* Implement high-order interpolation in 2D/3D
* Include missing header file and small clean-up
* Fix bug for FDTD build
* Small clean-up
* Modify current correction for staggered grids
* Implement comoving PSATD scheme (formulation with rho)
* Fix single-precision builds
* Do not implement rho-free formulation for comoving PSATD yet
* Invert sign of comoving velocity to match Galilean convention
* Fix two bugs in comoving PSATD algorithm
* Update benchmark of CI test momentum-conserving-gather
* Update benchmark of CI test PlasmaAccelerationMR
* Update documentation
* Clean up comoving PSATD class
* Clean up comoving PSATD class (more)
* Clean up comoving PSATD class (more)
* Implement changes requested in PR review
* Add 2D regression test for staggered Galilean PSATD
* Add 2D regression test for staggered comoving PSATD
* Unify input files for new CI tests to avoid duplication
* Fully rebase benchmarks changes on development
* Update benchmark of Galilean hybrid test after #1536
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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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* 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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* 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
* Added modifications for PICSAR galilean branch
* Averaged coefficients added
* 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
* Averaged fileds allocated on fine patch (Ex)
* Preparation for merging dev into galilean.
* remove TABs by hand
* Removed a tab.
* Redeclared v_galilean as a vector & related changed
* Added an automated test
* Moved v_galilean inside WarpX constructor
* Added analysis script for the automated test
* Changed name of the automated test to galilean_psatd
* Added InitializeSpectralCoefficients method
* Removed temporary comments
* Averaged fields added to FiledGather
* Added infinite order k[i]
* Setting kx_mod( kz_mod) = 0 for index = nx/2(-nz/2)
* 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
* Changing type of v_galilean from amrex::Vector to amrex::Array
* Changed back ng_fft to be equal nox_fft
* Changed v_galilean's type from amrex::vector to amrex::array
* Removed type
* Removed temporary comments
* Added flag 'do_time_averaging' to swith from unaveraged to averaged Galilean PSATD
* Updated doxygen
* Small fix on using 'do_time_averaging' flag
* Remove some commented Print statements
* [skip ci] Further cleanup
* Fix compilation
* Guard cells update of the averaged E,B fields
* Corrected included header file accordingly
* Removed EOL
* Removed EOL
* Corrected path of the included header file
* Updated choice of the spectral solver.
* Cleanup.
* use amrex::exp instead of std::exp
* no backward FFT for avg fields if avg is off
* Need to shift avg fields in MoveWindow
* Further cleaning
* Added 2D automated test for averaged PSATD
* Added automated 2D and 3D tests for averaged PSATD
* Removed comments
* Added specifications for averaged Galilean PSATD tests.
* Bug fixed - do FillBoundary of the averaged fields only if averaged is activated
* Do shiftMF of the averaged fields only if fft_do_time_averaging=true
* Add checksum json benchmarks for averaged Galilean PSATD
* Add missing indentation
* Add missing indentation
* Updated automated analysis script
* Updated diags period
* Fixed bug: no backtransform of the averaged fields when WARPX_DIM_RZ is set
* Fixed an uninitialized variable
* Clean-up
* Changed permissions for analysis_avg_*d.py
* Compactified variables initialization via conditional assignment
* Initialized averaged E_avg, B_avg fields
* Updated automated test for 2D averaged galilean PSATD
* Updated benchmark for 2D averaged galilean PSATD
* Updated automated 2D averaged PSATD test & benchmark
* Updated automated 3D averaged PSATD test & benchmark
* Fixed typo
* Updated benchmark averaged_galilean_3d_psatd
* Initialize the averaged fields only if the averaged Galilean PSATD algorithm is enabled
* Encreased time step for automated 3D averaged Galilean PSATD (to be equal c*dt=dz while dz/dx=3)
* Updated 3D automated test: specified standard deviations `.ux_th, .uy_th, .uz_th` along each direction
* Typo from the previous commit: enabled the averaged algorithm
* Trying out another input parameters for 3D averaged automated test with v_gal = v_plasma
* Update benchmark for previously added 3D averaged automated test
* Update 2D averaged automated test and corresponding benchmark
* Revert "Updated diags period"
This reverts commit 7334729b05e96589e020c981efdb430ca095991d.
* Cleanup: removed unwanted comment.
* Added descriptions of the 2D and 3D automated tests for the averaged Galilean PSATD.
* Updated value calculated via standard Galilean PSATD.
* Encreased relative error tolerance for 3D automated test for the averaged Galilean PSATD.
* Removed to avoid duplication since it already specified in the corresponding 2D/3D input scripts.
* Removed unwanted empty lines
* Added spaces after function's names
* Removed unwanted empty line
* Removed
* Fixed indentation
* Cleanup: removed #include <math.h>
* Cleanup: removed empty lines and fixed indentation
* Added 'AvgGalileanAlgorithm.cpp' to 'CMakeLists.txt'
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* Introduce option to update E with/without rho
* Clean up
* Include equations in docs
* Fix EOL whitespaces error
* Small clean-up
* Clean up
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* Implement periodic-single box option for spectral
* Fix out-of-bound in the periodic, single-box case
* Add documentation for periodic_single_box_fft
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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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* add warpx profiler wrapper
* call WX profiler wrapper instead of BL
* EOL and cleaning
* add doc on profile syncs
* do not use PROFILE macros in .H files
* replace WX_PROFILE with WARPX_PROFILE and use bool instead of int
* typo
* this file shouldn't be there
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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
Remi Lehe
Luca Fedeli
Michael E Rowan
MaxThevenet
Olga Shapoval
Axel Huebl
Tools
