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- Call `setVal` with default arguments
(number of components and ghost cells)
- Affects only functions used with multi-J time stepping:
- `MultiParticleContainer::DepositCurrent`
- `MultiParticleContainer::DepositCharge`
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* Rearrange in preparation for lifting do_not_deposit higher in the call stack
* Make do_not_deposit public, so callers can test on it
* Make all DepositCharge call sites respect WarpXParticleContainer::do_not_deposit
* Drop check for do_not_deposit in DepositCharge
* Fix comment to accurately describe np_to_depose
* Fix logic to account for other logic in AddSpaceChargeField
* Match zero charge density array to filled array in RZ PSATD case
* Structure control flow per @dpgrote's preference
* Reword comment for clarity
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* Species variables in diagnostics: deal with runtime components
* Remove ParticleStringNames namespace
* Use const reference in iteration variable
* Fix ion acc 2D test
* Output extra (e.g. initialized later with python) comps by default
* Always output theta in RZ
* Fix QED tests
* Fix Laser Acceleration RZ test
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simulations from checkpoints (#3194)
* Move the initialization of multi-physics module earlier
* Fix syntax error
* Initialize multi-physics modules also when restarting the simulation
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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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* initial work to move the Warning Logger into ablastr
* progress with warn manager class
* moved Warning Logger in ablastr
* fixed bugs
* Fix: `SpectralFieldDataRZ.cpp`
Missing include for `WarpX::getCosts(lev);`
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* fix miscellaneous issues found with clang tidy
* fix miscellaneous issues found with clang tidy
* moved default constructors and destructors to header
* fix issue
* Use default again
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* Current Deposition Interfaces: Always Pass `dt` & `relative_time`
* Fix CI Failures
* Fix 1D/RZ Warnings
* Fix RZ Bug
* Fix Bugs
* Minimize Changes, Fix Roundoff Errors
* Cleaning
* Remove dt From doDepositionShapeN
* Cleaning Esirkepov Deposition
* Cleaning Vay Deposition
* Fix Roundoff Errors
* Fix Roundoff Errors (continued)
* Fix Bug (RZ)
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* Cleaned up handling of v_galilean
* Missed one
* Update Source/WarpX.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/WarpX.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/WarpX.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/PhotonParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/FieldSolver/WarpXPushFieldsEM.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/WarpXParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/WarpXParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Diagnostics/ReducedDiags/ParticleExtrema.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/PhysicalParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/PhysicalParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Utils/WarpXUtil.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/RigidInjectedParticleContainer.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Particles/ElementaryProcess/Ionization.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/FieldSolver/WarpXPushFieldsEM.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* More cleanup
* Reset Galilean Benchmarks
* For mirrors, now include the Galilean shift
* Removed the flag since it is true for all calls
* Fix Source/FieldSolver/SpectralSolver/SpectralFieldDataRZ.cpp
* Update Source/WarpX.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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Just a missing space we saw in the warning message between the
sentences.
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* Clean up the use of ndt for collisions
* Update BackgroundStopping to match changes
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* initial work to add msg formatter
* wip
* replace AMREX_ALWAYS_ASSERT_WITH_MESSAGE with WarpX equivalent
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* Implement injection orthogal to plane
* Generalize momentum distribution for flux injection
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Revert "[pre-commit.ci] auto fixes from pre-commit.com hooks"
This reverts commit b0cd1891771a4c49c14abb7cb9df7374cee4458c.
* Revert "Generalize momentum distribution for flux injection"
This reverts commit 0a22b1d8fa68a3a5705d8f4824f757b6dee497f0.
* Rotate momentum initialization
* Correct flux number when the direction is normal to plane
* Update distribution of particles within a cell
* Clean-up injection code
* Add more documentation
* Add more comments
* Handle 1D case
* Only do the rotation for Gaussian flux profile
* Fix compilation error
* Correct compilation for GPU
* Start adding automated test
* Correct sign of velocity
* Update to add continuous injection
* Finalize test
* Correct processing of flux_normal_axis
* Add checksum
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Fix bug
* Update script
* Implement maximum injection time
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Add parameter tmin
* Make parameter optional ; update documentation
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* move BTD call before Redistribute
* define particle buffer, BTD particle functor, particle filter
* select particles on the slice
* add particle functors
* add Lorentz Transform
* fix conflict
* add call to loretnz operator
* storing Particles in buffer
* This is WIP. Added particle buffers, filled them, sent them for flush with number already flushed. Does not work for multiple flushes. Crashes for OpenPMD.
* trailing endif after rebase
* adding print statements and not flushing particles in OPENPMD if numpart is 0
* last timestep flush is ensured at the end of evolve loop
* fix bug in declaring uy uy new and computing uzp
* set particle Geom, BA, and DMAP for particle flush with plotfile
* set Particle BA Geom DMAP for particle buffer and no BTD transform for force flush
* separate compute and pack from flush
* Fix Typo: resizeable -> resizable
Fixes HDF5 BTD particle output.
* new class for plotfile particles for BTD
* copy particle_H and DATA and Header. some WIP print statements
* Merge plotfile
* clean print statements
* fix warning message
* struct declaration in header, fix warning
* doxygen comments and copyright
* clean print statements
* fix eol and override function warning
* tile data
* fix output species array size bug
* fix access for particle buffer size
* clean and move time-update
* add cur_time update back
* remove cur time update which was called twice
* dont access particles flushed already for full diagnostics
* cur time must be updated for RigidInjection BTD CI test to pass
* temporarily move call to BTD
* updating time and calling BTD before movewindow
* cleanup
* reset benchmarks and analysis script
* clean and add comments
* fix particle box array, geom, dmap
* reset benchmarks for multi_J rz and ElectrostaticSphereEB_mixedBC
* wip commit
* wip commit
* add SI conversion
* abort for openpmd bp backend if species is selected. Also write particle output for BTD only if write_species is 1
* add documentation for aborting if adios is used with openpmd and add other BTD input parameters
* Apply suggestions from code review
commit Axel's suggestions from review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* use bool instead of int
* fix doxygen format
* using h5 as backend in example test to ensure consistency with abort for particle output.
* fix doxygen comment
* reset benchmark again for comoving_2d_psatd galilean_2d_psatd multi_J_rz_psatd
* reset benchmark for background_mcc
* self-review suggestions
* reset benchmarks. Update with last snapshot full info
* Axel's PR suggestions
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's doxygen fix
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add comments
* fix eol
* improved exception handling for stringsteam
* PR suggestions
* Axels' suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's suggestions :)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* simplify logic
* suggestions from review (Axel/Reva)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* variable name change for clarity
* if num particles in tmp array is 0, return
* Use new BTD inputs to set up BTD for particles in the corresponding particle container
* unused var
* fix logic error
* speciesID undefined
* separate particle and field buffer calls and initialization for BTD. Data common to both are initialized separately
* rename variable so it does not ghost existing varname
* add more comments
* Assert that fields are on
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* redundant function definition
* unused variable
* unused variable zp
* 1D 2D 3D definition
* fix else
* Apply suggestions from code review
Add Prabhat's suggestion
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
* missing semicolon and ignore xp yp for 1D
* resetting benchmarks for boosted sims and mcc sim
* temporarily changing tolerance since the relative difference for momentum_z is 3.68e-3 and the current tolerance is 2.5e-3
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
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They should be specified in the lab frame
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* AMREX_SPACEDIM : Boundary Conditions
* AMREX_SPACEDIM : Parallelization
* Fix compilation
* AMREX_SPACEDIM : Initialization
* Fix Typo
* space
* AMREX_SPACEDIM : Particles
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* Python: Start 1D Support
Start supporting 1D builds in Python.
* Fix 1D: PML FillZero unused
... since PMLs are not yet supported in 1D.
* BeamRelevant: Fix unused p_pos0
* FromTXYEFileLaserProfile: Not Impl in 1D
* QED Schwinger: 1D not Implemented
Fix unused warnings, add aborts.
* 1D RealVect/IntVect: Initialization
Use explicit scalar constructors, no braces.
Fix warning in clang 10.
* 1D NCI Filter: Fix unused members & Init
Unimplemented, but throws warnings.
* PSATD: 1D not Implemented
- remove compile warnings
- start porting some parts
* NCIGodfreyFilter: Clean up 2D & Else
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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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* improve error msg
* eliminate final dot
* initial layout of the main classes
* progress
* progress with warnings
* print local errors
* progress with warning logger
* improved MsgLogger
* added file to test warnings
* added method to read debug warnings from inputfile
* progress towards collective gather of warnings
* add missing blank line in warning message
* move misplaced file
* refactoring
* fixed bugs
* progress
* fixed bugs
* fixed some bugs
* it finally works!
* add comments in WarpX.H
* add missing comment
* added comments to WarpX.cpp
* add profiler to WarpX.cpp
* expose option to enable 'warn immediately' feature in cmake
* Add comment to main.cpp
* add missing comment in WarpX.cpp
* add copyright and include guards to WarnManager_fwd.H
* cleaning and added comments to WarnManager.H
* updated test
* added fwd file for MsgLogger
* cleaning
* Added copyright in WarnManager.cpp
* Cleaning
* cleaning
* Add missing copyright
* cleaning
* clean and add comments to MsgLoggerSerialization.H
* cleaning MsgLogger_fwd.H
* cleaning
* continue cleaning MsgLogger
* added comments & bugfixing
* removed test file
* fixed bugs
* Update Source/Utils/MsgLogger/MsgLogger.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/WarpX.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLogger.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLogger.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLogger.cpp
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLoggerSerialization.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLoggerSerialization.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLoggerSerialization.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLoggerSerialization.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/MsgLogger/MsgLoggerSerialization.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/WarnManager.cpp
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/WarnManager.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/WarnManager.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Update Source/Utils/WarnManager.cpp
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* fixed bugs
* Update Source/Utils/MsgLogger/MsgLogger.cpp
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Added comment to explain rotation
* use last value computed by partial_sum
* fix bug
* now use error stream
* using anonymous namespace for helper functions
* print on both stderr and stdout
* now using runtime parameter to always print warnings
* added documentation
* using long int for counter
* sort affected warnings list
* add doc entry
* removed doc
* added documentation
* fixed bug
* fixed bug
* removing unnecessary text
* reformatting
* reformatting
* fixed bug
* fixed bug
* correction
* add warning_logger.rst to toctree in developers.rst
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
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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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* Use parser for more input parameters
* Fix PSATD compilation and apply suggestions from code review
* Avoid out of bound array access for num_particles_per_cell_each_dim
* Fix few input files with respect to num_particles_per_cell_each_dim
* Fix get that incorrectly became query
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* Add structure for proton-boron fusion module
* Fix clang compile error
* Generalize structure for other nuclear fusion types
* Workaround: try to use std::vectors to fix clang compile error
* Simplify workaround for clang
* Rebase on 2245 and add empty particle creation functor
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add couple of consts and runtime assert
* Add another const
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Initialize lasers when restarting + recalculate z position at each iteration
* Fix restart for rigid-injected particles
* Fix laser injection box at restart
* Use correct positions for the moving window of the BTD
* implement restart for laser particles
* add CI test for laser acceleration restarting
* writespace
* Revert "Fix restart for rigid-injected particles"
This reverts commit 33bf3a60126539b9566ead3115ff2bcdf4b80516.
* don't add lasers to all full diags, only checkpoints
* fix unused parameter warning
* move the call to reset the m_laser_injection_box into PostRestart
* bugfix for non-boosted frame simulations
* Read the mean velocity of the injected species
* Remove unused line
* Revert "Initialize lasers when restarting + recalculate z position at each iteration"
This reverts commit 322634c35aa996649d0e8fff9fb683d04f2ee121.
* Add new ReadHeader / WriteHeader functions
* Add WriteHeader/ReadHeader for laser particles
* Revert "add CI test for laser acceleration restarting"
This reverts commit 6ba0fb3c121027eecf8b5845f55080e5b187375d.
* Fix merge commit
* Correct reading of updated position
* Add laser in restart test
* Remove unused parameters
* Update regression tests
* Add benchmark files
* Update boundary conditions for restart_psatd
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* added tunable particle reflection from absorbing domain boundaries
* extended picmi.py to allow setting boundary reflection coefficients and added a CI test for the reflection implementation
* allow R(E) to be specified, except for embedded boundaries
* changed approach for particle reflection, now the ParticleBoundaries object will hold the reflection coefficient; reflection from EBs not implemented
* added functionality to reflect from EB; still needs to be tested for accuracy
* added support for energy dependent reflection models for domain boundaries
* fixed at least one issue causing CI fails - building reflection model parsers for not physical particle containers
* switched reflection coefficients to be functions of the velocity component perpendicular to the boundary rather than energy
* reverted initial work on reflecting from EBs
* changed naming convention for new CI test for particle reflection
* switched useMPI back to 1 in test
* breaking changes while trying to sort out GPU issue
* fixed issue with CUDA compilation - hopefully :)
* various code improvements from PR review suggestions
* fix of major issues
* no need to parse the reflection models at every step
* skip particles that are already flagged for removal in ApplyBoundaryConditions
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* OneStep_multiJ: Always Deposit rho in Component 0
* For Multi-J Algo Allocate only 1 Component
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Bug fixed: looping over all species now within 'OneStep_multij'
* Bug fixed: looping over all laser particles within DepositCharge in multi-J
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* Added B field to plasma lens
* Fix B field and updated CI test to include the B field
* Updated benchmark
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This is renaming the runtime added optical depth scalars for QED
physics just to create the same names in plotfile and openPMD output.
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* Implements a periodically repeating plasma lens
* Added documentation for plasma lenses
* Added m_n_lenses to avoid use of size in device code
* Change arrays to device arrays
* Put DeviceVectors in the MultiParticleContainer
* Update Source/Particles/MultiParticleContainer.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/Gather/GetExternalFields.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Added CI test
* Updated CI test
* LGTM clean up
* Moved literal namespace inside the routine
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Infrastructure for interacting particles with embedded boundary walls
* remove debug prints
* protect with AMREX_USE_EB
* fix for 2D XZ
* also update level set when regridding
* rename level set to 'DistanceToEB'
* add docstring for scrape particles.
* add assertion on maxLevel() since EB does not work with mesh refinement right now.
* m_eb_if_parser no longer exists
* add test for particle aborption at embedded boundaries
* fix bug I introduced refactoring
* add new test to suite
* fix test names
* fix 2D
* rookie python error
* fix filename in test
* fix script
* fix unused
* make sure we turn EB on in test
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* amrex::Parser
Replace WarpXParser with amrex::Parser. Roundoff errors are expected because
of additional optimization in amrex::Parser.
* Reset the Langmuir_multi_psatd_single_precision benchmark due to change in single precision parser
* enable Intel oneAPI CI again
* Update Source/EmbeddedBoundary/WarpXInitEB.cpp
* Replace hard-coded number in ParticleDiag with a constexpr
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* fix readability-container-size-empty warning raised by clang-tidy
* fix bug
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* Added ParticleBoundaries and reflecting boundary conditions
* Added ParticleBoundaries::AllNone
* Allowed different particle boundary conditions on each side of the domain
* Updated the documentation for particle boundaries
* Fix end of line space in Docs/source/running_cpp/parameters.rst
* Updated the reflecting BC to use boundary input group
* Fixes to reflective boundary conditions
* Bug fix in AsStored
* Added particle boundaries regression test particle_boundaries_3d
* Fixed particle_boundaries_3d.json
* Minor updates
* Added algo.particle_shape to test case
* Remove do_pml from test case
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
* Need to explicitly turn off pml in CI test
* Re-add include
* Fixed includes
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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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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* Added injection of a thermal flux from the domain surface
* Major fixes to NFluxPerCell injection
* Small fixes and clean up
* Fixed 'if WARPX_DIMS_RZ' to use ifdef
* Small fix to flux_normal_axis error message
* Fix typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Implemented query and getArrWithParser
* Updated parameters.rst regarding expressions for multiple floats
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electrostatic (#1807)
* Introduce new option skip_deposition
* Properly implement the option to skip deposition
* Skip deposition for electrostatic solver
* Correct typo
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Replace capture of a host-side array with unnamed members for E & B
field transport with a nicely named struct that transports the
Array4's as members.
This is harder to mix up and thus more self-documenting and solves an
issue with NVCC 10.0 of the form:
```
nvcc_internal_extended_lambda_implementation: In instantiation of '__nv_dl_wrapper_t<Tag, F1, F2, F3, F4, F5>::__nv_dl_wrapper_t(F1, F2, F3, F4, F5) [with Tag = __nv_dl_tag<int (*)(amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>&, amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>&, amrex::Box, const amrex::Array4<const double> (&)[6], int, int, const SchwingerFilterFunc&, const SmartCreate&, const SmartCreate&, const SchwingerTransformFunc&), filterCreateTransformFromFAB<1, amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>, amrex::Array4<const double> [6], int, const SchwingerFilterFunc&, const SmartCreate&, const SmartCreate&, const SchwingerTransformFunc&>, 1>; F1 = amrex::Array4<double>; F2 = const SchwingerFilterFunc; F3 = const amrex::Array4<const double> [6]; F4 = const amrex::Box; F5 = int*]':
/home/ubuntu/repos/WarpX/Source/Particles/ParticleCreation/FilterCreateTransformFromFAB.H:174:28: required from 'Index filterCreateTransformFromFAB(DstTile&, DstTile&, amrex::Box, const FABs&, Index, Index, FilterFunc&&, CreateFunc1&&, CreateFunc2&&, TransFunc&&) [with int N = 1; DstTile = amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>; FABs = amrex::Array4<const double> [6]; Index = int; FilterFunc = const SchwingerFilterFunc&; CreateFunc1 = const SmartCreate&; CreateFunc2 = const SmartCreate&; TransFunc = const SchwingerTransformFunc&]'
/home/ubuntu/repos/WarpX/Source/Particles/MultiParticleContainer.cpp:1169:167: required from here
nvcc_internal_extended_lambda_implementation:70:103: error: invalid initializer for array member 'const amrex::Array4<const double> __nv_dl_wrapper_t<__nv_dl_tag<int (*)(amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>&, amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>&, amrex::Box, const amrex::Array4<const double> (&)[6], int, int, const SchwingerFilterFunc&, const SmartCreate&, const SmartCreate&, const SchwingerTransformFunc&), filterCreateTransformFromFAB<1, amrex::ParticleTile<0, 0, 4, 0, amrex::ArenaAllocator>, amrex::Array4<const double> [6], int, const SchwingerFilterFunc&, const SmartCreate&, const SmartCreate&, const SchwingerTransformFunc&>, 1>, amrex::Array4<double>, const SchwingerFilterFunc, const amrex::Array4<const double> [6], const amrex::Box, int*>::f3 [6]'
```
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* Remove the avg_aux fields
* Update 3D benchmark
* Update benchmark in 2D
* Initialize Bfield_avg_cp
* Fix two whitespaces left out
* Fix two more whitespaces left out
Co-authored-by: Edoardo Zoni <59625522+EZoni@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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Edoardo Zoni
Phil Miller
Neïl Zaim
Remi Lehe
Axel Huebl
Luca Fedeli
David Grote
David Grote
Revathi Jambunathan
Prabhat Kumar
Andrew Myers
Roelof Groenewald
Olga Shapoval
Weiqun Zhang
Michael E Rowan
