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* Clang-tidy: add more misc-* checks to clang-tidy CI test
* address issues found with clang-tidy
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* pyAMReX: Build System
* CI Updates (Changed Options)
* Callback modernization (#4)
* refactor callbacks.py
* added binding code in `pyWarpX.cpp` to add or remove keys from the callback dictionary
* minor PR cleanups
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Added Python level reference to fetch the multifabs (#3)
* pyAMReX: Build System
* Added Python level reference to Ex_aux
* Now uses the multifab map
* Fix typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add initialization and finalize routines (#5)
A basic PICMI input file will now run to completion.
* Regression Tests: WarpX_PYTHON=ON
* Update Imports to nD pyAMReX
* IPO/LTO Control
Although pybind11 relies heavily on IPO/LTO to create low-latency,
small-binary bindings, some compilers will have troubles with that.
Thus, we add a compile-time option to optionally disable it when
needed.
* Fix: Link Legacy WarpXWrappers.cpp
* Wrap WarpX instance and start multi particle container
* Fix test Python_pass_mpi_comm
* Start wrapper for multiparticle container
* Add return policy
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update fields to use MultiFabs directly
Remove EOL white space
Removed old routines accessing MultiFabs
Update to use "node_centered"
* Fix compilation with Python
* Update fields.py to use modified MultiFab tag names
* Remove incorrect, unused code
* Add function to extract the WarpX MultiParticleContainer
* Complete class WarpXParticleContainer
* Wrap functions getNprocs / getMyProc
* restore `install___` callback API - could remove later if we want but should maintain backward compatibility for now
* add `gett_new` and `getistep` functions wrappers; fix typos in `callbacks.py`; avoid error in getting `rho` from `fields.py`
* Update callback call and `getNproc`/`getMyProc` function
* Replace function add_n_particles
* Fix setitem in fields.py for 1d and 2d
* also update `gett_new()` in `_libwarpx.py` in case we want to keep that API
* added binding for `WarpXParIter` - needed to port `libwarpx.depositChargeDensity()` which is an ongoing effort
* Wrap function num_real_comp
* added binding for `TotalNumberOfParticles` and continue progress on enabling 1d MCC test to run
* add `SyncRho()` binding and create helper function in `libwarpx.depositChargeDensity` to manage scope of the particle iter
* Clean up issues in fields.py
* update bindings for `get_particle_structs`
* Fix setitem in fields.py
* switch order of initialization for particle container and particle iterator
* switch deposit_charge loop to C++ code; bind `ApplyInverseVolumeScalingToChargeDensity`
* move `WarpXParticleContainer.cpp` and `MultiParticleContainer.cpp` to new Particles folder
* added binding for `ParticleBoundaryBuffer`
* More fixes for fields.py
* Fix: Backtraces from Python
Add the Python executable name with an absolute path, so backtraces
in AMReX work. See linked AMReX issue for details.
* Cleaning
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix: Backtraces from Python Part II
Do not add Python script name - it confuses the AMReX ParmParser to
build its table.
* Fix: CMake Dependencies for Wheel
This fixes a racecondition during `pip_install`: it was possible
that not all dimensions where yet build from pybind before we
start packing them in the wheel for pip install.
* MCC Test: Install Callbacks before Run
Otherwise hangs in aquiring the gil during shutdown.
* addition of `Python/pywarpx/particle_containers.py` and various associated bindings
* Fix: CMake Superbuild w/ Shared AMReX
We MUST build AMReX as a shared (so/dll/dylib) library, otherwise
all the global state in it will cause split-brain situations, where
our Python modules operate on different stacks.
* add `clear_all()` to callbacks in order to remove all callbacks at finalize
* add `-DWarpX_PYTHON=ON` to CI tests that failed to build
* add `get_comp_index` and continue to port particle data bindings
* Add AMReX Module as `libwarpx_so.amr`
Attribute to pass through the already loaded AMReX module with the
matching dimensionality to the simulation.
* Fix for fields accounting for guard cells
* Fix handling of ghost cells in fields
* Update & Test: Particle Boundary Scraping
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* CI: Python Updates
- modernize Python setups
- drop CUDA 11.0 for good and go 11.3+ as documented already
```
Error #3246: Internal Compiler Error (codegen): "there was an error in verifying the lgenfe output!"
```
* CI: Python Updates (chmod)
* Add support for cupy in fields.py
* Add MultiFab reduction routines
* CI: CUDA 11.3 is <= Ubuntu 20.04
* changed `AddNParticles` to take `amrex::Vector` arguments
* setup.py: WarpX_PYTHON=ON
* update various 2d and rz tests with new APIs
* add `-DWarpX_PYTHON_IPO=OFF` to compile string for 2d and 3d Python CI tests to speed up linking
* CI: -DpyAMReX_IPO=OFF
* CI: -DpyAMReX_IPO=OFF
actually adding `=OFF`
* CI: Intel Python
* CI: macOS Python Executable
Ensure we always use the same `python3` executable, as specified
by the `PATH` priority.
* CMake: Python Multi-Config Build
Add support for multi-config generators, especially on Windows.
* __init__.py: Windows DLL Support
Python 3.8+ on Windows: DLL search paths for dependent
shared libraries
Refs.:
- https://github.com/python/cpython/issues/80266
- https://docs.python.org/3.8/library/os.html#os.add_dll_directory
* CI: pywarpx Update
our setup.py cannot install pyamrex yet as a dependency.
* ABLASTR: `ablastr/export.H`
Add a new header to export public globals that are not covered by
`WINDOWS_EXPORT_ALL_SYMBOLS`.
https://stackoverflow.com/questions/54560832/cmake-windows-export-all-symbols-does-not-cover-global-variables/54568678#54568678
* WarpX: EXPORT Globals in `.dll` files
WarpX still uses a lot of globals:
- `static` member variables
- `extern` global variables
These globals cannot be auto-exported with CMake's
`WINDOWS_EXPORT_ALL_SYMBOLS` helper and thus we need to mark them
manually for DLL export (and import) via the new ABLASTR
`ablastr/export.H` helper macros.
This starts to export symbols in the:
- WarpX and particle container classes
- callback hook database map
- ES solver
* CI: pywarpx Clang CXXFLAGS Down
Move CXXFLAGS (`-Werror ...`) down until deps are installed.
* GNUmake: Generate `ablastr/export.H`
* CMake: More Symbol Exports for Windows
* `WarpX-tests.ini`: Simplify Python no-IPO
Also avoids subtle differences in compilation that increase
compile time.
* Update PICMI_inputs_EB_API.py for embedded_boundary_python_API CI test
* Fix Python_magnetostatic_eb_3d
* Update: Python_restart_runtime_components
New Python APIs
* Windows: no dllimport for now
* CI: Skip `PYINSTALLOPTIONS` For Now
* CMake: Dependency Bump Min-Versions
for external packages picked up by `find_package`.
* Fix F and G_fp names in fields.py
* Tests: Disable `Python_pass_mpi_comm`
* Wrappers: Cleanup
* pyWarpX: Include Cleaning
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* fields.py: Fix F and G Wrappers
Correct MultiFab names (w/o components).
* Remove unused in fields.py
* Windows: New Export Headers
- ABLASTR: `ablastr/export.H`
- WarpX: `Utils/export.H`
* removed `WarpInterface.py` since that functionality is now in `particle_containers.py`; removed parts of `WarpXWrappers.cpp` that have been ported to pyamrex
* CMake: Link OBJECT Target PRIVATE
* CMake: Remove OBJECT Target
Simplify and make `app` link `lib` (default: static). Remove OBJECT
target.
* Fix in fields.py for the components index
* Update get_particle_id/cpu
As implemented in pyAMReX with
https://github.com/AMReX-Codes/pyamrex/pull/165
* WarpX: Update for Private Constructor
* Import AMReX Before pyd DLL Call
Importing AMReX will add the `add_dll_directory` to a potentially
shared amrex DLL on Windows.
* Windows CI: Set PATH to amrex_Nd.dll
* CMake: AMReX_INSTALL After Python
In superbuild, Python can modify `AMReX_BUILD_SHARED_LIBS`.
* Clang Win CI: Manually Install requirements
Sporadic error is:
```
...
Installing collected packages: pyparsing, numpy, scipy, periodictable, picmistandard
ERROR: Could not install packages due to an OSError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\hostedtoolcache\\windows\\Python\\3.11.4\\x64\\Lib\\site-packages\\numpy\\polynomial\\__init__.py'
Consider using the `--user` option or check the permissions.
```
* Hopefully final fixes to fields.py
* Update getProbLo/getProbHi
* Set plasma length strength
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Fix fields method to remove CodeQL notice
* Update Comments & Some Finalize
* Move: set_plasma_lens_strength
to MPC
---------
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
Co-authored-by: David Grote <dpgrote@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Roelof Groenewald <regroenewald@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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(#4124)
* add few readability checks to clang-tidy CI test
* address all the issues found with clang-tidy
* fix bug
* fixed bug
* fix residual issue
* fix issue found with clang-tidy
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* Clang Tidy: add several modernize checks
* eliminate file included in commit by mistake
* fix bug
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* init some variables at declaration
* make code more readable
* avoid lossy function result cast
* Update Source/Initialization/WarpXInitData.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
* replace with equality
* Revert "replace with equality"
This reverts commit e3164f9e053d345b153d770ae107a7f68c4bb260.
* Update Source/Diagnostics/ComputeDiagFunctors/ParticleReductionFunctor.cpp
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
---------
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
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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
for more information, see https://pre-commit.ci
* 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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* Multi-Dim Buildsystem Support
* Docs
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amrex::Abort(Utils::TextMsg::Err("msg")) (#3879)
* use WARPX_ABORT_WITH_MSG instead of amrex::Abort(Utils::TextMsg::Err(msg)) [WIP]
* use WARPX_ABORT_WITH_MESSAGE
* fix typo
* fix missing parenthesis
* remove spaces to prevent automatic text wrapping
* remove wrong parenthesis
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* use_powi
* fix bug
* fix bug
* fix bug
* fix bug
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* Bug fix: loop over all azimuthal modes taking into account the shift `mode*n_fields`
* Bug fix: added missing speed of light factor in coefficient `c2`
* Bug fix: added missing `mode` as fourth optional component in `X5(i,j,k,mode)` and `X6(i,j,k,mode)` coefficients, used only with RZ multi-J averaged PSATD
* Reset benchmark of `multi_J_rz_psatd`
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* Introduce `warpx.grid_type` parameter
* Replace `or` with `||`
* Update examples with new user input syntax
* Fix `if` condition
* Improve error message
* Fix `if` condition
* Fix bugs
* Fix warning
* Fix RZ
* Debugging
* Fix RZ
* Fix bug
* Clean up
* More changes:
- set default algo parameters with hybrid grid
- all hybrid input parameters under warpx name
* Set default field gathering algo for hybrid grids
* Update documentation
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* Implement First-Order PSATD Equations
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix Unused Parameter Warning
* Fix RZ Build
* Fix Normalization of G to Match PML
* Add CI Test: 3D Uniform Plasma
* Cleaning
* Update 2D CI Checksums
* Update 3D CI Checksums
* Add F,G to CI Checksums of `uniform_plasma_multiJ`
* Allow User to Choose First-Order v. Second-Order
* Add WARPX_ALWAYS_ASSERT_WITH_MESSAGE
* Rename New Class `PsatdAlgorithmFirstOrder`
* Remove Inline Comment
* Update RZ CI Checksums
* Fix inline comment
* Use auxiliary variables to avoid divisions
* Use auxiliary variables to avoid divisions
* Make `nci_psatd_stability` dir and merge inputs
* Move all Galilean tests to `nci_psatd_stability`
* Fix CI
* Fix index for backward FFT of J
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Rename PsatdAlgorithm as PsatdAlgorithmJConstantInTime
* Add New Inputs: psatd.J_in_time, psatd.rho_in_time
* Update PSATD Classes
* Fix Bug for FDTD Build
* Fix Warning for RZ PSATD Build
* Fix Multi-J Loop w/ J Constant in Time
* Clean up
* Fix Error Message
* Fix Time of Charge Deposition for Rho Linear
* Add 3D Langmuir CI Tests w/ Multi-J Algo
* Fix Checksums of New CI Tests
* Remove Extra CI Tests (added in #3363)
* Fix CI Tests w/ Multi-J PSATD
* Add Docs for New Input Parameters
* Galilean/Comoving PSATD Not Compatible w/ J Linear
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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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(#3117)
* use formatted error messages
* fixed bug
* fixed bug
* fixed bugs
* fixed bug
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* use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort()
* fix bug
* Update Source/WarpX.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* use more uniform text formatting
* fixed bug
* fixed bug
* using Utils::TextMsg in more files
* fixed bug
* use Utils::TextMsg in more files
* fixed bug
* use Utils::TextMsg in more files
* fixed last merge conflict
* fixed bug
* fix indentation
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* 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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* Rename PSATD Classes
* Rename PsatdAlgorithmJLinear as PsatdAlgorithmJLinearInTime
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* Separate Class for Multi-J PSATD Algo
* Cleaning
* X1,...,X6 Real, not Complex
* Cleaning
* Improve Comments, Rename Jx as Jx_old (etc.)
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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
for more information, see https://pre-commit.ci
* 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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* Remove WarpX::J_linear_in_time
* Fix Bug
* Implement Deposition of Rho at Half Time
* Implement New Equations for E
* Fix New Equations for E
* Cleaning
* Fix Limits of X2, X3, X7
* Implement New Equations for F
* Implement New Equations for F
* Revert E Equations to Avoid Roundoff Changes
* Remove Quadratic Equations
* Remove Deposition of Rho at Half Time Step
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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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* Implement div(E)/div(B) Cleaning with Standard PSATD
* Cleaning
* Update Benchmark
* Add Nodal Synchronization of F,G
* OneStep_multiJ: Nodal Syncs, Damp PML
* OneStep_multiJ: Push PSATD Fields in PML
* div Cleaning Defaults (Domain v. PML)
* Include Fix of #2429 until Merged
* Reset Benchmark of Langmuir_multi_psatd_div_cleaning
* Multi-J: Remove PML Support
* Include Fix of #2474 Until Merged
* Exchange All Guard Cells for F,G
* Fix Defaults
* Update Test, Reset Benchmark
* Fix Defaults
* Cleaning
* Default update_with_rho=1 if do_dive_cleaning=1
* Update CI Test pml_psatd_dive_divb_cleaning
* Replace Warning with Abort
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psatd.update_with_rho=0 (#2571)
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* PSATD with div(B) Cleaning: Change Normalization of G
* Use New Normalization also in RZ
* Use New Normalization also in FDTD
* Reset Benchmark of Test divb_cleaning_3d
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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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* RZ PSATD: Time Averaging for Multi-J Algorithm
* Fix Wrong Signs in Bm
* Use Time Averaging in CI Test, Update Benchmark
* Minor Fix
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* RZ PSATD: Implement Multi-J Algorithm
* Implement J_linear_in_time Option
* Reduce Style Changes
* Move Copy/Zero/Scale Functions to SpectralFieldDataRZ
* Remove Unused Member m_n_rz_azimuthal_modes from SpectralSolverRZ
* Fix CI -Werror Warnings
* Implement Same Changes of #2116, Cleaning
* Fix Bug: Pass Correct dt to SpectralSolverRZ
* Add CI Test
* CI Test: Set random_theta = 0, Update Benchmark
* Remove random_theta from Inputs
* Update Benchmark of multi_J_rz_psatd
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* Multi-J Algo: Make div(E)/div(B) Cleaning Optional
* Remove Unnecessary Newlines
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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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* 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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Work-around for:
```
Source/FieldSolver/SpectralSolver/SpectralAlgorithms/GalileanPsatdAlgorithmRZ.cpp(145):
error #2985: identifier "PhysConst::ep0" is undefined in device code
```
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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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* Split Initialization Functions of Spectral Coefficients
* Simplify Initialization of Coefficients Without Averaging
* Do Not Store Coefficients C1,S1,C3,S3 With Averaging
* Simplify Initialization of Coefficients With Averaging
* Add amrex:: Prefix Following WarpX Style Guidelines
* Match Names Of Coefficients With/Without Averaging
* 'pow' Cannot Be Used in a Constant Expression
* Update Doxygen Documentation
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* PSATD+RZ: Fix Warnings
Fix a couple of warnings in PSATD + RZ.
* BesselRoots: Missing Include & using
* Kernel & Util: Unused Code & Var
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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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Luca Fedeli
Axel Huebl
Edoardo Zoni
Olga Shapoval
David Grote
Prabhat Kumar
Neïl Zaim
Remi Lehe
Michael E Rowan
