| Age | Commit message (Collapse) | Author | Files | Lines |
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* add more readability checks to clang-tidy CI test
* reformat check list
* starting to address issues found with clang-tidy£
* addressing issues
* remove check
* address issues
* address all issues
* address issue found with github code scanning
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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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* 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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* replace amrex::Abort with WarpX macros
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* adding back missing include
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* use amrex::Abort in a GPU kernel
* bump precision
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* Multi-Dim Buildsystem Support
* Docs
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* initial work to clean WarpX Utils
* remove AMRCore from Ionization tables
* progress
* refactoring of a part of the utils directory
* fix bug
* fixed bug
* fixed bug
* remove debug line accidentally slipped into the code
* remove debug line accidentally slipped into the code
* remove debug line accidentally slipped into the code
* cleaning
* fixed bug
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* 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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* initial work to add msg formatter
* wip
* replace AMREX_ALWAYS_ASSERT_WITH_MESSAGE with WarpX equivalent
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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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* 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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* 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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* CMake 3.20+ and CUDA: Modernized AMReX
Use modernized AMReX logic for CUDA builds with CMake 3.20+ as
supported by the latest AMReX updates.
* Resampling Trigger: Missing Include
AMReX update triggered missing include:
```
Source/Particles/Resampling/ResamplingTrigger.H(42):
error: namespace "amrex" has no member "Real"
```
* Update AMReX
Update AMReX to f7fd082bc8ab099d42784f69d6fe49dea3d388a7
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Fix a warning
```
warning C4138: '*/' found outside of comment
```
with MSVC.
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(#1385)
* Add option to only resample cells with high enough number of macroparticles
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Use amrex::ParallelForRNG for random number generation
In order to support RNG on non-Nvidia GPUs, we need to use
amrex::ParallelForRNG for kernels with calls to AMReX random number
generation functions.
* missing a RandomEngine argument
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* First working version of tests
* Add comments to test
* Add test in WarpX-test.ini and initial checksum json file
* Add resampling to input parameters doc
* Uncomment lines about checksum in analysis script + Fix minor typos
* Add momentum in plotfiles (for checksum) + Fix minor typoes
* Remove particle_theta from checksum json file
* Remove rho from checksum json file
* Fix syntax error in checksum json file
* Add benchmark values
* Update Docs/source/running_cpp/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Have one Resampling object per species
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* fix << declaration of galilean_shift shadows a member of WarpX >>
* fix << unused mu_stag >>
* fix << unused uxp, uyp, uzp >>
* renamed galilean_shift (member variable of WarpX class) into m_galilean_shift
* renamed v_galilean to m_v_galilean when appropriate
* fixed bug introduced in latest commit
* fix <<comparison of integer expressions of different signedness>>
* Update Source/FieldSolver/FiniteDifferenceSolver/MacroscopicEvolveE.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Initial commit (not working)
* First working version
* Cleaning and adding Doxygen comments
* Apply suggestions from code review
* Move findParticlesInEachCell to Utils/ParticleUtils
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* First version of resampling structure
* Remove new warnings
* Added Doxygen comments
* Minor modifications
* Add do_resampling() in OneStep_sub1
* Apply suggestions from code review
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Use mutable in ResamplingTrigger and replace run with operator()
* Apply suggestions from code review
Co-authored-by: MaxThevenet <maxence.thevenet@desy.de>
* Make LevelingThinning operator() final
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-authored-by: MaxThevenet <maxence.thevenet@desy.de>
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Luca Fedeli
Axel Huebl
Neïl Zaim
Edoardo Zoni
Weiqun Zhang
