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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
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* 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
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* 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
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* 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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* Clean up of MultiFab tagging
* Use [level=level] for the tag
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solver (#4034)
* explicitly check field `IndexType` appropriateness when using hybrid-PIC solver
* fix typo
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* Add "None" as an option for the Maxwell solver
* fixed some of the reasons for failing CI tests
* no longer pass `do_electrostatic` to `GuardCellManager`
* renamed `MaxwellSolverAlgo` to `ElectromagneticSolverAlgo`
* rename `do_electrostatic` to `electrostatic_solver_id`
* rename `maxwell_solver_id` to `electromagnetic_solver_id`
* start of hybrid solver logic
* changes requested during PR review
* remove `do_no_deposit` from tests without field evolution
* added `HybridSolveE.cpp`
* bulk of the hybrid solver implementation
* mostly reproduce 1d cold ion mirror results
* ion Bernstein modes reproduced with this version
* fix bug with reduced diagnostic FieldProbe in 1d
* added hybrid solver installation to PICMI and added example script generating ion-Bernstein modes
* enable the use of `FieldProbe` default parameter values
* use default field-probe values
* steady progress
* add `do_not_push` flag to picmi
* possibly use nodal fields
* added extra multifab for current calculated from curl B
* added `CalculateTotalCurrent` functions
* rewrote implementation to calculate J x curl B on a nodal grid first
* fill boundary for auxiliary MFs used during hybrid E solve
* properly handle nonzero resistivity
* updated hybrid model example
* clean up example scripts
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* fixed invalid memory access for GPU and other code cleanups
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* refinements on the example scripts
* added ion beam instability example
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* added EM modes and ion beam examples to CI test suite
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* started docs section on the hybrid model
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* more progress on documentation
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* added ion Landau damping verification test / example
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* add checksum benchmark for Landau damping example
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* added fields.py wrapper to access total current density in hybrid case
* refactored the charge deposition fix to be performed with the field data rather than individual particles
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* also correct current density at PEC boundary
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* made resistivity a parsed function of `rho`
* work on PEC boundary condition
* corrections pointed out during code review
* fix build fails due to unused variables
* fix issue with GPU builds
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* actually apply rho boundary correction in EM case
* take one sided derivative at PEC boundary when calculating div Pe
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* actually apply rho boundary correction in EM case
* removed specific treatment of E-field on PEC boundary for Ohm's law solver
* first round of CI fixes
* second round of CI fixes
* added description of deposition logic with PEC boundaries to documentation
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* third round of CI fixing
* move J and rho boundary handling to after `SyncRho` and `SyncCurrent` calls
* properly order the application of boundary conditions on rho, for electrostatic simulations
* fourth round of CI fixing
* moved calculation of total current (Ampere's law) to seperate function
* add random seed specification to `picmi`
* code clean-up -> renamed hybrid model to hybrid-PIC model
* added magnetic reconnection example
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* code cleanup & benchmark updates
* update PICMI class name for hybrid solver to `HybridPICSolver`
* don't apply J field boundary in
* don't apply J field boundary in `MultiParticleContainer::DepositCurrent`
* apply changes requested during code review
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Loosen tolerance on failing CI test
* Removed unused variable
* code cleanup: make use of `MultiParticleContainer::DepositCurrent` in `AddSpaceChargeFieldLabFrame`
* switch to using a rho_fp_temp multifab for old and averaged charge density field, also no longer require particles to move only one cell per step
* use `ablastr::coarsen::sample` namespace in `HybridPICSolveECartesian`
* switched to using `MultiFab::LinComb` instead of self written GPU kernels to calculated averaged or extrapolated current density
* add verbosity flag for the Ohm solver tests
* deal with fine versus coarse patches
* add theoretical instability growth / damping rates to hybrid-PIC examples
* update ion-Bernstein mode plot in documentation
* move the `ApplyRhofieldBoundary` call to after `SumBoundary`
* use a uniform calculation for the number of cells a given index is from the boundary
* remove unused variable
* limit number of ghost cells updated during PEC BC application
* the number of ghost cells to consider depends on whether the field is nodal or not
* attempt 1 to fix failing CI tests
* attempt 2 to fix failing CI tests and code cleanup
* attempt 3 to fix failing CI tests
* attempt 4 to fix failing CI tests and docs cleanup
* switched to using bibtex citations
* move hybrid solver input parameters documentation to its own section
* clean up ion beam instability analysis script
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Apply suggestions from code review
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* add inline comments describing the meaning of each argument for the `amrex::MultiFab::LinComb` calls used
* make `HybridPICSolver` a child class of `picmistandard.base._ClassWithInit`
* apply changes requested during code review
* add warning about using hybrid-PIC solver with Esirkepov current deposition
* add Stanier 2020 reference to recommend linear particles with hybrid-PIC
* add call to FillBoundary for `current_fp` - needed for accurate interpolation to nodal grid
* changes requested from code review
* Apply suggestions from code review
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* include physics accuracy check for ion beam instability; switch CI tests to use direct current deposition
* reset benchmark values after switching to direct current deposition
* update ion beam instability benchmark
* minor changes requested during code review
* remove guard cells for `enE_nodal_mf` as well as corresponding `FillBoundary` call
* refactor: moved hybrid-PIC specific multifabs and `CalculateElectronPressure()` to `HybridPICModel`
* add assert that load balancing is not used with the hybrid-PIC solver since the new multifabs are not yet properly redistributed
* move `CalculateCurrentAmpere` to `HybridPICModel`
* refactor: moved `HybridPICSolveE` to `HybridPICModel` class
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Luca Fedeli
Axel Huebl
David Grote
Roelof Groenewald
