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* Prevent NaNs in collisions between particles
* Avoid another division by 0
t# Please enter the commit message for your changes. Lines starting
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* Clang-tidy: add misc-definitions-in-headers check
* address issues found with clang-tidy
* remove std::cout added for debug purposes
* add back newline
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* added collider reduced diags
* added test
* fixed xy_ave and xy_std
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* fixed usage of IntVect and removed print
* Set up automated CI test
To-do:
- Fix bug (erroneous arithmetic operation)
- Remove unused parameters from input file
* Fix warning: set mass only if WARPX_QED
* Use amrex::ParticleReal for mass
* Update Make.package to fix GNU Make build
* reduced_data.value() only once
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* Merge `development` into `coll_rel_red_diags`
* updated 3d beam test
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* updated 3d test
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* `m_write_header` instead of `m_IsNotRestart`
* added angles
* updated 3d beam test
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* added 3 particle test
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* added warning
* updated diags names
* updated analysis multiple particles
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* added positrons to test
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* Update CI test
* Reuse input file parser from Tools
* Apply suggestions from code review
* Apply suggestions from code review
* changed order of diags and added docs
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* Apply WarpX style conventions
* Fix CodeQL alerts
* assert in RZ and removed fine ref levs
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* Fix compilation in 2D
* Fix compilation in RZ
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* minimized number of kernel launches and parallel ops
* updated constructor of ReduceDiags
* fixed based on comments
* updated docs: if QED not enable
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* fixed ReducedDiags constructor
* two passes instead of one for robusteness
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* fixed bugs
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* Fix 1D build (typo `wtot` instead of `w_tot`)
* refixed compile in RZ
* check io process in chi_ave computation
* updated test
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* Temporary fix: remove IOProcessor
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Apply suggestions from code review
* Remove `Debug` compilation mode from CI test
* CI test analysis: check all particles have same charge
* Use `m_beam_name` instead of `species_names`
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
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This is done by properly broadcasting the file geometry information
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* clang-tidy CI test: add selected google- checks
* address issues found with clang-tidy
* fixed bugs
* fix bugs
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* only print resampling message if `verbose` is on
* clang-tidy fix
Only use `const` qualification in function definitions, not in function declarations.
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* ChargeDeposition: Remove Global WarpX Variable
Remove Global WarpX variable use in `ChargeDeposition`.
* CurrentDeposition: Add Missing Include
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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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SignalHandling::CheckSignals() (#4240)
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* Add Python bindings to extract the timestep
* More secure array access
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* Work-Around: Segfault in MPI_Init with HIP
See:
https://docs.olcf.ornl.gov/systems/crusher_quick_start_guide.html#olcfdev-1655-occasional-seg-fault-during-mpi-init
* Move to ABLASTR
All that counts is that HIP is initialized before GPU-aware MPI.
* Add Exception
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In the spirit of a recent nvcc compiler bug, simplify the capture
logic from implicit to explicit for the particle filter lambda.
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* Remove AddToMultiFabMap functions from WarpX class
* fixed bug
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Add constant record components for position and positionOffset
in 1D3V and 2D3V simulations.
Follows our conventions in
https://warpx.readthedocs.io/en/latest/developers/dimensionality.html#conventions
and simplifies post-processing, e.g., emittance calculations.
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* Fix: WarpX Version
Fix the WarpX version info.
* Fix Version: pyWarpX
* Version: More Python __version__
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* Fix Repeated Plasma Lens: Start
The current implementation has problems finding the right
index of the current plasma lens if:
- the lens started before z=0
- the lens did not start between z=0...first-period
This should fix it.
* Document Start, Define an End
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* BoxArray in BTD has single box
* cleaning to remove all instances of max_box_size
* Assert BA size to be 1 for BTD and fix an inline comment
* fix typo
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Add an include guard to this header file.
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(#4116)
* include current density in diagnostic output even if an electromagnetic solver is not used
* do not redeposit current for the magnetostatic solver
* update CI benchmarks for tests that previously did not register current density
* fix remaining failing CI test
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* do not output current density in collision tests
* update `JFunctor` constructor doc-string
* code cleanup - reduce code duplication
* specify `Ex Ey Ez Bx By Bz` fields to plot for collision CI tests
* specify `Er Et Ez Br Bt Bz` as output for rz collision test
* rename `InterpolateToDst` to `InterpolateMFForDiag`
* only deposit current density once per diagnostic output (if not already deposited)
* write deposited current for all directions into `current_fp` during diagnostic step deposition
* use `amrex::make_alias` to directly deposit current density into `warpx.current_fp` during diagnostic step deposition
* add class variable `solver_deposits_current` to `FullDiagnostics` so that there is only one place where the determination is made whether current should be deposited during diagnostic output
* correct logic to determine `m_solver_deposits_current`
---------
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Fix: Remove Overly Exported Classes
Luckily, many of them should not contain global state.
* Add Missing WarpX.H Include
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* added nodal electrostatic solver
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* sphere test for electrostatic nodal solver
* add 3d single bunch test
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* adds single bunch ci test
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* updated tests
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* updated checksums nodal electrostatic
* Improve readability
* Change `assert` condition
* Clean up
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Extensive clean up of PlasmaInjection
* Small cleanup of parseMomentum
* Fix string argument reference
* Remove unneeded surface_flux
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(#4153)
* added guidelines
* added impose t_lab from file as an option
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* removed unused comment
* fixed unconsistent variable type
* removed space
* rearranged code changes
---------
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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
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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
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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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* Broadcast quantity & update tests
* Make only one rank create the lasy file
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---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* use same finite difference algo as for Yee with hybrid-PIC to calculate divE
* add `divE` and `divB` to field diagnostic in picmi.py
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* Add Python wrapper to set the lens strength
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* Correct missing `c_real`
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* Add assert message
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Fix continuous injection of lasers
- define new member functions nLasers and nContainers;
- loop over all containers, not just over all "species".
* Fix update of injection position for lasers
* Fix CodeQL issues
* Fix style
* Rename `ispecies` as `index`
* Rename functions to update injection and antenna positions
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* Add write_diagonstics_on_restart input option
* Add doc to new variable
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Use correct time step
---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Clang-tidy CI test: add few misc checks
* fix issue
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(#4164)
* clang-tidy CI test: add new readability checks
* address issues found with clang-tidy
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Remi Lehe
Luca Fedeli
Arianna Formenti
David Grote
Roelof Groenewald
Axel Huebl
Revathi Jambunathan
aveksler1
Ryan Sandberg
Ilian Kara-Mostefa
Edoardo Zoni
