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* CI: Shrink NVHPC Size
Try to shrink the size occupied in the NVHPC CI runs. Currently
running out-of-disk...
* NVHPC: Thin out Install
- remove profilers (big)
- remove static libs (big)
- remove examples (small)
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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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* BTD RZ test: add missing checksum analysis
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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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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Accidentially now always built AMReX was shared library,
which is only needed if we build with Python.
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* Remove unused/untested Python file
* Remove additional file
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Because breathe is not yet ready.
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Add an include guard to this header file.
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Frontier uses a Low-noise Mode Layout for its nodes which pins system
processes via the default core specification `-S 8` to the first core
every L3 region.
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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`
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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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* sphere test for electrostatic nodal solver
* add 3d single bunch test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* adds single bunch ci test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* updated tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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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* Implement boosted frame automated test (1D)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Implement boosted frame automated test (1D)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* time_chunk_size=50
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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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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* Update Python installation instructions on HPC
* Update Python installation instructions on HPC
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Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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We use too many cores when we compile and thus get our compile
processes killed by the system. Let's use a bit less to stay
in the limits.
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updates:
- [github.com/Lucas-C/pre-commit-hooks: v1.5.3 → v1.5.4](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.5.3...v1.5.4)
- [github.com/hadialqattan/pycln: v2.2.1 → v2.2.2](https://github.com/hadialqattan/pycln/compare/v2.2.1...v2.2.2)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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(#4153)
* added guidelines
* added impose t_lab from file as an option
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* removed unused comment
* fixed unconsistent variable type
* removed space
* rearranged code changes
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Python 3.7 went EOL last month. Time to bump up our supported
versions to 3.8+ as well.
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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
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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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* Broadcast quantity & update tests
* Make only one rank create the lasy file
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Update PICMI interface for Gaussian flux
* Update version of picmistandard
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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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Correct missing `c_real`
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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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- We do not need to cover year ranges (just the starting range).
- Update to exact wording of current notice texts.
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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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As discussed last week, we have a hard time tracking the Gitter
chat and organizing threads in it. GitHub discussions should
simplify that.
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* Clang-tidy CI test: add few misc checks
* fix issue
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Axel Huebl
Remi Lehe
Revathi Jambunathan
aveksler1
Edoardo Zoni
Ryan Sandberg
Ilian Kara-Mostefa
Marco Garten
Arianna Formenti
Roelof Groenewald
David Grote
pre-commit-ci[bot]
Luca Fedeli
