| Age | Commit message (Collapse) | Author | Files | Lines |
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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
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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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* Allocate fewer components for `rho`
* Fix compilation
* Use two components with dive_cleaning
* Fix Python script
* Fix PICMI script for 1D CI test
---------
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* Histogram 2D
A new functionality has been added. The files ParticleHistogram2D.cpp and ParticleHistogram2D.H allow the user to plot a 2D histogram that computes the number of particles for a given abscissa and ordinate.
* Modification to solve NVCC 11.8.0 GNUmake issue
ParticleHistogram2D.cpp added into Make.package
* Test for using openPMD
Test to activate the plug in for openPMD : #ifdef WARPX_USE_OPENPMD
Error message otherwise.
* Test for using openPMD continued
* New version of the ParticleHistogram2D option
The user can now choose the value of the weight via a value_function.
Another parameter was therefore added : w
The documentation has also been updated and an example (input file + python script for postprocessing) has been added to Examples/Physics_application/laser_ion
* Python script updated
The python script written for postprocessing the ParticleHistogram2D option has been renamed to pass a check test.
The argparse module has also been added to the code instead of the originally implemented command line interaction. Now the user must pass arguments when executing the script.
* Input files of the laser-ion example merged
The input file originally created for the 2D histogram has been merged with the initial input file "inputs" of the example.
* Correction of a display bug
* Help function for openPMD files
A help function has been created to find the correct file type when writing openPMDfiles.
Another update : the file type will be returned in the warpx_used_inputs file after running a simulation.
* Typo fixed in the python script used for 2D histograms visualisation
Typo for the shape of the data
* Typo in the help function file created
* Some typo fixed for checks
Modifications in the input file of the laser-ion example and in the ParticleHistogram2D.cpp file.
* Typo fixed : declaration on the WarpXOpenPMDFileType function outside #ifdef WARPX_USE_OPENPMD
* Typo for failing check NVCC 11.8.0 GNUmake
* Typo for failing check NVCC 11.8.0 GNUmake (continued)
* Typo for failing check NVCC 11.8.0 GNUmake (continued, abort message)
* .cpp file added to Make.package
* Time added to the data
Simulation time is now visible on Hist2D plots
* Update Docs/source/dataanalysis/reduced_diags.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/laser_ion/analysis_histogram_2D.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/laser_ion/analysis_histogram_2D.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ParticleHistogram2D.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ParticleHistogram2D.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ParticleHistogram2D.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/OpenPMDHelpFunction.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/OpenPMDHelpFunction.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Multiple hist2D active in the same simulation now possible
The laser-ion example as well as the documentation have been modified accordingly.
* Display enhancement for the laser-ion example
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---------
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Guarantee improved plasma stability for 2D with very low initial
target temperature when using Esirkepov current deposition with
energy-conserving field gather (default).
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* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* corrections pointed out during code review
* fix build fails due to unused variables
* fix issue with GPU builds
* actually apply rho boundary correction in EM case
* 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
* 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
* deal with fine versus coarse patches
* 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
---------
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>
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* change plotfile RZ allowed diag to r,t from x,y
* Change labeling in checksums
* add rz silver mueller analysis script
* make analysis_silver_mueller_rz.py executable
* change x,y fields to r,t in more tests
* x->r in MR RZ checksums
* correct analysis for plotfiles saved as 'boxlib'
* add self to creator list
* change rz diags in PICMI
* correct PICMI changes
* another y->t in an rz test
* update picmi plotfile rz btd names
* review suggestion to condense analysis
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Apply suggestions from code review
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---------
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Fix NUniformPerCell for 1D
* Fix CI benchmarks
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* Modify refined ijection CI to account for anisotropic ref ratio
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* change n_move based on new dt
* change variable name to be more specific
* Update Regression/WarpX-tests.ini
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* reset benchmark for RefineInjection because now it uses anisotropic refinement ratio
* add comment to show the formula for n_move
* Reset benchmark of `RefinedInjection`
* Remove wrong benchmark file
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* Start removing old BTD
* Remove GetCellCenteredData
* Remove do_backtransform_fields and do_backtransform_particles
* Remove more functions
* Remove more variables
* Update documentation
* Fix CI test `RigidInjection_BTD`
* Remove slicing from `BTD_ReducedSliceDiag`
* Rename `BTD_ReducedSliceDiag` as `LaserAcceleration_BTD`
* Query deprecated input and abort
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* Add warning to set zmin and zmax for ions
and also change the ion acceleration example to set these
parameters so that users are aware that memory overflow could
happen for production-size examples
furthermore, correct units in comment after definition of
r0 and Lcut
Replace zmin and zmax with variables for electrons
* Reset checksum for regression test
Reset benchmark for LaserIonAcc2d test because the particle
initialization in the input changed.
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plotfile/openPMD (#3424)
* print when writing openPMD, Ascent, Sensei
* remove unnecesssary variables, include min_digits
* print snapshot id when writing btd
* fix ascent print
* compile without warnings
* still working on Ascent
* still working Ascent
* Print when BTD buffer is flushed
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* print when writing openPMD, Ascent, Sensei
* remove unnecesssary variables, include min_digits
* print snapshot id when writing btd
* fix ascent print
* compile without warnings
* still working on Ascent
* still working Ascent
* Print when BTD buffer is flushed
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* add warning message if BTD not full
* adjust for CI, no in-situ vis BTD
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* revert to correct plotfile naming
* change warning topic to BTD
* nicer format for print statements
* extend examples to fill BTD
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Reset Checksums of BTD_ReducedSliceDiag
* Upgrade CI Test LaserAccelerationBoost
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* improve BTD warning notes
* edit final step notes
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* Fix formatting
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Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Correct particle positions outside refined injection
* Improve test
* Update benchmark
* Update Examples/Physics_applications/laser_acceleration/analysis_refined_injection.py
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* Added tridiag solve for 1D
* Added tridiag solver to WarpX.H
* Updated PICMI_inputs_1d.py to use float64
This was done so that it will compare to the tridiag to machine
precision
* Updated 1D capacitive_discharge test, adding pythonsolver flag
* Update capacitive_discharge analysis_1d.py file with updated reference data
* Add periodic boundary conditions, plus other fixes
* Added CI test Python_background_mcc_1d_tridiag
* Fix for parallel
* Fixed CI test file prefix for PICMI_inputs_1d.py
* Fixed comments
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* add 1d support to _libwarpx.py functions `get_particle_X`
* add coverage of 1d `_libwarpx.get_particle_z` to test suite
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Update comments in example input files: moving window now available along x, y, z.
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* Allow filtering in z with RZ FDTD
* Update the error message about filtering in RZ
* Turned z filtering on in laser_acceleration/inputs_rz
* Update LaserAccelerationRZ benchmark, including z filtering
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* `isort`: AMReX, WarpX, etc. as First Party
Mark the `amrex` and `pywarpx`, `picmistandard`, ... imports as first
party, so that they do not change if run locally or remotely pre/post
install.
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* Species variables in diagnostics: deal with runtime components
* Remove ParticleStringNames namespace
* Use const reference in iteration variable
* Fix ion acc 2D test
* Output extra (e.g. initialized later with python) comps by default
* Always output theta in RZ
* Fix QED tests
* Fix Laser Acceleration RZ test
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* Use amrex::RandomNormal in Maxwell-Boltzmann momentum injection
* Remove factor sqrt(2) in std calculation
* Update benchmarks
* Increase relative tolerance for Python_background_mcc checksum
* Update Source/Initialization/InjectorMomentum.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* initial commit for MCC to support relativistic particles
* proper calculation of collision energy when target mass is not much greater than projectile mass
* fix bug with scattered velocity rotation to lab frame
* refactor the MCC sequence for clarity
* use cross-section input to determine energy limits when calculating the maximum collision frequency
* code cleanup
* updated CI tests
* added Collisions section to Implementation Details in docs
* reset benchmark for mixed precision MCC test and other more code cleanup
* fix issue with single precision and simplified implementation
* use `double` for particle mass and energy calculations in MCC
* added comment to ImpactIonization.H explaining why `double`s are used for `energy` and `mass`
* switch to round off safe version of energy calculation and switched to using u instead of v for gamma*v in ParticleUtils.H
* update documentation
* simplified expression for collision energy, updated docs
* Add comment that the direct solver can be replaced for the MLMG solver once the issue with that solver is fixed (in the 1d MCC test)
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* Examples: LBC in Laser-Ion Example
* LoadBalanceCosts: num_cells & num_macro_particles
* Fix Script: Wrong Header Counting
Spliced out the first to columns twice.
* Fix Script: Blocking Factor
The script did not work if a direction only had one block
* Fix Script: 2D/3D
There is no generic way from the data we write to find this out,
without breaking corner cases such as one-block in one direction.
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* DRAFT for Moving Frame
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* Adds m_last_compute_step
* Generalized SetParticlePosition, semicolons and formatting
* Update Source/Diagnostics/ReducedDiags/FieldProbe.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Moved particle push before calculations. Condensed stuff.
* Fixed Velocity, added start and stop time functionality
* Documentation
* Apply suggestions from code review
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* Empty-Commit
* Fixed ParallelFor from review
* FP moving window in laser_acceleration 1d, 2d, 3d test
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* Line detector instead of point
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* [Draft] openPMD: RZ Modes
* Change 'theta' to 't' and 'J' to 'j'
* Docs: openPMD rz notes
* editing docs openPMD RZ note
* erase cartesian E,B,j from openPMD rz diags list
* openpmd rz: theta->t, exclude xyz dumps
* openpmd rz: axes r,z, save as comp[mode][r][z]
* catch logic bugs tracking when in rz mode
* change return type to c++17 tuple in helper fn
* allow divB functor to store in theta mode
* tuple bindings / account for theta mode variables
* only r,t,z componets in RZ, separate rz field init
* separate rz field init, arbitrary diags in RZ
* docs: xyz comps in cartesian, rtz in rz geometry
* docs : remove mention of dump_rz_modes
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* clarify documentation of InitializeFieldFunctorsRZ
* n_rz_modes = 1 if not in RZ
* style change for brackets
* style, documentation, clarify magic constants
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* add helper getVec
* transpose RZ openPMD data for proper viewing
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* safe for 2d and rz
* fix transpose order of limits, add tinyProfiler
* document transpose function, lack of optimization
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix divB num components
* keeping changes to openPMD+RZ, not general RZ
* divB made more similar to divE
* eliminate or document unused variables
* fix openPMD+RZ documentation
* change thetaMode parser to regex
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* replace n_rz_azimuthal_modes with warpx variable ncomps
* Ignore Unused Var in Cartesian
* add rz openpmd analysis
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix warnings: unused vars
* clarify documentation of dump_rz_modes
* cleaning up before sending to PR
* remove divB, divE, test in a different PR
* Update Source/Diagnostics/WarpXOpenPMD.cpp
fix Dxygen strings
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* clean up doxygen, note issue in divB
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* fixing rz_opmd test, still not passing
* Fix: Unused <diag>.dump_rz_modes
* updating openPMD+rz analysis
* Regression Setup: set `outputFile`
* Use HDF5 Backend
This is most likely installed by all developers, so we use it for
tests.
* Code Style Updates
* simplify test and reduce code redundancy
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* reduce redundancy 1 less line
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Keep HDF5
HDF5 is easier to install for developers and provided in CI.
* Style fixes
* Style fix
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
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* file_min_digits: 5->6
100k+ step runs are quite common in WarpX. To simplify
post-processing scripts, increase the default to pad to 6 digits.
This might break some hand-written scripts that use `?????`
wild-cards over `*` wildcards in regex and thus need to be updated.
But it at the same time simplifies regexes for analysis of data
series and listing of such file series.
* Update Scripts to Handle New File Names
* Fix CI Test pml_x_psatd
* Fix CI Test divb_cleaning_3d
* Fix CI Tests with EB Support
* Fix CI Tests with RZ Support
* Fix CI Tests with PICMI Support
* Use glob in Analysis of Collision Tests
* Use rstrip in Analysis of Collision Tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix CI Tests for Langmuir_multi_1d/psatd
* Fix CI Tests for LaserInjection_1d
* Checkpoint-Restart Tests: 5 Digits
`regtest.py` in `regression_testing` hard-codes 5 digits:
```diff
--- a/regtest.py
+++ b/regtest.py
@@ -734,7 +734,7 @@ def test_suite(argv):
shutil.move(test.diffDir, orig_diff_dir)
# get the file number to restart from
- restart_file = "%s_chk%5.5d" % (test.name, test.restartFileNum)
+ restart_file = "%s_chk%6.6d" % (test.name, test.restartFileNum)
```
* PICMI Restart Tests: `warpx_file_min_digits = 5`
Same as other CI restart tests: hard-coded value in regression
suite makes this necessary.
X-ref: https://github.com/AMReX-Codes/regression_testing/issues/119
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* define user attributes, parse them, initialize with respective parsers
* fix warning by using static_cast for int attribute as parser returns real
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* clean-up from self-review
* adding dimensionless velocity, gamma*v/c and time to parser argument
* add documentation
* typo in comment
* unused var
* device vector for kernels
* particle attribute in developer doc
* data ptr for device vector
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* ignore_unused
* Docs: Describe all particle attributes
including pre-defined ones :)
* Docs: Fix formatting (user params)
* Add: 1D and RZ Support
* Docs: Fix Typo in Function Declaration
* Laser-Ion Example: User-Defined Attrib.
Add two user-defined attributes to the laser-ion acceleration
example. This is a 2D test.
Documents the name in the table of commonly used, user-defined
attribute names. The attribute added is the original position
of particles, which I like to plot in "potential" plots that
correlate original position in the target with final energy.
* changing user-interface API with .attribute. and no need for separate 1D 2D 3D RZ code for parser. pos.x/y/z returns the right values
* Adding 1D, 3D, and rz tests
* attribute in inputs
* at(i)
* refinining names for inputs for laser ion and acceleration tests
* typo in input
* reset benchmarks for test-cases that included attributes
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* LWFA PICMI Tests: Add Electron Beam
* Remove Electron Beam from 1D Test
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* add SyncRho call to warpx_depositChargeDensity
* expose SyncRho to Python; add warpx_clearChargeDensity to reset rho_fp before deposition
* remove unneeded warpx_clearChargeDensity function
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add (default) option to depositChargeDensity to call SyncRho after deposition
* added option to depositChargeDensity to zero out rho_fp before deposition
* code cleanup
* import fields from inside depositChargeDensity
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
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* RZ FDTD: Filter Not Working (Abort)
* Update CI Tests and Benchmarks
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* added python wrapper function to deposit a specific species density in rho_fp
* added 1D ES input file with MCC that uses the charge deposition functionality
* reset rho_fp[lev] before depositing
* updated documentation
* switch to using simulation.extension in Poisson solver
* Apply suggestion from code review
Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
* suggested changes from code review
* add comment explaining why a direct Poisson solver is used
* removed direct solver in 1D example since it is actually slower than the MLMG solver
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* added docstring for warpx_depositChargeDensity
* fixed order of imports in new PICMI input file
Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Make moving window dimensionality consistent in PICMI
* update PICMI_inputs_plasma_acceleration_1d.py
* two elements for moving window velocity in RZ
* update RZ laser_acceration test
* update PICMI version
* update PICMI Langmuir RZ test
|
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* move BTD call before Redistribute
* define particle buffer, BTD particle functor, particle filter
* select particles on the slice
* add particle functors
* add Lorentz Transform
* fix conflict
* add call to loretnz operator
* storing Particles in buffer
* This is WIP. Added particle buffers, filled them, sent them for flush with number already flushed. Does not work for multiple flushes. Crashes for OpenPMD.
* trailing endif after rebase
* adding print statements and not flushing particles in OPENPMD if numpart is 0
* last timestep flush is ensured at the end of evolve loop
* fix bug in declaring uy uy new and computing uzp
* set particle Geom, BA, and DMAP for particle flush with plotfile
* set Particle BA Geom DMAP for particle buffer and no BTD transform for force flush
* separate compute and pack from flush
* Fix Typo: resizeable -> resizable
Fixes HDF5 BTD particle output.
* new class for plotfile particles for BTD
* copy particle_H and DATA and Header. some WIP print statements
* Merge plotfile
* clean print statements
* fix warning message
* struct declaration in header, fix warning
* doxygen comments and copyright
* clean print statements
* fix eol and override function warning
* tile data
* fix output species array size bug
* fix access for particle buffer size
* clean and move time-update
* add cur_time update back
* remove cur time update which was called twice
* dont access particles flushed already for full diagnostics
* cur time must be updated for RigidInjection BTD CI test to pass
* temporarily move call to BTD
* updating time and calling BTD before movewindow
* cleanup
* reset benchmarks and analysis script
* clean and add comments
* fix particle box array, geom, dmap
* reset benchmarks for multi_J rz and ElectrostaticSphereEB_mixedBC
* wip commit
* wip commit
* add SI conversion
* abort for openpmd bp backend if species is selected. Also write particle output for BTD only if write_species is 1
* add documentation for aborting if adios is used with openpmd and add other BTD input parameters
* Apply suggestions from code review
commit Axel's suggestions from review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* use bool instead of int
* fix doxygen format
* using h5 as backend in example test to ensure consistency with abort for particle output.
* fix doxygen comment
* reset benchmark again for comoving_2d_psatd galilean_2d_psatd multi_J_rz_psatd
* reset benchmark for background_mcc
* self-review suggestions
* reset benchmarks. Update with last snapshot full info
* Axel's PR suggestions
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's doxygen fix
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add comments
* fix eol
* improved exception handling for stringsteam
* PR suggestions
* Axels' suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Axel's suggestions :)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* simplify logic
* suggestions from review (Axel/Reva)
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* variable name change for clarity
* if num particles in tmp array is 0, return
* Use new BTD inputs to set up BTD for particles in the corresponding particle container
* unused var
* fix logic error
* speciesID undefined
* separate particle and field buffer calls and initialization for BTD. Data common to both are initialized separately
* rename variable so it does not ghost existing varname
* add more comments
* Assert that fields are on
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* redundant function definition
* unused variable
* unused variable zp
* 1D 2D 3D definition
* fix else
* Apply suggestions from code review
Add Prabhat's suggestion
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
* missing semicolon and ignore xp yp for 1D
* resetting benchmarks for boosted sims and mcc sim
* temporarily changing tolerance since the relative difference for momentum_z is 3.68e-3 and the current tolerance is 2.5e-3
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
|
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* Add PICMI Script for 2D Case
* Add PICMI Script for 3D Case
* Cleaning
* Add PICMI Script for 1D Case
* Add PICMI Script for RZ Case
* Remove Old PICMI Script
* Remove Old Test Python_LaserAccelerationMR
* inputs_3d: Move Inputs From runtime_params
* inputs_2d: Move Inputs From runtime_params
* Update PICMI Script for 2D Case
* Update PICMI Script for 3D Case
* inputs_1d: Move Inputs From runtime_params
* inputs_2d_rz: Move Inputs From runtime_params
* Rename inputs_2d_rz as inputs_rz
* Update PICMI Script for 1D Case
* Update PICMI Script for RZ Case
* inputs_rz: Fix Diagnostic Interval
* Fix Diagnostic Interval For All Inputs
* Add New Test For Each PICMI Script
* Remove Old PICMI Script From Workflow yml Files
* Dump RZ Modes for RZ Case
* LWFA PICMI: Add Shellbang
Add missing shellbang lines.
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
|
* Initial attempt at moving function into LibWarpX
* Bugfix - undefined structs in get_particle_theta
This is untested, identified by IDE/visual inspection only
* Unify newlines
* Delete libwarpx.clight (duplicated picmi.py)
See picmi.constants.c
* Change function descriptive comment to docstring
Also remove extra newline in __init__ beginning.
* Replace pywarpx/_libwarpx calls appropriately
* Fix atexit register of finalize function
* Reorder WarpX.py imports for pre-commit
* Use picmi.Simulation.extension = libwarpx alias
This will hopefully preempt user script changes if we restructure things
to allow multiple WarpX runs to be done within a single Python script.
* Fix libwarpx ref in WarpX.getProbLo/getProbHi
* Update get_particle_boundary_buffer doc reference
|
|
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
`.editorconfig`: isort options
https://github.com/PyCQA/isort/wiki/isort-Settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleaning: double np and lib
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
|
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* Docs: `geometry.dims` option
Add a new, required option to specify the geometry of an
inputs file at runtime.
* Check & Report Runtime Dims Mismatch
* Examples: add `geometry.dims`
* Deprecation Warning: `geometry.coord_sys`
* PICMI: `geometry.dims`
* Improve error message
sounds a bit better
* Improve Doc Description
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
|
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* Wrap shared object in a class to control its loading
* Fix libwarpx attribute references
* Updated callbacks.py for updated libwarpx
* Removed the wx module plus other clean up
* Further revision of how to use the pywarpx module.
Now, _libwarpx should not be imported by external scripts except in special circumstances.
* Updated documentation
* Clean up end of line whitespace
* Added more wrapping routines plus some clean up
* Fixed use of pywarpx in two examples
* Fix for getistep
* Fixed for the EB Python interface
* Silence a warning for our wrapper
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
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* Examples: Python ShellBang & Executable
Make sure that all PICMI scripts and all analysis Python scripts
in `Examples/` are:
- executable (`chmod a+x`)
- start with a shell-bang to `python3`
Now, all scripts can be run directly without a `python3 ...` prefix
and also default to the only right executable of Python on older
systems. (New systems always have a `python3` alias, too.)
* Revert a moved numpy
|
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Prepare to enable autofix bot from https://pre-commit.ci
|
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Hard coded, undocumented convention: turns out this must be the name
of the test that we define in the ini file. Logical, isn't it. Not.
Follow-up to #2593
|
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* modify requirements.txt and add input file for 1D Python pwfa
* add 1D Python plasma acceleration test to CI
* picmi version
* USE_PSATD=OFF for 1D
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Regression/WarpX-tests.ini
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Cartesian1D class in pywarpx/picmi.py
* requirements.txt: update picmistandard
* update picmi version
* requirements.txt: revert unintended changes
* 1D Laser Acceleration Test
* Update Examples/Physics_applications/laser_acceleration/inputs_1d
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add data_list to PICMI laser_acceleration test
* increase max steps and fix bug in pywarpx/picmi.py 1DCartesian moving window direction
* add data_lust to Python laser acceleration test
* picmistandard update
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
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* add github ci compile check for ascent
* now with less whitespace
* add ascent to insitu workflow
* Update .github/workflows/insitu.yml
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* more style
* try to run as existing user
* new container
* use env script
* path fix
* add ascent test
* fix space
* move test resources
* get into style
* style
* Ascent CI: Cleanup (#1)
- make sure inputs file stays up-to-date
- locate alongside example
* Update .github/workflows/insitu.yml
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update .github/workflows/insitu.yml
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* rename test file
* fix for cp
* improve color table for vol rendering
* now with rotation
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
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* Added embedded_circle test
* Add embedded_circle test files
* Removed diag files
* removed PICMI input file
* Update to use default regression analysis
* Added line breaks for spacing
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Added description
* Added Ar and Xe to pre-defined particle types
* added Boltzmann's constant to pre-defined constants and cleaned up the MCC CI test input
* Added Boltzmann's constant to warpx parser
* cleaned up embedded circle CI test input
* Remove duplicate entry.
Co-authored-by: kzhu-ME <kevin.zhu@modernelectron.com>
Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
|
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* Add pre-commit
Add basis for automated pre-commit checks.
Install locally via:
```bash
python3 -m pip install -U pre-commit
pre-commit install
```
See: https://pre-commit.com
* Cleanup: Whitespaces
* Cleanup: requirements.txt order
|
Axel Huebl
Remi Lehe
Luca Fedeli
Juliette Pech
Roelof Groenewald
Ryan Sandberg
David Grote
Prabhat Kumar
Marco Garten
Neïl Zaim
Tiberius Rheaume
Edoardo Zoni
Revathi Jambunathan
Peter Scherpelz
Cyrus Harrison
