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2023-09-13Add flag to set GPU-aware MPI from PICMI (#4298)Gravatar Remi Lehe 1-0/+7
2023-09-13Revert PR4266 - lower and uppers bounds (#4294)Gravatar Marco Garten 1-10/+0
The lower and upper bounds are already present within PICMI.
2023-09-12PICMI: Add `warpx_intervals` option to BTD (#4288)Gravatar David Grote 1-2/+22
* Add warpx_intervals option to BTD * Add warpx_intervals to LabFrameParticleDiagnostics
2023-09-08Add lower and upper bound params to regular diags in PICMI (#4266)Gravatar Marco Garten 1-0/+10
* Add lower and upper bound params to regular diags The parameters `warpx_lower_bound` and `warpx_upper_bound` can now be used in the definition of a `FieldDiagnostic` in PICMI. * Add docstring for lower and upper bound
2023-09-07Add particle resampling inputs to `picmi.py` (#4257)Gravatar Roelof Groenewald 1-1/+19
2023-09-07add symmetrize to PICMI (#4271)Gravatar Ryan Sandberg 1-0/+7
* add symmetrize to PICMI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * don't set defaults in PICMI - they don't matter --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-09-01PICMI: warpx.numprocs (#4255)Gravatar Axel Huebl 1-0/+9
Adding a parameter for `warpx.numprocs` in PICMI. https://warpx.readthedocs.io/en/latest/usage/parameters.html#distribution-across-mpi-ranks-and-parallelization https://warpx.readthedocs.io/en/latest/usage/domain_decomposition.html#simple-method
2023-08-31PICMI: LabFrameParticleDiagnostic w/ Species (#4254)Gravatar Axel Huebl 1-0/+41
Support the `species=...` argument in `PICMI_LabFrameParticleDiagnostic`.
2023-08-29Fix: PICMI BTD Diags (#4248)Gravatar Axel Huebl 1-2/+2
Typos.
2023-08-28Add LabFrameParticleDiagnostic to picmi (#4148)Gravatar David Grote 1-2/+66
2023-08-25Do not pre-processing routine in Python initialization (#4231)Gravatar Remi Lehe 1-4/+0
2023-08-24Fix: WarpX Version (#4218)Gravatar Axel Huebl 2-2/+13
* Fix: WarpX Version Fix the WarpX version info. * Fix Version: pyWarpX * Version: More Python __version__
2023-08-24Fix Python wrapper to extract `theta` (#4229)Gravatar Remi Lehe 1-3/+3
2023-08-22Remove unused/untested Python file (#4217)Gravatar Remi Lehe 2-145/+0
* Remove unused/untested Python file * Remove additional file
2023-08-12Transition to pyAMReX (#3474)Gravatar Axel Huebl 8-4032/+1404
* pyAMReX: Build System * CI Updates (Changed Options) * Callback modernization (#4) * refactor callbacks.py * added binding code in `pyWarpX.cpp` to add or remove keys from the callback dictionary * minor PR cleanups Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Added Python level reference to fetch the multifabs (#3) * pyAMReX: Build System * Added Python level reference to Ex_aux * Now uses the multifab map * Fix typo Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add initialization and finalize routines (#5) A basic PICMI input file will now run to completion. * Regression Tests: WarpX_PYTHON=ON * Update Imports to nD pyAMReX * IPO/LTO Control Although pybind11 relies heavily on IPO/LTO to create low-latency, small-binary bindings, some compilers will have troubles with that. Thus, we add a compile-time option to optionally disable it when needed. * Fix: Link Legacy WarpXWrappers.cpp * Wrap WarpX instance and start multi particle container * Fix test Python_pass_mpi_comm * Start wrapper for multiparticle container * Add return policy Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update fields to use MultiFabs directly Remove EOL white space Removed old routines accessing MultiFabs Update to use "node_centered" * Fix compilation with Python * Update fields.py to use modified MultiFab tag names * Remove incorrect, unused code * Add function to extract the WarpX MultiParticleContainer * Complete class WarpXParticleContainer * Wrap functions getNprocs / getMyProc * restore `install___` callback API - could remove later if we want but should maintain backward compatibility for now * add `gett_new` and `getistep` functions wrappers; fix typos in `callbacks.py`; avoid error in getting `rho` from `fields.py` * Update callback call and `getNproc`/`getMyProc` function * Replace function add_n_particles * Fix setitem in fields.py for 1d and 2d * also update `gett_new()` in `_libwarpx.py` in case we want to keep that API * added binding for `WarpXParIter` - needed to port `libwarpx.depositChargeDensity()` which is an ongoing effort * Wrap function num_real_comp * added binding for `TotalNumberOfParticles` and continue progress on enabling 1d MCC test to run * add `SyncRho()` binding and create helper function in `libwarpx.depositChargeDensity` to manage scope of the particle iter * Clean up issues in fields.py * update bindings for `get_particle_structs` * Fix setitem in fields.py * switch order of initialization for particle container and particle iterator * switch deposit_charge loop to C++ code; bind `ApplyInverseVolumeScalingToChargeDensity` * move `WarpXParticleContainer.cpp` and `MultiParticleContainer.cpp` to new Particles folder * added binding for `ParticleBoundaryBuffer` * More fixes for fields.py * Fix: Backtraces from Python Add the Python executable name with an absolute path, so backtraces in AMReX work. See linked AMReX issue for details. * Cleaning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: Backtraces from Python Part II Do not add Python script name - it confuses the AMReX ParmParser to build its table. * Fix: CMake Dependencies for Wheel This fixes a racecondition during `pip_install`: it was possible that not all dimensions where yet build from pybind before we start packing them in the wheel for pip install. * MCC Test: Install Callbacks before Run Otherwise hangs in aquiring the gil during shutdown. * addition of `Python/pywarpx/particle_containers.py` and various associated bindings * Fix: CMake Superbuild w/ Shared AMReX We MUST build AMReX as a shared (so/dll/dylib) library, otherwise all the global state in it will cause split-brain situations, where our Python modules operate on different stacks. * add `clear_all()` to callbacks in order to remove all callbacks at finalize * add `-DWarpX_PYTHON=ON` to CI tests that failed to build * add `get_comp_index` and continue to port particle data bindings * Add AMReX Module as `libwarpx_so.amr` Attribute to pass through the already loaded AMReX module with the matching dimensionality to the simulation. * Fix for fields accounting for guard cells * Fix handling of ghost cells in fields * Update & Test: Particle Boundary Scraping * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * CI: Python Updates - modernize Python setups - drop CUDA 11.0 for good and go 11.3+ as documented already ``` Error #3246: Internal Compiler Error (codegen): "there was an error in verifying the lgenfe output!" ``` * CI: Python Updates (chmod) * Add support for cupy in fields.py * Add MultiFab reduction routines * CI: CUDA 11.3 is <= Ubuntu 20.04 * changed `AddNParticles` to take `amrex::Vector` arguments * setup.py: WarpX_PYTHON=ON * update various 2d and rz tests with new APIs * add `-DWarpX_PYTHON_IPO=OFF` to compile string for 2d and 3d Python CI tests to speed up linking * CI: -DpyAMReX_IPO=OFF * CI: -DpyAMReX_IPO=OFF actually adding `=OFF` * CI: Intel Python * CI: macOS Python Executable Ensure we always use the same `python3` executable, as specified by the `PATH` priority. * CMake: Python Multi-Config Build Add support for multi-config generators, especially on Windows. * __init__.py: Windows DLL Support Python 3.8+ on Windows: DLL search paths for dependent shared libraries Refs.: - https://github.com/python/cpython/issues/80266 - https://docs.python.org/3.8/library/os.html#os.add_dll_directory * CI: pywarpx Update our setup.py cannot install pyamrex yet as a dependency. * ABLASTR: `ablastr/export.H` Add a new header to export public globals that are not covered by `WINDOWS_EXPORT_ALL_SYMBOLS`. https://stackoverflow.com/questions/54560832/cmake-windows-export-all-symbols-does-not-cover-global-variables/54568678#54568678 * WarpX: EXPORT Globals in `.dll` files WarpX still uses a lot of globals: - `static` member variables - `extern` global variables These globals cannot be auto-exported with CMake's `WINDOWS_EXPORT_ALL_SYMBOLS` helper and thus we need to mark them manually for DLL export (and import) via the new ABLASTR `ablastr/export.H` helper macros. This starts to export symbols in the: - WarpX and particle container classes - callback hook database map - ES solver * CI: pywarpx Clang CXXFLAGS Down Move CXXFLAGS (`-Werror ...`) down until deps are installed. * GNUmake: Generate `ablastr/export.H` * CMake: More Symbol Exports for Windows * `WarpX-tests.ini`: Simplify Python no-IPO Also avoids subtle differences in compilation that increase compile time. * Update PICMI_inputs_EB_API.py for embedded_boundary_python_API CI test * Fix Python_magnetostatic_eb_3d * Update: Python_restart_runtime_components New Python APIs * Windows: no dllimport for now * CI: Skip `PYINSTALLOPTIONS` For Now * CMake: Dependency Bump Min-Versions for external packages picked up by `find_package`. * Fix F and G_fp names in fields.py * Tests: Disable `Python_pass_mpi_comm` * Wrappers: Cleanup * pyWarpX: Include Cleaning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fields.py: Fix F and G Wrappers Correct MultiFab names (w/o components). * Remove unused in fields.py * Windows: New Export Headers - ABLASTR: `ablastr/export.H` - WarpX: `Utils/export.H` * removed `WarpInterface.py` since that functionality is now in `particle_containers.py`; removed parts of `WarpXWrappers.cpp` that have been ported to pyamrex * CMake: Link OBJECT Target PRIVATE * CMake: Remove OBJECT Target Simplify and make `app` link `lib` (default: static). Remove OBJECT target. * Fix in fields.py for the components index * Update get_particle_id/cpu As implemented in pyAMReX with https://github.com/AMReX-Codes/pyamrex/pull/165 * WarpX: Update for Private Constructor * Import AMReX Before pyd DLL Call Importing AMReX will add the `add_dll_directory` to a potentially shared amrex DLL on Windows. * Windows CI: Set PATH to amrex_Nd.dll * CMake: AMReX_INSTALL After Python In superbuild, Python can modify `AMReX_BUILD_SHARED_LIBS`. * Clang Win CI: Manually Install requirements Sporadic error is: ``` ... Installing collected packages: pyparsing, numpy, scipy, periodictable, picmistandard ERROR: Could not install packages due to an OSError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\hostedtoolcache\\windows\\Python\\3.11.4\\x64\\Lib\\site-packages\\numpy\\polynomial\\__init__.py' Consider using the `--user` option or check the permissions. ``` * Hopefully final fixes to fields.py * Update getProbLo/getProbHi * Set plasma length strength Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Fix fields method to remove CodeQL notice * Update Comments & Some Finalize * Move: set_plasma_lens_strength to MPC --------- Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: David Grote <dpgrote@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Dave Grote <grote1@llnl.gov> Co-authored-by: Roelof Groenewald <regroenewald@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-08-11In picmi.py, add G to fields to plot check (#4180)Gravatar David Grote 1-1/+1
2023-08-11Update PICMI interface for Gaussian flux (#4084)Gravatar Remi Lehe 1-1/+1
* Update PICMI interface for Gaussian flux * Update version of picmistandard
2023-08-11Enable `divE` field diagnostic with Ohm's law solver (#4178)Gravatar Roelof Groenewald 1-1/+1
* use same finite difference algo as for Yee with hybrid-PIC to calculate divE * add `divE` and `divB` to field diagnostic in picmi.py
2023-08-11Add Python wrapper to set the lens strength (#3748)Gravatar Remi Lehe 1-0/+22
* Add Python wrapper to set the lens strength * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct missing `c_real` * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add assert message --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-06-27Define new `InjectorFlux` object, and use it in `AddPlasmaFlux` (#4040)Gravatar Remi Lehe 1-3/+3
* Create flux injector object * Call new flux injector in AddPlasmaFlux * Update syntax in tests * Also test the flux parser * Remove the use of `density_min` and `density_max` for flux injection * Update PICMI interface * Update documentation * Remove .cpp file
2023-06-27Adding current density to Field Reduction reduced diagnostic (#3980)Gravatar Lizzette Corrales 1-1/+1
* Adding j in FieldReduction * Modiyfying input file with FieldReduced diag * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Diagnostics/ReducedDiags/FieldReduction.H * updating Field Reduction Docs to include current density * Update Source/Diagnostics/ReducedDiags/FieldReduction.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * adding cuurent density BackwardCompatibility to Field Reduction diagnostic * including E dot j density using the modifyed Field Reduction * fixing picmi interface * adding Edotj to automated python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Lizzette Corrales <lzcorrales@kong.dhcp.lbl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2023-06-15Added external field loading from file to picmi.py (#3945)Gravatar Camille Woicekowska 1-0/+9
* Added external field loading from file to picmi.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Python/pywarpx/picmi.py Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Added documentation * Removed init, documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated picmi version in requirements.txt * Updated picmi version in setup.py * Updated picmi version in requirements.txt * Updated name of call to picmi class * Adapted CI test for PICMI field loading from file * Added PICMI input script * Added .json file with new file name * fixed small errors * Fixed error in input script * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed old comments from code * fixed import, spacing in input script * fixed spacing * cleaned up input script * fixed typo * removed blocking factor * fixed name of test * correct ion species name * Added initial field to sim object --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
2023-06-12Cleanup unused parts of WarpX Python interface (#3971)Gravatar Remi Lehe 4-33/+2
* Cleanup unused parts of WarpX Python interface * Fix breaking Python import
2023-06-12Ohm's law solver (hybrid kinetic-fluid extension) (#3665)Gravatar Roelof Groenewald 6-0/+125
* 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 for more information, see https://pre-commit.ci * fixed invalid memory access for GPU and other code cleanups * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refinements on the example scripts * added ion beam instability example * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added EM modes and ion beam examples to CI test suite * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * started docs section on the hybrid model * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * more progress on documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added ion Landau damping verification test / example * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add checksum benchmark for Landau damping example * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 for more information, see https://pre-commit.ci * also correct current density at PEC boundary * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 for more information, see https://pre-commit.ci * actually apply rho boundary correction in EM case * take one sided derivative at PEC boundary when calculating div Pe * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * 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>
2023-06-02Add max_background_density to MCCollision (#3960)Gravatar David Grote 1-1/+7
2023-06-01Update picmi interface for MCCCollisions (#3953)Gravatar David Grote 1-6/+12
* Allow string expressions for MCCCollisions background density and temperature * Add check of whether value is str since special behavior is needed
2023-05-08Enable field ionization from PICMI (#3298)Gravatar Neïl Zaim 1-8/+17
* Enable field ionization from PICMI * Implement Dave's suggestions and add automated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update test benchmark * Add docstring for FieldIonization class --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-22Add python callback call when a break signal is recieved (#3849)Gravatar aveksler1 1-0/+20
* added onbreaksignal python callback * added documentation * fixed bug executing onbreaksignal callbacks at stoptime * applied suggestion from code review. * updated doc-strings
2023-04-19Add more PICMI options (#3773)Gravatar Remi Lehe 1-1/+10
* Add PICMI option to cover multiple cuts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Parse flux_min, flux_tmax from PICMI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Implement review comments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-17Fix particle reflecting boundaries in RZ (#3837)Gravatar David Grote 1-0/+6
* Fix the reflection of velocities in RZ * Add warpx_reflect_all_velocities to the PICMI interface
2023-04-13Add callback function before/after the initial Esolve (#3452)Gravatar Remi Lehe 1-1/+34
* Add callback function after the initial Esolve * Apply suggestions from code review * Change name of callback function * Update PR
2023-04-04Adding Amrex Bucket into WarpX Python interface. (#3590)Gravatar S. Eric Clark 4-0/+26
* Adding Amrex Bucket into WarpX Python interface. * Adding PICMI-like options in the Simulation class to control Amrex Arena parameters.
2023-03-30Add random seed specification to `picmi` (#3793)Gravatar Roelof Groenewald 1-0/+6
2023-03-23Fix add_particles to account for theta attribute with RZ (#3776)Gravatar David Grote 1-4/+12
* Fix add_particles to account for theta attribute with RZ * Add assertions in the number of attributes specified
2023-03-23PICMI Boundary: Silver-Mueller (#3709)Gravatar Axel Huebl 1-0/+1
* PICMI Boundary: Silver-Mueller Add support for silver-mueller boundary conditions in PICMI. * Dependencies: Update PICMI
2023-03-20PICMI: add `do_not_push` and `do_not_gather` (#3766)Gravatar Yinjian Zhao 1-0/+10
2023-03-10PICMI: add missing flags for latest algorithms (#3743)Gravatar Edoardo Zoni 1-2/+76
* PICMI: add missing flags for latest algorithms * Fix docstrings
2023-03-10Fix Bucket __getattr__ (#3747)Gravatar David Grote 1-1/+1
2023-03-09Implement PICMI flag to set `compute_max_step_from_btd` (#3740)Gravatar Remi Lehe 1-0/+7
* Implement PICMI flag for setting max_step from btd * Update Python/pywarpx/picmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-27Change plotfile RZ allowed diags to r,t from x,y (#3663)Gravatar Ryan Sandberg 1-25/+44
* 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 Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> --------- Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-22Reduced diagnostics: charge on the embedded boundary (#3648)Gravatar Remi Lehe 1-2/+20
* Prepare structure to compute charge inside boundary * Add calculation without embedded boundaries * Use EB area fraction * Skip cells that are not cut-cells * Choose point outside of the EB * Skip covered or regular boxes * Only compile with EB and 3D support * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test for charge on EB * Add automated test * Add automated Python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Avoid compilation error * Enable PICMI test * Rename ChargeInsideBoundary to ChargeOnEB * Update comments * Add parser for weighting * Call weighting function * Call weighting function * Add documentation * Update Python test * Add Python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix compilation errors * Fix access of attribute on GPU * Use difference in surface area * Pick smaller radius in test This is in order to avoid the influence of the boundaries * Update benchmark * Update benchmark * Properly add diagnostic * Update radius in analysis * Update analysis script * Relax tolerance * Fix tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Python tests * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Test one-eighth from Python * Add one-eighth charge in tests * Handle ChargeOnEB * Remove bug when handling charge on eb * Fix Python errors * Fix Python issues * Use more natural setting of tilebox --------- 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>
2023-02-21Renamed "particle_vel" to "particle_mom" (#3672)Gravatar Davide Terzani 1-3/+3
* Renamed particle_vel to particle_mom * Changed vel to u * Updated gitignore with vscode-specific folder * Updated docs for single particle * Revert "Updated gitignore with vscode-specific folder" This reverts commit cb44ef8d66c123daa93d6a13d5a1d88416e866bb. * Fixed typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed other typo * Add species indication in warning --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-02-21Add FieldReduction and ParticleHistogram to PICMI (#3697)Gravatar David Grote 2-21/+112
* Added FieldReduction and ParticleHistogram to ReducedDiagnostics * Add tests to reduced_diags/PICMI_inputs_loadbalancecosts.py * Clean up ReducedDiagnostics setting of argv
2023-02-20add flag to picmi `FieldDiagnostic` for whether particle data should be ↵Gravatar Roelof Groenewald 1-0/+5
saved along with the field data (#3699)
2023-01-13EB potential python interface (#3624)Gravatar David Grote 1-0/+13
* Add Python routine set_potential_EB to modify eb_potential * Add CI test
2023-01-06add local flag to ParticleBoundaryBuffer::getNumParticlesInContainer (#3586)Gravatar Roelof Groenewald 1-2/+6
2022-12-22Feature magnetostatic solver (#3551)Gravatar S. Eric Clark 3-3/+108
* Initial working Magnetostatic solver integration into warpx. Includes hooks in Python library, and a test problem. Build files updates. New solver algorithm and inputs. * Fixed indexing to allow Magnetostatic solver to work in RZ and 3D. * Removing trailing whitespace. * Adding basic regression testing with benchmarks. * Updated Regression test ini * Augmented test scripts to compare to analytical results for uniform beam. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updating CI tests for magnetostatic solver. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated magnetostatic CI tests to pass locally in regression testing framework. * Adjusting tolerance on magnetostatic_rz regression test to allow for noise in near zero fields. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Converted particle layout to Gridded instead of PsedupRandom to improve reproducibility of particle deposition for regression testing. * Dropped benchmark field comparisons with fields near zero. Dropped particle benchmark for magnetostatic_eb_rz regression test due to randomized particle theta adding noise to fields after a timestep. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Found and fixed a bug in syncronization of MultiFabs when interpolating between grids in the magnetostatic solver. Added Python output for nodal current and vector potential. Updated the CI tests to disable dynamic scheduling and enbale serialization of initial conditions. Updated benchmarks fro tests. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Adding random_theta flag to PICMI interface and updating RZ CI test and benchmark with change to disable randomized theta. * Added documentation to parameters.rst for relativistic-magnetostatic flag. Documentation corrections. Removal of commented source. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removing need to use do_current_centering. Updated current density inverse scaling support for nodal Jr in radius. Added flag to check for m_rz_random_theta when laying down particles in RZ. * Remove dA/dt term to decouple electrostatic and magnetostatic solvers. * Remove update of auxiliary fields * Adding non-Python test case for magnetostatic solver. Updating benchmarks. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Python/pywarpx/_libwarpx.py Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Diagnostics/Diagnostics.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/Evolve/WarpXEvolve.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.H Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Refactor names of functions for magnetostatic solver implementation. Remove current_fp_nodal python interface. Drop extraneous ghost cell exchanges. * Adding radial weighting at r=0 for Jr if nodal. * Splitting off Amrex bucket and adjustments to RZ radial weighting into different branches to be merged. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Switch name to labfame-electromagnetostatic * Update example scripts 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>
2022-11-28enable the use of `FieldProbe` default parameter values (#3538)Gravatar Roelof Groenewald 1-10/+10
2022-11-24allow initial fields to be set through the picmi interface (#3536)Gravatar Roelof Groenewald 1-0/+29
2022-11-18Adding an if statement for the last step diagnostic (#3436)Gravatar Yinjian Zhao 2-14/+11
* modified * Include max_step and stop_time as input parameters * Add comments * update * update * Fix CI test: apply suggestion from @ax3l * Do not force consistency between `max_step` and `stop_time` Co-authored-by: Dave Grote <grote1@llnl.gov> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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