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2023-09-13Clang tidy CI test: add misc-definitions-in-headers check (#4253)Gravatar Luca Fedeli 4-114/+160
* Clang-tidy: add misc-definitions-in-headers check * address issues found with clang-tidy * remove std::cout added for debug purposes * add back newline
2023-09-08Clang tidy CI test: add selected google-* checks (#4267)Gravatar Luca Fedeli 6-1/+5
* clang-tidy CI test: add selected google- checks * address issues found with clang-tidy * fixed bugs * fix bugs
2023-08-29Clang tidy CI test: add more readability checks to clang tidy CI test (#4146)Gravatar Luca Fedeli 25-223/+229
* add more readability checks to clang-tidy CI test * reformat check list * starting to address issues found with clang-tidy£ * addressing issues * remove check * address issues * address all issues * address issue found with github code scanning
2023-08-19Fix: Remove Overly Exported Classes (#4200)Gravatar Axel Huebl 1-3/+1
* Fix: Remove Overly Exported Classes Luckily, many of them should not contain global state. * Add Missing WarpX.H Include
2023-08-17Add nodal electrostatic solver (#3982)Gravatar Arianna Formenti 1-113/+232
* added nodal electrostatic solver * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * sphere test for electrostatic nodal solver * add 3d single bunch test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adds single bunch ci test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 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>
2023-08-14Clang-tidy: add more misc-* checks to clang-tidy CI test (#4170)Gravatar Luca Fedeli 4-7/+0
* Clang-tidy: add more misc-* checks to clang-tidy CI test * address issues found with clang-tidy
2023-08-12Transition to pyAMReX (#3474)Gravatar Axel Huebl 11-15/+20
* 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>
2023-08-11Enable `divE` field diagnostic with Ohm's law solver (#4178)Gravatar Roelof Groenewald 1-2/+4
* use same finite difference algo as for Yee with hybrid-PIC to calculate divE * add `divE` and `divB` to field diagnostic in picmi.py
2023-08-01Clang tidy CI test: add several readability checks to clang tidy CI test ↵Gravatar Luca Fedeli 6-32/+30
(#4124) * add few readability checks to clang-tidy CI test * address all the issues found with clang-tidy * fix bug * fixed bug * fix residual issue * fix issue found with clang-tidy
2023-07-31Clang tidy CI test: add some modernize checks to clang-tidy CI test (#4133)Gravatar Luca Fedeli 6-12/+14
* Clang Tidy: add several modernize checks * eliminate file included in commit by mistake * fix bug
2023-07-31remove WarpX::GetInstance() from PoissonBoundaryHandler::definePhiBCs (#4130)Gravatar Luca Fedeli 2-7/+10
2023-07-26Initialize variables at declaration if it improves readability (#4117)Gravatar Luca Fedeli 4-42/+12
* init some variables at declaration * make code more readable * avoid lossy function result cast * Update Source/Initialization/WarpXInitData.cpp Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> * replace with equality * Revert "replace with equality" This reverts commit e3164f9e053d345b153d770ae107a7f68c4bb260. * Update Source/Diagnostics/ComputeDiagFunctors/ParticleReductionFunctor.cpp Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> --------- Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2023-06-29Clean up of MultiFab tagging (#4014)Gravatar David Grote 1-14/+8
* Clean up of MultiFab tagging * Use [level=level] for the tag
2023-06-27Clang-tidy CI test: add bugprone-branch-clone check (#4030)Gravatar Luca Fedeli 1-9/+4
* add bugprone-branch-clone to clang-tidy CI test * Updating Inline Comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-06-27refactored `HybridPICModel::HybridPICSolveE` to more readable (#4044)Gravatar Roelof Groenewald 5-57/+33
2023-06-24Explicitly check field `IndexType` appropriateness when using hybrid-PIC ↵Gravatar Roelof Groenewald 2-6/+20
solver (#4034) * explicitly check field `IndexType` appropriateness when using hybrid-PIC solver * fix typo
2023-06-23added `WarpX::HybridPICDepositInitialRhoAndJ()` helper function to clean up ↵Gravatar Roelof Groenewald 1-0/+27
WarpX::Evolve (#4032)
2023-06-16correct seperate --> separate (#3998)Gravatar Luca Fedeli 1-1/+1
2023-06-16Generalize buffers for `SyncRho`, `SyncCurrent`, and related functions (#3995)Gravatar Edoardo Zoni 3-5/+5
2023-06-13Enforce const correctness using clang-tidy CI test (#3921)Gravatar Luca Fedeli 20-154/+162
* add clang-tidy workflow * fix missing newline * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make clang.14.sh executable * remove non explicitly selected checks * complete list of dependencies * fix bug * specify path of clang-tidy file * fix bug * add new check * remove one check * add magic numbers check * removed one check * keep only one check * Docs: Conda Dev w/ Boost (#3911) Add the `boost` package to the conda developer environment. Used for QED table generation. * Fix typo in Adastra cluster documentation (#3918) * add back three checks * prepare clang-tidy wrapper * actually use clang-tidy in the script * test * fix bug * actually use clang-tidy * fixed bug * fixed bug * fixed bug * fixed bug * remove all checks except the selected 3 * fixed bug * fixed bug * fixed bug * enforce const correctness using clang-tidy * remove one check * Fix Concurrency Issue * BLAS++/LAPACK++ for RZ+PSATD * Build all 4 WarpX DIMS * add few echo for test purposes * try to debug mysterious error * don't test RZ with clang-tidy * add back RZ test * add some const * fix bug * check also header files * remove header filter since it does not work as expected * fixed bug * check also WarpX headers * fix bugs * continue enforcing const correctness * continue enforcing const correctness * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug * fix bugs and add new const * clean .clang-tidy * make regex more precise according to Weiqun's suggestion * add more const * fix bugs * fix bug * silence warning on float comparison * fixed bug * fixed bugs * fix bug and add const * fixed bugs * fix bug * fix bug * fix bug * fixed bug * fix bug
2023-06-12Ohm's law solver (hybrid kinetic-fluid extension) (#3665)Gravatar Roelof Groenewald 14-2/+1325
* 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>
2023-06-12Replace amrex::Abort with WARPX_ABORT_WITH_MESSAGE (#3965)Gravatar Luca Fedeli 2-3/+3
* replace amrex::Abort with WarpX macros * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * adding back missing include * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * use amrex::Abort in a GPU kernel * bump precision
2023-06-01Fix: PSATD+RZ in SP (#3956)Gravatar Axel Huebl 2-13/+36
* Fix: PSATD+RZ in SP Fix the FFTW logic for RZ simulations using the PSATD field solver in single precision. Previously, the API was using the double precision interfaces for FFTW unconditionally. * Simplify Plans Reuse AnyFFT defines.
2023-05-22Multi-Dim Buildsystem Support (#3933)Gravatar Axel Huebl 7-69/+89
* Multi-Dim Buildsystem Support * Docs
2023-05-09Do not duplicate protected member of base class (#3915)Gravatar Edoardo Zoni 16-23/+0
2023-05-08Cleanup: rocFFT Includes (#3908)Gravatar Axel Huebl 1-3/+0
Newer versions fixed the include issue that required us to use `<cstddef>` includes before including rocFFT. Fixed with >4.3.
2023-05-08ROCm 5.2+ (#3906)Gravatar Axel Huebl 1-1/+5
* rocFFT: 5.2+ Compatible More careful include for old versions of rocFFT/ROCm. * ROCm: 5.2+
2023-05-05Change CartesianCKCAlgorithm.H (#3898)Gravatar Ilian Kara-Mostefa 1-1/+3
2023-05-04Replace 3 occurrencess of NULL with std::nullptr (#3893)Gravatar Luca Fedeli 2-3/+3
* replace NULL with std::nullptr everywhere * fix bug
2023-05-02Fix: rocFFT 5.5 (#3888)Gravatar Axel Huebl 1-1/+1
``` /opt/rocm-5.5.0/include/rocfft.h:16:2: error: "This file is deprecated. Use the header file from /opt/rocm-5.5.0/include/rocfft/rocfft.h by using #include <rocfft/rocfft.h>" [-Werror,-W#warnings] warning "This file is deprecated. Use the header file from /opt/rocm-5.5.0/include/rocfft/rocfft.h by using #include <rocfft/rocfft.h>" ^ ```
2023-05-01Use WARPX_ABORT_WITH_MESSAGE("msg") instead of ↵Gravatar Luca Fedeli 22-70/+70
amrex::Abort(Utils::TextMsg::Err("msg")) (#3879) * use WARPX_ABORT_WITH_MSG instead of amrex::Abort(Utils::TextMsg::Err(msg)) [WIP] * use WARPX_ABORT_WITH_MESSAGE * fix typo * fix missing parenthesis * remove spaces to prevent automatic text wrapping * remove wrong parenthesis
2023-04-20Use amrex::Math::powi<N>(x) in WarpX (#3846)Gravatar Luca Fedeli 3-33/+36
* use_powi * fix bug * fix bug * fix bug * fix bug
2023-04-12Reflect density from non-periodic boundaries during deposition (#3711)Gravatar Roelof Groenewald 1-2/+8
* 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 * 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 * [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 * 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>
2023-04-10`SyncRho`: Pass References To Charge MultiFabs (#3814)Gravatar Remi Lehe 2-3/+3
* `SyncRho`: Pass References To Charge MultiFabs * Keep a function SyncRho for the Python interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-10PSATD: call FFT of rho with explicit spectral index (#3720)Gravatar Edoardo Zoni 1-29/+19
2023-04-06code cleanup: make use of `MultiParticleContainer::DepositCurrent` in ↵Gravatar Roelof Groenewald 1-22/+2
`AddSpaceChargeFieldLabFrame` (#3807)
2023-04-04Make verboncoeur correction optional (#3802)Gravatar David Grote 1-38/+41
* Add radial_verboncoeur_correction input parameter * Change parameter to boundary.verboncoeur_axis_correction
2023-03-28Fix bugs related to azimuthal modes for multi-J algo in RZ geometry (#3764)Gravatar Olga Shapoval 2-12/+36
* Bug fix: loop over all azimuthal modes taking into account the shift `mode*n_fields` * Bug fix: added missing speed of light factor in coefficient `c2` * Bug fix: added missing `mode` as fourth optional component in `X5(i,j,k,mode)` and `X6(i,j,k,mode)` coefficients, used only with RZ multi-J averaged PSATD * Reset benchmark of `multi_J_rz_psatd`
2023-03-09New user input for grid type (collocated, staggered, hybrid) (#3683)Gravatar Edoardo Zoni 37-91/+92
* Introduce `warpx.grid_type` parameter * Replace `or` with `||` * Update examples with new user input syntax * Fix `if` condition * Improve error message * Fix `if` condition * Fix bugs * Fix warning * Fix RZ * Debugging * Fix RZ * Fix bug * Clean up * More changes: - set default algo parameters with hybrid grid - all hybrid input parameters under warpx name * Set default field gathering algo for hybrid grids * Update documentation
2023-03-04RZ FDTD: fix bug w/ div(E) cleaning (extra c2) (#3726)Gravatar Edoardo Zoni 1-2/+1
2023-02-21Fix Silver-Mueller boundary condition in 1D (#3703)Gravatar Remi Lehe 1-5/+2
* Fix Silver-Mueller boundary condition in 1D * Use WARPX_ZINDEX * Add automated test * Add benchmark
2023-02-03fix some issues in WarpX 1D (#3671)Gravatar Luca Fedeli 1-10/+18
2023-01-24Fix bug with PML in 2D when compiling with EB (#3637)Gravatar Remi Lehe 1-2/+8
* Fix condition to update PML in 2D * Add automated test: PML with EB compiled * Pass correct cell sizes * Update automated test * Update benchmark
2023-01-13EB potential python interface (#3624)Gravatar David Grote 2-1/+17
* Add Python routine set_potential_EB to modify eb_potential * Add CI test
2023-01-06For the tridiag, remove the guard cells since they are not needed (#3604)Gravatar David Grote 1-45/+30
* Removed the guard cells since they are not needed for the tridiag * Clean up the copy into the 1d array * For the upper boundary, use explicit indices instead of temporaries to make the code more clear
2023-01-02Fix a Bug in 1D ES (#3597)Gravatar Weiqun Zhang 1-4/+3
After the tri-diagonal solve, the data in the special single-box MultiFab need to be copied back to the normal MultiFab. However, when there was a bug for periodic boundary. The issue is the special MultiFab is really special. It has a nodal Box that grows the original nodal Box by 1 node in the lower boundary and 2 (why 2?) nodes in the upper boundary and these grown nodes are considered valid nodes, even though they do not have valid data. Therefore amrex::ParallelCopy with periodicity does not work in this case. For example, for a domain with 96 cells, the data at nodes 1 and 2 of the normal MultiFab could be written with the invalid data at nodes 97 and 98 of the special MultiFab. This bug is fixed by replacing it with a ParallelCopy without periodicity followed by a FillBoundary.
2022-12-22Feature magnetostatic solver (#3551)Gravatar S. Eric Clark 7-3/+520
* 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>
2022-12-22Adding radial weighting at r=0 for Jr if nodal. (#3589)Gravatar S. Eric Clark 1-17/+22
2022-12-19Clean up documentation (#3542)Gravatar David Grote 3-6/+5
* Fix comments for documentation * More fixes to comments for documentation * Fixes in the doc files * Fix typo in parameters.rst
2022-12-15Refactor update of auxiliary data for electrostatic solver (#3573)Gravatar Remi Lehe 1-6/+0
* Refactor update of auxiliary data for electrostatic solver * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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