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HS dev merge 24-02-28#139

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RevathiJambunathan merged 177 commits intoRevathiJambunathan:HarrisSheetinXRevathiJambunathan/WarpX:HarrisSheetinXfrom hklion:HSdevmerge_240228hklion/WarpX:HSdevmerge_240228Copy head branch name to clipboardFeb 29, 2024

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Commits on Nov 28, 2023

• add start/end moving step (ECP-WarpX#4437)

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Commits on Nov 29, 2023

• Frontier (OLCF): cupy (ECP-WarpX#4247)

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• Allow multiple injection sources per species (ECP-WarpX#4196)

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• Clang-Tidy Cache (ECP-WarpX#4453)

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Commits on Nov 30, 2023

• AMReX: Update to development (ECP-WarpX#4455)

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Commits on Dec 1, 2023

• Set amrex.omp_threads = "nosmt" (ECP-WarpX#4393)

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• Initial commit (ECP-WarpX#4460)

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• New Cache Strategy (ECP-WarpX#4456)

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• Make geometry.dims abort message more user-friendly (ECP-WarpX#4459)

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• Fix typo in "write_diagnostics_on_restart" (ECP-WarpX#4463)

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Commits on Dec 2, 2023

• Bugfix in fields.py mesh() with ghost cells included (ECP-WarpX#4466)

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• fix preprocessor defs for 1D in two locations (ECP-WarpX#4465)

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Commits on Dec 4, 2023

• Add external current handling to Ohm's law solver (ECP-WarpX#4405)

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Commits on Dec 5, 2023

• Release 23.12 (ECP-WarpX#4469)

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• Remove brew cache (ECP-WarpX#4470)

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• Doc: Restructure Examples (ECP-WarpX#4467)

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• Docs: Fix Many Small Errors & Warnings

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• Docs: Fix Formatting in parameters.rst

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• macOS CI: export CCACHE_DEPEND=1 (ECP-WarpX#4475)

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• Doc: Streamline Python Input (ECP-WarpX#4472)

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• Rename Depose -> Deposit (ECP-WarpX#4474)

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• Correct on-axis field boundary for RZ (ECP-WarpX#4464)

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• Fix typos in comments and docs (ECP-WarpX#4471)

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Commits on Dec 6, 2023

• pybind11: v2.11.1+ (ECP-WarpX#4473)

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• Set alpha mass directly from NIST data (ECP-WarpX#4478)

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• Add latex_theory/allbibs.bib to bibliography list and delete duplicates (ECP-WarpX#4481)

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Commits on Dec 9, 2023

• macOS CI: Fix brew installation (ECP-WarpX#4493)

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Commits on Dec 10, 2023

• sqrt -> std::sqrt (ECP-WarpX#4490)

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Commits on Dec 11, 2023

• Clang-Tidy: Update performance and readability (ECP-WarpX#4492)

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• Clang-Tidy CI: Keep Going after Errors (ECP-WarpX#4491)

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• Tidy-Clang: performance-type-promotion-in-math-fn (ECP-WarpX#4497)

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• Move external field parameters out of WarpX class (ECP-WarpX#4441)

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Commits on Dec 12, 2023

• [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#4500)

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• Custom class for bibliography style (ECP-WarpX#4482)

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• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4489)

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• Clang-tidy: enable readability-duplicate-include check in clang-tidy CI test (ECP-WarpX#4496)

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• Use more consistent species types in fusion module (ECP-WarpX#4480)

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• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4503)

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Commits on Dec 13, 2023

• workflow training neural network from warpx data (ECP-WarpX#4499)

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Commits on Dec 14, 2023

• Clang-Tidy: readability-braces-around-statements (ECP-WarpX#4511)

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• Clang-Tidy: readability-inconsistent-declaration-parameter-name (ECP-WarpX#4514)

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• Clang-tidy: enable no-malloc check in clang-tidy CI test (ECP-WarpX#4518)

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• Update descriptions of hybrid-PIC examples (ECP-WarpX#4479)

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• Bibliography: improved citations (ECP-WarpX#4513)

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• Doc: Fix Sphinx Warnings

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• Doc: Examples Before APIs

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Commits on Dec 15, 2023

• Bibliography: make author family names appear last (ECP-WarpX#4506)

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• Clang-Tidy: performance-noexcept-move-constructor (ECP-WarpX#4504)

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• Clang-Tidy: readability-qualified-auto (ECP-WarpX#4507)

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• Add ability to run checksum on openPMD files (ECP-WarpX#4519)

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• move function definition to cpp file (ECP-WarpX#4522)

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• Improve documentation for laser chirp (ECP-WarpX#4525)

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• Doc: Fix ChecksumAPI autofunction (ECP-WarpX#4524)

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Commits on Dec 16, 2023

• WarpXSumGuardCells: move function definitions in cpp file (ECP-WarpX#4521)

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• Spruce up amr.rst (ECP-WarpX#4529)

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• Doc: Extend a Simulation Workflow (ECP-WarpX#4520)

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• Fix chirp documentation (ECP-WarpX#4533)

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• Spruce up input_output.rst (ECP-WarpX#4532)

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• Spruce up cold_fluid_model.rst (ECP-WarpX#4531)

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• Spruce up boosted_frame.rst (ECP-WarpX#4530)

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• Documentation: numbered reference formatting (ECP-WarpX#4528)

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• Fix CI for ROCm 6.0 (ECP-WarpX#4527)

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• Spruce up ml_dataset_training.rst (ECP-WarpX#4512)

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• Spruce up PIC theory section (ECP-WarpX#4536)

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Commits on Dec 17, 2023

• Docs: rename and spruce up boundary conditions section (ECP-WarpX#4537)

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• Spruce up kinetic_fluid_hybrid_model.rst (ECP-WarpX#4534)

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• Doc: CUDA 11.7+ (ECP-WarpX#4538)

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• Add updated instructions for WarpX on Karolina (ECP-WarpX#4477)

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Commits on Dec 19, 2023

• [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#4539)

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• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4541)

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Commits on Dec 20, 2023

• WarpXAMReXInit: move include directive from header to cpp file (ECP-WarpX#4543)

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• Adding user defined keywords in Hybrid PIC Python class to allow for addition of constants when defining functions for resistivity and current. (ECP-WarpX#4550)

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Commits on Dec 21, 2023

• Clean up doc to improve readability (ECP-WarpX#4555)

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• add hybrid-PIC PoP reference to docs (ECP-WarpX#4551)

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• Fix reference (ECP-WarpX#4552)

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Commits on Dec 22, 2023

• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4559)

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• Add updated instructions for WarpX on Karolina (ECP-WarpX#4545)

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• Add DSMC module (ECP-WarpX#4125)

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• Fix: BeamRelevant 1D, 2D (ECP-WarpX#4558)

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Commits on Dec 23, 2023

• Update documentation for checksum (ECP-WarpX#4561)

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• Implicit electromagnetic solver using Picard iterations (ECP-WarpX#4071)

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• Fix default initialization of runtime attributes. (ECP-WarpX#4508)

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• Update explanation of why 2D simulations are not suitable for plasma-wakefield (ECP-WarpX#4544)

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Commits on Jan 2, 2024

• Change the sign of laser particles (ECP-WarpX#4568)

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• Add semi-implicit CI test (ECP-WarpX#4565)

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Commits on Jan 3, 2024

• Add filters for boundary scraping diagnostics (ECP-WarpX#4371)

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• Update the field probe diagnostic documentation (ECP-WarpX#4564)

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• Apply particle selection to BTDiagnostics (ECP-WarpX#4570)

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Commits on Jan 4, 2024

• Update dsmc and fusion binary collisions (ECP-WarpX#4572)

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• Beam-beam collision example (ECP-WarpX#4546)

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Commits on Jan 5, 2024

• Perlmutter: Load gpu Module (ECP-WarpX#4573)

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• Scale fields by a dimensionless number between 0 and 1 (ECP-WarpX#4575)

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• Beam-beam collision example follow-up (ECP-WarpX#4578)

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• Reduce tolerance for DSMC CI test (ECP-WarpX#4576)

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• Doc: Clean Example TODOs (ECP-WarpX#4584)

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Commits on Jan 6, 2024

• Read external fields from file in restarted simulation (ECP-WarpX#4547)

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• Release 24.01 (ECP-WarpX#4586)

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Commits on Jan 8, 2024

• Clang-tidy: enforce clang-tidy_readability_make_member_function_const check (ECP-WarpX#4510)

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• Implement correction to ADK for high fields (ECP-WarpX#4505)

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• fix doc for coarsening (ECP-WarpX#4588)

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• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4590)

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Commits on Jan 10, 2024

• Fix plasma injection from file for parallel runs (ECP-WarpX#4597)

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Commits on Jan 15, 2024

• Move input of galerkin_scheme upward to before the implicit check of it (ECP-WarpX#4607)

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Commits on Jan 16, 2024

• Docs: spruce up parameters.rst (ECP-WarpX#4609)

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• atomicAdd -> lockAdd (ECP-WarpX#4608)

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• Disambiguate the routine name initialize_inputs in picmi.py (ECP-WarpX#4554)

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• Fix undefined behavior in meanParticleVelocity (ECP-WarpX#4614)

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Commits on Jan 19, 2024

• Perlmutter (NERSC): January 2024 Update (ECP-WarpX#4620)

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• update cupy installation in Perlmutter dependencies (ECP-WarpX#4621)

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Commits on Jan 22, 2024

• Use RK4 to integrate the B-field in time in the hybrid-PIC algorithm (ECP-WarpX#4461)

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Commits on Jan 23, 2024

• Update picmi.ElectrostaticSolver child class in external Poisson solver test (ECP-WarpX#4622)

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• Add warpx_used_inputs_file in Python input (ECP-WarpX#4618)

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• Fix undefined behavior issue in WarpX initialization (ECP-WarpX#4615)

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• Doc: Fast, Local Compilation (ECP-WarpX#4603)

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Commits on Jan 24, 2024

• AMReX/pyAMReX/PICSAR: Weekly Update (ECP-WarpX#4630)

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• Temporary fix: disable hanging CI test (Python_background_mcc_1d_tridiag) (ECP-WarpX#4628)

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• Update pyAMReX (ECP-WarpX#4633)

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Commits on Jan 28, 2024

• Update Particle Container to Pure SoA (ECP-WarpX#3850)

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Commits on Jan 29, 2024

• Remove particles that are initialized in the EB (ECP-WarpX#4585)

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• Update DSMC picmi class initialization function (ECP-WarpX#4646)

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Commits on Jan 30, 2024

• AMReX: Weekly Update (ECP-WarpX#4647)

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• Fix neutral particle got pushed (ECP-WarpX#4643)

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• reactivate CI test (Python_background_mcc_1d_tridiag) (ECP-WarpX#4650)

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• Grammar Change in Theory Intro (ECP-WarpX#4617)

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• Revert "Update Particle Container to Pure SoA (ECP-WarpX#3850)" (ECP-WarpX#4652)

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  ax3l

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Commits on Jan 31, 2024

• AMReX: Latest development (ECP-WarpX#4654)

  ax3l

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Commits on Feb 1, 2024

• Docs: update instructions for Adastra supercomputer (CINES, France) (ECP-WarpX#4655)

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  lucafedeli88

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• Fix doc for doChargeConservingDepositionShapeNImplicit (ECP-WarpX#4658)

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• Add WarpX_CCACHE Option (ECP-WarpX#4637)

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• Update profile and job script for LUMI supercomputer (ECP-WarpX#4634)

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Commits on Feb 2, 2024

• Fix BTD/Scrape Flush Count with Filters (ECP-WarpX#4657)

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• Release 24.02 (ECP-WarpX#4660)

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  ax3l

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• Add install instructions for ALCF's Polaris (ECP-WarpX#4636)

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  roelof-groenewald

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• Implemented Villasenor and Buneman deposition routine for implicit solver (ECP-WarpX#4623)

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• Particle Container to Pure SoA Again (ECP-WarpX#4653)

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Commits on Feb 5, 2024

• Fix: Pre-Installed AMReX w/ CUDA (ECP-WarpX#4668)

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Commits on Feb 6, 2024

• Add hybrid resistivity current term (ECP-WarpX#4661)

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• CI: 4 Cores Linux/Win, 3 Cores macOS (ECP-WarpX#4673)

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• Update GitHub Action versions (ECP-WarpX#4674)

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Commits on Feb 8, 2024

• Update Polaris install instructions (ECP-WarpX#4664)

  roelof-groenewald

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• Minor fix in SLURM signal forwarding description (ECP-WarpX#4665)

  roelof-groenewald

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• ParticleHistogram2D change openPMD access type (ECP-WarpX#4659)

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• Fix docs for checksumAPI terminal call (ECP-WarpX#4677)

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• CI: NVHPC 24.1 (ECP-WarpX#4679)

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  ax3l

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• Update pyAMReX to development (ECP-WarpX#4680)

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• AMReX: Weekly Update (ECP-WarpX#4678)

  ax3l

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• Update openPMD-viewer documentation (ECP-WarpX#4682)

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• Apply filtering for the charge density in full diagnostics RZ PSATD (ECP-WarpX#4624)

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Commits on Feb 9, 2024

• Add automated test for spacecraft charging (ECP-WarpX#4413)

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Commits on Feb 10, 2024

• Fix: openPMD RZ Positions (ECP-WarpX#4686)

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Commits on Feb 12, 2024

• AMReX: Weekly Update (ECP-WarpX#4690)

  ax3l

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• Lassen (LLNL) TOSS3: Update (ECP-WarpX#4692)

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Commits on Feb 13, 2024

• Bugfix: sum guard cell values in current density diagnostic (ECP-WarpX#4596)

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• HPC3 (UCI): -j 8 (ECP-WarpX#4694)

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  ax3l

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• Add PICMI documentation for ReducedDiagnostics (ECP-WarpX#4693)

  RemiLehe

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• Obtain exact point of contact of Particles with EB (ECP-WarpX#4560)

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Commits on Feb 14, 2024

• Removed const modifier from LPInfo object on stack that was causing a… (ECP-WarpX#4696)

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Commits on Feb 16, 2024

• Adding a RZ version for the test "Point_of_contact_EB" (ECP-WarpX#4699)

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Commits on Feb 17, 2024

• Obtain exact time (real) when particles hit boundaries + test (ECP-WarpX#4695)

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Commits on Feb 20, 2024

• [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#4707)

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• Docs: update instructions for Fugaku supercomputer (Riken, Japan) (ECP-WarpX#4656)

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Commits on Feb 21, 2024

• Fix Particle Id Overflows (ECP-WarpX#4708)

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• Implementation of 4th order particle shape beyond implicit solver cases (ECP-WarpX#4706)

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  kale-j

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Commits on Feb 22, 2024

• Cleanup some docstrings (ECP-WarpX#4714)

  RemiLehe

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• Save the normal components in the particle buffer when there is EB (ECP-WarpX#4702)

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Commits on Feb 23, 2024

• Add focusing position to Gaussian beam initialization (ECP-WarpX#4639)

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• Update the documentation particles.rst in adding the new attributes (ECP-WarpX#4719)

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• Fix unresolved reference (ECP-WarpX#4722)

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  n01r

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• Improve Documentation for Laser-Ion Acceleration from Planar Target (ECP-WarpX#4569)

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Commits on Feb 24, 2024

• Update of the time saved for scraped particles on the boundaries (ECP-WarpX#4710)

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Commits on Feb 27, 2024

• AMReX: Weekly Update (ECP-WarpX#4728)

  ax3l

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• Position keyword now adds position variables in PICMI ParticleDiagnostic (ECP-WarpX#4721)

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  n01r

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• openPMD: Fix Particle Weight Dims in 1D/2D (ECP-WarpX#4717)

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  ax3l

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• Clang-Tidy: Fix Diagnostics Branch (ECP-WarpX#4731)

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• Exchange guard cells with the electrostatic solver (ECP-WarpX#4713)

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Commits on Feb 28, 2024

• Adding support for pml in domain for multiple patches (ECP-WarpX#4632)

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Commits on Feb 29, 2024

• Merge remote-tracking branch 'upstream/development' into HSdevmerge_240228

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