AMReX-Codes/amrex: AMReX 26.04

What's Changed

• Hypre: Remove unused code in HypreABecLap3 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5099
• PETSc: Fix potential memory leak by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5097
• PETSc: Remove unused code by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5091
• PETSc: Use PetscInt by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5090
• FFT::Clear: Clear the map after the stored plans are destroyed by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5089
• Doxygen PETSc by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5087
• Doxygen Boundary by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5096
• FFT: Use ParallelContext's communicator by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5088
• Nosync broadly by @ax3l in https://github.com/AMReX-Codes/amrex/pull/4957
• Hypre: Fix a typo in CMake by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5100
• Add new test and fix dual grid restart bug by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5075
• Use HYPRE capitalization consistently in Sphinx docs by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5071
• STL: Assert it's not empty by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5109
• EB: Validate lookup status in getLevel/getGeometry by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5107
• OpenBCSolver: Make define safer by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5129
• ReadAndBcastFile: Use the correct I/O process when sub-communicator is used. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5131
• ParallelDescriptor: Avoid the non-standard variable-length array by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5130
• FabArrayCopyDescriptor: Add assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5132
• Rename the NonManagedVector to NonManagedDeviceVector by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5124
• Hypre: Remove unimplemented 1d functions to avoid confusion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5103
• FillPatchSingleLevel: Robustify assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5121
• AmrMesh: Validate input by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5119
• Fujitsu MPI: Fix potential null-dereference by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5122
• MultiMask: Fix initval for multiple components by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5118
• StateDescriptor: Add assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5125
• StateDescriptor: Remove deprecated functions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5126
• BndryData: Robustify reuse check by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5116
• SpMatrix: Add assertion in communication by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5128
• Update Fortran BC type module by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5113
• Marching Cubes: Fix GPU memcpy by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5110
• EB: Assert there is no int overflow by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5111
• AmrLevel::FillPatch: Fix assertion by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5127
• Boundary: Fix forward declarations by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5114
• COMM_PROFILING: Fix size bug by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5135
• ParallelDescriptor: Assert team size is positive by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5134
• LineDistFcnElement2d::single_seg_cpdist: Fix degenerate case by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5106
• HypOptParse: Remove operator()(key, func) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5105
• Hypre: No need to call hypre if local row count is zero by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5104
• VisMF: Avoid UB-prone assertions on potentially empty strings by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5133
• FillPatcher: Robustify assertions by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5120
• BndryRegister: Make sure assertion does not access out-of-bound memory by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5112
• Mask: Fix writeOn/readFrom for multiple components by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5117
• FileSystem::Remove: Fix return value by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5136
• Workaround for deprecation warnings on Perlmutter by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5101
• Move PETSc Initialize and Finalize to amrex::Initialize and Finalize by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5098
• Fix caching mechanism for neighbor particle mask by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5080
• Fix restart where you lose a level and NReaders > NProcs() by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5074
• ParmParse: Add TOML-like features by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/4950
• Parser: Improve documentation and fix minor issues with help from Claude by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5144
• ParmParse: Refactor countval for TOML arrays by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5143
• Fix a warning in Fortran module by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5142
• Add Gpu::isStreamActive function by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5139
• Add FillBoundaryAndSync(Vector) by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5138
• Parser optimization by Claude by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5146
• ParmParse: Improve documentation and comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5148
• ParmParse: Support query/get a specific element from TOML array. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5149
• Fix bug in bisect by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5167
• Fix assertion in bisect by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5169
• Fix BaseFab::contains by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5171
• HDF5: Fix missing GPU device-to-host_copy in writing plotfile by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5174
• BLBackTrace: Fix null terminator by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5173
• Fix typo in N_VConstrMask_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5175
• SUNDIALS: Fix memory leak in N_VWL2Norm_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5177
• SUNDIALS: Fix a memory leak in N_VDestroy_MultiFab by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5176
• SUNDIALS: remove MemoryHelper's move operator= by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5178
• ParmParse: Fix printing TOML array by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5180
• ParmParse: accept true/false t/f for int keys by @charlesgwaldman in https://github.com/AMReX-Codes/amrex/pull/5150
• Fix hidden direction support for multilevel composite solves by @desjardi in https://github.com/AMReX-Codes/amrex/pull/5141
• Fix resource leaks in ParticleContainer::RestartHDF5 by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5185
• Fix InitFromBinary for the case that NP % NReaders != 0 by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5184
• Fix HDF5 handle leaks in early exits by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5187
• Make sure number of neighbor particles is preserved on swap by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5186
• ParmParse: Preserve quotes when printing strings by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5188
• Managed Arena: Do not pre-allocate if managed memory is not supported. by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5183
• Doxygen AmrCore by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5179
• Parser: fix self assignment of locals by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5189
• Doxygen Amr by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5190
• Fix Dual Grid restart with HDF5 format by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5137
• Fix tracer particle Timestamp to respect indices argument by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5194
• Fix empty vector dereference in HDF5 particle IO by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5195
• Add a comment to selectActualNeighbors by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5193
• Avoid clang warnings with -Wshadow-field by @charlesgwaldman in https://github.com/AMReX-Codes/amrex/pull/5197
• ParmParse::add: Improve TOML compatibility by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5196
• Filter transform fix by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5192
• Add comment that is safe to assume divisors are not zero in tracer mod by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5198
• Clean up RedistributeCPU by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/4529
• Add external GPU stream override support by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5199
• Fix GCC warning in AllGatherBoxes by @AlexanderSinn in https://github.com/AMReX-Codes/amrex/pull/5203
• Bump dorny/paths-filter from 3 to 4 by @dependabot[bot] in https://github.com/AMReX-Codes/amrex/pull/5202
• Fix assertions in particle IO to include runtime int comps by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5205
• Avoid undefined behavior in Random_int by having it always return 0 for n = 0. by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5206
• Add AGENTS.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5208
• Fix typo in Gitlab CI README by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5213
• Fix some typos in the docs by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5212
• Add section on using LLMs to CONTRIBUTING.md by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5211
• Sphinx Documentation: Minor wording fixes by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5217
• Fix typo in README.md by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5214
• Geometry: Exceptions by @ax3l in https://github.com/AMReX-Codes/amrex/pull/5219
• Geometry: Better assertion message by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5224
• Avoid invalid in AMReX_MFInterp_3D_C.H by @dpgrote in https://github.com/AMReX-Codes/amrex/pull/5215
• Implement pure-SoA HDF5 particle IO by @atmyers in https://github.com/AMReX-Codes/amrex/pull/5204
• FFT: Fix one-d mode in 2D & 3D builds by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5225
• Typos in .gitlab/README.md by @eebasso in https://github.com/AMReX-Codes/amrex/pull/5234
• ParReduce: Fix comments by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5238
• FilFC: Fix a copy-paste typo by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5240
• Fix facediv_int z indexing by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5239
• CI: Use C++20 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/4976
• Fix particle dual-grid test by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5255
• Bump Jimver/cuda-toolkit from 0.2.30 to 0.2.35 by @dependabot[bot] in https://github.com/AMReX-Codes/amrex/pull/5256
• Remove emoji in README.md by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5259
• Update CHANGES for 26.04 by @WeiqunZhang in https://github.com/AMReX-Codes/amrex/pull/5264

New Contributors

• @desjardi made their first contribution in https://github.com/AMReX-Codes/amrex/pull/5141

Full Changelog: https://github.com/AMReX-Codes/amrex/compare/26.03...26.04