chombo-discharge: v23.05

What's Changed

• Namespace bug fixes by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/7
• ParmParse redefine++ by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/15
• Removing files that were never supposed to be here by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/16
• Rename to chombo-discharge by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/18
• Removing tracking of PLY files. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/20
• Bug fix in cdr_solver which reset weights from data on wrong level. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/21
• Fallback option for Poisson by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/22
• Bug fix in cdr_gdnv by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/23
• Various minor fixes to jump_bc by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/25
• Resetting multigrid for poisson fallback by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/26
• Cleanup and inlining of jump_bc. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/30
• Time step computation for advection-diffusion code by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/31
• Removed file was not supposed to be tracked by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/32
• Support for runtime parsing of cell_tagger options. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/33
• Added plot variables runtime options to driver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/34
• Updated makefile for Betzy by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/35
• Fixed betzy makefiles and removed user configuration files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/36
• WIP: Renaming poisson_solver to field_solver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/37
• Minor readme update. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/38
• Removed calls to tiled code by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/42
• Implicit diffusion multigrid stopping criterion. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/43
• Air3 plasma model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/44
• streamer_air regtest by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/45
• Removing one-sided gradient and bad amr_mesh input by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/47
• Least squares interpolation and gradient by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/51
• New interface for electrostatic boundary conditions. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/52
• Bug fix after last PR by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/53
• Update copyright by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/59
• Update license by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/60
• Major update of code standard and documentation by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/58
• Removed file by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/62
• Removing specification of redistribution register size by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/63
• New interface for Eddington/Helmholtz radiative transfer by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/64
• Updated readme by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/65
• Cleanup of CdrPlasmaImexSdcStepper by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/66
• Updating electrostatics python setup tools by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/67
• Moving load balancing routines for Electrostatics by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/69
• New Helmholtz multigrid operator by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/73
• Cdr domain flux by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/75
• Lambda interfaces to common solvers by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/78
• Purge quadratic interpolation by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/80
• Refinement criterion based on surface curvature. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/81
• New multigrid solver for multifluid Helmholtz by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/82
• Updated closures by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/90
• Replacing multigrid kernels by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/91
• Code walk of AmrMesh by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/94
• Fixed restart bug in FieldSolver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/96
• Changed HDF5 identifiers for FieldSolver restart by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/97
• Runtime configurations of geometric grid refinement by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/98
• Improvement of curvature-based refinement by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/99
• Update options and inputs files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/100
• HDF5 and MPI guards by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/101
• Codewalk/geometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/103
• Codewalk of Source/CellTagger by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/104
• Codewalk of Source/ConvectionDiffusionReaction by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/105
• Code updates to Source/Driver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/106
• Formatting bug fix in pout() due to Timer by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/107
• Added runtime options to CdrPlasma/CellTaggers/StreamerTagger by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/108
• Bug fix in AMRUpdateResidual by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/110
• Adding examples folder with various programs by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/111
• Update docs in Source/Electrostatics by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/112
• Doc updates to Source/Elliptic by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/113
• Documenting implicit functions by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/114
• Docs to Source/Multifluid by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/115
• Generalizing bounding volume hierarchy to use k-ary trees. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/116
• Remove file which accidentally came in through last commit by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/117
• Multigrid interpolation performance optimization and cluster makefiles. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/118
• Timer improvement by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/119
• Optimization of EBMultigridInterpolator and monotone path routines by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/122
• Cache offsets in EBHelmholtzOp by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/123
• AggStencil optimization of EBMultigridInterpolator by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/124
• Guard against divide-by-zero in Helmholtz kernel by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/125
• Update example input scripts by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/126
• Fixing memory leaks after elliptic redesign by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/128
• Interpolator bug fix by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/129
• Update to Source/AmrMesh by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/131
• LEA model update by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/132
• E-field corrections with EBCF by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/135
• Fix coarsening criteria in streamer taggers by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/137
• Saturation charge BC to FieldSolverMultigrid by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/136
• Add reaction upwind method by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/138
• Memory leak by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/141
• Virtual destructor in EBHelmholtzNeumannDomainBC by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/142
• Fix cast from EBHelmholtzNeumannDomainBCFactory by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/143
• Fix memory leak in reaction upwinding by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/144
• Forgot a case where we also need upwind reactions by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/145
• Fixing curvature for profiled plane by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/146
• Changing reaction upwinding method to use face centroid values by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/147
• Face-centered gradient by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/148
• Add option to turn off initial load balancing when setting up simulations by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/149
• Reflux-free divergence operator by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/152
• Sign bug fix in outflow bc by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/153
• Add data parser for more easily reading input files. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/155
• Add introspective or constant computational loads for geometry generation by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/156
• Turn on/off profiling of PhaseRealm at runtime by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/157
• More redistribution options for hybrid divergences by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/158
• Add run-time profiling to ScanShop by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/159
• ScanShop redesign by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/160
• Minor improvements by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/161
• Performance optimizations to ScanShop by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/162
• Fix bug in electrode bcs when fetching with multiple electrodes by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/163
• Specify EB intersection algorithm for monte-carlo photons by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/164
• Update Betzy makefiles by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/167
• Added permittivity to plot files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/168
• Doc updates to sigma solver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/170
• Doc updates to Source/Utilities by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/172
• Doc updates to Source/RadiativeTransfer by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/173
• Particle redesign by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/151
• Missing MPI guards in Timer by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/174
• Update various particle functionality by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/175
• Docs to Physics/AdvectionDiffusion by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/176
• Update Physics/BrownianWalker by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/177
• Update Physics/Electrostatics by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/179
• Add doxygen to Physics/Geometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/181
• Introspective particle load balancing by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/182
• Code factoring and improvements by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/150
• Docs to Physics/RadiativeTransfer by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/183
• Fill ghost faces by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/185
• Update options file by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/187
• Start adding GitHub Actions by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/188
• Add Intel CI files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/189
• Add SIMD-safe loops for launching C++ kernels by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/190
• Remove Fortran from chombo-discharge by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/193
• Update chombo by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/198
• Installation instructions in docs by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/199
• Rework minimal plasma model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/202
• Update CdrPlasma model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/203
• Update HDF5 IO by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/206
• Put complex geometries in separate repo and clone as submodule by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/214
• Secondary emission on domain sides for JSON model by @FannySkirbekk in https://github.com/chombo-discharge/chombo-discharge/pull/207
• Continuation of CDR plasma rework. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/208
• Update EBGeometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/219
• Godunov integrator by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/220
• Fix FieldSolver plot bug by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/221
• Update EBGeometry and bindings by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/222
• Rename EBGeometry to EBGeometryIF by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/223
• Add docs to CI by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/229
• gh-pages deployment bug by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/230
• Second deployment bug by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/231
• Add doxygen to CI by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/232
• Update EBGeometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/236
• Add tracer particle module by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/227
• Extrapolated BC for JSON interface by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/237
• Add new class for regridding. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/239
• Add clang-format for consistent code formatting by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/241
• Use size_t for number of photons in cell by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/243
• Aggregate particle generation routines by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/244
• Add functionality for depositing RealVects by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/245
• Update input files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/248
• Update example files by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/249
• Add electrostatic examples and remove deprecated models by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/250
• Add convergence tests by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/252
• Update EBGeometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/253
• Mesh-based ODE solver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/256
• Update documentation by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/257
• Build and deploy pdf by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/258
• New corner transport upwind (CTU) discretization for advection by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/260
• Documentation of electrostatics module by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/261
• Remove TimeCode as global class. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/262
• Update documentation. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/263
• Skeleton for streamer inception model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/264
• Swap to CdrCTU for CdrPlasma examples by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/265
• Add SphereArray implicit function by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/266
• Explicit number of ghost cells to ScanShop by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/270
• Update Chombo by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/271
• Update EBGeometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/272
• Bugs by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/273
• Permit EB stencil change for deeper multigrid by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/281
• Rework particle code by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/282
• Restructure averaging methods. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/283
• Last PR exposed a few subtle bugs by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/287
• Add streamer inception model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/284
• Fix build errors and update EBGeometry by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/289
• Update kernels in DataOps by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/290
• Optimize Helmholtz operators for coefficient redefines by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/291
• Update documentation by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/295
• Add SurfaceODESolver by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/296
• Rename LookupTable by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/297
• Simpler regrid signature for particles by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/298
• Geometry needle by @FannySkirbekk in https://github.com/chombo-discharge/chombo-discharge/pull/233
• Redo prolongation and restriction operators. by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/301
• Add valid number of grid cells to Driver report by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/302
• New regrid method that does local remapping first by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/304
• Throw warning in LookupTable by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/305
• Optimizations for Helmholtz operators by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/306
• Bug fix in CTU slopes by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/307
• Add Ito-KMC plasma model by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/308
• Update documentation CI by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/315
• Update Ito-KMC functionality by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/317
• Update installation instructions by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/324
• Namespace bug fix in ParticleManagement by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/325
• Optimizations for linear solvers by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/327
• Add warning about newer versions of HDF5 by @rmrsk in https://github.com/chombo-discharge/chombo-discharge/pull/330

New Contributors

• @FannySkirbekk made their first contribution in https://github.com/chombo-discharge/chombo-discharge/pull/207

Full Changelog: https://github.com/chombo-discharge/chombo-discharge/commits/v23.05