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2021-12-03Replace AMREX_SPACEDIM: Boundary & Parallelization (#2620)Gravatar Prabhat Kumar 7-82/+82
* AMREX_SPACEDIM : Boundary Conditions * AMREX_SPACEDIM : Parallelization * Fix compilation * Update Source/Parallelization/WarpXComm_K.H
2021-12-02Mention that the potentail should be constant inside EB (#2618)Gravatar Remi Lehe 1-1/+3
* Mention that the potentail should be constant inside EB * Update text
2021-12-02Fix out-of-bound in Inverse FFT of F,G (#2619)Gravatar Edoardo Zoni 1-2/+2
2021-12-02Add 2D Langmuir Test w/ MR & PSATD (#2605)Gravatar Edoardo Zoni 2-0/+63
* Add 2D Langmuir Test w/ MR & PSATD * Add Missing Compile String
2021-12-02div(E,B) Cleaning Options for PSATD (#2403)Gravatar Edoardo Zoni 10-59/+148
* Implement div(E)/div(B) Cleaning with Standard PSATD * Cleaning * Update Benchmark * Add Nodal Synchronization of F,G * OneStep_multiJ: Nodal Syncs, Damp PML * OneStep_multiJ: Push PSATD Fields in PML * div Cleaning Defaults (Domain v. PML) * Include Fix of #2429 until Merged * Reset Benchmark of Langmuir_multi_psatd_div_cleaning * Multi-J: Remove PML Support * Include Fix of #2474 Until Merged * Exchange All Guard Cells for F,G * Fix Defaults * Update Test, Reset Benchmark * Fix Defaults * Cleaning * Default update_with_rho=1 if do_dive_cleaning=1 * Update CI Test pml_psatd_dive_divb_cleaning * Replace Warning with Abort
2021-12-02Release 21.12 (#2614)Gravatar Axel Huebl 10-16/+16
* AMReX: 21.12 * PICSAR: 21.12 * WarpX: 21.12
2021-12-01Fix installation location for libraries (#2583)Gravatar s9105947 1-1/+1
During configuration the installation location for libraries is given by dumping the cmake variable `CMAKE_INSTALL_LIBDIR`. This commit adjusts the installation of WarpX libraries (WarpX_LIB=ON) to respect this setting. Co-authored-by: Rolf Pfeffertal <tropf@users.noreply.github.com>
2021-11-30MergeBuffersForPlotfile: Barrier (#2608)Gravatar Axel Huebl 1-0/+6
Make sure that all MPI ranks are in sync, i.e., have closed the files that they wrote, before trying to merge them.
2021-12-01AMReX: Weekly Update (#2613)Gravatar Axel Huebl 4-4/+4
2021-11-30Dimensionality Docs: Default (#2609)Gravatar Axel Huebl 1-4/+4
Just adds the note that 3D is the default geometry.
2021-11-30Note that CCache 4.2 introduced large CUDA improvements (#2606)Gravatar Phil Miller 1-1/+1
2021-11-30Added parallel pragma to ApplyBoundaryConditions (#2612)Gravatar David Grote 1-0/+3
2021-11-30Fix segfault when importing _libwarpx without initializing WarpX (#2580)Gravatar Kevin Z. Zhu 2-2/+9
* Added check for if warpx was initialized when calling finalize * Renamed to be warpx_initialized * Fixed reference to global variable Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com> * Changed global variable to member of libwarpx * Fixed syntax errors * Remove custom arg from argv to avoid parmparse error Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
2021-11-30Throwing a warning if particle_shape>1 with EB (#2592)Gravatar Lorenzo Giacomel 1-2/+17
* Aborting if particle_shape!=1 with EB * Throw warning instead of aborting * Checking at runtime if EB is initialized * Added missing preprocessor directive * Ignoring an unused variable * Fix typo * Improve style Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-30Replaced duplicated current deposition documentation (#2604)Gravatar Remi Lehe 1-68/+32
2021-11-30CONTRIBUTING: Update/Modernize (#2600)Gravatar Axel Huebl 1-42/+77
* CONTRIBUTING: Update/Modernize - Add GitHub account setup - Add local git setup - Modernize for CMake workflows * Apply suggestions by Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-11-24requirements.txt - PICMI development version (#2588)Gravatar Axel Huebl 1-0/+6
Document in `requirements.txt` on how to install a pre-release version of PICMI.
2021-11-24C++17: Work-Around NVCC gatherParticles (#2596)Gravatar Axel Huebl 1-1/+2
The `noexcept` lambda does not compile in C++17 mode due to an NVCC compiler bug, at least in NVCC 11.3.109. Compiles in C++14 mode with the same compiler.
2021-11-23Fix Init of Vector Members (#2595)Gravatar Axel Huebl 3-4/+5
Fix default init of `Vector` member variables. The old construct is not valid C++. https://stackoverflow.com/a/11491003/2719194
2021-11-22Python: Start 1D Support (#2582)Gravatar Axel Huebl 16-31/+90
* Python: Start 1D Support Start supporting 1D builds in Python. * Fix 1D: PML FillZero unused ... since PMLs are not yet supported in 1D. * BeamRelevant: Fix unused p_pos0 * FromTXYEFileLaserProfile: Not Impl in 1D * QED Schwinger: 1D not Implemented Fix unused warnings, add aborts. * 1D RealVect/IntVect: Initialization Use explicit scalar constructors, no braces. Fix warning in clang 10. * 1D NCI Filter: Fix unused members & Init Unimplemented, but throws warnings. * PSATD: 1D not Implemented - remove compile warnings - start porting some parts * NCIGodfreyFilter: Clean up 2D & Else
2021-11-22Added abort error message to prevent using averaged Galilean PSATD with ↵Gravatar Olga Shapoval 1-0/+4
psatd.update_with_rho=0 (#2571)
2021-11-22Proton-boron fusion: compute initial momentum of produced alphas (#2330)Gravatar Neïl Zaim 7-32/+249
* Proton-boron fusion: initialize alphas momentum assuming isotropy * Remove constexpr underflow in single precision * Update Source/Particles/Collision/BinaryCollision/ProtonBoronFusionInitializeMomentum.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-22AMReX: Weekly Update (#2590)Gravatar Axel Huebl 4-4/+4
2021-11-22WarpX.cpp: Use Explicit Types, not `auto` (#2585)Gravatar Edoardo Zoni 1-16/+16
2021-11-21openPMD: 1D3V Support (#2586)Gravatar Axel Huebl 5-13/+28
Add 1D output support with openPMD.
2021-11-20Python: More Nullptr Checks (#2574)Gravatar Axel Huebl 1-0/+18
* Python: More Nullptr Checks I am debugging a couple of crashes while mitigating CI. One of them pointed to the locations here (`ValueError: NULL pointer access`), so I decided to add some checks. * Skip invalid tiles * Skip Empty Tiles But Check Pointer * Python: nullptr check in _array1d_from_pointer Make the methods `get_particle_structs` and `get_particle_boundary_buffer_structs` more robust.
2021-11-19added cost of MCC collisions to load balancing calculation (when using ↵Gravatar Roelof Groenewald 2-3/+33
Timers) (#2584)
2021-11-19add github ci compile check for ascent (#2483)Gravatar Cyrus Harrison 2-0/+115
* add github ci compile check for ascent * now with less whitespace * add ascent to insitu workflow * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * more style * try to run as existing user * new container * use env script * path fix * add ascent test * fix space * move test resources * get into style * style * Ascent CI: Cleanup (#1) - make sure inputs file stays up-to-date - locate alongside example * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update .github/workflows/insitu.yml Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * rename test file * fix for cp * improve color table for vol rendering * now with rotation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-19setup.py: beta -> stable (#2570)Gravatar Axel Huebl 1-1/+1
Mark the Python meta-data as production/stable.
2021-11-19RZ PSATD, make blocking_factor a power of 2 (#2572)Gravatar David Grote 1-3/+9
* With RZ PSATD, make blocking_factor a power of 2 * Fix typo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-11-19Bilinear Filter: Fix Warning (Vector) (#2575)Gravatar Axel Huebl 1-6/+6
GCC warns in some versions on the access here, since it cannot figure out the runtime size of the vectors. We can just replace `[]` with `.at()` to use a range-checked access that throws an exception instead of a segfault/UB when accessed out-of-bounds. In the preparation of the compute stencils, we don't have hot loops that benefit from non-range checked access, so that cost for improved safety is fine.
2021-11-191D3V Cartesian Support (#2307)Gravatar Prabhat Kumar 64-177/+1646
* Build System: Add 1D Geometry * test PR * test PR * 1D cartesian yee algorithm * fixed typo * Fixes for PML * 1D support related multiple changes * Fix compilation * change 1D to 1D_Z * 1D Field Gather and typo fix * 1D Charge Deposition * Particle Pusher * multiple changes related to 1D * 1D diagnostics and initialization * PlasmaInjector and PEC fixes for 1D * clean-up delete diags file * mobility 1D laser particle and bilinear filter * deleted diags files * update laser particle weight formula * delete diags files * Azure: Add 1D Cartesian Runner * 1D fixes for FieldProbe * Update Docs/source/developers/dimensionality.rst Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * 1d laser injection and langmuir test input files * 1d tests * clean up : delete print statements * analyse simulation result for laser injection and Langmuir tests * EOL * delete input files for which there are no automated tests * delete input files for which there are no automated tests * add ignore_unused to remove warnings * remove space * Fix compilation issues * fix error : macro name must be an identifier * Small bug fix * cleanup Python script for analysis * bug fix * bug fix * Update ParticleProbe: Check 1D in-domain * Update Source/Make.WarpX * Update .azure-pipelines.yml * Add USE_OPENPMD=FALSE to .azure-pipeline.yml * resolve conflict * resolve conflict * fix typo * Correct out-of-bound access * Fix Particle BC in WarpXParticleContainer and correct path to checksumAPI in python analysis scripts * EOL * Fix bug : accessing out of bound index of cell in 1D * remove 1d test for cartesian3d * Fix CI check * Slight style change * Address review comments * Fix GPU compilation Filter.cpp * Fix CI * Fix Indentation * Address review comments * More consistent ifdef for dimension bigger than 1 * Update Examples/Tests/Langmuir/analysis_langmuir_multi_1d.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update GNUmakefile Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Regression/prepare_file_ci.py Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/CartesianCKCAlgorithm.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/FieldSolver/FiniteDifferenceSolver/FiniteDifferenceAlgorithms/CartesianNodalAlgorithm.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Filter/Filter.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Filter/Filter.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Filter/Filter.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Filter/Filter.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Initialization/PlasmaInjector.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Initialization/PlasmaInjector.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add comment inline to explain twice push_back * Add amrex::Abort for NCIGodfreyFilter Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Remi Lehe <rlehe@lbl.gov>
2021-11-19Mini-PR: Improve Python particle attribute access CI test (#2581)Gravatar Roelof Groenewald 3-29/+41
* updated the Python particle attribute access CI test * additional fixes needed for tests to pass * changes requested by Axel during code review * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-18LaserInjectionFromTXYEFile Test: Use MPI (#2577)Gravatar Axel Huebl 1-1/+2
* WarpX tests: All MPI Enable MPI for the one regression test that does not use it. Still uses one rank there. This saves a compile per CI run. * add numprocs
2021-11-18Add WARPX_PROFILE calls to each python callback. (#2573)Gravatar Peter Scherpelz 3-13/+53
When python callbacks take some time, this is useful as otherwise many callbacks are lumped together in WarpX::Evolve::step.
2021-11-18WarpXComm.cpp: Use Explicit Types, not `auto` (#2578)Gravatar Edoardo Zoni 1-26/+29
* WarpXComm.cpp: Use Explicit Types, not `auto` * Use MultiFab* const instead of MultiFab* const&
2021-11-18Bug fixes and cleanup in load balancing (#2563)Gravatar Roelof Groenewald 9-210/+152
* added helper function to rebuild MultiFabs and iMultiFabs during load balancing and included rebuilding of EB multifabs * added redistribute call for the particle boundary buffer during load balancing * consistently use DistribtionMap rather than dmap in ElectrostaticSolver.cpp * applied suggested changes from code review by Phil Miller * removed default argument for redistribute in RemakeMultiFab * removed RemakeMultiFab() as a member of WarpX * Only remake EB multifabs if they are used Co-authored-by: Lorenzo Giacomel <47607756+lgiacome@users.noreply.github.com> * adapted existing particle scraping test (PICMI version) to also cover the redistribution of particle buffers from load balancing * added redeclaring of m_borrowing * Move redeclaring of m_borrow inside if statement for ECT solver algorihtm Co-authored-by: Lorenzo Giacomel <47607756+lgiacome@users.noreply.github.com> * added calls to MarkCells and ComputeFaceExtensions * fixed issue causing CI test to fail and copied conditionals from WarpXInitData.cpp to recompute EB quantities * Guard cells communication for EB data when re-gridding (#105) * Add 2D circle EB test (#2538) * Added embedded_circle test * Add embedded_circle test files * Removed diag files * removed PICMI input file * Update to use default regression analysis * Added line breaks for spacing * Added description * Fixed benchmark file * Added load balancing to test * Commented out load_balancing portion of test. This will be added back in once load balancing is fixed. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Added guard cells communication for EB data in regridding Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * moved all EB grid data calculations to a new function InitializeEBGridData() which is now called by both WarpX::InitLevelData and WarpX::RemakeLevel * Fix typo in doc string. Co-authored-by: Phil Miller <unmobile+gh@gmail.com> Co-authored-by: Lorenzo Giacomel <47607756+lgiacome@users.noreply.github.com> Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
2021-11-18WarpXMovingWindow.cpp: Add `amrex::` Prefix (#2579)Gravatar Edoardo Zoni 1-63/+63
2021-11-18Apply PEC to Split PML Fields (#2541)Gravatar Revathi Jambunathan 4-28/+59
2021-11-16Fix: GNUmake Python Link -g (#2568)Gravatar Axel Huebl 1-1/+1
On CPU links of the GNUmake Python lib, we forgot our `-g`, which we add to all build and optimization types. THis is part of the `LINKFLAGS` variable.
2021-11-16added superLU solver example to docs (#2567)Gravatar Roelof Groenewald 1-0/+7
2021-11-16Cell Center Macroscopic Properties (#2530)Gravatar Revathi Jambunathan 6-205/+188
* Cell Center Macroscopic Properties * Commit Suggestions from PR Review * Fix Error for 2D Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-11-16Clean up input files for tests with MCC (#2552)Gravatar Roelof Groenewald 7-82/+71
* Added embedded_circle test * Add embedded_circle test files * Removed diag files * removed PICMI input file * Update to use default regression analysis * Added line breaks for spacing Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Added description * Added Ar and Xe to pre-defined particle types * added Boltzmann's constant to pre-defined constants and cleaned up the MCC CI test input * Added Boltzmann's constant to warpx parser * cleaned up embedded circle CI test input * Remove duplicate entry. Co-authored-by: kzhu-ME <kevin.zhu@modernelectron.com> Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-16Enhanced inline documentation of EB related data (#2562)Gravatar Lorenzo Giacomel 3-8/+34
* Enhanced inline documentation of EB related data * Added ECT to the glossary * Made the EB documentation doxygen-compatible
2021-11-16Avoid code duplications in ECT face extension (#2557)Gravatar Lorenzo Giacomel 2-997/+338
* Refactoring the nborrow functions * Refactoring the one cell extension * Refactoring the eight cells extension * Enabling 2D * Bug fix * Some more improvements * Fixing templates * Switching the order of templates and AMREX_GPU_DEVICE * Adding the needed AMREX_GPU_DEVICE in WarpX.H * Fixing GPU related issues * Fixed a for loop bound * Making the new functions free * Suggestion from review * Suggestion from review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Suggestion from review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Improve loops over dimensions for 2D Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-16Fixes to the EB init (#2565)Gravatar Lorenzo Giacomel 1-3/+7
2021-11-16Add 2D circle EB test (#2538)Gravatar Kevin Z. Zhu 3-0/+137
* Added embedded_circle test * Add embedded_circle test files * Removed diag files * removed PICMI input file * Update to use default regression analysis * Added line breaks for spacing * Added description * Fixed benchmark file * Added load balancing to test * Commented out load_balancing portion of test. This will be added back in once load balancing is fixed. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-11-15Docs: Fix .rst Label in PML, rm .tex (#2537)Gravatar Axel Huebl 4-238/+6
Fix an auto-converted label in a `.rst` file for the manual. Remove the `PML.tex` file.
2021-11-15AMReX/PICSAR: Weekly Update (#2559)Gravatar Axel Huebl 5-9/+9
* AMReX: Weekly Update * PICSAR: Weekly Update
2021-11-15 I/O performance hints for Summit (#2495)Gravatar Jean Luca Bez 3-1/+77
* Fix conflict with upstream * Apply suggestions from code review * Remove space in the end of lines * Include suggestions from PR review * Generalize ROMIO Hints in Batch Scripts * Fix Comment * Fix Comment * Remove duplication * Formatting Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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