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2022-06-01Crusher: Update Modules (#3152)Gravatar Axel Huebl 1-3/+3
Module update on Crusher.
2022-06-01Boundary scraping diagnostic (#3064)Gravatar Remi Lehe 15-23/+324
* Initialize boundary scraping diagnostic * Add new file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Start fixing diagnostics * Define ReadParameters function * Define stubs for all required functions * Enable new diagnostics in one of the tests * Dump all particles at the end of the run * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use the same types for different pinned-memory particles * Use the same types for different pinned-memory particles * Fix compilation error * Finalize dumping buffer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Clean up file * Activate recording of particles at the boundary * New function getParticleBufferPointer * Pass a WarpXParticleContainer to the ParticleDiag * Handle timestamp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Revert to multi-level simulation * Add documentation and a few checks * Fix error with MPI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update varnames for RZ openPMD * Add automated test * Add automatic check * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Create new named component particle container * Fix compilation * Make WarpXParticleContainer derive from NamedParticleContainer * Transfer functions that are specific to the particle component maps * Move PIdx * Make PinnedMemoryParticleContainer derive from NamedComponentParticleContainer * Fix compilation * Avoid unnecessary MPI communications * Fix brittle code * Define function `make_alike` * Fix compilation * Add back const anotations * Fix typo * Update code * Fix compilation error * Fix indentation * Fix indentation * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix namespace * Improve Error Messages Further * Doxygen: Parameters of the Diag Constructor * Update `WarpX-tests.ini` ... so we can filter the test out if we build w/o openPMD. Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-06-01Acknowledge us: update DOIs (#3150)Gravatar Axel Huebl 1-7/+7
- properly link DOIs (pretty) - add arXiv for non-OA publication(s) - remove arXiv for OA publicaion(s)
2022-05-31AMReX no-MPI Gather Fixed (#3149)Gravatar Axel Huebl 2-5/+3
* CI: Add no-MPI Runtest * FieldProbe: Remove Work-Around #3134
2022-05-31Add 3D tests for proton boron fusion (#2450)Gravatar Neïl Zaim 4-0/+1104
* Add 3D tests for proton boron fusion * Add execute permission to analysis script * Fix Checksum path * Increase tolerance for energy check * Update benchmarks * Specify type of exception in try expect block * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add review suggestions Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Safe Runtime: <species>.do_not_deposit = 1 Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Remove division by zero warning in python analysis script * Update cross-section in the E > 3.5 MeV range * Increase some tolerances * Update benchmark Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-31Docs: Science Highlights (#3139)Gravatar Axel Huebl 3-2/+78
* Docs: Science Highlights Document science papers of ours and users that use WarpX. * Add: More LWFA Preprints :rocket: * Use Ordered (Numbered) Lists
2022-05-31AMReX: Weekly Update (#3147)Gravatar Axel Huebl 5-5/+5
2022-05-31Move MsgLogger to ablastr (#3148)Gravatar Luca Fedeli 13-53/+55
* move Msg Logger to ablastr * fixed bug * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-30Use Utils::TextMsg::Err and WARPX_ALWAYS_ASSERT_WITH_MESSAGE in more files ↵Gravatar Luca Fedeli 15-106/+137
(#3117) * use formatted error messages * fixed bug * fixed bug * fixed bugs * fixed bug
2022-05-30move serialization to ablastr (#3145)Gravatar Luca Fedeli 2-62/+69
2022-05-27Remove Extraneous `WARPX_DIM_RZ` in Gaussian Laser Init (#3144)Gravatar Ryan Sandberg 1-1/+1
2022-05-27Docs: Improve `collision_name>.species` (#3143)Gravatar Axel Huebl 1-2/+2
... for `background_stopping` we also just use one species.
2022-05-26Write Inputs to `warpx_used_inputs` (#3132)Gravatar Axel Huebl 3-2/+28
Write a general file `warpx_used_inputs` that contains all inputs of a simulation. This is needed, since we add & overwrite the inputs parameters in the inputs file with command-line options regularly. Writing the actually used inputs increases reproducibility of such workflows, especially in unsupervised scripted runs/optimizations.
2022-05-26Fix: Install ABLASTR (#3141)Gravatar Axel Huebl 1-1/+1
Since ABLASTR is a proper library now, we need to install it as well.
2022-05-26SpectralFieldDataRZ: Missing Utils Include (#3140)Gravatar Axel Huebl 1-0/+1
2022-05-25Fix: Field Probe no-MPI Gather (#3134)Gravatar Axel Huebl 1-2/+6
In AMReX, Gather without MPI was implemented as a no-OP. This applies a work-around so we can patch already released WarpX versions.
2022-05-25PML.cpp: missing util include (#3138)Gravatar Axel Huebl 1-0/+1
fix a missing include for `PML.cpp`
2022-05-25Reactivate Multi-J RZ PSATD Checksums (#2459)Gravatar Neïl Zaim 3-34/+29
* Try to reactivate Multi-J RZ PSATD checksums * Reduce size of test and add debug prints * No MPI in test * Revert "Reduce size of test and add debug prints" This reverts commit c8656710de7cdada71a7e8ff5a7c0e44d082e701. * Revert "No MPI in test" This reverts commit 1a0a682018800f606894f039c7c89f28998532b2. * Remove close to zero values from field outputs * Update benchmarks
2022-05-24Test Filter: Include Python Langmuir (#3129)Gravatar Axel Huebl 2-11/+8
* Test Filter: Include Python Langmuir * Reset Benchmarks (Python Langmuir) Co-authored-by: Tools <warpx@lbl.gov>
2022-05-24Specify particle precision (#3065)Gravatar Kevin Z. Zhu 23-256/+349
* Add precision to printed PIC parameters * Added WarpX_PARTICLE_PRECISION as a build option * Update types to ParticleReal * Updated libwarpx to inject particles with correct ParticleReal type * Fix syntax error * Add logic to avoid duplicate definitions * Use correct ParticleReal type in add_particles * Cleaned up code, addressed comments * Update Python/pywarpx/_libwarpx.py Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com> * Removed redundant functions, fixed some typing * Modified template functions * Cast d_w to Real * Fixed failing tests * Cast types to be consistent * removed in-tree-build from pip command * Added GPU device macros to PDim3 methods * rerun tests * Removed unecessary casting, update calls to use PDim3 instead of XDim3 * Refactored comments * Added mcc fields double precision, particles single precision test * Updated casting and formatting * Removed cast, updated declaration Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com> Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
2022-05-24Simplify the function computePhi (#3026)Gravatar Remi Lehe 1-56/+30
* Simplify the function computePhi * Allow to compile RZ without EB * Allow to compile RZ without EB * Deactivate semi-coarsening when both EB and RZ are used * Update Source/FieldSolver/ElectrostaticSolver.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-05-23CMake Pip: Unique Custom Targets (#3116)Gravatar Axel Huebl 1-4/+13
Add a prefix to custom targets so we do not collide if used as a CMake subproject, e.g., in ARTEMIS.
2022-05-23Docs: New Perlmutter Default Env, Microarch (#3127)Gravatar Axel Huebl 1-1/+6
* Docs: New Perlmutter Default Env The default environment on Perlmutter is now the one we already used, `PrgEnv-gnu`. Thus, we don't need to switch anymore. * Perlmutter: Build Microarch Tuned for Zen3, which is used on Login and Compute nodes alike: https://docs.nersc.gov/systems/perlmutter/system_details/ * Keep PrgEnv-gnu ... in case it changes again * Comment microarch flags
2022-05-23Fold Python tests into their corresponding base configurations, to better ↵Gravatar Phil Miller 4-49/+33
exploit ccache (#3107) * Fold Python tests into their corresponding base configurations, to better exploit ccache * Align 1D Python tests with rest of 1D tests * Remove archaic test exclusions * Reintroduce exclusion of Python_Langmuir test, since it currently fails
2022-05-24Add new class `NamedComponentParticleContainer` (#3100)Gravatar Remi Lehe 6-76/+190
* Add new class `NamedComponentParticleContainer` * Update docstrings * Fix compilation * Address review comments * Update Doxygen Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-05-24[pre-commit.ci] pre-commit autoupdate (#3128)Gravatar pre-commit-ci[bot] 1-2/+2
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.14 → v1.2.0](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.1.14...v1.2.0) - [github.com/hadialqattan/pycln: v1.3.2 → v1.3.3](https://github.com/hadialqattan/pycln/compare/v1.3.2...v1.3.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-23AMReX/PICSAR: Weekly Update (#3126)Gravatar Axel Huebl 6-6/+6
* AMReX: Weekly Update * PICSAR: Weekly Update
2022-05-23remove unused enum (#3124)Gravatar Luca Fedeli 1-7/+0
2022-05-23use fwd declaration for WarpXFaceInfoBox (#3125)Gravatar Luca Fedeli 8-8/+28
2022-05-23fix unnecessary double promotions (#3120)Gravatar Luca Fedeli 8-27/+27
2022-05-23Add `do_average` option to the particle fields diagnostic (#3067)Gravatar David Grote 10-76/+114
* Added do_average option to the particle fields diagnostic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated CI benchmark files * Updated CI benchmark files * Fix ParticleReductionFunctor comment * Changed maps to vector for code simplification * Change do_average to bool Co-authored-by: Hannah Klion <klion@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix from the merge Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Klion <klion@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-05-20Clarify error messages when parsing diagnostics input (#3122)Gravatar Hannah Klion 1-3/+3
2022-05-18ABLASTR: localIDtoGlobal (#3115)Gravatar Axel Huebl 3-24/+44
* ABLASTR: localIDtoGlobal Move the control of `localIDtoGlobal` to ABLASTR for particle IDs. * WarpX: Use ABLASTR now
2022-05-17Add workaround for Libfabric bug on Crusher to job script. (#3114)Gravatar Andrew Myers 2-0/+21
* Add workaround for Libfabric bug on Crusher to job script. * add known issues section for Crusher
2022-05-17Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ (#3071)Gravatar Axel Huebl 2-3/+37
* Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ Document how to install ADIOS2 (for openPMD `.bp`) and BLAS++/LAPACK++ (for PSATD in RZ) on Lassen at LLNL. * Update: ADIOS2~SST, BLAS++/LAPACK++ w/ ESSL
2022-05-17Avoid resizing ParticleBoundaryBuffer allocation to total particle count (#3068)Gravatar Phil Miller 1-26/+64
* Avoid resizing ParticleBoundaryBuffer allocation to total particle count * Switch atomic increments over to reductions
2022-05-17Use uniform error message formatting in more source files (#2964)Gravatar Luca Fedeli 46-359/+479
* use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * use more uniform text formatting * fixed bug * fixed bug * using Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed last merge conflict * fixed bug * fix indentation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-05-16[pre-commit.ci] pre-commit autoupdate (#3113)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.13 → v1.1.14](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.1.13...v1.1.14) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-16AMReX/PICSAR: Weekly Update (#3112)Gravatar Axel Huebl 6-6/+6
* AMReX: Weekly Update * PICSAR: Weekly Update
2022-05-16Add Headers to Input File Written by PICMI (#3093)Gravatar Edoardo Zoni 1-0/+12
* Add Headers to Input File Written by PICMI * Commit Suggestion by @dpgrote * Add Comment * Add Empty Line * Slightly Better Readable with a newline
2022-05-16CI: HIP with https (#3111)Gravatar Axel Huebl 1-2/+3
Small update in HIP docs: now supports HTTPS: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu
2022-05-16Stricter Tolerance for 3D Langmuir Tests (#3097)Gravatar Edoardo Zoni 1-1/+1
2022-05-16Add STL files support in pywarpx (#3089)Gravatar Lorenzo Giacomel 4-11/+53
* Added STL files support in pywarpx * Add new EB bucket * Added name to file headers * Fixing year in file headers * Checking that stl file and imp function are not both specified * Renamed EB bucket to EB2 * Adding STL documentation * Implement suggestions from code review Co-authored-by: lgiacome <lorenzo.giacome@cern.ch>
2022-05-16Fix Laser Injection in RZ (#3104)Gravatar Edoardo Zoni 1-1/+15
2022-05-16fix bug (#3110)Gravatar Luca Fedeli 1-1/+2
2022-05-13Fix Breaking Pip 22.1 Logic (#3106)Gravatar Axel Huebl 5-1/+6
* CI: Fix Windows Pip's `--no-build-isolation` says we have to have build-deps pre-installed. But Pip does offer no option to install those from `pyproject.toml`. * Pip 22.1: in-tree-build default And dropped the old option with a fatal error... classic. * Pip no-build isolation: pre-install build tools not installed in non-isolated builds - we want isolated builds, because they have a derministic path that we can cache with ccache
2022-05-11Fix Mirrors for RZ (NullifyMF) (#3101)Gravatar David Grote 1-3/+4
2022-05-11Doc: Improve Doxygen Links (#3099)Gravatar Axel Huebl 4-3/+13
* Doc: Improve Doxygen Links - download also openPMD-api tag files & link them - improve developer page: clearer links * Update: .gitignore
2022-05-11Fix Wrong Abort Message for PSATD w/ Time Averaging (#3098)Gravatar Edoardo Zoni 1-1/+1
2022-05-10Use queryWithParser to Parse v_particle_pml (#3096)Gravatar amadou38 2-1/+4
Use queryWithParser, instead of query, to parse v_particle_pml, in order to support functions like sin, cos, sqrt, etc.
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