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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.
2022-05-10Use uniform error message formatting for all the amrex::Abort() calls in ↵Gravatar Luca Fedeli 1-199/+232
WarpX.cpp (#2952) * use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp * fixed bug * fixed bug * Update Source/WarpX.cpp * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-05-09Apply shift for zmax>0 in old BTD (#3094)Gravatar Remi Lehe 1-2/+12
* Apply shift for zmax>0 in old BTD * BTD: also shift t_slice_lab
2022-05-09Add a python script to generate timestep duration plots (#3036)Gravatar Luca Fedeli 3-0/+118
* add script to generate timestep duration plots * disable transparent background * fix bugs * fix bug in doc * Update plot_timestep_duration.rst * add permissions * using argparse * using if __name__ == __main__: * add page in workflows * Update Docs/source/usage/workflows.rst * added missing file * Formatting
2022-05-09Fix miscellaneous issues found with clang tidy (#3083)Gravatar Luca Fedeli 10-35/+25
* fix miscellaneous issues found with clang tidy * fix miscellaneous issues found with clang tidy * moved default constructors and destructors to header * fix issue * Use default again
2022-05-09AMReX: Weekly Update (#3095)Gravatar Axel Huebl 5-5/+5
2022-05-06Apply shift in BTD for zmax different than 0 (#3091)Gravatar Remi Lehe 1-2/+3
* Include shift in t_lab when `zmax` is different than 0 * Revert "Include shift in t_lab when `zmax` is different than 0" This reverts commit 5f786f26ada3d9713221df653e28923557b5b614. * Apply shift in BTD for zmax > 0
2022-05-05Fix openPMD RZ with load-balancing (#3084)Gravatar Remi Lehe 2-8/+9
* Fix openPMD RZ with load-balancing * Fix compilation
2022-05-04Nuclear fusion: remove underflow warning in single precision (#3058)Gravatar Neïl Zaim 1-14/+8
* Nuclear fusion: remove underflow warning in single precision * Explicitly set underflowing constexprs as double * Also set alpha and beryllium masses as doubles
2022-05-04Close #3077 Fix RZ openPMD output with MR (#3082)Gravatar Remi Lehe 2-75/+74
* Update varnames for RZ openPMD * Add automated test
2022-05-04ABLASTR: `-fPIC` Control (#3081)Gravatar Axel Huebl 1-1/+20
Generalize and expose the control for position independent code compilation for ABLASTR. We could skip this if we solely build WarpX_APP, but if we build a shared WarpX library or a third party, like ImpactX, uses ablastr in a shared library (e.g., for Python bindings), then we need relocatable code.
2022-05-03Add velocity in pml as an input in function alpha (#3070)Gravatar amadou38 5-32/+50
* add velocity in pml as an input in function alpha * some changes on the variables * some changes on the variables * some changes on the variables * some changes on the variables, resquested changes, message error for v_particle_pml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-03Release 22.05 (#3076)Gravatar Axel Huebl 12-14/+17
* AMReX: 22.05 * PICSAR: 22.05 * WarpX: 22.05 * Fix issue with RZ electrostatic solver Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2022-05-03Abort if BTD selected for RZ, and unsupported field/particle varnames (#3074)Gravatar Revathi Jambunathan 4-3/+26
* abort if BTD selected for RZ, and unsupported field/particle varnames * add doc * particle fields to plot not supported for BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * WARPX_ALWAYS_ASSERT_WITH_MESSAGE * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use unified txt message syntax for abort * fix logic in assert Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-02Doc: Update Perlmutter Python/HDF5 (#3079)Gravatar Axel Huebl 1-6/+6
* Doc: Update Perlmutter Python/HDF5 Update Perlmutter modules after the last days' updates rolled out. * Perlmutter: Use CC for CXX Work-around `FindHDF5.cmake` issue (cannot find `HDF5_LIBRARIES`) which in turn is caused by Find MPI CXX picking up HDF5 libs already: https://gitlab.kitware.com/cmake/cmake/-/issues/22368#note_1181441
2022-05-02[pre-commit.ci] pre-commit autoupdate (#3078)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v1.3.1 → v1.3.2](https://github.com/hadialqattan/pycln/compare/v1.3.1...v1.3.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-05-02Use the same types for different pinned-memory particles (#3072)Gravatar Remi Lehe 6-10/+9
2022-04-28Update CUDA repo key (#3069)Gravatar Weiqun Zhang 1-2/+1
Nvidia has made changes in the signing keys. https://forums.developer.nvidia.com/t/notice-cuda-linux-repository-key-rotation/212771
2022-04-26Add profiling to ParticleBoundaryBuffer::gatherParticles (#3061)Gravatar Phil Miller 1-0/+5
This turned out to be a major portion of a particle-heavy simulation, and was being entirely attributed to WarpX::Evolve().
2022-04-25Doc: PICMI HPC System Update Requirements (#3060)Gravatar Axel Huebl 3-0/+9
Since these requirements (i.e., PICMI) change quite rapidly, document the line close to the `pip` install line.
2022-04-25AMReX: Weekly Update (#3059)Gravatar Axel Huebl 5-5/+5
2022-04-25Docs: Ascent 0.8.0 on Summit (#3057)Gravatar Axel Huebl 1-1/+1
Update the Ascent installation location to use Cyrus' new install for us.
2022-04-21Perlmutter: Boost Software Module (QED) (#3053)Gravatar Axel Huebl 2-1/+4
* Perlmutter: Boost Document a compatible Boost module on Perlmutter. This is needed for detailed table generation for the QED module (`WarpX_QED_TABLE_GEN=ON`). * CMake: Update PICSAR Include a fix for a compile error on CPU for QED table gen.
2022-04-21`Stencil.py`: Follow PEP 8 Coding Style (#3055)Gravatar Edoardo Zoni 1-60/+84
* `Stencil.py`: Follow PEP 8 Coding Style * Commit Suggestion by @dpgrote
2022-04-20Current Deposition Interfaces: Always Pass `dt` & `relative_time` (#2937)Gravatar Edoardo Zoni 7-106/+111
* Current Deposition Interfaces: Always Pass `dt` & `relative_time` * Fix CI Failures * Fix 1D/RZ Warnings * Fix RZ Bug * Fix Bugs * Minimize Changes, Fix Roundoff Errors * Cleaning * Remove dt From doDepositionShapeN * Cleaning Esirkepov Deposition * Cleaning Vay Deposition * Fix Roundoff Errors * Fix Roundoff Errors (continued) * Fix Bug (RZ)
2022-04-19add after diagnostic python callback (#3043)Gravatar Roelof Groenewald 3-2/+22
2022-04-19Fix a bug about particle weight. (#3052)Gravatar Yinjian Zhao 1-1/+1
Co-authored-by: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
2022-04-18Summit: Prepend Hostname & Mapping (#3040)Gravatar Axel Huebl 2-3/+9
Add an additional `jsrun` command on Summit so that one can easier map the run output to a hostname. Write a `task_host_mapping.txt` file for each run.
2022-04-18[pre-commit.ci] pre-commit autoupdate (#3049)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v1.2.5 → v1.3.1](https://github.com/hadialqattan/pycln/compare/v1.2.5...v1.3.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-04-18AMReX/PICSAR: Weekly Update (#3046)Gravatar Axel Huebl 5-5/+5
2022-04-16Avoid unnecessary construction of CopyParticleAttribs (#3042)Gravatar Weiqun Zhang 2-1/+6
If it's not used there is no reason to construct a CopyParticleAttribs object. In fact, it could result in a runtime `std::out_of_range` error in `std::map::at()` because `tmp_particle_data` is used in the CopyParticleAttribs constructor, but in `PhysicalParticleContainer::Evolve`, `tmp_particle_data` is properly prepared only when doing back transformed diagnostics.
generated by cgit v1.2.3 (git 2.46.0) at 2025-08-17 02:49:32 +0000