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2021-12-21CMake: openPMD on by default (#2698)Gravatar Axel Huebl 12-18/+18
openPMD builds are stable enough to be default-ON. Due to lacking heuristicst, we don't enable openPMD by default in GNUmake. (Further environments hints, e.g. `PKG_CONFIG_PATH`, or a system-path install are needed there.)
2021-12-21RZ correction in 2d RZ Poisson slver (#2697)Gravatar Weiqun Zhang 1-0/+2
Call MLNodeLaplacian::setRZCorrect, even when it's redundant when the coordinate system is 2d rz, so that the solver does not depend on the coordinate system set in amrex::Geometry.
2021-12-21Inputs: `geometry.dims` option (#2685)Gravatar Axel Huebl 112-168/+221
* Docs: `geometry.dims` option Add a new, required option to specify the geometry of an inputs file at runtime. * Check & Report Runtime Dims Mismatch * Examples: add `geometry.dims` * Deprecation Warning: `geometry.coord_sys` * PICMI: `geometry.dims` * Improve error message sounds a bit better * Improve Doc Description Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
2021-12-20[pre-commit.ci] pre-commit autoupdate (#2695)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pre-commit/pre-commit-hooks: v2.4.0 → v4.0.1](https://github.com/pre-commit/pre-commit-hooks/compare/v2.4.0...v4.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2021-12-20AMReX: Weekly Update (#2694)Gravatar Axel Huebl 4-4/+4
2021-12-20AMREX_ALWAYS_ASSERT -> AMREX_ASSERT for deposition bounds checks (#2688)Gravatar Andrew Myers 2-4/+4
* AMREX_ALWAYS_ASSERT -> AMREX_ASSERT for deposition bounds checks * fix unused * Apply suggestions from code review * Apply suggestions from code review * Simpler ignore + comment Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-19For Python inputs, values with temporary variables are wrapped in quotes (#2690)Gravatar David Grote 1-4/+8
2021-12-16Generalize Analysis Scripts: Number of Digits (plt) (#2683)Gravatar Axel Huebl 38-54/+100
* Update Scripts to Handle New File Names * Use glob in Analysis of Collision Tests * Use rstrip in Analysis of Collision Tests * Regex: Match ends-in-digits Thanks Phil! :) Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
2021-12-16added RZ support in libwarpx function _get_boundary_number (#2680)Gravatar Roelof Groenewald 1-1/+3
2021-12-16Wrap shared object in a class to control its loading (#2637)Gravatar David Grote 19-582/+599
* Wrap shared object in a class to control its loading * Fix libwarpx attribute references * Updated callbacks.py for updated libwarpx * Removed the wx module plus other clean up * Further revision of how to use the pywarpx module. Now, _libwarpx should not be imported by external scripts except in special circumstances. * Updated documentation * Clean up end of line whitespace * Added more wrapping routines plus some clean up * Fixed use of pywarpx in two examples * Fix for getistep * Fixed for the EB Python interface * Silence a warning for our wrapper Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-16AMREX_SPACEDIM : EB, Filter, Laser, Utils, and Diagnostics (#2677)Gravatar Prabhat Kumar 26-153/+153
* AMREX_SPACEDIM : EB and Filter * AMREX_SPACEDIM : Laser * AMREX_SPACEDIM : Utils * AMREX_SPACEDIM : Diagnostics * Fix Typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * AMREX_SPACEDIM : Warpx.cpp * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp 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> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-16Adding new inputs to picmi.ElectromagneticSolver (#2676)Gravatar Lorenzo Giacomel 1-0/+8
2021-12-16Doxygen: Fix Diags, FieldSolver, Parallelization & Particles (#2662)Gravatar Axel Huebl 29-24/+101
* Doxygen: Fix Diags, FieldSolver, Parallelization & Particles * Apply suggestions: Remi Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions: Roelof Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Apply suggestions: Luca Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Andrew * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Neil Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Apply suggestions: Roelof * Apply suggestions: Weiqun Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-12-15ABLASTR: Cleanups & Particle Moments (#2675)Gravatar Axel Huebl 12-71/+242
* ABLASTR: Cleanups - lowercase dir - nested directories - nested namespaces - functions: lowercase and snake_case - templates: prefix with `T_` - profiler: doc strings * Add: Particle Moments Co-authored-by: Remi Lehe <rlehe@lbl.gov> Co-authored-by: Remi Lehe <rlehe@lbl.gov>
2021-12-15CI: Azure Cache Ignore Errors (#2678)Gravatar Axel Huebl 1-0/+2
Sometimes, the Azure Pipelines Cache tasks fail because the service is not available, either for download or upload after a successful job. This marks the cache restore and upload steps as allowed to fail.
2021-12-15CI: Reduce Runtime of Some Galilean Tests (#2625)Gravatar Olga Shapoval 8-148/+148
* Modified 'averaged_galilean_3d_psatd' CI test to lower its run time. * Modified 'comoving_2d_psatd_hybrid' CI test to lower its run time. * Modified 'galilean_2d_psatd_hybrid' CI test to lower its run time. * Updated benchmarks.
2021-12-15Docs: Perlmutter Early Science (#2674)Gravatar Axel Huebl 1-0/+2
* Docs: Perlmutter Early Science Document how to perform large runs. * Change comment style Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-12-15Cori: c-blosc Support (#2636)Gravatar Axel Huebl 1-3/+24
Document setting up `c-blosc` on Cori for fast, lossless ADIOS2 openPMD output compression.
2021-12-15Examples: Python ShellBang & Executable (#2673)Gravatar Axel Huebl 84-66/+107
* Examples: Python ShellBang & Executable Make sure that all PICMI scripts and all analysis Python scripts in `Examples/` are: - executable (`chmod a+x`) - start with a shell-bang to `python3` Now, all scripts can be run directly without a `python3 ...` prefix and also default to the only right executable of Python on older systems. (New systems always have a `python3` alias, too.) * Revert a moved numpy
2021-12-15CI: Remove (`particle_`)`tolerance` (#2669)Gravatar Axel Huebl 2-189/+16
We compare field and particle tolerances now without silver files, using our checksum API. This allows us to reduce CI time a bit by skipping the build of plotfile tools.
2021-12-15pre-commit: check json (#2670)Gravatar Axel Huebl 1-0/+1
2021-12-14Fix: Missing EB `analysis.py` Permissions (#2672)Gravatar Axel Huebl 1-0/+0
This failed in other PRs: ``` PermissionError: [Errno 13] Permission denied: './analysis.py' ```
2021-12-14Fix: `pre-commit run -a` (#2671)Gravatar Axel Huebl 4-4/+1
Prepare to enable autofix bot from https://pre-commit.ci
2021-12-14ABLASTR: Fix Doxygen in `DepositCharge`Gravatar Axel Huebl 1-1/+1
2021-12-14Refactor DepositCharge so it can be called from ImpactX. (#2652)Gravatar Andrew Myers 11-178/+304
* Refactor DepositCharge so it can be called from ImpactX. * change thread_num * Fix namespace * remove all static WarpX:: members and methods from DepositChargeDoIt. * fix unused * Don't access ref_ratio unless lev != depos_lev * more unused * remove function to its own file / namespace * don't need a CMakeLists.txt for this * lower case namespace, rename file * Refactor: Profiler Wrapper Explicit control for synchronization instead of global state. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-13Adding EB multifabs to the Python interface (#2647)Gravatar Lorenzo Giacomel 8-0/+493
* Adding edge_lengths and face_areas to the Python interface * Added wrappers for the two new arrays of data * Adding a CI test * Fixed test name * Added customRunCmd * Added mpi in test
2021-12-13Add load balancing test (#2561)Gravatar Kevin Z. Zhu 4-26/+41
* 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 * 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. * Add load balancing to embedded_boundary test * Updated checksum * Added embedded_circle test * Add embedded_circle test files * removed PICMI input file * Update to use default regression analysis * Added load balancing to test * Commented out load_balancing portion of test. This will be added back in once load balancing is fixed. * Add load balancing to embedded_boundary test * added analysis.py file in order to relax tolerance on test * Ensure that timers are used to update load balancing algorithm * Updated test name retrieval Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Roelof <roelof.groenewald@modernelectron.com> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
2021-12-14AMReX/PICSAR: Weekly Update (#2666)Gravatar Axel Huebl 7-44/+44
* AMReX: Weekly Update * Reset: PEC_particle, RepellingParticles, subcyclingMR New AMReX grid layout routines split grids until they truly reach number of MPI ranks, if blocking factor allows. This changes some of our particle orders slightly.
2021-12-13Add anisotropic mesh refinement example (#2650)Gravatar Remi Lehe 2-0/+63
* Add anisotropic mesh refinement example * Update benchmark
2021-12-13Add high energy asymptotic fit for Proton-Boron total cross section (#2408)Gravatar Neïl Zaim 1-26/+72
* Add high energy asymptotic fit for Proton Boron total cross section * Write keV and MeV instead of kev and mev * Add @return doxystrings
2021-12-13Fix the scope of profiler for SYCL (#2668)Gravatar Weiqun Zhang 1-5/+5
In main.cpp, the destructor of the profiler was called after amrex::Finalize. This caused an error in SYCL due to a device synchronization call in the dtor, because the SYCL queues in amrex had been deleted. In this commit, we limit the scope of the profiler so that its destructor is called before the queues are deleted. Note that it was never an issue for CUDA/HIP, because the device synchronization calls in those backends do not need any amrex objects.
2021-12-13Add PML Support for multi-J Algorithm (#2603)Gravatar Edoardo Zoni 5-8/+233
* Add PML Support for multi-J Algorithm * Add CI Test
2021-12-13Fixing the initialization of the EB data in ghost cells (#2635)Gravatar Lorenzo Giacomel 4-57/+44
* Using ng_FieldSolver ghost cells in the EB data * Removed an unused variable * Fixed makeEBFabFactory also in in WarpXRgrid.cpp * Fixed end of line whitespace * Undoing #2607
2021-12-13Python: Add 3.10, Relax upper bound (#2664)Gravatar Axel Huebl 1-1/+2
There are no breaking changes in Python 3.10 that affect us. Giving the version compatibility of Python and it's ABI stability, there is no need at the moment to provide an upper limit. Thus, relaxed now in general.
2021-12-13Docs: Fix Warning Logger Typo (#2667)Gravatar Phil Miller 1-1/+1
2021-12-11ABLASTR Library (#2263)Gravatar Axel Huebl 6-41/+78
* [Draft] ABLASTR Library - CMake object library - include FFTW wrappers to start with * Add: MPIInitHelpers * Enable ABLASTR-only builds * Add alias WarpX::ablastr * ABLASTR: openPMD forwarding * make_third_party_includes_system: Avoid Collision * WarpX: depend on `ablastr` * Definitions: WarpX -> ablastr * CMake: Reduce build objects for ABLASTR Skip all object files that we do not use in builds. * CMake: app/shared links all object targets Our `PRIVATE` source/objects are not PUBLICly propagated themselves.
2021-12-11C++17: if constexpr for templates in ShapeFactors (#2659)Gravatar Luca Fedeli 1-150/+84
* use if constexpr to replace template specialization * Rmove Interface Annotations * Replace static_assert with amrex::Abort * Add includes & authors Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-11QED openPMD Tests: Specify H5 Backend (#2661)Gravatar Axel Huebl 1-2/+2
We default to ADIOS `.bp` if available. Thus, specify HDF5 assumption
2021-12-11ICC CI: Unbound Vars (`setvars.sh`) (#2663)Gravatar Axel Huebl 2-4/+4
Ignore: ``` /opt/intel/oneapi/compiler/latest/env/vars.sh: line 236: OCL_ICD_FILENAMES: unbound variable ```
2021-12-10`use_default_v_<galilean,comoving>` Only w/ Boosted Frame (#2654)Gravatar Edoardo Zoni 1-3/+18
2021-12-10fix for setting the boundary condition potentials in 1D ES simulations (#2649)Gravatar Roelof Groenewald 1-5/+5
2021-12-10use if constexpr to replace template specialization (#2660)Gravatar Luca Fedeli 1-106/+67
2021-12-10fix check for absolute library install path (#2646)Gravatar s9105947 1-1/+1
Co-authored-by: Hannes T <s9105947@users.noreply.github.com>
2021-12-10CMake: 3.18+ (#2651)Gravatar Axel Huebl 4-6/+6
With the C++17 switch, we required CMake 3.17+ since that one introduced the `cuda_std_17` target compile feature. It turns out that one of the many CUDA improvements in CMake 3.18+ is also to fix that feature for good, so we bump our requirement in CMake. Since CMake is easy to install, it's easier to require a clean newer version than working around a broken old one. Spotted first by Phil on AWS instances, thx!
2021-12-10Docs: `python3 -m pip` & Virtual Env (#2656)Gravatar Axel Huebl 7-14/+22
* Docs: `python3 -m pip` Use `python3 -m pip`: - works independent of PATH - always uses the right Python - is the recommended way to use `pip` * Dependencies: Python incl. venv Backported from #2556. Follow-up to #2653
2021-12-10PWFA 1D: Fix output nameGravatar Axel Huebl 3-2/+2
Hard coded, undocumented convention: turns out this must be the name of the test that we define in the ini file. Logical, isn't it. Not. Follow-up to #2593
2021-12-10Fix: analysis_default_regression.pyGravatar Axel Huebl 1-1/+2
Mismatched checksum file due to crude hard-coding.
2021-12-10Python/setup.py: picmistandard==0.0.18Gravatar Axel Huebl 1-1/+1
Forgotten in #2593
2021-12-09Azure: Ensure latest venv installedGravatar Axel Huebl 1-0/+1
2021-12-09Python GNUmake: Remove Prefix HacksGravatar Axel Huebl 1-20/+20
FREEEEDOM. venv power.
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