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2022-02-04CMake: Add More Pip Helpers (#2822)Gravatar Axel Huebl 5-55/+141
* CMake: Add More Pip Helpers Add and document more helpers to quickly and iteratively install our PICMI Python bindings with a one-liner from CMake. This should accelerate development cycles. * CI tests: Changed CMake target name * Update `.gitignore`: Python Workflows
2022-02-04Docs: NERSC Jupyter ipympl==0.8.6 (#2825)Gravatar Axel Huebl 1-1/+1
NERSC rolled out a new base environment, we now need to pin `ipympl` in version `0.8.6`.
2022-02-03Fix typo in laser assert (#2824)Gravatar Neïl Zaim 1-1/+1
2022-02-03Fixing the computation of ECT Rho Field (#2711)Gravatar Lorenzo Giacomel 8-112/+219
* Fixed computation of ECT Rho * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Adding a missing preprocessor directive * Updated contributors list * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fixed an abort message * Fix in Source/Initialization/WarpXInitData.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Added some comments * Made EvolveRhoCartesianECT not static Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: lgiacome <lorenzo.giacome@cern.ch> 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> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-02-03Rename PSATD Classes (#2805)Gravatar Edoardo Zoni 15-90/+90
* Rename PSATD Classes * Rename PsatdAlgorithmJLinear as PsatdAlgorithmJLinearInTime
2022-02-02Release 22.02 (#2820)Gravatar Axel Huebl 11-14/+14
* AMReX: 22.02 * PICSAR: 22.02 * WarpX: 22.02
2022-02-023D LWFA PICMI Test: Add Electron Beam (#2723)Gravatar Edoardo Zoni 2-16/+57
* LWFA PICMI Tests: Add Electron Beam * Remove Electron Beam from 1D Test
2022-02-02Docs: Glossary (ECP, LDRD, BLAST & ABLASTR) (#2813)Gravatar Axel Huebl 2-0/+6
* Docs: Glossary (ECP, LDRD, BLAST & ABLASTR) Add new glossary entries. * Clarify ECP & DOE
2022-02-02QED example inputs: simplify initialization of product species (#2816)Gravatar Neïl Zaim 6-236/+108
* QED example inputs: simplify initialization of product species * Update benchmark
2022-02-02Docs: NERSC `ipympl` Work-Around (#2815)Gravatar Axel Huebl 2-2/+9
Document a work-around to get `ipympl` widgets to work on NERSC's Jupyter service. Also x-ref the upstream issue: https://github.com/matplotlib/ipympl/issues/416
2022-02-02Add myself to .zenodo.json (#2817)Gravatar Lorenzo Giacomel 1-0/+5
Co-authored-by: lgiacome <lorenzo.giacome@cern.ch>
2022-02-02Docs: Improve Provisioning Perf Tests (#2780)Gravatar Axel Huebl 1-9/+14
* Docs: Improve Provisioning Perf Tests Reduce startup time of the performance tests on Summit. Update Python venv only manually. * Clarify wording
2022-02-02Read species size correctly (#2799)Gravatar Revathi Jambunathan 4-24/+29
* read species size correctly for the ith buffer, instead of reading buffer size for the 2D array * call write_Species before accessing species specific attributes * using at and not clearing m_output_species, but only clearing for ith buffer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use .at().at() * Modernize for loops (range based) * Add Test (see #2738) * revert buffer cleaning * allocate output species vector with num_buffers * Use Warning Logger This allows us to collect these warnings centrally and abort on if we want to. 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>
2022-02-01Fix Bug with Damped BCs & MR (#2809)Gravatar Edoardo Zoni 2-9/+11
2022-02-01CI: Do Not Set `diag1.file_prefix` in `runtime_params` (#2811)Gravatar Edoardo Zoni 1-4/+4
2022-02-01Doc: Document `run_test.sh` manipulation (#2812)Gravatar Axel Huebl 2-8/+31
Add references and instructions to manipulate `run_test.sh` configs.
2022-02-01Prepare for CI: Remove PGI (#2814)Gravatar Axel Huebl 1-2/+1
Remove an outdated "COMP = PGI" setting that has not been used for years (likely not been used since OpenACC experiments in the Fortran times).
2022-02-01allow `add_particles` to be called with empty numpy arrays i.e. injecting ↵Gravatar Roelof Groenewald 1-5/+0
zero particles (#2808)
2022-02-01AMReX: Update latest (#2810)Gravatar Axel Huebl 5-5/+5
2022-02-01Add abort on warning threshold (#2751)Gravatar Luca Fedeli 5-16/+65
* add abort on warning threshold * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add white endline * fix issue with QED tests * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * removed lines from another branch * increase abort threshold for examples with a ionizable species * fix issues with absolute tolerance for self field * Revert "fix issues with absolute tolerance for self field" This reverts commit 588e022d3edbb97ff8efc33d21439449f498a9bc. * increase threshold for some tests where a warning stating that max norm of rho equal to 0 is raised * increase threhshold for another test * setting abort on warning is now the default for CI tests 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>
2022-01-31[pre-commit.ci] pre-commit autoupdate (#2806)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.10 → v1.1.11](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.1.10...v1.1.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-02-01Summit: Fix Batch Template (#2807)Gravatar Axel Huebl 1-1/+1
That EOL should be at the beginning of the line. Thanks to Cho for catching this!
2022-01-31Add Modern Electron contributors to .zenodo.json (#2800)Gravatar Peter Scherpelz 1-0/+32
* Add Modern Electron contributors to zenodo * Complete zenodo ORCID entries
2022-01-31BTD: clean left over comment (#2804)Gravatar Revathi Jambunathan 1-2/+0
2022-01-31`Langmuir_multi_psatd_div_cleaning`: Remove G Benchmark (#2803)Gravatar Edoardo Zoni 2-3/+2
2022-01-31Separate Class for Multi-J PSATD Algo (#2748)Gravatar Edoardo Zoni 7-197/+632
* Separate Class for Multi-J PSATD Algo * Cleaning * X1,...,X6 Real, not Complex * Cleaning * Improve Comments, Rename Jx as Jx_old (etc.)
2022-01-29FieldProbe: Fixed Assert Typo (#2802)Gravatar Tiberius Rheaume 1-1/+1
2022-01-27Docs: Update Acknowledgement & Citations (#2783)Gravatar Axel Huebl 3-9/+47
* Docs: Update Acknowledgement & Citations * Fix wording Co-authored-by: David Grote <dpgrote@lbl.gov> * Fix spelling: Double Firstname Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Zenodo: Update References Co-authored-by: David Grote <dpgrote@lbl.gov> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-01-27Fix: Move MPI Thread Level Check (#2786)Gravatar Axel Huebl 4-14/+28
* Fix: Move MPI Thread Level Check Move the MPI thread level check (requested vs. provided) into `InitData()`. This is needed, since we will access the warning logger, which itself needs to be accessed via a WarpX instance. This is also cleaner than just moving this behind the constructor in `main.cpp`, as we have less functions to call around the `WarpX` object usage. * Fix MPI=OFF
2022-01-26Fix Docs of MinAndMaxPositions (#2787)Gravatar Axel Huebl 1-1/+1
Fix order of returned tuple (doc string).
2022-01-26Add Python callbacks before and after collisions (#2791)Gravatar Roelof Groenewald 3-3/+36
* add python callbacks before and after collisions * re-order callback declarations
2022-01-26Regressions: Remove Tolerance (#2789)Gravatar Axel Huebl 1-1/+0
... otherwise we build the `fvarnames` tools automatically.
2022-01-26style fixes in WarpXWrappers.cpp (#2792)Gravatar Roelof Groenewald 1-17/+17
2022-01-26fix typo in docstring for ImpactIonizationTransformFunc constructor (#2793)Gravatar Roelof Groenewald 1-1/+0
2022-01-26Add tiny profiling to reduced diagnostics (#2794)Gravatar Neïl Zaim 1-0/+3
2022-01-26expose WarpXParticleContainer::sumParticleCharge to Python (#2790)Gravatar Roelof Groenewald 4-1/+28
2022-01-26udpate zenodo (#2784)Gravatar Hannah Klion 1-0/+5
Co-authored-by: Hannah Klion <hannah.klion@gmail.com>
2022-01-25Add SyncRho call to warpx_depositChargeDensity (#2777)Gravatar Roelof Groenewald 5-8/+16
* add SyncRho call to warpx_depositChargeDensity * expose SyncRho to Python; add warpx_clearChargeDensity to reset rho_fp before deposition * remove unneeded warpx_clearChargeDensity function * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add (default) option to depositChargeDensity to call SyncRho after deposition * added option to depositChargeDensity to zero out rho_fp before deposition * code cleanup * import fields from inside depositChargeDensity Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-25Update .zenodo.json (#2782)Gravatar Prabhat Kumar 1-0/+5
2022-01-25Funding/Acknowledgements: CEA-LIDYL. (#2781)Gravatar Axel Huebl 1-0/+3
2022-01-25RZ FDTD: Filter Not Working (Abort) (#2775)Gravatar Edoardo Zoni 5-109/+107
* RZ FDTD: Filter Not Working (Abort) * Update CI Tests and Benchmarks
2022-01-24Docs: Crusher Load `cce` module (#2770)Gravatar Axel Huebl 1-0/+1
* Docs: Crusher Load `cce` module Without that module, HIP RDC builds do not work. https://docs.olcf.ornl.gov/systems/crusher_quick_start_guide.html#compilers * cce/13.0.0 -> cce/13.0.1 * Crusher: load `cce` after `rocm`
2022-01-24AMReX: Update latest (#2773)Gravatar Axel Huebl 4-4/+4
2022-01-24PML Exchanges: Less Duplicate Code (#2394)Gravatar Edoardo Zoni 4-162/+85
Similarly to #2375, I'm trying to see if we can reduce the amount of duplicate code, in this case for the functions `Exchange<E,B>` of the PML class. Open for discussion.
2022-01-24CI: GNUmake (#2769)Gravatar Axel Huebl 3-1/+38
Since we migrated also Azure regression tests to CMake now, we should add a GNUmake build to CI, so we don't accidentally lose this capability (we will not duplicate the whole CI matrix). Does a standard CUDA build without dependencies but enabling PSATD.
2022-01-24RZ: Add error message when using 0 order for azimuthal decomposition (#2772)Gravatar Neïl Zaim 2-0/+5
2022-01-24remove check on geometry (#2771)Gravatar Luca Fedeli 1-7/+0
2022-01-21Access species specific charge density from python (#2710)Gravatar Roelof Groenewald 8-3/+346
* added python wrapper function to deposit a specific species density in rho_fp * added 1D ES input file with MCC that uses the charge deposition functionality * reset rho_fp[lev] before depositing * updated documentation * switch to using simulation.extension in Poisson solver * Apply suggestion from code review Co-authored-by: Phil Miller <phil.miller@intensecomputing.com> * suggested changes from code review * add comment explaining why a direct Poisson solver is used * removed direct solver in 1D example since it is actually slower than the MLMG solver * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * added docstring for warpx_depositChargeDensity * fixed order of imports in new PICMI input file Co-authored-by: Phil Miller <phil.miller@intensecomputing.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-20AMReX: Update latest (#2752)Gravatar Axel Huebl 4-4/+4
2022-01-20Implement PML for the outer RZ boundary with PSATD (#2211)Gravatar David Grote 28-47/+966
* Initial version of RZ PSATD PML BCs * Cleaned up some bugs * Add support of do_pml_in_domain option * Cleaned up stuff for building * Fix PMLPsatdAlgorithm macro * Removed unneeded variable from SpectralSolverRZ * Change length 3 arrays to length 2 (for 2D) * Cleanup around DampPML * Added more checks of pml[lev] * Added CI test for RZ PML * Added code to update the corner guard cells * Further updates * Added CI test * Fixed EOL space * Updated CI benchmarks, removing round off fields * Changes to CI missed on previous commit * Various fixes for clean up * More fixes for clean up * Further cleanup * Updated benchmark * Fixed benchmarks file * Minor cleanup * Added round off benchmark values * Fixed testname in analysis_pml_psatd_rz.py * Update comment in analysis file * Put pml_rz code in RZ and PSATD macro blocks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add geometry.dims input to CI test input file, inputs_rz * Cleanup to match recent changes Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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