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2022-12-21CI: Unbreak macOS Python3 (#3587)Gravatar Axel Huebl 1-1/+1
2022-12-21Allow const_dt with EM and check it for ES (#3561)Gravatar David Grote 5-5/+14
* Allow const_dt with EM and check it for ES * Update PR according to comments * Fix typo * Fix invalid reference to m_const_dt * Fixed another invalid reference to m_const_dt * Remove erroneous setting of `const_dt` test * Add doc for const_dt Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2022-12-21Include fusion reactions in documentation (#3570)Gravatar Remi Lehe 1-16/+51
* Include fusion reactions in documentation * Finalize documentation * Update documentation * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-12-21Docs: Fix HTML5 for Install Logos (#3588)Gravatar Axel Huebl 1-1/+1
With the update tot HTML5 in docutils, we need to modernize our CSS code that does fancy logos in the user install section.
2022-12-21Add accelerator lattice, starting with quadrupoles (#3063)Gravatar David Grote 40-7/+1856
* Initial version of accelerator lattice * Clean up EOL white space * Small clean up for GPU * Fixed up consts * Added hard edge fraction plus other clean ups * More clean up * Restructure to work on GPUs * Now this grabs its own copies of particle info * Updates, including adding dBdx * Small cleanup in Quad * Small fixes for GPU * More cleanup for GPU * More GPU cleanup * Rewrite of the accelerator lattice implementation to better handle GPU * Fix struct forward definition * Another forward definition fix * Bug fix * Added LatticeElementBase * Removed zcenters array * Added CI test case * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Clean up in CI analysis.py * Cleanup of coding * Added CI test hard_edged_quadrupoles_moving * Added Lorentz transform between boosted frame and lab frame * Fixes for working in the boosted frame * Added boosted CI test * Change input name, adding the prefix "lattice." * Added plasma lens lattice element This will replace the external field plasma lens * Fixed CI analysis script to look for "lattice.quad" * Added checks of lattice element input * Added documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed duplicate call to lattice finder UpdateIndices * Added extensive comments * Reworked the input to use the MAD like description This is the same as the method used in ImpactX * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove old lines from inputs_lattice_3d * Added "lattice" element type * Fixed some Real and ParticleReals * [pre-commit.ci] pre-commit autoupdate (#3246) updates: - [github.com/hadialqattan/pycln: v2.0.1 → v2.0.3](https://github.com/hadialqattan/pycln/compare/v2.0.1...v2.0.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ABLASTR: Update Poisson Solver API (#3243) Update the Poisson Solver API to be more usable. Needed for ImpactX. * Docs: New OLCF Machine (#3228) * D-T fusion (#3153) * initial work * fixed bugs and added species * update documentation * delete unused file * Add properties for neutron, hydrogen isotopes, helium isotopes * Update code to be more consistent * Correct typo * Parse deuterium-tritium fusion * Start putting in place the files for deuterium-tritium * Update documentation * Prepare structures for deuterium tritium * Fix typo * Fix compilation * Add neutron * Add correct formula for the cross-section * Correct compilation error * Fix nuclear fusion * Reset benchmarks * Prepare creation functor for 2-product fusion * First implementation of momentum initialization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use utility function for fusion * Minor modification of variable names * Fix GPU compilation * Fix single precision compilation * Update types * Use util function in P-B fusion * Correct compilation errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct errors * Update values of mass and charge * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Correct compilation error * Correct compilation error * Correct compilation error * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Reset benchmark * Use helium particle in proton-boron, to avoid resetting benchmark * Fixed proton-boron test * Revert "Fixed proton-boron test" This reverts commit 73c8d9d0be8417d5cd08a23daeebbc322c984808. * Incorporate Neil's recommendations * Reset benchmarks * Correct compilation errors * Add new deuterium tritium automated test * Correct formula of cross-section * Correct cross-section * Improve analysis script * Add test of energy conservation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add test of conservation of momentum * Progress in analysis script * Fix error in the initial energy of the deuterium particles * Add check of isotropy * Clean up the test script * Rewrite p_sq formula in a way to avoids machine-precision negative numbers * Add checksum * Clean up code * Apply suggestions from code review * Update PR according to comments * Update benchmark * Address additional comments * Numerical Literals Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Docs: gaussian beam `q_tot` is not optional (#3249) * Fix a bug in GPU version of Hankel Transform (#3253) amrex::Array4 is a 4D array that can be accessed with three spatial indices plus an optional component index. We must always provide all three spatial indices even in 2D. * Add Python Callback Call when Checkpointing Signal is Received (#3251) * CI: Add Missing Regression Analysis (NCI corrector) (#3252) * Fixes to allow mixed precision, ParticleReal float, Real double (#3239) * Fixes to allow mixed precision, ParticleReal float, Real double * Fix for the optical depth * A different way of fixing QuantumSynchrotronEvolveOpticalDepth * In the QED code, consistently use ParticleReal * Use ParticleReal type consistently * Fix typo Docs/source/usage/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix typo Docs/source/usage/parameters.rst Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Fix small error in plasma lens lattice documentation * Small addition to the documentation * Fix the residence correction to allow short elements * Updated CI benchmarks * Added check of lattice to isNoOp * Updated the hard_edged_quadrupoles CI benchmarks It is not clear why there was a change, but the difference is essentially round off in the E field. The important thing is that the particles are still correct. * Update Source/AcceleratorLattice/AcceleratorLattice.H Add include statements Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/AcceleratorLattice/LatticeElements/LatticeElementBase.H Add includes Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Renamed to README.rst and updated headers * Made d_lattice_element_finder optional type * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Include `<optional>` * Docs: Developer AccLattice Inclusion 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: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-12-20[pre-commit.ci] pre-commit autoupdate (#3580)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pycqa/isort: 5.11.1 → v5.11.3](https://github.com/pycqa/isort/compare/5.11.1...v5.11.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-12-20Fix typo in documentation for Haswell (#3583)Gravatar Remi Lehe 1-1/+1
2022-12-19managed memory for user defined attribs in addplasma (#3576)Gravatar Revathi Jambunathan 1-25/+66
2022-12-19Docs: Profiler Sync (Debug) (#3571)Gravatar Axel Huebl 1-0/+4
Document the `amrex.use_profiler_syncs` option in our debugging section.
2022-12-19Clean up documentation (#3542)Gravatar David Grote 31-92/+100
* Fix comments for documentation * More fixes to comments for documentation * Fixes in the doc files * Fix typo in parameters.rst
2022-12-19Docs: rst Formatting Issue in GB PaperGravatar Axel Huebl 1-6/+6
2022-12-16Add a new section on domain decomposition to the docs. (#3572)Gravatar Andrew Myers 5-90/+86
* Add a new section on domain decomposition to the docs. * Remove old parallelization section and migrate more info
2022-12-16Docs: add ``photo_species`` input param and fix typo (#3575)Gravatar Arianna Formenti 1-1/+5
* Docs: add photo_species input param and fix typo This PR makes the following changes to the _Input Parameters_ page of the documentation: - Adds the input parameter ``particles.photon_species`` to the Particle Initialization section. - Fixes a typo in the section _Lookup tables and other settings for QED modules_ under the bullet point about ``qed_qs.lookup_table_mode`` (from ``qed_bw.save_table_in`` to ``qed_qs.save_table_in``) * [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>
2022-12-15Refactor update of auxiliary data for electrostatic solver (#3573)Gravatar Remi Lehe 2-10/+4
* Refactor update of auxiliary data for electrostatic solver * [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>
2022-12-15Allow surface flux injection from the domain boundary (#3554)Gravatar David Grote 6-18/+59
* Fix to AddPlasmaFlux to allow flux surface to be on the domain boundary * Update FluxInjection3D.json since the particle positions changed * Update comments in AddPlasmaFlux
2022-12-13Fix Syntax in .zenodo.jsonGravatar Axel Huebl 1-0/+1
follow-up to last commit updating contributors
2022-12-13Typo: Fewer Ranks (Perf. Hint) (#3569)Gravatar Axel Huebl 1-2/+2
* Typo: Fewer Ranks (Perf. Hint) * fix warning message (space) Co-authored-by: lucafedeli88 <luca.fedeli@cea.fr>
2022-12-13Release 22.12 (#3565)Gravatar Axel Huebl 11-14/+14
* AMReX: 22.12 * PICSAR: 22.12 * WarpX: 22.12
2022-12-12CodeQL Filter: One Level DeeperGravatar Axel Huebl 1-0/+1
2022-12-12CI CodeQL: Filter Third Party (#3563)Gravatar Axel Huebl 2-0/+27
Filter out third party warnings, i.e., from AMReX, PICSAR, and openPMD.
2022-12-13[pre-commit.ci] pre-commit autoupdate (#3564)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pycqa/isort: 5.10.1 → 5.11.1](https://github.com/pycqa/isort/compare/5.10.1...5.11.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-12-13Update documentation to compile and run on LUMI supercomputer (#3562)Gravatar Luca Fedeli 3-8/+57
* update example profile * update documentation for LUMI * Fix minor typo Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-12-09CI: CodeQL w/ 🔍Gravatar Axel Huebl 1-1/+1
2022-12-09Improve memory footprint for ParticleInitialize (#3392)Gravatar Revathi Jambunathan 5-38/+59
2022-12-09CI: Source Checks on ubuntu 22.04 (#3558)Gravatar Axel Huebl 1-1/+1
Updated Doxygen from 1.8.17 to 1.9.1
2022-12-09Renamed currents in Vay deposition from `j` to `D` (#3557)Gravatar Arianna Formenti 2-35/+36
* Renamed Vay currents from j to D * [pre-commit.ci] auto fixes from pre-commit.com hooks
2022-12-08CI: Concurrency Limit CodeQLGravatar Axel Huebl 1-0/+4
Same as other runners: aborts when new updates are pushed to safe CI time.
2022-12-08Add CodeQL workflow for GitHub code scanning (#3555)Gravatar lgtm-com[bot] 2-29/+63
* Add CodeQL workflow for GitHub code scanning * Remove: old LGTM config * Fix: CodeQL Deps Co-authored-by: LGTM Migrator <lgtm-migrator@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-12-08Docs: Repo Vis Link (#3553)Gravatar Axel Huebl 1-1/+1
2022-12-08ABLASTR: Coarsen Functions (#3433)Gravatar Axel Huebl 32-546/+640
* ABLASTR: Coarsen Functions Move coarsen functions to ABLASTR. Rename by property of the coarsening function. * Remove unused imports Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2022-12-08Highlights & References: Gordon Bell (#3552)Gravatar Axel Huebl 4-5/+25
* Highlights & References: Gordon-Bell Add our award-winning Gordon Bell paper in documentation :) * Update Landing Pages
2022-12-07PSATD: Implement First-Order Equations (#3466)Gravatar Edoardo Zoni 37-292/+957
* Implement First-Order PSATD Equations * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix Unused Parameter Warning * Fix RZ Build * Fix Normalization of G to Match PML * Add CI Test: 3D Uniform Plasma * Cleaning * Update 2D CI Checksums * Update 3D CI Checksums * Add F,G to CI Checksums of `uniform_plasma_multiJ` * Allow User to Choose First-Order v. Second-Order * Add WARPX_ALWAYS_ASSERT_WITH_MESSAGE * Rename New Class `PsatdAlgorithmFirstOrder` * Remove Inline Comment * Update RZ CI Checksums * Fix inline comment * Use auxiliary variables to avoid divisions * Use auxiliary variables to avoid divisions * Make `nci_psatd_stability` dir and merge inputs * Move all Galilean tests to `nci_psatd_stability` * Fix CI * Fix index for backward FFT of J Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-12-06Zenodo: Move Gunther to ContributorsGravatar Axel Huebl 1-5/+5
2022-12-07Fix the CUDA Aware part of the Perlmutter script. (#3549)Gravatar kngott 1-1/+1
As a Gordon Bell winner, I take no responsibility for this bug. But, I'll fix it. And it gives solid performance enhancement, so I will take responsibility for that. 😄
2022-12-06[pre-commit.ci] pre-commit autoupdate (#3547)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/mgedmin/check-manifest: 0.48 → 0.49](https://github.com/mgedmin/check-manifest/compare/0.48...0.49) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-12-05Update docutils version (#3546)Gravatar David Grote 3-281/+529
* Update Docs/Doxyfile * Update Docs/requirements.txt versions * Update Docs/source/index.rst
2022-12-02Check rho pointer in `if` conditions for charge deposition (#3544)Gravatar Edoardo Zoni 1-2/+4
2022-12-02Clean up examples folders (#3545)Gravatar Edoardo Zoni 146-307/+307
* Clean up examples folders * Use `snake_case` names * Rename `nci_corrector` as `nci_fdtd_stability`
2022-11-30PSATD: Rewrite Equations with/without Rho (#3343)Gravatar Edoardo Zoni 1-83/+64
2022-11-29Fix Esirkepov deposition in 1D (#3537)Gravatar Remi Lehe 3-22/+20
* Fix Esirkepov deposition in 1D * Clean up code * Update benchmarks * Update benchmark
2022-11-29[pre-commit.ci] pre-commit autoupdate (#3540)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v4.4.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-11-28fix bug with reduced diagnostic FieldProbe in 1d (#3535)Gravatar Roelof Groenewald 2-2/+5
2022-11-28enable the use of `FieldProbe` default parameter values (#3538)Gravatar Roelof Groenewald 3-38/+36
2022-11-28AMReX/PICSAR: Weekly Update (#3539)Gravatar Edoardo Zoni 5-5/+5
2022-11-24Take into account mean velocity in gaussian flux injection (#3514)Gravatar Remi Lehe 8-18/+325
* Take into account normal mean velocity in gaussian flux injection * Avoid negative u * Adjust threshold to switch from one method to the other * Fix compilation error * Fix compilation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Raise error if momentum is positive * Fix compilation * Add correct import statement * Fix compilation * Fix automated test * Update checksum * Relax tolerance * Add analysis script * Add CI test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add checksum file * Make the code clearer Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-11-24allow initial fields to be set through the picmi interface (#3536)Gravatar Roelof Groenewald 1-0/+29
2022-11-23Speed up Vay current deposition (#3529)Gravatar AlexanderSinn 1-95/+91
* Speed up Vay current deposition by about 3 times * add endif * test 2D * fix ( * cleaning + check if i_new == i_old
2022-11-22Assert for `diag_type` (prevent input typos) (#3532)Gravatar Revathi Jambunathan 1-0/+3
2022-11-21AMReX/PICSAR: Weekly Update (#3530)Gravatar Edoardo Zoni 6-5/+7
* AMReX/PICSAR: Weekly Update * Fix bug
2022-11-19Bugfix for "particle coordinates" with plane field probe reduced diagnostic ↵Gravatar Roelof Groenewald 2-45/+53
(#3497) * changed the method by which the grid coordinates are generated for "plane" field probe * use amrex::literals to avoid implicit cast * Restrict function arguments * make failing compilers happy Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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