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2022-12-22CMake: ADIOS1 off by default (#3591)Gravatar Axel Huebl 1-0/+1
We will deprecate ADIOS1 and will not build it by default anymore in the upcoming release. Since we only use ADIOS2 in WarpX and builds are sometimes fragile with ADIOS1, we just disable it now in superbuilds already.
2022-12-22Adding radial weighting at r=0 for Jr if nodal. (#3589)Gravatar S. Eric Clark 1-17/+22
2022-12-21Avoid touching device memory on host in FieldProbe (#3579)Gravatar Weiqun Zhang 1-16/+23
The implementation here can be optimized by using shared memory. However, instead of doing it here, I am going to add a helper function to AMReX. Also removed an unnecessary synchronization, because there is a synchronization in the destructor of the particle iterator.
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
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