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2022-08-15Move handling of do_not_deposit to physics callers (#3225)Gravatar Phil Miller 1-0/+1
* Rearrange in preparation for lifting do_not_deposit higher in the call stack * Make do_not_deposit public, so callers can test on it * Make all DepositCharge call sites respect WarpXParticleContainer::do_not_deposit * Drop check for do_not_deposit in DepositCharge * Fix comment to accurately describe np_to_depose * Fix logic to account for other logic in AddSpaceChargeField * Match zero charge density array to filled array in RZ PSATD case * Structure control flow per @dpgrote's preference * Reword comment for clarity
2022-08-15AMReX: Weekly Update (#3315)Gravatar Axel Huebl 5-5/+5
2022-08-12Fill Guard Cells of Fields and Currents Independently (#3302)Gravatar Edoardo Zoni 20-89/+120
* Fill Guard Cells of Fields and Currents Independently * Fill Guard Cells of Averaged Fields as Regular Fields
2022-08-12Enable Particle RZ BackTransformed Diagnostics (#3309)Gravatar Remi Lehe 2-4/+7
* Enable particle RZ BackTransformed diagnostics * Add warning + compute theta * [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>
2022-08-12Docs: Add Input Parameter `psatd.use_default_v_galilean` (#3304)Gravatar Edoardo Zoni 1-8/+9
2022-08-11`isort`: AMReX, WarpX, etc. as First Party (#3307)Gravatar Axel Huebl 12-3/+15
* `isort`: AMReX, WarpX, etc. as First Party Mark the `amrex` and `pywarpx`, `picmistandard`, ... imports as first party, so that they do not change if run locally or remotely pre/post install.
2022-08-10Initialize particle runtime attributes inside AddNParticles (#3272)Gravatar Neïl Zaim 12-35/+267
* Initialize particle runtime attributes before calling AddNParticles * Avoid Multiplication result converted to larger type warning * Directly initialize runtime attributes inside AddNParticles * Update doxygen comment
2022-08-08PICMI: Fix Bug in Class `Species` Init (#3286)Gravatar Edoardo Zoni 1-17/+20
2022-08-08Fix out of bounds array access with Particle Scraping + Continuous Injection ↵Gravatar Neïl Zaim 1-0/+4
(#3294) * Fix out of boundary access with Particle Scraping + Continuous Injection * Explicit type of particles * Change type of particles
2022-08-08AMReX: Weekly Update (#3293)Gravatar Axel Huebl 5-5/+5
2022-08-08Doc: PICMI Parameters (#3291)Gravatar Axel Huebl 3-23/+134
This adds all currently defined PICMI parameters to the user-facing docs.
2022-08-05Use extended box array in setting par GDB for BTD (#3285)Gravatar Revathi Jambunathan 2-4/+5
* uise extended box array in setting par GDB for BTD * add synchronize in BTD particle functor
2022-08-04`CoarsenIO::Coarsen` : `mf_tmp` to be constructed with `ngrowvect` (#3288)Gravatar Revathi Jambunathan 1-1/+1
2022-08-04Fix Checksums & Analysis: Skip cpu & id (#2924)Gravatar Yinjian Zhao 123-680/+13
* Checksum: Ignore cpu & id Both are dependent on MPI parallelism and differ if run with one or more MPI ranks, as well if run on CPU (NOACC, OMP) or GPU (CUDA, HIP, SYCL). * Benchmarks: Remove cpu/id from JSON * Update Script Further - fixes: field/species property, not species itself - comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-08-04Species variables in diagnostics: deal with runtime components (#3218)Gravatar Neïl Zaim 13-110/+74
* Species variables in diagnostics: deal with runtime components * Remove ParticleStringNames namespace * Use const reference in iteration variable * Fix ion acc 2D test * Output extra (e.g. initialized later with python) comps by default * Always output theta in RZ * Fix QED tests * Fix Laser Acceleration RZ test
2022-08-04Regressions: remove tolerance (#3287)Gravatar Axel Huebl 1-1/+0
We do `tolerance` and `abs_tolerance` checks via our checksums. This avoids that we need to build the AMReX plotfile tools in CI, which: - take long time to build - use GNUmake - fail to build on macOS M1 Thus, do not add these sections to CI tests.
2022-08-04Docs: Update Intro PFS OLCF (#3284)Gravatar Axel Huebl 12-26/+80
* Docs: Update Intro PFS OLCF 1. put more emphasis on reading the system docs for HPC systems 2. duplicate information form the system docs about purge times, because you already skipped 1. again, didn't you * All Systems: BOLD read the Sys Docs
2022-08-04Docs: Lassen HDF5 Perf. Hints (#3264)Gravatar Axel Huebl 2-2/+22
* Docs: Lassen HDF Perf. Hints Copy the IBM GPFS Performance hints we use on Summit to Lassen. * Remove duplicate line
2022-08-03Implement output of scraped particles at domain boundaries (#3274)Gravatar David Grote 22-83/+150
* Implement scraping from all boundaries * Update input script * Output all particles to the same buffer * Dump different boundaries into different files * Avoid writing species that are not allocated * Improve documentation * Allow output of some boundaries only * Correct compilation error * Fixes and updates to BoundaryScraping * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci 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>
2022-08-02`SyncCurrent`: Pass References To Current MultiFabs (#3277)Gravatar Edoardo Zoni 6-15/+43
* `SyncCurrent`: Pass References To Current MultiFabs * Add Doxygen for `SyncCurrent`
2022-08-01[pre-commit.ci] pre-commit autoupdate (#3278)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v2.0.4 → v2.1.1](https://github.com/hadialqattan/pycln/compare/v2.0.4...v2.1.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-08-01Remove duplicated parameter in QED inputs (#3275)Gravatar Neïl Zaim 4-16/+0
2022-08-01Release 22.08 (#3276)Gravatar Axel Huebl 11-13/+13
* AMReX: 22.08 * PICSAR: 22.08 * WarpX: 22.08
2022-07-29Docs: Typos Frontier Section (#3273)Gravatar Axel Huebl 2-3/+3
Fix little typos in the Crusher/Frontier docs.
2022-07-29Remove duplicated parameter <species_name>.x/y/z_rms in parameters docs (#3268)Gravatar Neïl Zaim 1-1/+0
2022-07-29Frontier: Update Submission Scripts (#3267)Gravatar Axel Huebl 1-5/+12
Update the submission scripts, since the Slurm configs changed.
2022-07-29Update `background_mcc_dp_psp` benchmark (#3271)Gravatar David Grote 1-1/+1
2022-07-27Fix: mpi4py requirement for `--target pip_install` (#3265)Gravatar Axel Huebl 2-1/+8
Installs `mpi4py` if not already found during ``` cmake --build build -j 4 --target pip_install ```
2022-07-27Starting with the pusher, consistently use ParticleReal (#3259)Gravatar David Grote 15-156/+157
* Starting with the pusher, consistently use ParticleReal * Update benchmarks for background_mcc_dp_psp
2022-07-27ParticleReal for external fields and collisions (#3262)Gravatar David Grote 17-312/+313
* Use ParticleReal consistently in GetExternalFields * Use ParticleReal in Collision code * Use ParticleReal in Algorithms/KineticEnergy.H * Fix _prt in Algorithms/KineticEnergy.H
2022-07-26Frontier: Update JobscriptGravatar Axel Huebl 1-2/+2
`--cpus-per-task=8` is currently not working
2022-07-25[pre-commit.ci] pre-commit autoupdate (#3261)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v2.0.3 → v2.0.4](https://github.com/hadialqattan/pycln/compare/v2.0.3...v2.0.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-07-25AMReX: Weekly Update (#3260)Gravatar Axel Huebl 5-5/+5
2022-07-24Bug fix for BTD - particle BA, and geom, same as field buffer (#3056)Gravatar Revathi Jambunathan 6-106/+160
* fix BTD particle container BA, geom, and add assert for probhi == 0 * fix bug with mesh-refinement * delete commented line * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * with offset added, we dont need the assert anymore * similar to plotfile, openpmd also initializes tmp from pinned pc, and no need to reset BA * commenting out the assert * changes consistent with #3201 * unused var warning fix * Compute snapshot box at init, expand and shrink buffer BA and particle BA before and after redistribute, close buffer when klab_current == k_lo for that buffer * unused var * turning off particle output in BTD CI tests for plotfiles * reset particle BA only if species output is finite * add particle output for plotfile format for BTD tests * add openpmd diags back in 2d test case * fix input to have the right format Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-07-24Poisson Solver: Fix Bug w/ Semi-coarsening and EB (#3247)Gravatar Edoardo Zoni 1-1/+1
2022-07-22Fixes to allow mixed precision, ParticleReal float, Real double (#3239)Gravatar David Grote 5-2143/+2143
* 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
2022-07-22CI: Add Missing Regression Analysis (NCI corrector) (#3252)Gravatar Edoardo Zoni 3-0/+84
2022-07-22Add Python Callback Call when Checkpointing Signal is Received (#3251)Gravatar Roelof Groenewald 3-1/+17
2022-07-22Fix a bug in GPU version of Hankel Transform (#3253)Gravatar Weiqun Zhang 1-6/+6
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.
2022-07-19Docs: gaussian beam `q_tot` is not optional (#3249)Gravatar Neïl Zaim 1-1/+1
2022-07-19D-T fusion (#3153)Gravatar Remi Lehe 15-8/+868
* 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>
2022-07-18Docs: New OLCF Machine (#3228)Gravatar Axel Huebl 4-0/+202
2022-07-18ABLASTR: Update Poisson Solver API (#3243)Gravatar Axel Huebl 2-14/+23
Update the Poisson Solver API to be more usable. Needed for ImpactX.
2022-07-18[pre-commit.ci] pre-commit autoupdate (#3246)Gravatar pre-commit-ci[bot] 1-1/+1
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>
2022-07-18AMReX: Weekly Update (#3244)Gravatar Axel Huebl 5-5/+5
2022-07-14Remove Unused Allocations of Averaged MultiFabs (#3237)Gravatar Edoardo Zoni 1-18/+30
2022-07-14CMake: 3.20+ (#3196)Gravatar Axel Huebl 5-12/+6
We already use this version in ImpactX. The main reason is a severe simplifcation of CMake CUDA search logic that we can rely on. X-Ref.: https://github.com/AMReX-Codes/amrex/blob/2d931f63cb4d611d0d23d694726889647f8a482d/Tools/CMake/AMReXParallelBackends.cmake#L55
2022-07-13Refactor code in fusion module to avoid machine-precision issues (#3229)Gravatar Remi Lehe 3-14/+16
* Refactor code in fusion module to avoid machine-precision issues * Update formula
2022-07-12Fix: Write Used Inputs Once (#3234)Gravatar Axel Huebl 1-4/+6
Ooopsi, nearly killed a PFS again :D Only the IO processor should write this and not every rank on the planet.
2022-07-12Update 2D nuclear fusion test input file (#3230)Gravatar Neïl Zaim 2-65/+65
* Update 2D nuclear fusion test input file * Update Benchmarks
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