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2023-07-31clang-tidy CI test: add misc-misleading-bidirectional check (#4140)Gravatar Luca Fedeli 1-0/+1
2023-07-31AMReX: Weekly Update (#4142)Gravatar Axel Huebl 5-5/+5
2023-07-28remove superfluous includes from LatticeElements (#4131)Gravatar Luca Fedeli 6-9/+0
2023-07-27Fix bug with MLMG solver, always pass ghost cells to `SumBoundary` (#4078)Gravatar Edoardo Zoni 4-66/+16
* Must pass number of ghost cells to call `SumBoundary` * Apply suggestions from #4093 * Add inline comments on possible performance optimization
2023-07-27Improve script to compute PSATD stencil (#4016)Gravatar Edoardo Zoni 2-153/+188
* Improve script to compute PSATD stencil * Make it work both in 2D and 3D * Parse input file into dictionary * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use more lists * Move parser function to separate file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Use more lists * Apply suggestions from code review * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove TODO comment * Apply suggestions from code review * Apply suggestions from code review --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-07-27fix BTD doc (#4089)Gravatar Revathi Jambunathan 1-1/+15
* fix BTD doc * Apply suggestions from code review Axel's fix to typos Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> --------- Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-07-27Fix the writing of raw rho_fp (#4114)Gravatar David Grote 1-3/+4
2023-07-26Initialize variables at declaration if it improves readability (#4117)Gravatar Luca Fedeli 21-214/+107
* init some variables at declaration * make code more readable * avoid lossy function result cast * Update Source/Initialization/WarpXInitData.cpp Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> * replace with equality * Revert "replace with equality" This reverts commit e3164f9e053d345b153d770ae107a7f68c4bb260. * Update Source/Diagnostics/ComputeDiagFunctors/ParticleReductionFunctor.cpp Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> --------- Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2023-07-26AMReX: Update (Plotfile Write) (#4126)Gravatar Axel Huebl 6-6/+6
* AMReX: Update (Plotfile Write) Update AMReX to latest `development` to include compile fixes for `ParticleTransformation` and plotfile writing. * Azure: Increase timeoutInMinutes 2hrs to 3hrs for uncached builds. Need to check why some of the combinations rebuild currently.
2023-07-26exclude cppcoreguidelines-init-variables (#4118)Gravatar Luca Fedeli 1-0/+1
2023-07-26remove unused upper_bound algorithm (#4123)Gravatar Luca Fedeli 2-50/+0
2023-07-26Tools: Update Copyright String (#4120)Gravatar Axel Huebl 1-3/+2
Use a modern, short version referring our license model and keep per-file autorship notes.
2023-07-25[pre-commit.ci] pre-commit autoupdate (#4115)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/hadialqattan/pycln: v2.1.5 → v2.1.6](https://github.com/hadialqattan/pycln/compare/v2.1.5...v2.1.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-07-25Clang tidy CI test: add modernize-concat-nested-namespaces check to clang ↵Gravatar Luca Fedeli 4-15/+8
tidy CI test (#4098) * clang-tidy CI test: add modernize-concat-nested-namespaces check * fix modernize-concat-nested-namespaces issue found with clang-tidy
2023-07-25WarpX class: move a couple of function definitions (#4097)Gravatar Luca Fedeli 2-20/+26
* move function declarations from WarpX.H to WarpX.cpp
2023-07-25Clang-tidy: add cppcoreguidelines-interfaces-global-init check (#4107)Gravatar Luca Fedeli 1-0/+1
2023-07-24Fix timestep duration plot script download link (#4105)Gravatar Marco Garten 1-1/+1
Previously, this just was a relative link to the file which could not be resolved. Now it downloads the plot script.
2023-07-24Update perlmutter_gpu.sbatch (#4100)Gravatar kngott 1-1/+1
Tweak tasks per node. 32 is with hyper threads.
2023-07-24exclude some checks from clang-tidy CI test (#4108)Gravatar Luca Fedeli 1-0/+5
2023-07-24AMReX/PICSAR: Weekly Update (#4111)Gravatar Axel Huebl 6-6/+6
* AMReX: Weekly Update * PICSAR: Weekly Update
2023-07-24Merge MPI Reduction Calls (#4051)Gravatar Weiqun Zhang 5-48/+17
2023-07-21Fix `chi_min` and `chi_max` in `ParticleExtrema` reduced diags (#4101)Gravatar Arianna Formenti 1-10/+13
* moved reduce ops out of loop over boxes and added io process number * fixed position of reduce data eval * moved chi_min_f chi_max_f outside loop over levels * [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>
2023-07-21Update inputs files in WarpX (#4103)Gravatar Weiqun Zhang 10-25/+25
Due to the recent changes in amrex::ParmParse, we must use the line continuation character '\' for values spanning multiple lines. For Parser expression, we could either double quotes to enclose the whole string or use `\` as line continuation. The old style multi-line values were removed in AMReX to avoid mistakes like algo.current_deposition = direct # galilean psatd.use_default_v_galilean # Forgot = 1 Here, `psatd.use_default_v_galilean` is silently ignored because with the old style multi-line support it becomes part of the values for the previous definition (i.e., `algo.current_deposition = direct psatd.use_default_v_galilean`). This case will now abort.
2023-07-20Fix: Ablastr PoissonSolver Constant (#4090)Gravatar Axel Huebl 1-1/+2
Seen in ImpactX: ``` build/_deps/fetchedablastr-src/Source/ablastr/fields/PoissonSolver.H:163:31: error: use of undeclared identifier 'PhysConst' rho[lev]->mult(-1._rt/PhysConst::ep0); // TODO: when do we "un-multiply" this? We need to document this side-effect! ^ ```
2023-07-18AMReX: Weekly Update (#4092)Gravatar Axel Huebl 5-5/+5
2023-07-18Remove specification of nsys version (#4048)Gravatar Remi Lehe 1-13/+1
2023-07-17Remove field probe raw_fields option (#4074)Gravatar David Grote 3-37/+11
* Remove field probe raw_fields option * Fix error message * Remove unused variables * Remove more unused variables
2023-07-18Release 23.07 (#4088)Gravatar Axel Huebl 11-13/+13
* AMReX: 23.07 * PICSAR: 23.07 * WarpX: 23.07
2023-07-17 Clang-tidy CI test: add some performance checks in clang-tidy CI test (#4077)Gravatar Luca Fedeli 5-9/+15
* add some performance checks in clang-tidy CI test * fix few smalle performance issues found with clang-tidy * fix bug * fixed bug * fixed performance issue
2023-07-17Update Adastra documentation (#4082)Gravatar Luca Fedeli 3-34/+213
* update Adastra documentation * fix issues in the documentation * fixed issues * fixed issue * fixed issue * replace some 'Frontier' with 'Adastra' in adastra documentation
2023-07-17 Update LUMI documentation (#4087)Gravatar Luca Fedeli 3-30/+212
* add almost all missing bugprone checks in clang-tidy CI test * disable bugprone-misplaced-widening-cast check * fix issue of type bugprone-integer-division * initial update of the documentation * update LUMI profile * updates & addition of install dependencies script * update doc * fix bug
2023-07-14ablastr: fix missing/superfluous `#include` directives (#4080)Gravatar Luca Fedeli 17-28/+33
* use iwyu on ablastr * fix bug * add missing include * always include AMReX_ParallelDescriptor in Logger.cpp
2023-07-13Add reduced diag precision input parameter (#4079)Gravatar David Grote 3-1/+11
* Add precision input parameter for reduced diags * Add documentation * Allow parsing of the precision input parameter
2023-07-13Update Intel compiler installation (#4081)Gravatar Weiqun Zhang 1-5/+8
2023-07-13Clang-tidy CI test: make bugprone checks list more compact (#4075)Gravatar Luca Fedeli 1-57/+1
2023-07-11Clang-tidy CI test: add almost all missing bugprone clang-tidy checks (#4064)Gravatar Luca Fedeli 2-1/+53
* add almost all missing bugprone checks in clang-tidy CI test * disable bugprone-misplaced-widening-cast check * fix issue of type bugprone-integer-division
2023-07-11Clang-tidy CI test: add more bugprone clang-tidy checks (#4047)Gravatar Luca Fedeli 1-0/+3
2023-07-10Clang-tidy CI test: add few bugprone clang-tidy checks (#4046)Gravatar Luca Fedeli 1-0/+4
* add few bugprone checks in clang-tidy CI * [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>
2023-07-10main.cpp: change warpx_amrex_init into warpx::initialization::amrex_init (#4055)Gravatar Luca Fedeli 4-31/+41
* change warpx_amrex_init into warpx::initialization::amrex_init * fix bug
2023-07-10explicitly exclude bugprone-easily-swappable-parameters check from ↵Gravatar Luca Fedeli 1-0/+1
clang-tidy CI test (#4060)
2023-07-10Update GitHub actions CI test to use Ascent 0.9.2 (#4067)Gravatar Cyrus Harrison 1-1/+1
2023-07-10Fix `max_grid_size` for RZ PSATD (#4073)Gravatar David Grote 1-3/+4
2023-07-10Fix clang-tidy `bugprone-branch-clone` warning (#4072)Gravatar Edoardo Zoni 1-28/+18
2023-07-06Impose t_lab in Lorentz Transformation for externally loaded particles (#3996)Gravatar Ilian Kara-Mostefa 2-13/+16
* Impose t_lab from the openPMD file, set t_lab=0 by default for handwritten species * Clear commented out print statement * Move x and y coordinates accordingly
2023-06-30Docs: Karolina (IT4I) (#4012)Gravatar Axel Huebl 7-0/+635
* Docs: Karolina (IT4I) Document how to use the Karolina supercomputer at IT4I.cz * ADIOS2: w/o HDFVol Layer * Add OpenBLAS for RZ+PSATD * GPU Visibility Work-Around * Add GPU Job Script Co-authored-by: "Andrei Berceanu <andrei.berceanu@eli-np.ro>" * Typo: PBS * Activate Env On Install * uodate GPUs per node * pbs pinning Maybe not the closest CPU-GPU, but at least 1:1. * Update Modules, Job Script * [Draft] CPU: Slight Update Modules and job script are to do. * Fix: /scratch
2023-06-30Allow `FieldProbe` in RZ geometry (#4057)Gravatar Roelof Groenewald 5-15/+23
* allow `FieldProbe` in RZ geometry * hard code the FieldProbe number of outputs to 11 * add note in the docs about `raw_fields` only outputting the n=0 azimuthal mode
2023-06-30Continuous injection of moving plasma (#3958)Gravatar Edoardo Zoni 10-72/+186
* Continuous injection of moving plasma * Fix const correctness * Fix bugs in calculation of v_bulk * Fix restart * Use range-based for loops where possible * Apply suggestions from code review * Fix bug related to managed memory * Apply suggestions from code review * Exclude case with `moving_window_v = 0` * Add to WarpXParticleContainer virtual function that returns pointer to plasma injector * Add to WarpXParticleContainer member variable for current injection position * Fix bugs * Fix bug: use continue instead of return
2023-06-30Use GPU compatible kernel in `sumParticleCharge` (#3949)Gravatar Roelof Groenewald 1-7/+11
* use GPU compatible kernel in `sumParticleCharge` * Add omp threading if GPU is not used. Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> --------- Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2023-06-30Docs: update openPMD tutorials link (#4061)Gravatar Ilian Kara-Mostefa 1-1/+1
2023-06-30Allocate fewer `rho` components for ES, MS, hybrid-PIC solvers (#4036)Gravatar Remi Lehe 3-14/+18
* Allocate fewer components for `rho` * Fix compilation * Use two components with dive_cleaning * Fix Python script * Fix PICMI script for 1D CI test --------- Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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