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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>
2023-06-30RigidInjection: properly transform z_inject to boosted frame (#4059)Gravatar Remi Lehe 1-1/+5
2023-06-29Fix typo in docs of hybrid PIC scheme (#4058)Gravatar Roelof Groenewald 1-1/+1
2023-06-29Clean up of MultiFab tagging (#4014)Gravatar David Grote 7-225/+233
* Clean up of MultiFab tagging * Use [level=level] for the tag
2023-06-28Replace unsed WARPX_DIM_2D with AMREX_SPACEDIM==2 (#4039)Gravatar Luca Fedeli 1-2/+2
* replace WARPX_DIM_2D, since it is not used anymore * fixed bug
2023-06-28AMReX: Weekly Update (#4053)Gravatar Axel Huebl 5-5/+5
2023-06-28remove dependency of VectorPoissonSolver.H on WarpX (#4054)Gravatar Luca Fedeli 1-6/+4
2023-06-28Doc: Link All Tests in Examples (#4056)Gravatar Axel Huebl 1-0/+7
Although we want to document them with more detail, this is the right location to link the integration tests already.
2023-06-27Kernel Fusion in Reduced Diagnostics for Fields (#4050)Gravatar Weiqun Zhang 1-84/+29
The 8 kernels in ReducedDiags/FieldMaximum is merged into one. Also, we can call one MPI Reduce on all 8 numbers.
2023-06-27Define new `InjectorFlux` object, and use it in `AddPlasmaFlux` (#4040)Gravatar Remi Lehe 8-23/+227
* Create flux injector object * Call new flux injector in AddPlasmaFlux * Update syntax in tests * Also test the flux parser * Remove the use of `density_min` and `density_max` for flux injection * Update PICMI interface * Update documentation * Remove .cpp file
2023-06-27Doc: Summit SciPy -j10 (#4045)Gravatar Axel Huebl 1-1/+1
We can use the latest SciPy if we avoid over-using the provided resources on the head-node. Compile with `-j 10` instead of `-j` now.
2023-06-27Adding current density to Field Reduction reduced diagnostic (#3980)Gravatar Lizzette Corrales 6-12/+64
* Adding j in FieldReduction * Modiyfying input file with FieldReduced diag * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Diagnostics/ReducedDiags/FieldReduction.H * updating Field Reduction Docs to include current density * Update Source/Diagnostics/ReducedDiags/FieldReduction.H Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * adding cuurent density BackwardCompatibility to Field Reduction diagnostic * including E dot j density using the modifyed Field Reduction * fixing picmi interface * adding Edotj to automated python test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Lizzette Corrales <lzcorrales@kong.dhcp.lbl.gov> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2023-06-27Clang-tidy CI test: add bugprone-branch-clone check (#4030)Gravatar Luca Fedeli 8-80/+94
* add bugprone-branch-clone to clang-tidy CI test * Updating Inline Comments Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-06-27refactored `HybridPICModel::HybridPICSolveE` to more readable (#4044)Gravatar Roelof Groenewald 5-57/+33
2023-06-27Doc: Summit Scipy Install (#4023)Gravatar Ryan Sandberg 1-11/+13
* fix some build issues * downgrade scipy version to what can install on Summit * make sure to remove tmp build dir * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update * Cleaning --------- 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>
2023-06-26Remove Custom momentum and density injector (#4037)Gravatar Remi Lehe 9-158/+7
2023-06-24Explicitly check field `IndexType` appropriateness when using hybrid-PIC ↵Gravatar Roelof Groenewald 2-6/+20
solver (#4034) * explicitly check field `IndexType` appropriateness when using hybrid-PIC solver * fix typo
2023-06-24change default current deposition algorithm to `direct` with hybrid-PIC ↵Gravatar Roelof Groenewald 2-4/+6
solver (#4033)
2023-06-23added `WarpX::HybridPICDepositInitialRhoAndJ()` helper function to clean up ↵Gravatar Roelof Groenewald 3-31/+41
WarpX::Evolve (#4032)
2023-06-23abort simulation if a user attempts to use an external field applied ↵Gravatar Roelof Groenewald 1-0/+9
directly to the particles with the hybrid-PIC solver (#4020)
2023-06-23Doc: HPC Machines Source Py Env (#4029)Gravatar Axel Huebl 4-0/+5
Make sure the Python environment is active on very first dependency install, before we start compiling.
2023-06-23Doc: HPC3 (UCI) HDF5 & GPU Visibility (#4021)Gravatar Axel Huebl 2-3/+4
* Doc: HPC3 (UCI) HDF5 & GPU Visibility Switch the HDF5 module to one that is picked up well by our build logic. Slurm is not well configured to properly address GPU visibility per MPI rank. Thus, we define the node layouts during compile-time. * GPUS_PER_NODE: In CMake Looks like there is no env var support. * GPU Visibility: Via SLURM_LOCALID Not necessarily ideally pinned, but a good start.
2023-06-23Doc: IPAC22 Tan et al. Dielectric (#4027)Gravatar Axel Huebl 1-0/+5
Document the IPAC22 proceeding article by Tan et al.
2023-06-22Clean up GpuArray init in ABLASTR interp modules (#4028)Gravatar Edoardo Zoni 2-78/+18
2023-06-22Doc: IPAC23 Paper (#4017)Gravatar Axel Huebl 2-1/+21
Document the IPAC23 paper, which uses WarpX to train an ML model for ImpactX.
2023-06-22add modernize-avoid-bind check to clang-tidy CI test (#4025)Gravatar Luca Fedeli 1-0/+1
2023-06-22Move MPIInitHelpers into ablastr (#4026)Gravatar Luca Fedeli 9-29/+36
* move MPIInitHelper into ablastr * fix bug * fix bug
2023-06-22For ReducedDiags, write header on restart if file does not exist (#4022)Gravatar David Grote 16-21/+23
2023-06-21Fixes to remove compilation warnings (#4015)Gravatar David Grote 2-9/+9
* Fixes to remove compilation warnings * Further cleanup in FieldProbe.cpp * Fix Bug, Use Assign Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-06-21Doc: HPC QED & Multi-Dim (#4013)Gravatar Axel Huebl 18-26/+28
Update HPC machine instructions to enable multi-dims, PSATD and QED table non-defaults for all machines where these dependencies are met. This ensures users will get an as-feature- complete-as-possible install.
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