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2022-09-01Spack Envs: Debian (#3360)Gravatar Axel Huebl 7-1/+128
* Spack Envs: Debian Add default compilers on Debian to our Spack environments. * Debian: have `lsb-release` installed See: https://github.com/spack/spack/pull/32479
2022-09-01Fix a bug in AddPlasma (#3351)Gravatar Weiqun Zhang 1-20/+18
When warpx.refine_plasma=1, there was an error in the logic like below. if (lrefine_injection) { Box fine_overlap_box = ...; if (fine_overlap_box.ok()) { pcounts[index] = ...; } // the else part was missing } else { pcounts[index] = ...; }
2022-09-01ABLASTR: Add Nodal Gather Functions (#3357)Gravatar Axel Huebl 4-19/+78
Add nodal field gather functions to ABLASTR for scalar and vector fields. This currently only implements 1st order (CIC) shape. Co-authored-by: Remi Lehe <rlehe@lbl.gov> Co-authored-by: Remi Lehe <rlehe@lbl.gov>
2022-08-31make variables constexpr (#3354)Gravatar Luca Fedeli 3-3/+3
2022-08-31Perlmutter: Work-Around CUDA-Aware MPI & Slurm (#3349)Gravatar Axel Huebl 1-2/+4
* Perlmutter: Work-Around CUDA-Aware MPI & Slurm There are known HPE bugs on Perlmutter that can blow up simulations (segfault) with CUDA-aware MPI. We avoid the respective Slurm options now and just manually control the exposed GPUs per MPI rank. * Add: `gpus-per-node`
2022-08-29Fix few "magic constants" & undefined variables found with clang-tidy (#3346)Gravatar Luca Fedeli 4-23/+41
* fix few issues found with clang tidy * fix bug
2022-08-29AMReX: Weekly Update (#3348)Gravatar Axel Huebl 5-5/+5
2022-08-29Python: 3.7+ (#3342)Gravatar Axel Huebl 7-9/+11
* Python: 3.7+ Python 3.6 is now end-of-life. Bump support to 3.7+. * CUDA CI: Python3 Update
2022-08-28Docs: Add description of Python APIs in `libwarpx` (#3310)Gravatar Roelof Groenewald 3-97/+266
* add mention of callbacks and some libwarpx functions to the docs * reformatted various function docstrings in `_libwarpx.py` and added them to the docs * Add subsection Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-08-26Fix Bugs w/ Current Correction and Vay Deposition (#3290)Gravatar Edoardo Zoni 12-112/+402
* Fix Bugs w/ Current Correction and Vay Deposition * Vay Deposition and Current Correction Cannot be Combined Together * Add Comment for Future Implementation of Vay Deposition w/ MR * Add Comment for Future Implementation of Vay Deposition w/ MR * Define SyncCurrentAndRho, Clean Up * Vay Deposition: Remove Extra FFT of Rho * Fix Bug in RZ Geometry (Double Filtering) * Add 2D Galilean Test w/o Periodic Single Box * Add RZ Galilean Test w/o Periodic Single Box * Add 3D Galilean Test w/o Periodic Single Box
2022-08-26Fixed plasma lens residence correction to allow a short lens (#3318)Gravatar David Grote 5-11/+111
* Fixed plasma lens residence correction to allow a short lens * Added CI test with a short plasma lens
2022-08-25Order-independent `rho_<species>` with RZ and openPMD (#3338)Gravatar Ryan Sandberg 3-3/+26
* order-independent rho_<species> * add test to check rho_<species> is order-agnostic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make analysis naming more consistent Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-08-23Use proper units for momenta, in BoundaryScrapingDiagnostic (#3240)Gravatar Remi Lehe 7-35/+16
* Use proper units for momenta, in BoundaryScrapingDiagnostic * Fix fetch of attribs in particlesConvertUnits Co-authored-by: Dave Grote <grote1@llnl.gov>
2022-08-23Docs: Improve Nsight Systems Section (#3102)Gravatar thierry 1-1/+11
* avoid details bugs with nsight system analysis I added the header of the sbatch file for nsight system analysis, a little description of the useful output files for the analysis and a warning for the execution of the sbatch file. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Docs/source/developers/profiling.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Docs/source/developers/profiling.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update profiling.rst * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: remove ill-placed anchor * Fix ill-removed section * Fix Formatting * Update Wording 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>
2022-08-22Spack: Fix Typo in curl (previous commit)Gravatar Axel Huebl 1-1/+1
2022-08-22MultiParticleContainer: Prevent Bugs in Some `setVal` Calls (#3266)Gravatar Edoardo Zoni 1-4/+4
- Call `setVal` with default arguments (number of components and ghost cells) - Affects only functions used with multi-J time stepping: - `MultiParticleContainer::DepositCurrent` - `MultiParticleContainer::DepositCharge`
2022-08-22Performance Hint: Too Many Boxes / GPU (#3269)Gravatar Axel Huebl 1-4/+33
Print a performance hint if too many boxes are used per GPU.
2022-08-22Docs: Spack Desktop Environment (#3326)Gravatar Axel Huebl 5-52/+483
Add Spack environment files for developer desktop/laptop computers.
2022-08-22[pre-commit.ci] pre-commit autoupdate (#3334)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.3.0 → v1.3.1](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.3.0...v1.3.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-08-22AMReX: Weekly Update (#3333)Gravatar Axel Huebl 5-5/+5
2022-08-22CI: Clean up Analysis of Galilean Tests (#3322)Gravatar Edoardo Zoni 4-174/+109
* CI: Clean up Analysis of Galilean Tests * Update Reference Energy Values * Update Reference Energy Tolerances * Improve Inline Comment
2022-08-22Remove outdated comments from example input files (#3332)Gravatar Luca Fedeli 5-5/+5
Update comments in example input files: moving window now available along x, y, z.
2022-08-22Updated Docs/README.md (#3328)Gravatar David Grote 1-1/+2
2022-08-20shift BTD lab frame bounds by half a cell to prevent round off errors (#3330)Gravatar Revathi Jambunathan 1-2/+5
* shift BTD lab frame bounds by half a cell to prevent round off errors * [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>
2022-08-19Docs: Add NAPAC'22 Paper (#3314) (#3316)Gravatar Axel Huebl 1-0/+5
Add our latest NAPAC'22 paper to the documented references. Will replace with a JACOW reference once proceedings are out.
2022-08-18Fix Docs for `psatd.update_with_rho` (#3325)Gravatar Edoardo Zoni 2-3/+3
2022-08-18Wheel: Separate Directory (#3320)Gravatar Axel Huebl 3-13/+7
* Wheel: Separate Directory The `pip_install` target did not yet work on Windows, because it has no universal wildcard `*` support for our pip install logic. Fix this by creating the wheel in a sub-directory and installing it by "finding all wheels for `pywarpx` in a given prefix". - Avoid wildcards by using a separate directory. - Avoid downloading deps during `wheel` build again. * Fix: Manifest follow-up to #3265
2022-08-18Docs: Lassen diable MPI-I/O file lock (#3303)Gravatar Axel Huebl 1-0/+7
Workaround a OpenMPI bug that uses file locking on Lassen (OLCF). Performance is still not going up...
2022-08-17Allow filtering in z with RZ FDTD (#3281)Gravatar David Grote 3-57/+58
* Allow filtering in z with RZ FDTD * Update the error message about filtering in RZ * Turned z filtering on in laser_acceleration/inputs_rz * Update LaserAccelerationRZ benchmark, including z filtering
2022-08-15Docs: Add NAPAC'22 Paper (#3314)Gravatar Axel Huebl 1-0/+5
Add our latest NAPAC'22 paper to the documented references. Will replace with a JACOW reference once proceedings are out.
2022-08-15ABLASTR: Fix Missing Include (#3313)Gravatar Axel Huebl 2-1/+2
See if this missing include, which would import dllexport, fixes symbol errors on Windows in ImpactX.
2022-08-15Windows CI: Abort on First Error (#3312)Gravatar Axel Huebl 1-0/+11
Our Windows CI does not abort on the first failing command. This could, in the future, lead to false-positive tests.
2022-08-15Move handling of do_not_deposit to physics callers (#3225)Gravatar Phil Miller 7-78/+86
* 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
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