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2023-04-20Add check in `addPlasma` and `addPlasmaFlux` to respect `random_theta` (#3585)Gravatar S. Eric Clark 7-95/+95
* Adding additional check in addPlasma and addPlasmaFlux to respect the random_theta flag, otherwise acts deterministically. * Reset RZ benchmarks --------- Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2023-04-19Add more PICMI options (#3773)Gravatar Remi Lehe 1-1/+10
* Add PICMI option to cover multiple cuts * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Parse flux_min, flux_tmax from PICMI * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Implement review comments --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-19Correct sign of the `ChargeOnEB` diagnostic (#3851)Gravatar Remi Lehe 3-17/+17
* Correct sign of the ChargeOnEB diagnostic * Properly indent documentation
2023-04-17AMReX/PICSAR: Update to New Particle APIs (#3848)Gravatar Axel Huebl 13-17/+30
* AMReX: Weekly Update * Particles: Update WarpX APIs
2023-04-17Fix particle reflecting boundaries in RZ (#3837)Gravatar David Grote 3-4/+33
* Fix the reflection of velocities in RZ * Add warpx_reflect_all_velocities to the PICMI interface
2023-04-17Doc: Tunneling Jupyter (#3841)Gravatar Axel Huebl 3-0/+68
* Doc: Tunneling Jupyter Document how to tunnel Jupyter servers. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add explicit headless command to workflow * Fix quotes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-17AMReX: Weekly Update (#3845)Gravatar Axel Huebl 5-5/+5
2023-04-16AMReX/PICSAR: Weekly Update (#3822)Gravatar Axel Huebl 9-64/+64
* AMReX: Weekly Update * AMReX: Include Fix Roundoff Domain 3247 * Reset Benchmarks * AMReX: Include PR 3248 * Update Checksums
2023-04-14Doc: HPSS Permissions (#3840)Gravatar Axel Huebl 1-0/+5
Document to change the default permissions of HPSS archives to be group (as in *project*) readable.
2023-04-13Doc: AAC22 Proceeding (#3836)Gravatar Axel Huebl 1-2/+7
Add AAC22 proceeding paper (preprint).
2023-04-13amrex.the_arena_is_managed=0 (#3825)Gravatar Axel Huebl 2-1/+10
Disable managed memory by default for performance and non-bugness. Please disable explicitly if needed for some of the current scripting tasks, e.g., in the current Python bindings.
2023-04-13Add callback function before/after the initial Esolve (#3452)Gravatar Remi Lehe 4-4/+42
* Add callback function after the initial Esolve * Apply suggestions from code review * Change name of callback function * Update PR
2023-04-13Doc: Typo "CUDA" in HIP ProfilesGravatar Axel Huebl 3-3/+3
2023-04-13Docs: LPA Collision Papers (#3827)Gravatar Axel Huebl 1-0/+10
Add Yin's LPA collision papers.
2023-04-12Doc: Perlmutter CFS for SW & Optimas (#3835)Gravatar Axel Huebl 4-34/+45
Updates the installation location of software to use CFS. HOME has only 40GB of quota, which can fill quickly when pulling in large ML packages. Also adds optimas for GPU including pytorch dependency.
2023-04-12Reflect density from non-periodic boundaries during deposition (#3711)Gravatar Roelof Groenewald 32-191/+935
* refactored the charge deposition fix to be performed with the field data rather than individual particles * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * also correct current density at PEC boundary * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * corrections pointed out during code review * fix build fails due to unused variables * fix issue with GPU builds * actually apply rho boundary correction in EM case * first round of CI fixes * second round of CI fixes * added description of deposition logic with PEC boundaries to documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * third round of CI fixing * move J and rho boundary handling to after `SyncRho` and `SyncCurrent` calls * properly order the application of boundary conditions on rho, for electrostatic simulations * fourth round of CI fixing * don't apply J field boundary in `MultiParticleContainer::DepositCurrent` * apply changes requested during code review * Apply suggestions from code review Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Loosen tolerance on failing CI test * Removed unused variable * deal with fine versus coarse patches * move the `ApplyRhofieldBoundary` call to after `SumBoundary` * use a uniform calculation for the number of cells a given index is from the boundary * remove unused variable * limit number of ghost cells updated during PEC BC application * the number of ghost cells to consider depends on whether the field is nodal or not --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-04-12Docs: Perlmutter CPU (#3831)Gravatar Axel Huebl 5-75/+272
Document Perlmutter (NERSC) CPU usage.
2023-04-12Doc: Frontier Module Updates (#3832)Gravatar Axel Huebl 2-15/+8
* Doc: Frontier Cray HDF5 Work-Around Document the HDF5 workaround for the current Frontier Cray Modules. * Frontier: Update Modules
2023-04-11DD fusion anneutronic branch (#3789)Gravatar Johan Carlsson 1-2/+4
* Allow DD fusion products to be tritium + protium For deuterium-deuterium (DD) fusion there are two branches: | He-3 + n (neutronic branch, 50% probability) d + d -> < | t + p (anneutronic branch, 50% probability) Currently in Warpx anneutronic DD fusion only works when the species of the fusion products are tritium (or hydrogen3) and proton. If protium (or hydrogen1) are specified instead of proton, the simulation aborts with the following error message: amrex::Abort::0::ERROR: Product species of proton-boron fusion must be of type helium3 and neutron, or tritium and proton !!! The proposed diff allows anneutronic DD fusion to produce either protium / hydrogen1 or proton. It also corrects the error message. * Shows that DD fusion cannot produce protium Input deck that demonstrates how anneutronic DD fusion in the development branch cannot produce protium, only proton. Some options of the anneutronic DD branch: 1) tritium + proton (currently the only option) 2) tritium + protium (added in this branch) 3) triton + proton (another alternative) Option 1) seems inconsistent (why include the electron mass in one fusion product species but not in the other?). Option 2) is enabled by the diff in this branch. Option 3) would require adding a triton species (and deuteron and helion species for consistency). * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove test file --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2023-04-11Add message if user sets old flag `warpx.do_nodal` (#3749)Gravatar Edoardo Zoni 1-0/+6
* Add message if user sets old flag `warpx.do_nodal` * Update PICMI version --------- Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2023-04-10`SyncRho`: Pass References To Charge MultiFabs (#3814)Gravatar Remi Lehe 5-15/+26
* `SyncRho`: Pass References To Charge MultiFabs * Keep a function SyncRho for the Python interface * [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>
2023-04-10Clean up calls to FillBoundary in FDTD part of `OneStep_nosub` (#3607)Gravatar Edoardo Zoni 1-4/+5
* Clean up calls to FillBoundary in FDTD part of `OneStep_nosub` * Remove commented-out code * Exchange guard cells of F,G before evolving B
2023-04-10CI: add RZ Langmuir test w/ multi-J PSATD (#3612)Gravatar Edoardo Zoni 2-0/+47
* CI: add RZ Langmuir test w/ multi-J PSATD * Run test with 4 grids and 2 MPI procs * Use 2 azimuthal modes in new test
2023-04-10Improve Python script to plot PSATD stencils (#3668)Gravatar Edoardo Zoni 1-159/+117
* Improve Python script to plot PSATD stencils * Improve explanation printed to standard output Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov> * Fix warning, improve docstrings * Handle exception where signal does not reach double machine precision --------- Co-authored-by: Ryan Sandberg <RSandberg@lbl.gov>
2023-04-10PSATD: call FFT of rho with explicit spectral index (#3720)Gravatar Edoardo Zoni 3-31/+33
2023-04-10Bug fix: use current finest level in loops over levels (#3798)Gravatar Edoardo Zoni 2-2/+10
2023-04-10Lattice: Line Docs & Rename (#3815)Gravatar Axel Huebl 4-8/+33
* Lattice: Line Docs & Rename Rename the `lattice` element type to `line` and add documentation for it. * Add `{}` for Dave :)
2023-04-07Contributing page update (#3819)Gravatar Juliette Pech 1-1/+1
'(between quotation marks)' has been removed
2023-04-07Glossary update (#3818)Gravatar Juliette Pech 1-0/+1
ALS has been added to the glossary
2023-04-07ChargeOnEB: use atomic add on CPU, instead of critical (#3816)Gravatar Remi Lehe 1-4/+1
2023-04-07Fix loading particles from openPMD (#3810)Gravatar Remi Lehe 1-12/+17
* Read particle offset when loading particles from openPMD * Fix compilation errors * Use loadChunk * Use correct mass
2023-04-07GitHub Actions: macOS has 3 Cores (#3813)Gravatar Axel Huebl 1-2/+2
https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
2023-04-06CI: Retry Simplify (#3812)Gravatar Axel Huebl 2-10/+13
Only write number of retries in a single location.
2023-04-06Charge on EB: Use `fp` field instead of `aux` (#3809)Gravatar Remi Lehe 1-3/+3
2023-04-06code cleanup: make use of `MultiParticleContainer::DepositCurrent` in ↵Gravatar Roelof Groenewald 2-28/+7
`AddSpaceChargeFieldLabFrame` (#3807)
2023-04-06openPMD-api 0.15.1 (#3771)Gravatar Axel Huebl 15-77/+40
* openPMD-api 0.15.1 Prepare tests for openPMD-api `0.15.1`. * Deprecated: `openPMD::shareRaw` Update to newer syntax. * Use replace_all from openPMD-api * openPMD: Remove Duplicate Compile Defs * CI: openPMD-api 0.15.1
2023-04-06Glossary: IO, LPI Again (#3808)Gravatar Axel Huebl 1-1/+2
More glossary entries
2023-04-06Implement thread-safe ChargeOnEB diagnostic (#3804)Gravatar Remi Lehe 1-1/+4
* Do not use threads in ChargeOnEB diagnostic * Use OpenMP critical for the atomic add
2023-04-04Adding Amrex Bucket into WarpX Python interface. (#3590)Gravatar S. Eric Clark 4-0/+26
* Adding Amrex Bucket into WarpX Python interface. * Adding PICMI-like options in the Simulation class to control Amrex Arena parameters.
2023-04-04Make verboncoeur correction optional (#3802)Gravatar David Grote 4-38/+56
* Add radial_verboncoeur_correction input parameter * Change parameter to boundary.verboncoeur_axis_correction
2023-04-04[pre-commit.ci] pre-commit autoupdate (#3803)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.4.2 → v1.5.1](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.4.2...v1.5.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-04-02CI: Retry Apt Repos (#3801)Gravatar Axel Huebl 10-10/+71
Since Intel Repos are often out-of-sync with each others for apt packages provided (checksum errors), we try to pause and retry up to five times to get them installed. Also set apt retries to 3 for `apt update`.
2023-04-02Release 23.04 (#3800)Gravatar Axel Huebl 11-13/+13
* AMReX: 23.04 * PICSAR: 23.04 * WarpX: 23.04
2023-04-02Doc: Update Funding (#3799)Gravatar Axel Huebl 1-0/+4
* Doc: Update Funding Update new CAMPA funding (SciDAC-5). Add ABLASTR seed funding (LBNL LDRD). * Unintentional change
2023-04-01CI: CMake-Easyinstall New Link (#3796)Gravatar Axel Huebl 8-8/+8
New Download Link
2023-04-01Frontier: User Early Access Docs (#3795)Gravatar Axel Huebl 1-11/+11
Update docs after today's webinar.
2023-03-30Docs: Frontier/Crusher ROCm 5.3/4 Perf (#3780)Gravatar Axel Huebl 3-0/+24
* Docs: Frontier/Crusher ROCm 5.3/4 Perf Document the performance regressions in ROCm 5.3/4 * Add ROCm issue numbers
2023-03-30Add random seed specification to `picmi` (#3793)Gravatar Roelof Groenewald 1-0/+6
2023-03-28Slurm & LSF: How to Checkpoint & Terminate (#3778)Gravatar Axel Huebl 1-0/+22
* Slurm: How to Checkpoint & Terminate Add a first concrete example how to gracefully checkpoint and terminate a WarpX simulation that runs into an HPC system's walltime. If this works well, we will add this to all HPC templates. * Signal Handling for LSF x-ref https://www.ibm.com/docs/en/spectrum-lsf/10.1.0?topic=options-wa * Simplified
2023-03-28Output enabled diagnostics (and checkpoint) on interrupt (#3790)Gravatar Roelof Groenewald 1-2/+5
* output enabled diagnostics on interupt by default * add flag to output LastTimestep diagnostics if the PIC loop was interrupted by an OS signal
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