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2023-02-22Fix getBulkMomentum for Maxwellian distributions (#3705)Gravatar David Grote 1-20/+21
* Fix getBulkMomentum for Maxwellian distributions * Add more "_rt" to real literals * More cleanup
2023-02-22Add option to increase `max_step` or `stop_time` to fill BTD (#3693)Gravatar Ryan Sandberg 5-8/+49
* add option to increase max_step to fill BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make sure code compiles locally * allow for unspecified max step if setting by BTD * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clarify docs, match default max_step value * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review shortening flag name * add example input script, fix bugf * check stop_time and max_step * account for stop time * Fix logic, improve documentation * [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>
2023-02-22Doc: Perlmutter 80 GB GPUs (#3706)Gravatar Axel Huebl 2-1/+10
Perlmutter (NERSC) now has 256 nodes with A100 that have 80 GB instead of 40 GB. Nice!
2023-02-21Fix Silver-Mueller boundary condition in 1D (#3703)Gravatar Remi Lehe 4-5/+82
* Fix Silver-Mueller boundary condition in 1D * Use WARPX_ZINDEX * Add automated test * Add benchmark
2023-02-21Doc: HPC build/bin (#3675)Gravatar Axel Huebl 11-9/+53
Hint where to find the executable after build.
2023-02-21AMReX: Weekly Update (#3701)Gravatar Axel Huebl 5-5/+5
2023-02-21Renamed "particle_vel" to "particle_mom" (#3672)Gravatar Davide Terzani 33-118/+146
* Renamed particle_vel to particle_mom * Changed vel to u * Updated gitignore with vscode-specific folder * Updated docs for single particle * Revert "Updated gitignore with vscode-specific folder" This reverts commit cb44ef8d66c123daa93d6a13d5a1d88416e866bb. * Fixed typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed other typo * Add species indication in warning --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-02-21Add warning message in RZ for < 2 azimuthal modes (#3655)Gravatar Davide Terzani 1-0/+13
* Add warning message in RZ for < 2 azimuthal modes * Simplify if statements C++ operator precedence doesn't require double parenthesis in `if` statements Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-02-21GetExternalEBField: Use AMReX's CompileTimeOption ParallelFor (#3696)Gravatar Weiqun Zhang 4-14/+56
This greatly improves the performance on AMD and Intel GPUs when GetExternalEBField is not used.
2023-02-21Add FieldReduction and ParticleHistogram to PICMI (#3697)Gravatar David Grote 3-24/+137
* Added FieldReduction and ParticleHistogram to ReducedDiagnostics * Add tests to reduced_diags/PICMI_inputs_loadbalancecosts.py * Clean up ReducedDiagnostics setting of argv
2023-02-20add flag to picmi `FieldDiagnostic` for whether particle data should be ↵Gravatar Roelof Groenewald 1-0/+5
saved along with the field data (#3699)
2023-02-10Update Crusher Modules to cce/15.0.0 and others (#3688)Gravatar Marco Garten 2-5/+25
Module changes were suggested by HPE on 2023/02/08 due to problems with building ImpactX on cce/14.0.2. Hence we update WarpX dependencies accordingly, too.
2023-02-09Pass seed for gpu in ResetRandomSeed (#3682)Gravatar David Grote 1-4/+8
2023-02-08Updated gitignore with vscode-specific folder (#3685)Gravatar Davide Terzani 1-0/+5
2023-02-08CI & Bug Fixes: 1D & 2D Compile (#3680)Gravatar Axel Huebl 4-10/+102
* CI: 1D & 2D Compile Add a modern CI entry that compiles 1D and 2D with `-Werror` and many warnings enabled. * Fix: 1D Field Init in z * Fix 1D: filterCreateTransformFromFAB * CI Job: Rename * CI: 1D/2D EB Off Not yet working.
2023-02-08Fix bug in mirror with F,G fields (#3681)Gravatar Edoardo Zoni 1-24/+41
2023-02-07Bug fix: retain particles in boundary buffer during Redistribute() (#3679)Gravatar Roelof Groenewald 1-1/+2
2023-02-06Pre-Commit: Smaller Files & NB (#3678)Gravatar Axel Huebl 2-14/+17
* Pre-Commit: Smaller Files & NB - Reduce threshold of "large file" from 50KB to 40KB. - Remove Jupyter notebook output if present. * [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>
2023-02-06AMReX: Weekly Update (#3677)Gravatar Axel Huebl 5-5/+5
2023-02-03 Bug fix : Coarse patch dx for external field init (#3674)Gravatar Revathi Jambunathan 3-11/+18
* fix coarse patch dx for external field init * rename var * Update Source/Initialization/WarpXInitData.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * reset benchmark for PEC_mr test case --------- Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-02-03Clean warning on unused function (#3656)Gravatar Remi Lehe 1-2/+0
2023-02-03Add all the elements from Z=87 (Fr) to Z=100 (Fm) to the ionization table ↵Gravatar Luca Fedeli 3-7/+1787
(#3670) * add elements between Z=87 and Z=100 to the ionization table * update documentation
2023-02-03Fix a bug in 1D PEC (#3669)Gravatar Prabhat Kumar 3-12/+38
* Fix a bug in 1D PEC * remove print statement used for debugging * reset benchmark for LaserInjection_1d because a bug was fixed in 1D pec * use correct data file in last commit for LaserInjection_1d * update benchmark for LaserAcceleration_1d since it uses pec * use data at correct time step * fix yt version to get nonzero particle output in LaserAcceleration_1d.json * fix yt version to get nonzero particle output in LaserAcceleration_1d.json
2023-02-03fix some issues in WarpX 1D (#3671)Gravatar Luca Fedeli 3-16/+32
2023-02-02RZ: abort if warpx.numprocs[0] > 1 with PSATD (#3615)Gravatar Olga Shapoval 1-0/+6
* RZ: added abort message if warpx.numprocs[0] > 1 is set. * Clean-up. * More clean-up. * Clean up alignment * Narrow down domain decomposition abort message to spectral solvers with RZ --------- Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2023-02-02Docs: Update Crusher (OLCF) Submission (#3601)Gravatar Axel Huebl 1-1/+2
Update the Crusher (OLCF) job submission template as seen since the last system update by Weiqun. > now I get > srun: error: Unable to create step for job 238051: More > processors requested than permitted. > It seems that after the most recent shutdown of crusher a few days > ago, -c 8 no longer works. The mapping without -c 8 is probably > still fine, because I can see 64 unique GPUs, assuming we can trust > HIP's uuid. I checked the Frontier template and that one currently does not yet configure these options.
2023-02-02Doc: NAPAC22 DOI (#3614)Gravatar Axel Huebl 1-2/+3
Add the DOI to our NAPAC22 paper.
2023-02-02Release 23.02 (#3667)Gravatar Axel Huebl 11-13/+13
* AMReX: 23.02 * PICSAR: 23.02 * WarpX: 23.02
2023-02-02Doc: Add ARTEMIS Publications (#3647)Gravatar Axel Huebl 1-3/+15
* Docs: Add ARTEMIS Publication Add an ARTEMIS paper :) * Two More :) Co-authored-by: Zhi (Jackie) Yao <58234082+jackieyao0114@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Newline * Fix Space --------- Co-authored-by: Zhi (Jackie) Yao <58234082+jackieyao0114@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-02-02add elements from Z=55 to Z=85 to the ionization table (#3666)Gravatar Luca Fedeli 2-6/+2978
2023-02-02ADIOS2: Fix BTD Particle Resize w/ Empty Ranks (#3657)Gravatar Axel Huebl 1-0/+55
* ADIOS2: Fix BTD Resize w/ Empty Ranks For ADIOS2 BP4 and BP5 writes, setting an update of a variable's (openPMD record's) shape is not sufficient to drop all meta-data on disk. In situations where the last write to a BTD stage only adds further particles from a few ranks, we need to pad with zero-block writes so ADIOS2 `Put` gets called. Backend details: - BP4 (as of ADIOS 2.8): last MPI rank's `Put` meta-data wins - BP5 (as of ADIOS 2.8): everyone has to write an empty block * [Draft] Start Duplicating All Put Logic Jeeeeeze. * Better Work-Around Compact and general, including MR situations.
2023-02-01Use a simpler expression for particle energy for reduced diagnostics. (#3650)Gravatar David Grote 1-18/+8
2023-02-01Docs: Spack Binary Caches (#3628)Gravatar Axel Huebl 3-4/+25
Spack now has binary caches for some popular platforms. They are for rolling (`development`) and stable releases. Since Spack's official docs will point users to install the rolling release of Spack, we will document to use the rolling binary cache.
2023-02-01Docs: Summit Jupyter HDF5 Back (#3629)Gravatar Axel Huebl 1-9/+4
* Docs: Summit Jupyter HDF5 Back The issues on OLCF Jupyter to read HDF5 data from GPFS production directories have been resolved. We can use the previous work-around again and reads will not get stuck. * Simplify * Update File Systems
2023-02-01Perlmutter (NERSC): New Boost Module (#3651)Gravatar Axel Huebl 1-1/+1
Just like #3619, stolen from E4S-22.05 deployment path. ```console $ spack spec /lmdngkt boost@1.79.0%gcc@11.2.0+atomic+chrono~clanglibcpp~container~context~contract~coroutine+date_time~debug+exception~fiber+filesystem+graph~graph_parallel~icu+iostreams~json+locale+log+math~mpi+multithreaded~nowide~numpy~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded~stacktrace+system~taggedlayout+test+thread+timer~type_erasure~versionedlayout+wave cxxstd=17 patches=57a8401,a440f96 visibility=hidden arch=cray-sles15-zen3 ```
2023-02-01Fix NUniformPerCell for 1D (#3659)Gravatar David Grote 5-61/+61
* Fix NUniformPerCell for 1D * Fix CI benchmarks
2023-02-01updates classical radiation reaction entry in docs (#3661)Gravatar Arianna Formenti 1-1/+4
* updated classical radiation reaction entry in docs * [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>
2023-01-31Add Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe to the ↵Gravatar Luca Fedeli 2-63/+1075
ionization table (#3652) * add Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe to the ionization tables * fix bug
2023-01-31[pre-commit.ci] pre-commit autoupdate (#3653)Gravatar pre-commit-ci[bot] 1-2/+2
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.4.1 → v1.4.2](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.4.1...v1.4.2) - [github.com/pycqa/isort: 5.11.5 → 5.12.0](https://github.com/pycqa/isort/compare/5.11.5...5.12.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-01-30CI: Unbreak Pre-CommitGravatar Axel Huebl 1-1/+1
https://github.com/PyCQA/isort/releases/tag/5.11.5
2023-01-30Docs: CCache Perlmutter (NERSC) (#3619)Gravatar Axel Huebl 1-0/+3
Stolen from E4S-22.05 deployment path.
2023-01-30Implement linear interpolation for both cell-centered and nodal data types ↵Gravatar Prabhat Kumar 14-221/+223
(#3638) * use two points and correct weights for higher order interpolation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * better alignment * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Parallelization/WarpXComm_K.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Reset CI benchmarks * apply review suggestion * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * white space --------- 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> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2023-01-30add K,Ca,Sc,Zn,Ga,Ge,As,Se,Br to ionization tables (#3646)Gravatar Luca Fedeli 2-12/+593
2023-01-30AMReX/PICSAR: Weekly Update (#3634)Gravatar Axel Huebl 5-5/+5
* AMReX: Weekly Update * 225c605680e825e1f0793780746b4112d4262381
2023-01-29Clean loadbalance params (#3632)Gravatar Hannah Klion 2-7/+31
* add tables for heuristic weights to documentation * re-format tables * only read in load balancing parameters when used
2023-01-29change github actions to use ascent 0.9.0 container (#3642)Gravatar Cyrus Harrison 1-1/+1
2023-01-28Add ionization support for Titanium (#3645)Gravatar Marco Garten 2-11/+43
* Add ionization support for Titanium This commit adds ionization support for Titanium as asked for in WarpX Issue 3641. * [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>
2023-01-28Docs: Fix `n_rz_azimuthal_modes` (#3643)Gravatar Axel Huebl 1-1/+1
Renamed a while ago and docs were outdated.
2023-01-25Fix few includes in WarpXAMReXInit.cpp/H and TextMsg.cpp using IWYU tool (#3627)Gravatar Luca Fedeli 3-1/+6
* Fix a couple of include directives * fix bug * Update Source/Initialization/WarpXAMReXInit.H Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * remove unnecessary AMReX.H include Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2023-01-24[pre-commit.ci] pre-commit autoupdate (#3635)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.3.1 → v1.4.1](https://github.com/Lucas-C/pre-commit-hooks/compare/v1.3.1...v1.4.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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