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2022-03-28Change particle filter parser to check it as a boolean instead of comparing ↵Gravatar Hannah Klion 2-5/+4
to 0.5 (#3007) * change particle filter functor to be a boolean check instead of comparing to 0.5 * update documentation * update doxygen
2022-03-28Docs: Fix syntax issues in parameters.rst (#3009)Gravatar Phil Miller 1-10/+11
2022-03-28Use Utils::TextMsg::Err in Message Logger (#3000)Gravatar Luca Fedeli 1-2/+3
2022-03-28Clean up handling of `v_galilean` (#2989)Gravatar David Grote 22-212/+152
* Cleaned up handling of v_galilean * Missed one * Update Source/WarpX.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/WarpX.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/WarpX.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/PhotonParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/FieldSolver/WarpXPushFieldsEM.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Diagnostics/ReducedDiags/FieldProbe.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/WarpXParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/WarpXParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Diagnostics/ReducedDiags/ParticleExtrema.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Utils/WarpXUtil.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/RigidInjectedParticleContainer.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/ElementaryProcess/QEDPhotonEmission.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/ElementaryProcess/QEDPairGeneration.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/Particles/ElementaryProcess/Ionization.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Update Source/FieldSolver/WarpXPushFieldsEM.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * More cleanup * Reset Galilean Benchmarks * For mirrors, now include the Galilean shift * Removed the flag since it is true for all calls * Fix Source/FieldSolver/SpectralSolver/SpectralFieldDataRZ.cpp * Update Source/WarpX.H Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-03-28Docs: Fix Missing "s" in <digs>.adios2_engine.parameters (#3002)Gravatar Axel Huebl 1-1/+1
Fix a typo in the `<digs>.adios2_engine.parameters.NumAggregators` example.
2022-03-27Docs: Updates Profiling Perlmutter (#2993)Gravatar Axel Huebl 1-9/+46
Fix issues we encountered.
2022-03-25Add Field Probe to Laser Ion Test (#2998)Gravatar Tiberius Rheaume 1-1/+27
2022-03-25Synchronize all nodal points in sub-cycling loop (#2995)Gravatar Remi Lehe 1-0/+6
2022-03-22add openPMD test for particle_fields_diags to CI (#2975)Gravatar Hannah Klion 3-10/+50
* add openPMD test for particle_fields_diags to CI * Specify HDF5 for openpmd output in test * remove unnecessary variable redefinition * Increase tolerance for checksum check in single precision Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-03-22Perform mesh refinement taggin on GPU (#2990)Gravatar Weiqun Zhang 2-16/+18
2022-03-22openPMD RZ modes dumped in thetaMode (#2878)Gravatar Ryan Sandberg 14-107/+599
* [Draft] openPMD: RZ Modes * Change 'theta' to 't' and 'J' to 'j' * Docs: openPMD rz notes * editing docs openPMD RZ note * erase cartesian E,B,j from openPMD rz diags list * openpmd rz: theta->t, exclude xyz dumps * openpmd rz: axes r,z, save as comp[mode][r][z] * catch logic bugs tracking when in rz mode * change return type to c++17 tuple in helper fn * allow divB functor to store in theta mode * tuple bindings / account for theta mode variables * only r,t,z componets in RZ, separate rz field init * separate rz field init, arbitrary diags in RZ * docs: xyz comps in cartesian, rtz in rz geometry * docs : remove mention of dump_rz_modes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * clarify documentation of InitializeFieldFunctorsRZ * n_rz_modes = 1 if not in RZ * style change for brackets * style, documentation, clarify magic constants * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add helper getVec * transpose RZ openPMD data for proper viewing * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * safe for 2d and rz * fix transpose order of limits, add tinyProfiler * document transpose function, lack of optimization * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix divB num components * keeping changes to openPMD+RZ, not general RZ * divB made more similar to divE * eliminate or document unused variables * fix openPMD+RZ documentation * change thetaMode parser to regex * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replace n_rz_azimuthal_modes with warpx variable ncomps * Ignore Unused Var in Cartesian * add rz openpmd analysis * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix warnings: unused vars * clarify documentation of dump_rz_modes * cleaning up before sending to PR * remove divB, divE, test in a different PR * Update Source/Diagnostics/WarpXOpenPMD.cpp fix Dxygen strings Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * clean up doxygen, note issue in divB * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixing rz_opmd test, still not passing * Fix: Unused <diag>.dump_rz_modes * updating openPMD+rz analysis * Regression Setup: set `outputFile` * Use HDF5 Backend This is most likely installed by all developers, so we use it for tests. * Code Style Updates * simplify test and reduce code redundancy * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reduce redundancy 1 less line * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Keep HDF5 HDF5 is easier to install for developers and provided in CI. * Style fixes * Style fix Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-03-21openPMD: Handle Zero Particles Well (#2980)Gravatar Axel Huebl 4-215/+262
* openPMD: Handle Zero Particles Well When a time step for output encounters zero particles in a species, then we still want to dump them as "empty" species in openPMD. That simplifies post-processing a lot and we have the mechanisms in openPMD for it :) * openPMD: Emtpy Particle Writes Write empty records for iterations (steps or lab steps for BTD, respectively) without particles in a species. * Re-order: ED-PIC & Constant Particle Records - set attributes once - set constant records once - clean up into appropriate functions * Enable BTD for ADIOS :) Works now as well :tada: * Fix lingo in comments (Reva) Thank you!! :) Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
2022-03-22Vay Deposition: Separate Arrays, Correct Index Types w/ FFTs (#2965)Gravatar Edoardo Zoni 9-178/+168
* Refactoring * Separate Arrays (Fine Patch) * Add Aborts w/ Current Centering, MR * Cleaning * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-03-21Hybrid Algorithms: Add FDTD Support for Centering (#2327)Gravatar Edoardo Zoni 8-228/+254
* Hybrid Algorithms: Add FDTD Support for Centering * Current Centering Incompatible with Esirkepov Deposition * Remove FDTD v. PSATD Runtime Conditions * Add CI Test * Rename coefs as coeffs in getFornbergStencilCoefficients * amrex::Vector: Use at() Instead of Operator [] * Reset Benchmark * Reset Benchmark * Cleaning * Reduce Size of New CI Test * Reset Benchmark * Fix Bug
2022-03-21AMReX: Update latest commit (#2987)Gravatar Axel Huebl 5-5/+5
2022-03-21Measure time taken in the moving window (#2985)Gravatar Remi Lehe 1-0/+2
2022-03-21Add profile region for Evolve (#2983)Gravatar Remi Lehe 1-0/+1
2022-03-21Streamline profiling documentation (#2971)Gravatar Remi Lehe 3-49/+117
* Streamline profiling documentation * Add Updates: Full Profile, OLCF Links, Commas * Spelling of Section Titles * nsys: Add Environment Options Especially for unwritable /tmp, which happens often in HPC. * nsys: add mkdir for TMPDIR Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Update documentation Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-03-18LaserAccelection_1d: Use same build as other 1D tests (#2982)Gravatar Phil Miller 1-2/+2
2022-03-18Doc: Major Cori Update (#2978)Gravatar Axel Huebl 4-38/+38
* Doc: Major Cori Update Update Cori instructions after the major upgrade yesterday. Before using the new modules, remove the old, pre-build software: ```bash rm -rf $HOME/sw/knl $HOME/sw/haswell $HOME/sw/gpu $HOME/sw/cori_gpu ``` * Cori: Work-Around ADIOS 2.7.1 ZeroMQ Disable due to https://github.com/ornladios/ADIOS2/issues/2709 * Fix haswell/knl mismatch
2022-03-18Minimum digits for plotfile cell and particle data is 5 (#2973)Gravatar Revathi Jambunathan 1-6/+15
* minimum digits for plotfile cell and particle data is 5 * Apply suggestions from code review * Update Source/Diagnostics/BTDiagnostics.cpp * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-03-17Removed used of separate bc arguments (#2977)Gravatar David Grote 1-22/+18
2022-03-17Docs: Cori Python & Testing (#2969)Gravatar Axel Huebl 1-1/+55
- improve the `--force-reinstall` logic to not trigger a forced re-install of WarpX Python dependencies - install WarpX Python dependencies upfront - add a first "testing" section to show how to run `./run_tests.sh` on Cori
2022-03-17openPMD: Only Write up to Finest Level (#2970)Gravatar Axel Huebl 4-13/+31
Now that we support "dynamic" levels, we need to differentiate between the maximum allowed refinement level (maxLevel) and the currently maximum used level (finestLevel) of a simulation.
2022-03-16fix documentation with pml_has_particles instead of the old ↵Gravatar Revathi Jambunathan 1-1/+1
do_particles_in_pml (#2974)
2022-03-16RZ: Use WarpX::ncomps more consistently (#2951)Gravatar Axel Huebl 4-19/+20
* RZ: Use WarpX::ncomps more consistently We used `2*modes - 1` in many places, which is harder to follow then the variable we have. * Update Comments * Replace leftover `ncomp` -> `m_ncomps`
2022-03-16ABLASTR: Full Library (#2968)Gravatar Axel Huebl 3-12/+12
* CMake: ABLASTR as library previously only an object collection. * CMake: Fix `set_warpx_binary_name` Should only change WarpX library and app build, not the library name of ABLASTR. * Use ABLASTR_ALWAYS_ASSERT_WITH_MESSAGE Over AMReX and WarpX equivalent macros.
2022-03-15Initialize buffer data only for the required levels in the output (#2967)Gravatar Revathi Jambunathan 1-0/+8
2022-03-15[pre-commit.ci] pre-commit autoupdate (#2966)Gravatar pre-commit-ci[bot] 1-2/+2
updates: - [github.com/hadialqattan/pycln: v1.2.4 → v1.2.5](https://github.com/hadialqattan/pycln/compare/v1.2.4...v1.2.5) - [github.com/mgedmin/check-manifest: 0.47 → 0.48](https://github.com/mgedmin/check-manifest/compare/0.47...0.48) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-03-14FAQ: Forward Declarations (#2957)Gravatar Axel Huebl 2-10/+52
* FAQ: Forward Declarations * Fwd Declarations: Extend Example
2022-03-14Langmuir 2D Tests: Better Analysis Plots (#2960)Gravatar Edoardo Zoni 1-15/+24
* Langmuir 2D Tests: Better Analysis Plots * Remove Unused Import
2022-03-14FFT of J: Use Spectral Index of Correct MR Level (#2961)Gravatar Edoardo Zoni 1-8/+18
2022-03-14FFT of J: Use Correct Current w/ Current Centering (#2962)Gravatar Edoardo Zoni 1-5/+1
2022-03-14QED: Add Space in Multiline Warnings (#2956)Gravatar Axel Huebl 1-2/+2
Just a missing space we saw in the warning message between the sentences.
2022-03-13Add by-cell averages of particle properties (#2892)Gravatar Hannah Klion 15-15/+724
* Add ParticleReductionFunctor * Adds a by-cell particle average diagnostic * Averaged quantity is given by an input parser in (x,y,z,ux,uy,uz) * Coordinates in these parsers are in the WarpX convention * Users specify which species the averages are calculated for. The averages are calculated for each given species individually. * If there are no particles in a cell, the average will be zero. * add documentation for ParticleReductionFunctor * add test for cell-averaged particle diagnostics * set benchmarks for praticle_fields_diags and particle_fields_diags_single_precision * small changes to parameter docs and test script (addressing David's comments) * Apply suggestions from code review * remove unnecessary comments in python test script * remove unused variable * fixed inaccurate comments * use static_cast<int> pattern * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add comment in ParticleReductionFunctor.H * warpx.serialize_ics -> warpx.serialize_initial_conditions * AMREX_SPACEDIM to WARPX_DIM_3D and WARPX_DIM_XZ * fix compile errors from dimensionality conditionals * fix compile errors * Apply suggestions from code review * clarify docs * add include headers * update docs Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-03-12Load-balancing heuristic weights: not negative by default (#2963)Gravatar Remi Lehe 2-3/+3
2022-03-11WarpX/PICSAR Version Define: File (#2959)Gravatar Axel Huebl 12-39/+83
* WarpX/PICSAR Version Define: File Move the `-D` defines that contain the latest WarpX commit to a config file. Using always the latest commit counteracts `ccache` since the signature of the compilation call changes every commit. * Avoid Rebuilding WarpX.cpp * Support WarpXVersion.H in GNU Make * AMReX: Update to latest commit Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
2022-03-11ABLASTR: Move TextMsg (#2953)Gravatar Axel Huebl 13-119/+218
* ABLASTR: Move TextMsg Since this is used in a ABLASTR header, we need to compile this in ABLASTR, so ImpactX can use it as well. Otherwise we have missing symbols for that utility. * Fix typo in GNUmake * Apply Wording Update for Doxygen Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
2022-03-10Default CFL to 0.999 instead of 0.7 (#2940)Gravatar Maxence Thévenet 3-6/+6
* default CFL to 0.999 instead of 0.7, and update doc * Apply suggestions from code review * set CFL explicitly in tests to avoid failing tests * set cfl to 0.7 in CI test ion_stopping Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-03-10CMake: pip_install w/o MPI (#2950)Gravatar Axel Huebl 1-2/+3
We automatically trigger a dependency to `mpi4py` when MPI is used. This makes sure this requirement stays consistent.
2022-03-10Clean Pip Staging Directory (#2954)Gravatar Axel Huebl 2-4/+17
* Clean Pip Staging Directory The distutils staging (`build` -> `_tmppythonbuild`) directory that pip uses to collect build artifacts is not by default cleaned between multiple `pip` runs. This can be confusing when we recompile, because old `libwarpx*` files can be still in it that are not present in our own `build/lib/`. This cleans that staging directory before builds now. It also sets the whole `build_base` so that no artifact lands in the default, which was `build/`. So far, `bdist.linux-x86_64/` still was out-of-tree. * Python_background_mcc_1d: Add CMake Options Add missing CMake options in `WarpX-tests.ini`. This must have been merged in parallel to when we modernized our regression tests end of last year. #2556
2022-03-10Clean up the use of ndt for collisions (#2944)Gravatar David Grote 11-32/+28
* Clean up the use of ndt for collisions * Update BackgroundStopping to match changes
2022-03-10fix ambiguity in Parser from amrex and ExternalFieldInitType (#2955)Gravatar Revathi Jambunathan 2-4/+4
2022-03-09allow diagnostic data_list to be None (#2949)Gravatar Ryan Sandberg 1-88/+91
2022-03-09move MCC modules to a new folder inside "Particles/Collision/" (#2945)Gravatar Roelof Groenewald 10-8/+15
2022-03-08Add background stopping (#2884)Gravatar David Grote 12-15/+771
* Added BackgroundStopping * Added BackgroundStopping CI test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * For background stopping, allowed parsed background density and temperature * Updated background stopping CI test * For background stopping, temperature is specified in Kelvin * Added documentation for background stopping * Added ion stopping plus other fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Made dt level dependent * Revert "Made dt level dependent" This reverts commit 1aed9654d24ff1411a7b5fd8558891e0688f0032. The collisions should be done using the time step of the lowest level. * Add a comment about dt * Add const declaration * Added comment regarding stopped particle * Several fixes and clean up of the documentation * Update CI benchmark Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2022-03-08Make error and info messages visually uniform (#2939)Gravatar Luca Fedeli 70-354/+586
* initial work to add msg formatter * wip * replace AMREX_ALWAYS_ASSERT_WITH_MESSAGE with WarpX equivalent
2022-03-07doxygen comments for static variables in WarpX class (#2935)Gravatar Revathi Jambunathan 1-5/+41
2022-03-07properly handle MCC collision subcycling (#2934)Gravatar Roelof Groenewald 3-3/+10
2022-03-07AMReX: Update latest commit (#2932)Gravatar Axel Huebl 5-5/+5
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