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2021-06-30Add OpenMP for FFTW (#2040)Gravatar Axel Huebl 1-0/+4
* CMake: Find out if FFTW supports OpenMP Add a heuristics that also works with PkgConfig to query OpenMP support in FFTW. Enable by default if we build with the OpenMP compute backend unless explicitly disabled. Add a macro to control the source-code, since FFTW does not offer a public define for this. * FFTW: Initialize Threads Co-authored-by: Severin Diederichs <severin.diederichs@desy.de> Co-authored-by: Severin Diederichs <severin.diederichs@desy.de>
2021-06-28Docs: Update Repo-Structure (#2039)Gravatar Axel Huebl 2-11/+17
- update build system references - move "evolve" term to glossary - update titles to typical spelling - minor formatting
2021-06-28Check verbose parameter before printing out step info (#2033)Gravatar Michael Kieburtz 1-6/+9
* Check verbose parameter before printing out step info * moved walltime outside of verbose check * renamed wall_time to evolve_time
2021-06-28Multi-J scheme (#1828)Gravatar Remi Lehe 22-221/+1342
* Introduce new option skip_deposition * Properly implement the option to skip deposition * Skip deposition for electrostatic solver * Correct typo * Add Index Enumerator and Equations for F/G Without Averaging * Define new functions for current deposition and charge deposition * Disable interpolation between levels * Correct compilation error in RZ mode * Add argument for relative time * Add Index Enumerator and Equations for F/G With Averaging * [skip ci] Add new OneStep function * Fix compilation errors * Correct more compilation errors * [skip ci] Fix compilation * Split the PSATD push into separate functions * Add guards for rho field * [skip ci] Use new functions in OneStep * [skip ci] Separate the inverse transform of E_avg, B_avg * Add deposition of rho * [skip ci] Prevent deposition of rho if unallocated * Fix error in deposition function * Add subcycling of current deposition * [skip ci] Add inverse transform of averaged fields * [skip ci] Move component of rho * Add function to copy J * Temporarily deactivate contribution from F * [skip ci] Implement call to linear in J * Add psatd time averaging for multiJ * [skip ci] Fix implementation of averaging * [skip ci] Implement divE cleaning * Fix Bug for RZ Builds * Fix Bug for RZ Builds * Fix Bug in Init of PML Spectral Solvers * Cleaning * Cleaning * Add div(B) Cleaning (G Equation) * Multi-J Not Implemented with Galilean PSATD or PMLs * Add 2D CI Test Using Multi-J Scheme * Add More Inline Comments * Add More Inline Comments & Doxygen * Add Doxygen for Constructor of SpectralSolver * More Doxygen in Class SpectralSolver * Add Doxygen for New Functions in WarpXPushFieldsEM.cpp * Add Doxygen for New Functions in WarpX/MultiParticleContainer * do_dive/b_cleaning Must Be True With linear_in_J Option * Cast multij_n_depose to Real in Divisions * New Input Syntax * Add const where Possible, Fix Warnings * Docs for New Input Syntax, Fix Abort Messages * Consistent Use of Idx, IdxAvg, IdxLin * Improve Documentation of psatd.J_linear_in_time * Use const Type Qualifier whenever Possible * Simplify Initialization of Pointer ion_lev * Improve Doxygen * Update documentation * Add Note on NCI to Docs * Make warpx.do_multi_J_n_depositions Not Optional * Simplify Logic in getRequiredNumberOfFields * Use More const Type Qualifiers Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2021-06-28Docs: Fix Include RST linksGravatar Axel Huebl 1-1/+1
Little formatting issues when linking to references
2021-06-28AMReX/PICSAR: Weekly Update (#2038)Gravatar Axel Huebl 2-2/+2
Update AMReX to AMReX-Codes/amrex@55cb40092910183729ca81e6eef3d0ce386af317 No changes im PICSAR since last update. ``` ./Tools/Release/updatePICSAR.py ./Tools/Release/updateAMReX.py ```
2021-06-25Evolve: Avoid Resetting Walltime (#2032)Gravatar nruof 1-7/+7
* Moved walltime to WarpX.H so that it doesn't reset for each sim.step() call * Move Real walltime to static instance in WarpXEvolve.cpp and rename all instances of walltime to evolve_time
2021-06-24Use "Include What You Use" on WarpX (#1947)Gravatar Luca Fedeli 279-733/+3221
* initial tests with IWYU * added a couple of forward declarations * used iwyu on more files * progress * used iwyu on more files * progress with iwyu * progress with iwyu * fixed bug * progress with iwyu * progress with IWYU * progress with IWYU * fixed bug * fixed bug * progress with IWYU * progress with IWYU + use forward declarations in WarpX.H * first try with .def files * fix bugs * progress with IWYU * progress with IWYU * progress with iwyu * correct copyright * fixed bug * fixed bugs * fix missing include * fixed bug * fix bug * fix bug introduced during last bugfix * use iwyu on newly added files * add space * fix bug * fix missing include * fix missing include * fix missing include * fixed bugs * fixed bug * attempt at fixing issue with math functions * added missing include * fixed missing include * using _fwd.H * fixed bug * progress with iwyu * update AMReX branch * enforce alphabetic order * progress with iwyu * use right version of amrex * use right version of amrex for tests * fixed bug * fix another bug * fix missing include * fix missing include * fix missing include * updated amrex * initial work to document new include strategy * updated documentation * Fix rst & private includes * Remove accidentially added files * Fix rst code blocks * one more rst block Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-06-24Refactored basestring to str (#2030)Gravatar kzhu-ME 1-6/+6
2021-06-23DepositCurrent: Const Arguments (#2025)Gravatar Axel Huebl 4-46/+46
2021-06-21Laser: warnin antenna of a box; Allow zero amplitude (#1989)Gravatar Luca Fedeli 2-8/+19
* add check of laser antenna position * implement axel suggestions * disable laser if antenna is out the box * fix bug * Update Source/Particles/LaserParticleContainer.cpp * implement neil's solution * remove unnecessary include * fix initial status of m_enabled * adding back a check * add back check * add back check * removed unnecessary comment Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
2021-06-21Add option to not dump first and last timestep (#1530)Gravatar Neïl Zaim 8-3/+27
* Add option to not dump first and last timestep * Add new function MultiDiagnostics::FilterComputePackFlushLastTimestep
2021-06-21Add damped to BC_map (#2021)Gravatar David Grote 1-1/+1
2021-06-21AMReX/PICSAR: Weekly Update (#2024)Gravatar Axel Huebl 2-2/+2
Update AMReX to https://github.com/AMReX-Codes/amrex/commit/c797f6b6979aea63cc6bda574765c29ba89e7b9c No changes im PICSAR since last update. ``` ./Tools/Release/updatePICSAR.py ./Tools/Release/updateAMReX.py ```
2021-06-21Make FieldReduction more robust with respect to multiline parser inputs (#2008)Gravatar Neïl Zaim 2-2/+8
* Add multi-line example * Replace newlines and following whitespaces by single whitespaces * Update Source/Diagnostics/ReducedDiags/FieldReduction.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-06-17Avoid calling `AddPlasma` when using `AddPlasmaFlux` (#2014)Gravatar David Grote 1-1/+4
2021-06-16AMReX: (#2020)Gravatar Axel Huebl 2-2/+2
Update AMReX to https://github.com/AMReX-Codes/amrex/commit/501626901f500b45fce5102c01d15cd8f74c7187 ``` ./Tools/Release/updateAMReX.py ``` Updated to include https://github.com/AMReX-Codes/amrex/pull/2116 This PR mitigates: - do no allocated managed memory for received buffers as managed (with preferred location on-device): they are used only on host and caused crases with `amrex.the_arena_is_managed=0`
2021-06-16Silver-Mueller: Avoid Managed Memory (#2019)Gravatar Axel Huebl 3-24/+26
Avoid relying on managed memory usage in Silver-Mueller boundary conditions. Previously, we initialized the coefficients on the host, copied them to device and then accidentially used the device memory on the host again, as we calculated some constants. This now keeps the initial host-memory around so we can use it for host-only operations.
2021-06-16don't use RealVector in laser particle initialization. (#2018)Gravatar Andrew Myers 1-4/+4
2021-06-14callbacks.py: Fix bound method py2 -> py3 syntax (#2012)Gravatar peterscherpelz 1-1/+1
2021-06-14AMReX: fc9bc1e3efdaead0253d0a55dcf1abb7abc06bd7 (#2016)Gravatar Axel Huebl 2-2/+2
2021-06-11Fix Offset: PushPX -> evolve_opt (#2011)Gravatar Axel Huebl 3-23/+23
* Fix Offset: PushPX -> evolve_opt Comparing to the `doParticlePush()` above, the `ux`/`uy`/`uz` SoA attributes seem to lack the particle offset in `PushPX`. Also simplifies the offset calculation to reside off-kernel, which saves 8 bytes cmem and some index indirection logic for the compiler. * RigidInjected Particle: Fix Offset Looks like this is missing here, too?
2021-06-09ion_map_ids: static & const access (#2010)Gravatar Axel Huebl 3-6/+9
This fixes the `ion_map_ids` atom-to-number object: - declare static, so the file can be included in multiple translation units - use `.at()`: - missing entries do not cause an insertion - missing entries will throw - access is `const`, so we can declare the whole object `static const` as well.
2021-06-09Add Total Particle & Field Momentum to Reduced Diagnostics (#1908)Gravatar Edoardo Zoni 12-125/+794
* Add Field Momentum To Reduced Diagnostics * Add Particle Momentum To Reduced Diagnostics * Cover Particle/Field Momentum in CI Test reduced_diags * Clean Up Implementation of Photons Case * Fix Bug in Field Momentum and Improve Analysis of CI Test * Fix 'includes' Following @ax3l's Suggestions * Interpolate On The Fly, Do Not Allocate Cell-Centered MultiFabs * Update/Improve Docs * Fix include, Remove Unused Variable * Write Total Momentum Divided by Sum of Weights, Test Output * Write Total Energy Divided by Sum of Weights, Test Output * Divide by Wtot Only if Not Zero * Use New Tuple-Level Reductions Available in AMReX * Use Tuple-level Reduction for Field Momentum
2021-06-08[Docs] openPMD: fix block formatting (compressors)Gravatar Axel Huebl 1-4/+7
Fix .rst block highlighting
2021-06-08Fix kernel timer: use after free (#2006)Gravatar Axel Huebl 4-23/+71
* KernelTimer: Fix Cost Use-After-Free AMReX' ParallelFor is async, the free of the cost function occurs too early can can lead to use-after-free's from the kernel. * CMake: WarpX_GPUCLOCK on CUDA/HIP Make conditional on supported backends. * Add addition to global cost array As we abstracted this from the original research prototypes (https://doi.org/10.5281/zenodo.4708449) to merge this to mainline in 1406, we forgot to add the addition to `*costs` at this point. Measurements were done with the code linked in the zenodo archive. * Cleaning: Move m_cost assignment more in Not too important, but with a default nullptr now possible. * synchronize -> streamSynchronize Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-06-07Call function ReadBCParams() during python execution (#1972)Gravatar roelof-groenewald 12-5/+158
* added ReadBCParams() function call to python execution and added a test of the electrostatic solver executing from python * added separate specification of particle boundary conditions in picmi setup and adjusted the inputs for existing tests to follow the new practice * updated input for rz PICMI test and renamed the electrostatic test to follow standard practice * added arguments for particle boundary conditions to Langmuir RZ test * added dictionary to picmi.py to map from picmistandard field boundary condition specifications to that of WarpX * fixes for failing unit tests; added key, pair 'none' to picmi dictionary of field BCs * also using 'none' for upper boundary condition for RZ test Python_Langmuir_rz_multimode
2021-06-07Added injection of a thermal flux from a plane (#1892)Gravatar David Grote 12-3/+639
* Added injection of a thermal flux from the domain surface * Major fixes to NFluxPerCell injection * Small fixes and clean up * Fixed 'if WARPX_DIMS_RZ' to use ifdef * Small fix to flux_normal_axis error message * Fix typo Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-06-07add m_u (#2003)Gravatar Luca Fedeli 3-0/+5
2021-06-07AMReX: Weekly Update (#2005)Gravatar Axel Huebl 2-2/+2
2021-06-04Disable Separable Compilation (GPU) (#1999)Gravatar Axel Huebl 3-4/+40
* Disable Separable Compilation (GPU) Disable relocatable device code (RDC) aka "separable compilation". We do not need it unless we use in situ vis. This addresses issues with CUDA 11.3.0 on Perlmutter, reduces build complexity and can potentially create more efficient code. * Update AMReX Update to eb2fb8eb11d4df88d5b6c04a68f2971a6c3b97f0, so we include https://github.com/AMReX-Codes/amrex/pull/2083
2021-06-03Spectral: Missing Include (#2001)Gravatar Axel Huebl 1-0/+2
Fix a build error with the latest AMReX version due to a missing include.
2021-06-03remove superfluous semicolon (#2000)Gravatar Luca Fedeli 1-1/+1
2021-06-02 CMake 3.20+ and CUDA: Modernized AMReX (#1998)Gravatar Axel Huebl 4-6/+16
* CMake 3.20+ and CUDA: Modernized AMReX Use modernized AMReX logic for CUDA builds with CMake 3.20+ as supported by the latest AMReX updates. * Resampling Trigger: Missing Include AMReX update triggered missing include: ``` Source/Particles/Resampling/ResamplingTrigger.H(42): error: namespace "amrex" has no member "Real" ``` * Update AMReX Update AMReX to f7fd082bc8ab099d42784f69d6fe49dea3d388a7
2021-06-01openPMD: Expose ADIOS2 Operators (Compressors) (#1983)Gravatar Axel Huebl 4-7/+111
* openPMD: Expose ADIOS2 Operators (Compressors) Expose ADIOS2 Operators (at the moment: one operator max) in WarpX inputs. This allows the user to select ZFP or Blosc compression without changing the input file. We can later on define short-hand notions for this. For now we give the parameters control out for the expert user and document good examples. * Rename: adios2_operator (openPMD) In that scheme, this only works with ADIOS2 atm.
2021-06-01Release 21.06 (#1996)Gravatar Axel Huebl 8-10/+10
* AMReX/PICSAR: 21.06 * WarpX: 21.06
2021-06-01Docs: Ookami (Stony Brook) (#1991)Gravatar Axel Huebl 2-0/+149
* Docs: Ookami (Stony Brook) Add Ookami build instructions. * Add Suggestions from Luca Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> * Add 4x12 MPI/OMP ups, forgot to add * Ookami: Finalize Batch & Storage Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
2021-06-01[mini-PR] improve error message in case of wrong type of a reduced diag (#1986)Gravatar Luca Fedeli 1-1/+1
* improve error msg * eliminate final dot
2021-06-01CoarsenIO: Replace Copy with ParallelCopy (#1992)Gravatar Axel Huebl 1-1/+1
Fix a warning from AMReX by migrating to the newer, recommended interface.
2021-06-01Use Python Indexing in Reduced Diags Headers (#1990)Gravatar Edoardo Zoni 13-208/+124
* Use Python Indexing in Reduced Diags Headers * Use Automatic Counter For Column Numbers
2021-05-31pytables: missing option dependencyGravatar Axel Huebl 1-0/+1
crashes if missing
2021-05-31Docs: Update Summit Perf. Tests (#1994)Gravatar Axel Huebl 5-14/+25
Update instructions to fix new errors
2021-05-31Minor update to Schwinger documentation (#1995)Gravatar Neïl Zaim 1-2/+4
2021-05-28Added new option <diag>.openpmd_encoding (#1979)Gravatar guj 4-20/+81
* Added new option <diag>.openpmd_encoding, which can be either file/group/variable With the encoding being group/variable, there will be one file generated for all iterations. * fixed tab * fixed style * backward compatibility for openpmd-api versions < 0.14 * eol * Update Docs/source/usage/parameters.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * used inline instead of lamba, encoding decision is moved up at FlushFormatOpenPMD * making file based the default so scripts can work as is * Update Docs/source/usage/parameters.rst Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Unify defaults of variables Co-authored-by: Junmin Gu <junmin@login1.summit.olcf.ornl.gov> Co-authored-by: Junmin Gu <junmin@login3.summit.olcf.ornl.gov> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-05-27replaced query with get for a parameter which should be always explicit (#1985)Gravatar Luca Fedeli 1-1/+1
2021-05-27Removed the call to zero out phi data before electrostatic (labframe) field ↵Gravatar roelof-groenewald 2-2/+1
solve, so that the potential of the previous step is used as a starting guess for the solution of the Poisson equation. (#1968)
2021-05-26Parser: Fix Operator Issues; Field Energy: Cleanups (#1987)Gravatar Edoardo Zoni 3-15/+7
* Follow up on PR #1944 * Fix Bug, Use Better Parser Syntax
2021-05-26Docs: Spock (OLCF) (#1988)Gravatar Axel Huebl 3-0/+118
* Docs: Spock (OLCF) Add an initial instruction on how to build on Spock (OLCF) for AMD rocm GPUs (HIP). This works around the missing Cray `PrgEnv-hip` that could be used with the compiler wrappers. * Missing -L: Via $CRAYLIBS_X86_64 Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-05-24using amrex::Math::abs (#1982)Gravatar Revathi Jambunathan 1-1/+2
2021-05-24Add generic field reduction reduced diag (#1944)Gravatar Neïl Zaim 23-88/+505
* Add generic field reduction reduced diag * Make ComputeFieldReduction public * Apply suggestions from code review * Apply suggestions from Luca and Edoardo * Fix syntax error * Fix typo in example input file Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it>
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