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Remerge upstream/development and gradient descent (#182)
* Apply shift in BTD for zmax different than 0 (ECP-WarpX#3091) * Include shift in t_lab when `zmax` is different than 0 * Revert "Include shift in t_lab when `zmax` is different than 0" This reverts commit 5f786f2. * Apply shift in BTD for zmax > 0 * AMReX: Weekly Update (ECP-WarpX#3095) * Fix miscellaneous issues found with clang tidy (ECP-WarpX#3083) * fix miscellaneous issues found with clang tidy * fix miscellaneous issues found with clang tidy * moved default constructors and destructors to header * fix issue * Use default again * Add a python script to generate timestep duration plots (ECP-WarpX#3036) * add script to generate timestep duration plots * disable transparent background * fix bugs * fix bug in doc * Update plot_timestep_duration.rst * add permissions * using argparse * using if __name__ == __main__: * add page in workflows * Update Docs/source/usage/workflows.rst * added missing file * Formatting * Apply shift for zmax>0 in old BTD (ECP-WarpX#3094) * Apply shift for zmax>0 in old BTD * BTD: also shift t_slice_lab * Use uniform error message formatting for all the amrex::Abort() calls in WarpX.cpp (ECP-WarpX#2952) * use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp * fixed bug * fixed bug * Update Source/WarpX.cpp * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <[email protected]> * Use queryWithParser to Parse v_particle_pml (ECP-WarpX#3096) Use queryWithParser, instead of query, to parse v_particle_pml, in order to support functions like sin, cos, sqrt, etc. * Fix Wrong Abort Message for PSATD w/ Time Averaging (ECP-WarpX#3098) * Doc: Improve Doxygen Links (ECP-WarpX#3099) * Doc: Improve Doxygen Links - download also openPMD-api tag files & link them - improve developer page: clearer links * Update: .gitignore * Fix Mirrors for RZ (NullifyMF) (ECP-WarpX#3101) * Fix Breaking Pip 22.1 Logic (ECP-WarpX#3106) * CI: Fix Windows Pip's `--no-build-isolation` says we have to have build-deps pre-installed. But Pip does offer no option to install those from `pyproject.toml`. * Pip 22.1: in-tree-build default And dropped the old option with a fatal error... classic. * Pip no-build isolation: pre-install build tools not installed in non-isolated builds - we want isolated builds, because they have a derministic path that we can cache with ccache * fix bug (ECP-WarpX#3110) * Fix Laser Injection in RZ (ECP-WarpX#3104) * Add STL files support in pywarpx (ECP-WarpX#3089) * Added STL files support in pywarpx * Add new EB bucket * Added name to file headers * Fixing year in file headers * Checking that stl file and imp function are not both specified * Renamed EB bucket to EB2 * Adding STL documentation * Implement suggestions from code review Co-authored-by: lgiacome <[email protected]> * Stricter Tolerance for 3D Langmuir Tests (ECP-WarpX#3097) * CI: HIP with https (ECP-WarpX#3111) Small update in HIP docs: now supports HTTPS: https://rocmdocs.amd.com/en/latest/Installation_Guide/Installation-Guide.html#ubuntu * Add Headers to Input File Written by PICMI (ECP-WarpX#3093) * Add Headers to Input File Written by PICMI * Commit Suggestion by @dpgrote * Add Comment * Add Empty Line * Slightly Better Readable with a newline * AMReX/PICSAR: Weekly Update (ECP-WarpX#3112) * AMReX: Weekly Update * PICSAR: Weekly Update * [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#3113) updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.13 → v1.1.14](Lucas-C/pre-commit-hooks@v1.1.13...v1.1.14) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Use uniform error message formatting in more source files (ECP-WarpX#2964) * use WARPX_ALWAYS_ASSERT_WITH_MESSAGE instead of Abort() * fix bug * Update Source/WarpX.cpp Co-authored-by: Axel Huebl <[email protected]> * use more uniform text formatting * fixed bug * fixed bug * using Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed bug * use Utils::TextMsg in more files * fixed last merge conflict * fixed bug * fix indentation Co-authored-by: Axel Huebl <[email protected]> * Avoid resizing ParticleBoundaryBuffer allocation to total particle count (ECP-WarpX#3068) * Avoid resizing ParticleBoundaryBuffer allocation to total particle count * Switch atomic increments over to reductions * Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ (ECP-WarpX#3071) * Lassen (LLNL): ADIOS2, BLAS++ & LAPACK++ Document how to install ADIOS2 (for openPMD `.bp`) and BLAS++/LAPACK++ (for PSATD in RZ) on Lassen at LLNL. * Update: ADIOS2~SST, BLAS++/LAPACK++ w/ ESSL * Add workaround for Libfabric bug on Crusher to job script. (ECP-WarpX#3114) * Add workaround for Libfabric bug on Crusher to job script. * add known issues section for Crusher * ABLASTR: localIDtoGlobal (ECP-WarpX#3115) * ABLASTR: localIDtoGlobal Move the control of `localIDtoGlobal` to ABLASTR for particle IDs. * WarpX: Use ABLASTR now * Clarify error messages when parsing diagnostics input (ECP-WarpX#3122) * Add `do_average` option to the particle fields diagnostic (ECP-WarpX#3067) * Added do_average option to the particle fields diagnostic * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated CI benchmark files * Updated CI benchmark files * Fix ParticleReductionFunctor comment * Changed maps to vector for code simplification * Change do_average to bool Co-authored-by: Hannah Klion <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> * Fix from the merge Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Hannah Klion <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> * fix unnecessary double promotions (ECP-WarpX#3120) * use fwd declaration for WarpXFaceInfoBox (ECP-WarpX#3125) * remove unused enum (ECP-WarpX#3124) * AMReX/PICSAR: Weekly Update (ECP-WarpX#3126) * AMReX: Weekly Update * PICSAR: Weekly Update * [pre-commit.ci] pre-commit autoupdate (ECP-WarpX#3128) updates: - [github.com/Lucas-C/pre-commit-hooks: v1.1.14 → v1.2.0](Lucas-C/pre-commit-hooks@v1.1.14...v1.2.0) - [github.com/hadialqattan/pycln: v1.3.2 → v1.3.3](hadialqattan/pycln@v1.3.2...v1.3.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add new class `NamedComponentParticleContainer` (ECP-WarpX#3100) * Add new class `NamedComponentParticleContainer` * Update docstrings * Fix compilation * Address review comments * Update Doxygen Co-authored-by: Axel Huebl <[email protected]> * Fold Python tests into their corresponding base configurations, to better exploit ccache (ECP-WarpX#3107) * Fold Python tests into their corresponding base configurations, to better exploit ccache * Align 1D Python tests with rest of 1D tests * Remove archaic test exclusions * Reintroduce exclusion of Python_Langmuir test, since it currently fails * Docs: New Perlmutter Default Env, Microarch (ECP-WarpX#3127) * Docs: New Perlmutter Default Env The default environment on Perlmutter is now the one we already used, `PrgEnv-gnu`. Thus, we don't need to switch anymore. * Perlmutter: Build Microarch Tuned for Zen3, which is used on Login and Compute nodes alike: https://docs.nersc.gov/systems/perlmutter/system_details/ * Keep PrgEnv-gnu ... in case it changes again * Comment microarch flags * CMake Pip: Unique Custom Targets (ECP-WarpX#3116) Add a prefix to custom targets so we do not collide if used as a CMake subproject, e.g., in ARTEMIS. * Simplify the function computePhi (ECP-WarpX#3026) * Simplify the function computePhi * Allow to compile RZ without EB * Allow to compile RZ without EB * Deactivate semi-coarsening when both EB and RZ are used * Update Source/FieldSolver/ElectrostaticSolver.cpp Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Axel Huebl <[email protected]> * Specify particle precision (ECP-WarpX#3065) * Add precision to printed PIC parameters * Added WarpX_PARTICLE_PRECISION as a build option * Update types to ParticleReal * Updated libwarpx to inject particles with correct ParticleReal type * Fix syntax error * Add logic to avoid duplicate definitions * Use correct ParticleReal type in add_particles * Cleaned up code, addressed comments * Update Python/pywarpx/_libwarpx.py Co-authored-by: Peter Scherpelz <[email protected]> * Removed redundant functions, fixed some typing * Modified template functions * Cast d_w to Real * Fixed failing tests * Cast types to be consistent * removed in-tree-build from pip command * Added GPU device macros to PDim3 methods * rerun tests * Removed unecessary casting, update calls to use PDim3 instead of XDim3 * Refactored comments * Added mcc fields double precision, particles single precision test * Updated casting and formatting * Removed cast, updated declaration Co-authored-by: Peter Scherpelz <[email protected]> Co-authored-by: Peter Scherpelz <[email protected]> * Test Filter: Include Python Langmuir (ECP-WarpX#3129) * Test Filter: Include Python Langmuir * Reset Benchmarks (Python Langmuir) Co-authored-by: Tools <[email protected]> * Reactivate Multi-J RZ PSATD Checksums (ECP-WarpX#2459) * Try to reactivate Multi-J RZ PSATD checksums * Reduce size of test and add debug prints * No MPI in test * Revert "Reduce size of test and add debug prints" This reverts commit c865671. * Revert "No MPI in test" This reverts commit 1a0a682. * Remove close to zero values from field outputs * Update benchmarks * PML.cpp: missing util include (ECP-WarpX#3138) fix a missing include for `PML.cpp` * Fix: Field Probe no-MPI Gather (ECP-WarpX#3134) In AMReX, Gather without MPI was implemented as a no-OP. This applies a work-around so we can patch already released WarpX versions. * SpectralFieldDataRZ: Missing Utils Include (ECP-WarpX#3140) * Fix: Install ABLASTR (ECP-WarpX#3141) Since ABLASTR is a proper library now, we need to install it as well. * Write Inputs to `warpx_used_inputs` (ECP-WarpX#3132) Write a general file `warpx_used_inputs` that contains all inputs of a simulation. This is needed, since we add & overwrite the inputs parameters in the inputs file with command-line options regularly. Writing the actually used inputs increases reproducibility of such workflows, especially in unsupervised scripted runs/optimizations. * Docs: Improve `collision_name>.species` (ECP-WarpX#3143) ... for `background_stopping` we also just use one species. * Remove Extraneous `WARPX_DIM_RZ` in Gaussian Laser Init (ECP-WarpX#3144) * move serialization to ablastr (ECP-WarpX#3145) * Use Utils::TextMsg::Err and WARPX_ALWAYS_ASSERT_WITH_MESSAGE in more files (ECP-WarpX#3117) * use formatted error messages * fixed bug * fixed bug * fixed bugs * fixed bug * Move MsgLogger to ablastr (ECP-WarpX#3148) * move Msg Logger to ablastr * fixed bug * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed bug Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * AMReX: Weekly Update (ECP-WarpX#3147) * Docs: Science Highlights (ECP-WarpX#3139) * Docs: Science Highlights Document science papers of ours and users that use WarpX. * Add: More LWFA Preprints 🚀 * Use Ordered (Numbered) Lists * Add 3D tests for proton boron fusion (ECP-WarpX#2450) * Add 3D tests for proton boron fusion * Add execute permission to analysis script * Fix Checksum path * Increase tolerance for energy check * Update benchmarks * Specify type of exception in try expect block * Apply suggestions from code review Co-authored-by: Axel Huebl <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add review suggestions Co-authored-by: Remi Lehe <[email protected]> * Safe Runtime: <species>.do_not_deposit = 1 Co-authored-by: Remi Lehe <[email protected]> * Remove division by zero warning in python analysis script * Update cross-section in the E > 3.5 MeV range * Increase some tolerances * Update benchmark Co-authored-by: Remi Lehe <[email protected]> Co-authored-by: Axel Huebl <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Revert ""Gradient descent" convergence to steady-state (#176)" This reverts commit e31338f. * update changelog and version * Gradient Descent (#181) * Added ArbitraryDistributionVolumeEmitter * Updated particle weight calculation * renamed thermionic_emission test directory to emission * arbitrary seed from uniform distribution * Bug fixes and changes to test * add test for arbitrary seeding * Changed position sampling, added test * Removed unused imports and code * revert traceback printout * Added comments for binning particle positions * increased rtol for test * Allow input of any 2d array, add interpolation of 2d array onto current simulation grid * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated changelog * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated changelog * update version * created steady_state_descent.py file * Added coarsening algorithm * Added ability to read numpy data and coarsen grid * Added regression function calculation * Solve system of equations rather than curve fit * Use skimage block_reduce * Hard coded inverse exponential solve * take mean if exponential equation can't be solved * Added special cases to use linear regression * Update docstring * Added command line arguments * Modified linear regression logic and added main function * Added entry point * Change output file name * Change output file name * Fixed interpolate grid * updated arbitrary distribution emitter test * Fix interpolation logic * Changed to take in exact prediction timestep rather than a multiple * Added ability to specify save directory * Updated docstrings, removed unneeded files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added gradient descent test, refactored code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Changed test parameters * Increase rtol of arbitrary seed test by 0.01 * Update mewarpx/mewarpx/utils_store/plasma_density_oracle.py Co-authored-by: Roelof Groenewald <[email protected]> * Update changelog * Update version * Add controller for plasma density oracle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * WIP oracle control * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Allow oracle control bins to be overridden * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added command line arguments * Fixed bugs, added info logging * added ability to modify run_script * removed unnecessary code * Cleaned up code * Refactored code to be clearer * Update docstrings * Added test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added documentation about oracle_control * Updated changelog * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fixed TOTAL_TIME calculation * update wheel in docker build * change numpy to oldest-supported-numpy for docker * Updated formatting and documentation Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <[email protected]> Co-authored-by: Axel Huebl <[email protected]> Co-authored-by: Luca Fedeli <[email protected]> Co-authored-by: amadou38 <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: David Grote <[email protected]> Co-authored-by: Lorenzo Giacomel <[email protected]> Co-authored-by: lgiacome <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Phil Miller <[email protected]> Co-authored-by: Andrew Myers <[email protected]> Co-authored-by: Hannah Klion <[email protected]> Co-authored-by: Phil Miller <[email protected]> Co-authored-by: Peter Scherpelz <[email protected]> Co-authored-by: Peter Scherpelz <[email protected]> Co-authored-by: Tools <[email protected]> Co-authored-by: Neïl Zaim <[email protected]> Co-authored-by: Ryan Sandberg <[email protected]>
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