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2022-01-12AMReX/PICSAR: Weekly Update (#2731)Gravatar Axel Huebl 5-5/+5
* AMReX: Weekly Update * Azure: 90->120min Uncached Python builds go just over 90min.
2022-01-12Initialize EB grid data on restart. (#2689)Gravatar Andrew Myers 4-0/+159
* Initialize EB grid data on restart. * Add restart test with EBs. Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com>
2022-01-12Fix PML with anisotropic refinement ratio (#2734)Gravatar Weiqun Zhang 3-82/+90
* Fix PML with anisotropic refinement ratio Use IntVect instead of int for the number of cells in PML so that anisotropic refinement ratio can be properly handled. * Reset Benchmark of Langmuir_multi_2d_MR_anisotropic Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-01-11More efficient PML BoxArray (#2631)Gravatar Weiqun Zhang 17-232/+364
* More efficient PML BoxArray If the union of the grids is a single rectangular domain, we can simplify the process and generate more efficient PML BoxArray. * Update Source/BoundaryConditions/PML.cpp Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions from code review * reset Python_wrappers benchmark * fix the computation of sigmas for the new BoxArray * Revert "reset Python_wrappers benchmark" This reverts commit 2999304571d525076ba6c1f7cbbcef6e9acafabb. * fix warning * fix 1d * initialize to quiet NaN * Reset Benchmark: pml_x_psatd - maximum relative error: 2.50e-06 - new implementation: 10 PML grids - old implementation: 24 PML grids * Reset Benchmark: LaserAccelerationMR - maximum relative error: 2.73e-04 - new implementation: (18,8,8) PML grids - old implementation: (48,18,18) PML grids * Reset Benchmark: LaserOnFine - maximum relative error: 6.44e-05 - new implementation: (2,6,6) PML grids - old implementation: (2,12,12) PML grids * Reset Benchmark: PlasmaAccelerationMR - maximum relative error: 6.84e-04 - new implementation: (10,6,6) PML grids - old implementation: (24,12,12) PML grids * Reset Benchmark: RefinedInjection - maximum relative error: 2.55e-04 - new implementation: (18,8,8) PML grids - old implementation: (48,18,18) PML grids * Reset Benchmark: momentum-conserving-gather - maximum relative error: 7.43e-04 - new implementation: (10,6,6) PML grids - old implementation: (24,12,12) PML grids * Reset Benchmark: subcyclingMR - maximum relative error: 2.41e-05 - new implementation: (6,6,6) PML grids - old implementation: (12,12,12) PML grids * Reset Benchmark: Langmuir_multi_2d_MR - maximum relative error: 1.32e-01 (B numerical artifact) - new implementation: (0,20,20) PML grids - old implementation: (0,52,40) PML grids * Reset Benchmark: Langmuir_multi_2d_MR_psatd - maximum relative error: 1.05e-01 (B numerical artifact) - new implementation: (0,20,20) PML grids - old implementation: (0,52,40) PML grids * Reset Benchmark: Python_LaserAccelerationMR - maximum relative error: 2.73e-04 - new implementation: (18,8,8) PML grids - old implementation: (48,18,18) PML grids * Reset Benchmark: Python_wrappers - maximum relative error: 1.07e-08 - new implementation: 8 PML grids - old implementation: 16 PML grids * Reset Benchmark: pml_psatd_dive_divb_cleaning - maximum relative error: 4.91e-03 - new implementation: 24 PML grids - old implementation: 98 PML grids * Remove an assertion. We will fix it later * Reset Benchmark: Langmuir_multi_2d_MR_anisotropic - maximum relative error: 1.07e-01 (B numerical artifact) - new implementation: (0,16,16) PML grids - old implementation: (0,40,34) PML grids * Reset Benchmark: PEC_field_mr - maximum relative error: 3.98e-02 - new implementation: (0,2,2) PML grids - old implementation: (0,2,2) PML grids (different number of ghost cells on coarse PML patch) Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
2022-01-11Sort the argument list that Python writes to the inputs files (#2732)Gravatar David Grote 1-4/+7
2022-01-09Multi-J: J Always Linear in Time (#2679)Gravatar Edoardo Zoni 21-109/+90
* Remove WarpX::J_linear_in_time * Fix Bug * Implement Deposition of Rho at Half Time * Implement New Equations for E * Fix New Equations for E * Cleaning * Fix Limits of X2, X3, X7 * Implement New Equations for F * Implement New Equations for F * Revert E Equations to Avoid Roundoff Changes * Remove Quadratic Equations * Remove Deposition of Rho at Half Time Step
2022-01-07Particle Buffer for Backtransformed Diagnostics (#1898)Gravatar Revathi Jambunathan 50-414/+1801
* move BTD call before Redistribute * define particle buffer, BTD particle functor, particle filter * select particles on the slice * add particle functors * add Lorentz Transform * fix conflict * add call to loretnz operator * storing Particles in buffer * This is WIP. Added particle buffers, filled them, sent them for flush with number already flushed. Does not work for multiple flushes. Crashes for OpenPMD. * trailing endif after rebase * adding print statements and not flushing particles in OPENPMD if numpart is 0 * last timestep flush is ensured at the end of evolve loop * fix bug in declaring uy uy new and computing uzp * set particle Geom, BA, and DMAP for particle flush with plotfile * set Particle BA Geom DMAP for particle buffer and no BTD transform for force flush * separate compute and pack from flush * Fix Typo: resizeable -> resizable Fixes HDF5 BTD particle output. * new class for plotfile particles for BTD * copy particle_H and DATA and Header. some WIP print statements * Merge plotfile * clean print statements * fix warning message * struct declaration in header, fix warning * doxygen comments and copyright * clean print statements * fix eol and override function warning * tile data * fix output species array size bug * fix access for particle buffer size * clean and move time-update * add cur_time update back * remove cur time update which was called twice * dont access particles flushed already for full diagnostics * cur time must be updated for RigidInjection BTD CI test to pass * temporarily move call to BTD * updating time and calling BTD before movewindow * cleanup * reset benchmarks and analysis script * clean and add comments * fix particle box array, geom, dmap * reset benchmarks for multi_J rz and ElectrostaticSphereEB_mixedBC * wip commit * wip commit * add SI conversion * abort for openpmd bp backend if species is selected. Also write particle output for BTD only if write_species is 1 * add documentation for aborting if adios is used with openpmd and add other BTD input parameters * Apply suggestions from code review commit Axel's suggestions from review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * use bool instead of int * fix doxygen format * using h5 as backend in example test to ensure consistency with abort for particle output. * fix doxygen comment * reset benchmark again for comoving_2d_psatd galilean_2d_psatd multi_J_rz_psatd * reset benchmark for background_mcc * self-review suggestions * reset benchmarks. Update with last snapshot full info * Axel's PR suggestions Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Axel's doxygen fix Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * add comments * fix eol * improved exception handling for stringsteam * PR suggestions * Axels' suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Axel's suggestions :) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * simplify logic * suggestions from review (Axel/Reva) Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * variable name change for clarity * if num particles in tmp array is 0, return * Use new BTD inputs to set up BTD for particles in the corresponding particle container * unused var * fix logic error * speciesID undefined * separate particle and field buffer calls and initialization for BTD. Data common to both are initialized separately * rename variable so it does not ghost existing varname * add more comments * Assert that fields are on * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * redundant function definition * unused variable * unused variable zp * 1D 2D 3D definition * fix else * Apply suggestions from code review Add Prabhat's suggestion Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com> * missing semicolon and ignore xp yp for 1D * resetting benchmarks for boosted sims and mcc sim * temporarily changing tolerance since the relative difference for momentum_z is 3.68e-3 and the current tolerance is 2.5e-3 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> Co-authored-by: Prabhat Kumar <89051199+prkkumar@users.noreply.github.com>
2022-01-04Python Script to Compute PSATD Stencil (#2364)Gravatar Edoardo Zoni 3-0/+482
* Add Python Script Stencil.py * Add More Modular Functions, Docstrings * Only 3D * Parse Error Threshold (Optional) * Move Script from Source/Utils to Tools/DevUtils * Fix EOL White Spaces * Replace Parser with Main, Cleaning * Correct Initial Docstring * Fix Figure Name for Generic Path * Improve Inline Comments * Improve Comment * Remove Unused Import * Add Documentation * Remove Parentheses from if Statements * Rename sin as sin_kn * No Capital Letters in Variable Names * Cleaning Function plot_stencil * Use os.path.join * Improve Comments * Import Python Standard Libraries Before Others * [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>
2022-01-04Add Coulomb collision and nuclear fusion subfolders (#2389)Gravatar Neïl Zaim 11-7/+8
2022-01-04Allow Dirichlet BCs on r boundaries in RZ (electrostatic) (#2714)Gravatar Roelof Groenewald 5-22/+32
* allow Dirichlet BCs in r when r_min != 0 with ES RZ simulations * handle the rmax boundary condition setting properly when rmin == 0 * add ability to specify rmin and rmax potentials through picmi
2022-01-04Release 22.01 (#2718)Gravatar Axel Huebl 11-13/+13
* AMReX: 22.01 * PICSAR: 22.01 * WarpX: 22.01
2022-01-04Docs: Add New Inputs (Manual) (#2717)Gravatar Axel Huebl 1-3/+8
Add the new 1D/2D/3D/RZ AMReX and Python scripts in our user-facing manual section for the LWFA test case.
2022-01-04Docs: Spack Dev - Relax MPL Pin (#2715)Gravatar Axel Huebl 1-1/+1
Relax the pinned version of `matplotlib`, documented in our Spack developer enviornment documentation. This caused problems (tried to re-compile and did not find freetype) on Ubuntu 20.04. We pinned this earlier, since yt was incompatible.
2022-01-04Add PICMI Scripts for LWFA Tests (#2700)Gravatar Edoardo Zoni 18-198/+822
* Add PICMI Script for 2D Case * Add PICMI Script for 3D Case * Cleaning * Add PICMI Script for 1D Case * Add PICMI Script for RZ Case * Remove Old PICMI Script * Remove Old Test Python_LaserAccelerationMR * inputs_3d: Move Inputs From runtime_params * inputs_2d: Move Inputs From runtime_params * Update PICMI Script for 2D Case * Update PICMI Script for 3D Case * inputs_1d: Move Inputs From runtime_params * inputs_2d_rz: Move Inputs From runtime_params * Rename inputs_2d_rz as inputs_rz * Update PICMI Script for 1D Case * Update PICMI Script for RZ Case * inputs_rz: Fix Diagnostic Interval * Fix Diagnostic Interval For All Inputs * Add New Test For Each PICMI Script * Remove Old PICMI Script From Workflow yml Files * Dump RZ Modes for RZ Case * LWFA PICMI: Add Shellbang Add missing shellbang lines. Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-30[pre-commit.ci] pre-commit autoupdate (#2712)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.0.1...v4.1.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2021-12-29Regression Testing: Use Mainline & CMake (#2556)Gravatar Axel Huebl 8-58/+237
* Regression testing: Use mainline * Update WarpX-tests.ini - Add `cmakeSetupOpts =` - Add `-DWarpX_DIMS`: Not an AMReX convention, so we cannot rely on `dim = ...` - Skip building unneeded tools - Add `install_pip` target: Calling `python -m pip wheel .` and install re-using the build directory. This is mainly for our CI Python regression scrips, users and package managers should just use `python -m pip wheel .` and `... install *whl` directly. * LaserInjectionFromTXYEFile: General Exe Generalize executable globber in script * Docs: Update Regression Testing (CMake) * Azure: Ninja Builds (CMake)
2021-12-29CI: mpi4py breaking setuptools API (#2713)Gravatar Axel Huebl 4-9/+29
setuptools keeps breaking its API, which currently breaks `mpi4py` installs. Until a new mpi4py release is cut, this will serve as a work-around
2021-12-23Test particle scraping for EB in RZ. (#2691)Gravatar Yinjian Zhao 7-14/+129
* Modify WarpXFaceExtensions.cpp and WarpXInitEB.cpp. * Remove an assertion. * Update particle scraping for RZ * Apply suggestions from code review * Add automated test. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix CI issues * Change permissions 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>
2021-12-23Adding staircased EB in the PMLs (#2693)Gravatar Lorenzo Giacomel 10-73/+246
* Adding EB to PMLs * Fix to guard cells * Initializing EB data only if AMREX_USE_EB * Not compiling at all EB initialization when EB is off * Bug fix (wrong order of PML init arguments)
2021-12-22Docs: Add Missing Default for warpx.serialize_ics (#2706)Gravatar Edoardo Zoni 1-1/+1
2021-12-23removed distinct functions computePhiRZ and computePhiCartesian since these ↵Gravatar Roelof Groenewald 2-177/+51
function now share mostly the same code (#2709)
2021-12-22Change _libwarpx.py functions to LibWarpX class methods (#2696)Gravatar Peter Scherpelz 16-2016/+1927
* Initial attempt at moving function into LibWarpX * Bugfix - undefined structs in get_particle_theta This is untested, identified by IDE/visual inspection only * Unify newlines * Delete libwarpx.clight (duplicated picmi.py) See picmi.constants.c * Change function descriptive comment to docstring Also remove extra newline in __init__ beginning. * Replace pywarpx/_libwarpx calls appropriately * Fix atexit register of finalize function * Reorder WarpX.py imports for pre-commit * Use picmi.Simulation.extension = libwarpx alias This will hopefully preempt user script changes if we restructure things to allow multiple WarpX runs to be done within a single Python script. * Fix libwarpx ref in WarpX.getProbLo/getProbHi * Update get_particle_boundary_buffer doc reference
2021-12-22Add embedded BC in RZ. (#2602)Gravatar Yinjian Zhao 11-74/+184
* Start to add embedded BC in RZ. * Add . * Remove scaling * Fix compilation error * Update * Can compile. * Add call linop.setRZ(true). * Remove lines 264 to 312 and 343 to 345. * Add assert. * Remove an assert. * Add an automated test. * Change to MLEBNodeFDLaplacian. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix compilation error * Update the test selection * Correct compilation error * Move test to another worker * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add new required argument * Update Examples/Tests/ElectrostaticSphereEB/inputs_rz * Update Examples/Tests/ElectrostaticSphereEB/analysis_rz.py * Update analysis script 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>
2021-12-22ParticleMoments: Deduct Lambda Ret Type (#2705)Gravatar Axel Huebl 1-8/+3
We can auto-deduct the return type of the tuples in the particle moments lambdas by using the `amrex::makeTuple` factory function.
2021-12-21Doxygen: include `static` functions (#2701)Gravatar Axel Huebl 1-1/+1
We use this for ODR-friendly specifications of public functions in ABLASTR. https://stackoverflow.com/a/22103109
2021-12-21Add runtime option to use DM that is 'similar' to the mother grids in the ↵Gravatar Andrew Myers 6-6/+27
PML. (#2665) * add runtime option to use DM that is 'similar' to the mother grids in the PML. * update amrex * toggle similar dm * add runtime option to use DM that is 'similar' to the mother grids in the PML. * toggle similar dm * bump tolerance * document option * Change default PML behavior for psatd_dive_test Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
2021-12-21pre-commit: Python imports (#2686)Gravatar Axel Huebl 118-238/+478
* pre-commit: Python imports Add two new Python rules to: - remove unused imports - sort imports according to PEP8 * pre-commit: Python imports Add two new Python rules to: - remove unused imports - sort imports according to PEP8 `.editorconfig`: isort options https://github.com/PyCQA/isort/wiki/isort-Settings * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * move import os (mpl) * move import yt (mpl) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Cleanup around matplotlib.use * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Cleaning: double np and lib Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2021-12-21Update AMReX (RZ Poisson) (#2699)Gravatar Axel Huebl 4-4/+4
Update AMReX to the latest `development`.
2021-12-21CMake: openPMD on by default (#2698)Gravatar Axel Huebl 12-18/+18
openPMD builds are stable enough to be default-ON. Due to lacking heuristicst, we don't enable openPMD by default in GNUmake. (Further environments hints, e.g. `PKG_CONFIG_PATH`, or a system-path install are needed there.)
2021-12-21RZ correction in 2d RZ Poisson slver (#2697)Gravatar Weiqun Zhang 1-0/+2
Call MLNodeLaplacian::setRZCorrect, even when it's redundant when the coordinate system is 2d rz, so that the solver does not depend on the coordinate system set in amrex::Geometry.
2021-12-21Inputs: `geometry.dims` option (#2685)Gravatar Axel Huebl 112-168/+221
* Docs: `geometry.dims` option Add a new, required option to specify the geometry of an inputs file at runtime. * Check & Report Runtime Dims Mismatch * Examples: add `geometry.dims` * Deprecation Warning: `geometry.coord_sys` * PICMI: `geometry.dims` * Improve error message sounds a bit better * Improve Doc Description Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
2021-12-20[pre-commit.ci] pre-commit autoupdate (#2695)Gravatar pre-commit-ci[bot] 1-1/+1
updates: - [github.com/pre-commit/pre-commit-hooks: v2.4.0 → v4.0.1](https://github.com/pre-commit/pre-commit-hooks/compare/v2.4.0...v4.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2021-12-20AMReX: Weekly Update (#2694)Gravatar Axel Huebl 4-4/+4
2021-12-20AMREX_ALWAYS_ASSERT -> AMREX_ASSERT for deposition bounds checks (#2688)Gravatar Andrew Myers 2-4/+4
* AMREX_ALWAYS_ASSERT -> AMREX_ASSERT for deposition bounds checks * fix unused * Apply suggestions from code review * Apply suggestions from code review * Simpler ignore + comment Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-19For Python inputs, values with temporary variables are wrapped in quotes (#2690)Gravatar David Grote 1-4/+8
2021-12-16Generalize Analysis Scripts: Number of Digits (plt) (#2683)Gravatar Axel Huebl 38-54/+100
* Update Scripts to Handle New File Names * Use glob in Analysis of Collision Tests * Use rstrip in Analysis of Collision Tests * Regex: Match ends-in-digits Thanks Phil! :) Co-authored-by: Edoardo Zoni <ezoni@lbl.gov> Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
2021-12-16added RZ support in libwarpx function _get_boundary_number (#2680)Gravatar Roelof Groenewald 1-1/+3
2021-12-16Wrap shared object in a class to control its loading (#2637)Gravatar David Grote 19-582/+599
* Wrap shared object in a class to control its loading * Fix libwarpx attribute references * Updated callbacks.py for updated libwarpx * Removed the wx module plus other clean up * Further revision of how to use the pywarpx module. Now, _libwarpx should not be imported by external scripts except in special circumstances. * Updated documentation * Clean up end of line whitespace * Added more wrapping routines plus some clean up * Fixed use of pywarpx in two examples * Fix for getistep * Fixed for the EB Python interface * Silence a warning for our wrapper Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-16AMREX_SPACEDIM : EB, Filter, Laser, Utils, and Diagnostics (#2677)Gravatar Prabhat Kumar 26-153/+153
* AMREX_SPACEDIM : EB and Filter * AMREX_SPACEDIM : Laser * AMREX_SPACEDIM : Utils * AMREX_SPACEDIM : Diagnostics * Fix Typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * AMREX_SPACEDIM : Warpx.cpp * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp 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> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-12-16Adding new inputs to picmi.ElectromagneticSolver (#2676)Gravatar Lorenzo Giacomel 1-0/+8
2021-12-16Doxygen: Fix Diags, FieldSolver, Parallelization & Particles (#2662)Gravatar Axel Huebl 29-24/+101
* Doxygen: Fix Diags, FieldSolver, Parallelization & Particles * Apply suggestions: Remi Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> * Apply suggestions: Roelof Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Apply suggestions: Luca Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Andrew * Apply suggestions: Edoardo Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> * Apply suggestions: Neil Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> * Apply suggestions: Roelof * Apply suggestions: Weiqun Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov> Co-authored-by: Remi Lehe <remi.lehe@normalesup.org> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Luca Fedeli <luca.fedeli@for.unipi.it> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
2021-12-15ABLASTR: Cleanups & Particle Moments (#2675)Gravatar Axel Huebl 12-71/+242
* ABLASTR: Cleanups - lowercase dir - nested directories - nested namespaces - functions: lowercase and snake_case - templates: prefix with `T_` - profiler: doc strings * Add: Particle Moments Co-authored-by: Remi Lehe <rlehe@lbl.gov> Co-authored-by: Remi Lehe <rlehe@lbl.gov>
2021-12-15CI: Azure Cache Ignore Errors (#2678)Gravatar Axel Huebl 1-0/+2
Sometimes, the Azure Pipelines Cache tasks fail because the service is not available, either for download or upload after a successful job. This marks the cache restore and upload steps as allowed to fail.
2021-12-15CI: Reduce Runtime of Some Galilean Tests (#2625)Gravatar Olga Shapoval 8-148/+148
* Modified 'averaged_galilean_3d_psatd' CI test to lower its run time. * Modified 'comoving_2d_psatd_hybrid' CI test to lower its run time. * Modified 'galilean_2d_psatd_hybrid' CI test to lower its run time. * Updated benchmarks.
2021-12-15Docs: Perlmutter Early Science (#2674)Gravatar Axel Huebl 1-0/+2
* Docs: Perlmutter Early Science Document how to perform large runs. * Change comment style Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
2021-12-15Cori: c-blosc Support (#2636)Gravatar Axel Huebl 1-3/+24
Document setting up `c-blosc` on Cori for fast, lossless ADIOS2 openPMD output compression.
2021-12-15Examples: Python ShellBang & Executable (#2673)Gravatar Axel Huebl 84-66/+107
* Examples: Python ShellBang & Executable Make sure that all PICMI scripts and all analysis Python scripts in `Examples/` are: - executable (`chmod a+x`) - start with a shell-bang to `python3` Now, all scripts can be run directly without a `python3 ...` prefix and also default to the only right executable of Python on older systems. (New systems always have a `python3` alias, too.) * Revert a moved numpy
2021-12-15CI: Remove (`particle_`)`tolerance` (#2669)Gravatar Axel Huebl 2-189/+16
We compare field and particle tolerances now without silver files, using our checksum API. This allows us to reduce CI time a bit by skipping the build of plotfile tools.
2021-12-15pre-commit: check json (#2670)Gravatar Axel Huebl 1-0/+1
2021-12-14Fix: Missing EB `analysis.py` Permissions (#2672)Gravatar Axel Huebl 1-0/+0
This failed in other PRs: ``` PermissionError: [Errno 13] Permission denied: './analysis.py' ```
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