CI: Add Missing Python Analysis for EB Test #2147
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ax3l
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Jul 30, 2021
ax3l
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Jul 30, 2021
| @@ -2114,12 +2114,13 @@ dim = 3 | |||
| addToCompileString = USE_EB=TRUE | |||
| restartTest = 0 | |||
| useMPI = 1 | |||
| numprocs = 4 | |||
| numprocs = 1 | |||
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@lgiacome I'll just ping you here for a follow-up issue or PR :)
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* CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated mewarpx with recent changes to _libwarpx.add_particles * fix broken test - test_mepicmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com>
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* Update memaster with new upstream/development (#42) * CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated mewarpx with recent changes to _libwarpx.add_particles * fix broken test - test_mepicmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Add runinfo from warp to warpx * Doc string edit Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com>
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* Added timeseries class * Added flux_diagnostic file * Nruof/runinfo minimal (#44) * Update memaster with new upstream/development (#42) * CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated mewarpx with recent changes to _libwarpx.add_particles * fix broken test - test_mepicmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Add runinfo from warp to warpx * Doc string edit Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Ported more flux diags from warp * Renamed FluxDiag to FluxDiagnostic * Remove js, species conversion in runinfo * Add TimeSeriesPlot * Typo util -> mwxutil * Added test for Timeseries * Added test file for Timeseries * Added appendable array * Added parallel_util and added test for flux diag * Renamed columns and added current checks to test * Update runinfo.py and flux_diagnostic, up to FluxCalcDataFrame * Updated flux_diagnostic.py * Fixed indexing issues, flux diagnostics and plotting now works for injected particles * Added test for flux diag pickle and plot, refactored code * Removed mpi4py, added dill to requirements * Refactored docstring and record_injectedparticles function * revert changes to diag file save locations * Added save_dir to fluxdiagnostic call * Renamed save_dir to write_dir * Refactored code based on review, and made appendable array fit better with python 3 * Removed scraper object Co-authored-by: Nicholas William Ruof <86024944+nruof@users.noreply.github.com> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: nruof <nicholas.ruof@modernelectron.com>
roelof-groenewald
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* Added timeseries class * Added flux_diagnostic file * Nruof/runinfo minimal (#44) * Update memaster with new upstream/development (#42) * CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated mewarpx with recent changes to _libwarpx.add_particles * fix broken test - test_mepicmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Add runinfo from warp to warpx * Doc string edit Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Ported more flux diags from warp * Renamed FluxDiag to FluxDiagnostic * Remove js, species conversion in runinfo * Add TimeSeriesPlot * Typo util -> mwxutil * Added test for Timeseries * Added test file for Timeseries * Added appendable array * Added parallel_util and added test for flux diag * Renamed columns and added current checks to test * Update runinfo.py and flux_diagnostic, up to FluxCalcDataFrame * Updated flux_diagnostic.py * Fixed indexing issues, flux diagnostics and plotting now works for injected particles * Added test for flux diag pickle and plot, refactored code * Change to use upper case variables to use with runinfo * Update runinfo for warpx * Add dill to requirements and remove mpi4py * Remove unused lines from warp * Removed functions that will not be used * doc string format Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> * Spacing * Type in doc string * Doc string update * Update mewarpx/mewarpx/runinfo.py Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> Co-authored-by: kzhu-ME <kevin.zhu@modernelectron.com> Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com>
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* CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Add predefined density profile to parameters documentation (ECP-WarpX#2155) * Release 21.08 (ECP-WarpX#2158) * AMReX/PICSAR: 21.08 * WarpX: 21.08 * initialize guard cells for macroscopic properties (ECP-WarpX#2159) * openPMD: Style Cleaning (Dec/Def) (ECP-WarpX#2160) In our code base, definitions and declarations of functions need a space after their name. This makes them easy to search for. Ref.: https://warpx.readthedocs.io/en/21.08/developers/contributing.html#style-and-conventions * openPMD: Use Steps if != BTD (ECP-WarpX#2157) * openPMD: Use Steps if != BTD For all but back-transformed diagnostics, we can use efficient, temporally sequentially increasing writes to iteration numbers for iterations. This allows us to give a guarantee to HPC I/O libraries on how to arrange data, e.g., we can use ADIOS2 BeginStep() and EndStep(). This enables paths to: - streaming workflows, such as ADIOS2 SST or SSC, where we stage data over the network instead of using files https://openpmd-api.readthedocs.io/en/0.14.0/usage/streaming.html This mitigates: - host-side memory aggregation for ADIOS2 with openPMD `groupBased` iteration encoding https://openpmd-api.readthedocs.io/en/0.14.0/backends/adios2.html#memory-usage * openPMD: Open Iterations Explicitly Explicitly open iterations. Usually, file-open operations are delayed until the first load/storeChunk operation is flush-ed. In parallel contexts where we might want to do only particle writes from a few ranks but no field wries in the future, this will avoid that we run into hangs from the non-collective nature of the first flush. The Streaming API (i.e., Series::writeIterations()) will call this method implicitly as well, but back-transformed diags (particles) might still need this. * openPMD: 0.13.0+ Needed for streaming API and collective open. * openPMD: Missing Include (ECP-WarpX#2162) Fix compile issue on Conda-Forge (Windows with Clang). * PEC Analysis: Remove Unused Imports (ECP-WarpX#2165) Fix a LGTM warning on unused imports in our PEC analysis scripts. * BinaryCollision: use more general particle data structure (ECP-WarpX#2137) * Added B field to plasma lens (ECP-WarpX#2163) * Added B field to plasma lens * Fix B field and updated CI test to include the B field * Updated benchmark * Fixed bug where specifying write_dir for particle diagnostic did not work (ECP-WarpX#2167) * Add particle weight as an explicit argument for _libwarpx.py::add_particles() (ECP-WarpX#2161) * added particle weight as an explicit argument for _libwarpx.py::add_particles() * changes requested during code review * RZ PSATD: Time Averaging for Multi-J Algorithm (ECP-WarpX#2141) * RZ PSATD: Time Averaging for Multi-J Algorithm * Fix Wrong Signs in Bm * Use Time Averaging in CI Test, Update Benchmark * Minor Fix * Shift parsing of physical/mathematical constants from hard-coding to table lookup (ECP-WarpX#2128) * Shift parsing of physical/mathematical constants from hard-coding to table lookup * Make constants map local and static for now, until there's a reason for it to be accessible/modifiable * Accept rewording * Accept rewording Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * Moved some routines to .cpp file (ECP-WarpX#2168) * In add_particles, used None for input parameter values (ECP-WarpX#2169) * More cleanup of particle boundaries (ECP-WarpX#2171) * Moved some routines to .cpp file * Moved more stuff to a header file * make parameter less prone to numerical issues in single precision (ECP-WarpX#2173) * ES Solver: Fix SP Build (ECP-WarpX#2174) Fix HIP: ``` /home/runner/work/WarpX/WarpX/Source/FieldSolver/ElectrostaticSolver.cpp:434:9: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing] 1.-beta[0]*beta[0], 1.-beta[1]*beta[1], 1.-beta[2]*beta[2])}); ^~~~~~~~~~~~~~~~~~ /home/runner/work/WarpX/WarpX/build_sp/_deps/fetchedamrex-src/Src/Base/AMReX_SPACE.H:151:31: note: expanded from macro 'AMREX_D_DECL' ^ /home/runner/work/WarpX/WarpX/Source/FieldSolver/ElectrostaticSolver.cpp:434:9: note: insert an explicit cast to silence this issue 1.-beta[0]*beta[0], 1.-beta[1]*beta[1], 1.-beta[2]*beta[2])}); ^~~~~~~~~~~~~~~~~~ ``` * EB: RZ Warnings (ECP-WarpX#2176) Not an implementation yet, just adding aborts and silencing warnings. * fix typo (ECP-WarpX#2175) * Fix: Performance Tests (Boundary) (ECP-WarpX#2178) The performance tests were aborting since we changed the boundary condition inputs last month. This fixes it. * CI: Cover Performance Tests (ECP-WarpX#2179) * CI: Cover Performance Tests Make sure their syntax stays up-to-date. * Performance Test in CI: Fake Output Add "fake" output so we do not have unused variables when the tests are run. * reverted (or fixed) various unneccesary changes between ME fork and upstream/development Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Co-authored-by: David Grote <grote1@llnl.gov> Co-authored-by: Kevin Z. Zhu <86268612+KZhu-ME@users.noreply.github.com> Co-authored-by: Phil Miller <unmobile+gh@gmail.com> Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>
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* Test file for particle scraping * Added wrapper to get number of particle species tracked by the scraper Not sure if this is going to be useful, but it demonstrates a method to get information from the ParticleBoundaryBuffer into Python. * Stubbed out the main wrapper functions * Added parameters to wrapper * Added wrapper for getting the number of particles scraped of a species on a boundary * Added timeseries class * Added flux_diagnostic file * Nruof/runinfo minimal (#44) * Update memaster with new upstream/development (#42) * CI: Add Missing Python Analysis for EB Test (ECP-WarpX#2147) * CI: Add Missing Python Analysis for EB Test * Use 1 MPI Process for Azure * a few _rt (ECP-WarpX#2146) * PSATD: div Cleaning Implemented only with psatd.J_linear_in_time=1 (ECP-WarpX#2142) * BTD: Don't Flush If Written (ECP-WarpX#2148) Written BTD buffers for lab snapshot data are reset to zero size (count). When we do the final write of all partly filled buffers in `FilterComputePackFlushLastTimestep`, we should not write such already completed backtransformed lab snapshots again. * openPMD: `groupBased` Option Missing (ECP-WarpX#2149) The `groupBased` iteration encoding (input: `g`) was not parsed. * Remove predefined constants from example input files (ECP-WarpX#2153) * BTD_ReducedSliceDiag: BTD Plotfiles (ECP-WarpX#2152) By accident, the 2nd test did not use plotfile output. * Allow extra particle attributes (besides ux, uy, uz and w) to be set at particle creation in AddNParticles() (ECP-WarpX#2115) * exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index * added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation * added function to get index of a particle component given the PID name * changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id * changed warpx_addRealComp to accept a species name as input and only add the new component for that species * added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime * changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index * updated test according to PR ECP-WarpX#2119 changes * removed unneeded BL_ASSERT(nattr == 1) statement * fixed bug in add_particles to correctly determine the number of extra attributes * fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species * use isinstance(attr, ndarray) rather than type(attr) is np.ndarray * generalize_runtime_comps_io * fix OpenPMD * fix OpenPMD * fix plot flags in WritePlotFile * fix offset and comment * changed extra pid test to not use an underscore in the pid name * switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays * License update in test file Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * fix typo * added a test with unique_particles=False * Apply suggestions from code review Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated docstring and comments Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> * updated mewarpx with recent changes to _libwarpx.add_particles * fix broken test - test_mepicmi.py Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Add runinfo from warp to warpx * Doc string edit Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> * Ported more flux diags from warp * Renamed FluxDiag to FluxDiagnostic * added picmi arguments to scrape particles at the domain boundary * Remove js, species conversion in runinfo * Added wrapper to get the full particle buffer into python * rearanged the getBuffer properties code a little * Added test for Timeseries * Added test file for Timeseries * Added docstrings +other suggested changes * Added appendable array * Added num_particles_impacted_boundary docstring * fixed mistake in docstring * Changed boundary parameter to be a string for clarity * Fixed issue with the boundary parameter for scraping * Added parallel_util and added test for flux diag * Added appendable array * initial commit of scraping diagnostic functionality added to assemblies.py - does not work yet * changes that should be included in upstream PR as well * partly working implementation of SurfaceFluxDiag * Added wrapper to get number of particle species tracked by the scraper Not sure if this is going to be useful, but it demonstrates a method to get information from the ParticleBoundaryBuffer into Python. * Stubbed out the main wrapper functions * Added parameters to wrapper * Added wrapper for getting the number of particles scraped of a species on a boundary * added picmi arguments to scrape particles at the domain boundary * Added wrapper to get the full particle buffer into python * rearanged the getBuffer properties code a little * Added docstrings +other suggested changes * Added num_particles_impacted_boundary docstring * fixed mistake in docstring * Changed boundary parameter to be a string for clarity * Fixed issue with the boundary parameter for scraping * Fixed issue with the boundary input for scraping stats wrapper * Added demonstration of particle scraping wrapper * Added analysis.py file * Fix typo in one of the dimension maps Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Added before esolve to warpx evolve * added test for the scraped particle buffer wrappers * added a comment for a needed future improvement * Moved python PICMI particle boundary scrape test * Add support for EB buffer * protect for AMREX_USE_EB, static_assert that EB and RZ aren't both on. * fix unused * add inputs file * add test * fix bugs, remove print * fix test * fix test path. * remove no-op code * adding clear particles method * attempt at adding time stamp * Readded python test files * Renamed test file to the correct name * Renamed test file to the correct name * Removed old test * added special functionality to get the timestep at which particles were scraped * added special functionality to get the timestep at which particles were scraped * removed debug print * added python wrapper for the clearParticles() function of the scraper buffer * added special wrapper function to get the timesteps at which the particles in the boundary buffer were scraped * adapted the record_scrapedparticles function to work with data from multiple tiles * added python wrapper for the clearParticles() function of the scraper buffer * added special wrapper function to get the timesteps at which the particles in the boundary buffer were scraped * updated test to match the non-PICMI test for the particle scraper buffer * Fixed formatting mistake in docstring * removed duplicate get_particle_boundary_buffer function * Fixed 'metools' reference in docstring Co-authored-by: Nicholas William Ruof <86024944+nruof@users.noreply.github.com> * Start to mewarp flux diag accuracy test * Progress on flux diag accuracy test * Renamed some metools to mewarpx * quick fix for runinfo RecursionError * Finished porting test and moved it into test_flux_diagnostic.py * Add note about energy and charge multiplied by -1 for scraped particles Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com> * Removed whitespace * Add newline to docstring in _libwarpx.get_particle_boundary_buffer * Remove test_particle_scraping_stats * Changed mcc_wrapper to add E_total pid to all species * Cleanup from code review - Removed some newlines that aren't upstream - Removed some unused imports in the flux diag test - Added a newline in a docstring * Move code for enabling scraping into init_scraper - Also remove the init_scraper flag because init_scraper() is called from init_conductors() * removed test_calc_dt, which I accidently added * fixed issue with printing currents for each conductor during flux diag output and other requested change from PR review Co-authored-by: mkieburtz <michaelkieburtz@gmail.com> Co-authored-by: kzhu-ME <kevin.zhu@modernelectron.com> Co-authored-by: Nicholas William Ruof <86024944+nruof@users.noreply.github.com> Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com> Co-authored-by: MaxThevenet <maxence.thevenet@desy.de> Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com> Co-authored-by: atmyers <atmyers2@gmail.com> Co-authored-by: nruof <nicholas.ruof@modernelectron.com> Co-authored-by: Phil Miller <phil.miller@intensecomputing.com>
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The Python analysis for the CI test
embedded_boundary_cubewas missing.Also, I had to use 1 MPI process for the test to pass successfully. The maximum would be 2 on Azure (while it was set to 4 before), but changing it to 2 seems to require a slightly larger tolerance (@lgiacome this might need to be investigated further).