Add filter for particle histogram #1643
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NeilZaim
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Jan 21, 2021
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| import sys | ||
| sys.path.insert(1, '../../../../warpx/Regression/Checksum/') | ||
| import checksumAPI | ||
|
|
||
| filename = sys.argv[1] |
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It looks like the checksum were not tested in the analysis script, so I added them.
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So the benchmarks were failing but it seems to be unrelated to this PR (I tried reverting the changes of the PR, except for these lines, which activate the checksum test in the analysis script, and got the same thing).
Most notably, the electric field checksums are now higher by a factor 100 (almost exactly) and the magnetic field checksums are now higher by a factor 10000 (almost exactly). Should we worry about this? (for now I've updated the benchmark but this can be reverted)
@MaxThevenet Do you know if there is a reason why the checksum were not tested in this analysis script?
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Hm, WarpX-tests.ini might need to add to runtime_params = the options warpx.do_dynamic_scheduling=0 warpx.serialize_ics=1 for this test ([initial_distribution])?
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Good idea, I've added that in the latest commit. It didn't change the benchmarks though (it would have been surprising if this changed the magnetic field by 4 orders of magnitude).
The difference is probably due to something that changed in the code since those benchmark values were added. Do you think it's worth tracking it down?
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I think it's fine - the B-field is essentially close to zero and we changed the microscopic random number generator in the PR. LGTM, this test is more about the init of the particles, which looks good (densities, positions, momentum, et al.)
NeilZaim
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Jan 21, 2021
| @@ -22,6 +22,7 @@ warpx.cfl = 1.e-8 | |||
| ############ PLASMA ############# | |||
| ################################# | |||
| particles.species_names = gaussian maxwell_boltzmann maxwell_juttner beam | |||
| particles.rigid_injected_species = beam | |||
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I've added this because we currently have some unused parameters (zinject_plane, rigid_advance, etc.).
NeilZaim
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…rpX#1624) * Fix bug in momentum-conserving interpolation function * Reset checksum benchmark for CI test momentum-conserving-gather Unused Params: Check after Step 0 (ECP-WarpX#1596) An early check for unused parameters after the first step. Add Superparticle version of getParticlePosition. (ECP-WarpX#1640) * Add Superparticle version of GetParticlePosition. * move unpack_particle to a free function and rename * no longer need SuperPType * Update Source/Particles/Pusher/GetAndSetPosition.H * remove templating from get_particle_position * remove template * Add missing include Co-authored-by: Axel Huebl <[email protected]> Distribution mapping and cost plotting (ECP-WarpX#1444) * Distribution mapping and cost plotting Cleanup Cleanup Cleanup EOL Unused import * Cost initializes to 0.0 * plot slices of 3D * WIP * WIP docs * docs * docs * docs * docs * docs * docs * docs * docs * EOL SpeciesProperties: C, N, O, Cu (ECP-WarpX#1638) * SpeciesProperties: C, N, O, Cu Add more ionic species as pre-defined particle species. * Cu: Add to Ionization Energies Fix 2D: ParticleHistogram (ECP-WarpX#1635) Fix out-of-bounds access in particle histogram in non-3D. Fix FilterFunctor in non-3D (ECP-WarpX#1633) Fix an out-of-bounds access to positions in 2D & RZ for filter functors. openPMD: ionizationLevel (ECP-WarpX#1622) * openPMD: ionizationLevel Write out the ionizationLevel with openPMD. * openPMD Record Repetitions: Use Lambdas openPMD: Particle Filter (Container) (ECP-WarpX#1632) * openPMD: Particle Filter (Container) A fresh implementation of particle filters for openPMD diagnostics using the generalized `PhysicalParticleContainer` approach that we also use in plotfiles 🎉 * Ion Example: Filter & Coarsen Test diagnostics filter & coarsen functions in CI. Test reduced diagnostics (histograms). Define: _OPENMP -> AMREX_USE_OMP (ECP-WarpX#1520) * Define: _OPENMP -> AMREX_USE_OMP Replace the define check of `_OPENMP` with the explicit backend control of `AMREX_USE_OMP` for parallel constructs. Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency pulls it in for linear algebra, I/O, etc. This can led to confusion if the user explicitly requested a serial build. Also, we might want to use OpenMP functionality here and there for auxiliary functions w/o having to use the AMReX OpenMP backend, i.e. because we compile for GPUs. * Add missing amrex::Gpu::notInLaunchRegion Start: PerformanceHints After Init (ECP-WarpX#1630) Start a helper routine that gives performance hints after initialization of the simulation. Fix number of guard cells in PML with 2D PSATD (ECP-WarpX#1648) Remove unused lines about particle filters (ECP-WarpX#1646) Add parameter for default galilean velocity (ECP-WarpX#1097) * Add parameter for default galilean velocity * Apply suggestions from code review Co-authored-by: Edoardo Zoni <[email protected]> * Fix bug in constructor of PhysicalParticleContainer * Use new input parameter in CI test Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> Cleaned up field diagnostic in picmi interface (ECP-WarpX#1649) Use pinned memory for tmp particles in diags. (ECP-WarpX#1644) * Use pinned memory for tmp particles in diags. * openPMD: pinned memory (tmp particles) Co-authored-by: Axel Huebl <[email protected]> Replace an always false test with an abort (ECP-WarpX#1655) * replace always false test with abort * fix bug [mini-PR] Broken link to scripts (ECP-WarpX#1651) CI: Ubuntu-latest -> 20.04 (ECP-WarpX#1654) Start Embedded Boundary development (ECP-WarpX#1641) * Start Embedded Boundary development Modify the build system for embedded boundary (EB) support. Currently EB is a compile time option that must be explicitly enabled. For GNU Make, one can enable it with `USE_EB=TRUE`, whereas for CMake, `-DAMReX_EB=ON`. Later we could decide to enable EB by default with all regular geometry. Add a simple geometry initialization function, WarpX::InitEB. By default, the geometry is all regular. A few basic types such as box, cylinder, plane, sphere, etc. are supported via ParmParse runtime parameters. See `amrex/Src/EB/AMReX_EB2.cpp` for more details. Later, we could build more complex geometry using constructive solid geometry (CSG). ( https://en.wikipedia.org/wiki/Constructive_solid_geometry ) See `amrex/Tutorials/EB/GeometryGeneration` for an example of CSG. There is also a STL ( https://en.wikipedia.org/wiki/STL_(file_format) ) approach under development in AMReX. Add a new member, m_factory, to WarpX class. This object can be used to obtain geometry information such as whether a cell is cut, edge centroids, etc. Currently we are not using these factories to build MultiFabs for field data to embed the geometry information into the data containers. We could do that later if it is needed or it makes things more convenient. Nevertheless, this should be sufficient to start the EB development of the field solver. It's not clear to me yet how many ghost cells are needed for the geometry information. It's currently one, and can be adjusted. In the future, when particle and embedded boundary interaction is considered, we can use `amrex::FillSignedDistance` function to obtain signed distance function on the nodes. With that information, one should be able to determine where and when a particle collides with the embedded boundary. * resize factory vector * CMake: Require AMReX_EB for embedded boundaries * Add AMReX_Config.H et al. Explicit includes are most robust to make sure defines are set with future refactorings. * rename Factory fieldFactory Co-authored-by: Axel Huebl <[email protected]> Add filter for particle histogram (ECP-WarpX#1643) * Add filter for particle histogram * Update benchmarks * Update benchmark again * Use serialize_ics in test + proper usage of RandomEngine * Laser-Ion Acc. (2D3V): Test Hist Filter Co-authored-by: Axel Huebl <[email protected]> Take time step into account to compute guard cells for J and rho (ECP-WarpX#1607) * Use IntVect for ng_J and ng_rho * Compute guard cells for J and rho based on dt * Reset some CI benchmarks * Fix rebase commit * Add back +1 cell for rho: fix remaining out-of-bound accesses * Simplify ASSERTS using new interface of amrex::numParticlesOutOfRange Modern setup.py: CMake-Driven, Multi-Dimensional (ECP-WarpX#1647) This adds a new, project-centric setup.py file. With this file, all dimensions (2D, 3D, RZ) of WarpX can be built and packaged at once, using the CMake build logic. Build & install: ```bash pip wheel -v . pip install *whl ``` Updates for electrostatic solver (ECP-WarpX#1604) * Fix electrostatic solver with momentum conservation * Fix electrostatic, adding call to FillBoundaryAux * For electrostatic, removed unneeded extra calls to UpdateAux and FillBoundary * For electrostatic, calculate fields at the end of the time step * Updated ElectrostaticSphere analysis script to use fields from end of time step Reset broken benchmark for CI test initial_distribution (ECP-WarpX#1661) make sure we redefine the tmp particle tiles when we load balance. (ECP-WarpX#1658) [mini-PR] Add particle tiling documentation (ECP-WarpX#1665) * tiling wip * do_tiling documentation * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Luca Fedeli <[email protected]> Co-authored-by: Luca Fedeli <[email protected]> fix inconsistent formatting (ECP-WarpX#1666) parameter.rst fixes (ECP-WarpX#1663) requirements.txt: fix overspecification (ECP-WarpX#1668) I accidentally added the patch-level for version-compatible matching This removes the patch-level for `~=` matching for the packages that have a >=1 major version already. scipy 1.5+ (ECP-WarpX#1670) Sufficient since it was last release in december and works well. The 3.5 release series still builds wheels for Python 3.6 for Ubuntu oldstable (18.04). Remove redundant "do_qed" option in inputfile (ECP-WarpX#1667) * removed redundant do_qed option in inputfile * fixed bug remove semicolons (ECP-WarpX#1662) fixTypo for pml has particles parameter for docs (ECP-WarpX#1671) load balance efficiency reduced diagnostic eol minor eol
mrowan137
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Feb 3, 2021
…rpX#1624) * Fix bug in momentum-conserving interpolation function * Reset checksum benchmark for CI test momentum-conserving-gather Unused Params: Check after Step 0 (ECP-WarpX#1596) An early check for unused parameters after the first step. Add Superparticle version of getParticlePosition. (ECP-WarpX#1640) * Add Superparticle version of GetParticlePosition. * move unpack_particle to a free function and rename * no longer need SuperPType * Update Source/Particles/Pusher/GetAndSetPosition.H * remove templating from get_particle_position * remove template * Add missing include Co-authored-by: Axel Huebl <[email protected]> Distribution mapping and cost plotting (ECP-WarpX#1444) * Distribution mapping and cost plotting Cleanup Cleanup Cleanup EOL Unused import * Cost initializes to 0.0 * plot slices of 3D * WIP * WIP docs * docs * docs * docs * docs * docs * docs * docs * docs * EOL SpeciesProperties: C, N, O, Cu (ECP-WarpX#1638) * SpeciesProperties: C, N, O, Cu Add more ionic species as pre-defined particle species. * Cu: Add to Ionization Energies Fix 2D: ParticleHistogram (ECP-WarpX#1635) Fix out-of-bounds access in particle histogram in non-3D. Fix FilterFunctor in non-3D (ECP-WarpX#1633) Fix an out-of-bounds access to positions in 2D & RZ for filter functors. openPMD: ionizationLevel (ECP-WarpX#1622) * openPMD: ionizationLevel Write out the ionizationLevel with openPMD. * openPMD Record Repetitions: Use Lambdas openPMD: Particle Filter (Container) (ECP-WarpX#1632) * openPMD: Particle Filter (Container) A fresh implementation of particle filters for openPMD diagnostics using the generalized `PhysicalParticleContainer` approach that we also use in plotfiles 🎉 * Ion Example: Filter & Coarsen Test diagnostics filter & coarsen functions in CI. Test reduced diagnostics (histograms). Define: _OPENMP -> AMREX_USE_OMP (ECP-WarpX#1520) * Define: _OPENMP -> AMREX_USE_OMP Replace the define check of `_OPENMP` with the explicit backend control of `AMREX_USE_OMP` for parallel constructs. Doing so avoids that we accidentially turn on OpenMP, e.g. if a dependency pulls it in for linear algebra, I/O, etc. This can led to confusion if the user explicitly requested a serial build. Also, we might want to use OpenMP functionality here and there for auxiliary functions w/o having to use the AMReX OpenMP backend, i.e. because we compile for GPUs. * Add missing amrex::Gpu::notInLaunchRegion Start: PerformanceHints After Init (ECP-WarpX#1630) Start a helper routine that gives performance hints after initialization of the simulation. Fix number of guard cells in PML with 2D PSATD (ECP-WarpX#1648) Remove unused lines about particle filters (ECP-WarpX#1646) Add parameter for default galilean velocity (ECP-WarpX#1097) * Add parameter for default galilean velocity * Apply suggestions from code review Co-authored-by: Edoardo Zoni <[email protected]> * Fix bug in constructor of PhysicalParticleContainer * Use new input parameter in CI test Co-authored-by: Edoardo Zoni <[email protected]> Co-authored-by: Edoardo Zoni <[email protected]> Cleaned up field diagnostic in picmi interface (ECP-WarpX#1649) Use pinned memory for tmp particles in diags. (ECP-WarpX#1644) * Use pinned memory for tmp particles in diags. * openPMD: pinned memory (tmp particles) Co-authored-by: Axel Huebl <[email protected]> Replace an always false test with an abort (ECP-WarpX#1655) * replace always false test with abort * fix bug [mini-PR] Broken link to scripts (ECP-WarpX#1651) CI: Ubuntu-latest -> 20.04 (ECP-WarpX#1654) Start Embedded Boundary development (ECP-WarpX#1641) * Start Embedded Boundary development Modify the build system for embedded boundary (EB) support. Currently EB is a compile time option that must be explicitly enabled. For GNU Make, one can enable it with `USE_EB=TRUE`, whereas for CMake, `-DAMReX_EB=ON`. Later we could decide to enable EB by default with all regular geometry. Add a simple geometry initialization function, WarpX::InitEB. By default, the geometry is all regular. A few basic types such as box, cylinder, plane, sphere, etc. are supported via ParmParse runtime parameters. See `amrex/Src/EB/AMReX_EB2.cpp` for more details. Later, we could build more complex geometry using constructive solid geometry (CSG). ( https://en.wikipedia.org/wiki/Constructive_solid_geometry ) See `amrex/Tutorials/EB/GeometryGeneration` for an example of CSG. There is also a STL ( https://en.wikipedia.org/wiki/STL_(file_format) ) approach under development in AMReX. Add a new member, m_factory, to WarpX class. This object can be used to obtain geometry information such as whether a cell is cut, edge centroids, etc. Currently we are not using these factories to build MultiFabs for field data to embed the geometry information into the data containers. We could do that later if it is needed or it makes things more convenient. Nevertheless, this should be sufficient to start the EB development of the field solver. It's not clear to me yet how many ghost cells are needed for the geometry information. It's currently one, and can be adjusted. In the future, when particle and embedded boundary interaction is considered, we can use `amrex::FillSignedDistance` function to obtain signed distance function on the nodes. With that information, one should be able to determine where and when a particle collides with the embedded boundary. * resize factory vector * CMake: Require AMReX_EB for embedded boundaries * Add AMReX_Config.H et al. Explicit includes are most robust to make sure defines are set with future refactorings. * rename Factory fieldFactory Co-authored-by: Axel Huebl <[email protected]> Add filter for particle histogram (ECP-WarpX#1643) * Add filter for particle histogram * Update benchmarks * Update benchmark again * Use serialize_ics in test + proper usage of RandomEngine * Laser-Ion Acc. (2D3V): Test Hist Filter Co-authored-by: Axel Huebl <[email protected]> Take time step into account to compute guard cells for J and rho (ECP-WarpX#1607) * Use IntVect for ng_J and ng_rho * Compute guard cells for J and rho based on dt * Reset some CI benchmarks * Fix rebase commit * Add back +1 cell for rho: fix remaining out-of-bound accesses * Simplify ASSERTS using new interface of amrex::numParticlesOutOfRange Modern setup.py: CMake-Driven, Multi-Dimensional (ECP-WarpX#1647) This adds a new, project-centric setup.py file. With this file, all dimensions (2D, 3D, RZ) of WarpX can be built and packaged at once, using the CMake build logic. Build & install: ```bash pip wheel -v . pip install *whl ``` Updates for electrostatic solver (ECP-WarpX#1604) * Fix electrostatic solver with momentum conservation * Fix electrostatic, adding call to FillBoundaryAux * For electrostatic, removed unneeded extra calls to UpdateAux and FillBoundary * For electrostatic, calculate fields at the end of the time step * Updated ElectrostaticSphere analysis script to use fields from end of time step Reset broken benchmark for CI test initial_distribution (ECP-WarpX#1661) make sure we redefine the tmp particle tiles when we load balance. (ECP-WarpX#1658) [mini-PR] Add particle tiling documentation (ECP-WarpX#1665) * tiling wip * do_tiling documentation * Update Docs/source/running_cpp/parameters.rst Co-authored-by: Luca Fedeli <[email protected]> Co-authored-by: Luca Fedeli <[email protected]> fix inconsistent formatting (ECP-WarpX#1666) parameter.rst fixes (ECP-WarpX#1663) requirements.txt: fix overspecification (ECP-WarpX#1668) I accidentally added the patch-level for version-compatible matching This removes the patch-level for `~=` matching for the packages that have a >=1 major version already. scipy 1.5+ (ECP-WarpX#1670) Sufficient since it was last release in december and works well. The 3.5 release series still builds wheels for Python 3.6 for Ubuntu oldstable (18.04). Remove redundant "do_qed" option in inputfile (ECP-WarpX#1667) * removed redundant do_qed option in inputfile * fixed bug remove semicolons (ECP-WarpX#1662) fixTypo for pml has particles parameter for docs (ECP-WarpX#1671) Move getCosts Always synchronize nodal points of PML MultiFabs (ECP-WarpX#1669) * Always synchronize nodal points of PML MultiFabs * Reset benchmark for CI test pml_x_psatd * Use new separate functions NodalSyncPML minor
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Close #1637: this adds the possibility to use a filter function in the ParticleHistogram reduced diag.
The filter is tested in the same CI test as the ParticleHistogram reduced diag (which is only in 3D).