Age | Commit message (Collapse) | Author | Files | Lines |
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Update modules after the last upgrade of Perlmutter (NERSC).
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* Removed the guard cells since they are not needed for the tridiag
* Clean up the copy into the 1d array
* For the upper boundary, use explicit indices instead of temporaries to make the code more clear
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* Correct particle positions outside refined injection
* Improve test
* Update benchmark
* Modifications for vector refinement ratio
* Update getPosition function
* Update code for anisotropic injection
* Correct compilation
* Correct code for RZ and 1D
* Correct indentation
* Correct integer overflow, as suggested by Weiqun
* Generalize interpolation routines in diagnostics for anisotropic ref ratio
* Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/Diagnostics/FlushFormats/FlushFormatPlotfile.cpp
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* Update Source/Utils/Interpolate.H
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* Update Source/Utils/Interpolate.cpp
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* Update Source/Utils/Interpolate_K.H
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* Update Source/Utils/Interpolate.H
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* apply review suggestion
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Correct particle positions outside refined injection
* Improve test
* Update benchmark
* Modifications for vector refinement ratio
* Update getPosition function
* Update code for anisotropic injection
* Correct compilation
* Correct code for RZ and 1D
* Correct indentation
* Correct integer overflow, as suggested by Weiqun
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* Correct density
* update
* Add test
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* Update Regression/WarpX-tests.ini
* update
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* Apply suggestions from code review
* update
* Fix shadowing of variables
* Simplify code
* Correct density
* Update checksum
* Update exponential fit
* Remove unused global variable
* Add comment on exponential fit
* Cleaning
* Cleaning
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Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* AMReX: 23.01
* PICSAR: 23.01
* WarpX: 23.01
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* Fix typos noticed in reviewing existing changes
* Fix a typo in test case name
* Plasma Lens: Rename Benchmark
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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updates:
- [github.com/pycqa/isort: v5.11.3 → 5.11.4](https://github.com/pycqa/isort/compare/v5.11.3...5.11.4)
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After the tri-diagonal solve, the data in the special single-box MultiFab
need to be copied back to the normal MultiFab. However, when there was a
bug for periodic boundary. The issue is the special MultiFab is really
special. It has a nodal Box that grows the original nodal Box by 1 node in
the lower boundary and 2 (why 2?) nodes in the upper boundary and these
grown nodes are considered valid nodes, even though they do not have valid
data. Therefore amrex::ParallelCopy with periodicity does not work in this
case. For example, for a domain with 96 cells, the data at nodes 1 and 2 of
the normal MultiFab could be written with the invalid data at nodes 97 and
98 of the special MultiFab. This bug is fixed by replacing it with a
ParallelCopy without periodicity followed by a FillBoundary.
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* Initial working Magnetostatic solver integration into warpx. Includes hooks in Python library, and a test problem. Build files updates. New solver algorithm and inputs.
* Fixed indexing to allow Magnetostatic solver to work in RZ and 3D.
* Removing trailing whitespace.
* Adding basic regression testing with benchmarks.
* Updated Regression test ini
* Augmented test scripts to compare to analytical results for uniform beam.
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* Updating CI tests for magnetostatic solver.
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* Updated magnetostatic CI tests to pass locally in regression testing framework.
* Adjusting tolerance on magnetostatic_rz regression test to allow for noise in near zero fields.
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* Converted particle layout to Gridded instead of PsedupRandom to improve reproducibility of particle deposition for regression testing.
* Dropped benchmark field comparisons with fields near zero. Dropped particle benchmark for magnetostatic_eb_rz regression test due to randomized particle theta adding noise to fields after a timestep.
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* Found and fixed a bug in syncronization of MultiFabs when interpolating between grids in the magnetostatic solver. Added Python output for nodal current and vector potential. Updated the CI tests to disable dynamic scheduling and enbale serialization of initial conditions. Updated benchmarks fro tests.
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* Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Adding random_theta flag to PICMI interface and updating RZ CI test and benchmark with change to disable randomized theta.
* Added documentation to parameters.rst for relativistic-magnetostatic flag. Documentation corrections. Removal of commented source.
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* Removing need to use do_current_centering. Updated current density inverse scaling support for nodal Jr in radius. Added flag to check for m_rz_random_theta when laying down particles in RZ.
* Remove dA/dt term to decouple electrostatic and magnetostatic solvers.
* Remove update of auxiliary fields
* Adding non-Python test case for magnetostatic solver. Updating benchmarks.
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* Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp
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* Update Python/pywarpx/_libwarpx.py
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* Update Python/pywarpx/_libwarpx.py
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* Update Python/pywarpx/_libwarpx.py
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* Update Python/pywarpx/_libwarpx.py
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* Update Source/Diagnostics/Diagnostics.cpp
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* Update Source/Evolve/WarpXEvolve.cpp
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* Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.H
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Refactor names of functions for magnetostatic solver implementation. Remove current_fp_nodal python interface. Drop extraneous ghost cell exchanges.
* Adding radial weighting at r=0 for Jr if nodal.
* Splitting off Amrex bucket and adjustments to RZ radial weighting into different branches to be merged.
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* Update Source/FieldSolver/MagnetostaticSolver/MagnetostaticSolver.cpp
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* Switch name to labfame-electromagnetostatic
* Update example scripts
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* AMReX: Weekly Update
* Fix Intel CI: dpcpp -> icpx
Intel has deprecated `dpcpp`. We are supposed to use `icpx -fsycl` now for
SYCL code.
* Add -fsycl
Co-authored-by: Weiqun Zhang <weiqunzhang@lbl.gov>
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We will deprecate ADIOS1 and will not build it by default anymore
in the upcoming release. Since we only use ADIOS2 in WarpX and
builds are sometimes fragile with ADIOS1, we just disable it
now in superbuilds already.
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The implementation here can be optimized by using shared memory. However,
instead of doing it here, I am going to add a helper function to AMReX.
Also removed an unnecessary synchronization, because there is a
synchronization in the destructor of the particle iterator.
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* Allow const_dt with EM and check it for ES
* Update PR according to comments
* Fix typo
* Fix invalid reference to m_const_dt
* Fixed another invalid reference to m_const_dt
* Remove erroneous setting of `const_dt` test
* Add doc for const_dt
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Include fusion reactions in documentation
* Finalize documentation
* Update documentation
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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With the update tot HTML5 in docutils, we need to modernize
our CSS code that does fancy logos in the user install section.
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* Initial version of accelerator lattice
* Clean up EOL white space
* Small clean up for GPU
* Fixed up consts
* Added hard edge fraction plus other clean ups
* More clean up
* Restructure to work on GPUs
* Now this grabs its own copies of particle info
* Updates, including adding dBdx
* Small cleanup in Quad
* Small fixes for GPU
* More cleanup for GPU
* More GPU cleanup
* Rewrite of the accelerator lattice implementation to better handle GPU
* Fix struct forward definition
* Another forward definition fix
* Bug fix
* Added LatticeElementBase
* Removed zcenters array
* Added CI test case
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* Clean up in CI analysis.py
* Cleanup of coding
* Added CI test hard_edged_quadrupoles_moving
* Added Lorentz transform between boosted frame and lab frame
* Fixes for working in the boosted frame
* Added boosted CI test
* Change input name, adding the prefix "lattice."
* Added plasma lens lattice element
This will replace the external field plasma lens
* Fixed CI analysis script to look for "lattice.quad"
* Added checks of lattice element input
* Added documentation
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* Removed duplicate call to lattice finder UpdateIndices
* Added extensive comments
* Reworked the input to use the MAD like description
This is the same as the method used in ImpactX
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* Remove old lines from inputs_lattice_3d
* Added "lattice" element type
* Fixed some Real and ParticleReals
* [pre-commit.ci] pre-commit autoupdate (#3246)
updates:
- [github.com/hadialqattan/pycln: v2.0.1 → v2.0.3](https://github.com/hadialqattan/pycln/compare/v2.0.1...v2.0.3)
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* ABLASTR: Update Poisson Solver API (#3243)
Update the Poisson Solver API to be more usable. Needed for ImpactX.
* Docs: New OLCF Machine (#3228)
* D-T fusion (#3153)
* initial work
* fixed bugs and added species
* update documentation
* delete unused file
* Add properties for neutron, hydrogen isotopes, helium isotopes
* Update code to be more consistent
* Correct typo
* Parse deuterium-tritium fusion
* Start putting in place the files for deuterium-tritium
* Update documentation
* Prepare structures for deuterium tritium
* Fix typo
* Fix compilation
* Add neutron
* Add correct formula for the cross-section
* Correct compilation error
* Fix nuclear fusion
* Reset benchmarks
* Prepare creation functor for 2-product fusion
* First implementation of momentum initialization
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* Use utility function for fusion
* Minor modification of variable names
* Fix GPU compilation
* Fix single precision compilation
* Update types
* Use util function in P-B fusion
* Correct compilation errors
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* Correct errors
* Update values of mass and charge
* Correct compilation error
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* Correct compilation error
* Correct compilation error
* Correct compilation error
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* Reset benchmark
* Use helium particle in proton-boron, to avoid resetting benchmark
* Fixed proton-boron test
* Revert "Fixed proton-boron test"
This reverts commit 73c8d9d0be8417d5cd08a23daeebbc322c984808.
* Incorporate Neil's recommendations
* Reset benchmarks
* Correct compilation errors
* Add new deuterium tritium automated test
* Correct formula of cross-section
* Correct cross-section
* Improve analysis script
* Add test of energy conservation
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* Add test of conservation of momentum
* Progress in analysis script
* Fix error in the initial energy of the deuterium particles
* Add check of isotropy
* Clean up the test script
* Rewrite p_sq formula in a way to avoids machine-precision negative numbers
* Add checksum
* Clean up code
* Apply suggestions from code review
* Update PR according to comments
* Update benchmark
* Address additional comments
* Numerical Literals
Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* Docs: gaussian beam `q_tot` is not optional (#3249)
* Fix a bug in GPU version of Hankel Transform (#3253)
amrex::Array4 is a 4D array that can be accessed with three spatial indices
plus an optional component index. We must always provide all three spatial
indices even in 2D.
* Add Python Callback Call when Checkpointing Signal is Received (#3251)
* CI: Add Missing Regression Analysis (NCI corrector) (#3252)
* Fixes to allow mixed precision, ParticleReal float, Real double (#3239)
* Fixes to allow mixed precision, ParticleReal float, Real double
* Fix for the optical depth
* A different way of fixing QuantumSynchrotronEvolveOpticalDepth
* In the QED code, consistently use ParticleReal
* Use ParticleReal type consistently
* Fix typo Docs/source/usage/parameters.rst
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* Fix typo Docs/source/usage/parameters.rst
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* Fix small error in plasma lens lattice documentation
* Small addition to the documentation
* Fix the residence correction to allow short elements
* Updated CI benchmarks
* Added check of lattice to isNoOp
* Updated the hard_edged_quadrupoles CI benchmarks
It is not clear why there was a change, but the difference is
essentially round off in the E field. The important thing is that the
particles are still correct.
* Update Source/AcceleratorLattice/AcceleratorLattice.H
Add include statements
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* Update Source/AcceleratorLattice/LatticeElements/LatticeElementBase.H
Add includes
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* Renamed to README.rst and updated headers
* Made d_lattice_element_finder optional type
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* Include `<optional>`
* Docs: Developer AccLattice Inclusion
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- [github.com/pycqa/isort: 5.11.1 → v5.11.3](https://github.com/pycqa/isort/compare/5.11.1...v5.11.3)
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Document the `amrex.use_profiler_syncs` option in our debugging
section.
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* Fix comments for documentation
* More fixes to comments for documentation
* Fixes in the doc files
* Fix typo in parameters.rst
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* Add a new section on domain decomposition to the docs.
* Remove old parallelization section and migrate more info
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* Docs: add photo_species input param and fix typo
This PR makes the following changes to the _Input Parameters_
page of the documentation:
- Adds the input parameter ``particles.photon_species``
to the Particle Initialization section.
- Fixes a typo in the section _Lookup tables and other settings for QED modules_
under the bullet point about ``qed_qs.lookup_table_mode``
(from ``qed_bw.save_table_in`` to ``qed_qs.save_table_in``)
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* Refactor update of auxiliary data for electrostatic solver
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* Fix to AddPlasmaFlux to allow flux surface to be on the domain boundary
* Update FluxInjection3D.json since the particle positions changed
* Update comments in AddPlasmaFlux
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follow-up to last commit updating contributors
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* Typo: Fewer Ranks (Perf. Hint)
* fix warning message (space)
Co-authored-by: lucafedeli88 <luca.fedeli@cea.fr>
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* AMReX: 22.12
* PICSAR: 22.12
* WarpX: 22.12
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Filter out third party warnings, i.e., from
AMReX, PICSAR, and openPMD.
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updates:
- [github.com/pycqa/isort: 5.10.1 → 5.11.1](https://github.com/pycqa/isort/compare/5.10.1...5.11.1)
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* update example profile
* update documentation for LUMI
* Fix minor typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Updated Doxygen from 1.8.17 to 1.9.1
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* Renamed Vay currents from j to D
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Same as other runners: aborts when new updates are pushed to safe CI
time.
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* Add CodeQL workflow for GitHub code scanning
* Remove: old LGTM config
* Fix: CodeQL Deps
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* ABLASTR: Coarsen Functions
Move coarsen functions to ABLASTR.
Rename by property of the coarsening function.
* Remove unused imports
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* Highlights & References: Gordon-Bell
Add our award-winning Gordon Bell paper in documentation :)
* Update Landing Pages
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* Implement First-Order PSATD Equations
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* Fix Unused Parameter Warning
* Fix RZ Build
* Fix Normalization of G to Match PML
* Add CI Test: 3D Uniform Plasma
* Cleaning
* Update 2D CI Checksums
* Update 3D CI Checksums
* Add F,G to CI Checksums of `uniform_plasma_multiJ`
* Allow User to Choose First-Order v. Second-Order
* Add WARPX_ALWAYS_ASSERT_WITH_MESSAGE
* Rename New Class `PsatdAlgorithmFirstOrder`
* Remove Inline Comment
* Update RZ CI Checksums
* Fix inline comment
* Use auxiliary variables to avoid divisions
* Use auxiliary variables to avoid divisions
* Make `nci_psatd_stability` dir and merge inputs
* Move all Galilean tests to `nci_psatd_stability`
* Fix CI
* Fix index for backward FFT of J
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As a Gordon Bell winner, I take no responsibility for this bug.
But, I'll fix it. And it gives solid performance enhancement, so I will take responsibility for that. 😄
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