| Age | Commit message (Collapse) | Author | Files | Lines |
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* added collider reduced diags
* added test
* fixed xy_ave and xy_std
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* fixed usage of IntVect and removed print
* Set up automated CI test
To-do:
- Fix bug (erroneous arithmetic operation)
- Remove unused parameters from input file
* Fix warning: set mass only if WARPX_QED
* Use amrex::ParticleReal for mass
* Update Make.package to fix GNU Make build
* reduced_data.value() only once
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* Merge `development` into `coll_rel_red_diags`
* updated 3d beam test
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* updated 3d test
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* `m_write_header` instead of `m_IsNotRestart`
* added angles
* updated 3d beam test
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* added 3 particle test
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* added warning
* updated diags names
* updated analysis multiple particles
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* added positrons to test
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* Update CI test
* Reuse input file parser from Tools
* Apply suggestions from code review
* Apply suggestions from code review
* changed order of diags and added docs
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* Apply WarpX style conventions
* Fix CodeQL alerts
* assert in RZ and removed fine ref levs
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* Fix compilation in 2D
* Fix compilation in RZ
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.H
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* minimized number of kernel launches and parallel ops
* updated constructor of ReduceDiags
* fixed based on comments
* updated docs: if QED not enable
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* fixed ReducedDiags constructor
* two passes instead of one for robusteness
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* fixed bugs
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* Fix 1D build (typo `wtot` instead of `w_tot`)
* refixed compile in RZ
* check io process in chi_ave computation
* updated test
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* Temporary fix: remove IOProcessor
* Update Source/Diagnostics/ReducedDiags/ColliderRelevant.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Apply suggestions from code review
* Remove `Debug` compilation mode from CI test
* CI test analysis: check all particles have same charge
* Use `m_beam_name` instead of `species_names`
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
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* BTD RZ test: add missing checksum analysis
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(#4116)
* include current density in diagnostic output even if an electromagnetic solver is not used
* do not redeposit current for the magnetostatic solver
* update CI benchmarks for tests that previously did not register current density
* fix remaining failing CI test
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* do not output current density in collision tests
* update `JFunctor` constructor doc-string
* code cleanup - reduce code duplication
* specify `Ex Ey Ez Bx By Bz` fields to plot for collision CI tests
* specify `Er Et Ez Br Bt Bz` as output for rz collision test
* rename `InterpolateToDst` to `InterpolateMFForDiag`
* only deposit current density once per diagnostic output (if not already deposited)
* write deposited current for all directions into `current_fp` during diagnostic step deposition
* use `amrex::make_alias` to directly deposit current density into `warpx.current_fp` during diagnostic step deposition
* add class variable `solver_deposits_current` to `FullDiagnostics` so that there is only one place where the determination is made whether current should be deposited during diagnostic output
* correct logic to determine `m_solver_deposits_current`
---------
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* added nodal electrostatic solver
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* sphere test for electrostatic nodal solver
* add 3d single bunch test
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* adds single bunch ci test
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* updated tests
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* updated checksums nodal electrostatic
* Improve readability
* Change `assert` condition
* Clean up
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Implement boosted frame automated test (1D)
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* Implement boosted frame automated test (1D)
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* time_chunk_size=50
---------
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Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* pyAMReX: Build System
* CI Updates (Changed Options)
* Callback modernization (#4)
* refactor callbacks.py
* added binding code in `pyWarpX.cpp` to add or remove keys from the callback dictionary
* minor PR cleanups
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Added Python level reference to fetch the multifabs (#3)
* pyAMReX: Build System
* Added Python level reference to Ex_aux
* Now uses the multifab map
* Fix typo
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add initialization and finalize routines (#5)
A basic PICMI input file will now run to completion.
* Regression Tests: WarpX_PYTHON=ON
* Update Imports to nD pyAMReX
* IPO/LTO Control
Although pybind11 relies heavily on IPO/LTO to create low-latency,
small-binary bindings, some compilers will have troubles with that.
Thus, we add a compile-time option to optionally disable it when
needed.
* Fix: Link Legacy WarpXWrappers.cpp
* Wrap WarpX instance and start multi particle container
* Fix test Python_pass_mpi_comm
* Start wrapper for multiparticle container
* Add return policy
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update fields to use MultiFabs directly
Remove EOL white space
Removed old routines accessing MultiFabs
Update to use "node_centered"
* Fix compilation with Python
* Update fields.py to use modified MultiFab tag names
* Remove incorrect, unused code
* Add function to extract the WarpX MultiParticleContainer
* Complete class WarpXParticleContainer
* Wrap functions getNprocs / getMyProc
* restore `install___` callback API - could remove later if we want but should maintain backward compatibility for now
* add `gett_new` and `getistep` functions wrappers; fix typos in `callbacks.py`; avoid error in getting `rho` from `fields.py`
* Update callback call and `getNproc`/`getMyProc` function
* Replace function add_n_particles
* Fix setitem in fields.py for 1d and 2d
* also update `gett_new()` in `_libwarpx.py` in case we want to keep that API
* added binding for `WarpXParIter` - needed to port `libwarpx.depositChargeDensity()` which is an ongoing effort
* Wrap function num_real_comp
* added binding for `TotalNumberOfParticles` and continue progress on enabling 1d MCC test to run
* add `SyncRho()` binding and create helper function in `libwarpx.depositChargeDensity` to manage scope of the particle iter
* Clean up issues in fields.py
* update bindings for `get_particle_structs`
* Fix setitem in fields.py
* switch order of initialization for particle container and particle iterator
* switch deposit_charge loop to C++ code; bind `ApplyInverseVolumeScalingToChargeDensity`
* move `WarpXParticleContainer.cpp` and `MultiParticleContainer.cpp` to new Particles folder
* added binding for `ParticleBoundaryBuffer`
* More fixes for fields.py
* Fix: Backtraces from Python
Add the Python executable name with an absolute path, so backtraces
in AMReX work. See linked AMReX issue for details.
* Cleaning
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* Fix: Backtraces from Python Part II
Do not add Python script name - it confuses the AMReX ParmParser to
build its table.
* Fix: CMake Dependencies for Wheel
This fixes a racecondition during `pip_install`: it was possible
that not all dimensions where yet build from pybind before we
start packing them in the wheel for pip install.
* MCC Test: Install Callbacks before Run
Otherwise hangs in aquiring the gil during shutdown.
* addition of `Python/pywarpx/particle_containers.py` and various associated bindings
* Fix: CMake Superbuild w/ Shared AMReX
We MUST build AMReX as a shared (so/dll/dylib) library, otherwise
all the global state in it will cause split-brain situations, where
our Python modules operate on different stacks.
* add `clear_all()` to callbacks in order to remove all callbacks at finalize
* add `-DWarpX_PYTHON=ON` to CI tests that failed to build
* add `get_comp_index` and continue to port particle data bindings
* Add AMReX Module as `libwarpx_so.amr`
Attribute to pass through the already loaded AMReX module with the
matching dimensionality to the simulation.
* Fix for fields accounting for guard cells
* Fix handling of ghost cells in fields
* Update & Test: Particle Boundary Scraping
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* CI: Python Updates
- modernize Python setups
- drop CUDA 11.0 for good and go 11.3+ as documented already
```
Error #3246: Internal Compiler Error (codegen): "there was an error in verifying the lgenfe output!"
```
* CI: Python Updates (chmod)
* Add support for cupy in fields.py
* Add MultiFab reduction routines
* CI: CUDA 11.3 is <= Ubuntu 20.04
* changed `AddNParticles` to take `amrex::Vector` arguments
* setup.py: WarpX_PYTHON=ON
* update various 2d and rz tests with new APIs
* add `-DWarpX_PYTHON_IPO=OFF` to compile string for 2d and 3d Python CI tests to speed up linking
* CI: -DpyAMReX_IPO=OFF
* CI: -DpyAMReX_IPO=OFF
actually adding `=OFF`
* CI: Intel Python
* CI: macOS Python Executable
Ensure we always use the same `python3` executable, as specified
by the `PATH` priority.
* CMake: Python Multi-Config Build
Add support for multi-config generators, especially on Windows.
* __init__.py: Windows DLL Support
Python 3.8+ on Windows: DLL search paths for dependent
shared libraries
Refs.:
- https://github.com/python/cpython/issues/80266
- https://docs.python.org/3.8/library/os.html#os.add_dll_directory
* CI: pywarpx Update
our setup.py cannot install pyamrex yet as a dependency.
* ABLASTR: `ablastr/export.H`
Add a new header to export public globals that are not covered by
`WINDOWS_EXPORT_ALL_SYMBOLS`.
https://stackoverflow.com/questions/54560832/cmake-windows-export-all-symbols-does-not-cover-global-variables/54568678#54568678
* WarpX: EXPORT Globals in `.dll` files
WarpX still uses a lot of globals:
- `static` member variables
- `extern` global variables
These globals cannot be auto-exported with CMake's
`WINDOWS_EXPORT_ALL_SYMBOLS` helper and thus we need to mark them
manually for DLL export (and import) via the new ABLASTR
`ablastr/export.H` helper macros.
This starts to export symbols in the:
- WarpX and particle container classes
- callback hook database map
- ES solver
* CI: pywarpx Clang CXXFLAGS Down
Move CXXFLAGS (`-Werror ...`) down until deps are installed.
* GNUmake: Generate `ablastr/export.H`
* CMake: More Symbol Exports for Windows
* `WarpX-tests.ini`: Simplify Python no-IPO
Also avoids subtle differences in compilation that increase
compile time.
* Update PICMI_inputs_EB_API.py for embedded_boundary_python_API CI test
* Fix Python_magnetostatic_eb_3d
* Update: Python_restart_runtime_components
New Python APIs
* Windows: no dllimport for now
* CI: Skip `PYINSTALLOPTIONS` For Now
* CMake: Dependency Bump Min-Versions
for external packages picked up by `find_package`.
* Fix F and G_fp names in fields.py
* Tests: Disable `Python_pass_mpi_comm`
* Wrappers: Cleanup
* pyWarpX: Include Cleaning
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* fields.py: Fix F and G Wrappers
Correct MultiFab names (w/o components).
* Remove unused in fields.py
* Windows: New Export Headers
- ABLASTR: `ablastr/export.H`
- WarpX: `Utils/export.H`
* removed `WarpInterface.py` since that functionality is now in `particle_containers.py`; removed parts of `WarpXWrappers.cpp` that have been ported to pyamrex
* CMake: Link OBJECT Target PRIVATE
* CMake: Remove OBJECT Target
Simplify and make `app` link `lib` (default: static). Remove OBJECT
target.
* Fix in fields.py for the components index
* Update get_particle_id/cpu
As implemented in pyAMReX with
https://github.com/AMReX-Codes/pyamrex/pull/165
* WarpX: Update for Private Constructor
* Import AMReX Before pyd DLL Call
Importing AMReX will add the `add_dll_directory` to a potentially
shared amrex DLL on Windows.
* Windows CI: Set PATH to amrex_Nd.dll
* CMake: AMReX_INSTALL After Python
In superbuild, Python can modify `AMReX_BUILD_SHARED_LIBS`.
* Clang Win CI: Manually Install requirements
Sporadic error is:
```
...
Installing collected packages: pyparsing, numpy, scipy, periodictable, picmistandard
ERROR: Could not install packages due to an OSError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\hostedtoolcache\\windows\\Python\\3.11.4\\x64\\Lib\\site-packages\\numpy\\polynomial\\__init__.py'
Consider using the `--user` option or check the permissions.
```
* Hopefully final fixes to fields.py
* Update getProbLo/getProbHi
* Set plasma length strength
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* Fix fields method to remove CodeQL notice
* Update Comments & Some Finalize
* Move: set_plasma_lens_strength
to MPC
---------
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
Co-authored-by: David Grote <dpgrote@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Roelof Groenewald <regroenewald@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Due to the recent changes in amrex::ParmParse, we must use the line
continuation character '\' for values spanning multiple lines. For Parser
expression, we could either double quotes to enclose the whole string or use
`\` as line continuation.
The old style multi-line values were removed in AMReX to avoid mistakes like
algo.current_deposition = direct
# galilean
psatd.use_default_v_galilean # Forgot = 1
Here, `psatd.use_default_v_galilean` is silently ignored because with the
old style multi-line support it becomes part of the values for the previous
definition (i.e., `algo.current_deposition = direct
psatd.use_default_v_galilean`). This case will now abort.
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* Allocate fewer components for `rho`
* Fix compilation
* Use two components with dive_cleaning
* Fix Python script
* Fix PICMI script for 1D CI test
---------
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
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* Create flux injector object
* Call new flux injector in AddPlasmaFlux
* Update syntax in tests
* Also test the flux parser
* Remove the use of `density_min` and `density_max` for flux injection
* Update PICMI interface
* Update documentation
* Remove .cpp file
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* Adding j in FieldReduction
* Modiyfying input file with FieldReduced diag
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* Update Source/Diagnostics/ReducedDiags/FieldReduction.H
* updating Field Reduction Docs to include current density
* Update Source/Diagnostics/ReducedDiags/FieldReduction.H
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
* adding cuurent density BackwardCompatibility to Field Reduction diagnostic
* including E dot j density using the modifyed Field Reduction
* fixing picmi interface
* adding Edotj to automated python test
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---------
Co-authored-by: Lizzette Corrales <lzcorrales@kong.dhcp.lbl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
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* Added external field loading from file to picmi.py
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* Update Python/pywarpx/picmi.py
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
* Added documentation
* Removed init, documentation
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* Updated picmi version in requirements.txt
* Updated picmi version in setup.py
* Updated picmi version in requirements.txt
* Updated name of call to picmi class
* Adapted CI test for PICMI field loading from file
* Added PICMI input script
* Added .json file with new file name
* fixed small errors
* Fixed error in input script
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* Removed old comments from code
* fixed import, spacing in input script
* fixed spacing
* cleaned up input script
* fixed typo
* removed blocking factor
* fixed name of test
* correct ion species name
* Added initial field to sim object
---------
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Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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* Add "None" as an option for the Maxwell solver
* fixed some of the reasons for failing CI tests
* no longer pass `do_electrostatic` to `GuardCellManager`
* renamed `MaxwellSolverAlgo` to `ElectromagneticSolverAlgo`
* rename `do_electrostatic` to `electrostatic_solver_id`
* rename `maxwell_solver_id` to `electromagnetic_solver_id`
* start of hybrid solver logic
* changes requested during PR review
* remove `do_no_deposit` from tests without field evolution
* added `HybridSolveE.cpp`
* bulk of the hybrid solver implementation
* mostly reproduce 1d cold ion mirror results
* ion Bernstein modes reproduced with this version
* fix bug with reduced diagnostic FieldProbe in 1d
* added hybrid solver installation to PICMI and added example script generating ion-Bernstein modes
* enable the use of `FieldProbe` default parameter values
* use default field-probe values
* steady progress
* add `do_not_push` flag to picmi
* possibly use nodal fields
* added extra multifab for current calculated from curl B
* added `CalculateTotalCurrent` functions
* rewrote implementation to calculate J x curl B on a nodal grid first
* fill boundary for auxiliary MFs used during hybrid E solve
* properly handle nonzero resistivity
* updated hybrid model example
* clean up example scripts
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* fixed invalid memory access for GPU and other code cleanups
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* refinements on the example scripts
* added ion beam instability example
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* added EM modes and ion beam examples to CI test suite
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* started docs section on the hybrid model
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* more progress on documentation
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* added ion Landau damping verification test / example
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* add checksum benchmark for Landau damping example
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* added fields.py wrapper to access total current density in hybrid case
* refactored the charge deposition fix to be performed with the field data rather than individual particles
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* also correct current density at PEC boundary
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* made resistivity a parsed function of `rho`
* work on PEC boundary condition
* corrections pointed out during code review
* fix build fails due to unused variables
* fix issue with GPU builds
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* actually apply rho boundary correction in EM case
* take one sided derivative at PEC boundary when calculating div Pe
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* actually apply rho boundary correction in EM case
* removed specific treatment of E-field on PEC boundary for Ohm's law solver
* first round of CI fixes
* second round of CI fixes
* added description of deposition logic with PEC boundaries to documentation
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* third round of CI fixing
* move J and rho boundary handling to after `SyncRho` and `SyncCurrent` calls
* properly order the application of boundary conditions on rho, for electrostatic simulations
* fourth round of CI fixing
* moved calculation of total current (Ampere's law) to seperate function
* add random seed specification to `picmi`
* code clean-up -> renamed hybrid model to hybrid-PIC model
* added magnetic reconnection example
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* code cleanup & benchmark updates
* update PICMI class name for hybrid solver to `HybridPICSolver`
* don't apply J field boundary in
* don't apply J field boundary in `MultiParticleContainer::DepositCurrent`
* apply changes requested during code review
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Loosen tolerance on failing CI test
* Removed unused variable
* code cleanup: make use of `MultiParticleContainer::DepositCurrent` in `AddSpaceChargeFieldLabFrame`
* switch to using a rho_fp_temp multifab for old and averaged charge density field, also no longer require particles to move only one cell per step
* use `ablastr::coarsen::sample` namespace in `HybridPICSolveECartesian`
* switched to using `MultiFab::LinComb` instead of self written GPU kernels to calculated averaged or extrapolated current density
* add verbosity flag for the Ohm solver tests
* deal with fine versus coarse patches
* add theoretical instability growth / damping rates to hybrid-PIC examples
* update ion-Bernstein mode plot in documentation
* move the `ApplyRhofieldBoundary` call to after `SumBoundary`
* use a uniform calculation for the number of cells a given index is from the boundary
* remove unused variable
* limit number of ghost cells updated during PEC BC application
* the number of ghost cells to consider depends on whether the field is nodal or not
* attempt 1 to fix failing CI tests
* attempt 2 to fix failing CI tests and code cleanup
* attempt 3 to fix failing CI tests
* attempt 4 to fix failing CI tests and docs cleanup
* switched to using bibtex citations
* move hybrid solver input parameters documentation to its own section
* clean up ion beam instability analysis script
* Apply suggestions from code review
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|
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|
|
* make sure isort output good for black
|
|
* Starting to develop on the integration of lasy RZ coordinates
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* Allocating time_chunk_size outside GPU ParallelFor
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---------
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* Add waterbag generation in injector
* Fix typo in average
* Renamed distribution from waterbag to uniform
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* Fixed typo in Docs
* Add test for uniform distribution
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Created via:
```bash
./run_test.sh initial_distribution
```
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* Histogram 2D
A new functionality has been added. The files ParticleHistogram2D.cpp and ParticleHistogram2D.H allow the user to plot a 2D histogram that computes the number of particles for a given abscissa and ordinate.
* Modification to solve NVCC 11.8.0 GNUmake issue
ParticleHistogram2D.cpp added into Make.package
* Test for using openPMD
Test to activate the plug in for openPMD : #ifdef WARPX_USE_OPENPMD
Error message otherwise.
* Test for using openPMD continued
* New version of the ParticleHistogram2D option
The user can now choose the value of the weight via a value_function.
Another parameter was therefore added : w
The documentation has also been updated and an example (input file + python script for postprocessing) has been added to Examples/Physics_application/laser_ion
* Python script updated
The python script written for postprocessing the ParticleHistogram2D option has been renamed to pass a check test.
The argparse module has also been added to the code instead of the originally implemented command line interaction. Now the user must pass arguments when executing the script.
* Input files of the laser-ion example merged
The input file originally created for the 2D histogram has been merged with the initial input file "inputs" of the example.
* Correction of a display bug
* Help function for openPMD files
A help function has been created to find the correct file type when writing openPMDfiles.
Another update : the file type will be returned in the warpx_used_inputs file after running a simulation.
* Typo fixed in the python script used for 2D histograms visualisation
Typo for the shape of the data
* Typo in the help function file created
* Some typo fixed for checks
Modifications in the input file of the laser-ion example and in the ParticleHistogram2D.cpp file.
* Typo fixed : declaration on the WarpXOpenPMDFileType function outside #ifdef WARPX_USE_OPENPMD
* Typo for failing check NVCC 11.8.0 GNUmake
* Typo for failing check NVCC 11.8.0 GNUmake (continued)
* Typo for failing check NVCC 11.8.0 GNUmake (continued, abort message)
* .cpp file added to Make.package
* Time added to the data
Simulation time is now visible on Hist2D plots
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* Multiple hist2D active in the same simulation now possible
The laser-ion example as well as the documentation have been modified accordingly.
* Display enhancement for the laser-ion example
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* Implement legacy mode
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* break application of PEC to rho into separate loops over boxes
* round #1: fix failing CI tests
* also apply the fix to the `ApplyPECtoJfield`
* round 2: fix failing CI tests
* round 3: fix failing CI tests
* refactor PEC handling for charge and current density
* removed unused variable
* round 4: fix failing CI tests
* Fix `mirrorfac` calculation for `rho`
* only apply rho and J PEC boundaries for Cartesian grid (for now) in `SyncCurrentAndRho()`
* use the same kernel to apply PEC boundary to rho and J
* perform J and rho PEC application for RZ but warn about incorrect results if r_max is PEC
* do not apply PEC boundary for rho and J to r-max in RZ
* set warning level to medium and increase abort_on_warning_threshold to high for failing CI tests
|
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* Enable field ionization from PICMI
* Implement Dave's suggestions and add automated test
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* Update test benchmark
* Add docstring for FieldIonization class
---------
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* Imported openPMD
* Unable to add E
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* corrected errors
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* Clean up .H file
* Extract grid coordinates
* Corrected field name
* Implement laser oscillations
* More correct position
* More correct position
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* Cleaned up code
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* Implementation of a 2D test
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Co-authored-by: Camille Woicekowski <camille.meala@berkeley.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
|
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Guarantee improved plasma stability for 2D with very low initial
target temperature when using Esirkepov current deposition with
energy-conserving field gather (default).
|
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* AMReX: 23.05
* PICSAR: 23.05
* WarpX: 23.05
* Update ES EB RZ Tests
- slightly relaxed Phi
- better selection of r outside cutcells
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* Use GPU shared memory to accelerate charge deposition (#66)
* WIP Apply charge deposition unconditionally in scratch memory
* Ensure enough threads to touch every value in the array, even if there are no particles
* Zero out the shared memory before accumulating into it
* Replace box-aware accumulation of final results with simple pointers
* Remove unused code
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* Wording
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* Restore non-GPU code path
* Pick apart #if stuff to allow better formatting and comprehension
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* Abort on insufficient shared memory, rather than falling back to global memory
* Fix silly whitespace
* Fix stray tab character
* Sort and bin particles, pass bins to charge deposition
* Contribute on a binned tile basis; memory errors now
* Initialize array to the extent we actually allocated
* Make sure we initialize the vector the tboxes with invalid Box objects
* in 2D, we make sure we use the same particle position to tile box mapping as amrex
* go ahead and skip empty bins in deposit charge
* Quiet warning from HIP
* Avoid signed/unsigned comparison
* Code compiles for CPU ...
* Rename intermediate buffer back to reduce extraneous diff bits
* Remove another extraneous diff bit
* Leave DPC++ out in the cold, since it expects different syntax for GPU-specific code
* Reset failing value of rho that only slightly changes
* Try tiling over ng_rho to capture particles moved into guard cells
* Match box expansion in both call sites - maybe the third is also necessary
* Grow last box by ng_rho as well.
* Match macro syntax
* Use WarpX dimensionality macros instead of AMREX_SPACEDIM
* Add support for 1D case
* Update benchmark checksums for ME tests
* Fix macro used for 1D
* Fix CUDA compilation
* Rename variable to simplify diff
* Clear up assertions now that stuff is working
* Fix comment referring to current in ChargeDeposition.H
* Fix warning about unused variable after assertion change
* add runtime option
* Convert flag variable from int to bool
* Switch AMREX_SPACEDIM conditions to use WARPX_DIM_* macros
* Once again, leave DPC++ out in the cold, as it doesn't support the same syntax as CUDA and HIP
* Grow charge deposition boxes by the necessary amount
* Mark a variable only used for assertions to suppress warnings
* Fix compilation error for 1D
* Re-add missing 1D support
* Fix other bits of codfe specific to CUDA and HIP, and not DPC++
* restore missing accumulation of thread local charge into main fab.
* reset benchmark for background_mcc because randomization makes it very sensitive
* reset benchmark for Langmuir_multi_psatd_div_cleaning because diffing field is a numerical artifact
* Calm nvcc about function missing a return
* reset benchmark for background_mcc because it's randomized and numerically chaotic
* reset benchmark for LaserAccelerationBoost because of numerical shift in momentum from charge deposition order
* Remove extra nesting level
* Skip sorting the particles and just access them according to the binned permutation
* Load permutation pointer outside GPU kernel
* Revert background_mcc benchmark values
* Loosen overly-strict checksum tolerances in single-precision tests, rather than changing target values
* Revert embedded_circle
* Convert AMREX_ALWAYS_ASSERT to AMREX_ASSERT for particle bounds checking
* Match assertion macro change from #2939
* Fix indentation
* Disable shared memory charge deposition by default
* Ignore variable only used in assertion
* Add documentation of added input parameter warpx.do_shared_mem_charge_deposition
* Add comments as suggested by Remi
* Docs: Fix syntax issues in parameters.rst
* Convert error check to unconditional assertion as requested
* Make some arguments const to ease refactoring
* Finished DepositCurrent function
Ready to call the function from CurrentDeposition.H, but currently there
is only a dummy function there
* AMReX: Weekly Update
* Reset: `reduced_diags_single_precision`
* Reset: `background_mcc_dp_psp`
* Merged with develop. runs on mpi no gpu
* All funcs implemented. Compiles with bugs
* Fixed typo in CurrentDeposition
* Working on 2D version. there is bug
jz doesn't line up correctly
* Fixed 2d bug
* Removed some debugging lines
* Cleaning up comments
* Added an input param for threads per block
* Added a variable NS and START/STOP
* Added a region for kernel
* Not working on tilesize > 1 1 1
* Implemented Andrews new algo for max tilesize
* Reduce the amount of shared memory needed by re-using the same buffer for all three components
* Made default tilesize sort_bin_size LAST V1 COMMIT
* bugfix - don't add 0.0 cells back to global memory.
* Need to take abs before checking > 0.0
* Ran Whitespace Fixer As instructed
* Updated Comments
* change default tpb for current deposition to 128
* clean up comments
* quiet compiler warning
* remove unused variables
* refactor shared current depo code
* forgot to check in file
* fix cpu compilation
* fix uninitialized
* fix typo
* fix bad merge
* Fixed default tilesize bug
Previously had defualted shared_tilesize to sort_bin_size. This was
overwritting the shared_tilesize. Some scanning shows that sort_bin_size
isn't a very good default for tilesize anyways, so the new default is 1
1 1.
* changed shared tilesize default to 6 6 8
Decision based on scan over tilesizes and ppc by @atmyers and @kaplannp
* Put in switches for default tilesize 288 3d 144 2d
Tested correctness in 2 and 3 d
* Simplified parcticle contribution section
In accordance to @AlexanderSinn feedback, and tested RZ, 2D, 3D
* Cleanup tbox construction and depos->(depos+1)/2
in accordance to changes proposed by @AlexanderSinn. Tested on 3D 2D and
RZ
* Restored shared to previous version from 6acab48
Changes from before broke single precision
* Found new spot to benefit from (depos_order+1)/2
* Cleaned up sloppy comments
* Throw error on shared if no hip or cuda
This commit makes the assumption that if you use shared, you must be
using HIP or CUDA. This allows us to remove a bunch of macros that tried
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Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
Co-authored-by: Phil Miller <phil@intensecomputing.com>
Co-authored-by: Tools <warpx@lbl.gov>
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* Squashed commit of the following:
commit 5452b0a818e952fc8ac989a306b0ea83738243f1
Merge: a21dda0f 90b72e80
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Sep 23 13:22:03 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
commit a21dda0f1bad8ee8601104c3322631d5f385ffdd
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Sep 23 13:13:23 2022 -0700
Update
commit 3394416cc0f7dc1e4742249b469957bedbfd5e84
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 24 13:37:30 2022 -0700
Update Examples/Tests/LoadExternalField/*
commit f0650b02e2f2d8d9719163ed5d4fd932a9d62a5b
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 24 12:41:11 2022 -0700
parameters.rst added
commit a96a3eb3a181d6e1a649a43bc9eb2e00e4e0ef57
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 15:15:43 2022 -0700
Add 3D test
commit caf213cdff02213cf0ff7389b399898bc76951b5
Merge: e85a7105 2b60afe8
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:02:35 2022 -0700
Merge branch 'add_external_fields' of https://github.com/Yin-YinjianZhao/WarpX into add_external_fields
commit e85a7105dceb80bc8769062a306248f57ac0939d
Merge: d00ce279 642f6c0f
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:01:59 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
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commit d00ce2790ae56148bd717baa7c8e074a2d12a6bf
Merge: fbaf5226 c21244d1
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 12:01:42 2022 -0700
minor
commit fbaf5226ee92444b618029ad56722f8e54918448
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 18 11:57:46 2022 -0700
The automated test of RZ passed, cleaning up needed.
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commit 0a52f2976b58cdbb48673387decce61aabf61561
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 17 13:51:40 2022 -0700
Add RZ test, but has a bug.
commit 2c6e1537e9fa1f630134e64800b2d509088481b8
Merge: d3b6b0cd b4686616
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 13:37:01 2022 -0700
Merge branch 'development' of https://github.com/ECP-WarpX/WarpX into add_external_fields
commit d3b6b0cd8eb34a5832bc8b439e96744f7a01a2ce
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 13:36:36 2022 -0700
Do not use WARPX_EXTERNAL_FIELD
commit a32207ab2c4476feab0cb4b1e9a65a6181c7bf81
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Wed Aug 10 10:50:18 2022 -0700
In the middle of clean up.
commit dcfcb02b9e053391c59cef50c692e84cf379fb8a
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 9 11:08:42 2022 -0700
RZ OpenPMD bug fixed, but code is messy, and chunk load is not done.
commit dec17c35d025ac4d40dcaca4b68853959e176782
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 9 10:43:58 2022 -0700
Has bug using RZ OpenMPD
commit b32e6efdd766f5986d66b213479d7c84587fca7e
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Aug 5 13:17:04 2022 -0700
Add OpenPMD 3D.
commit 7b7f48e2ae751d0393703c912116f5cb4d4dffbc
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Thu Aug 4 15:50:00 2022 -0700
Revert "minor"
This reverts commit 01e022958bad3057737e57fda4ecfaed22778b51.
commit 01e022958bad3057737e57fda4ecfaed22778b51
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Tue Aug 2 15:03:24 2022 -0700
minor
commit 774e591959fce76f94dcb96ae17f43c71ee7b931
Author: Yin-YinjianZhao <yinjianzhao@lbl.gov>
Date: Fri Jul 29 11:13:14 2022 -0700
Make 1d work
commit 5db4e862104459e5511dad9869764866dc88e62d
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Fri Jul 29 10:27:03 2022 -0700
Make xz working
commit 03c3d0062e301c1dd525a50f7ea84c2ccad6d679
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Date: Fri Jul 29 09:38:43 2022 -0700
Make rz workiong
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Merge: 0c1c7b7b a514e793
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Merge branch 'add_external_fields' of https://github.com/Yin-YinjianZhao/WarpX into add_external_fields
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Date: Wed Jun 22 14:01:42 2022 -0700
Fix a bug.
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Use txt file.
commit 61fb96d9219598d10dab6a729eb4db7278583d2e
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Thu May 26 13:51:58 2022 -0700
Now the loaded external field does not match the provided external field data.
commit 7354a1abcd3b36e97d2145eff0c4b1da0a3aca27
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Wed May 18 15:21:15 2022 -0700
Try to add new arguments in the doGatherShapeN function, such that external fields can be added.
commit 3a0db5fcbaf4298c7cf59ba4443f3cdf7a21094b
Author: Yinjian Zhao <yin@Yinjians-MacBook-Air.local>
Date: Tue May 10 14:35:53 2022 -0700
Changed to mfi.growntilebox() to include the guard cells.
commit 33e3393eb6bf769a2d92043c1012796b8212e653
Merge: 53201644 32fe8aac
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Date: Thu May 5 13:37:24 2022 -0700
A bug needs to be fixed related to the growth of cells.
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A bug needs to be fixed related to the growth of cells.
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Date: Tue May 3 15:54:25 2022 -0700
In the middle.
commit 698e8f3e69dac5945b332c67570272bf2f4ae168
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Date: Tue May 3 09:32:54 2022 -0700
In the middle.
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In the middle of reading data.
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Draft.
commit 85e16cafbf65cf502b82943d5bae98c4e1d750df
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Date: Mon Apr 18 15:15:22 2022 -0700
Minor: change tag.
commit 0b7d2723c225cc4eed09eb58ad7f049d6baa650a
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Date: Mon Apr 18 15:04:19 2022 -0700
Allocate MultiFabs for the external E and B fields.
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* Fix copy-paste errors
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* Drop unused includes
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* Rename function to slightly better reflect substance
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* Specify type argument for interpolation to avoid mixture
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* Move assertion about max levels to earlier in initialization
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---------
Co-authored-by: Tools <warpx@lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Lattice: Line Docs & Rename
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* Prepare structure to compute charge inside boundary
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* Fix Silver-Mueller boundary condition in 1D
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* Added FieldReduction and ParticleHistogram to ReducedDiagnostics
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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.
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* 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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* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* 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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Correct errors
* Update values of mass and charge
* Correct compilation error
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Correct compilation error
* Correct compilation error
* Correct compilation error
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fix typo Docs/source/usage/parameters.rst
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* 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
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/AcceleratorLattice/LatticeElements/LatticeElementBase.H
Add includes
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Renamed to README.rst and updated headers
* Made d_lattice_element_finder optional type
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Include `<optional>`
* Docs: Developer AccLattice Inclusion
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>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>
Co-authored-by: Neïl Zaim <49716072+NeilZaim@users.noreply.github.com>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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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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Arianna Formenti
Edoardo Zoni
Roelof Groenewald
Ilian Kara-Mostefa
Axel Huebl
Remi Lehe
Weiqun Zhang
Lizzette Corrales
Luca Fedeli
Camille Woicekowska
Ryan Sandberg
Davide Terzani
Juliette Pech
Neïl Zaim
Andrew Myers
Phil Miller
S. Eric Clark
David Grote
Prabhat Kumar
Yinjian Zhao
