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* Clean up examples folders
* Use `snake_case` names
* Rename `nci_corrector` as `nci_fdtd_stability`
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* file_min_digits: 5->6
100k+ step runs are quite common in WarpX. To simplify
post-processing scripts, increase the default to pad to 6 digits.
This might break some hand-written scripts that use `?????`
wild-cards over `*` wildcards in regex and thus need to be updated.
But it at the same time simplifies regexes for analysis of data
series and listing of such file series.
* Update Scripts to Handle New File Names
* Fix CI Test pml_x_psatd
* Fix CI Test divb_cleaning_3d
* Fix CI Tests with EB Support
* Fix CI Tests with RZ Support
* Fix CI Tests with PICMI Support
* Use glob in Analysis of Collision Tests
* Use rstrip in Analysis of Collision Tests
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix CI Tests for Langmuir_multi_1d/psatd
* Fix CI Tests for LaserInjection_1d
* Checkpoint-Restart Tests: 5 Digits
`regtest.py` in `regression_testing` hard-codes 5 digits:
```diff
--- a/regtest.py
+++ b/regtest.py
@@ -734,7 +734,7 @@ def test_suite(argv):
shutil.move(test.diffDir, orig_diff_dir)
# get the file number to restart from
- restart_file = "%s_chk%5.5d" % (test.name, test.restartFileNum)
+ restart_file = "%s_chk%6.6d" % (test.name, test.restartFileNum)
```
* PICMI Restart Tests: `warpx_file_min_digits = 5`
Same as other CI restart tests: hard-coded value in regression
suite makes this necessary.
X-ref: https://github.com/AMReX-Codes/regression_testing/issues/119
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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* Initial attempt at moving function into LibWarpX
* Bugfix - undefined structs in get_particle_theta
This is untested, identified by IDE/visual inspection only
* Unify newlines
* Delete libwarpx.clight (duplicated picmi.py)
See picmi.constants.c
* Change function descriptive comment to docstring
Also remove extra newline in __init__ beginning.
* Replace pywarpx/_libwarpx calls appropriately
* Fix atexit register of finalize function
* Reorder WarpX.py imports for pre-commit
* Use picmi.Simulation.extension = libwarpx alias
This will hopefully preempt user script changes if we restructure things
to allow multiple WarpX runs to be done within a single Python script.
* Fix libwarpx ref in WarpX.getProbLo/getProbHi
* Update get_particle_boundary_buffer doc reference
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* Docs: `geometry.dims` option
Add a new, required option to specify the geometry of an
inputs file at runtime.
* Check & Report Runtime Dims Mismatch
* Examples: add `geometry.dims`
* Deprecation Warning: `geometry.coord_sys`
* PICMI: `geometry.dims`
* Improve error message
sounds a bit better
* Improve Doc Description
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
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* Wrap shared object in a class to control its loading
* Fix libwarpx attribute references
* Updated callbacks.py for updated libwarpx
* Removed the wx module plus other clean up
* Further revision of how to use the pywarpx module.
Now, _libwarpx should not be imported by external scripts except in special circumstances.
* Updated documentation
* Clean up end of line whitespace
* Added more wrapping routines plus some clean up
* Fixed use of pywarpx in two examples
* Fix for getistep
* Fixed for the EB Python interface
* Silence a warning for our wrapper
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Examples: Python ShellBang & Executable
Make sure that all PICMI scripts and all analysis Python scripts
in `Examples/` are:
- executable (`chmod a+x`)
- start with a shell-bang to `python3`
Now, all scripts can be run directly without a `python3 ...` prefix
and also default to the only right executable of Python on older
systems. (New systems always have a `python3` alias, too.)
* Revert a moved numpy
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* added tunable particle reflection from absorbing domain boundaries
* extended picmi.py to allow setting boundary reflection coefficients and added a CI test for the reflection implementation
* allow R(E) to be specified, except for embedded boundaries
* changed approach for particle reflection, now the ParticleBoundaries object will hold the reflection coefficient; reflection from EBs not implemented
* added functionality to reflect from EB; still needs to be tested for accuracy
* added support for energy dependent reflection models for domain boundaries
* fixed at least one issue causing CI fails - building reflection model parsers for not physical particle containers
* switched reflection coefficients to be functions of the velocity component perpendicular to the boundary rather than energy
* reverted initial work on reflecting from EBs
* changed naming convention for new CI test for particle reflection
* switched useMPI back to 1 in test
* breaking changes while trying to sort out GPU issue
* fixed issue with CUDA compilation - hopefully :)
* various code improvements from PR review suggestions
* fix of major issues
* no need to parse the reflection models at every step
* skip particles that are already flagged for removal in ApplyBoundaryConditions
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* support only new boundary interface. set pml flags to 0 as default
* use new boundary interface in Examples/Modules/
* use new boundary interface in the input for tests in Examples/Physical_applications
* use new boundary interface in the input for tests in Examples/Tests
* use new bc
* fix typo
* fix typo
* Update Examples/Tests/SingleParticle/inputs_2d
* fix bc in input
* specific bc for electrostatic inputs
* resetting benchmark for PEC particle CI test after fixing the default pml flags from 1 to 0
* Update Examples/Physics_applications/laser_acceleration/inputs_2d_rz
* remove documentation on previous boundary input
* Comment to clarify where in the code is_periodic is appended and how it is defined
* add default parameters for BC in doc
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* Infrastructure for interacting particles with embedded boundary walls
* remove debug prints
* protect with AMREX_USE_EB
* fix for 2D XZ
* also update level set when regridding
* rename level set to 'DistanceToEB'
* add docstring for scrape particles.
* add assertion on maxLevel() since EB does not work with mesh refinement right now.
* m_eb_if_parser no longer exists
* add test for particle aborption at embedded boundaries
* fix bug I introduced refactoring
* add new test to suite
* fix test names
* fix 2D
* rookie python error
* fix filename in test
* fix script
* fix unused
* make sure we turn EB on in test
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Edoardo Zoni
Axel Huebl
Peter Scherpelz
David Grote
Roelof Groenewald
Revathi Jambunathan
Andrew Myers
