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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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* Correct density
* update
* Add test
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Update Regression/WarpX-tests.ini
* update
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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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>
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Edoardo Zoni <59625522+EZoni@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`
* changes requested during PR review
* remove `do_no_deposit` from tests without field evolution
* Fix doc-string in `GuardCellManager.H`
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Updated 1D CI tests with particles
* Updated required version of yt to 4.1.0
* Fixed CI analysis of collisionXYZ
Fixed the fetching of the particle data
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* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
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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
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* 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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* added Coulomb collision installation to picmi.py
* added comment saying the input values for the new PICMI test comes from inputs_2d
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* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
* pre-commit: Python imports
Add two new Python rules to:
- remove unused imports
- sort imports according to PEP8
`.editorconfig`: isort options
https://github.com/PyCQA/isort/wiki/isort-Settings
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Cleaning: double np and lib
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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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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* Update Scripts to Handle New File Names
* Use glob in Analysis of Collision Tests
* Use rstrip in Analysis of Collision Tests
* Regex: Match ends-in-digits
Thanks Phil! :)
Co-authored-by: Edoardo Zoni <ezoni@lbl.gov>
Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
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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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* Add rotation.
* Fix a small bug
* Add automated test.
* rename inputs_rz
* Add json
* minor
* add comment.
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update analysis_collision_rz.py
* Fix missing import
* Change tolerance.
* Add warnings
* Apply suggestions from code review
* Move assert.
* fix end-of-Line whitespaces.
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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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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* Define New Input Parameter interpolation.shape_factors_order
* Use New Input Parameter, Remove Obsolete Ones
* Add New Input Parameter to PICMI Interface
* Update Docs, Use New Input Parameter in Remaining Input Files
* Cleaning
* New Name: algo.particle_shape
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* Add CI coverage for the plotfile particle filter function
* Minor fix in analysis script
* Test all 3 particle filters in 2D/3D/RZ
* Dirty trick to deal with same ID from multiple MPI ranks + enforce 100 characters per line rule
* Fix CI when running on a single MPI rank
* Add new module to avoid duplicate code
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* Unify intervals notation
* Fix diagnostic intervals with PICMI
* Use new syntax in updated Larmor test
* Update PICMI to comply with the standard
* Update new hybrid test
* Update particles_in_PML test input files
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* Update inputs_3d
* Update inputs_2d
* Add ndt
* Doc
* Doc
* Update inputs_3d
* Update inputs_2d
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Input: Remove n<something> options
The information in
- lasers.nlasers
- particles.nspecies
- collisions.ncollisions
is redundant with their `<...>.names` counter-part and requires users
to change info at two locations. We just remove this now since we can
query the size of names automatically in the parser.
* Examples: remove n<something>
Removes:
- lasers.nlasers
- particles.nspecies
- collisions.ncollisions
from examples.
* QED: Update nspecies
* Removed nspecies and nlasers from the Python interface
Co-authored-by: Dave Grote <grote1@llnl.gov>
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* add a checksum module for regtests
* All capabilities to checksum tests
* update tests to generate a clean benchmark
* call checksum tests from analysis scripts
* Add checksum json benchmarks
* add missing script, better printing and increase tol
* eol
* fix permission, and bump tolerance
* chmod +x checksumAPI.py
* update benchmarks, probably old ones were wrong due to parallelization
* remove unused variable, thanks lgtm
* special handling when the benchmark is 0
* non-zero but very small CFL for 1 step for init tests
* reset erroneous Python benchmarks
* slightly bump tolerance for initial distribution test
* too small dr results in nans
* improve prints, tolerance handling, and fix tests
* typo
* enable tolerance and fields/particles optional comparison to fix tests
* more minor cleaning in space charge initialization tests
* update Python benchmarks for serial runs
* Run Python tests with 1 rank instead of 2
* fields that are zero should not be in reg tests
* Add developer documentation on checksum regression tests
Co-authored-by: Tools <warpx@lbl.gov>
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* Create subsection for diags documentation in input parameters list
* Replace old diags with new ones IN DOC ONLY
* eol whitespace
* Check first CI test with new diags, before changing all of them
* use diags in all CI
* oops, had forgotten all examples except Tests/
* Updated picmi interface to use the new diagnostics
* fix bug in how field functors are initialized for diags
* fix bug: should always dump output at the end of simulation
* eol
* update test parameters in ini file
* Further fixes to picmi for new diagnostics
* Updates PICMI input files to use the new diagnostics
* avoid dumping final plotfile twoce
* update test to run with new diags
* fix typo introduced when fixing merge conflicts
* had accidentally removed the max_step here, so the run never ended on TravisCI
* Add Diagnostics.py for picmi with new diagnostics
* Adding m_ for member variables in new diags (#934)
* fixing bug to initialize CellCenterFunctor for Bx
* diag_name renamed to m_diag_name
* some more diag members made m_
* renaming member variable mf_avg to m_mf_output
* fixing m_mf_output to mf_dst in comments
* Python documentation updates (#936)
* Update Python documentation
* Added numpy as a requirement for the Python installation
* Cleaned EOL white space in Python documentation
* Add periodictable to the Python packages required
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Added periodictable to required packages for pure Python version
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Add hostname to LoadBalanceCosts reduced diagnostic (#902)
* Add hostname to reduced diags
EOL
Fix rd loadbalancecosts test
AMREX_USE_MPI
EOL
move macro to source file
Review changes
eol
add GPU ID if running on GPU
eol
Typo in comment
use vectors to get rid of C-style memory management
Fix for test
eol
* Compute number of unique box data fields in analysis script
* analysis script
* Use amrex Tokenize to split string
* Update WarpXUtil.cpp
* Update WarpXUtil.H
* [mini] Add contact us section to documentation (#941)
* add contact us section to doc
* Update Docs/source/contact_us.rst
Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov>
* Update Docs/source/contact_us.rst
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
* stop calling the old WritePlotFile functions
* fix new diags, problem with rho and PSATD and particle output variables
* remove more deprecated code for old diags
* Move checkpoint capability to new diagnostics
* error if user asks custom output for checkpoint
* eol
* some more old diags code deleted
* further cleaning
* eol
* further cleaning, make sure that WarpX compiles with USE_OPENPMD
* remove old diags parameters
* use new option to change the plotfile name
* typo
* do not need checkpoint files
* adapt to new option for checkpoint
* removed unread options as they make tests crash
* remove warpx_checkInt from the Python layer
* remove some more python wrappers
* add checkpoint capability with 2 diags in new output
* fix bug in MultiDiagnostics, and (should) fix checkpoint-restart test
* fix restart CI test
* avoid issue when writing the last plotfile twice
* dpgrote's fix for the Python tests
* update doc for diagnostics
* stop requesting ndiags, this is read from the list of diags
* awk to remove ndiags from all example input files
* Removed diagnostics.ndiags from picmi interface
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
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cleanup_examples_input_files: synchronize with 'dev' branch before requesting PR review.
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- remove wrong extension '.rt' from previous commits ('rt' string
denotes regression tests and does not represent a file extension)
- put back string 'rt' in input file names wherever needed
- update entries in Regression/WarpX-tests.ini for Travis CI
- add entries in Regression/WarpX-tests.ini corresponding to input files
previously not tested: now testing only run (no analysis)
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- add strings '2d' or '3d' for dimensionality of test case
- use '.' only to separate file names from file extensions
- use uniform file extension '.rt' in all input files
- change permission of input file in /particle_pusher/ from executable
to read/write
- update entries in /Regression/WarpX-tests.ini for Travis CI: comment
out two tests where parameter 'dim' does not match dimensionality in
input file
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Roelof Groenewald
Yinjian Zhao
David Grote
Edoardo Zoni
Axel Huebl
Revathi Jambunathan
NeilZaim
MaxThevenet
Tools
Edoardo Zoni
