| Age | Commit message (Collapse) | Author | Files | Lines |
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* Clean up examples folders
* Use `snake_case` names
* Rename `nci_corrector` as `nci_fdtd_stability`
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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
for more information, see https://pre-commit.ci
* move import os (mpl)
* move import yt (mpl)
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Cleanup around matplotlib.use
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* 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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* Draw Gaussian beam position with amrex random engine
* Update benchmarks
* Update tolerance in space-charge tests
* Update benchmark for space charge initialization test
* Update benchmarks
* Update benchmark
* Clean-up code
* Update benchmarks
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* AMReX/PICSAR: Weekly Update (#2478)
Weekly update to latest AMReX.
Weekly update to latest PICSAR (no changes).
```
./Tools/Release/updatePICSAR.py
./Tools/Release/updateAMReX.py
```
* Update benchmarks
* Update benchmarks for 3D tests
* Update benchmarks
* Update benchmark
* Update benchmark
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Simplify momentum initialization in example input files
* Update benchmarks
* Trigger Build
* Apply suggestions from code review
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Add more amrex prefix
* Remove using namespace amrex in PlasmaInjector.cpp
* Fix compilation with OpenPMD
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* ChecksumAPI: yt 4+ ds.force_periodicity()
Mitigate issues of the form
```
RuntimeError: yt attempted to read outside the boundaries of a non-periodic domain along dimension 0.
Region left edge = -7.5e-06 code_length, Region right edge = 7.500000000000002e-06 code_length
Dataset left edge = -7.5e-06 code_length, Dataset right edge = 7.5e-06 code_length
This commonly happens when trying to compute ghost cells up to the domain boundary. Two possible solutions are to select a smaller region that does not border domain edge (see https://yt-project.org/docs/analyzing/objects.html?highlight=region)
or override the periodicity with
ds.force_periodicity()
```
* make yt3 compatible
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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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simulations (#1761)
* Update copyright notices
* allow specification of boundary potentials at runtime when using Dirichlet boundary conditions in the electrostatic solver (labframe)
* added parsing to boundary potentials specified at runtime to allow time dependence through a mathematical expression with t (time)
* updated to picmistandard 0.0.14 in order to set the electrostatic solver convergence threshold
* update docs
* various changes requested during PR review
* fixed issue causing old tests to break and added a new test for time varying boundary potentials
* possibly a fix for the failed time varying boundary condition test
* changed permission on the analysis file for the time varying BCs test
* switched to using yt for data analysis since h5py is not available
* made changes compatible with PR#1730; changed potential boundary setting routine to use the ParallelFor construct and set all boundaries in a single call
* fixed typo in computePhiRZ
* updated docs and fixed other minor typos
* fixed bug in returning from loop over dimensions when setting boundary potentials rather than continuing
* changed to setting potentials on domain boundaries rather than tilebox boundaries and changed picmi.py to accept boundary potentials
* now using domain.surroundingNodes() to get the proper boundary cells for the physical domain
* fixed typo in variable name specifying z-boundary potential
* changed boundary value parameter for Dirichlet BC to boundary.field_lo/hi and changed setPhiBC() to only loop over the grid points when a boundary value has changed
* switched specifying potential boundary values though individual inputs of the form boundary.potential_lo/hi_x/y/z and incorporated the new BC formalism through FieldBoundaryType::Periodic and FieldBoundaryType::PEC rather than Geom(0).isPeriodic(idim)
* removed incorrect check of whether the potential boundary values are already correct, also had to change the input to test space_charge_initialization_2d to comply with the new boundary condition input parameters and finally changed permissions to analysis_fields.py file for the embedded boundary test since it was failing
* remove line from WarpX-tests.ini that was incorrectly added during upstream merge
* changed input file for relativistic space charge initialization to new boundary condition specification
* fixed outdated comment and updated documentation to reflect that the Dirichlet BCs can also be specified when using the relativistic electrostatic field solver
* moved call to get domain boundaries inside the loop over levels
* cleaned up the code some by using domain.smallEnd and domain.bigEnd rather than lbound and ubound
* added check that a box contains boundary cells before launching a loop over that box cells to set the boundary conditions
Co-authored-by: Peter Scherpelz <peter.scherpelz@modernelectron.com>
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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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* 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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* always print error and tolerance before ASSERT in CI tests
* eol
* fix typos
* more typo
* typo
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Do not assume a location of the python interpreter.
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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
- match few input file names with corresponding Python scripts names
- update entries in /Regression/WarpX-tests.ini for Travis CI
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Edoardo Zoni
Axel Huebl
Remi Lehe
Neïl Zaim
roelof-groenewald
MaxThevenet
Tools
Edoardo Zoni
