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* Clean up examples folders
* Use `snake_case` names
* Rename `nci_corrector` as `nci_fdtd_stability`
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* Added `none` as an option for fields_to_plot
* Added CI test case
* Further updates, for picmi and CI tests
* Skip the call to amrex::WriteMultiLevelPlotfile when writing no fields
* Now clears m_varnames_fields
* Don't allocate m_mf_output if no varnames
* Updated WarpX-tests.ini
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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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* 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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* Gaussian Beam PICMI: Add openPMD Argument
Add an `--diagformat` option to switch between plotfiles and openPMD
for the Gaussian Beam PICMI example.
* CI: openPMD + PICMI on Windows
* Regression Test: Add openPMD PICMI
* format -> warpx_format
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* Filter Always ON by Default
* Fix CI Tests
* Update Docs
* Fix CI Test dirichletbc
* Default WarpX::use_filter = 0 with RZ FDTD, Add Warnings
* Set WarpX::use_kspace_filter = true by Default, too
* RZ: Fix Bug with PSATD Binary and FDTD Runtime Solver
* Default use_kspace_filter = true, Fix Runtime Issue with Rho Functor
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* added ReadBCParams() function call to python execution and added a test of the electrostatic solver executing from python
* added separate specification of particle boundary conditions in picmi setup and adjusted the inputs for existing tests to follow the new practice
* updated input for rz PICMI test and renamed the electrostatic test to follow standard practice
* added arguments for particle boundary conditions to Langmuir RZ test
* added dictionary to picmi.py to map from picmistandard field boundary condition specifications to that of WarpX
* fixes for failing unit tests; added key, pair 'none' to picmi dictionary of field BCs
* also using 'none' for upper boundary condition for RZ test Python_Langmuir_rz_multimode
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* Read boundary and set periodicity, enumerate BC types, added support for periodic
* separate particle and field boudnary structs
* Update comment for particle struct
* default pml is 0, and reset lo, hi, and do_pml to 1
* turn on pml for MR
* eol
* remove duplication
* resolving commit conflict
* explicitly setting pml_HI_MR
* default pml lo and hi to 0, and set MR pml lo and hi to the domain values if fine patch coincides with domain boundary
* set lo and hi flag for pml when do pml = 1 and domain is non-periodic
* remove commented line
* add doc
* Update Source/Utils/WarpXUtil.cpp
remove empty line
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Docs/source/usage/parameters.rst
lower case for input
* add do_pml flags for IonAcc2d and PlasmaMirror
* add pml = true in PICMI for gaussian beam and plasma acceleration
* pml is the default field BC
* adding temporary defaults for field and particle BC using periodicity
* fix temp initialization
* set default to pec if input sets pml to 0
* fix typo
* logic for both old and new pml interface
* fix eol
* change examples to original pml input with default values
* Update Docs/source/usage/parameters.rst
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* fix comments
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Docs: fix .rst list
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* add functor for doing the tmp particles copy for the back-transformed diagnosti
* merge the particle push options into one kernel
* EOL
* fix assertion
* add a FieldGatherandPushPX method to PhysicalParticleContainer
* handle offset in copyAttribs
* allow this functor to be constructed even it we aren't doing the back transformed diagnostics
* EOL
* update the overloads of PushPX for the Photon and RigidInjected ParticleContainers
* function for dispatching the right field gather
* init this val to 0.0
* fix some typos
* handle scaling the fields for rigid injection
* EOL
* don't need to get pointers to E and B arrays in PushPX any more.
* actually I can't remove these yet
* EOL
* variable order bug
* move the QED stuff to the proper place
* EOL
* make sure we don't build these functors unless the runtime options are toggled
* EOL
* perform the field gather prior to the photon particle push
* remove E and B components and FieldGather methods. Reimplement PushP for rigid injected and physical particles
* update ionization to do field gather inline
* remove E and B from the particle diagnostics
* don't write E or B in these tests for particles
* add missing files
* remove EB from the Regtest ini file too
* no need to do this twice
* important typo
* also do the gather inline for the QED processes that need to
* move these sources inside ifdef for QED
* fix bug in RZ
* remove some fields from the Python tests.
* remove all particle E and B comps from json benchmarks
* don't assert that Ey is the langmuir output
* remove uy from this output
* update test
* restore the mesh fields I turned off by mistake
* turn off field IO for a few python tests I missed
* fix typo
* reset Langmuir_multi benchmark
* update Langmuir_multi_nodal benchmark
* update single precision langmuir bench
* update psatd single precision languir one too
* also do ionization_lab
* finally, ionizaiton_boost
* update benchmarks_json/Langmuir_multi_psatd.json
* update benchmarks_json/Langmuir_multi_psatd_current_correction.json
* update benchmarks_json/Langmuir_multi_psatd_momentum_conserving.json
* update benchmarks_json/Langmuir_multi_psatd_nodal.json
* remove the particle E and B from the choices in the docs
* fix offset bug
* also add the Gather subdirectory
* Update Source/WarpX.H
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* add docstring for LowerCornerWithGalilean
* add new source files to CMakeLists.txt
* also need to update the GPU regression tests
* update the name of the output file for this python test
* remove field gather call from FieldDiagnostics
* fix typo in docstring
* init fields to 0
* add docstring to the CopyParticleAttribs constructor
* some explicit amrex::namepace
Co-authored-by: MaxThevenet <mthevenet@lbl.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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* Implemented new particle diagnostics in picmi
* Cleaned up picmi adding new particle diagnostics
* In PICMI examples, use name option for diagnostics
* For travis, update ubuntu version to bionic
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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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Edoardo Zoni
David Grote
Axel Huebl
roelof-groenewald
Revathi Jambunathan
Andrew Myers
MaxThevenet
Luca Fedeli
