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* Added specification of the version picmistandard
* Set the requirement of Python version >= 3.6
* Add Python version requirement to the docs
* Add comment about Python version to docs
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* mention the use of amrex:: prefix in CONTRIBUTINH
* forgot eol
* incorporate review suggestions.
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Minor updates to Schwinger tests
* Update Examples/Modules/qed/schwinger/analysis_schwinger.py
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Set tests in parallel with 2 threads and 2 procs
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
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* crash for deprecated input parameters
* typo
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Document how to use ADIOS2 (new module) on Summit with openPMD.
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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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* update libensemble scripts
* Update Tools/LibEnsemble/readme.txt
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
* avoid notebook-type readme in WarpX repo.
This file has been pushed to the LibEnsemble repo.
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>
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Document the conventions that go with the three dimensional
compilation variants of WarpX and what they imply in build and
source.
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Homebrew needs a `brew update` to detect new packages.
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* Initial work to add back QED particle generation
* Work in progress: port old QED routines
* Add two distinct CopyFuncs
* modified getMFItInfo and CopyFunc (not working)
* bugfixing & work to add back QED particle creation routines
* bugfixing
* added back quantum photon emission
* bugfixing
* bugfixing
* added back pair generation (still some bugs in photon emission)
* removed unwanted check
* bugfixing
* bugfixing
* bugfixing
* Moved QED folder
* added comments + some refactoring
* added comments
* remove some virtual functions to make lgtm happy
* updated tests
* added PhysicalParticleType
* bugfixing
* added copyright
* improved comments
* improved comments
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* moved inclusion of QEDInternals folder
* moved some inclusion directives between Make files
* moved some inclusion directives between Make files (forgot to add a file)
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/PhysicalParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* corrected alignment
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
* removed some unnecessary amrex::
* add missing comment
* Replaced BL_PROFILE with WARPX_PROFILE
* bugfixing and making some variables const
* removed some moves
* removed some moves
* started to change tau into optical_depth_BW or optical_depth_QSR
* Using initialization policy to initialize optical depth
* bugfixing
* forgot to add a file
* fixed bug
* Revert "fixed bug"
This reverts commit a3fb98d10cc30327635aeaa71451a05ca2229ff4.
* Define doQEDSchwinger function
* Read input parameters for Schwinger process
* Update Source/Particles/ElementaryProcess/QEDPairGeneration.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Added doQEDEvents to OneStep_sub1
* add a bunch of const
* add _rt suffix
* Update Source/Particles/MultiParticleContainer.cpp
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* added path to included files
* Introduced a templated AmIA<something> function using physical_species
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Update Source/Particles/ElementaryProcess/QEDPhotonEmission.H
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* added paths to included headers
* updated documentation
* updated examples
* bugfixing
* bugfixing
* fixing examples
* fixed example
* fixed example
* correct a misprint in error message
* fixed issue related to 1./mass for photons
* Add skeleton of doQEDSchwinger function
* Linked to PICSAR to calculate pair production rate
* Added missing header file
* fix conflicts in QEDPhotonEmission.H
* Written first version of FilterCreateTransformFromFAB.H
* Cleanup some useless comments
* Update Source/Particles/ElementaryProcess/QEDInternals/SchwingerProcessWrapper.H
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Particles/ParticleCreation/FilterCreateTransformFromFAB.H
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Particles/ParticleCreation/FilterCreateTransformFromFAB.H
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Minor revisions and improvements
* Remove trailing white spaces
* Write filter function
* Remove print
* Some debugging and cleaning
* Write tranform function
* remove transform_dummy
* Added some tests
* Remove EOL whitespaces
* update prepare_file_travis.py
* Should fix error in automated tests
* Make the tests run in parallel
* Put path relative to Source/ in includes
* update include path
* Actually resolve conflicts
* put dVdt and weight_index as members of filter and transform functions
* a bit of debugging on GPU
* Add comments and documentation
* Fix typos
* Add assert for single precision
* Update Docs/source/running_cpp/parameters.rst
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Particles/MultiParticleContainer.H
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Update Source/Particles/ParticleCreation/FilterCreateTransformFromFAB.H
Co-Authored-By: Luca Fedeli <luca.fedeli.88@gmail.com>
* Add profiler and minor modifications
* Fix typo
* Update asserts so that module works with momentum conserving algo
* update assert if particles are created in analysis script
* Apply suggestions from code review
Co-Authored-By: MaxThevenet <mthevenet@lbl.gov>
* Add comments to FilterCopyTransform and FilterCreateTransform functions
* Add const and comment
* Update Source/Particles/ParticleCreation/FilterCreateTransformFromFAB.H
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Update test for new diags and remove AllContainerType
* Update Regression/WarpX-tests.ini
* update test
* update tests
* Split Schwinger test into 4 separate tests
* Change name of analysis script
* update tests
* Combine all analysis scripts into a single one
Co-authored-by: Luca Fedeli <luca.fedeli@cea.fr>
Co-authored-by: Luca Fedeli <luca.fedeli.88@gmail.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: Neil <nzaim@iram-fe-003981.extra.cea.fr>
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* host / device function for gathering fields to a single particle
* fix the doxygen comments for the many-particle version of field gather.
* EOL
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* Move interpolation functions for MR to new folder
* Preparatory clean-up of old namespace Average for future MR functions
* Add interpolation for MR in new namespace Coarsen
* Change file names Average.H/.cpp to Coarsen.H/.cpp
* Remove Source/Parallelization/WarpXComm.H (not necessary anymore)
* Coarsening for IO and MR in separate files
* Clean up IO and MR Coarsen namespaces
* Remove old interpolation functions (charge and current)
* Void commit: trigger Travis CI build
* Fix GPU build
* Void commit: trigger Travis CI build
* Add Python script to test interpolation points/weights in 1D
* Move using-directives inside namespaces
* Add Doxygen documentation and comments
* Minor style changes
* Improve new Python script
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Rationale:
The parser conditionally includes CUDA qualifiers in GPU builds.
There is only CUDA C++, no CUDA C. C is (mostly) a subset of C++.
Consequently: those are now C++ files :-)
Simplifies build logic with build system generators.
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* Relax PSATD check on boxes, so that PSATD momentum-conserving can be used
* Increase tolerance of test
* Add automated tests for momentum-conserving PSATD
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Fixes include paths and missing includes in diagnostics.
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* Update parameters.rst
Add in situ visualization control parameters
* Update parameters.rst
* fix the end-of-line whitespaces issues
Co-authored-by: Ge <lge@pc97608.t-mobile.com>
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Document explicit steps to build WarpX with openPMD support on
Summit.
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* Load Particles: external_file MPI Support
Split and add MPI support for particle loading from an openPMD
file.
Changes input file to allow overwriting the charge and mass by
user input (with a warning). Allows to add "weighting" to
files as constant record (ED-PIC extension).
Co-Authored-By: Ligia Diana Amorim <ldianaamorim@lbl.gov>
Co-Authored-By: Maxence Thevenet <mthevenet@lbl.gov>
* Remove RZ guard.
Particles are 3D, if this is not yet working we can fix it
later.
Co-authored-by: Ligia Diana Amorim <ldianaamorim@lbl.gov>
Co-authored-by: Maxence Thevenet <mthevenet@lbl.gov>
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* add option to write (or not) all modes when running RZ
* do not dump rz modes in Langmuir_multi_rz
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* Start implementing PSATD push without rho.
TODO: 1) fix unit test pml_x_psatd;
2) try new PSATD push in PML;
3) avoid intro of new derived class?
* Correct PSATD push to fix PML test.
* Few improvements on new PSATD push:
- new class name is 'PsatdAlgorithmMixed' (both rho and J are used);
- new algorithm parameter to choose between available implementations:
parameter name is 'psatd_push', possible values are 'standard' for
old implementation using rho via Gauss law and continuity equation
and 'mixed' for new implementation using rho via Gauss law and J for
all remaining terms.
* Fix style error (tabs vs four white spaces).
* Improve comments for available PSATD algorithms.
* Correct few typos in latest comments.
* Implement first current correction:
- new member function 'CurrentCorrection' in class SpectralSolver;
- correction applied only without subcycling (in function 'OneStep_nosub');
- TODO: add correction when subcycling is used (in function 'OneStep_sub1');
- back to old implementation of PSATD push of E and B (class 'PsatdAlgorithmMixed' removed);
- TODO: PML unit test 'pml_x_psatd' does not pass.
* Small cleanup:
- remove residual option for choice of PSATD push algorithm (only one choice now);
- improve comments.
* Implement div(E) diagnostics for spectral case.
* split travis tests in bigger matrix
* split more TravisCI tests, add electrostatic, use defaults values
* typo
* Move computation of div(E) to base class SpectralBaseAlgorithm.
* need to split psatd too
* consistent variable names and use function to avoid duplication
* fix typo for qed tests
* typo
* also need to update run_tests.sg
* Update copyright tags.
* change matrix
* Add test of div(E) vs rho/epsilon_0 in PML test.
* Small clean-up.
* Small clean-up
* Remove option for current correction from input files of two new tests (not used)
* Small clean-up: remove unnecessary references
* More clean-up (minimize style changes to keep PR simple).
* Add specific 2D/3D tests for current correction:
- 'Langmuir_multi_2d_psatd_cc': same input file as 'Langmuir_multi_2d_psatd',
except for current correction and output of divE;
- 'Langmuir_multi_psatd_cc': same input file (3D) as 'Langmuir_multi_psatd',
except for current correction and output of divE;
- add corresponding Python scripts for analysis: same as previous ones,
except for check on L-infinity spatial norm of rho/epsilon_0 vs div(E);
- revert changes on old tests: do not use current correction in old tests
(benchmarks on Battra do not need to be updated).
* Improve comments.
* Start implementation of new averaging with staggering:
- face-to-cell-center and edge-to-cell-center replaced so far;
- TODO: node-to-cell-center and 1D behavior (AMREX_SPACEDIM=1).
* Remove unrelated style changes (cleaner PR).
* Avoid duplication of input files and analysis scripts for new tests
* Improve comments for Doxygen documentation.
* Improve comments for Doxygen documentation.
* Small clean-up
* first implementation of Diags base classes
* Small clean-up
* Small clean-up
* Fix erroneous non-ASCII character
* Small clean-up
* Auxiliary function for current correction in class WarpX to keep OneStep_nosub clean
* Remove unrelated style changes (cleaner PR)
* Improve comments
* Instrument virtual function 'CurrentCorrection'
* Trying to fix build error detected by LGTM analysis only
* add example, temporarily
* Continue implementation of new averaging with staggering:
- new function takes reference to single MultiFab (no vector);
- TODO: node-to-cell-center still in progress.
* Fix small bug and clean up
* Fix bug in loop over n=0,...,ncomp-1 and clean up
* add more functions
* Add Doxygen documentation and clean up
* Small clean-up in Doxygen documentation
* Compile in single precision: add _rt suffix to avoid unnecessary conversions
* Avoid accessing staggering index directly from IntVect in innermost loops
* Implement periodic-single box option for spectral
* Fix out-of-bound in the periodic, single-box case
* Replace do-while loop with for loop (default ncomp=1)
* Remove temporary pointer and pass reference to MultiFab (instead of MultiFab*)
* Replace AMREX_LAUNCH_HOST_DEVICE_LAMBDA with ParallelFor
* cleaning and initialize output mf
* use general average routine
* move flush in new class, and implemented the Plotfile derived class
* add comments
* eol
* free memory in destructor
* typo
* typo
* no need to clear MF pointers there
* though shalt not break existing tests
* FlushRaw doesnt have to be virtual for now
* The importance of being constant
* Capability to select fields in output files
* EOL
* revert to old inputs
* const in right place
* avoid brace initializer there
* oops, fix logic error in is_in
* Use old name for output image of new 2D test
* user can choose flush interval, same behavior as plot_int
* Small clean-up in Doxygen documentation
* Add option to plot raw fields
* eol
* replace ter flush with dump to avoid confusion
* add options
* Diagnostics stores a vector of functors to compute diags on the fly
* eol
* Field gather from diags to sync particle quantities
* New diagnostics handle RZ with same behavior as old ones
* cleaning and doc
* const ref for string
* smarter for loop from Axel and typo fix from Reva
* Functors to compute some fields
* simplify code following Dave's comments
* Create subfolders and add more output options (divE etc.)
* eol
* Add documentation for periodic_single_box_fft
* For periodic, single-box, apply current correction after guard cell exchange
* rename mode_avg to convertRZmodes2cartesian
* Update CellCenterFunctor.H
* fill varnames and vector of functors at the same time
* output rho_new, not rho_old
* WarpX instance not needed here
* add const
* little bit more of reorganization
* Travis CI: force 2 MPI processes only for numprocs > 2
* Use special FFT (PR #834) and new diagnostics (PR #844) in new tests
* Improve Doxygen documentation
* Move option do_current_correction from warpx to psatd
* Fix path to output files for tests using new diagnostics
* Fix additional paths to output files for new diagnostics
* Add input paramter do_current_correction to documentation
* Fix test Langmuir_multi_psatd_hybrid: do not plot divE
* Remove input parameter amr.plot_int in tests using new diagnostics
* Trigger failing source/style checks on Travis CI
* Fix build error due to public include
* Add missing const keywords
* Change test names and corresponding analysis scripts
* Improve Python script for analysis
* Do not rename output files in old CI tests (without current correction)
* Fix output file name prefix for some tests
* Trigger Travis CI build after AMReX bug fix
* Void commit: trigger Travis CI build
* Fix some tests failing due to recent changes in master
* Use new diagnostics for particle output correctly
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Print tolerance and error in Python analysis
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Print tolerance and error in Python analysis
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Improve documentation
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
* Fix EOL white spaces
* Fix name of particle output variables
Co-authored-by: MaxThevenet <mthevenet@lbl.gov>
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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Cleanup
Cleanup
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David Grote
MaxThevenet
NeilZaim
Axel Huebl
Remi Lehe
Andrew Myers
Edoardo Zoni
lge0303
Michael E Rowan
