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* add component names to checkpoint
* read in particle components and add the missing ones on restart
* do not add components if one by the name already exists
* sign error
* Better warning messages
* Update Source/Diagnostics/ParticleIO.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add CI test for restarting particles with runtime-added attributes
* remove unused module
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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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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* Various updated related to defining embedded boundaries in Python
* Fix typo in comment
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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* Add a class to output checkpoint diagnostics in picmi
* Add argument to picmi Simulation for restarting from a checkpoint
* Changes to make the checkpoint work
* Change inheritance for Checkpoint and rename variables in Simulation
* Remove file exists check
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* Added wrapper to get number of particle species tracked by the scraper
Not sure if this is going to be useful, but it demonstrates a method to get information
from the ParticleBoundaryBuffer into Python.
* Stubbed out the main wrapper functions
* Added parameters to wrapper
* Added wrapper for getting the number of particles scraped of a species on a boundary
* added picmi arguments to scrape particles at the domain boundary
* Added wrapper to get the full particle buffer into python
* rearanged the getBuffer properties code a little
* Added docstrings +other suggested changes
* Added num_particles_impacted_boundary docstring
* fixed mistake in docstring
* Changed boundary parameter to be a string for clarity
* Fixed issue with the boundary parameter for scraping
* Fixed issue with the boundary input for scraping stats wrapper
* Added demonstration of particle scraping wrapper
* Added analysis.py file
* Fix typo in one of the dimension maps
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
* Added before esolve to warpx evolve
* added test for the scraped particle buffer wrappers
* Moved python PICMI particle boundary scrape test
* Renamed test file to the correct name
* Removed old test
* added special functionality to get the timestep at which particles were scraped
* removed debug print
* added python wrapper for the clearParticles() function of the scraper buffer
* added special wrapper function to get the timesteps at which the particles in the boundary buffer were scraped
* updated test to match the non-PICMI test for the particle scraper buffer
* Fix uncaught rebase mistake
* re-activated picmi test of accessing the scraped particle buffers via python
* added documentation for the new parameters involved in the scraped particle buffer and fixed remaining issue with picmi test
* changes requested during code review
Co-authored-by: mkieburtz <michaelkieburtz@gmail.com>
Co-authored-by: Roelof <roelof.groenewald@modernelectron.com>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>
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* added functionality to save particle positions from the previous step
* copied WarpX variable to local variable to fix issue with GPU and DPC++ compilation
* switched to using a species attribute to toggle whether previous positions are saved so it can be turned on for only a subset of species if desired
* changed variable name to be more verbose
* added CI test of saving the previous particle positions
* start of a table in the documentation to describe commonly used runtime attributes
* generate test benchmark data from results obtained with a 2 processor run - the same as what is done during the test
* relaxed tolerance on test
* regenerate CI test reference data with USE_PSATD=TRUE
* Update Docs/source/developers/particles.rst
Co-authored-by: Phil Miller <unmobile+gh@gmail.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* do_pml not parsed. remove code that was added to support both types of boundary interface
* add paranthesis
* fix eol and move to BackwardCompatibility
* missing semicolon
* Update Source/WarpX.cpp
* clean input files in examples
* delete do_pml in performance test input
* fixing an example input file in docs
* Update Source/WarpX.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* cleaning up docs
* Update Docs/source/usage/parameters.rst
* fix eol
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Implemented new style BTD in picmi
* Added rho_species. Added documentation
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(#2167)
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* added functionality to picmi.py to initialize MCC collisions from python runscripts
* bug fix and copyright declaration change
* add Boltzmann's constant to picmi.py
* added test for picmi MCC setup
* set diagnostic output name for test and cleaned up analysis.py
* fixed style issue with EOL white space after merge
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* added functionality to picmi.py to allow an embedded boundary to be set from a python run script
* added test: embedded sphere run from python (the test is the same as ElectrostaticSphereEB)
* added a line to prepare_file_travis.py so that tests with USE_EB=True are not included in Python CI test list
* fixed import path in analysis.py file for new test
* added WarpX_EB flag to setup.py so that embedded boundary functionality can be included in pip installs of pywarpx
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* For RZ, changed the sign of the density corrections near the axis
* Further fixes for deposition correction near axis
* Yet one more sign fix for charge density
* For RZ spectral solver, filled in the guard cells below the radial axis
* Fix white space at end of line
* In RZ spectral backtransform, ensure box is valid
* For RZ inverse volume scaling, fixed use of nGrow to use nGrowVect
* Temporary fix adding damped cells in the domain interior
* Bug fix for RZ PSATD scalar backward transform
* Fixes for damping of the fields in the z-guards
* Bug fix in DampFieldsInGuards
* Bug fix in DampFieldsInGuards (for tiling)
* Added warpx_amr_check_input input parameter
* Removed unneeded damp and zero_in_domain input
* Removed damping related code from picmi
* Improved some comments in code copying field to the radial guard cells
* Update Source/FieldSolver/SpectralSolver/SpectralFieldDataRZ.cpp
Simplify the expression for the sign
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Updated benchmarks
* Updated tolerance for Langmuir analysis script
* Updated CI test galilean_rz_psatd_current_correction
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* Added functionality to pass mpi comm from python script to amrex during initialization
* Fixed missing _ in MPI._sizeof()
* Added functions to get the current processor's rank and total number of processors
* Renamed MPI_Comm to _MPI_Comm_type and defined _MPI_Comm_type in except statement
* Updated comment to explain why mpi4py needs to be imported before loading libwarpx
* Removed ifdef flags that prevent amrex_init_with_inited_mpi from being declared when MPI is off
* Changed amrex_init_with_inited_mpi to be declared even when not using mpi, but will be defined to be functionally the same as amrex_init
* Defined MPI = None to signify whether MPI is used, to add another check when initializing amrex
* Changed ifdef blocks in WarpXWrappers.cpp/h to fix compile errors.
Added ifdef block to conditionally declare amrex_init_with_inited_mpi in WarpXWrappers.h to prevent compile error when not using MPI. Removed ifdef block to declare/define same function in WarpXWrappers.cpp since function needs to be declared even when MPI is not used, but will never be called in that case.
* Changed BL_USE_MPI to AMREX_USE_MPI and removed incorrect MPI=None statement
* Changed BL_USE_MPI to AMREX_USE_MPI
* Added test to verify correct passing of MPI communicator to amrex
* Added ability to pass mpi_comm to sim.step
* Change test to check for differeing outputs when passed different inputs
* Removed obsolete comments refactored program to use more shared code
* Refactored comments
* Updated description to match test
* Removed unecessary imports and updated comments
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* Added warpx_solver_verbosity input parameter
- This input paramter is for the electrostatic solver to pass into
MLMG::setVerbose(int)
- Originally this value was hardcoded to 2
* readded accidently deleted line
* Handle the default solver_verbosity value on the C++ side
* Verbosity parameter now works the same as warpx.self_fields_max_iters
- The input parameter for mlmg verbosity is now warpx.self_fields_verbosity
- It still has a default value of 2.
* fixed missing comma
* added missing parameter to function call
* Added documentation entry for warpx.self_fields_verbosity
* corrected documentation
* fixed formatting mistsake
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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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* 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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* Added multiple particles injection source
* Added documentation for MultipleParticles
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* Load balance params now input as algo.
* load balance params to algo
* Backward compatibility and knapsack_factor_doc
* Update Docs/source/running_cpp/parameters.rst
* backward_strings
* picmi
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* Updates to match picmi version 0.0.14
Added call to register constants.
* Python: Bump Versions
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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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 ElectrostaticSolver in picmi
* Added relativistic option to picmi ElectrostaticSolver
* Update PICMI version
* Fix electrostatic with picmi
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Docs: PSATD Runtime Option
* Tests: PSATD Runtime Option
Add new runtime option to PSATD regression test matrix.
* PICMI: PSATD runtime option
* Source: PSATD Runtime Option
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* use_filter now controls physical and k-space filtering
* Added backward compatibility error if use_kspace_filter is set
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* Update picmi constants to match the values in PhysConst
* In picmi, use string q_e for charge instead of float with charge_state = +-1
* Updated benchmarks of picmi tests
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(#1361)
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* added the phase argument for the gaussian laser
* removed signature
* added laser phase to picmi api
* added doc string for phi0
* Update parameters.rst
typo fix
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* PICMI: read flag for laser continuous injection
* Simplify assignment of do_continuous_injection
* Update PICMI version
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Initial version of use_damp_in_z_guard option
* Fix typo in WarpX.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Changed use_damp_in_z_guard to use_damp_fields_in_z_guard
* Added documentatin for use_damp_fields_in_z_guard
* Clean up for use_damp_fields_in_z_guard
* Added use_damp_fields_in_z_guard to picmi interface, and moved it to the psatd input group
* For RZ spectral, damping of the fields is on by default when not periodic
* Updated documentation for use_damp_fields_in_z_guard
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
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* picmi - For 2D, changed arguments to expect length 2 lists
* picmi - For 2D, guard_cells should be length 2
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* PICMI Added applied fields
* PICMI fixed typo in Constants
* Change picmistandard version requirement to 0.0.9
* Increment required picmi version
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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This fixes a small bug in the `picmi.ParticleListDistribution` class.
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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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* Rename Input to `algo.maxwell_solver`
Rename the input option `algo.maxwell_fdtd_solver` to
`algo.maxwell_solver` and throw a useful error message for users
using the old option.
This is in preparation to unify FDTD and PSATD input control to
reduce mutually exclusive binary variants of WarpX.
* MW Solver Name: Update Examples
Update all example to use the new algo.maxwell_solver option.
* Fix typo in comutation of dt
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* Added k-space filter for RZ spectral solver
* Added SpectralBinomialFilter files for RZ spectral solver
* Added RZspectral binomial filter to CMakeLists.txt
* Update Docs/source/running_cpp/parameters.rst
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Docs/source/running_cpp/parameters.rst
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/FieldSolver/SpectralSolver/SpectralBinomialFilter.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/FieldSolver/SpectralSolver/SpectralBinomialFilter.cpp
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Update Source/FieldSolver/SpectralSolver/SpectralFieldDataRZ.H
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* Fixed literals in SpectralBinomialFilter.cpp
* For RZ spectral, apply filter to rho old and new
* Added SpectralBinomialFilter::InitFilterArray
* For SpectralBinomialFilter, combine R and Z into one routine
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* For SpectralBinomialFilter, combine R and Z into one routine, part 2
Co-authored-by: Edoardo Zoni <59625522+EZoni@users.noreply.github.com>
* For SpectralBinomialFilter, combine R and Z into one routine, part 3
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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* Clean up implementation of current correction:
- abort when current correction runs with psatd.periodic_single_box_fft=0
- rename input parameter from psatd.do_current_correction to psatd.current_correction
- add nodal tests in 2D and 3D (using direct current deposition)
- change 2D test: use Esirkepov deposition, instead of direct, as in 3D test
- add/update relevant checksum benchmarks
* Small clean-up
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Andrew Myers
Neïl Zaim
Roelof Groenewald
Remi Lehe
Michael Kieburtz
David Grote
Nicholas Ruof
Phil Miller
Revathi Jambunathan
Kevin Z. Zhu
Peter Scherpelz
Michael Kieburtz
Edoardo Zoni
Michael E Rowan
Axel Huebl
Igor Andriyash
