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* Beginnings of signal handling machinery
* Add tentative logic to make checkpoint call
* Adapt formatting slightly
* Add calls to read signals and set up signal handlers
* Initialize signal flag array
* Add parsing of signal names, and fix some whitespace issues
* Skip signal setup on Windows
* added checkpoint and break signal inputs to picmi.py
* Address initial review requests
* Correct comment to match changed code
* Convert maximum signal number to a symbolic name
* Always parse signal input, and error out on Windows or wherever it may be unsupported
* Typo fix
* Add missing reset of checkpoint signal flag
* Add reset of break signal, in support of Python or library usage
* Test for a configured checkpoint diag when asked to checkpoint on a signal
* Fix typo in Linux code path
* Clean up MPI support
* Use symbolic name for maximum signal number
* Fix unused variable in the no-MPI case
* Add missing header inclusions
* Switch signal parsing to an enumerated table
* Test signal handling for Linux, not GNU C library
* Avoid another magic number
* Update MPI_Ibcast call to match symbolic array length
* Update loop over signal flags to use symbolic limit
* Match #includes to usage
* Add omitted C++ std <atomic> header include
* Guard entire set of signal definitions as *nix-only, not for Windows
* Broaden Windows exclusion to avoid zero-length array that displeases MSVC++
* Check return value from sigaction()
* Convert conditional calls to Abort() to assertions
* Move check for platform support to input parsing
* Shift signal handling code over toward ABLASTR to share with ImpactX and Hipace++
* Minor cleanup
* A bit more cleanup
* Fix formatting nits
* Add AMReX error handling on MPI calls
* Add ABLASTR signal handling code to GNU makefile too
* Document new input parameters
* Use ABLASTR assertion macros in ABLASTR code
* Convert requests limit value to a requests array size
* Generalize signal handling to an arbitrary set of potential actions
* Rename class to match usage and file name
* Stick stuff in ABLASTR namespace
* Indent conditional includes as requested
Co-authored-by: Roelof <roelof.groenewald@modernelectron.com>
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* Rename `serialize_ics` as `serialize_initial_conditions`
* Add Backward Compatibility Check
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Add for all diagnostics the equivalent of `<diag>.file_min_digits`.
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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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* Set geometry earlier in Python
* Fix comment typos
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* Make moving window dimensionality consistent in PICMI
* update PICMI_inputs_plasma_acceleration_1d.py
* two elements for moving window velocity in RZ
* update RZ laser_acceration test
* update PICMI version
* update PICMI Langmuir RZ test
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* allow Dirichlet BCs in r when r_min != 0 with ES RZ simulations
* handle the rmax boundary condition setting properly when rmin == 0
* add ability to specify rmin and rmax potentials through picmi
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* Initial attempt at moving function into LibWarpX
* Bugfix - undefined structs in get_particle_theta
This is untested, identified by IDE/visual inspection only
* Unify newlines
* Delete libwarpx.clight (duplicated picmi.py)
See picmi.constants.c
* Change function descriptive comment to docstring
Also remove extra newline in __init__ beginning.
* Replace pywarpx/_libwarpx calls appropriately
* Fix atexit register of finalize function
* Reorder WarpX.py imports for pre-commit
* Use picmi.Simulation.extension = libwarpx alias
This will hopefully preempt user script changes if we restructure things
to allow multiple WarpX runs to be done within a single Python script.
* Fix libwarpx ref in WarpX.getProbLo/getProbHi
* Update get_particle_boundary_buffer doc reference
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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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* modify requirements.txt and add input file for 1D Python pwfa
* add 1D Python plasma acceleration test to CI
* picmi version
* USE_PSATD=OFF for 1D
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Regression/WarpX-tests.ini
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Cartesian1D class in pywarpx/picmi.py
* requirements.txt: update picmistandard
* update picmi version
* requirements.txt: revert unintended changes
* 1D Laser Acceleration Test
* Update Examples/Physics_applications/laser_acceleration/inputs_1d
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* Update Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration_1d.py
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* add data_list to PICMI laser_acceleration test
* increase max steps and fix bug in pywarpx/picmi.py 1DCartesian moving window direction
* add data_lust to Python laser acceleration test
* picmistandard update
Co-authored-by: Prabhat Kumar <prabhatkumar@kraken.dhcp.lbl.gov>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* PICMI: Add amr.max_grid_size_<x,y,z>
* Set All Flags in Python
* PICMI: Add amr.blocking_factor_<x,y,z>
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* added option to specify absolute tolerance for the MLMG solver used in the electrostatic field solve
* added absolute tolerance argument to the documentation
* fixed bug introduced during copy and paste
* expanded documentation for MLMG solver absolute tolerance (added unit) and added a link to the AMReX documentation describing the MLMG solver parameters
* possibly more robust handling of the MLMG convergence
* switched from std::max to amrex::max to hopefully fix compiler complaints
* updated checksum values for MCC test (background_mcc); the values changed only slightly, presumably due to a difference in the initial field solve which would now have the absolute tolerance value included, but since the Python version of this same test (which uses the direct solver) still passes the change is assumed to be inconsequential
* another try to fix the compile issues
* print a message to notify user if the max norm of rho is zero
* Apply suggestions from code review
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
* switched print statements to the new warning logger
Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>
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* PICMI: Add div(E),div(B) Cleaning Options
* Update PICMI Version: 0.0.15
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* Use os.path.join in picmi.py for portability
* Apply suggestions from code review
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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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Phil Miller
David Grote
David Grote
Ryan Sandberg
Roelof Groenewald
Edoardo Zoni
Axel Huebl
Prabhat Kumar
Peter Scherpelz
Lorenzo Giacomel
Kevin Z. Zhu
Andrew Myers
Neïl Zaim
Remi Lehe
Michael Kieburtz
Nicholas Ruof
Phil Miller
Revathi Jambunathan
Michael Kieburtz
Michael E Rowan
