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* Python: generalize library search (Win)
* CMake: Honor Multi-Config Lib Alias
For multi-config build generators (MSVC, Ninja opt-in), we
have a deeper build structure based on the build type. Honor
this structure for the (Python) library alias/symlink.
* CI: Windows with Python
Co-authored-by: Dave Grote <dpgrote@lbl.gov>
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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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* Update: AMReX/PICSAR to 21.10
* WarpX: 21.10
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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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between C++ and Python (#2285)
* added missing parts to allow an external Poisson solver to be used instead of the MLMG solver
* added rho and phi wrappers to fields.py
* added an example of using an external Poisson solver
* need to run PICMI test on 2 processors same as non-PICMI version in order to compare plotfiles
* changes requested during PR review
* pass dictionary to eval statement when calculating boundary potential
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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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* Update: AMReX/PICSAR to 21.09
* WarpX: 21.09
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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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of the Electrostatic solver (#2143)
* refactored parts of the electrostatic solver to allow an outside Poisson solver to be installed
* added callback to install a Poisson solver that can be used instead of the MLMG solver
* added call to the poissonsolver callback if one is installed and updated ElectrostaticSolver.cpp to calculate the electric field directly in amrex if EBs are used
* fixed issue causing ElectrostaticSphereEB test to crash
* fixed the logic for when to call computeE
* added function to allow charge density to be deposited in rho_fp from outside WarpX
* fixed inconsistency between labframe and relativistic electrostatic simulation setup
* fixed typo
* fixed issue that caused ElectrostaticSphere test to fail and removed unnecessary call to multiply E_y by -1 when doing a 2d simulation
* revert edit to error handling string
* changes requested during PR review
* additional change requested during PR review
* fixed typo
* revert unnecessary changes
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loaded (#2215)
* Improved error handling when the libwarpx shared library can't be loaded
* Removed extra newline
* Improved check and ended program on error
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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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_libwarpx.py::add_particles() (#2161)
* added particle weight as an explicit argument for _libwarpx.py::add_particles()
* changes requested during code review
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(#2167)
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* AMReX/PICSAR: 21.08
* WarpX: 21.08
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particle creation in AddNParticles() (#2115)
* exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index
* added functionality to AddNParticles() to allow extra particle attributes to also be set during particle creation
* added function to get index of a particle component given the PID name
* changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id
* changed warpx_addRealComp to accept a species name as input and only add the new component for that species
* added a test of the pywarpx bridge to get particle data and add new particle attributes at runtime
* changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index
* updated test according to PR #2119 changes
* removed unneeded BL_ASSERT(nattr == 1) statement
* fixed bug in add_particles to correctly determine the number of extra attributes
* fixed bug in AddNParticles if fewer attribute values are passed than the number of extra arrays for the species
* use isinstance(attr, ndarray) rather than type(attr) is np.ndarray
* generalize_runtime_comps_io
* fix OpenPMD
* fix OpenPMD
* fix plot flags in WritePlotFile
* fix offset and comment
* changed extra pid test to not use an underscore in the pid name
* switched _libwarpx.py::add_particles to use kwargs to accept the weight and extra attribute arrays
* License update in test file
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* fix typo
* added a test with unique_particles=False
* Apply suggestions from code review
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* updated docstring and comments
Co-authored-by: atmyers <atmyers2@gmail.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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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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* changed all particle interacting functions in libwarpx to use the species name rather than id, also changed the functions to get particle array data to use the component name rather than index
* removed unneeded function declaration
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* exposes AddRealComp to Python to allow extra particle attributes to be added at runtime; also includes a new function to grab a particle data array from the name of the component rather than the index
* added function to get index of a particle component given the PID name
* changed new get component index and get_particle_arrays_from_comp_name functions to take species name as argument rather than species id
* changed warpx_addRealComp to accept a species name as input and only add the new component for that species
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* Replace injection_style = python with injection_style = none
* Update Docs
* Add Default injection_style = none
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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 explanatory comments in timestepper.py
* Add comments to WarpInterface.py
* Added comments to WarpXPIC.py
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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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* Add possibility to start and stop moving window
* Update Benchmark laserInjection_2d
* Update Source/Diagnostics/BTDiagnostics.cpp
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
* modification of the MoveWindow function in the python interface
* False to True for move j in python function
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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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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* AMReX/PICSAR: 21.07
* WarpX: 21.07
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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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* AMReX/PICSAR: 21.06
* WarpX: 21.06
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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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* Deploy new Azure worker, for the embedded boundary test
* Correct missing end of line
* Update amrex version
* Update PICSAR version
* Update WarpX version
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I forgot to bump the version for the last release with our script.
Will do better next time.
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* Added multiple particles injection source
* Added documentation for MultipleParticles
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* Add "." to libwarpx Aliases
Add a "." to the suffix of the short-hand `libwarpx.<DIM>.<so|dll>`
libs. This unifies the suffix with the structure in executables and
makes it easier to find a "long" version of the library (not in this
PR).
Also fixes the suffix naming on Windows to ".dll", since this is
a true C/C++ library, not a Python module (aka not a shared library
following Python entry points and conventions).
* CMake: Add library alias in install
Also add the expected library alias in CMake install prefixes.
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Axel Huebl
Andrew Myers
Neïl Zaim
Roelof Groenewald
Remi Lehe
Michael Kieburtz
David Grote
Nicholas Ruof
Phil Miller
Revathi Jambunathan
Kevin Z. Zhu
Peter Scherpelz
Edoardo Zoni
thomas clark
Michael Kieburtz
