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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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* 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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* 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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* 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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* CMake: libwarpx
Reorder CMake builds to collect everything in an object
file library, which is then used to link out a shared library
and the WarpX executable app.
* setup.py: Install up to 3 libs at once
Inside CMake build dir:
```
PYWARPX_LIB_DIR=$PWD/lib python3 -m pip wheel ../Python/
```
* Docs: CMake + Python
* CI: Python CMake Package
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* Fixes to the Python interface for accessing field and particle data
* In Python wrapper, cleaned up how ngrow is handled
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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 - convert True/False to 1/0
* picmi - update picmi input files to use True/False for booleans
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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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Roelof Groenewald
Peter Scherpelz
nruof
Edoardo Zoni
KZhu-ME
David Grote
thomas clark
Michael Kieburtz
Axel Huebl
Michael E Rowan
NeilZaim
Igor Andriyash
