Age | Commit message (Collapse) | Author | Files | Lines |
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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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* Wrap shared object in a class to control its loading
* Fix libwarpx attribute references
* Updated callbacks.py for updated libwarpx
* Removed the wx module plus other clean up
* Further revision of how to use the pywarpx module.
Now, _libwarpx should not be imported by external scripts except in special circumstances.
* Updated documentation
* Clean up end of line whitespace
* Added more wrapping routines plus some clean up
* Fixed use of pywarpx in two examples
* Fix for getistep
* Fixed for the EB Python interface
* Silence a warning for our wrapper
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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* Adding edge_lengths and face_areas to the Python interface
* Added wrappers for the two new arrays of data
* Adding a CI test
* Fixed test name
* Added customRunCmd
* Added mpi in test
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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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* added _getitem1d and _setitem1d to fields.py
* refactored fields.py to reduce duplicate code for different dimensions
* fixed some bugs with the refactor
* changes requested during code review
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* Added check for if warpx was initialized when calling finalize
* Renamed to be warpx_initialized
* Fixed reference to global variable
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
* Changed global variable to member of libwarpx
* Fixed syntax errors
* Remove custom arg from argv to avoid parmparse error
Co-authored-by: Peter Scherpelz <31747262+peterscherpelz@users.noreply.github.com>
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* Python: Start 1D Support
Start supporting 1D builds in Python.
* Fix 1D: PML FillZero unused
... since PMLs are not yet supported in 1D.
* BeamRelevant: Fix unused p_pos0
* FromTXYEFileLaserProfile: Not Impl in 1D
* QED Schwinger: 1D not Implemented
Fix unused warnings, add aborts.
* 1D RealVect/IntVect: Initialization
Use explicit scalar constructors, no braces.
Fix warning in clang 10.
* 1D NCI Filter: Fix unused members & Init
Unimplemented, but throws warnings.
* PSATD: 1D not Implemented
- remove compile warnings
- start porting some parts
* NCIGodfreyFilter: Clean up 2D & Else
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* Python: More Nullptr Checks
I am debugging a couple of crashes while mitigating CI.
One of them pointed to the locations here
(`ValueError: NULL pointer access`), so I decided to add some checks.
* Skip invalid tiles
* Skip Empty Tiles But Check Pointer
* Python: nullptr check in _array1d_from_pointer
Make the methods `get_particle_structs` and
`get_particle_boundary_buffer_structs` more robust.
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* Add pre-commit
Add basis for automated pre-commit checks.
Install locally via:
```bash
python3 -m pip install -U pre-commit
pre-commit install
```
See: https://pre-commit.com
* Cleanup: Whitespaces
* Cleanup: requirements.txt order
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buffers (#2498)
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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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* Add Python Wrappers for F,G in PML
* Add Getters for F,G Nodal Flags
* Fix Bug in <F,G>FPPMLWrapper (Default Level)
* Fix Bug in F,G Nodal Flags
* Use GetPML Method for F,G Nodal Flags
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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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Fixed indexing for PML fields.
Add all of the fixes to the setitems routines.
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* PICMI: Add div(E),div(B) Cleaning Options
* Update PICMI Version: 0.0.15
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* Fix fields indexing
* Added additional documentation
* Fixed comment
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* Use os.path.join in picmi.py for portability
* Apply suggestions from code review
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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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* 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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* 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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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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