HS dev merge 24-02-28 #139
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* add start/end moving step * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * set the default parameters to be None in start/end_moving_window_step * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix the indent --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: root <root@Tiga>
Documenting cupy installation for Frontier.
* Extensive clean up of PlasmaInjection * Small cleanup of parseMomentum * Fix string argument reference * Remove unneeded surface_flux * Allow multiple injection sources per species * Add documentation * Some clean up * Bug fix * Add ParmParseWithOptionalGroup * Used langmuir/inputs_2d as a CI test case * Update documentation * Each source must have injection_style specified * Fix in documentation * Small clean up in Examples/Tests/langmuir/inputs_2d * Add documentation to ParmParseWithOptionalGroup * Update nuclear_fusion tests to use multiple injection_source * Clean up "const int" * Make explicit double and float in ParmParseWithOptionalGroup * Make charge and mass ParticleReal * Update Deuterium_Tritium_Fusion_3D.json * Move ParmParseWithOptionalGroup to Utils and update method names * Allow the injection_style to be the same for all sources * Revert the nuclear_fusion/inputs_deuterium_tritium_rz test * Revert the changes to Examples/Tests/langmuir/inputs_2d * Small cleanup to use references insteads of pointers * Update Source/Particles/PhysicalParticleContainer.H Co-authored-by: Remi Lehe <[email protected]> * Rework the ParmParse get routines * Update doc regarding moving windows * Further rework, now cleaning up the query routines * Rework the handling of the optional group name in input parameter parsing * Fix consts * Add multiple source capability to the PICMI interface * Small clean up in picmi --------- Co-authored-by: Remi Lehe <[email protected]>
Use ccache in the clang-tidy CI. This allows us to skip clang-tidy checks on files that are not changed as reported by ccache.
``` ./Tools/Release/updateAMReX.py ```
Improve the performance on Intel and AMD CPUs by default: Avoid oversubscribing the physical number of CPU threads, as is default in OpenMP.
If a cache is updated during a job, GitHub does not store the new cache unless it's not found with the primary key. To work around that, we use the git hash in the cache name. When the cache action tries to load the cache using the primary key, it's always a miss. It will then try to load a cache using the restore-keys. If the cache is updated during CI, the new version will be stored under the primary key's name. In this new strategy, a new PR will use the cache associated with the latest development branch. The updated cache will be stored and become private to that PR. Any updates to the PR will also create new updated caches. But we don't need to keep all the copies. We only need to keep the latest version of the cache associated with the PR. So we use a workflow (clean-cache.yml) to clean up the old caches. After a PR is closed, we use clean-cache-postpr.yml to clean up all the caches associated with the PR. There is no easy way to get the PR number of the PR that triggers the cleanup workflow. Thus, we store the PR number as an artifact for the cleanup workflow. It turns out ccache encounters internal errors in some CIs on Ubuntu 20.04. Switching to the latest ccache solves the issues.
* fix type on "write diagnostics on restart" write_diagnostics_on_restart was write_diagonstics_on_restart * fix all instances of typo * Delete install.sh
* add `WarpX::getedgelengths` and WarpX::getfaceareas` functions to return pointers to those multifabs * add external current support to the hybrid-PIC solver * add external current specification (for hybrid-PIC scheme) to picmi * add RZ support for `FiniteDifferenceSolver::CalculateCurrentAmpere` * allow an initial Bz field to be set in RZ * code cleanup and addition of CI test * avoid lambda capture issue * update documentation to show external current implementation * revert unwanted changes * restore RZ support that was lost during rebase * fix segfault when EB support is OFF * fix codeQL issue * add some details to docs * the external current only needs to be calculated once per field solve step * add description of `hybrid_pic_model.J[x/y/z]_external_grid_function(x, y, z, t)` to the documentation
* AMReX: 23.12 * pyAMReX: 23.12 * WarpX: 23.12
The size of the brew cache is huge. It can be as big as more than 6 GB. Since we only have 10 GB GitHub cache space, the brew cache is disabled in the macOS CI. It should not increase the time for the macOS CI too much. Without any cache, it usually takes less than 10 minutes to install all the brew packages.
* Doc: Restructure Examples Restructure examples by science case. * Doc: Fix visualized field name. * Doc: `:py:function:` with trailing () Co-authored-by: Roelof Groenewald <[email protected]>
Mostly file names that changed or were not yet created.
More formatting issues in a list.
Without it, the hit rate of ccache is very low.
Start to streamline the PICMI Python input.
* Correct on-axis fields for RZ * Update checksum file * Clean commented-out code
* Fix typos and spelling * More typos * Typos 2023 Nov 27 * 2023 Nov 30 Update * Docs typos * Fix "arbitrary" * 2023 Dec 01 typos * Particles * ablastr - FieldSolver * Filter * Fluids * Docs + Tools * Change back to "lamda" * Fix typo Co-authored-by: Roelof Groenewald <[email protected]> * Fix cylindrical --------- Co-authored-by: Axel Huebl <[email protected]> Co-authored-by: Roelof Groenewald <[email protected]>
Update pybind11 to the latest release.
* Set alpha mass directly from NIST data * Delete extra line
…ates (ECP-WarpX#4481) * Add `latex_theory/allbibs.bib` to conf.py * Delete additional redundant reference and make intro.rst match intro.tex
It appears that we need to call brew upgrade.
Unlike std::sqrt that has overloads for double and float, sqrt is a C function that takes a double. If the argument is a float, it will have to be promoted to double first.
For performance and readability, instead of including checks explicitly, switch to excluding checks explicitly. These checks are excluded because currently WarpX fails at them. Add portability and diagnostic checks.
Add `--keep-going` to the make command in Clang-Tidy CI. With that, the job will keep going and show all the clang-tidy check errors instead of stopping on the first error.
* Adding of the bool `radially_weighted` as variable in the class Species * Remove error message * Fix bug with radially-weighted * Fix weighting of particles * ghost_cells problems fixed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * modification of particle_containers to track the particle * Add PICMI interface for BoundaryScrapingDiagnostic * Add first iteration of the input script * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * second draft, < 2 min, good results * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * adding a draft of analysis code for spacecraft_charging * adding spacecraft_charging at the very end * adding spacecraft_charging analysis * Revert "Add PICMI interface for BoundaryScrapingDiagnostic" This reverts commit 521dc5d. * Revert changes in fields.py * Update PlasmaInjector.cpp Trying to fix the error during the test: /home/runner/work/WarpX/WarpX/Source/Initialization/PlasmaInjector.cpp:72:5: warning: 'zmax' should be initialized in a member initializer of the constructor [cppcoreguidelines-prefer-member-initializer] zmax = std::numeric_limits<amrex::Real>::max(); * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update PlasmaInjector.cpp Adding "amrex::Real" to define xmin,ymin,zmin,xmax,ymax,zmax * Update PlasmaInjector.cpp * modelisation code * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * new version gathering the electrons and the protons * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * deplaced in the Physics_applications file * not necessary * analysis file * changes in some syntaxes and adding checksum test * add png file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replaced by new syntax * change of syntax and keep just one version * Add checksum json file * Update PICMI_inputs_rz.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove changes related to radially-weighted * Update Regression/WarpX-tests.ini * Make script executable * Update format of automated test * Update test * adding description * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update PICMI_inputs_rz.py * Update analysis.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update PICMI_inputs_rz.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update PICMI_inputs_rz.py * Update PICMI_inputs_rz.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update PICMI_inputs_rz.py * analysis changed: I wish it works now * Update WarpX-tests.ini adding the outputFile * Update filename * Update checksum * Update Examples/Physics_applications/spacecraft_charging/analysis.py * Update PICMI_inputs_rz.py From a random to an identical test * Update analysis.py * Update spacecraft_charging.json * Update spacecraft_charging.json * Update analysis.py --------- Co-authored-by: Remi Lehe <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Fix: openPMD RZ Positions Fix the particle position write in openPMD with SoA particle layout. For the openPMD I/O backend, we transform the r,z,theta particle components back to x,y,z. * Updates for CI
Update small typos and simplify source directory.
Reduce the compile parallelism to avoid getting build processes killed by the watchdog daemon.
* modifying the function ParticleSraper using bisection method * adding a variable const amrex::dt for the ScraperParticle function * adding the variable dt to ScraperParticle function * adding the variable dt in the ScraperParticle function * not real change * Fix compilation * Remove mutable * new folder for the test of calculation of the point of contact in the case of one particle and EB * make it quicker * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make it quicker * case in 3D * deleating diags files * fix some issues * EB as a sphere * first draft of analysis * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add of getPosition but doesn t work * some changes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * version Rémi non modifiée * reset the version of ParticleScraper.H with the branch development * adding the dt variable to make the file consistent with the modifications from the branch bisection * still 2 errors * still one error * some changes but still errors * WORKSgit add Source/Particles/ParticleBoundaryBuffer.cpp, but only in CPU * Update ParticleBoundaryBuffer.cpp Make it work for GPU * works for GPU * works for GPU * works * works but not for RZ * adding a test for a tolerance of 0.1% * comma missed * addind checkout + change of some details * add point_of_contact_EB_3d * updates with checksum and changes in calling diags folders * ready to be tested * ready to be tested * midification of one comment * adding test for 3d * the code works for RZ * json file for the point_of_contact test in rz * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Delete Examples/Tests/point_of_contact_EB/.ipynb_checkpoints/inputs_rz-checkpoint * Update analysis.py * Update ParticleBoundaryBuffer.cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestions from code review * Update Source/EmbeddedBoundary/ParticleScraper.H * Update Source/EmbeddedBoundary/ParticleScraper.H * Update Source/EmbeddedBoundary/ParticleScraper.H * Update Source/Particles/ParticleBoundaryBuffer.cpp * Add type for phi_value * Fix compilation * Update ParticleScraper.H lines updated for OpenMP parallelized * Update Source/Particles/ParticleBoundaryBuffer.cpp * Avoid GPU compilation errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Particles/ParticleBoundaryBuffer.cpp * Update Source/Particles/ParticleBoundaryBuffer.cpp * Update Source/Particles/ParticleBoundaryBuffer.cpp * Update WarpX-test.ini * Remove particles that are initialized in the EB * Fix error whereby the momentum was not particle-dependent * Add back the BeamBeam test * Apply suggestions from code review * Make analysis script executable * Correct format of analysis file * Update ParticleBoundaryBuffer.cpp syntax changed for saving the exact position * Update ParticleBoundaryBuffer.cpp try an other syntax for the positions * Update ParticleBoundaryBuffer.cpp fix a error * Update ParticleBoundaryBuffer.cpp change syntax due to new commits in WarpX * Update ParticleBoundaryBuffer.cpp little error in taping fixed * Update ParticleBoundaryBuffer.cpp fix issue in RZ. Now 'theta' --> 'y' in RZ * back to the previous version theta='theta' in RZ * udate syntax to be consistent with the merge * Update ParticleScraper.H * Update analysis.py * Update ParticleBoundaryBuffer.cpp coherent with the updates of development * modification due to the merge * Update analysis.py * Update analysis.py * Update Point_of_contact_EB_rz.json * changes of coordinates analysis in RZ * Update Point_of_contact_EB_rz.json * Update WarpXOpenPMD.cpp * Update Point_of_contact_EB_rz.json * Update analysis_rz.py * delete in tests in RZ * deleting RZ tests in Regression file * Update WarpXOpenPMD.cpp * Update analysis.py * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update WarpX-tests.ini * Update Examples/Tests/point_of_contact_EB/analysis.py Co-authored-by: Remi Lehe <[email protected]> * Update analysis.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update analysis.py * Update analysis.py * Update Examples/Tests/point_of_contact_EB/inputs_3d Co-authored-by: Remi Lehe <[email protected]> * Update Examples/Tests/point_of_contact_EB/inputs_3d Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp --------- Co-authored-by: Remi Lehe <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
ECP-WarpX#4696) * Removed const modifier from LPInfo object on stack that was causing a warning from not being initialized properly. * Changing instantiation of LPInfo to make consistent with usage elsewhere in AMReX and avoiding compile time warning. * LPInfo in PoissonSolver can be adjusted for semi-coarsening, so reverting back to non-const.
* adding RZ example * Update particle_containers.py * Update Point_of_contact_EB_rz.json
…rpX#4695) * adding the time * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update particle_containers.py * Update ParticleBoundaryBuffer.cpp * Update PICMI_inputs_rz.py * Update PICMI_inputs_rz.py * Update particle_containers.py * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * fix issue * fix issue * issue fixed * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update analysis_rz.py * Update analysis_rz_filter.py * Update analysis.py * Update PICMI_inputs_scrape.py * Update PICMI_inputs_reflection.py * Update particle_containers.py * Update PICMI_inputs_reflection.py * Update PICMI_inputs_scrape.py * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update ParticleBoundaryBuffer.cpp --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <[email protected]>
updates: - [github.com/Lucas-C/pre-commit-hooks: v1.5.4 → v1.5.5](Lucas-C/pre-commit-hooks@v1.5.4...v1.5.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…P-WarpX#4656) * update instructions for the Fugaku supercomputer * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add missing instruction * update Fugaku instructions * fix bug * fix bug * fix bug * fix bug * fix bug * fix bug * fix issue with Fujitsu compiler * update install_dependencies script to save some space * delete BinaryCollision move constructor * update compilation instructions * update submission script --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* AMReX: Weekly Update * pyAMReX: Weekly Update * Azure: Bump up Timeout to 4hrs * Fix `ParticleContainer`: `amrex::Long pid` overflows ``` error: narrowing conversion from 'amrex::Long' (aka 'long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions,-warnings-as-errors] ``` * Cleanup: no AoS
…es (ECP-WarpX#4706) * Merged with latest Modified shape factors written for Villasenor algorithm to use simpler (mathematically equivalent) expressions * Added test Added test for particle_shape=4 Choice of 2d Langmuir wave case is based on cost (resolution would need to be increased relative to existing 3d tests) Fixed bugs related to rebase * Removed tabs Removed tabs that did not properly convert to whitespace * Undid custom settings in regression testing * Update Source/Particles/WarpXParticleContainer.cpp
…CP-WarpX#4702) * modifications for adding the normal components * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update analysis.py * Update ParticleBoundaryBuffer.cpp * Update NodalFieldGather.H * Update NodalFieldGather.H * Update NodalFieldGather.H * Update Docs/source/usage/parameters.rst Co-authored-by: Remi Lehe <[email protected]> * Update Source/EmbeddedBoundary/ParticleScraper.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/EmbeddedBoundary/ParticleScraper.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/EmbeddedBoundary/ParticleScraper.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/ablastr/particles/NodalFieldGather.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/ablastr/particles/NodalFieldGather.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/ablastr/particles/NodalFieldGather.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/ablastr/particles/NodalFieldGather.H Co-authored-by: Remi Lehe <[email protected]> * Update Source/ablastr/particles/NodalFieldGather.H Co-authored-by: Remi Lehe <[email protected]> * Update DistanceToEB.H * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update DistanceToEB.H * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Remi Lehe <[email protected]> * makes it concise * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleScraper.H * updates * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update DistanceToEB.H * Update DistanceToEB.H --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Lehe <[email protected]>
* add focusing position * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * removed prints * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix stashed * generalized to focal distance * first test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ci test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix formatting in benchmark checksums * updated test and start docs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * focal distance is optional * updated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed unused variables vbulk * updated docs * updated test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reset benchmark * vx vy mistake * fix conversion error clang tidy * fix clang tidy error * fix typo * Update Docs/source/usage/parameters.rst Co-authored-by: Remi Lehe <[email protected]> * Update Examples/Tests/gaussian_beam/analysis_focusing_beam.py Co-authored-by: Remi Lehe <[email protected]> * Update Examples/Tests/gaussian_beam/analysis_focusing_beam.py Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Examples/Tests/gaussian_beam/analysis_focusing_beam.py Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * integrate comments by remi * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused variable * reset benchmark * fix v_dot_n * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * Update Source/Particles/PhysicalParticleContainer.cpp Co-authored-by: Remi Lehe <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Tools <[email protected]> Co-authored-by: Remi Lehe <[email protected]>
…CP-WarpX#4719) * Update particles.rst * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update particles.rst * Update particles.rst --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
The variable `species` was an unresolved reference and needed to accessed via `self.species` instead. Fixed also a word `specie` where `species` was meant.
…CP-WarpX#4569) * Update laser-ion acc example - add PICMI input - add vis script - update docs - add Python regression test - update phase space analysis script - add checksum regression test * Update docs with figures from hi-res runs * Add captions * Fix checksum regression tests * Change outputs to h5 for CI * Fix: Do Not Deselect Positions * Synchronize PICMI and Inputs More - Species selections - Filter details * Fix checksum regression test Update checksums in Python_LaserIonAcc2d Co-authored-by: Axel Huebl <[email protected]>
…-WarpX#4710) * modifications of the names and change of timeScraped into delta * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update analysis.py * updates * Update parameters.rst * Update parameters.rst * Update parameters.rst * Update parameters.rst * Update parameters.rst * Update parameters.rst * Update parameters.rst * Update analysis.py * Update parameters.rst * Update particle_containers.py * Update ParticleBoundaryBuffer.cpp * Update analysis.py * Update ParticleBoundaryBuffer.cpp * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * update name * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Revathi Jambunathan <[email protected]> * Update Source/Particles/ParticleBoundaryBuffer.cpp Co-authored-by: Revathi Jambunathan <[email protected]> * Update ParticleBoundaryBuffer.cpp * Update ParticleBoundaryBuffer.cpp * Update Docs/source/usage/parameters.rst Co-authored-by: Remi Lehe <[email protected]> * Update analysis.py * Update analysis.py * Update particle_containers.py * Update particle_containers.py * Update analysis.py * Update analysis.py --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Revathi Jambunathan <[email protected]> Co-authored-by: Remi Lehe <[email protected]>
…tic (ECP-WarpX#4721) * Position keyword in ParticleDiags now adds pos Prior to recently, the `'position'` string in the input of the PICMI `ParticleDiagnostic` did not add the positions because they were written out automatically. That has been changed and so we are adding them to the list of variables now. Also added the class `LabFrameParticleDiagnostic` to the docs. * Fix dimension-specific cases and examples - in picmi.py, the dimensions were not checked and so it would try to add variables that do not exist for a species in a lower dimension - in examples, some coordinates were named wrongly for lower dimensions than 2 but it did not matter before since positions were added automatically
* openPMD: Fix Particle Weight Dims Weighting of a macro particle is a count in 3D and RZ sims, but a count per line in 2D and a count per surface in 1D. This reflects this now in the `weighting` attribute `unitDimensions`. * Simplify * Spaces
Keep for readability as is.
* Exchange guard cells for electrostatic solver * Update calls to fillboundary * Update checksums * Add automated test * Update benchmark * Add automated test for energy conservation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update Examples/Tests/energy_conserving_thermal_plasma/analysis.py * Update Regression/WarpX-tests.ini * Fix automated test * Update benchmarks * Apply suggestions from code review Co-authored-by: Luca Fedeli <[email protected]> * Update input script --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Luca Fedeli <[email protected]>
* this works only on single proc, but lifts the assumption of single patch for do pml in domain * fix cbl * building reduced ba and cba * Removing print statements * removing comment * assert that box length must be greater than size of pml when its grown inwards * same assertion for box length for coarse grid * simplified_list and no need for assert in coarse, but if fine works, coarse should * boxlist instead of simplified list * comments * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * CI test for double patch with particles entering and leaving pml inside the patch * checksum for new particles in pml 2d mr test with double patch * renaming plt to diag1 again * include level 0 maxfield to capture no j damping effect * removing incorect comment about heavy paritcle in input --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
RevathiJambunathan
merged commit 1efba85
into
RevathiJambunathan:HarrisSheetinX
19 of 26 checks passed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.