Render issue in RST in PASC24 entry.

* initial implementation of the grid based merging routine

* add compiler directives for different dimensions

* avoid implicit capture of `this` in lambda

* code clean-up

* use `PIdx::x` for r-coordinate while 4667 is still being reviewed

* fix clang-tidy errors

* another clang-tidy fix

* improve doc-strings

* use iterative heap sort since "SYCL kernel cannot call a recursive function"

* fix clang-tidy error

* fix sorting bug; add documentation and CI test

* add dummy CI benchmark file to get proper values

* update benchmark values based on Azure results

* rename `GridBasedMerging` -> `VelocityCoincidenceThinning`

* use `Algorithms::KineticEnergy`

* reorganize merging loop

* update CI benchmark values

* Relativistic correction in product particles' velocity calculation

* update benchmark values after changing energy calculation

* handle edge case with zero cluster momentum

* call redistribute after particle resampling to remove invalid particles

* use unsigned ints for indexing

* Revert "use unsigned ints for indexing"

This reverts commit abe027f3402cf0e7c51c4599a0a50b9e8a6b817a.

* call `Redistribute` before merging

* code clean-up

* also check for `std::isnan` in edge case handling

* add reference for grid based merging

* check that cluster has total weight > 0 before merging

* add defense against numerical error leading to nan

* make resampling message more verbose

* use `deleteInvalidParticles` instead of `Redistribute`

* remove default values for merging parameters

* remove doc-string default specifications in picmi.py

* apply suggestions from code review

* update benchmark values; avoid possible nans

* add assert to prevent merging of photons

* add `BackwardCompatibility` check to `LevelingThinning`

* implement option for Cartesian velocity mesh

* use `enum` for velocity grid types

* fix Windows `uint` issue and clang-tidy error

* use `Reduce` functions for GPU compatibility

* merge kernels finding min and max velocities

* take array of du values in picmi

* avoid checking velocity grid type for every particle

* fix issue in picmi

* use array input for velocity bin sizes

Update the ADIOS2 v2.10.0 installation, do not create campaign
directories (we do not use them yet).

* AMReX: Weekly Update

* pyAMReX: Weekly Update

* `isort`: First Party Modules

Declare `amrex` and `pywarpx` our first party modules, even if they
are not installed. This resolves inconsistencies when sorting imports
in developer or remote runs (pre-commit.com CI).

* [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>

* add missing include

* add missing include

* openPMD-api: 0.15.2

This patch release mostly improves reads.
https://openpmd-api.readthedocs.io/en/0.15.2/install/changelog.html#id1

* 0.15.1+

- technically also works
- we forgot to bump the installed version in 0.15.2

* [Draft] Open Governance Model

This is a first draft of the open governance model for WarpX,
developed after discussion with the current leadership team.

The goal of the governance model is to:
- document and make transparent our decision structure,
- structure and openly credit sensible roles,
- clarify appointment and offboarding,
- encourage participation, engagement and growth.

Thoughts that guided the initial document include:
- accurately reflecting our successful project workflows,
- evolving it for shared responsibiliy and co-ownership,
- avoiding unnecessary overheads and deadlocks,
- be flexible enough to enable later introduction of sub-roles
  and further formalization, depending on community growth.

* Review Session today

* Clarify SC permissions are for each member.

* Fix Typo: Groenewald

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* Added TC Veto Overwrite Rule

* Documentation & Link to (Access) Developer Meeting Notes

* Added Jean-Luc also to TC

---------

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* Great Lakes Cluster (UMich)

Document how to use the Great Lakes Cluster at the
University of Michigan.

* Fix c-blosc2 typos

* Parallel HDF5 for CUDA-aware MPI

New module added on the system.

* Fix GPU Visibility

Ensure one MPI rank sees exactly one, unique GPU.

* Add `#SBATCH --gpu-bind=single:1`

* Add clean-up message.

- link domain decomposition for `numprocs` option
- remove outdated warning

* initial implementation of the grid based merging routine

* add compiler directives for different dimensions

* avoid implicit capture of `this` in lambda

* code clean-up

* use `PIdx::x` for r-coordinate while 4667 is still being reviewed

* fix clang-tidy errors

* another clang-tidy fix

* improve doc-strings

* use iterative heap sort since "SYCL kernel cannot call a recursive function"

* fix clang-tidy error

* fix sorting bug; add documentation and CI test

* add dummy CI benchmark file to get proper values

* update benchmark values based on Azure results

* rename `GridBasedMerging` -> `VelocityCoincidenceThinning`

* use `Algorithms::KineticEnergy`

* reorganize merging loop

* update CI benchmark values

* Relativistic correction in product particles' velocity calculation

* update benchmark values after changing energy calculation

* handle edge case with zero cluster momentum

* call redistribute after particle resampling to remove invalid particles

* use unsigned ints for indexing

* Revert "use unsigned ints for indexing"

This reverts commit abe027f3402cf0e7c51c4599a0a50b9e8a6b817a.

* call `Redistribute` before merging

* code clean-up

* also check for `std::isnan` in edge case handling

* add reference for grid based merging

* check that cluster has total weight > 0 before merging

* add defense against numerical error leading to nan

* make resampling message more verbose

* use `deleteInvalidParticles` instead of `Redistribute`

* remove default values for merging parameters

* remove doc-string default specifications in picmi.py

* apply suggestions from code review

* update benchmark values; avoid possible nans

* add assert to prevent merging of photons

* add `BackwardCompatibility` check to `LevelingThinning`

* Reorder particle boundary handling and call to `Redistribute`

* split boundary buffer gathering into separate functions for domain and embedded boundaries

* rename `scrapeParticles` -> `scrapeParticlesAtEB`

* DepositCharge: Component 1 Allocated?

* Move assert

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

---------

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

Downgrade the regression testing scripts to work around
  https://github.com/AMReX-Codes/regression_testing/issues/136

* Add function to set value of `do_no_push`

* clang-tidy fix

Pull in the latest `development`.

* Add M. Haseeb in the list of developers

* Update .zenodo.json

Co-authored-by: Muhammad Haseeb <14217455+mhaseeb123@users.noreply.github.com>

---------

Co-authored-by: Muhammad Haseeb <14217455+mhaseeb123@users.noreply.github.com>

* add thermal boundary specification to picmi.py

* include thermal boundary handling for Cartesian grids

* opt gpu accel of particle collisions

* minor updates in .gitignore

* fix for consistent and correct particle collision error

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci



* minor bug fixing

* [minor]: remove stale code and clean up comments

* undo erroneously pushed changes in GNUmakefile

* undo erroneously pushed inputs_3d

* revert errors from obsolete code plus minor improvements

* fix for a possible segfault

* replace std::min with amrex::min for future compatibility

* clang-tidy updates

* Update random seed

* Update benchmark files

* Update .gitignore

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>

* Update .gitignore

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>

* Use bisect function

* Simplify the code

* Update benchmark and fix style

* use `BinaryCollision` class for DSMC collisions

* comment out explicit delete of `ScatteringProcess` constructor

* fix first GPU compilation issue

* fix RZ issue

* avoid copying `binary_collision_functor`

* fix merge error

* do not keep `ScatteringProcess` instances in `DSMCFunc`

* only keep array of `ScatteringProcess::Executor`s

* fix clang-tidy errors and reset benchmark

* fix default collision type issue

* copy cross-section data to `DSMCFunc`

* update checksum after fixing issue with cross-section arrays

* move logic to set up cross-section interpolators to `DSMCFunc.cpp` file

* use internal `struct`s in collision filter functors

* clean-up and fixing clang-tidy issues

* second clang-tidy fix attempt

* update `DSMCFunc` with new collision pair parallelization strategy

* fix DSMC CI benchmark file values

* Fix clang-tidy error

* update reference density array for DSMC CI test

* Only call redistribute if collision type has product species

* fix clang-tidy error

* another clang-tidy error fix

* Appropriately set `local` parameter in `Redistribute` call.

* set `Redistribute` arguments appropriately

* check if weight is numerically zero

* Apply suggestions from code review

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci



* add docstring for `CollisionPairFilter` function arguments

* Use `insert` rather than `push_back` & `rotate`

Co-authored-by: Remi Lehe <remi.lehe@normalesup.org>

* apply suggestions from a few of the review comments

* reduce differences between `SplitAndScatterFunc.H` and `ParticleCreationFunc.H`

* use `deleteInvalidParticles` from #4849

* avoid unnecessary duplication when species1 == species2

* Apply suggestions from code review

* Apply suggestions from code review

* [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: Remi Lehe <remi.lehe@normalesup.org>
Co-authored-by: roelof-groenewald <regroenewald@gmail.com>
Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* AMReX: Weekly Update

* pyAMReX: Weekly Update

* Always update guard cells in WarpXSumGuardCells

* Apply suggestions from code review

* Update benchmarks

* Update capacitive discharge test

* Update benchmarks

* Update Regression/WarpX-tests.ini

* Update Examples/Tests/ohm_solver_EM_modes/analysis_rz.py

* Update Examples/Physics_applications/capacitive_discharge/analysis_dsmc.py

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* Update benchmark

* Update box position

* Update checksum

---------

Co-authored-by: Roelof Groenewald <40245517+roelof-groenewald@users.noreply.github.com>

* add openpmd-viewer to conda install instructions

* add optimas example to documentation