Wakis v0.6.0

🚀 New Features

🖼️ Plotting
- Unified plotting tools for both MPI and non-MPI simulations.
- plot1D now supports field visualization independently of MPI use.
- Plot2D supports parallel execution.
- Error handling added for plot3D and plot3DonSTL when use_mpi = True.
- Support for dpi and return_handles in plot utilities to further customize plots.
- Enhanced examples and notebook suite visualization cells.
🧱 GridFIT3D
- Added mpi_initialize() to handle domain decomposition (Z-slicing).
- New method mpi_gather_asGrid() to retrieve the full global grid from distributed subdomains.
- Full support for multi-GPU domain decomposition through cupy (CUDA-aware, Linux only).
- Improved communication layer for subdomain synchronization via ghost cells.
⚡ SolverFIT3D
- MPI-compatible time-stepping routine mpi_one_step() using a leapfrog scheme.
- mpi_communicate() to send/receive boundary field values between subdomains.
- mpi_gather() to retrieve field data as a NumPy array and mpi_gather_asField() to reconstruct a Field object.
- MPI-safe support integrated into update() and field getter logic.
- Introduced save_state() method for checkpointing during MPI runs together with load_state(). Added support for MPI save state too.
- Feature in progress: multiGPU support (use_GPU=True when use_MPI=True) for distributed simulations (Linux only!).
- Added missing docstrings (Numpy-style)
📥 Sources
- Beam:
  - Added plot(t) to visualize beam current evolution.
  - Generalized update() to work with or without MPI.
  - Enhanced support for time-aligned injection with beta and MPI shifts.
  - New example for MPI+GPU simulation (topic in progress).
🌊 WakeSolver
- Refactored to internally store the full longitudinal domain.
- skip_cells now acts only at analysis level, preserving resolution.
  - add_space and use_edt retained for compatibility, but add_space is deprecated for new parameter skip_cells, more adequate to its utility (i.e. skip cells in the integration path).
- Future-ready structure for distributed wake solving with MPI-aware GPU.
- Improved numerical robustness by preventing indexing errors in WakePotential integration -> solves issue #12
- Enhanced extrapolation method with iddefix.
- New example 004 for wakefield simulation with MPI+GPU configuration.
🛡️ Security & Documentation
- Added SECURITY.md to describe supported versions and vulnerability reporting.
- Improved installation guide with Miniforge (supports both Windows/Linux) and MPI setup instructions.
- Added new issue templates for Bug Report and Feature Request with markdown formatting and emojis for readability.
- Addition of the Physics Guide, with detailed physics models and numerical methods explanations.
- User's guide updated to include Wake extrapolation with iddefix, Wake function calculation with neffint, and power loss calculation with BIHC.
- Added a Table of Contents (ToC) to the documentation for easier navigation.
- Expanded installation guide with multiGPU configuration and MPI-aware domain partitioning.

💗 Other Tag highlights

🔁 Nightly tests with GitHub Actions:
- Enabled infrastructure for MPI-based test cases (test_003, test_005).
- Improved test coverage for MPI and GPU simulations.
- MultiGPU end-to-end tests for distributed domain synchronization.
📁 Examples:
- notebook 003 → MPI wakefield simulation using mpi4py.
- notebook 005 → Full MPI simulation inside Jupyter using ipyparallel + mpi4py.
- New example 003 with MPI + GPU configuration for large-scale simulations.
📁 Notebooks:
- 005 → Full MPI simulation inside Jupyter using ipyparallel + mpi4py.
- New Jupyter notebook showcasing multiGPU configuration.

🐛 Bugfixes

Fixed crash in plot3D and plot3DonSTL when use_mpi=True.
Fixed default use_mpi=True to now default to False for general usage.
Fixed a typo in beam injection routine solver.z.min().
Fixed potential rounding error in wake potential integration with negligible performance impact (~0.1ns) -> solves issue #12
Corrected default beam injection time to align with CST Wakefield Solver reference in beta<1 cases.
Fixed minor typos in the documentation.
Fixed synchronization issues with MPI runs when saving states.
Resolved encoding issues when installing in Windows editable mode.
Corrected result folder naming in GPU example 002.

👋👩‍💻 New Contributors

@mctfr – PR #11 Contributed improvements to installation instructions in the documentation.

📝 Full changelog

git log v0.5.1... --date=short --pretty=format:"* %ad %d %s (%aN)" | copy

78 commits	📚 Docs	🧪 Tests	🐛 Fixes	🎨 Style	✨ Features	Other
% of Commits	30.3%	10.5%	9.2%	10.5%	22.4%	17.1

2025-05-27 docs: add docstrings for mpi_gather and mpi_gather_asField (elenafuengar)
2025-05-26 tests: fix mpi folder creation issues (elenafuengar)
2025-05-23 tests: only allowed 2 procs per CI workflow... (elenafuengar)
2025-05-23 tests: reduce MPI pipeline to only 007 (elenafuengar)
2025-05-23 fix: update run workflow name (elenafuengar)
2025-05-23 tests: add MPI CI/CD on manual py3.10 (elenafuengar)
2025-05-23 test: add 007 to pytest pipeline (elenafuengar)
2025-05-22 style: remove duplicates, prepare for release (elenafuengar)
2025-05-23 tests: passing 007 for single core and mpiexec! (elenafuengar)
2025-05-19 fix: nightly test report fix (elenafuengar)
2025-05-14 style: move mpl.plt import (elenafuengar)
2025-05-13 docs: update release draft, prepare for deployment (elenafuengar)
2025-05-09 feature: multiGPU working (Ubuntu) -but needs optimization (elenafuengar)
2025-05-09 style: revise GPU example 002, fix folder result name (Elena De La Fuente Garcia)
2025-05-09 build: fix encoding when installing editable in Windows (Elena De La Fuente Garcia)
2025-05-08 docs: add miniforge (Windows/Linux) to python installation guide (elenafuengar)
2025-05-08 docs: fix reference typo (elenafuengar)
2025-05-07 feature: support save_state for MPI runs (elenafuengar)
2025-05-06 docs: fix few mistakes spotted after RTD deployment (elenafuengar)
2025-05-06 docs: minor changes to adapt to the physics guide content (elenafuengar)
2025-05-06 docs: revised physics guide, make html passed (elenafuengar)
2025-05-05 docs: first version of physics guide (elenafuengar)
2025-05-02 feat: new example for MPI+GPU simulation (in progress) (elenafuengar)
2025-04-29 docs: update installation with MPI-GPU findings (elenafuengar)
2025-04-24 Update README.md (Elena de la Fuente García)
2025-04-24 Create SECURITY.md (Elena de la Fuente García)
2025-04-24 Update and rename feature-request-💡.md to feature-request.md (Elena de la Fuente García)
2025-04-24 Update bug-report.md (Elena de la Fuente García)
2025-04-24 Update and rename bug-report-🐛.md to bug-report.md (Elena de la Fuente García)
2025-04-24 Update and rename 💡feature-request-.md to feature-request-💡.md (Elena de la Fuente García)
2025-04-24 Add issue templates (bug & feature) (Elena de la Fuente García)
2025-04-09 docs: small typo in readme (Elena de la Fuente García)
2025-04-07 docs: update readme with playground contents (elenafuengar)
2025-04-02 build: update release draft version to 0.6.0 (elenafuengar)
2025-04-02 tests: add MPI test files and test script in progress (elenafuengar)
2025-04-02 build: add neffint, iddefix and bihc as dependencies (elenafuengar)
2025-04-02 style: fix results folder and plot kwargs (elenafuengar)
2025-03-29 docs: update release.md (elenafuengar)
2025-03-29 docs: small typo (elenafuengar)
2025-03-27 style: revised notebook 004, in particular the iddefix extrapolation (elenafuengar)
2025-03-27 feature: include wakefield simulation in example 003 (elenafuengar)
2025-03-27 docs: fix sidebar TOC in conf.py, add TOC to installation and user guide, minor fixes (elenafuengar)
2025-03-27 feature: add wakefield simulation to MPI example and extrapolation to fully decayed (elenafuengar)
2025-03-27 feature: MPI wakefield simulation with solver.wakesolve is now working (elenafuengar)
2025-03-27 docs: update MPI installation after testing on imp machines (elenafuengar)
2025-03-27 docs: fix in index.md for missing logo (elenafuengar)
2025-03-26 docs: prepare v0.5.2 release (elenafuengar)
2025-03-26 feature: support for MPI in wakesolve in progress + refact: wakesolve saves now all longitudinal values, skip_cells will only be applied inside WakeSolver. add_space and use_edt kept for legacy (elenafuengar)
2025-03-26 test: adjust tes_001 to WakeSolver refactor in previous commit (elenafuengar)
2025-03-26 fix: add if statement in wake potential calculation to catch rounding errors (profiler indicates only 0.1ns overhead) + refact: add_space now deprecated for skip_cells'. This parameter now adjusts the slicing of z instead of modyfing zmin and zmax, since solver.wakesolve` will now save all the longitudinal data (elenafuengar)
2025-03-26 fix: typo in solver.z.min() (elenafuengar)
2025-03-25 fix: change default to False for MPI (elenafuengar)
2025-03-21 feature: notebook 005 containing working MPI example using ipyparallel and mpi4py, using MPI methods ins...

Wakis v0.5.1

Minor fixes and updates

🚀 New Features

Plotting
- Allow passing camera position to solver's 3D plots plot3D and plor3DnSTL

💗 Other Tag highlights

🔁 Nightly tests with GitHub actions:
- 003 -> coverage for grid inspect and plot_solid
📁 Examples:
- 003 -> MPI wakefield simulation with mpi4py
📁 Notebooks:
- 005 -> MPI example in jupyter notebooks with ipyparallel+ mpi4py

🐛 Bugfixes

__version__ now matches PyPI release and tag
gridFIT3D.plot_solids() fix typo in the opacity assignment
example/001 fixed stl_solids parameter in grid.inspect() call

📝Full changelog

v0.5.0...v0.5.1

2025-03-12 fix: typo in ocpacity, variable overwritten (elenafuengar)
2025-03-12 test: add coverage for grid.inspect and grid.plot_solids (elenafuengar)
2025-03-12 fix: add_stl use keys not stl file path, add default parameters and uncomment (elenafuengar)
2025-03-11 feature: allow passing camera position as argument on 3D plotting routines (elenafuengar)
2025-03-11 test: study different pml_func profiles and compare smoothness and derivatives (elenafuengar)
2025-03-10 docs: update release.md for next version (elenafuengar)
2025-03-07 docs: update supported python versions 3.8+ <3.12 (elenafuengar)
2025-03-07 docs: update version (elenafuengar)
2025-03-07 docs: update CITATION.cff with v0.5.0 doi (Elena de la Fuente García)
2025-03-07 docs: add zenodo badge to readme.md (Elena de la Fuente García)

@MaltheRaschke

Wakis v0.5.0

🚀 New Features

🧱 Geometry import:
- Functions to read .STP files, exporting each solid into an .STL file indicating the name and material: wakis.geometry.generate_stl_solids_from_stp(stp_file)
- Functions to extract from .STP files solid names, colors, and materials: wakis.geometry.extract_XXX(stp_file) to easily build the input dictionaries needed for GridFIT3D
⚡Solver:
- New maximal timestep calculation for high-conductive regions based on CFL + relaxation time criterion
- New methods: save_state(), load_state() to export and import the fields at a particular simulation timestep (HDF5 format). Method reset_fields() to clear fields before restarting a simulation.
- Perfect Matching Layers (PML) boundary conditions: First version out!
🖼️ Plotting:
- solver.plot3DonSTL Field on STL solid using pyvista.sample interpolation algorithm
  - Interactive plane clipping on plot3DonSTL
  - Field shown on clipping plane
- grid.plot_solids() 3D plot with the imported solids and the position in the simulation bounding box when bounding_box=True
📥Sources:
- Add plot(t) method to plot the source over the simulation time t
- Custom amplitude as an attribute self.amplitude
- Custom phase as an attribute self.phase
- Custom injection time self.tinj
- For PlaneWave allow for truncation at specific number of self.nodes injected
🌱 Ecosytem:
- Wake extrapolation of partially decayed wakes coupling with [IDDEFIX]: https://github.com/ImpedanCEI/IDDEFIX:
  - IDDEFIX is a physics-informed machine learning framework that fits a resonator-based model (parameterized by R, f, Q) to wakefield simulation data using Evolutionary Algorithms. It leverages Differential Evolution to optimize these parameters, enabling efficient classification and extrapolation of electromagnetic wakefield behavior. This allows for reduced simulation time while maintaining long-term accuracy, akin to time-series forecasting in machine learning
- Impedance to wake function conversion using non-equidistant Fourier transform with: [`neffint]: https://github.com/ImpedanCEI/neffint
  - Neffint is an acronym for Non-equidistant Filon Fourier integration. This is a python package for computing Fourier integrals using a method based on Filon's rule with non-equidistant grid spacing.
- Beam-induced power loss calculations for different beam shapes and filling schemes using ['BIHC`]: https://github.com/ImpedanCEI/BIHC
  - Beam Induced Heating Computation (BIHC) tool is a package that allows the estimation of the dissipated power due to the passage of a particle beam inside an accelerator component. The dissipated power value depends on the characteristics of the particle beam (beam spectrum and intensity) and on the characteristics of the considered accelerator component (beam-coupling impedance).

💗 Other Tag highlights

🔁 Nightly tests with GitHub actions: 000 - 005
📁 notebooks: containing interactive examples
📁 examples: major cleanup, examples on CPU and GPU

🐛 Bugfixes

Patch representation when a list is passed in Plot2D
ipympl added as a dependency to wakis['notebook'] installation
Injection time to account for relativistic beta in sources

👋👩‍💻New Contributors

@MaltheRaschke made their first contribution in #4

Full Changelog: v0.4.0...v0.5.0

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Wakis v0.6.0

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Wakis v0.5.1

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Wakis v0.5.0

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Releases: ImpedanCEI/wakis

Wakis v0.6.0

Wakis v0.6.0

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Wakis v0.5.1

Wakis v0.5.1

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Wakis v0.5.0

Wakis v0.5.0

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