.cargo/config.toml | 6 +- doc/docs-header.html => .docs-header.html | 0 .github/workflows/publish_book.yml | 62 -- CITATION.cff | 22 + Cargo.toml | 4 +- LICENSE.md => LICENSE | 0 README.md | 6 +- build_website.sh | 92 ++ cellular_raza-benchmarks/.cargo/config.toml | 2 + cellular_raza-benchmarks/Cargo.toml | 3 +- cellular_raza-benchmarks/benches/cell_sorting.rs | 2 +- cellular_raza-book/.gitignore | 1 - cellular_raza-book/book.toml | 15 - cellular_raza-book/mdbook-admonish.css | 352 ------- .../src/AbstractionLayers/Concepts.md | 1 - .../src/AbstractionLayers/User-Space.md | 1 - cellular_raza-book/src/Benchmarking/Algorithms.md | 1 - .../src/Benchmarking/BenchmarkBackends.md | 1 - .../src/Benchmarking/Benchmarking.md | 1 - cellular_raza-book/src/Benchmarking/Hardware.md | 1 - .../src/DesignPrinciples/Backends.md | 8 - .../DesignPrinciples/BackendsFeatureComparison.md | 1 - .../src/DesignPrinciples/Concepts.md | 32 - .../src/DesignPrinciples/DesignPrinciples.md | 65 -- .../src/DesignPrinciples/User-Space.md | 1 - .../src/Developers/CodingGuidelines.md | 1 - .../src/Developers/DesigningNewConcepts.md | 1 - cellular_raza-book/src/Developers/Developers.md | 1 - .../src/Developers/HowToWriteBackend.md | 1 - cellular_raza-book/src/SUMMARY.md | 21 - cellular_raza-book/src/UserGuides/FirstSim.md | 1 - .../src/UserGuides/PredefinedCellularModules.md | 1 - .../src/UserGuides/StartFromPreviousSimualtion.md | 1 - cellular_raza-book/src/UserGuides/UserGuides.md | 15 - cellular_raza-book/src/about_cellular_raza.md | 107 -- .../src/media/cellular_raza_square.svg | 59 -- cellular_raza-book/src/media/rust-svgrepo-com.svg | 2 - cellular_raza-building-blocks/.cargo/config.toml | 5 + cellular_raza-building-blocks/.docs-header.html | 32 + cellular_raza-building-blocks/Cargo.toml | 12 +- .../src/cell_building_blocks/cycle.rs | 11 +- .../src/cell_building_blocks/interaction.rs | 41 +- .../src/cell_building_blocks/mechanics.rs | 120 ++- .../src/cell_models/mod.rs | 4 + .../src/cell_models/modular_cell.rs | 105 +- .../src/cell_models/pool_bacteria.rs | 449 ++++++++ .../src/domains/cartesian_cuboid_2_vertex.rs | 20 +- .../src/domains/cartesian_cuboid_n.rs | 177 ++-- cellular_raza-building-blocks/src/lib.rs | 15 +- cellular_raza-concepts-derive/.cargo/config.toml | 5 + cellular_raza-concepts-derive/Cargo.toml | 6 +- cellular_raza-concepts-derive/src/lib.rs | 921 ++++++++++++---- cellular_raza-concepts/.cargo/config.toml | 2 + cellular_raza-concepts/Cargo.toml | 4 + cellular_raza-concepts/src/cell.rs | 20 +- cellular_raza-concepts/src/cycle.rs | 246 ++++- cellular_raza-concepts/src/domain_new.rs | 9 +- cellular_raza-concepts/src/errors.rs | 10 +- cellular_raza-concepts/src/interaction.rs | 9 +- cellular_raza-concepts/src/lib.rs | 314 +++--- cellular_raza-concepts/src/mechanics.rs | 6 +- cellular_raza-concepts/src/prelude.rs | 7 - cellular_raza-core-derive/src/lib.rs | 258 ----- cellular_raza-core-derive/tests/identical.rs | 17 - cellular_raza-core-derive/tests/mod.rs | 2 - cellular_raza-core-proc-macro/.cargo/config.toml | 5 + .../Cargo.toml | 15 +- .../README.md | 0 cellular_raza-core-proc-macro/src/aux_storage.rs | 673 ++++++++++++ cellular_raza-core-proc-macro/src/communicator.rs | 290 ++++++ cellular_raza-core-proc-macro/src/from_map.rs | 203 ++++ cellular_raza-core-proc-macro/src/lib.rs | 229 ++++ .../src/simulation_aspects.rs | 210 ++++ cellular_raza-core-proc-macro/src/testing.rs | 120 +++ cellular_raza-core/.cargo/config.toml | 5 + cellular_raza-core/.docs-header.html | 32 + cellular_raza-core/Cargo.toml | 11 +- .../src/backend/chili/aux_storage.rs | 1101 ++++++++++++++++++-- .../src/backend/chili/datastructures.rs | 741 ++++++++----- cellular_raza-core/src/backend/chili/errors.rs | 70 +- cellular_raza-core/src/backend/chili/mod.rs | 38 +- cellular_raza-core/src/backend/chili/setup.rs | 28 +- .../src/backend/chili/simulation_flow.rs | 1062 ++++++++++++------- cellular_raza-core/src/backend/chili/solvers.rs | 261 +++++ .../src/backend/cpu_os_threads/config.rs | 33 +- .../backend/cpu_os_threads/domain_decomposition.rs | 39 +- .../src/backend/cpu_os_threads/errors.rs | 10 +- .../src/backend/cpu_os_threads/prelude.rs | 12 +- .../src/backend/cpu_os_threads/supervisor.rs | 20 +- .../src/backend/cpu_rayon/concepts.rs | 2 +- cellular_raza-core/src/backend/cpu_rayon/engine.rs | 12 +- cellular_raza-core/src/backend/mod.rs | 55 +- cellular_raza-core/src/lib.rs | 40 +- cellular_raza-core/src/proc_macro.rs | 92 ++ cellular_raza-core/src/storage/concepts.rs | 151 ++- cellular_raza-core/src/storage/mod.rs | 13 +- cellular_raza-core/src/time.rs | 324 ++++++ cellular_raza-examples/autophagy_pyo3/Cargo.toml | 2 +- .../autophagy_pyo3/src/simulation.rs | 5 +- cellular_raza-examples/cell_sorting/src/main.rs | 2 +- .../pool_model_pyo3/analysis.ipynb | 58 +- .../pool_model_pyo3/cr_pool_model.py | 7 +- .../pool_model_pyo3/pool_paper_spatial.py | 53 +- .../pool_model_pyo3/potential.ipynb | 62 ++ cellular_raza-examples/pool_model_pyo3/run_sim.py | 49 +- .../pool_model_pyo3/src/bacteria_properties.rs | 163 +-- cellular_raza-examples/pool_model_pyo3/src/lib.rs | 1 - .../pool_model_pyo3/src/simulation.rs | 10 +- cellular_raza-examples/template/Cargo.toml | 15 + cellular_raza-examples/template/src/main.rs | 193 ++++ .../.devcontainer/devcontainer.json | 21 + cellular_raza-homepage/.gitignore | 11 + cellular_raza-homepage/.gitpod.yml | 15 + cellular_raza-homepage/LICENSE | 21 + cellular_raza-homepage/content/_index.md | 31 + cellular_raza-homepage/content/about.md | 6 + .../benchmarks/2024-02-thread-scaling/_index.md | 14 + .../2024-02-thread-scaling/scaling_1.png | Bin 0 -> 93746 bytes .../content/benchmarks/_index.md | 13 + cellular_raza-homepage/content/guides/_index.md | 19 + .../content/guides/building-blocks.md | 9 +- .../content/guides/getting-started.md | 6 +- .../content/guides/introduction.md | 47 + .../content/guides/load-previous-simulation.md | 4 + .../content/guides/physical-domain.md | 4 + .../content/guides/predefined-celll-models.md | 4 + cellular_raza-homepage/content/internals/_index.md | 21 + .../content/internals/backends/_index.md | 6 + .../content/internals/backends/chili/_index.md | 20 + .../internals/backends/chili/build_aux_storage.md | 5 + .../internals/backends/chili/build_communicator.md | 4 + .../content/internals/backends/chili/overview.md | 4 + .../internals/backends/cpu-os-threads/_index.md | 4 + .../content/internals/coding-guidelines.md | 16 + .../content/internals/concepts/_index.md | 5 + .../content/internals/concepts/cell/_index.md | 4 + .../content/internals/concepts/cell/cycle.md | 4 + .../content/internals/concepts/cell/interaction.md | 4 + .../content/internals/concepts/cell/mechanics.md | 5 + .../content/internals/concepts/cell/reactions.md | 4 + .../content/internals/concepts/domain/_index.md | 5 + .../content/internals/concepts/domain/boundary.md | 4 + .../internals/concepts/domain/decomposition.md | 4 + .../internals/concepts/domain/fluid-dynamcis.md | 4 + .../content/internals/roadmap.md | 22 +- .../content/internals/storage/_index.md | 4 + .../content/internals/time/_index.md | 4 + .../content/publications/_index.md | 12 + cellular_raza-homepage/content/showcase/_index.md | 19 + .../showcase/cell-sorting/cell_sorting_end.png | Bin 0 -> 492571 bytes .../content/showcase/cell-sorting/index.md | 6 + .../content/showcase/pool-model/index.md | 6 + .../showcase/pool-model/snapshot_00012000.png | Bin 0 -> 149903 bytes cellular_raza-homepage/go.mod | 5 + cellular_raza-homepage/go.sum | 2 + cellular_raza-homepage/hugo.yaml | 68 ++ cellular_raza-homepage/netlify.toml | 6 + .../static/logos}/cellular_raza.svg | 0 .../static/logos}/cellular_raza_dark_mode.svg | 0 cellular_raza/.cargo/config.toml | 7 +- cellular_raza/.docs-header.html | 32 + cellular_raza/Cargo.toml | 15 +- cellular_raza/README.md | 4 +- cellular_raza/src/lib.rs | 16 +- cellular_raza/src/prelude.rs | 3 +- rustfmt.toml | 10 + 166 files changed, 8026 insertions(+), 2798 deletions(-)