├── .github └── workflows │ ├── release.yml │ └── wheels.yml ├── .gitignore ├── .gitmodules ├── .zenodo.json ├── AUTHORS ├── CMakeLists.txt ├── LICENSE ├── MANIFEST.in ├── README.md ├── conda.recipe ├── bld.bat ├── build.sh └── meta.yaml ├── ecell4 ├── CMakeLists.txt ├── bd │ ├── BDFactory.hpp │ ├── BDPropagator.cpp │ ├── BDPropagator.hpp │ ├── BDSimulator.cpp │ ├── BDSimulator.hpp │ ├── BDWorld.hpp │ ├── CMakeLists.txt │ ├── functions3d.cpp │ ├── functions3d.hpp │ ├── samples │ │ ├── CMakeLists.txt │ │ └── hardbody.cpp │ └── tests │ │ ├── BDSimulator_test.cpp │ │ ├── BDWorld_test.cpp │ │ └── CMakeLists.txt ├── core │ ├── AABB.cpp │ ├── AABB.hpp │ ├── AABBSurface.cpp │ ├── AABBSurface.hpp │ ├── Attribute.cpp │ ├── Attribute.hpp │ ├── BDMLWriter.hpp │ ├── Barycentric.cpp │ ├── Barycentric.hpp │ ├── BoundaryCondition.hpp │ ├── CMakeLists.txt │ ├── Circle.hpp │ ├── CompartmentSpace.cpp │ ├── CompartmentSpace.hpp │ ├── CompartmentSpaceHDF5Writer.hpp │ ├── Cone.hpp │ ├── Context.cpp │ ├── Context.hpp │ ├── Cylinder.cpp │ ├── Cylinder.hpp │ ├── Doxyfile │ ├── DynamicPriorityQueue.hpp │ ├── EventScheduler.hpp │ ├── HCPLatticeSpace.cpp │ ├── HCPLatticeSpace.hpp │ ├── Identifier.hpp │ ├── Integer3.cpp │ ├── Integer3.hpp │ ├── Journal.cpp │ ├── Journal.hpp │ ├── LatticeSpaceCellListImpl.cpp │ ├── LatticeSpaceCellListImpl.hpp │ ├── LatticeSpaceHDF5Writer.hpp │ ├── LatticeSpaceVectorImpl.cpp │ ├── LatticeSpaceVectorImpl.hpp │ ├── Mesh.cpp │ ├── Mesh.hpp │ ├── Model.cpp │ ├── Model.hpp │ ├── ModelWrapper.hpp │ ├── MoleculePool.hpp │ ├── NetfreeModel.cpp │ ├── NetfreeModel.hpp │ ├── NetworkModel.cpp │ ├── NetworkModel.hpp │ ├── ObjectIDContainer.hpp │ ├── OffLatticeSpace.cpp │ ├── OffLatticeSpace.hpp │ ├── Particle.hpp │ ├── ParticleSpace.cpp │ ├── ParticleSpace.hpp │ ├── ParticleSpaceCellListImpl.cpp │ ├── ParticleSpaceCellListImpl.hpp │ ├── ParticleSpaceHDF5Writer.hpp │ ├── ParticleSpaceRTreeImpl.cpp │ ├── ParticleSpaceRTreeImpl.hpp │ ├── PeriodicRTree.hpp │ ├── PlanarSurface.cpp │ ├── PlanarSurface.hpp │ ├── Polygon.cpp │ ├── Polygon.hpp │ ├── PolygonHDF5Writer.cpp │ ├── PolygonHDF5Writer.hpp │ ├── Quantity.hpp │ ├── RandomNumberGenerator.cpp │ ├── RandomNumberGenerator.hpp │ ├── ReactionRule.cpp │ ├── ReactionRule.hpp │ ├── ReactionRuleDescriptor.hpp │ ├── Real3.hpp │ ├── Rod.cpp │ ├── Rod.hpp │ ├── STLFileIO.cpp │ ├── STLFileIO.hpp │ ├── Segment.hpp │ ├── SerialIDGenerator.hpp │ ├── Shape.hpp │ ├── Simulator.hpp │ ├── SimulatorBase.hpp │ ├── SimulatorFactory.hpp │ ├── Space.hpp │ ├── Species.cpp │ ├── Species.hpp │ ├── Sphere.cpp │ ├── Sphere.hpp │ ├── StructureType.hpp │ ├── SubvolumeSpace.cpp │ ├── SubvolumeSpace.hpp │ ├── SubvolumeSpaceHDF5Writer.hpp │ ├── Triangle.cpp │ ├── Triangle.hpp │ ├── TriangleView.hpp │ ├── UnitSpecies.cpp │ ├── UnitSpecies.hpp │ ├── VacantType.hpp │ ├── VoxelPool.hpp │ ├── VoxelSpaceBase.cpp │ ├── VoxelSpaceBase.hpp │ ├── VoxelView.hpp │ ├── WorldInterface.hpp │ ├── collision.cpp │ ├── collision.hpp │ ├── comparators.hpp │ ├── config.h.in │ ├── converter.hpp │ ├── exceptions.hpp │ ├── extras.cpp │ ├── extras.hpp │ ├── functions.hpp │ ├── geometry.cpp │ ├── geometry.hpp │ ├── observers.cpp │ ├── observers.hpp │ ├── shape_operators.hpp │ ├── tests │ │ ├── Barycentric_test.cpp │ │ ├── CMakeLists.txt │ │ ├── CompartmentSpace_test.cpp │ │ ├── EventScheduler_test.cpp │ │ ├── LatticeSpace_test.cpp │ │ ├── NetfreeModel_test.cpp │ │ ├── NetworkModel_test.cpp │ │ ├── ObjectIDContainer_test.cpp │ │ ├── OffLatticeSpace_test.cpp │ │ ├── ParticleSpaceRTreeImpl_test.cpp │ │ ├── ParticleSpace_test.cpp │ │ ├── PeriodicRTree_test.cpp │ │ ├── Polygon_test.cpp │ │ ├── RandomNumberGenerator_test.cpp │ │ ├── ReactionRule_test.cpp │ │ ├── Real3_test.cpp │ │ ├── STLIO_test.cpp │ │ ├── Shape_test.cpp │ │ ├── Species_test.cpp │ │ ├── SubvolumeSpace_test.cpp │ │ ├── Triangle_test.cpp │ │ ├── extras_test.cpp │ │ └── geometry_test.cpp │ ├── triangle_geometry.cpp │ ├── triangle_geometry.hpp │ ├── type_name_of.hpp │ └── types.hpp ├── egfrd │ ├── .gitignore │ ├── .hgignore │ ├── AUTHORS │ ├── AnalyticalPair.hpp │ ├── AnalyticalSingle.hpp │ ├── BDPropagator.hpp │ ├── BDSimulator.hpp │ ├── CMakeLists.txt │ ├── COPYING │ ├── ChangeLog │ ├── ConsoleAppender.hpp │ ├── Domain.hpp │ ├── DomainID.hpp │ ├── EGFRDSimulator.hpp │ ├── INSTALL │ ├── Logger.cpp │ ├── Logger.hpp │ ├── MatrixSpace.hpp │ ├── Multi.hpp │ ├── NEWS │ ├── NetworkRulesAdapter.hpp │ ├── Pair.hpp │ ├── ParticleContainer.hpp │ ├── ParticleSimulator.hpp │ ├── ParticleTraits.hpp │ ├── Polygon.hpp │ ├── PotentialField.hpp │ ├── README │ ├── ReactionRecord.hpp │ ├── ReactionRecorder.hpp │ ├── ReactionRecorderWrapper.hpp │ ├── ReactionRuleInfo.hpp │ ├── Real3Type.hpp │ ├── ShapedDomain.hpp │ ├── Shell.hpp │ ├── ShellID.hpp │ ├── Single.hpp │ ├── VolumeClearer.hpp │ ├── World.hpp │ ├── egfrd.hpp │ ├── exceptions.hpp │ ├── generator.hpp │ ├── geometry.hpp │ ├── linear_algebra.hpp │ ├── pyport.patch │ ├── samples │ │ ├── CMakeLists.txt │ │ ├── mymapk.cpp │ │ ├── polygon.cpp │ │ └── wscript │ ├── sorted_list.hpp │ ├── structures.hpp │ ├── tests │ │ └── GreensFunction3DRadInf_test.cpp │ ├── twofold_container.hpp │ └── utils │ │ ├── array_helper.hpp │ │ ├── array_traits.hpp │ │ ├── collection_contains.hpp │ │ ├── fun_composition.hpp │ │ ├── math.hpp │ │ ├── memberwise_compare.hpp │ │ ├── pair.hpp │ │ ├── pointer_as_ref.hpp │ │ ├── random.hpp │ │ ├── range.hpp │ │ └── stringizer.hpp ├── gillespie │ ├── CMakeLists.txt │ ├── GillespieFactory.hpp │ ├── GillespieSimulator.cpp │ ├── GillespieSimulator.hpp │ ├── GillespieWorld.cpp │ ├── GillespieWorld.hpp │ ├── samples │ │ ├── CMakeLists.txt │ │ └── simple.cpp │ └── tests │ │ ├── CMakeLists.txt │ │ ├── GillespieSimulator_test.cpp │ │ └── GillespieWorld_test.cpp ├── meso │ ├── CMakeLists.txt │ ├── MesoscopicFactory.hpp │ ├── MesoscopicSimulator.cpp │ ├── MesoscopicSimulator.hpp │ ├── MesoscopicWorld.cpp │ ├── MesoscopicWorld.hpp │ ├── samples │ │ ├── CMakeLists.txt │ │ └── simple-meso.cpp │ └── tests │ │ ├── CMakeLists.txt │ │ └── MesoscopicSimulator_test.cpp ├── ode │ ├── CMakeLists.txt │ ├── ODEFactory.hpp │ ├── ODESimulator.cpp │ ├── ODESimulator.hpp │ ├── ODEWorld.cpp │ ├── ODEWorld.hpp │ ├── samples │ │ ├── CMakeLists.txt │ │ ├── dissociation.cpp │ │ ├── equilibrium.cpp │ │ ├── equilibrium2.cpp │ │ ├── equilibrium_new.cpp │ │ ├── odesimulator2.cpp │ │ └── run_test.cpp │ └── tests │ │ ├── CMakeLists.txt │ │ ├── ODESimulator_new_test.cpp │ │ └── ODESimulator_test.cpp ├── python_api │ ├── CMakeLists.txt │ ├── bd.cpp │ ├── core.cpp │ ├── egfrd.cpp │ ├── gillespie.cpp │ ├── main.cpp │ ├── meso.cpp │ ├── model.hpp │ ├── observers.hpp │ ├── ode.cpp │ ├── python_api.hpp │ ├── random_number_generator.hpp │ ├── reaction_rule_descriptor.hpp │ ├── sgfrd.cpp │ ├── shape.hpp │ ├── simulator.hpp │ ├── simulator_factory.hpp │ ├── spatiocyte.cpp │ ├── type_caster.hpp │ └── world_interface.hpp ├── sgfrd │ ├── BDPropagator.hpp │ ├── BDSimulator.hpp │ ├── Birth.hpp │ ├── CMakeLists.txt │ ├── Multi.hpp │ ├── MultiContainer.hpp │ ├── Pair.hpp │ ├── ReactionInfo.hpp │ ├── SGFRDEvent.hpp │ ├── SGFRDFactory.hpp │ ├── SGFRDSimulator.cpp │ ├── SGFRDSimulator.hpp │ ├── SGFRDWorld.cpp │ ├── SGFRDWorld.hpp │ ├── Shell.hpp │ ├── ShellContainer.hpp │ ├── ShellID.hpp │ ├── ShellVisitorApplier.hpp │ ├── ShellVisitors.hpp │ ├── Single.hpp │ ├── StructureRegistrator.hpp │ ├── distance.hpp │ ├── distance_calculator.hpp │ ├── expected.hpp │ ├── samples │ │ ├── CMakeLists.txt │ │ ├── bdonly.cpp │ │ ├── diffusion.cpp │ │ ├── plane10x10.stl │ │ ├── reaction.cpp │ │ ├── reaction.inp │ │ ├── rebinding_bd.cpp │ │ └── sphere.stl │ ├── statistics.hpp │ └── tracer.hpp └── spatiocyte │ ├── CMakeLists.txt │ ├── OffLattice.hpp │ ├── OneToManyMap.hpp │ ├── ReactionEvent.cpp │ ├── SpatiocyteEvent.hpp │ ├── SpatiocyteFactory.hpp │ ├── SpatiocyteReactions.cpp │ ├── SpatiocyteReactions.hpp │ ├── SpatiocyteSimulator.cpp │ ├── SpatiocyteSimulator.hpp │ ├── SpatiocyteWorld.cpp │ ├── 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