OpenMP solvers #110
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| #pragma once | ||
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| #include <array> | ||
| #include <span> | ||
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| #include "types.h" | ||
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| namespace physicore { | ||
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| /** | ||
| * @brief Uniform Cartesian mesh for spatial domain discretization. | ||
| * | ||
| * Provides axis-aligned structured grid with uniform spacing. | ||
| * Used by both reaction-diffusion and mechanics modules for domain partitioning. | ||
| * | ||
| * Supports 1D, 2D, and 3D domains with configurable voxel sizes and bounding boxes. | ||
| * Enables efficient spatial queries: position-to-voxel mapping and voxel linearization. | ||
| * | ||
| * @see reactions-diffusion/biofvm for diffusion solver usage | ||
| * @see mechanics/physicell for mechanics engine usage | ||
| */ | ||
| class cartesian_mesh | ||
| { | ||
| public: | ||
| /// @brief Constructor | ||
| /// @param dims Number of spatial dimensions (1, 2, or 3) | ||
| /// @param bounding_box_mins Minimum coordinates of domain bounds | ||
| /// @param bounding_box_maxs Maximum coordinates of domain bounds | ||
| /// @param voxel_shape Size of each voxel in each dimension | ||
| explicit cartesian_mesh(index_t dims, std::array<sindex_t, 3> bounding_box_mins, | ||
| std::array<sindex_t, 3> bounding_box_maxs, std::array<index_t, 3> voxel_shape); | ||
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| /// @brief Get total number of voxels in the mesh | ||
| [[nodiscard]] std::size_t voxel_count() const; | ||
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| /// @brief Get volume of a single voxel | ||
| [[nodiscard]] index_t voxel_volume() const; | ||
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| /// @brief Find voxel indices containing the given position | ||
| /// @param position Spatial coordinates (must match dims) | ||
| /// @return Voxel indices in x, y, z order | ||
| [[nodiscard]] std::array<index_t, 3> voxel_position(std::span<const real_t> position) const; | ||
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| /// @brief Get the center position of a voxel | ||
| /// @param position Voxel indices | ||
| /// @return Center coordinates in x, y, z order | ||
| [[nodiscard]] std::array<real_t, 3> voxel_center(std::array<index_t, 3> position) const; | ||
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| /// @brief Convert 3D voxel indices to linear index | ||
| /// @param x, y, z Voxel indices | ||
| /// @return Linear index for use in flat arrays | ||
| [[nodiscard]] std::size_t linearize(index_t x, index_t y, index_t z) const; | ||
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| // Member data (public for direct access, following biofvm pattern) | ||
| index_t dims; ///< Number of spatial dimensions | ||
| std::array<sindex_t, 3> bounding_box_mins; ///< Minimum domain coordinates | ||
| std::array<sindex_t, 3> bounding_box_maxs; ///< Maximum domain coordinates | ||
| std::array<index_t, 3> voxel_shape; ///< Size of each voxel | ||
| std::array<index_t, 3> grid_shape; ///< Number of voxels per dimension | ||
| }; | ||
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| } // namespace physicore |
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| #pragma once | ||
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| namespace physicore { | ||
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| #if defined(_MSC_VER) | ||
| #define PHYSICORE_RESTRICT __restrict | ||
| #elif defined(__GNUC__) || defined(__clang__) | ||
| #define PHYSICORE_RESTRICT __restrict__ | ||
| #else | ||
| #define PHYSICORE_RESTRICT | ||
| #endif | ||
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| } // namespace physicore |
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| #pragma once | ||
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| #include <cassert> | ||
| #include <concepts> | ||
| #include <functional> | ||
| #include <memory> | ||
| #include <string> | ||
| #include <unordered_map> | ||
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| namespace physicore { | ||
| template <class Base> | ||
| class factory_registry | ||
| { | ||
| public: | ||
| using ptr_t = std::unique_ptr<Base>; | ||
| using factory_func_t = std::function<ptr_t()>; | ||
| using map_t = std::unordered_map<std::string, factory_func_t>; | ||
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| bool register_factory(std::string name, factory_func_t&& f); | ||
| ptr_t get(const std::string& name); | ||
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| private: | ||
| map_t factories_; | ||
| }; | ||
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| template <class Base> | ||
| bool factory_registry<Base>::register_factory(std::string name, factory_func_t&& f) | ||
| { | ||
| auto [it, emplaced] = factories_.try_emplace(std::move(name), std::move(f)); | ||
| return emplaced; | ||
| } | ||
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| template <class Base> | ||
| typename factory_registry<Base>::ptr_t factory_registry<Base>::get(const std::string& name) | ||
| { | ||
| auto it = factories_.find(name); | ||
| if (it == factories_.end()) | ||
| { | ||
| return nullptr; | ||
| } | ||
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| return it->second(); | ||
| } | ||
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| template <class Derived, class Registry> | ||
| struct generic_registry_adder | ||
| { | ||
| explicit generic_registry_adder(std::string name) | ||
| { | ||
| Registry::instance().register_factory(std::move(name), []() { return std::make_unique<Derived>(); }); | ||
| } | ||
| }; | ||
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| } // namespace physicore |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,78 @@ | ||
| #include "common/cartesian_mesh.h" | ||
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| #include <cassert> | ||
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| namespace physicore { | ||
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| cartesian_mesh::cartesian_mesh(index_t dims, std::array<sindex_t, 3> bounding_box_mins, | ||
| std::array<sindex_t, 3> bounding_box_maxs, std::array<index_t, 3> voxel_shape) | ||
| : dims(dims), | ||
| bounding_box_mins(bounding_box_mins), | ||
| bounding_box_maxs(bounding_box_maxs), | ||
| voxel_shape(voxel_shape), | ||
| grid_shape({ 1, 1, 1 }) | ||
| { | ||
| if (dims >= 1) | ||
| { | ||
| grid_shape[0] = (bounding_box_maxs[0] - bounding_box_mins[0] + voxel_shape[0] - 1) / voxel_shape[0]; | ||
| } | ||
| if (dims >= 2) | ||
| { | ||
| grid_shape[1] = (bounding_box_maxs[1] - bounding_box_mins[1] + voxel_shape[1] - 1) / voxel_shape[1]; | ||
| } | ||
| if (dims >= 3) | ||
| { | ||
| grid_shape[2] = (bounding_box_maxs[2] - bounding_box_mins[2] + voxel_shape[2] - 1) / voxel_shape[2]; | ||
| } | ||
| } | ||
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| std::size_t cartesian_mesh::voxel_count() const | ||
| { | ||
| return (std::size_t)grid_shape[0] * (std::size_t)grid_shape[1] * (std::size_t)grid_shape[2]; | ||
| } | ||
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| index_t cartesian_mesh::voxel_volume() const { return voxel_shape[0] * voxel_shape[1] * voxel_shape[2]; } | ||
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| std::array<index_t, 3> cartesian_mesh::voxel_position(std::span<const real_t> position) const | ||
| { | ||
| assert(position.size() == (size_t)dims); | ||
| assert(position[0] <= bounding_box_maxs[0] && position[0] >= bounding_box_mins[0]); | ||
| if (dims >= 2) | ||
| assert(position[1] <= bounding_box_maxs[1] && position[1] >= bounding_box_mins[1]); | ||
| if (dims >= 3) | ||
| assert(position[2] <= bounding_box_maxs[2] && position[2] >= bounding_box_mins[2]); | ||
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| switch (position.size()) | ||
| { | ||
| case 1: | ||
| return { (index_t)((position[0] - (real_t)bounding_box_mins[0]) / (real_t)voxel_shape[0]), 0, 0 }; | ||
| case 2: | ||
| return { (index_t)((position[0] - (real_t)bounding_box_mins[0]) / (real_t)voxel_shape[0]), | ||
| (index_t)((position[1] - (real_t)bounding_box_mins[1]) / (real_t)voxel_shape[1]), 0 }; | ||
| case 3: | ||
| return { (index_t)((position[0] - (real_t)bounding_box_mins[0]) / (real_t)voxel_shape[0]), | ||
| (index_t)((position[1] - (real_t)bounding_box_mins[1]) / (real_t)voxel_shape[1]), | ||
| (index_t)((position[2] - (real_t)bounding_box_mins[2]) / (real_t)voxel_shape[2]) }; | ||
| default: | ||
| assert(false); // Should never reach here | ||
| return { 0, 0, 0 }; | ||
| } | ||
| } | ||
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| std::array<real_t, 3> cartesian_mesh::voxel_center(std::array<index_t, 3> position) const | ||
| { | ||
| assert(position[0] < grid_shape[0]); | ||
| assert(position[1] < grid_shape[1]); | ||
| assert(position[2] < grid_shape[2]); | ||
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| return { (real_t)(position[0] * voxel_shape[0] + bounding_box_mins[0]) + ((real_t)voxel_shape[0] / (real_t)2.0), | ||
| (real_t)(position[1] * voxel_shape[1] + bounding_box_mins[1]) + ((real_t)voxel_shape[1] / (real_t)2.0), | ||
| (real_t)(position[2] * voxel_shape[2] + bounding_box_mins[2]) + ((real_t)voxel_shape[2] / (real_t)2.0) }; | ||
| } | ||
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| std::size_t cartesian_mesh::linearize(index_t x, index_t y, index_t z) const | ||
| { | ||
| return x + y * grid_shape[0] + z * grid_shape[0] * grid_shape[1]; | ||
| } | ||
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| } // namespace physicore |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,26 +1,43 @@ | ||
| #pragma once | ||
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| #include <memory> | ||
| #include <optional> | ||
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| #include <common/cartesian_mesh.h> | ||
| #include <common/timestep_executor.h> | ||
| #include <common/types.h> | ||
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| #include "mechanical_agent_container.h" | ||
| #include "serializer.h" | ||
| #include "solver.h" | ||
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| namespace physicore::mechanics::physicell { | ||
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| class environment : public timestep_executor | ||
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Check warning on line 16 in mechanics/physicell/include/physicell/environment.h
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| { | ||
| public: | ||
| environment(real_t timestep, index_t dims, index_t agent_types_count, index_t substrates_count); | ||
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| void run_single_timestep() override; | ||
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| void serialize_state(real_t current_time) override; | ||
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| real_t mechanics_timestep; | ||
| bool automated_spring_adhesion = false; | ||
| bool virtual_wall_at_domain_edges = true; | ||
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| serializer_ptr serializer; | ||
| solver_ptr solver; | ||
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| std::unique_ptr<mechanical_agent_container> agents; | ||
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| // Mesh data for spatial queries | ||
| void set_mesh(cartesian_mesh mesh) { this->mesh_ = std::move(mesh); } | ||
| const cartesian_mesh& get_mesh() const; | ||
| bool has_mesh() const { return mesh_.has_value(); } | ||
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| private: | ||
| std::optional<cartesian_mesh> mesh_; | ||
| }; | ||
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| } // namespace physicore::mechanics::physicell | ||
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