[1.3.45] 2025-08-21

* Fixed errors in the `radiation_StanfordBunny` and `energybalance_StanfordBunny` samples that were using the deprecated `Context::setPrimitiveData()` signature with explicit type and size parameters.
* Added automatic version change detection and CUDA object file cleanup improvements to the CMake build system
* Enhanced benchmark collection and reporting in `utilities/run_benchmarks.sh`
* Enhanced OpenMP configuration for macOS with automatic Apple Clang + libomp setup via Homebrew detection
* Added OpenMP installation step to GitHub Actions macOS workflow for improved CI compatibility

- Added comprehensive ray-tracing implementation with new `CollisionDetection_RayTracing.cpp` module
- Implemented advanced ray-tracing data structures including `RayQuery`, `HitResult`, `RayTracingStats`, `RayPacket`, and `RayStream` for efficient batch ray processing
- Added GPU-accelerated ray casting with warp-efficient CUDA kernels for optimal performance
- Introduced Structure-of-Arrays (SoA) BVH layout (`BVHNodesSoA`) for improved memory access patterns and cache efficiency
- Added SIMD-optimized ray-AABB intersection tests using AVX2/SSE instructions
- Implemented streaming ray tracer interface for optimal GPU utilization with memory usage statistics
- Enhanced spatial query capabilities including cone intersection queries, voxel ray path length calculations, and proximity-based collision detection
- Added advanced geometry operations for gap detection, optimal path finding, and attraction point detection within perception cones
- Implemented thread-safe primitive caching system for safe multi-threaded ray casting operations
- Added comprehensive GPU memory management with allocation and transfer optimizations
- Enhanced CMakeLists.txt with improved CUDA support and compilation handling
- Extended `HitResult` structure with `path_length` field for unobstructed voxel path length calculations in LiDAR processing
- Added `calculateVoxelPathLengths()` method for efficient ray path length calculations through individual voxels with OpenMP parallelization
- Enhanced `performGridRayIntersection()` to return detailed `HitResult` objects for each hit instead of simple hit counts
- Added ray classification methods `getRayClassificationCounts()` for Beer's law calculations with hit_before/hit_after statistics

- Fixed an error with `Visualizer::setColorbarRange()` where it was setting the color of values clipped below the lower bound incorrectly by implementing proper bounds checking for normalized color positions.

- Fixed `RadiationModel::updateGeometry()` to properly handle cases when called with an empty Context by adding a check for zero primitives and returning early with a warning message.

- Updated integration with enhanced collision detection capabilities for improved geometric operations

Author: bnbailey-psl

.github/workflows/mac_selftests.yaml

@@ -24,6 +24,8 @@ jobs:
         run: /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
       - name: Install XQuartz
         run: brew install Caskroom/cask/xquartz
+      - name: Install OpenMP support
+        run: brew install libomp
 
       - name: Bash script
         run: |

core/CMake_project.cmake

@@ -1,5 +1,6 @@
 option(ENABLE_OPENMP "Enable building with OpenMP" ON)
 option(BUILD_TESTS "Build test executables" OFF)
+option(BUILD_BENCHMARKS "Build performance benchmark executables" OFF)
 
 
 # Set CMake policies to avoid warnings on newer CMake versions
@@ -83,6 +84,22 @@ message( STATUS "[Helios] Last configured Helios Git commit hash: ${HELIOS_PREVI
 
 if(NOT HELIOS_PREVIOUS_COMMIT STREQUAL GIT_COMMIT_HASH)
   message(STATUS "[Helios] Git commit version change detected, automatically re-configuring...")
+  
+  # Clean CUDA object files to prevent linking issues with stale objects
+  find_package(CUDAToolkit QUIET)
+  if(CUDAToolkit_FOUND)
+    message(STATUS "[Helios] Cleaning CUDA object files due to version change...")
+    file(GLOB_RECURSE CUDA_OBJECTS 
+      "${CMAKE_BINARY_DIR}/**/*.cu.o"
+      "${CMAKE_BINARY_DIR}/**/*.cudafe*"
+      "${CMAKE_BINARY_DIR}/**/cmake_device_link.o"
+    )
+    if(CUDA_OBJECTS)
+      file(REMOVE ${CUDA_OBJECTS})
+      message(STATUS "[Helios] Removed ${CMAKE_CURRENT_LIST_SIZE} CUDA object files")
+    endif()
+  endif()
+  
   # update cache for next time
   set(HELIOS_PREVIOUS_COMMIT "${GIT_COMMIT_HASH}" CACHE STRING "Last configured Helios Git commit" FORCE)
 endif()
@@ -164,7 +181,59 @@ endforeach(PLUGIN)
 target_compile_definitions(helios PUBLIC $<$<CONFIG:Debug>:HELIOS_DEBUG>  $<$<CONFIG:RelWithDebInfo>:HELIOS_DEBUG> )
 
 if( ENABLE_OPENMP )
-    find_package(OpenMP)
+    # First try standard OpenMP detection
+    find_package(OpenMP QUIET)
+    
+    # If OpenMP not found and we're on macOS with Apple Clang, try automatic libomp configuration
+    if(NOT OpenMP_CXX_FOUND AND CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+        message(STATUS "[Helios] Configuring OpenMP for Apple Clang on macOS...")
+        
+        # Find Homebrew
+        find_program(BREW NAMES brew)
+        if(BREW)
+            # Check if libomp is installed
+            execute_process(COMMAND ${BREW} ls libomp 
+                           RESULT_VARIABLE BREW_RESULT_CODE 
+                           OUTPUT_QUIET ERROR_QUIET)
+            
+            if(NOT BREW_RESULT_CODE)
+                # Get libomp prefix
+                execute_process(COMMAND ${BREW} --prefix libomp 
+                               OUTPUT_VARIABLE LIBOMP_PREFIX 
+                               OUTPUT_STRIP_TRAILING_WHITESPACE)
+                
+                # Configure OpenMP for Apple Clang + libomp
+                set(OpenMP_CXX_FLAGS "-Xpreprocessor;-fopenmp")
+                set(OpenMP_CXX_LIB_NAMES "omp")
+                set(OpenMP_omp_LIBRARY "${LIBOMP_PREFIX}/lib/libomp.dylib")
+                set(OpenMP_CXX_INCLUDE_DIRS "${LIBOMP_PREFIX}/include")
+                
+                # Add include directory globally for compatibility
+                include_directories("${LIBOMP_PREFIX}/include")
+                
+                # Create OpenMP target if it doesn't exist
+                if(NOT TARGET OpenMP::OpenMP_CXX)
+                    add_library(OpenMP::OpenMP_CXX SHARED IMPORTED)
+                    set_target_properties(OpenMP::OpenMP_CXX PROPERTIES
+                        IMPORTED_LOCATION "${OpenMP_omp_LIBRARY}"
+                        INTERFACE_COMPILE_OPTIONS "-Xpreprocessor;-fopenmp"
+                        INTERFACE_INCLUDE_DIRECTORIES "${OpenMP_CXX_INCLUDE_DIRS}"
+                        INTERFACE_LINK_LIBRARIES "${OpenMP_omp_LIBRARY}")
+                endif()
+                
+                set(OpenMP_FOUND TRUE)
+                set(OpenMP_CXX_FOUND TRUE)
+                
+                message(STATUS "[Helios] Automatically configured OpenMP using Homebrew libomp from ${LIBOMP_PREFIX}")
+            else()
+                message(WARNING "[Helios] OpenMP requires libomp on macOS. Install with: brew install libomp")
+            endif()
+        else()
+            message(WARNING "[Helios] OpenMP on macOS requires Homebrew. Install from https://brew.sh then run: brew install libomp")
+        endif()
+    endif()
+    
+    # Final OpenMP configuration
     if (OpenMP_CXX_FOUND)
         message( STATUS "[Helios] Enabling OpenMP support" )
         target_link_libraries(helios PUBLIC OpenMP::OpenMP_CXX)

doc/CHANGELOG.md

@@ -1,5 +1,39 @@
 # Changelog
 
+# [1.3.45] 2025-08-21
+
+* Fixed errors in the `radiation_StanfordBunny` and `energybalance_StanfordBunny` samples that were using the deprecated `Context::setPrimitiveData()` signature with explicit type and size parameters.
+* Added automatic version change detection and CUDA object file cleanup improvements to the CMake build system
+* Enhanced benchmark collection and reporting in `utilities/run_benchmarks.sh`
+* Enhanced OpenMP configuration for macOS with automatic Apple Clang + libomp setup via Homebrew detection
+* Added OpenMP installation step to GitHub Actions macOS workflow for improved CI compatibility
+
+## CollisionDetection
+- Added comprehensive ray-tracing implementation with new `CollisionDetection_RayTracing.cpp` module
+- Implemented advanced ray-tracing data structures including `RayQuery`, `HitResult`, `RayTracingStats`, `RayPacket`, and `RayStream` for efficient batch ray processing
+- Added GPU-accelerated ray casting with warp-efficient CUDA kernels for optimal performance
+- Introduced Structure-of-Arrays (SoA) BVH layout (`BVHNodesSoA`) for improved memory access patterns and cache efficiency
+- Added SIMD-optimized ray-AABB intersection tests using AVX2/SSE instructions
+- Implemented streaming ray tracer interface for optimal GPU utilization with memory usage statistics
+- Enhanced spatial query capabilities including cone intersection queries, voxel ray path length calculations, and proximity-based collision detection
+- Added advanced geometry operations for gap detection, optimal path finding, and attraction point detection within perception cones
+- Implemented thread-safe primitive caching system for safe multi-threaded ray casting operations
+- Added comprehensive GPU memory management with allocation and transfer optimizations
+- Enhanced CMakeLists.txt with improved CUDA support and compilation handling
+- Extended `HitResult` structure with `path_length` field for unobstructed voxel path length calculations in LiDAR processing
+- Added `calculateVoxelPathLengths()` method for efficient ray path length calculations through individual voxels with OpenMP parallelization
+- Enhanced `performGridRayIntersection()` to return detailed `HitResult` objects for each hit instead of simple hit counts
+- Added ray classification methods `getRayClassificationCounts()` for Beer's law calculations with hit_before/hit_after statistics
+
+## Visualizer
+- Fixed an error with `Visualizer::setColorbarRange()` where it was setting the color of values clipped below the lower bound incorrectly by implementing proper bounds checking for normalized color positions.
+
+## Radiation
+- Fixed `RadiationModel::updateGeometry()` to properly handle cases when called with an empty Context by adding a check for zero primitives and returning early with a warning message.
+
+## Plant Architecture
+- Updated integration with enhanced collision detection capabilities for improved geometric operations
+
 # [1.3.44] 2025-08-10
 
 * Added `BUILD_TESTS` CMake option to conditionally build test executables instead of building them by default

doc/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = Helios
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v1.3.44
+PROJECT_NUMBER         = v1.3.45
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/DoxygenLayout.xml

@@ -9,23 +9,23 @@
       <tab type="user" visible="yes" url="@ref IO" title="File I/O"/>
     </tab>
     <tab type="usergroup" visible="yes" url="@ref PlugIns" title="Plugins" intro="">
-      <tab type="user" visible="yes" url="@ref VisualizerDoc" title="Visualizer"/>
-      <tab type="user" visible="yes" url="@ref RadiationDoc" title="Radiation Model"/>
-      <tab type="user" visible="yes" url="@ref EnergyBalanceDoc" title="Energy Balance Model"/>
-      <tab type="user" visible="yes" url="@ref BLConductanceDoc" title="Boundary-Layer Conductance"/>
-      <tab type="user" visible="yes" url="@ref LiDARDoc" title="Terrestrial LiDAR"/>
       <tab type="user" visible="yes" url="@ref AerialLiDARDoc" title="Aerial LiDAR"/>
+      <tab type="user" visible="yes" url="@ref BLConductanceDoc" title="Boundary-Layer Conductance"/>
+      <tab type="user" visible="yes" url="@ref CanopyGeneratorDoc" title="Canopy Generator"/>
+      <tab type="user" visible="yes" url="@ref EnergyBalanceDoc" title="Energy Balance Model"/>
+      <tab type="user" visible="yes" url="@ref LeafOpticsDoc" title="Leaf Optics Model"/>
+      <tab type="user" visible="yes" url="@ref ParameterOptimizationDoc" title="Model Parameter Optimization Utility"/>
       <tab type="user" visible="yes" url="@ref PhotosynthesisDoc" title="Photosynthesis Models"/>
-      <tab type="user" visible="yes" url="@ref StomatalDoc" title="Stomatal Conductance Models"/>
-      <tab type="user" visible="yes" url="@ref SolarPositionDoc" title="Solar Position and Fluxes Model"/>
-      <tab type="user" visible="yes" url="@ref VoxelIntersectionDoc" title="Voxel Intersection"/>
       <tab type="user" visible="yes" url="@ref PlantArchitectureDoc" title="Plant Architecture"/>
-      <tab type="user" visible="yes" url="@ref CanopyGeneratorDoc" title="Canopy Generator"/>
-      <tab type="user" visible="yes" url="@ref WeberPennDoc" title="Weber-Penn Tree"/>
       <tab type="user" visible="yes" url="@ref PlantHydraulicsDoc" title="Plant Hydraulics Model"/>
-      <tab type="user" visible="yes" url="@ref ParameterOptimizationDoc" title="Model Parameter Optimization Utility"/>
-      <tab type="user" visible="yes" url="@ref LeafOpticsDoc" title="Leaf Optics Model"/>
       <tab type="user" visible="yes" url="@ref ProjectBuilderDoc" title="Project Builder"/>
+      <tab type="user" visible="yes" url="@ref RadiationDoc" title="Radiation Model"/>
+      <tab type="user" visible="yes" url="@ref SolarPositionDoc" title="Solar Position and Fluxes Model"/>
+      <tab type="user" visible="yes" url="@ref StomatalDoc" title="Stomatal Conductance Models"/>
+      <tab type="user" visible="yes" url="@ref LiDARDoc" title="Terrestrial LiDAR"/>
+      <tab type="user" visible="yes" url="@ref VisualizerDoc" title="Visualizer"/>
+      <tab type="user" visible="yes" url="@ref VoxelIntersectionDoc" title="Voxel Intersection"/>
+      <tab type="user" visible="yes" url="@ref WeberPennDoc" title="Weber-Penn Tree"/>
     </tab>
     <tab type="usergroup" visible="yes" url="@ref Tutorials" title="Tutorials" intro="">
       <tab type="user" visible="yes" url="@ref context_selftest_tutorial" title="Tutorial 0: Context Self-Test"/>

doc/UserGuide.dox

@@ -141,23 +141,23 @@
   4. Class: C++ class associated with the plug-in and the class constructor(s).
   5. Usage: Explanation of plug-in member functions for performing various tasks related to the plug-in. In general, these explanations will comprise the majority of the plug-in documentation.
 
-  - \subpage VisualizerDoc "Visualizer: visualization of model geometry and data"
-  - \subpage WeberPennDoc "Weber-Penn Tree: Procedural tree architecture generation"
-  - \subpage RadiationDoc "Radiation Model: GPU-accelerated ray-tracing radiation transport model"
-  - \subpage EnergyBalanceDoc "Energy Balance Model: Surface energy balance solution"
+  - \subpage AerialLiDARDoc "Aerial LiDAR: Processing and visualizing aerial LiDAR data"
   - \subpage BLConductanceDoc "Boundary-Layer Conductance: Perform boundary-layer conductance model calculations based on several possible models."		
+  - \subpage CanopyGeneratorDoc "Canopy Generator: Simple generation of different type of plant and canopy geometries."
+  - \subpage EnergyBalanceDoc "Energy Balance Model: Surface energy balance solution"
+  - \subpage LeafOpticsDoc "Leaf Optics: Implementation of the PROSPECT-PRO leaf optical model of leaf reflectance and transmittance spectra."
   - \subpage LiDARDoc "LiDAR: Processing and visualizing terrestrial LiDAR data"
-  - \subpage AerialLiDARDoc "Aerial LiDAR: Processing and visualizing aerial LiDAR data"
+  - \subpage ParameterOptimizationDoc "Parameter Optimization: Utility for optimization of model parameters."
   - \subpage PhotosynthesisDoc "Photosynthesis Model: Photosynthetic assimilation model"
-  - \subpage StomatalDoc "Stomatal Conductance Model: Model for the conductance of water vapor through stomatal pores"
-  - \subpage SolarPositionDoc "Solar Position Model: Model for the position of the sun in the sky, as well as models of solar radiation flux and longwave flux from the sky."
-  - \subpage VoxelIntersectionDoc "Voxel Intersection: Determine planar primitive elements that lie within voxel primitives."
-  - \subpage CanopyGeneratorDoc "Canopy Generator: Simple generation of different type of plant and canopy geometries."
   - \subpage PlantArchitectureDoc "Plant Architecture: Flexible procedural plant generation with dynamic growth and phenology."
   - \subpage PlantHydraulicsDoc "Plant Hydraulics: Models the water potentials, water contents, hydraulic conductances, and hydraulic capacitances."
-  - \subpage ParameterOptimizationDoc "Parameter Optimization: Utility for optimization of model parameters."
-  - \subpage LeafOpticsDoc "Leaf Optics: Implementation of the PROSPECT-PRO leaf optical model of leaf reflectance and transmittance spectra."
   - \subpage ProjectBuilderDoc "GUI and XML interface for creating and running Helios projects."
+  - \subpage RadiationDoc "Radiation Model: GPU-accelerated ray-tracing radiation transport model"
+  - \subpage SolarPositionDoc "Solar Position Model: Model for the position of the sun in the sky, as well as models of solar radiation flux and longwave flux from the sky."
+  - \subpage StomatalDoc "Stomatal Conductance Model: Model for the conductance of water vapor through stomatal pores"
+  - \subpage VisualizerDoc "Visualizer: visualization of model geometry and data"
+  - \subpage VoxelIntersectionDoc "Voxel Intersection: Determine planar primitive elements that lie within voxel primitives."
+  - \subpage WeberPennDoc "Weber-Penn Tree: Procedural tree architecture generation"
 
 */
 

doc/html/_a_p_i.html

@@ -84,7 +84,7 @@
   <td id="projectlogo"><img alt="Logo" src="Helios_logo_small.png"></td>
   <td id="projectalign">
    <div id="projectname">
-       <span id="projectnumber">&#160;v1.3.44</span>
+       <span id="projectnumber">&#160;v1.3.45</span>
    </div>
   </td>
      <td id="searchbox-container">        <div id="MSearchBox" class="MSearchBoxInactive">

doc/html/_aerial_li_d_a_r_8cpp.html

@@ -84,7 +84,7 @@
   <td id="projectlogo"><img alt="Logo" src="Helios_logo_small.png"></td>
   <td id="projectalign">
    <div id="projectname">
-       <span id="projectnumber">&#160;v1.3.44</span>
+       <span id="projectnumber">&#160;v1.3.45</span>
    </div>
   </td>
      <td id="searchbox-container">        <div id="MSearchBox" class="MSearchBoxInactive">

doc/html/_aerial_li_d_a_r_8cpp_source.html

@@ -84,7 +84,7 @@
   <td id="projectlogo"><img alt="Logo" src="Helios_logo_small.png"></td>
   <td id="projectalign">
    <div id="projectname">
-       <span id="projectnumber">&#160;v1.3.44</span>
+       <span id="projectnumber">&#160;v1.3.45</span>
    </div>
   </td>
      <td id="searchbox-container">        <div id="MSearchBox" class="MSearchBoxInactive">

doc/html/_aerial_li_d_a_r_8cu.html

@@ -84,7 +84,7 @@
   <td id="projectlogo"><img alt="Logo" src="Helios_logo_small.png"></td>
   <td id="projectalign">
    <div id="projectname">
-       <span id="projectnumber">&#160;v1.3.44</span>
+       <span id="projectnumber">&#160;v1.3.45</span>
    </div>
   </td>
      <td id="searchbox-container">        <div id="MSearchBox" class="MSearchBoxInactive">