[1.3.28] 2025-02-25

+++++ NEW PLUG-IN ++++++
- project builder plug-in added. GUI and XML interface for creating projects. This is still in beta testing. Credit to Sean Banks for this addition.

++Substantial expansion of self-tests for boundarylayerconductance, energybalance, photosynthesis, solarposition, stomatalconductance, syntheticannotation, and visualizer plug-ins
++New documentation theme

*Context*
- Many upgrades to substantially improve performance for CPU code.
- Upgrades to OBJ file writing, including making Gazebo compatable and adding option to write normals to OBJ files. Credit to LeRoy Corentin for this addition.

*Radiation*
- Minor change in RadiationModel::runBand() to set all primitive data values in a single Context method call for efficiency.
- Changed up logic for radiation property setting. If a spectrum is specified for reflectivity or transmissivity, this can be overridden for a single band by specifying the primitive data "reflectivity_[bandname]" or "transmissivity_[bandname]".

*Plant Architecture*
- cowpeaLeafPrototype_unifoliate_OBJ() asset function was incorrect in the last commit, and would cause an error if used.
- The plugin now writes primitive data "object_label" for all organs it creates.
- Some minor fixes to bean OBJ assets.
- Removed erroneous organ labels in MaizeTassel.obj and TomatoFlower.obj assets.

*Boundary-layer Conductance*
- Corrected spelling of 'Pohlhausen'. This should still be backward compatible, as it also accepts the spelling "Polhausen".

*Photosynthesis*
- The way parameters are set for the FvCB model has been clarified to be more explicitly clear about how temperature response is being treated.

Co-authored-by: Kyle Rizzo <ktrizzo@users.noreply.github.com>
Co-authored-by: Ismael Mayanja <IsmaelMayanja@users.noreply.github.com>
Co-authored-by: Sean Banks <smbanx@users.noreply.github.com>

Author: 4 people

core/CMake_project.txt

@@ -18,10 +18,6 @@ if ( WIN32 )
         set( CMAKE_ARCHIVE_OUTPUT_DIRECTORY_${OUTPUTCONFIG} "${CMAKE_BINARY_DIR}/lib" )
     endforeach(OUTPUTCONFIG)
 endif()
-if( CMAKE_BUILD_TYPE STREQUAL Debug )
-    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DHELIOS_DEBUG" )
-    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHELIOS_DEBUG")
-endif()
 cmake_policy(SET CMP0079 NEW)
 set(CMAKE_WARN_DEPRECATED OFF CACHE BOOL "" FORCE)
 
@@ -50,17 +46,16 @@ foreach(PLUGIN ${PLUGINS})
 endforeach(PLUGIN)
 include_directories( "${PLUGIN_INCLUDE_PATHS};${CMAKE_CURRENT_SOURCE_DIRECTORY}" )
 
+if( CMAKE_BUILD_TYPE STREQUAL Debug OR CMAKE_BUILD_TYPE STREQUAL "RelWithDebInfo" )
+    target_compile_definitions(helios PRIVATE HELIOS_DEBUG)
+endif()
+
 if( ENABLE_OPENMP )
     find_package(OpenMP)
     if (OpenMP_CXX_FOUND)
         message( "-- Enabling experimental OpenMP support" )
-        target_link_libraries(${EXECUTABLE_NAME} OpenMP::OpenMP_CXX)
-        target_compile_definitions(${EXECUTABLE_NAME} PRIVATE USE_OPENMP)
-        if ( WIN32 )
-            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /openmp")
-        else()
-            set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
-        endif()
+        target_link_libraries(helios PUBLIC OpenMP::OpenMP_CXX)
+        target_compile_definitions(helios PUBLIC USE_OPENMP)
     else()
         if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
             message(WARNING "You are using Apple Clang compiler, which does not support OpenMP. The program will compile without OpenMP support.")

core/include/Context.h

@@ -2539,86 +2539,185 @@ class Context{
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const int& data );
+    void setPrimitiveData( uint UUID, const char* label, const int& data );
+
+    //! Add data value (int) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<int> &data );
 
     //! Add data value (uint) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const uint& data );
+    void setPrimitiveData( uint UUID, const char* label, const uint& data );
+
+    //! Add data value (uint) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<uint> &data );
 
     //! Add data value (float) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const float& data );
+    void setPrimitiveData( uint UUID, const char* label, const float& data );
+
+    //! Add data value (float) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<float> &data );
 
     //! Add data value (double) associated with a primitive element
     /**
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const double& data );
+    void setPrimitiveData( uint UUID, const char* label, const double& data );
+
+    //! Add data value (double) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<double> &data );
 
     //! Add data value (vec2) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::vec2& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::vec2& data );
+
+    //! Add data value (vec2) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<vec2> &data );
 
     //! Add data value (vec3) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::vec3& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::vec3& data );
+
+    //! Add data value (vec3) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<vec3> &data );
 
     //! Add data value (vec4) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::vec4& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::vec4& data );
+
+    //! Add data value (vec4) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<vec4> &data );
 
     //! Add data value (int2) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::int2& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::int2& data );
+
+    //! Add data value (int2) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<int2> &data );
 
     //! Add data value (int3) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::int3& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::int3& data );
+
+    //! Add data value (int3) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<int3> &data );
 
     //! Add data value (int4) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const helios::int4& data );
+    void setPrimitiveData( uint UUID, const char* label, const helios::int4& data );
+
+    //! Add data value (int4) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<int4> &data );
 
     //! Add data value (string) associated with a primitive element
     /**
      * \param[in] UUID Unique universal identifier of Primitive element
      * \param[in] label Name/label associated with data
      * \param[in] data Primitive data value (scalar)
      */
-    void setPrimitiveData( const uint& UUID, const char* label, const std::string& data );
+    void setPrimitiveData( uint UUID, const char* label, const std::string& data );
+
+    //! Add data value (string) associated with a vector of primitive elements. Each element in UUIDs maps to each element in data.
+    /**
+     * \note the size of UUIDs and data must match
+     * \param[in] UUIDs Unique universal identifiers of Primitive elements
+     * \param[in] label Name/label associated with data
+     * \param[in] data Primitive data value (vector)
+     */
+    void setPrimitiveData( const std::vector<uint> &UUIDs, const char* label, const std::vector<std::string> &data );
 
     //! Add data associated with a primitive element
     /**
@@ -2628,7 +2727,7 @@ class Context{
      * \param[in] size Number of data elements
      * \param[in] data Pointer to primitive data
      */
-    void setPrimitiveData( const uint& UUIDs, const char* label, HeliosDataType type, uint size, void* data );
+    void setPrimitiveData( uint UUID, const char* label, HeliosDataType type, uint size, void* data );
 
     //! Add data value (int) associated with a primitive element
     /**
@@ -5947,23 +6046,26 @@ class Context{
     //! Write geometry in the Context to a Wavefront file (.obj)
     /**
      * \param[in] filename Base filename of .obj and .mtl file
+     * \param[in] write_normals true if we should write the normal vectors
      */
-    void writeOBJ( const std::string &filename ) const;
+    void writeOBJ( const std::string &filename, bool write_normals = false ) const;
 
     //! Write geometry in the Context to a Wavefront file (.obj) for a subset of UUIDs
     /**
      * \param[in] filename Base filename of .obj and .mtl file
      * \param[in] UUIDs Vector of UUIDs for which geometry should be written
+     * \param[in] write_normals true if we should write the normal vectors
      */
-    void writeOBJ( const std::string &filename, const std::vector<uint> &UUIDs ) const;
+    void writeOBJ( const std::string &filename, const std::vector<uint> &UUIDs, bool write_normals = false ) const;
 
     //! Write geometry in the Context to a Wavefront file (.obj)
     /**
      * \param[in] filename Base filename of .obj and .mtl file
      * \param[in] UUIDs Vector of UUIDs for which geometry should be written
      * \param[in] primitive_dat_fields A .dat file will be written containing primitive data given in this vector (for Unity visualization)
+     * \param[in] write_normals true if we should write the normal vectors
      */
-    void writeOBJ( const std::string &filename, const std::vector<uint> &UUIDs, const std::vector<std::string> &primitive_dat_fields ) const;
+    void writeOBJ( const std::string &filename, const std::vector<uint> &UUIDs, const std::vector<std::string> &primitive_dat_fields, bool write_normals = false ) const;
 
     //! Set simulation date by day, month, year
     /**

core/include/global.h

@@ -45,6 +45,7 @@ constexpr float PI_F = 3.14159265358979323846f;
 #include <memory>
 #include <ctime>
 #include <map>
+#include <unordered_map>
 #include <algorithm>
 #include <ctime>
 #include <random>