Add tetrahedral grid (#230)

* Add NestedDensityTreePolicy
- changed DensityTreePolicy & TreePolicy consequently
- added extra contains & intersects to Box

* Fix formatting, warning, and minor merge error

* move min/max level test into needsSubdivide()

* streamline property names and add documentation

* verify that inner box is nonempty

* tetra construction functional

* grid construction fully working
cleaned up unused stuff from voronoi
started work on PathSegmentGenerator

* working PathSegmentGenerator

* started work on efficient ray traversal

* implemented traversal from maria et al.

* tetgen functional

* refactored to Tetrahedron.cpp
added TetraMeshSpatialGrid options
added NeedsSubdivide as tetgen unsuitable

* fixed  traversal edge case
changed search tree to use vertices instead of centroids

* functional centroid kd-tree using breadth-first search of neighbors

* updated traversal algo to Martie (2017)

* temp fix for edge cases
(vertex intersection still not working)

* almost functional traversal with edge cases
only entry vertex intersection isn't working

* traversal funtioncal, uses plane intersection if unsure
small fixes to prepare TetraMeshSpatialGrid

* sped up Tetra::inside

* used traversal in CellIndex and refactored some code

* tetra stats

* fixes and var test

* var fix

* minVolume

* small fix; removed unused code

* started cleanup

* removed adaptive construction
added all Tetra classes
started work on refining Delaunay

* removed unnecessary code

* added refine option to Tetra grid
marked potential oversight in Voro
`TetraMeshSnapshot::readAndClose` still needs to infer cell properties from vertex properties

* moved class Tetrahedron to class TetraMeshSnapshot
removed unused code

* started basic tetra implemenation
moved all tetra code to TetraMeshSpatialGrid
removed unnecessary code/classes and fixed small oversights
added tetgen LICENSE

* removed unnecessary code
fixed compile errors

* formatted code

* formatting

* used block search structure

* temp: moved Tetra and Face to hpp to make it compile
reformatted code

* cleanup and documentation

* documentation

* rename property and fix small oversight in path generator

* final refactoring and documentation

* remove debug files

* avoid warnings with clang - not yet for other compilers

* fix warnings for GCC and MSVC

* try to fix warnings for GCC on MinGW

* add build check with Intel oneAPI

* try intel oneAPI runner again

* try oneAPI checker once more

* cosmetic updates to source code

* add error if no grid

* add 8 corner vertices to cover full domain

* trivial adjustments to comments

---------

Co-authored-by: Peter Camps <[email protected]>

.github/workflows/check-builds.yml

@@ -1,8 +1,7 @@
 # GitHub action workflow that checks the build process on multiple platforms.
 #
 # The workflow builds the code (without MPI and without MakeUp)
-# using GCC on Ubuntu and using Clang on macOS, in two different jobs.
-# Other compiler/platform combinations can be added if the need arises.
+# using various compilers and operating systems, in different jobs.
 # The workflow fails if there are any build errors and/or warnings.
 #
 name: Check builds
@@ -86,3 +85,30 @@ jobs:
     - name: Build
       shell: cmd
       run: cd release && cmake --build . -j 2
+
+  # Intel on Ubuntu
+  check_build_intel:
+    # job name, displayed in the action log
+    name: Build using Intel oneAPI on Ubuntu
+    # run this job on the Github-provided runner with a recent Ubuntu version
+    runs-on: ubuntu-22.04
+    # steps that make up this job
+    steps:
+    # checkout using a recent version of the checkout action
+    - name: Checkout
+      uses: actions/checkout@v3
+    # add Intel oneAPI to apt repository
+    - name: add oneAPI to apt
+      run: |
+        wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+        echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        sudo apt update
+    # install Intel oneAPI
+    - name: install oneAPI
+      run: sudo apt install intel-oneapi-compiler-dpcpp-cpp
+    # configure the build files through CMake
+    - name: Configure
+      run: cmake -B release -DCMAKE_C_COMPILER=/opt/intel/oneapi/compiler/latest/bin/icx -DCMAKE_CXX_COMPILER=/opt/intel/oneapi/compiler/latest/bin/icpx -DCMAKE_BUILD_TYPE:STRING=Release -DWARNINGS_AS_ERRORS:BOOL=ON -DBUILD_DOX_STYLE:BOOL=ON -DBUILD_SMILE_SHAPES:BOOL=ON -DBUILD_SMILE_TOOL:BOOL=ON -L
+    # perform the actual build (Ubuntu runners have 2 cores)
+    - name: Build
+      run: make -C release -j 2

SKIRT/CMakeLists.txt

@@ -10,6 +10,7 @@
 # add all relevant subdirectories; each subdirectory defines a single target
 add_subdirectory(fitsio)
 add_subdirectory(voro)
+add_subdirectory(tetgen)
 add_subdirectory(mpi)
 add_subdirectory(utils)
 add_subdirectory(core)

SKIRT/core/CMakeLists.txt

@@ -22,8 +22,9 @@ target_link_libraries(${TARGET} schema fundamentals)
 include_directories(../../SMILE/schema ../../SMILE/fundamentals)
 
 # add SKIRT library dependencies
-target_link_libraries(${TARGET} fitsio voro mpi utils)
+target_link_libraries(${TARGET} fitsio voro mpi utils tetgen)
 include_directories(../fitsio ../voro ../mpi ../utils)
+include_directories(SYSTEM ../tetgen)  # suppress warnings in tetgen header
 
 # adjust C++ compiler flags to our needs
 include("../../SMILE/build/CompilerFlags.cmake")

SKIRT/core/SimulationItemRegistry.cpp

@@ -256,6 +256,7 @@
 #include "TTauriDiskGeometry.hpp"
 #include "TemperatureProbe.hpp"
 #include "TemperatureWavelengthCellLibrary.hpp"
+#include "TetraMeshSpatialGrid.hpp"
 #include "ThemisDustMix.hpp"
 #include "ToddlersSED.hpp"
 #include "ToddlersSEDFamily.hpp"
@@ -494,6 +495,7 @@ SimulationItemRegistry::SimulationItemRegistry(string version, string format)
     ItemRegistry::add<FileTreeSpatialGrid>();
     ItemRegistry::add<AdaptiveMeshSpatialGrid>();
     ItemRegistry::add<VoronoiMeshSpatialGrid>();
+    ItemRegistry::add<TetraMeshSpatialGrid>();
 
     // spatial grid policies
     ItemRegistry::add<TreePolicy>();