Fix mesh mutation frequency (#74)

* build: Update geometry central version
* build: do not search for netcdf

* fix: do not split or collapse around notable vertices
* fix: respect initial timestep for mesh update frequencies

Due to variable time stepping algorithms the time step can vary with system configuration. The modified time step was used for updating mutation/prescription counters leading to difficult to predict behavior.

* fix: Adding an aggressive exclusion criteria for split/collapse processing when fixed boundary conditions are used

!Modifies split/collapse behavior for fixed boundary simulations

* refactor!: change mesh update periods to be double
* refactor: update python type hints

* feat: geodesic distance calculations relative to user defined vertices
* feat: add Gaussian force to visualization
* feat: add function to remove low valency vertices and add to split-collapse

---------

Signed-off-by: Christopher T. Lee <ctlee@ucsd.edu>
Co-authored-by: Xiaoyi Wu <xiw135@ucsd.edu>

.github/workflows/ci.yaml

@@ -59,46 +59,46 @@ jobs:
           cmake --build . --config Release -j 4
           ctest -C Release -V -j 4
 
-  # build_macos:
-  #   name: Build-Test macOS
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: [macos-15]
-  #   runs-on: ${{ matrix.os }}
-  #   defaults:
-  #     run:
-  #       shell: bash
-  #   steps:
-  #     - uses: actions/checkout@v3
-  #       with:
-  #         fetch-depth: 0
-  #         submodules: recursive
+  build_macos:
+    name: Build-Test macOS
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          submodules: recursive
 
-  #     - uses: actions/setup-python@v5
-  #       id: pyexe
-  #       with:
-  #         python-version: '3.10'
+      - uses: actions/setup-python@v5
+        id: pyexe
+        with:
+          python-version: '3.10'
 
-  #     # - name: Setup python libs
-  #     #   id: pyexe
-  #     #   run: |
-  #     #     python3 --version
-  #     #     # python3 -m pip install pytest
-  #     #     py_exe_path=$(which python3)
-  #     #     echo ::set-output name=path::$py_exe_path
+      # - name: Setup python libs
+      #   id: pyexe
+      #   run: |
+      #     python3 --version
+      #     # python3 -m pip install pytest
+      #     py_exe_path=$(which python3)
+      #     echo ::set-output name=path::$py_exe_path
 
-  #     - name: Resolve dependencies
-  #       run: brew install netcdf eigen pybind11 netcdf-cxx
+      - name: Resolve dependencies
+        run: brew install netcdf eigen pybind11 netcdf-cxx
 
-  #     - name: Build
-  #       run: |
-  #         mkdir -p build && cd build;
-  #         cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.python-path }} --log-level=DEBUG ..
-  #         cmake --build . --config Release -j 4
+      - name: Build
+        run: |
+          mkdir -p build && cd build;
+          cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_PYMEM3DG=ON -DSUITESPARSE=OFF -DWITH_NETCDF=ON -DPython_EXECUTABLE:FILEPATH=${{ steps.pyexe.outputs.python-path }} --log-level=DEBUG ..
+          cmake --build . --config Release -j 4
 
-  #     - name: Test
-  #       run: ctest -C Release -V -j 4
+      - name: Test
+        run: ctest -C Release -V -j 4
 
 
   # build_windows:
@@ -211,7 +211,7 @@ jobs:
     name: Deploy to PyPI
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
     runs-on: ubuntu-latest
-    needs: [build_linux]
+    needs: [build_linux, build_macos]
     defaults:
       run:
         shell: bash

include/mem3dg/solver/integrator/integrator.h

@@ -74,6 +74,8 @@ class DLL_PUBLIC Integrator {
   // key parameters (read/write)
   /// characteristic time step
   double characteristicTimeStep;
+  // Original time step at construction
+  double baseTimeStep;
   // total simulation time
   double totalTime = std::numeric_limits<double>::max();
   /// period of saving output data
@@ -132,7 +134,8 @@ class DLL_PUBLIC Integrator {
   Integrator(System &system_, double characteristicTimeStep_, double tolerance_,
              std::string outputDirectory_)
       : timeStep(characteristicTimeStep_), system(system_),
-        characteristicTimeStep(characteristicTimeStep_), tolerance(tolerance_),
+        characteristicTimeStep(characteristicTimeStep_),
+        baseTimeStep(characteristicTimeStep_), tolerance(tolerance_),
         outputDirectory(outputDirectory_) {
     ifDisableIntegrate = true;
     ifPrintToConsole = true;

include/mem3dg/solver/mesh_process.h

@@ -61,7 +61,7 @@ struct MeshProcessor {
    */
   struct MeshMutator {
     /// period of mesh mutation
-    std::size_t mutateMeshPeriod = std::numeric_limits<std::size_t>::max();
+    double mutateMeshPeriod = std::numeric_limits<double>::max();
 
     /// Whether edge flip
     bool isFlipEdge = false;

include/mem3dg/solver/parameters.h

@@ -162,7 +162,7 @@ struct Parameters {
     /// domain of shape variation
     double geodesicMask = -1;
     /// period of updating mask
-    std::size_t updateMaskPeriod = std::numeric_limits<std::size_t>::max();
+    double updateMaskPeriod = std::numeric_limits<double>::max();
 
     /**
      * @brief check parameter conflicts
@@ -175,22 +175,22 @@ struct Parameters {
     std::function<Eigen::Matrix<bool, Eigen::Dynamic, 1>(const Geometry &)>
         prescribeNotableVertex = NULL;
     /// period of updating geodesic distance from notableVertex calculation
-    std::size_t updateGeodesicsPeriod = std::numeric_limits<std::size_t>::max();
+    double updateGeodesicsPeriod = std::numeric_limits<double>::max();
     /// period of updating notable vertex based functional
     /// prescribeNotableVertex
-    std::size_t updateNotableVertexPeriod =
-        std::numeric_limits<std::size_t>::max();
+    double updateNotableVertexPeriod = std::numeric_limits<double>::max();
   };
 
   struct Protein {
     /// interior point parameter for protein density
     double proteinInteriorPenalty = 0; // 1e-6
     /// prescription of protein density
-    std::function<EigenVectorX1d(double, EigenVectorX1d, EigenVectorX1d)>
+    std::function<EigenVectorX1d(const Geometry &, double, EigenVectorX1d,
+                                 EigenVectorX1d)>
         prescribeProteinDensityDistribution = NULL;
     /// period of updating protein density distribution
-    std::size_t updateProteinDensityDistributionPeriod =
-        std::numeric_limits<std::size_t>::max();
+    double updateProteinDensityDistributionPeriod =
+        std::numeric_limits<double>::max();
   };
 
   struct Spring {

include/mem3dg/solver/system.h

@@ -650,6 +650,8 @@ class DLL_PUBLIC System {
    */
   bool processSplitCollapseQueued();
 
+  bool removeLowValencyVertices(std::size_t degree = 4);
+
   /**
    * @brief global smoothing after mutation of the mesh
    * @param initStep initial guess of time step

include/mem3dg/type_utilities.h

@@ -342,6 +342,10 @@ inline auto toMatrix(gcs::VertexData<gc::Vector3> &vector) {
   return gc::EigenMap<double, 3>(vector);
 }
 
+inline const auto toMatrix(const gcs::VertexData<gc::Vector3> &vector) {
+  return gc::EigenMap<double, 3>(vector);
+}
+
 } // namespace mem3dg
 
 namespace std {