Merge pull request #9 from dfvankomen/master

feat: Functionality to get refinement flags from mesh object (useful for multi-refinement types)
paralab · Aug 19, 2024 · 667dc53 · 667dc53
2 parents 07b5d37 + 1d71824
commit 667dc53
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Showing 26 changed files with 144 additions and 96 deletions.
diff --git a/FEM/examples/src/dgVecTest.cpp b/FEM/examples/src/dgVecTest.cpp
@@ -69,7 +69,7 @@ int main(int argc, char** argv) {
     Point pt_min(d_min, d_min, d_min);
     Point pt_max(d_max, d_max, d_max);
     //@note that based on how the functions are defined (f(x), dxf(x), etc) the
-    //compuatational domain is equivalent to the grid domain.
+    // compuatational domain is equivalent to the grid domain.
     std::function<double(double, double, double)> func =
         [d_min, d_max](const double x, const double y, const double z) {
             double xx = (x / (1u << m_uiMaxDepth)) * (d_max - d_min) + d_min;

diff --git a/ODE/examples/testLTSBlkVec.cpp b/ODE/examples/testLTSBlkVec.cpp
@@ -69,7 +69,7 @@ int main(int argc, char** argv) {
     Point pt_min(d_min, d_min, d_min);
     Point pt_max(d_max, d_max, d_max);
     //@note that based on how the functions are defined (f(x), dxf(x), etc) the
-    //compuatational domain is equivalent to the grid domain.
+    // compuatational domain is equivalent to the grid domain.
     std::function<double(double, double, double)> func =
         [d_min, d_max](const double x, const double y, const double z) {
             double xx = (x / (1u << m_uiMaxDepth)) * (d_max - d_min) + d_min;

diff --git a/ODE/include/blkAsync.h b/ODE/include/blkAsync.h
@@ -41,7 +41,7 @@ class BlockAsyncVector {
 
    public:
     /**@brief: default constructor.*/
-    BlockAsyncVector(){};
+    BlockAsyncVector() {};
 
     /**@brief: default destructor*/
     ~BlockAsyncVector() {

diff --git a/ODE/include/ctx.h b/ODE/include/ctx.h
@@ -238,10 +238,10 @@ class Ctx {
 
    public:
     /**@brief: default constructor*/
-    Ctx(){};
+    Ctx() {};
 
     /**@brief: default destructor*/
-    ~Ctx(){};
+    ~Ctx() {};
 
     /**@brief: derived class static cast*/
     inline DerivedCtx& asLeaf() { return static_cast<DerivedCtx&>(*this); }

diff --git a/ODE/include/enuts.h b/ODE/include/enuts.h
@@ -456,14 +456,16 @@ class ExplicitNUTS : public ETS<T, Ctx> {
 
     /**@brief: compute weight for a wpart. */
     static unsigned int getOctWeight(const ot::TreeNode* pNode) {
-        const unsigned int finest_t =
-            wpart_meta.tfac(wpart_meta.lmax, wpart_meta.lmin,
-                            wpart_meta.lmax);  // m_uiAppCtx->getBlkTimestepFac(m_uiLevMax,m_uiLevMin,m_uiLevMax);
-                                               // // finest  time level.
-        const unsigned int coarset_t =
-            wpart_meta.tfac(wpart_meta.lmin, wpart_meta.lmin,
-                            wpart_meta.lmax);  // m_uiAppCtx->getBlkTimestepFac(m_uiLevMin,m_uiLevMin,m_uiLevMax);
-                                               // // coarset time level.
+        const unsigned int finest_t = wpart_meta.tfac(
+            wpart_meta.lmax, wpart_meta.lmin,
+            wpart_meta
+                .lmax);  // m_uiAppCtx->getBlkTimestepFac(m_uiLevMax,m_uiLevMin,m_uiLevMax);
+                         // // finest  time level.
+        const unsigned int coarset_t = wpart_meta.tfac(
+            wpart_meta.lmin, wpart_meta.lmin,
+            wpart_meta
+                .lmax);  // m_uiAppCtx->getBlkTimestepFac(m_uiLevMin,m_uiLevMin,m_uiLevMax);
+                         // // coarset time level.
         const unsigned int weight =
             ((coarset_t - finest_t) /
              (wpart_meta.tfac(pNode->getLevel(), wpart_meta.lmin,

diff --git a/ODE/include/enutsOp.h b/ODE/include/enutsOp.h
@@ -72,7 +72,7 @@ class ENUTSOp {
      * @brief Destroy the ENUTSOp object
      *
      */
-    ~ENUTSOp(){};
+    ~ENUTSOp() {};
 
     /**
      * @brief Diagonal op. of time scaling $P_{\Delta t}$ and its inverse

diff --git a/ODE/include/inverseCtx.h b/ODE/include/inverseCtx.h
@@ -32,9 +32,9 @@ class InverseCtx {
     launcher::Launcher* m_uiJobLauncher = NULL;
 
    public:
-    InverseCtx(){};
+    InverseCtx() {};
 
-    ~InverseCtx(){};
+    ~InverseCtx() {};
 
     /**@brief: derived class static cast*/
     DerivedInverseCtx& asLeaf() {

diff --git a/ODE/include/rk.h b/ODE/include/rk.h
@@ -126,15 +126,15 @@ class RK {
     // END UNUSED
 
     /** One time step iteration iteration for RK45 update*/
-    virtual void performSingleIteration(){};
+    virtual void performSingleIteration() {};
 
     /** apply intial conditions*/
-    virtual void applyInitialConditions(){};
+    virtual void applyInitialConditions() {};
 
     /**function to apply boundary conditions. */
-    virtual void applyBoundaryConditions(){};
+    virtual void applyBoundaryConditions() {};
 
-    virtual void rkSolve(){};
+    virtual void rkSolve() {};
 
     /**@brief free memeory of the mesh*/
     inline void freeMesh() { delete m_uiMesh; };

diff --git a/ODE/include/sdc.h b/ODE/include/sdc.h
@@ -76,7 +76,7 @@ class SDC {
     /**
      * @brief Construct a new SDC object
      */
-    SDC(){};
+    SDC() {};
 
     /**
      * @brief Destroy the SDC object

diff --git a/examples/src/meshBenchmark.cpp b/examples/src/meshBenchmark.cpp
@@ -155,9 +155,10 @@ void meshBenchMark(char* ptsFile, bool genPts, unsigned int numPts,
         SFC::parSort::SFC_treeSort(
             pNodesConstructed, pNodesSorted, pNodesConstructed, pNodesBalanced,
             tol, maxDepth, root, ROOT_ROT_ID, 1, TS_BALANCE_OCTREE, sf_k, comm);
-        t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_bal = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                          // - t1).count();
+        t2    = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
+        t_bal = t2 -
+                t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                     // - t1).count();
         if (!rank) std::cout << RED << "2:1 balance end" << NRM << std::endl;
         pNodesConstructed.clear();
 
@@ -184,8 +185,10 @@ void meshBenchMark(char* ptsFile, bool genPts, unsigned int numPts,
         ot::Mesh mesh(pNodesBalanced, stencilSz, eleOrder, comm, false,
                       ot::FEM_CG);
         t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_mesh = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                           // - t1).count();
+        t_mesh =
+            t2 -
+            t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                 // - t1).count();
         if (!rank)
             std::cout << RED << "mesh generation end" << NRM << std::endl;
 
@@ -279,9 +282,10 @@ void meshBenchMark(char* ptsFile, bool genPts, unsigned int numPts,
             &(*(pNodesConstructed.begin())), pNodesConstructed.size(),
             pNodesSorted, pNodesConstructed, pNodesBalanced, maxDepth, maxDepth,
             root, ROOT_ROT_ID, 1, TS_BALANCE_OCTREE);
-        t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_bal = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                          // - t1).count();
+        t2    = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
+        t_bal = t2 -
+                t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                     // - t1).count();
         if (!rank) std::cout << RED << "2:1 balance end" << NRM << std::endl;
 
         t_bal_g[0] = t_bal;
@@ -314,8 +318,10 @@ void meshBenchMark(char* ptsFile, bool genPts, unsigned int numPts,
             cg_sz = mesh.getDegOfFreedom();
         }
         t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_mesh = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                           // - t1).count();
+        t_mesh =
+            t2 -
+            t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                 // - t1).count();
         if (!rank)
             std::cout << RED << "mesh generation end" << NRM << std::endl;
 

diff --git a/examples/src/meshE2NCheck.cpp b/examples/src/meshE2NCheck.cpp
@@ -299,9 +299,10 @@ int main(int argc, char** argv) {
         SFC::parSort::SFC_treeSort(
             pNodesConstructed, pNodesSorted, pNodesConstructed, pNodesBalanced,
             tol, maxDepth, root, ROOT_ROT_ID, 1, TS_BALANCE_OCTREE, sf_k, comm);
-        t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_bal = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                          // - t1).count();
+        t2    = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
+        t_bal = t2 -
+                t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                     // - t1).count();
         if (!rank) std::cout << RED << "2:1 balance end" << NRM << std::endl;
         pNodesConstructed.clear();
 
@@ -355,8 +356,10 @@ int main(int argc, char** argv) {
         t1 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
         ot::Mesh mesh(pNodesBalanced, stencilSz, 4, comm);
         t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_mesh = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                           // - t1).count();
+        t_mesh =
+            t2 -
+            t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                 // - t1).count();
         if (!rank)
             std::cout << RED << "mesh generation end" << NRM << std::endl;
 

diff --git a/examples/src/meshLooping.cpp b/examples/src/meshLooping.cpp
@@ -107,8 +107,9 @@ int main(int argc, char** argv) {
             tmpNodes, pNodesSorted, pNodesConstructed, pNodesBalanced, tol,
             maxDepth, root, ROOT_ROT_ID, 1, TS_BALANCE_OCTREE, sf_k, comm);
         auto t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_bal = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                          // - t1).count();
+        t_bal   = t2 -
+                t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                     // - t1).count();
         if (!rank) std::cout << RED << "2:1 balance end" << NRM << std::endl;
         par::Mpi_Reduce(&t_bal, &t_g, 1, MPI_MAX, 0, comm);
         DendroIntL localSz = pNodesBalanced.size();
@@ -131,8 +132,10 @@ int main(int argc, char** argv) {
         t1 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
         ot::Mesh mesh(pNodesBalanced, stencilSz, 1, comm);
         t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_mesh = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                           // - t1).count();
+        t_mesh =
+            t2 -
+            t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                 // - t1).count();
         if (!rank)
             std::cout << RED << "mesh generation end" << NRM << std::endl;
         par::Mpi_Reduce(&t_mesh, &t_g, 1, MPI_MAX, 0, comm);
@@ -151,8 +154,9 @@ int main(int argc, char** argv) {
             tmpNodes, pNodesSorted, pNodesConstructed, pNodesBalanced, tol,
             maxDepth, root, ROOT_ROT_ID, 1, TS_BALANCE_OCTREE, sf_k, comm);
         auto t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_bal = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                          // - t1).count();
+        t_bal   = t2 -
+                t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                     // - t1).count();
         if (!rank) std::cout << RED << "2:1 balance end" << NRM << std::endl;
         par::Mpi_Reduce(&t_bal, &t_g, 1, MPI_MAX, 0, comm);
         DendroIntL localSz = pNodesBalanced.size();
@@ -174,8 +178,10 @@ int main(int argc, char** argv) {
         t1 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
         ot::Mesh mesh(pNodesBalanced, stencilSz, 1, comm);
         t2 = MPI_Wtime();  // std::chrono::high_resolution_clock::now();
-        t_mesh = t2 - t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
-                           // - t1).count();
+        t_mesh =
+            t2 -
+            t1;  // std::chrono::duration_cast<std::chrono::milliseconds>(t2
+                 // - t1).count();
         if (!rank)
             std::cout << RED << "mesh generation end" << NRM << std::endl;
         par::Mpi_Reduce(&t_mesh, &t_g, 1, MPI_MAX, 0, comm);

diff --git a/examples/src/zoltan_hilbert.cpp b/examples/src/zoltan_hilbert.cpp
@@ -417,9 +417,9 @@ void ZoltanHibertLBandSort(DendroIntL grainSz, unsigned int dim,
 
     //}
 
-    auto zz_local_start = std::chrono::system_clock::now();  // MPI_Wtime();
+    auto zz_local_start     = std::chrono::system_clock::now();  // MPI_Wtime();
 
-    ZOLTAN_ID_TYPE localPts     = mesh.numLocalPts;
+    ZOLTAN_ID_TYPE localPts = mesh.numLocalPts;
 
     ZOLTAN_ID_TYPE *permutedIds = new ZOLTAN_ID_TYPE[localPts];
     Zoltan_Order(zz, NUM_GID_SIZE, mesh.numLocalPts, mesh.globalIds,

diff --git a/include/TreeNode.h b/include/TreeNode.h
@@ -952,7 +952,7 @@ class Mpi_datatype<ot::TreeNode> {
             (static_cast<ot::TreeNode *>(inout))[i] =
                 (((first.getLevel()) > (second.getLevel())) ? first : second);
         }  // end for
-    }      // end function
+    }  // end function
 
     static void Node_MAX(void *in, void *inout, int *len, MPI_Datatype *dptr) {
         for (int i = 0; i < (*len); i++) {
@@ -961,7 +961,7 @@ class Mpi_datatype<ot::TreeNode> {
             (static_cast<ot::TreeNode *>(inout))[i] =
                 ((first > second) ? first : second);
         }  // end for
-    }      // end function
+    }  // end function
 
     static void Node_MIN(void *in, void *inout, int *len, MPI_Datatype *dptr) {
         for (int i = 0; i < (*len); i++) {
@@ -970,7 +970,7 @@ class Mpi_datatype<ot::TreeNode> {
             (static_cast<ot::TreeNode *>(inout))[i] =
                 ((first < second) ? first : second);
         }  // end for
-    }      // end function
+    }  // end function
 
     /* static void Node_NCA(void *in, void *inout, int* len, MPI_Datatype *
      dptr) { for(int i = 0; i < (*len); i++) { ot::TreeNode first =

diff --git a/include/asyncExchangeContex.h b/include/asyncExchangeContex.h
@@ -38,7 +38,7 @@ class AsyncExchangeContex {
     /**@brief batched requests for recv */
     std::vector<MPI_Request> m_recv_req;
 
-    AsyncExchangeContex(){};
+    AsyncExchangeContex() {};
 
     /**@brief creates an async ghost exchange contex*/
     AsyncExchangeContex(const void* var) {
@@ -51,7 +51,7 @@ class AsyncExchangeContex {
     }
 
     /**@brief : defaut destructor*/
-    ~AsyncExchangeContex(){};
+    ~AsyncExchangeContex() {};
 
     /**@brief allocates send buffer for ghost exchange*/
     inline void allocateSendBuffer(size_t bytes) {

diff --git a/include/dtypes.h b/include/dtypes.h
@@ -84,15 +84,15 @@ class Mpi_datatype<bool> {
                 (((static_cast<bool *>(in))[i]) ||
                  ((static_cast<bool *>(inout))[i]));
         }  // end for
-    }      // end function
+    }  // end function
 
     static void bool_LAND(void *in, void *inout, int *len, MPI_Datatype *dptr) {
         for (int i = 0; i < (*len); i++) {
             ((static_cast<bool *>(inout))[i]) =
                 (((static_cast<bool *>(in))[i]) &&
                  ((static_cast<bool *>(inout))[i]));
         }  // end for
-    }      // end function
+    }  // end function
 
    public:
     /**

diff --git a/include/launcher.h b/include/launcher.h
@@ -45,7 +45,7 @@ class Launcher {
         m_uiCoresPerNode = cores_per_node;
     }
 
-    ~Launcher(){};
+    ~Launcher() {};
 
     int alloc_sub_communicator(unsigned int njobs) {
         int rank_g, npes_g;

diff --git a/include/mesh.h b/include/mesh.h
@@ -2621,6 +2621,11 @@ class Mesh {
     void getFinerFaceNeighbors(unsigned int ele, unsigned int dir,
                                unsigned int *child) const;
 
+    /**
+     * @brief Extract the raw refinement flags from all local elements
+     */
+    std::vector<unsigned int> getAllRefinementFlags();
+
     /**
      * @brief Set the Mesh Refinement flags, for the local portion of the mesh.
      Note that coarsening happens if all the children are
@@ -2826,24 +2831,30 @@ inline bool Mesh::computeOveralppingNodes(const ot::TreeNode &parent,
 
                 if (!(((child.getX() - parent.getX()) * dp * dc + k * Lc * dp) %
                       (Lp * dc)))
-                    index[0] = ((child.getX() - parent.getX()) * dp * dc +
-                                k * Lc * dp) /
-                               (Lp * dc);  //((child.getX()-parent.getX())*m_uiElementOrder
-                                           //+ k*Lc)/Lp;
+                    index[0] =
+                        ((child.getX() - parent.getX()) * dp * dc +
+                         k * Lc * dp) /
+                        (Lp *
+                         dc);  //((child.getX()-parent.getX())*m_uiElementOrder
+                               //+ k*Lc)/Lp;
 
                 if (!(((child.getY() - parent.getY()) * dp * dc + k * Lc * dp) %
                       (Lp * dc)))
-                    index[1] = ((child.getY() - parent.getY()) * dp * dc +
-                                k * Lc * dp) /
-                               (Lp * dc);  //((child.getY()-parent.getY())*m_uiElementOrder
-                                           //+ k*Lc)/Lp;
+                    index[1] =
+                        ((child.getY() - parent.getY()) * dp * dc +
+                         k * Lc * dp) /
+                        (Lp *
+                         dc);  //((child.getY()-parent.getY())*m_uiElementOrder
+                               //+ k*Lc)/Lp;
 
                 if (!(((child.getZ() - parent.getZ()) * dp * dc + k * Lc * dp) %
                       (Lp * dc)))
-                    index[2] = ((child.getZ() - parent.getZ()) * dp * dc +
-                                k * Lc * dp) /
-                               (Lp * dc);  //((child.getZ()-parent.getZ())*m_uiElementOrder
-                                           //+ k*Lc)/Lp;
+                    index[2] =
+                        ((child.getZ() - parent.getZ()) * dp * dc +
+                         k * Lc * dp) /
+                        (Lp *
+                         dc);  //((child.getZ()-parent.getZ())*m_uiElementOrder
+                               //+ k*Lc)/Lp;
 
                 if (!stateX && index[0] < (m_uiElementOrder + 1)) stateX = true;
 

diff --git a/include/point.h b/include/point.h
@@ -126,7 +126,7 @@ class Mpi_datatype<Point> {
             Point p2 = (static_cast<Point *>(inout))[i];
             (static_cast<Point *>(inout))[i] += p1;
         }  // end for
-    }      // end function
+    }  // end function
 
    public:
     /**