f/gcl

.gitmodules

@@ -2,6 +2,3 @@
 	path = reg_tests/mesh
 	url = https://github.com/Exawind/meshes.git
         ignore = dirty
-[submodule "wind-utils"]
-	path = wind-utils
-	url = https://github.com/Exawind/wind-utils.git

include/Realm.h

@@ -454,7 +454,7 @@ class Realm {
   ABLForcingAlgorithm *ablForcingAlg_;
   BdyLayerStatistics* bdyLayerStats_{nullptr};
   std::unique_ptr<MeshMotionAlg> meshMotionAlg_;
-
+    
   std::vector<Algorithm *> propertyAlg_;
   std::map<PropertyIdentifier, ScalarFieldType *> propertyMap_;
   std::vector<Algorithm *> initCondAlg_;

include/edge_kernels/ContinuityEdgeSolverAlg.h

@@ -30,11 +30,12 @@ class ContinuityEdgeSolverAlg : public AssembleEdgeSolverAlgorithm
 
 private:
   unsigned coordinates_ {stk::mesh::InvalidOrdinal};
-  unsigned velocityRTM_ {stk::mesh::InvalidOrdinal};
+  unsigned velocity_ {stk::mesh::InvalidOrdinal};
   unsigned pressure_ {stk::mesh::InvalidOrdinal};
   unsigned densityNp1_ {stk::mesh::InvalidOrdinal};
   unsigned Gpdx_ {stk::mesh::InvalidOrdinal};
   unsigned edgeAreaVec_ {stk::mesh::InvalidOrdinal};
+  unsigned edgeFaceVelMag_{stk::mesh::InvalidOrdinal};
   unsigned Udiag_ {stk::mesh::InvalidOrdinal};
 };
 

include/edge_kernels/ScalarOpenEdgeKernel.h

@@ -0,0 +1,61 @@
+// Copyright 2017 National Technology & Engineering Solutions of Sandia, LLC
+// (NTESS), National Renewable Energy Laboratory, University of Texas Austin,
+// Northwest Research Associates. Under the terms of Contract DE-NA0003525
+// with NTESS, the U.S. Government retains certain rights in this software.
+//
+// This software is released under the BSD 3-clause license. See LICENSE file
+// for more details.
+//
+
+#ifndef SCALAROPENEDGEKERNEL_H
+#define SCALAROPENEDGEKERNEL_H
+
+#include "kernel/Kernel.h"
+#include "KokkosInterface.h"
+#include "FieldTypeDef.h"
+
+namespace sierra {
+namespace nalu {
+
+class SolutionOptions;
+
+template<typename BcAlgTraits>
+class ScalarOpenEdgeKernel : public NGPKernel<ScalarOpenEdgeKernel<BcAlgTraits>>
+{
+public:
+  ScalarOpenEdgeKernel(
+    const stk::mesh::MetaData&,
+    const SolutionOptions&,
+    ScalarFieldType*,
+    ScalarFieldType*,
+    ElemDataRequests&);
+
+  KOKKOS_FORCEINLINE_FUNCTION
+  ScalarOpenEdgeKernel() = default;
+
+  KOKKOS_INLINE_FUNCTION
+  virtual ~ScalarOpenEdgeKernel() = default;
+
+  using Kernel::execute;
+
+  KOKKOS_FUNCTION
+  virtual void execute(
+    SharedMemView<DoubleType**, DeviceShmem>&,
+    SharedMemView<DoubleType*, DeviceShmem>&,
+    ScratchViews<DoubleType, DeviceTeamHandleType, DeviceShmem>&);
+
+private:
+  unsigned scalarQ_ { stk::mesh::InvalidOrdinal };
+  unsigned bcScalarQ_ { stk::mesh::InvalidOrdinal };
+  unsigned openMassFlowRate_ {stk::mesh::InvalidOrdinal};
+
+  const DoubleType relaxFac_;
+
+  MasterElement* meFC_{nullptr};
+};
+
+}  // nalu
+}  // sierra
+
+
+#endif /* SCALAROPENEDGEKERNEL_H */

include/mesh_motion/FrameBase.h

@@ -53,6 +53,10 @@ class FrameBase
   {
   }
 
+  stk::mesh::PartVector get_partvec() {
+    return partVec_;
+  };
+
 protected:
   //! Reference to the STK Mesh BulkData object
   stk::mesh::BulkData& bulk_;

include/mesh_motion/FrameNonInertial.h

@@ -40,6 +40,7 @@ class FrameNonInertial : public FrameBase
   MotionBase::TransMatType compute_transformation(
     const double,
     const double*);
+
 };
 
 } // nalu

include/mesh_motion/MeshMotionAlg.h

@@ -23,6 +23,8 @@ class MeshMotionAlg
 
   void post_compute_geometry();
 
+  stk::mesh::PartVector get_partvec();
+
 private:
   MeshMotionAlg() = delete;
   MeshMotionAlg(const MeshMotionAlg&) = delete;

include/mesh_motion/MotionDeformingInterior.h

@@ -0,0 +1,65 @@
+#ifndef MOTIONDEFORMINGINTERIOR_H
+#define MOTIONDEFORMINGINTERIOR_H
+
+#include "MotionBase.h"
+
+namespace sierra{
+namespace nalu{
+
+class MotionDeformingInterior : public MotionBase
+{
+public:
+  MotionDeformingInterior(
+    stk::mesh::MetaData&,
+    const YAML::Node&);
+
+  virtual ~MotionDeformingInterior()
+  {
+  }
+
+  virtual void build_transformation(const double, const double*);
+
+  /** Function to compute motion-specific velocity
+   *
+   * @param[in] time           Current time
+   * @param[in] compTrans      Transformation matrix
+   *                           for points other than xyz
+   * @param[in] mxyz           Model coordinates
+   * @param[in] mxyz           Transformed coordinates
+   */
+  virtual ThreeDVecType compute_velocity(
+    const double time,
+    const TransMatType& compTrans,
+    const double* mxyz,
+    const double* cxyz );
+
+  /** perform post compute geometry work for this motion
+   *
+   * @param[in] computedMeshVelDiv flag to denote if divergence of
+   *                               mesh velocity already computed
+   */
+  void post_compute_geometry(
+    stk::mesh::BulkData&,
+    stk::mesh::PartVector&,
+    stk::mesh::PartVector&,
+    bool& computedMeshVelDiv );
+
+private:
+  MotionDeformingInterior() = delete;
+  MotionDeformingInterior(const MotionDeformingInterior&) = delete;
+
+  void load(const YAML::Node&);
+
+  void scaling_mat(const double, const double*);
+
+  ThreeDVecType xyzMin_;
+  ThreeDVecType xyzMax_;
+
+  ThreeDVecType amplitude_ = {{0.0,0.0,0.0}};
+  ThreeDVecType frequency_ = {{0.0,0.0,0.0}};
+};
+
+} // nalu
+} // sierra
+
+#endif /* MOTIONDEFORMINGINTERIOR_H */

include/mesh_motion/MotionRotation.h

@@ -31,6 +31,17 @@ class MotionRotation : public MotionBase
     const double* mxyz,
     const double* cxyz );
 
+  /** perform post compute geometry work for this motion
+   *
+   * @param[in] computedMeshVelDiv flag to denote if divergence of
+   *                               mesh velocity already computed
+   */
+  void post_compute_geometry(
+    stk::mesh::BulkData&,
+    stk::mesh::PartVector&,
+    stk::mesh::PartVector&,
+    bool& computedMeshVelDiv );
+
 private:
   MotionRotation() = delete;
   MotionRotation(const MotionRotation&) = delete;

include/mesh_motion/MotionWaves.h

@@ -0,0 +1,65 @@
+#ifndef MOTIONWAVES_H
+#define MOTIONWAVES_H
+
+#include "MotionBase.h"
+
+namespace sierra{
+namespace nalu{
+
+class MotionWaves : public MotionBase
+{
+public:
+  MotionWaves(
+    stk::mesh::MetaData&,
+    const YAML::Node&);
+
+  virtual ~MotionWaves()
+  {
+  }
+
+virtual void build_transformation(const double, const double*);
+
+  /** Function to compute motion-specific velocity
+   *
+   * @param[in] time           Current time
+   * @param[in] compTrans      Transformation matrix
+   *                           for points other than xyz
+   * @param[in] mxyz           Model coordinates
+   * @param[in] mxyz           Transformed coordinates
+   */
+  virtual ThreeDVecType compute_velocity(
+    const double time,
+    const TransMatType& compTrans,
+    const double* mxyz,
+    const double* cxyz );
+
+  /** perform post compute geometry work for this motion
+   *
+   * @param[in] computedMeshVelDiv flag to denote if divergence of
+   *                               mesh velocity already computed
+   */
+	void post_compute_geometry(
+		stk::mesh::BulkData&,
+    stk::mesh::PartVector&,
+    stk::mesh::PartVector&,
+    bool& computedMeshVelDiv );
+
+private:
+  MotionWaves() = delete;
+  MotionWaves(const MotionWaves&) = delete;
+
+  void load(const YAML::Node&);
+
+  void translation_mat(const ThreeDVecType&);
+
+  std::string waveModel_{"Sinusoidal_full_domain"};   
+  double amplitude_{0.1};
+  double waveperiod_{1.0};
+	double wavelength_{1.0};
+	double sealevelz_{0.0};
+};
+
+} // nalu
+} // sierra
+
+#endif /* MOTIONWAVES_H */

include/ngp_algorithms/GeometryAlgDriver.h

@@ -49,6 +49,9 @@ class GeometryAlgDriver : public NgpAlgDriver
   //! Reset fields before calling algorithms
   virtual void pre_work() override;
 
+  //! Pre work for mesh motion
+  virtual void mesh_motion_prework();
+
   //! Synchronize fields after algorithms have done their work
   virtual void post_work() override;
 

include/ngp_algorithms/MdotEdgeAlg.h

@@ -33,11 +33,12 @@ class MdotEdgeAlg : public Algorithm
 
 private:
   unsigned coordinates_ {stk::mesh::InvalidOrdinal};
-  unsigned velocityRTM_ {stk::mesh::InvalidOrdinal};
+  unsigned velocity_ {stk::mesh::InvalidOrdinal};
   unsigned pressure_ {stk::mesh::InvalidOrdinal};
   unsigned densityNp1_ {stk::mesh::InvalidOrdinal};
   unsigned Gpdx_ {stk::mesh::InvalidOrdinal};
   unsigned edgeAreaVec_ {stk::mesh::InvalidOrdinal};
+  unsigned edgeFaceVelMag_{stk::mesh::InvalidOrdinal};
   unsigned Udiag_ {stk::mesh::InvalidOrdinal};
   unsigned massFlowRate_ {stk::mesh::InvalidOrdinal};
 };

include/ngp_algorithms/MeshVelocityAlg.h

@@ -0,0 +1,92 @@
+// Copyright 2017 National Technology & Engineering Solutions of Sandia, LLC
+// (NTESS), National Renewable Energy Laboratory, University of Texas Austin,
+// Northwest Research Associates. Under the terms of Contract DE-NA0003525
+// with NTESS, the U.S. Government retains certain rights in this software.
+//
+// This software is released under the BSD 3-clause license. See LICENSE file
+// for more details.
+//
+
+#ifndef MESHVELOCITYALG_H
+#define MESHVELOCITYALG_H
+
+#include "Algorithm.h"
+#include "ElemDataRequests.h"
+#include "FieldTypeDef.h"
+
+#include "stk_mesh/base/Types.hpp"
+
+namespace sierra {
+namespace nalu {
+
+class Realm;
+
+template<typename AlgTraits>
+class MeshVelocityAlg : public Algorithm
+{
+public:
+  MeshVelocityAlg(Realm&, stk::mesh::Part*);
+
+  virtual ~MeshVelocityAlg() = default;
+
+  virtual void execute() override;
+
+private:
+  ElemDataRequests elemData_;
+
+  unsigned modelCoords_{stk::mesh::InvalidOrdinal};
+  unsigned currentCoords_{stk::mesh::InvalidOrdinal};
+  unsigned meshDispNp1_{stk::mesh::InvalidOrdinal};
+  unsigned meshDispN_{stk::mesh::InvalidOrdinal};
+  unsigned faceVelMag_{stk::mesh::InvalidOrdinal};
+  unsigned sweptVolumeNp1_{stk::mesh::InvalidOrdinal};
+  unsigned sweptVolumeN_{stk::mesh::InvalidOrdinal};
+
+  MasterElement* meSCS_{nullptr};
+
+  const double isoParCoords_[57] = {
+      0.00, -1.00, -1.00,    // surf 1    1->2  0  8
+      1.00,  0.00, -1.00,    // surf 2    2->3  1  9
+      0.00,  1.00, -1.00,    // surf 3    3->4  2 10
+     -1.00,  0.00, -1.00,    // surf 4    1->4  3 11
+      0.00,  0.00, -1.00,    //                 4 12
+      0.00, -1.00,  1.00,    // surf 5    5->6  5 13
+      1.00,  0.00,  1.00,    // surf 6    6->7  6 14
+      0.00,  1.00,  1.00,    // surf 7    7->8  7 15
+     -1.00,  0.00,  1.00,    // surf 8    5->8  8 16
+      0.00,  0.00,  1.00,    //                 9 17
+      1.00, -1.00,  0.00,    // surf 10   2->6 10 18
+     -1.00, -1.00,  0.00,    // surf 9    1->5 11 19
+      0.00, -1.00,  0.00,    //                12 20
+     -1.00,  1.00,  0.00,    // surf 12   4->8 14 21
+      1.00,  1.00,  0.00,    // surf 11   3->7 13 22
+      0.00,  1.00,  0.00,    //                15 23
+      1.00,  0.00,  0.00,    //                16 24
+     -1.00,  0.00,  0.00,    //                17 25
+      0.00,  0.00,  0.00,    //                18 26
+  };
+
+  const int scsFaceNodeMap_[12][4] = {
+      {12,  0,  4, 18},
+      {16,  1,  4, 18},
+      {2,   4, 18, 15},
+      {3,  17, 18,  4},
+      {5,  12, 18,  9},
+      {9,   6, 16, 18},
+      {9,   7, 15, 18},
+      {8,   9, 18, 17},
+      {11, 12, 18, 17},
+      {12, 10, 16, 18},
+      {14, 15, 18, 16},
+      {13, 17, 18, 15}
+  };
+
+  double isoCoordsShapeFcn_[152];
+};
+
+}  // nalu
+}  // sierra
+
+
+
+#endif /* MESHVELOCITYALG_H */