Oscillating mesh motion (#1329)

* oscillating kernel: compiling with pieces in place

* add bichromatic, use get_required as needed

* formatting etc

* hook for parsing, avoid dividing by 0

* running reg test

* tweaks to reg test input + norm

include/mesh_motion/MotionOscillationKernel.h

@@ -0,0 +1,58 @@
+#ifndef MOTIONOscillationKERNEL_H
+#define MOTIONOscillationKERNEL_H
+
+#include "NgpMotion.h"
+
+namespace sierra {
+namespace nalu {
+
+class MotionOscillationKernel : public NgpMotionKernel<MotionOscillationKernel>
+{
+public:
+  MotionOscillationKernel(const YAML::Node&);
+
+  MotionOscillationKernel() = default;
+
+  virtual ~MotionOscillationKernel() = default;
+
+  /** Function to compute motion-specific transformation matrix
+   *
+   * @param[in] time Current time
+   * @param[in] xyz  Coordinates
+   * @return Transformation matrix
+   */
+  KOKKOS_FUNCTION
+  virtual mm::TransMatType
+  build_transformation(const double& time, const mm::ThreeDVecType& xyz);
+
+  /** Function to compute motion-specific velocity
+   *
+   * @param[in]  time      Current time
+   * @param[in]  compTrans Transformation matrix
+   *                       including all motions
+   * @param[in]  mxyz      Model coordinates
+   * @param[in]  cxyz      Transformed coordinates
+   * @return Velocity vector associated with coordinates
+   */
+  KOKKOS_FUNCTION
+  virtual mm::ThreeDVecType compute_velocity(
+    const double& time,
+    const mm::TransMatType& compTrans,
+    const mm::ThreeDVecType& mxyz,
+    const mm::ThreeDVecType& cxyz);
+
+private:
+  void load(const YAML::Node&);
+
+  mm::ThreeDVecType direction_{0.0, 0.0, 1.0};
+
+  double period_{0.0};
+  double amplitude_{0.0};
+  double period_2nd_{0.0};
+  double amplitude_2nd_{0.0};
+};
+
+} // namespace nalu
+} // namespace sierra
+
+#endif /* MOTIONOscillationKERNEL_H */

reg_tests/CTestList.cmake

@@ -246,6 +246,7 @@ if(NOT ENABLE_CUDA AND NOT ENABLE_ROCM)
 
   if (ENABLE_TIOGA AND ENABLE_HYPRE)
     add_test_r(oversetRotCylNGPHypre 2)
+    add_test_r(oversetOscCylNGPHypre 2)
     if (ENABLE_TRILINOS_SOLVERS)
       add_test_r(oversetRotCylinderHypre 2)
       add_test_r(oversetRotCylMultiRealm 2)

reg_tests/test_files/oversetOscCylNGPHypre/oversetOscCylNGPHypre.norm.gold

@@ -0,0 +1,10 @@
+0.1032040329331224 1 0.003
+0.03111868191476334 2 0.006
+0.03802955274794819 3 0.009
+0.04192027057100021 4 0.012
+0.0328423923794225 5 0.015
+0.01992606763318192 6 0.018
+0.00798146926560496 7 0.021
+0.003208226735370011 8 0.024
+0.006417074116005693 9 0.027
+0.006891712098202526 10 0.03

reg_tests/test_files/oversetOscCylNGPHypre/oversetOscCylNGPHypre.yaml

@@ -0,0 +1,218 @@
+# -*- mode: yaml -*-
+
+Simulations:
+  - name: sim1
+    time_integrator: ti_1
+    optimizer: opt1
+
+# Hypre memory and other configurations
+hypre_config:
+    memory_pool_mbs: 1500
+    use_vendor_spgemm: no
+    use_vendor_spmv: no
+    use_vendor_sptrans: no
+
+linear_solvers:
+
+  - name: solve_mom
+    type: hypre
+    method: hypre_gmres
+    preconditioner: boomerAMG
+    tolerance: 1e-12
+    max_iterations: 200
+    kspace: 15
+    output_level: 0
+    segregated_solver: yes
+    write_matrix_files: no
+    simple_hypre_matrix_assemble: no
+    dump_hypre_matrix_stats: no
+    recompute_preconditioner_frequency: 1
+    reuse_linear_system: yes
+    write_preassembly_matrix_files: no
+
+    # File containing hypre specific configuration options
+    hypre_cfg_file: ../../hypre_settings/hypre_blade_resolved.yaml
+    # YAML node used for this linear solver
+    hypre_cfg_node: hypre_simple_precon
+
+  - name: solve_elliptic
+    type: hypre
+    method: hypre_gmres
+    preconditioner: boomerAMG
+    tolerance: 1e-12
+    max_iterations: 200
+    kspace: 75
+    output_level: 0
+    write_matrix_files: no
+    simple_hypre_matrix_assemble: no
+    dump_hypre_matrix_stats: no
+    recompute_preconditioner_frequency: 1
+    reuse_linear_system: yes
+    write_preassembly_matrix_files: no
+
+    # File containing hypre specific configuration options
+    hypre_cfg_file: ../../hypre_settings/hypre_blade_resolved.yaml
+    # YAML node used for this linear solver
+    hypre_cfg_node: hypre_elliptic
+
+realms:
+
+  - name: realm_1
+    mesh: ../../mesh/oversetCylinder.g
+    use_edges: yes
+    automatic_decomposition_type: rcb
+
+    equation_systems:
+      name: theEqSys
+      max_iterations: 2
+      decoupled_overset_solve: yes
+
+      solver_system_specification:
+        velocity: solve_mom
+        pressure: solve_elliptic
+
+      systems:
+
+        - LowMachEOM:
+            name: myLowMach
+            max_iterations: 1
+            convergence_tolerance: 1e-7
+
+    initial_conditions:
+
+      - constant: ic_1
+        target_name:
+          - Unspecified-2-HEX
+          - Unspecified-3-HEX
+        value:
+          pressure: 0.0
+          velocity: [1.0,0.0,0.0]
+
+    material_properties:
+      target_name:
+          - Unspecified-2-HEX
+          - Unspecified-3-HEX
+      specifications:
+        - name: density
+          type: constant
+          value: 1.00
+
+        - name: viscosity
+          type: constant
+          value: 0.005
+
+    boundary_conditions:
+
+    - inflow_boundary_condition: bc_1
+      target_name: inlet
+      inflow_user_data:
+        velocity: [1.0,0.0,0.0]
+        pressure: 0.0
+
+    - open_boundary_condition: bc_2
+      target_name: outlet
+      open_user_data:
+        pressure: 0.0
+        velocity: [0.0,0.0,0.0]
+
+    - symmetry_boundary_condition: bc_3
+      target_name: top
+      symmetry_user_data:
+
+    - symmetry_boundary_condition: bc_4
+      target_name: bottom
+      symmetry_user_data:
+
+    - wall_boundary_condition: bc_5
+      target_name: wall
+      wall_user_data:
+        user_function_name:
+         velocity: wind_energy
+        user_function_string_parameters:
+         velocity: [interior]
+
+    - symmetry_boundary_condition: bc_6
+      target_name: side11
+      symmetry_user_data:
+
+    - symmetry_boundary_condition: bc_7
+      target_name: side12
+      symmetry_user_data:
+
+    - symmetry_boundary_condition: bc_8
+      target_name: side21
+      symmetry_user_data:
+
+    - symmetry_boundary_condition: bc_9
+      target_name: side22
+      symmetry_user_data:
+
+    - overset_boundary_condition: bc_overset
+      overset_connectivity_type: tioga
+      overset_user_data:
+        tioga_options:
+          symmetry_direction: 2
+          set_resolutions: yes
+        mesh_group:
+          - overset_name: interior
+            mesh_parts: [ Unspecified-2-HEX ]
+            wall_parts: [ wall ]
+            ovset_parts: [ overset1 ]
+
+          - overset_name: wake
+            mesh_parts: [ Unspecified-3-HEX]
+
+    mesh_motion:
+      - name: interior
+        mesh_parts: [ Unspecified-2-HEX ]
+        motion:
+         - type: oscillation
+           period: 1.25
+           amplitude: 1.5
+           direction: [0.0, 0.0, 1.0]
+
+    solution_options:
+      name: myOptions
+
+      options:
+        - hybrid_factor:
+            velocity: 1.0
+
+        - limiter:
+            pressure: no
+            velocity: no
+
+        - projected_nodal_gradient:
+            pressure: element
+            velocity: element
+
+    restart:
+      restart_data_base_name: rst/cyl.rst
+      restart_frequency: 100
+      restart_start: 100
+
+    output:
+      output_data_base_name: out/cyl.e
+      output_frequency: 10
+      output_node_set: no
+      output_variables:
+       - velocity
+       - pressure
+       - dpdx
+       - mesh_displacement
+       - iblank
+       - iblank_cell
+
+
+Time_Integrators:
+  - StandardTimeIntegrator:
+      name: ti_1
+      start_time: 0
+      termination_step_count: 10
+      time_step: 0.003
+      time_stepping_type: fixed
+      time_step_count: 0
+      second_order_accuracy: yes
+
+      realms:
+        - realm_1

src/mesh_motion/CMakeLists.txt

@@ -8,6 +8,7 @@ target_sources(nalu PRIVATE
    ${CMAKE_CURRENT_SOURCE_DIR}/MotionRotationKernel.C
    ${CMAKE_CURRENT_SOURCE_DIR}/MotionScalingKernel.C
    ${CMAKE_CURRENT_SOURCE_DIR}/MotionTranslationKernel.C
+   ${CMAKE_CURRENT_SOURCE_DIR}/MotionOscillationKernel.C
    ${CMAKE_CURRENT_SOURCE_DIR}/MotionWavesKernel.C
    ${CMAKE_CURRENT_SOURCE_DIR}/TurbineSurrogateKernel.C
 )

src/mesh_motion/FrameBase.C

@@ -5,6 +5,7 @@
 #include "mesh_motion/MotionScalingKernel.h"
 #include "mesh_motion/MotionRotationKernel.h"
 #include "mesh_motion/MotionTranslationKernel.h"
+#include "mesh_motion/MotionOscillationKernel.h"
 #include "mesh_motion/TurbineSurrogateKernel.h"
 #include "mesh_motion/MotionWavesKernel.h"
 #include "NaluParsing.h"
@@ -70,6 +71,8 @@ FrameBase::load(const YAML::Node& node)
           new MotionDeformingInteriorKernel(meta_, motion_def));
       else if (type == "rotation")
         motionKernels_[i].reset(new MotionRotationKernel(motion_def));
+      else if (type == "oscillation")
+        motionKernels_[i].reset(new MotionOscillationKernel(motion_def));
       else if (type == "scaling")
         motionKernels_[i].reset(new MotionScalingKernel(meta_, motion_def));
       else if (type == "translation")