Add Stokes flow example (#54)

* Add stokes flow example

* Add test config

examples/CMakeLists.txt

@@ -3,4 +3,5 @@
 # SPDX-License-Identifier: MIT
 
 add_subdirectory(poisson)
-add_subdirectory(linelast)
+add_subdirectory(linelast)
+add_subdirectory(stokes)

examples/stokes/CMakeLists.txt

@@ -0,0 +1,15 @@
+# Copyright 2024 Lawrence Livermore National Security, LLC. See the top-level LICENSE file for details.
+#
+# SPDX-License-Identifier: MIT
+
+file(COPY stokes.sampling.yml DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes)
+file(COPY array.8.yml DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes)
+
+file(COPY generate_configs.py DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes)
+file(COPY setup_stokes.sh DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes)
+
+file(COPY meshes/square.o3.mesh DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes/meshes)
+file(COPY meshes/square-circle.msh.mfem DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes/meshes)
+file(COPY meshes/square-triangle.msh.mfem DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes/meshes)
+file(COPY meshes/square-star.msh.mfem DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes/meshes)
+file(COPY meshes/square-square.msh.mfem DESTINATION ${CMAKE_BINARY_DIR}/examples/stokes/meshes)

examples/stokes/array.8.yml

@@ -0,0 +1,116 @@
+main:
+#mode: run_example/sample_generation/build_rom/single_run
+  mode: single_run
+  use_rom: true
+  solver: stokes
+
+mesh:
+  type: component-wise
+  component-wise:
+# you can try other config files you generated by specifying it here.
+    global_config: "configs/test.box-channel.8x8.h5"
+    components:
+      - name: "empty"
+        file: "meshes/square.o3.mesh"
+      - name: "square-circle"
+        file: "meshes/square-circle.msh.mfem"
+      - name: "square-square"
+        file: "meshes/square-square.msh.mfem"
+      - name: "square-triangle"
+        file: "meshes/square-triangle.msh.mfem"
+      - name: "square-star"
+        file: "meshes/square-star.msh.mfem"
+
+domain-decomposition:
+  type: interior_penalty
+
+discretization:
+  order: 2
+  full-discrete-galerkin: false
+
+solver:
+  direct_solve: true
+  use_amg: true
+  max_iter: 1000000
+  print_level: 0
+  absolute_tolerance: 1.0e-10
+  relative_tolerance: 1.0e-10
+
+visualization:
+  enabled: true
+  visualize_error: true
+  unified_paraview: false
+  file_path:
+    prefix: paraview/8x8/stokes_array_output
+
+parameterized_problem:
+  name: flow_past_array
+  #name: stokes_channel
+
+single_run:
+  choose_from_random_sample: false
+  flow_past_array:
+    nu: 1.1
+    u0_x: 1.5
+    u0_y: -0.8
+    du_x: 0.
+    du_y: 0.
+  stokes_channel:
+    nu: 1.1
+    U: 1.5
+    L: 4.
+    x0: 2.
+
+sample_generation:
+  type: "random"
+  random_sample_generator:
+    number_of_samples: 100
+  maximum_number_of_snapshots: 100
+  parameters:
+    - key: mesh/component-wise/global_config
+      type: filename
+      minimum: 0
+      maximum: 99
+      format: "boxchannel_sample/8x8_samples/box-channel.8x8.%06d.h5"
+    - key: single_run/flow_past_array/u0_x
+      type: double
+      minimum: -1.5
+      maximum: 1.5
+    - key: single_run/flow_past_array/u0_y
+      type: double
+      minimum: -1.5
+      maximum: 1.5
+
+basis:
+  prefix: "basis/stokes_basis"
+  number_of_basis: 36
+  tags:
+    - name: "empty"
+    - name: "square-circle"
+    - name: "square-square"
+    - name: "square-triangle"
+    - name: "square-star"
+  svd:
+    save_spectrum: true
+    update_right_sv: false
+  visualization:
+    enabled: false
+    prefix: stokes_comp
+
+model_reduction:
+  rom_handler_type: mfem
+  linear_solver_type: direct
+  linear_system_type: spd
+# This is the input for saving ROM matrix/rhs system.
+  save_linear_system:
+    enabled: true
+    prefix: rom-system/stokes.8x8
+  preconditioner: gs
+  # individual/universal
+  subdomain_training: universal
+  save_operator:
+    level: component
+    prefix: "stokes_comp"
+  compare_solution:
+    enabled: true
+

examples/stokes/generate_configs.py

@@ -0,0 +1,24 @@
+import sys
+# Add path to root utils/python/ directory to find config scripts
+sys.path.insert(0, "../../../utils/python/")
+
+from config import Empty, ObjectInSpace
+from box_channel_config import BoxChannelConfig
+
+if __name__ == "__main__":
+    comp_list = {'empty': Empty(),
+                 'circle': ObjectInSpace('square-circle'),
+                 'square': ObjectInSpace('square-square'),
+                 'triangle': ObjectInSpace('square-triangle'),
+                 'star': ObjectInSpace('square-star'),}
+
+    example = BoxChannelConfig(2,2)
+    for name, comp in comp_list.items():
+        example.addComponent(comp)
+
+    example.GenerateAllConfigs(0)
+
+    test = BoxChannelConfig(8,8)
+    for name, comp in comp_list.items():
+        test.addComponent(comp)
+    test.CreateRandomConfig('test.box-channel.8x8.h5')