optional gmsh integration for rectangles and boxes.

.github/workflows/CI_every_commit.yml

@@ -28,6 +28,7 @@ jobs:
         shell: pwsh # putting in a shell command makes for compile linking problems later
         # (if you use the shell here, cannot use 'compiler' package, but mpi only seems to work with it)
         run: |
+          conda install -n base mamba
           bash ./install.sh test-environment
           conda activate test-environment
           conda list

demo/documented/Yaml_Examples/0-wind_farm_2D.yaml

@@ -60,11 +60,10 @@ domain:
 
     # ########################### Circle Domain #########################
     type: circle                                  
-    mesh_type: mshr         # squircular, elliptic, stretch
+    mesh_type: gmsh         # squircular, elliptic, stretch
     radius: 1200            # x-range of the domain | m
     center: [0.0, 0.0]      # y-range of the domain | m
     nt: 62                  # segments around circle| -
-    res: 50                 # resolution for mshr   | -
     # ###################################################################
 
 

demo/documented/Yaml_Examples/1-wind_farm_2D_layout_opt.yaml

@@ -57,7 +57,7 @@ domain:
 
     ########################### Circle Domain #########################
     type: circle                                  
-    mesh_type: mshr         # squircular, elliptic, stretch
+    mesh_type: gmsh         # squircular, elliptic, stretch
     radius: 1500            # x-range of the domain | m
     center: [0.0, 0.0]      # y-range of the domain | m
     nt: 50                  # segments around circle| -

demo/documented/Yaml_Examples/7-wind_farm_2D_OM.yaml

@@ -18,8 +18,8 @@ wind_farm:
     type: grid            #                          |
     grid_rows: 1          # Number of rows           | -
     grid_cols: 2          # Number of columns        | -
-    ex_x: [-882, 882]     # x-extent of the farm     | m
-    ex_y: [-882, 882]     # y-extent of the farm     | m
+    ex_x: [-720, 720]     # x-extent of the farm     | m
+    ex_y: [-720, 720]     # y-extent of the farm     | m
     jitter: 0            # Randomly perturb turbines| m
     seed: 8675309         # random seed for repeats  | -
     ##################################################################
@@ -57,11 +57,10 @@ domain:
 
     ########################### Circle Domain #########################
     type: circle                                  
-    mesh_type: mshr         # squircular, elliptic, stretch
+    mesh_type: gmsh         # squircular, elliptic, stretch
     radius: 1500            # x-range of the domain | m
     center: [0.0, 0.0]      # y-range of the domain | m
     nt: 20                  # segments around circle| -
-    res: 10                 # resolution for mshr   | -
     ###################################################################
 
 

environment.yaml

@@ -3,23 +3,25 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  # - python=3.7
+  - python=3.9 #3.10 causes CI to hang in parallel
+  - mpich
+  # - mpich=4.1.2=hd33e60e_101
+  # - mpich=4.0.3
   - coveralls
   - dolfin-adjoint=2019.1.0
-  - fenics=2019.1.0=py39*_26
+  - fenics
   - hdf5
   - jsonschema
   - matplotlib
   - memory_profiler
-  - mshr
   - openmdao
   - pandas
   - pyoptsparse
   - pytest
   - pytest-cov
   - pytest-mpi
   - pyyaml
-  - scipy=1.7.0
+  - scipy
   - slepc
   - sphinx<7.0.0
   - pip
@@ -34,4 +36,6 @@ dependencies:
     - networkx
     - pulp
     - fatpack
+    - gmsh
+    - meshio
     - -e .

install.sh

@@ -1,23 +1,15 @@
 #!/bin/bash 
 
-### Run this to use conda in the script
-source $(conda info --base)/etc/profile.d/conda.sh
-
-# ### Create the Environment
-# conda create -y --name $1
-# conda activate $1
+### Create some names
+conda_base_path=$(conda info --base)
+env_name=$1
 
-# ### Install conda-forge dependencies 
-# conda install -y -c conda-forge fenics=2019.1.0=py38_9 dolfin-adjoint matplotlib scipy=1.4.1 slepc mshr hdf5 pyyaml memory_profiler pytest pytest-cov pytest-mpi coveralls pandas
-
-# ### Install the new tsfc compiler
-# pip install git+https://github.com/blechta/[email protected]
-# pip install git+https://github.com/blechta/[email protected]
-# pip install git+https://github.com/blechta/[email protected]
-# pip install git+https://github.com/mdolab/[email protected]
-# pip install singledispatch networkx pulp openmdao fatpack
+### Run this to use conda in the script
+source ${conda_base_path}/etc/profile.d/conda.sh
 
-# ### Install editible version of WindSE
-# pip install -e .
+### Create the Environment with mamba
+conda create --yes --name ${env_name} --channel conda-forge python=3.9 mamba
+conda activate ${env_name}
 
-conda env create --name ${1} --file environment.yaml
+### Install dependencies from environment
+mamba env update --prefix ${conda_base_path}/envs/${env_name} --file environment.yaml --prune 

tests/9-Regression/2D_Rectangle_Steady_gmsh.yaml

@@ -0,0 +1,81 @@
+# General options
+general:
+    # name: 3D_Wind_Farm      # Name of the output folder
+    output: ["mesh","initial_guess","height","turbine_force","solution"]
+    dolfin_adjoint: True
+    debug_mode: True
+
+# Wind Farm Parameters:
+wind_farm:
+
+    ########################## Grid Wind Farm #########################
+    type: grid            #                          |
+    grid_rows: 2          # Number of rows           | -
+    grid_cols: 4          # Number of columns        | -
+    ex_x: [-600, 600]     # x-extent of the farm     | m
+    ex_y: [-300, 300]     # y-extent of the farm     | m
+    ###################################################################
+
+turbines:
+    type: disk            # Use actuator Disks       |
+    HH: 90                # Hub Height               | m
+    RD: 126.0             # Turbine Diameter         | m
+    thickness: 20.0       # Effective Thickness      | m
+    yaw: 0.349            # Yaw                      | rads
+    axial: 0.33           # Axial Induction          | -
+
+domain:
+
+    ########################### Box Domain ############################
+    type: rectangle        #                       |
+    x_range: [-1200, 1200] # x-range of the domain | m
+    y_range: [-600, 600]   # y-range of the domain | m
+    nx: 128                # Number of x-nodes     | -
+    ny:  64                # Number of y-nodes     | -
+    mesh_type: gmsh
+    ###################################################################
+
+refine:
+    # warp_type: split
+    # warp_percent: 0.7     # percent of cells moved       | -
+    # warp_height: 250       # move cell below this value   | m
+    refine_custom:
+        1:
+            type: box
+            x_range: [-1000,1200]
+            y_range: [-400, 400]
+            # z_range: [0, 200]
+
+    turbine_num: 1         # number of turbine refinements| -
+    turbine_factor: 1.25   # turbine radius multiplier    | -
+
+function_space:
+    type: taylor_hood
+
+boundary_conditions:
+    vel_profile: uniform
+    HH_vel: 8.0
+    # k: 0.4
+    # inflow_angle: 1.13
+    ######## Uncomment to test out custom BCs for BoxDomain ##########
+    boundary_types:
+        inflow: ["west"]
+        no_stress: ["east"]
+        free_slip: ["north","south"]
+    ##################################################################
+
+problem:
+    type: taylor_hood
+    viscosity: 5
+    lmax: 50
+
+solver:
+    # nonlinear_solver: newton
+    # newton_relaxation: 0.9
+    type: steady
+    save_power: true
+
+optimization:
+    control_types: [layout,yaw]
+    layout_bounds: [[-720, 720],[-450, 450]]
+    gradient: True

tests/9-Regression/3D_Box_Steady_gmsh.yaml

@@ -0,0 +1,82 @@
+# General options
+general:
+    # name: 3D_Wind_Farm      # Name of the output folder
+    output: ["mesh","initial_guess","height","turbine_force","solution"]
+    dolfin_adjoint: True
+    debug_mode: True
+
+# Wind Farm Parameters:
+wind_farm:
+
+    ########################## Grid Wind Farm #########################
+    type: grid            #                          |
+    grid_rows: 2          # Number of rows           | -
+    grid_cols: 4          # Number of columns        | -
+    ex_x: [-600, 600]     # x-extent of the farm     | m
+    ex_y: [-300, 300]     # y-extent of the farm     | m
+    ###################################################################
+
+turbines:
+    type: disk            # Use actuator Disks       |
+    HH: 90                # Hub Height               | m
+    RD: 126.0             # Turbine Diameter         | m
+    thickness: 20.0       # Effective Thickness      | m
+    yaw: 0.349            # Yaw                      | rads
+    axial: 0.33           # Axial Induction          | -
+
+domain:
+
+    ########################### Box Domain ############################
+    type: box              #                       |
+    x_range: [-1200, 1200] # x-range of the domain | m
+    y_range: [-600, 600]   # y-range of the domain | m
+    z_range: [0.04, 640]   # z-range of the domain | m
+    nx: 16                 # Number of x-nodes     | -
+    ny:  8                 # Number of y-nodes     | -
+    nz:  8                 # Number of z-nodes      | -
+    mesh_type: gmsh
+    ###################################################################
+
+refine:
+    warp_type: split
+    warp_percent: 0.7     # percent of cells moved       | -
+    warp_height: 250       # move cell below this value   | m
+    refine_custom:
+        1:
+            type: box
+            x_range: [-1000,1200]
+            y_range: [-400, 400]
+            z_range: [0, 200]
+
+    turbine_num: 1         # number of turbine refinements| -
+    turbine_factor: 1.25   # turbine radius multiplier    | -
+
+function_space:
+    type: linear
+
+boundary_conditions:
+    vel_profile: log
+    HH_vel: 8.0
+    k: 0.4
+    # inflow_angle: 1.13
+    ######## Uncomment to test out custom BCs for BoxDomain ##########
+    boundary_types:
+        inflow: ["west"]
+        no_stress: ["east"]
+        free_slip: ["top","north","south"]
+        no_slip: ["bottom"]
+    ##################################################################
+
+problem:
+    type: stabilized
+    viscosity: 5
+    lmax: 50
+
+solver:
+    type: steady
+    save_power: true
+
+optimization:
+    control_types: [layout,yaw]
+    layout_bounds: [[-720, 720],[-450, 450]]
+    gradient: True

tests/9-Regression/Truth_Data/2D_Rectangle_Steady_gmsh_truth.yaml

@@ -0,0 +1,108 @@
+GenericWindFarm:
+  min_x: -537.0
+  max_x: 537.0
+  avg_x: 0.0
+  min_y: -237.0
+  max_y: 237.0
+  avg_y: 0.0
+  min_z: 90.0
+  max_z: 90.0
+  avg_z: 90.0
+  min_yaw: 0.349
+  max_yaw: 0.349
+  avg_yaw: 0.349
+DomainManager:
+  dim: 2
+  x_min: -1200.0
+  x_max: 1200.0
+  y_min: -600.0
+  y_max: 600.0
+  volume: 2879999.9999999944
+  ID_east: 1
+  SA_east: 1199.9999999999993
+  ID_north: 2
+  SA_north: 2399.999999999999
+  ID_west: 3
+  SA_west: 1199.9999999999998
+  ID_south: 4
+  SA_south: 2399.999999999999
+FunctionSpaceManager:
+  velocity_dofs: 199784
+  pressure_dofs: 25045
+  total_dofs: 224829
+BoundaryManager:
+  min_x: 8.0
+  max_x: 8.0
+  avg_x: 8.0
+  min_y: 0.0
+  max_y: 0.0
+  avg_y: 0.0
+  min_p: 0.0
+  max_p: 0.0
+  avg_p: 0.0
+  min_initial_values: 0.0
+  max_initial_values: 8.0
+  avg_initial_values: 3.5544169124089864
+  num_bc: 7
+ProblemManager:
+  int_nu_T: 3.6195476564638705e-12
+  int_tf_x: -0.017779690602830505
+  int_tf_y: -0.006469952285041019
+SolverManager:
+  min_x_vel: 3.1513290589444534
+  max_x_vel: 10.314223723630104
+  avg_x_vel: 7.999999999999985
+  min_y_vel: -1.5355717615335474
+  max_y_vel: 1.7312382083757618
+  avg_y_vel: -0.012640362247818808
+OptimizationManager:
+  n_controls: 24
+  obj_value0: 0.09657585867884727
+  val0_x_0: -537.0
+  val0_y_0: -237.0
+  val0_x_1: -179.0
+  val0_y_1: -237.0
+  val0_x_2: 179.0
+  val0_y_2: -237.0
+  val0_x_3: 537.0
+  val0_y_3: -237.0
+  val0_x_4: -537.0
+  val0_y_4: 237.0
+  val0_x_5: -179.0
+  val0_y_5: 237.0
+  val0_x_6: 179.0
+  val0_y_6: 237.0
+  val0_x_7: 537.0
+  val0_y_7: 237.0
+  val0_yaw_0: 0.349
+  val0_yaw_1: 0.349
+  val0_yaw_2: 0.349
+  val0_yaw_3: 0.349
+  val0_yaw_4: 0.349
+  val0_yaw_5: 0.349
+  val0_yaw_6: 0.349
+  val0_yaw_7: 0.349
+  grad_x_0: -8.33214537992983e-06
+  grad_y_0: -2.0118478496424273e-05
+  grad_x_1: -5.802770168646045e-07
+  grad_y_1: -6.845843664967294e-07
+  grad_x_2: 2.423778555536142e-06
+  grad_y_2: 1.1422838544789697e-05
+  grad_x_3: 8.578153855238626e-06
+  grad_y_3: 1.6946275983151124e-05
+  grad_x_4: -1.0314760814733896e-05
+  grad_y_4: 2.8272220694531887e-05
+  grad_x_5: -8.751615197887761e-07
+  grad_y_5: -8.281878532430593e-06
+  grad_x_6: 1.6008364572576094e-06
+  grad_y_6: -1.2717509235006934e-05
+  grad_x_7: 6.279591155513218e-06
+  grad_y_7: -1.6236312575846403e-05
+  grad_yaw_0: -0.0072120688648149335
+  grad_yaw_1: -0.004558722084702321
+  grad_yaw_2: -0.004826849442760917
+  grad_yaw_3: -0.006876464533418879
+  grad_yaw_4: -0.007472719447171188
+  grad_yaw_5: -0.004770395674441498
+  grad_yaw_6: -0.004642931548333499
+  grad_yaw_7: -0.005883549707396079