Allow NumPy v2.0+

.github/workflows/pr.yml

@@ -30,10 +30,10 @@ jobs:
     #   - the content of pyproject.toml changes
     #   - you manually change the value of the CACHE_NUMBER below
     # Else the existing cache is used.
-    - name: Setup Mambaforge
+    - name: Setup Miniforge
       uses: conda-incubator/setup-miniconda@v2
       with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           activate-environment: test-env
           use-mamba: true
@@ -45,8 +45,6 @@ jobs:
       shell: bash
 
     # create a conda yaml file
-    # for some reason Windows installs capytaine 1.4 instead of latest.
-    # CHANGE: Capytaine version
     - name: Create environment.yml file
       run: |
         echo "name: test-env" >> environment.yml;
@@ -139,4 +137,4 @@ jobs:
       shell: bash -l {0}
       run: |
         git fetch --tags
-        python3 docs/build_docs.py
+        python3 docs/build_docs.py --build production

.github/workflows/push.yml

@@ -30,10 +30,10 @@ jobs:
     #   - the content of pyproject.toml changes
     #   - you manually change the value of the CACHE_NUMBER below
     # Else the existing cache is used.
-    - name: Setup Mambaforge
+    - name: Setup Miniforge
       uses: conda-incubator/setup-miniconda@v2
       with:
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           activate-environment: test-env
           use-mamba: true
@@ -45,8 +45,6 @@ jobs:
       shell: bash
 
     # create a conda yaml file
-    # for some reason Windows installs capytaine 1.4 instead of latest.
-    # CHANGE: Capytaine version
     - name: Create environment.yml file
       run: |
         echo "name: test-env" >> environment.yml;
@@ -138,7 +136,7 @@ jobs:
       shell: bash -l {0}
       run: |
         git fetch --tags
-        python3 docs/build_docs.py
+        python3 docs/build_docs.py --build production
 
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3

.github/workflows/release.yml

@@ -62,7 +62,7 @@ jobs:
       shell: bash -l {0}
       run: |
         git fetch --tags
-        python3 docs/build_docs.py
+        python3 docs/build_docs.py --build production
 
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3

docs/build_docs.py

@@ -3,6 +3,7 @@
 import shutil
 import re
 import yaml
+import argparse 
 
 from sphinx.application import Sphinx
 
@@ -17,6 +18,10 @@
 html_dir = os.path.join(build_dir, 'html')
 doctree_dir = os.path.join(build_dir, 'doctrees')
 
+parser = argparse.ArgumentParser()
+parser.add_argument('-b', '--build', nargs=1, type=str,
+                    choices=['debug', 'production'],
+                    default='debug')
 
 def linkcheck():
     app = Sphinx(source_dir,
@@ -51,36 +56,56 @@ def cleanup():
         f.write(data2)
 
 
-def build_doc(version, tag, home_branch):
-    os.environ['current_version'] = version
-    subprocess.run(f'git checkout {tag}', shell=True)
-    subprocess.run(
-        f"git checkout {home_branch} -- {os.path.join(source_dir, 'conf.py')}", shell=True)
-    subprocess.run(
-        f"git checkout {home_branch} -- {os.path.join(docs_dir, 'versions.yaml')}", shell=True)
-    subprocess.run(
-        f"git checkout {home_branch} -- {os.path.join(source_dir, '_templates/versions.html')}", shell=True)
+def build_doc(version, tag, home_branch, build):
+    if build != 'debug':
+        os.environ['current_version'] = version
+        subprocess.run(f'git checkout {tag}', shell=True)
+        subprocess.run(
+            f"git checkout {home_branch} -- {os.path.join(source_dir, 'conf.py')}",
+            shell=True)
+        subprocess.run(
+            f"git checkout {home_branch} -- {os.path.join(docs_dir, 'versions.yaml')}",
+            shell=True)
+        subprocess.run(
+            f"git checkout {home_branch} -- {os.path.join(source_dir, '_templates/versions.html')}",
+            shell=True)
     source.make_theory_animations
     linkcheck()
     html()
     cleanup()
-    subprocess.run(
-        f"git checkout {home_branch}", shell=True)
+    if build != 'debug':
+        subprocess.run(
+            f"git checkout {home_branch}", shell=True)
 
 
-if __name__ == '__main__':
-    home_name = 'latest'
-    with open(os.path.join(docs_dir, 'versions.yaml'), 'r') as v_file:
-        versions = yaml.safe_load(v_file)
-    home_branch = versions[home_name]
-    build_doc(home_name, home_branch, home_branch)
-    print(f"Moving HTML pages to {os.path.join(docs_dir, 'pages')}...")
-    shutil.copytree(html_dir, os.path.join(docs_dir, 'pages'))
+def move_pages(dest_dir=None):
+    if dest_dir is None:
+        print(f"Moving HTML pages to {os.path.join(docs_dir, 'pages')}...")
+        shutil.copytree(
+            html_dir, os.path.join(docs_dir, 'pages'))
+    else:
+        print(f"Moving HTML pages to {os.path.join(docs_dir, 'pages', dest_dir)}...")
+        shutil.copytree(
+            html_dir, os.path.join(docs_dir, 'pages', dest_dir))
     print('Done.')
-    for name, tag in versions.items():
-        if name != home_name:
-            build_doc(name, tag, home_branch)
-            print(f"Moving HTML pages to {os.path.join(docs_dir, 'pages', name)}...")
-            shutil.copytree(html_dir, os.path.join(docs_dir, 'pages', name))
-            print('Done.')
+
+
+if __name__ == '__main__':
+    args = parser.parse_args()
+    build = args.build
+    if build == 'debug':
+        print(f'Building docs in current branch...')
+        build_doc('latest', '', '', build)
+        move_pages()
+    else:
+        home_name = 'latest'
+        with open(os.path.join(docs_dir, 'versions.yaml'), 'r') as v_file:
+            versions = yaml.safe_load(v_file)
+        home_branch = versions[home_name]
+        build_doc(home_name, home_branch, home_branch, build)
+        move_pages()
+        for name, tag in versions.items():
+            if name != home_name:
+                build_doc(name, tag, home_branch, build)
+                move_pages(dest_dir=name)
     shutil.rmtree(html_dir)

docs/source/references.rst

@@ -21,3 +21,4 @@ Bibliography
     Grasberger:2023aa
     Strofer:2023vw
     Coe2020Initial
+    DEVIN2024119124

docs/source/wecopttool_refs.bib

@@ -99,3 +99,13 @@ @article{Bacelli2014Numerical
 	title = {Numerical optimal control of wave energy converters},
 	volume = {6},
 	year = {2014}}
+
+@article{DEVIN2024119124,
+	title = {High-dimensional control co-design of a wave energy converter with a novel pitch resonator power takeoff system},
+	author = {Michael C. Devin and Daniel T. Gaebele and Carlos A. Michelén Ströfer and Jeff T. Grasberger and Jantzen Lee and Ryan G. Coe and Giorgio Bacelli},
+	journal = {Ocean Engineering},
+	volume = {312},
+	pages = {119124},
+	year = {2024},
+	issn = {0029-8018},
+	doi = {10.1016/j.oceaneng.2024.119124}}

examples/tutorial_1_WaveBot.ipynb

@@ -32,6 +32,7 @@
    "source": [
     "import autograd.numpy as np\n",
     "import capytaine as cpy\n",
+    "from capytaine.io.meshio import load_from_meshio\n",
     "import matplotlib.pyplot as plt\n",
     "from scipy.optimize import brute\n",
     "\n",
@@ -135,7 +136,11 @@
     "#### WEC geometry mesh\n",
     "Now we will create a surface mesh for the WEC hull and store it using the `FloatingBody` object from Capytaine.\n",
     "The WaveBot mesh is pre-defined in the `wecopttool.geom` module, so we will call it directly from there.\n",
-    "Note that the Capytaine `from_meshio` method can also import from other file types (STL, VTK, MSH, etc.), click [here](https://pypi.org/project/meshio/) for the full list of compatible mesh file types."
+    "Note that the Capytaine `from_meshio` method can also import from other file types (STL, VTK, MSH, etc.), click [here](https://pypi.org/project/meshio/) for the full list of compatible mesh file types.\n",
+    "\n",
+    "We also apply an internal lid which helps eliminate irregular frequency spikes. \n",
+    "The lid position was chosen by iterating through a series of mesh size factors and lid positions to move the frequency spikes above the range of interest. \n",
+    "See the `capytaine` documentation [here](https://capytaine.github.io/stable/index.html#) for more details. "
    ]
   },
   {
@@ -145,9 +150,14 @@
    "outputs": [],
    "source": [
     "wb = wot.geom.WaveBot()  # use standard dimensions\n",
-    "mesh_size_factor = 0.5 # 1.0 for default, smaller to refine mesh\n",
+    "mesh_size_factor = 0.2 # 1.0 for default, smaller to refine mesh\n",
     "mesh = wb.mesh(mesh_size_factor)\n",
-    "fb = cpy.FloatingBody.from_meshio(mesh, name=\"WaveBot\")"
+    "\n",
+    "# create mesh object for WaveBot and add internal lid\n",
+    "mesh_obj = load_from_meshio(mesh, 'WaveBot')\n",
+    "lid_mesh = mesh_obj.generate_lid(-2e-2)\n",
+    "\n",
+    "fb = cpy.FloatingBody(mesh=mesh_obj, lid_mesh=lid_mesh, name=\"WaveBot\")"
    ]
   },
   {
@@ -359,7 +369,7 @@
     "nsubsteps = 4\n",
     "\n",
     "def const_f_pto(wec, x_wec, x_opt, waves): # Format for scipy.optimize.minimize\n",
-    "    f = pto.force_on_wec(wec, x_wec, x_opt, waves, nsubsteps)\n",
+    "    f = pto.force(wec, x_wec, x_opt, waves, nsubsteps)\n",
     "    return f_max - np.abs(f.flatten())\n",
     "\n",
     "ineq_cons = {'type': 'ineq',\n",
@@ -974,7 +984,7 @@
     "    f_max = 750.0\n",
     "\n",
     "    def const_f_pto(wec, x_wec, x_opt, waves):\n",
-    "        f = pto.force_on_wec(wec, x_wec, x_opt, waves, nsubsteps)\n",
+    "        f = pto.force(wec, x_wec, x_opt, waves, nsubsteps)\n",
     "        return f_max - np.abs(f.flatten())\n",
     "\n",
     "    ineq_cons = {'type': 'ineq', 'fun': const_f_pto}\n",

examples/tutorial_2_AquaHarmonics.ipynb

@@ -23,6 +23,7 @@
    "outputs": [],
    "source": [
     "import capytaine as cpy\n",
+    "from capytaine.io.meshio import load_from_meshio\n",
     "import autograd.numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "from matplotlib import cm\n",
@@ -68,6 +69,7 @@
    "metadata": {},
    "source": [
     "Next we create a `FloatingBody` object from the mesh in Capytaine, which we will use to calculate the hydrodynamics.\n",
+    "We add a lid mesh to remove irregular frequency spikes, similar to [Tutorial 1](https://github.com/sandialabs/WecOptTool/blob/main/examples/tutorial_1_WaveBot.ipynb).\n",
     "We can visualize a 3D rendering of the mesh now as well."
    ]
   },
@@ -77,7 +79,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fb = cpy.FloatingBody.from_meshio(mesh, name=\"AquaHarmonics\")\n",
+    "mesh_obj = load_from_meshio(mesh, 'WaveBot')\n",
+    "lid_mesh = mesh_obj.generate_lid(-5e-2)\n",
+    "\n",
+    "fb = cpy.FloatingBody(mesh=mesh_obj, lid_mesh=lid_mesh, name=\"AquaHarmonics\")\n",
     "fb.add_translation_dof(name=\"Heave\")\n",
     "ndof = fb.nb_dofs\n",
     "fb.show_matplotlib()"
@@ -125,7 +130,7 @@
    "outputs": [],
    "source": [
     "amplitude = 0.5\n",
-    "wavefreq =  0.24/2 \n",
+    "wavefreq = 0.24/2 \n",
     "phase = 30\n",
     "wavedir = 0\n",
     "\n",

examples/tutorial_3_LUPA.ipynb

@@ -39,6 +39,7 @@
     "\n",
     "import gmsh, pygmsh\n",
     "import capytaine as cpy\n",
+    "from capytaine.io.meshio import load_from_meshio\n",
     "import autograd.numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
@@ -103,9 +104,10 @@
     "Here we create the mesh based on the dimensions provided by Oregon State University using `pygmsh`, available [here](https://pypi.org/project/pygmsh/).\n",
     "This is the same package used by `geom.py` (click [here](https://sandialabs.github.io/WecOptTool/api_docs/wecopttool.geom.html) for API documentation) containing the predefined WaveBot and AquaHarmonics meshes used in the previous tutorials.\n",
     "\n",
-    "The float has a hole where the spar passes through it, though OSU has found that this hole creates a large spike in the BEM results at about 4.5 rad/s.\n",
-    "There is not much energy in the waves at this frequency in the wave spectrum we will be using, so this spike should not significantly affect our results.\n",
-    "If you would like to remove this spike and create smoother BEM results, set `hole = False` in the cell below."
+    "The float has a hole where the spar passes through it. \n",
+    "In previous versions of this tutorial, the hole was larger than the spar and led to a large spike in the BEM results. \n",
+    "The spike has been resolved by making the hole smaller so that the float is flush with the spar.\n",
+    "Like the other tutorials, a lid is added to remove any irregular frequency spikes. "
    ]
   },
   {
@@ -121,20 +123,16 @@
     "h1 = 0.5  \n",
     "h2 = 0.21\n",
     "freeboard = 0.3\n",
-    "r3 = 0.10/2 + 0.05  # hole radius\n",
-    "hole = True # set to False to remove spike in BEM results\n",
+    "r3 = 0.05  # hole radius\n",
     "with pygmsh.occ.Geometry() as geom:\n",
     "    gmsh.option.setNumber('Mesh.MeshSizeFactor', mesh_size_factor)\n",
     "    cyl = geom.add_cylinder([0, 0, 0], [0, 0, -h1], r1)\n",
     "    cone = geom.add_cone([0, 0, -h1], [0, 0, -h2], r1, r2)\n",
     "    geom.translate(cyl, [0, 0, freeboard])\n",
     "    geom.translate(cone, [0, 0, freeboard]) \n",
-    "    if hole:\n",
-    "        tmp = geom.boolean_union([cyl, cone])\n",
-    "        bar = geom.add_cylinder([0, 0, 10], [0,0,-20], r3)\n",
-    "        geom.boolean_difference(tmp, bar)\n",
-    "    else:\n",
-    "        geom.boolean_union([cyl, cone])\n",
+    "    tmp = geom.boolean_union([cyl, cone])\n",
+    "    bar = geom.add_cylinder([0, 0, 10], [0,0,-20], r3)\n",
+    "    geom.boolean_difference(tmp, bar)\n",
     "    mesh_float = geom.generate_mesh()"
    ]
   },
@@ -152,8 +150,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# lid\n",
+    "mesh_obj = load_from_meshio(mesh_float, 'float')\n",
+    "lid_mesh = mesh_obj.generate_lid(z=-1e-2)\n",
+    "\n",
     "# floating body\n",
-    "float_fb = cpy.FloatingBody.from_meshio(mesh_float, name='float')\n",
+    "float_fb = cpy.FloatingBody(mesh=mesh_obj, lid_mesh=lid_mesh, name=\"float\")\n",
     "float_fb.add_translation_dof(name='Heave')"
    ]
   },
@@ -221,8 +223,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# lid\n",
+    "mesh_obj = load_from_meshio(mesh_spar, 'float')\n",
+    "lid_mesh = mesh_obj.generate_lid(z=-1e-2)\n",
+    "\n",
     "# floating body\n",
-    "spar_fb = cpy.FloatingBody.from_meshio(mesh_spar, name='spar')\n",
+    "spar_fb = cpy.FloatingBody(mesh=mesh_obj, lid_mesh=lid_mesh, name=\"spar\")\n",
     "spar_fb.add_translation_dof(name='Heave')"
    ]
   },