Test capytaine lids

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\")"
    ]
   },
   {

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",
+    "Again, we add a lid mesh to remove irregular frequency spikes.\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

@@ -39,11 +39,13 @@
     "\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",
     "from scipy.optimize import brute\n",
     "\n",
+    "\n",
     "import wecopttool as wot\n",
     "\n",
     "## set colorblind-friendly colormap for plots\n",
@@ -103,9 +105,10 @@
     "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 +124,16 @@
     "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 +151,12 @@
    "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 +224,12 @@
    "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')"
    ]
   },

examples/tutorial_4_Pioneer.ipynb

@@ -35,6 +35,7 @@
    "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 scipy.linalg import block_diag\n",
@@ -148,7 +149,7 @@
     "                             h2=17.321 * in2m,\n",
     "                             scale_factor=1,\n",
     "                             freeboard=freeboard)\n",
-    "mesh = hull_geom.mesh(mesh_size_factor=0.5)\n",
+    "mesh = hull_geom.mesh(mesh_size_factor=0.3)\n",
     "_ = hull_geom.plot_cross_section()"
    ]
   },
@@ -253,7 +254,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pnr_fb = cpy.FloatingBody.from_meshio(mesh, name=\"Pioneer\")\n",
+    "mesh_obj = load_from_meshio(mesh, 'Pioneer')\n",
+    "lid_mesh = mesh_obj.generate_lid(-4e-2)\n",
+    "\n",
+    "pnr_fb = cpy.FloatingBody(mesh=mesh_obj, lid_mesh=lid_mesh, name=\"WaveBot\")\n",
     "pnr_fb.add_rotation_dof(name='Pitch')\n",
     "pnr_fb.center_of_mass = np.array([0., 0., buoy_props['CG']])\n",
     "pnr_fb.rotation_center = pnr_fb.center_of_mass\n",