Test capytaine lids (#363)

* Update CONTRIBUTING.md to indicate PRs should be to the new `dev` branch * Update RELEASING.md to reflect new workflow with the `dev` branch * Set Default uniform_shift to False (#313) * Make uniform shift default false and fix test_core * Allow for non-uniform shift for impedance * update docstrings (#326) * damping naming and consistently change radiation damping (#328) * run CI + codeQL on dev PRs/pushses * Fix test failures (#330) * fix tests * fix pioneer * actually test power solution for irregular wave (#327) * Update test_integration with new scaling (#333) * Phase Realizations Demo and Docs (#315) * Pioneer tutorial realizations demo Add frequency array and realization study to beginning of pioneer tutorial * Update pioneer * Clean pioneer and update docs * remove print * Units * Update pioneer plots * Waves before frequencies * Explain less frequencies * Minor updates * Update pioneer * Merge branch 'dev' of https://github.com/sandialabs/WecOptTool into phases_demo * issue 321 fd_to_td() bug (#329) * bug bix : DC and Nyquist frequency should not be devided by two before ifft * Changed td_to_fd to scale single sided frequency components rather than TD signal * minor bug fix from issue332 #332 * nodf -> ndof (#334) * add DOI for Daniel's paper (#336) * Tutorial cleanup (#339) * run CI on PRs against dev branch * revamped tutorial 1, including fix for #293 * more tutorial cleanup and editorial changes * more cleanup and incorporated changes in #315 * fixed tutorial 2 colormaps * finishing touches * reverted a few accidental changes * fixes as per Jeff's review comments --------- Co-authored-by: Ryan Coe <[email protected]> * Utils dev - replaces old utilities PR (#343) * run CI on PRs against dev branch * coppied fundamental utility files * import utilities module * added utilities funtions to tut1 * added bem plot from utils * added bem plot from utils * updated sankey plot * updated check_radiation_damping * cleared outputs * corrected bug * changed Zi to hydro_impedance to be consistent with our variables name python convention * PR review edits * add grid to plots * removed draft functions in utilities.py * typo * Fixed one more typo I found while reviewing Daniel's changes --------- Co-authored-by: Ryan Coe <[email protected]> Co-authored-by: Michael Devin <[email protected]> * Post process docstrings; use loops for multiple realizations (#337) * post_processing docstrings - examples - parameters (order) * handle multiple phase realizations internally * Update wecopttool/core.py * making outputs lists * Update implementation to function with tutorial 1 for now * Update tutorials * Update LUPA * Make sure same WEC is passed in * Add test_utilities Revert "Add test_utilities" This reverts commit 27399f0. * Update utilities module * Update utilities * Update test_utilities * Update tutorial 1 utilities call --------- Co-authored-by: Carlos A. Michelén Ströfer <[email protected]> Co-authored-by: Carlos A. Michelén Ströfer <[email protected]> Co-authored-by: jtgrasb <[email protected]> Co-authored-by: jtgrasb <[email protected]> * v3.0.0 * Lower tolerance for new test to fix CI failing occasionally * hyperlinks no longer have formatting, plus other small adjustments (#348) * Merge to dev, not main (#349) * Dev version of documentation site (#347) * added initial file changes based on sphinx_multiversion docs and WEC-Sim implementation * removed sphinx-multiversion since it is no longer supported and made manual multiversion * now uses absolute paths, commented out linkcheck for debugging * fixed docstring errors in utilities module * updating files again that somehow got reverted * fixing path in conf.py * don't run tutorials (will revert later) * handle file moves correctly, fixed if statement to make other versions appear * fixed two bugs in versions template * reverted temp changes, changes latest to main * switched latest to main * main branch now in root directory of pages * fixed URLs with change from last commit * make other branches visible before building * switched main branch tag for more testing * fixed typo * switched dev branch to an existing branch * renamed main to latest, changed version.html file name to avoid confusion * added prints about moving files so Sphinx output isn't misleading * fixed typo with quotations * changed versions.html name back because that broke things I guess * modified contributing documentation to reflect changes * add logic to remove duplicate 'latest' branch * Fixed pathing when already on latest * remove typo * Troubleshooting complete, switching back to correct branches for deployment * Removed extra word in docstring * removed redundant function * fixed pathing so returns to same file (and fixes tutorial/API docs) * changed latest branch for demonstration * switched back latest branch for deployment * updated with new Capytaine docs URL * Add warnings when adding inertia and hydrostatic stiffness automatically (#346) * CI workflow cleanup (#352) * removed conda environment from workflows since newer capytaine/wavespectra work with Windows * fixed unnecessary capitalization * still create CI conda environment to fix Mac environment failures * added conda env fully back in, push workflow deploys docs, split PR workflow * conda environment activates again * mambaforge instead of miniforge * manual cache reset * reset to older version of setup-miniconda to troubleshoot * Specify NumPy version <2.0 since it breaks autograd * v3.0.1 (#360) * Revert "v3.0.1 (#360)" (#361) This reverts commit f79ff8b. * Update pyproject.toml * Test out lid feature * Add lid to pioneer and remove extra files * Revert LUPA and add lid comment * Revert LUPA bem data * Fix pioneer * Test lid LUPA * Update LUPA with lid * LUPA lid * Revert LUPA unnecessary changes * Resolve Daniel's suggestions --------- Co-authored-by: Carlos A. Michelén Ströfer <[email protected]> Co-authored-by: Ryan Coe <[email protected]> Co-authored-by: Daniel Gaebele <[email protected]> Co-authored-by: Michael Devin <[email protected]> Co-authored-by: Carlos A. Michelén Ströfer <[email protected]> Co-authored-by: mcdevin <[email protected]>
sandialabs · Oct 29, 2024 · 71c826a · 71c826a
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diff --git a/examples/data/bem.nc b/examples/data/bem.nc
diff --git a/examples/tutorial_1_WaveBot.ipynb b/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\")"
    ]
   },
   {

diff --git a/examples/tutorial_2_AquaHarmonics.ipynb b/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",

diff --git a/examples/tutorial_3_LUPA.ipynb b/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')"
    ]
   },

diff --git a/examples/tutorial_4_Pioneer.ipynb b/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",