Pioneer tutorial updates (empirical impedance model and nonlinear spring) (sandialabs#362)

* 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 (sandialabs#313)

* Make uniform shift default false and fix test_core

* Allow for non-uniform shift for impedance

* update docstrings (sandialabs#326)

* damping naming and consistently change radiation damping (sandialabs#328)

* run CI + codeQL on dev PRs/pushses

* Fix test failures (sandialabs#330)

* fix tests

* fix pioneer

* actually test power solution for irregular wave (sandialabs#327)

* Update test_integration with new scaling (sandialabs#333)

* Phase Realizations Demo and Docs (sandialabs#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 (sandialabs#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 sandialabs#332

* nodf -> ndof (sandialabs#334)

* add DOI for Daniel's paper (sandialabs#336)

* Tutorial cleanup (sandialabs#339)

* run CI on PRs against dev branch

* revamped tutorial 1, including fix for sandialabs#293

* more tutorial cleanup and editorial changes

* more cleanup and incorporated changes in sandialabs#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 (sandialabs#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 (sandialabs#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 (sandialabs#348)

* Merge to dev, not main (sandialabs#349)

* Dev version of documentation site (sandialabs#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 (sandialabs#346)

* Add data and update tutorial 4

* CI workflow cleanup (sandialabs#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 (sandialabs#360)

* Revert "v3.0.1 (sandialabs#360)" (sandialabs#361)

This reverts commit f79ff8b.

* Update pyproject.toml

* Update pioneer tutorial with nl spring and empirical model

* Clear outputs

* Consolidate empirical data and fix small issues

* Remove consolidation file

---------

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]>

Author: 5 people

examples/data/pioneer_empirical_data.nc

@@ -41,7 +41,6 @@
     "from scipy.linalg import block_diag\n",
     "import xarray as xr\n",
     "from math import comb\n",
-    "from wavespectra.construct.frequency import pierson_moskowitz\n",
     "\n",
     "import wecopttool as wot\n",
     "\n",
@@ -76,11 +75,9 @@
     "fend = 1.875\n",
     "nfreq_irreg = 150\n",
     "f1_irreg = fend / nfreq_irreg\n",
-    "freq_irreg = wot.frequency(f1_irreg, nfreq_irreg, False) # False -> no zero frequency\n",
     "\n",
     "f1_reg = .325/2\n",
-    "nfreq_reg = 12\n",
-    "freq_reg = wot.frequency(f1_reg, nfreq_reg, False) # False -> no zero frequency"
+    "nfreq_reg = 12"
    ]
   },
   {
@@ -100,7 +97,8 @@
     "nrealizations = 2\n",
     "\n",
     "fp = 1/Tp\n",
-    "efth = pierson_moskowitz(freq=freq_irreg, hs=Hs, fp=fp)\n",
+    "spectrum = lambda f: wot.waves.pierson_moskowitz_spectrum(f, fp, Hs)\n",
+    "efth = wot.waves.omnidirectional_spectrum(f1_irreg, nfreq_irreg, spectrum, \"Pierson-Moskowitz\")\n",
     "waves_irregular = wot.waves.long_crested_wave(efth, nrealizations=nrealizations)"
    ]
   },
@@ -280,9 +278,14 @@
    "outputs": [],
    "source": [
     "rho = 1025. # kg/m^3\n",
+    "freq_reg = wot.frequency(f1_reg, nfreq_reg, False) # False -> no zero frequency\n",
     "bem_data_reg = wot.run_bem(pnr_fb, freq_reg)\n",
     "omega_reg = bem_data_reg.omega.values\n",
     "\n",
+    "freq_irreg = wot.frequency(f1_irreg, nfreq_irreg, False) # False -> no zero frequency\n",
+    "bem_data_irreg = wot.run_bem(pnr_fb, freq_irreg)\n",
+    "omega_irreg = bem_data_irreg.omega.values\n",
+    "\n",
     "bem_data_irreg = wot.run_bem(pnr_fb, freq_irreg)\n",
     "omega_irreg = bem_data_irreg.omega.values\n",
     "\n",
@@ -307,19 +310,12 @@
    "outputs": [],
    "source": [
     "# load in the empirical data\n",
-    "datafile = 'data/pioneer_empirical_data.npz'\n",
-    "\n",
-    "with np.load(datafile) as empirical_data:\n",
-    "    # Access the data within the 'with' block\n",
-    "    omega_data = empirical_data['omega_data']\n",
-    "    exc_coeff_data = empirical_data['exc_coeff_data']\n",
-    "    Zi_data = empirical_data['Zi_data']\n",
-    "    Zi_stiffness = empirical_data['Zi_stiffness']\n",
-    "\n",
-    "dof_names = [\"Pitch\"]\n",
-    "directions = [0]\n",
+    "datafile = 'data/pioneer_empirical_data.nc'\n",
+    "empirical_data = xr.load_dataset(datafile)\n",
     "\n",
-    "exc_coeff_data, Zi_data = wot.utilities.create_dataarray(Zi_data, exc_coeff_data, omega_data, directions, dof_names)\n",
+    "exc_coeff_data = empirical_data.exc_coeff_data_real + 1j*empirical_data.exc_coeff_data_imag\n",
+    "Zi_data = empirical_data.Zi_data_real + 1j*empirical_data.Zi_data_imag\n",
+    "Zi_stiffness = empirical_data.Zi_stiffness\n",
     "\n",
     "# here extrapolation for impedance and padding with zeros for the excitation\n",
     "exc_coeff_intrp_reg = exc_coeff_data.interp(omega = omega_reg, method='linear', kwargs={\"fill_value\": 0})\n",
@@ -503,12 +499,7 @@
     "pto_impedance = np.array([[pto_impedance_11, pto_impedance_12],\n",
     "                        [pto_impedance_21, pto_impedance_22]])\n",
     "\n",
-    "pto = wot.pto.PTO(ndof, \n",
-    "                  kinematics=[1], \n",
-    "                  controller=wot.controllers.unstructured_controller(), \n",
-    "                  impedance=pto_impedance, \n",
-    "                  loss=None, \n",
-    "                  names=None)\n"
+    "pto = wot.pto.PTO(ndof, kinematics=[1], controller=None, impedance=pto_impedance, loss=None, names=None)\n"
    ]
   },
   {
@@ -856,7 +847,7 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(nrows=5, sharex=True, figsize=(12, 12))\n",
-    "t = wec_tdom.sel(realization=0).time.values\n",
+    "t = wec_tdom[0].time.values\n",
     "\n",
     "# Positions\n",
     "ax[0].plot(t, fw_pos*180/np.pi, label='Flywheel', c='k')\n",
@@ -881,7 +872,7 @@
     "ax1 = ax[1].twinx()\n",
     "ax1.tick_params(axis='y', labelcolor='b')\n",
     "# when using an impedance model, the excitation force cannot be split up into Froude-Krylov and diffraction\n",
-    "wec_tdom.sel(realization=0)['force'].sel(type='excitation').plot(ax=ax1, c='b') \n",
+    "wec_tdom[0]['force'].sel(type='excitation').plot(ax=ax1, c='b') \n",
     "ax1.set_ylabel('Excitation torque [N-m]', color='b')\n",
     "ax1.set_title('Torque')\n",
     "\n",
@@ -937,8 +928,8 @@
     "Zi = Zi_intrp_reg\n",
     "Rad_res = np.real(Zi.squeeze())\n",
     "\n",
-    "Fex = wec_fdom.sel(realization=0).force.sel(type=['excitation'])\n",
-    "Vel = wec_fdom.sel(realization=0).vel\n",
+    "Fex = wec_fdom[0].force.sel(type=['excitation'])\n",
+    "Vel = wec_fdom[0].vel\n",
     "\n",
     "P_max_absorbable = (np.abs(Fex)**2/(8*Rad_res) ).squeeze().sum('omega').item() # after Falnes Eq. 6.10\n",
     "P_opt_excitation = 2*P_max_absorbable # after Falnes Eq. 6.10\n",
@@ -1043,12 +1034,7 @@
     "pto_impedance = np.array([[pto_impedance_11, pto_impedance_12],\n",
     "                        [pto_impedance_21, pto_impedance_22]])\n",
     "\n",
-    "pto = wot.pto.PTO(ndof, \n",
-    "                  kinematics=[1], \n",
-    "                  controller=wot.controllers.unstructured_controller(), \n",
-    "                  impedance=pto_impedance, \n",
-    "                  loss=None, \n",
-    "                  names=None)\n",
+    "pto = wot.pto.PTO(ndof, kinematics=[1], controller=None, impedance=pto_impedance, loss=None, names=None)\n",
     "\n",
     "wec_lin = wot.WEC.from_impedance(freq_irreg, \n",
     "                            Zi_intrp_irreg,\n",
@@ -1135,7 +1121,7 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(nrows=5, sharex=True, figsize=(12, 12))\n",
-    "t = wec_tdom.sel(realization=0).time.values\n",
+    "t = wec_tdom[0].time.values\n",
     "\n",
     "# Positions\n",
     "ax[0].plot(t, fw_pos*180/np.pi, label='Flywheel', c='k')\n",
@@ -1159,7 +1145,7 @@
     "\n",
     "ax1 = ax[1].twinx()\n",
     "ax1.tick_params(axis='y', labelcolor='b')\n",
-    "wec_tdom.sel(realization=0)['force'].sel(type=['excitation']).plot(ax=ax1, c='b')\n",
+    "wec_tdom[0]['force'].sel(type=['excitation']).plot(ax=ax1, c='b')\n",
     "ax1.set_ylabel('Excitation torque [N-m]', color='b')\n",
     "ax1.set_title('Torque')\n",
     "\n",

examples/tutorial_4_Pioneer.ipynb

@@ -153,14 +153,14 @@ def plot_bode_impedance(impedance: DataArray,
     influenced_dofs = impedance.influenced_dof.values
     mag = 20.0 * np.log10(np.abs(impedance))
     phase = np.rad2deg(np.unwrap(np.angle(impedance)))
-    freq = impedance.omega.values/2/np.pi
+    freq = impedance.omega.values/2/np.pi   
     if fig_axes is None:
         fig, axes = plt.subplots(
-            2*len(radiating_dofs),
+            2*len(radiating_dofs), 
             len(influenced_dofs),
-            tight_layout=True,
-            sharex=True,
-            figsize=(3*len(radiating_dofs), 3*len(influenced_dofs)),
+            tight_layout=True, 
+            sharex=True, 
+            figsize=(3*len(radiating_dofs), 3*len(influenced_dofs)), 
             squeeze=False
             )
     else:
@@ -276,7 +276,7 @@ def calculate_power_flows(wec,
     return power_flows
 
 
-def plot_power_flow(power_flows: dict[str, float],
+def plot_power_flow(power_flows: dict[str, float], 
     tolerance: Optional[float] = None,
 )-> tuple(Figure, Axes):
     """Plot power flow through a WEC as Sankey diagram.