capytaine 2.1__cp312-cp312-win_amd64.whl

capytaine/green_functions/delhommeau.py

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+"""Variants of Delhommeau's method for the computation of the Green function."""
+# Copyright (C) 2017-2024 Matthieu Ancellin
+# See LICENSE file at <https://github.com/capytaine/capytaine>
+
+import os
+import logging
+from functools import lru_cache
+from importlib import import_module
+
+import numpy as np
+
+from capytaine.meshes.meshes import Mesh
+from capytaine.meshes.collections import CollectionOfMeshes
+from capytaine.tools.prony_decomposition import exponential_decomposition, error_exponential_decomposition
+from capytaine.tools.cache_on_disk import cache_directory
+
+from capytaine.green_functions.abstract_green_function import AbstractGreenFunction
+
+LOG = logging.getLogger(__name__)
+
+_default_parameters = dict(
+    tabulation_nr=676,
+    tabulation_rmax=100.0,
+    tabulation_nz=372,
+    tabulation_zmin=-251.0,
+    tabulation_nb_integration_points=1000,
+    tabulation_method="scaled_nemoh3",
+    finite_depth_prony_decomposition_method="fortran",
+    floating_point_precision="float64"
+)
+
+
+class Delhommeau(AbstractGreenFunction):
+    """The Green function as implemented in Aquadyn and Nemoh.
+
+    Parameters
+    ----------
+    tabulation_nr: int, optional
+        Number of tabulation points for horizontal coordinate.
+        If 0 is given, no tabulation is used at all.
+        Default: 676
+    tabulation_rmax: float, optional
+        Maximum value of r range for the tabulation. (Minimum is zero.)
+        Only used with the :code:`"scaled_nemoh3"` method.
+        Default: 100.0
+    tabulation_nz: int, optional
+        Number of tabulation points for vertical coordinate.
+        If 0 is given, no tabulation is used at all.
+        Default: 372
+    tabulation_zmin: float, optional
+        Minimum value of z range for the tabulation. (Maximum is zero.)
+        Only used with the :code:`"scaled_nemoh3"` method.
+        Default: -251.0
+    tabulation_nb_integration_points: int, optional
+        Number of points for the numerical integration w.r.t. :math:`theta` of
+        Delhommeau's integrals
+        Default: 1000
+    tabulation_method: string, optional
+        Either :code:`"legacy"` or :code:`"scaled_nemoh3"`, which are the two
+        methods currently implemented.
+        Default: :code:`"scaled_nemoh3"`
+    finite_depth_prony_decomposition_method: string, optional
+        The implementation of the Prony decomposition used to compute the
+        finite water_depth Green function. Accepted values: :code:`'fortran'`
+        for Nemoh's implementation (by default), :code:`'python'` for an
+        experimental Python implementation.
+        See :func:`find_best_exponential_decomposition`.
+    floating_point_precision: string, optional
+        Either :code:`'float32'` for single precision computations or
+        :code:`'float64'` for double precision computations.
+        Default: :code:`'float64'`.
+
+    Attributes
+    ----------
+    fortran_core:
+        Compiled Fortran module with functions used to compute the Green
+        function.
+    tabulation_method_index: int
+        Integer passed to Fortran code to describe which method is used.
+    tabulated_r_range: numpy.array of shape (tabulation_nr,) and type floating_point_precision
+    tabulated_z_range: numpy.array of shape (tabulation_nz,) and type floating_point_precision
+        Coordinates of the tabulation points.
+    tabulated_integrals: numpy.array of shape (tabulation_nr, tabulation_nz, 2, 2) and type floating_point_precision
+        Tabulated Delhommeau integrals.
+    """
+
+    fortran_core_basename = "Delhommeau"
+
+
+    def __init__(self, *,
+                 tabulation_nr=_default_parameters["tabulation_nr"],
+                 tabulation_rmax=_default_parameters["tabulation_rmax"],
+                 tabulation_nz=_default_parameters["tabulation_nz"],
+                 tabulation_zmin=_default_parameters["tabulation_zmin"],
+                 tabulation_nb_integration_points=_default_parameters["tabulation_nb_integration_points"],
+                 tabulation_method=_default_parameters["tabulation_method"],
+                 finite_depth_prony_decomposition_method=_default_parameters["finite_depth_prony_decomposition_method"],
+                 floating_point_precision=_default_parameters["floating_point_precision"],
+                 ):
+
+        self.floating_point_precision = floating_point_precision
+
+        self.fortran_core = import_module(f"capytaine.green_functions.libs.{self.fortran_core_basename}_{self.floating_point_precision}")
+
+        self.tabulation_method = tabulation_method
+        fortran_indices_for_methods = {
+                'legacy': self.fortran_core.delhommeau_integrals.legacy_method,
+                'scaled_nemoh3': self.fortran_core.delhommeau_integrals.scaled_nemoh3_method,
+                              }
+        self.tabulation_method_index = fortran_indices_for_methods[tabulation_method]
+
+        self._create_or_load_tabulation(tabulation_nr, tabulation_rmax, tabulation_nz, tabulation_zmin, tabulation_nb_integration_points)
+
+        self.finite_depth_prony_decomposition_method = finite_depth_prony_decomposition_method
+
+        self.exportable_settings = {
+            'green_function': self.__class__.__name__,
+            'tabulation_nr': tabulation_nr,
+            'tabulation_rmax': tabulation_rmax,
+            'tabulation_nz': tabulation_nz,
+            'tabulation_zmin': tabulation_zmin,
+            'tabulation_nb_integration_points': tabulation_nb_integration_points,
+            'tabulation_method': tabulation_method,
+            'finite_depth_prony_decomposition_method': finite_depth_prony_decomposition_method,
+            'floating_point_precision': floating_point_precision,
+        }
+
+        self._hash = hash(self.exportable_settings.values())
+
+    def __hash__(self):
+        return self._hash
+
+    def __str__(self):
+        # Print only the non-default values.
+        to_be_printed = []
+        for name, value in self.exportable_settings.items():
+            if name in _default_parameters and value != _default_parameters[name]:
+                to_be_printed.append(f"{name}={repr(value)}")
+        return f"{self.__class__.__name__}({', '.join(to_be_printed)})"
+
+    def __repr__(self):
+        # Same as __str__ except all values are printed even when they are the
+        # default value.
+        to_be_printed = []
+        for name, value in self.exportable_settings.items():
+            if name in _default_parameters:
+                to_be_printed.append(f"{name}={repr(value)}")
+        return f"{self.__class__.__name__}({', '.join(to_be_printed)})"
+
+    def _repr_pretty_(self, p, cycle):
+        p.text(self.__repr__())
+
+    def _create_or_load_tabulation(self, tabulation_nr, tabulation_rmax,
+                                   tabulation_nz, tabulation_zmin,
+                                   tabulation_nb_integration_points):
+        """This method either:
+            - loads an existing tabulation saved on disk
+            - generates a new tabulation with the data provided as argument and save it on disk.
+        """
+
+        # Normalize inputs
+        tabulation_rmax = float(tabulation_rmax)
+        tabulation_zmin = float(tabulation_zmin)
+
+        filename = "tabulation_{}_{}_{}_{}_{}_{}_{}_{}.npz".format(
+            self.fortran_core_basename, self.floating_point_precision,
+            self.tabulation_method,
+            tabulation_nr, tabulation_rmax, tabulation_nz, tabulation_zmin,
+            tabulation_nb_integration_points
+        )
+        filepath = os.path.join(cache_directory(), filename)
+
+        if os.path.exists(filepath):
+            LOG.info("Loading tabulation from %s", filepath)
+            loaded_arrays = np.load(filepath)
+            self.tabulated_r_range = loaded_arrays["r_range"]
+            self.tabulated_z_range = loaded_arrays["z_range"]
+            self.tabulated_integrals = loaded_arrays["values"]
+
+        else:
+            LOG.warning("Precomputing tabulation, it may take a few seconds.")
+            self.tabulated_r_range = self.fortran_core.delhommeau_integrals.default_r_spacing(
+                    tabulation_nr, tabulation_rmax, self.tabulation_method_index
+                    )
+            self.tabulated_z_range = self.fortran_core.delhommeau_integrals.default_z_spacing(
+                    tabulation_nz, tabulation_zmin, self.tabulation_method_index
+                    )
+            self.tabulated_integrals = self.fortran_core.delhommeau_integrals.construct_tabulation(
+                    self.tabulated_r_range, self.tabulated_z_range, tabulation_nb_integration_points
+                    )
+            LOG.debug("Saving tabulation in %s", filepath)
+            np.savez_compressed(
+                filepath, r_range=self.tabulated_r_range, z_range=self.tabulated_z_range,
+                values=self.tabulated_integrals
+            )
+
+    @lru_cache(maxsize=128)
+    def find_best_exponential_decomposition(self, dimensionless_omega, dimensionless_wavenumber):
+        """Compute the decomposition of a part of the finite water_depth Green function as a sum of exponential functions.
+
+        Two implementations are available: the legacy Fortran implementation from Nemoh and a newer one written in Python.
+        For some still unexplained reasons, the two implementations do not always give the exact same result.
+        Until the problem is better understood, the Fortran implementation is the default one, to ensure consistency with Nemoh.
+        The Fortran version is also significantly faster...
+
+        Results are cached.
+
+        Parameters
+        ----------
+        dimensionless_omega: float
+            dimensionless angular frequency: :math:`kh \\tanh (kh) = \\omega^2 h/g`
+        dimensionless_wavenumber: float
+            dimensionless wavenumber: :math:`kh`
+        method: string, optional
+            the implementation that should be used to compute the Prony decomposition
+
+        Returns
+        -------
+        Tuple[np.ndarray, np.ndarray]
+            the amplitude and growth rates of the exponentials
+        """
+
+        LOG.debug(f"\tCompute Prony decomposition in finite water_depth Green function "
+                  f"for dimless_omega=%.2e and dimless_wavenumber=%.2e",
+                  dimensionless_omega, dimensionless_wavenumber)
+
+        if self.finite_depth_prony_decomposition_method.lower() == 'python':
+            # The function that will be approximated.
+            @np.vectorize
+            def f(x):
+                return self.fortran_core.initialize_green_wave.ff(x, dimensionless_omega, dimensionless_wavenumber)
+
+            # Try different increasing number of exponentials
+            for n_exp in range(4, 31, 2):
+
+                # The coefficients are computed on a resolution of 4*n_exp+1 ...
+                X = np.linspace(-0.1, 20.0, 4*n_exp+1)
+                a, lamda = exponential_decomposition(X, f(X), n_exp)
+
+                # ... and they are evaluated on a finer discretization.
+                X = np.linspace(-0.1, 20.0, 8*n_exp+1)
+                if error_exponential_decomposition(X, f(X), a, lamda) < 1e-4:
+                    break
+
+            else:
+                LOG.warning("No suitable exponential decomposition has been found"
+                            "for dimless_omega=%.2e and dimless_wavenumber=%.2e",
+                            dimensionless_omega, dimensionless_wavenumber)
+
+        elif self.finite_depth_prony_decomposition_method.lower() == 'fortran':
+            lamda, a, nexp = self.fortran_core.old_prony_decomposition.lisc(dimensionless_omega, dimensionless_wavenumber)
+            lamda = lamda[:nexp]
+            a = a[:nexp]
+
+        else:
+            raise ValueError("Unrecognized method name for the Prony decomposition.")
+
+        # Add one more exponential function (actually a constant).
+        # It is not clear where it comes from exactly in the theory...
+        a = np.concatenate([a, np.array([2])])
+        lamda = np.concatenate([lamda, np.array([0.0])])
+
+        return a, lamda
+
+    def evaluate(self, mesh1, mesh2, free_surface=0.0, water_depth=np.inf, wavenumber=1.0, adjoint_double_layer=True, early_dot_product=True):
+        r"""The main method of the class, called by the engine to assemble the influence matrices.
+
+        Parameters
+        ----------
+        mesh1: Mesh or CollectionOfMeshes or list of points
+            mesh of the receiving body (where the potential is measured)
+            if only S is wanted or early_dot_product is False, then only a list of points as an array of shape (n, 3) can be passed.
+        mesh2: Mesh or CollectionOfMeshes
+            mesh of the source body (over which the source distribution is integrated)
+        free_surface: float, optional
+            position of the free surface (default: :math:`z = 0`)
+        water_depth: float, optional
+            constant depth of water (default: :math:`+\infty`)
+        wavenumber: float, optional
+            wavenumber (default: 1.0)
+        adjoint_double_layer: bool, optional
+            compute double layer for direct method (F) or adjoint double layer for indirect method (T) matrices (default: True)
+        early_dot_product: boolean, optional
+            if False, return K as a (n, m, 3) array storing ∫∇G
+            if True, return K as a (n, m) array storing ∫∇G·n
+
+        Returns
+        -------
+        tuple of numpy arrays
+            the matrices :math:`S` and :math:`K`
+        """
+
+        wavenumber = float(wavenumber)
+
+        if free_surface == np.inf: # No free surface, only a single Rankine source term
+
+            a_exp, lamda_exp = np.empty(1), np.empty(1)  # Dummy arrays that won't actually be used by the fortran code.
+
+            coeffs = np.array((1.0, 0.0, 0.0))
+
+        elif water_depth == np.inf:
+
+            a_exp, lamda_exp = np.empty(1), np.empty(1)  # Idem
+
+            if wavenumber == 0.0:
+                coeffs = np.array((1.0, 1.0, 0.0))
+            elif wavenumber == np.inf:
+                coeffs = np.array((1.0, -1.0, 0.0))
+            else:
+                coeffs = np.array((1.0, 1.0, 1.0))
+
+        else:  # Finite water_depth
+            if wavenumber == 0.0 or wavenumber == np.inf:
+                raise NotImplementedError("Zero or infinite frequencies not implemented for finite depth.")
+            else:
+                a_exp, lamda_exp = self.find_best_exponential_decomposition(
+                    wavenumber*water_depth*np.tanh(wavenumber*water_depth),
+                    wavenumber*water_depth,
+                )
+                coeffs = np.array((1.0, 1.0, 1.0))
+
+        if isinstance(mesh1, Mesh) or isinstance(mesh1, CollectionOfMeshes):
+            collocation_points = mesh1.faces_centers
+            nb_collocation_points = mesh1.nb_faces
+            if ( adjoint_double_layer == False ):
+                early_dot_product_normals = np.zeros((nb_collocation_points, 3))  # Should not be used
+            else:
+                early_dot_product_normals = mesh1.faces_normals
+        elif isinstance(mesh1, np.ndarray) and mesh1.ndim ==2 and mesh1.shape[1] == 3:
+            # This is used when computing potential or velocity at given points in postprocessing
+            collocation_points = mesh1
+            nb_collocation_points = mesh1.shape[0]
+            early_dot_product_normals = np.zeros((nb_collocation_points, 3))  # Should not be used
+            if ( adjoint_double_layer == False ):
+                raise NotImplementedError("Using a list of points as collocation points is not supported in computing adjoint double layer matrices.")
+        else:
+            raise ValueError(f"Unrecognized input for {self.__class__.__name__}.evaluate")
+
+        if self.floating_point_precision == "float32":
+            dtype = "complex64"
+        elif self.floating_point_precision == "float64":
+            dtype = "complex128"
+        else:
+            raise NotImplementedError
+
+        S = np.empty((nb_collocation_points, mesh2.nb_faces), order="F", dtype=dtype)
+        K = np.empty((nb_collocation_points, mesh2.nb_faces, 1 if early_dot_product else 3), order="F", dtype=dtype)
+
+        # Main call to Fortran code
+        self.fortran_core.matrices.build_matrices(
+            collocation_points,  early_dot_product_normals,
+            mesh2.vertices,      mesh2.faces + 1,
+            mesh2.faces_centers, mesh2.faces_normals,
+            mesh2.faces_areas,   mesh2.faces_radiuses,
+            *mesh2.quadrature_points,
+            wavenumber, water_depth,
+            coeffs,
+            self.tabulation_method_index, self.tabulated_r_range, self.tabulated_z_range, self.tabulated_integrals,
+            lamda_exp, a_exp,
+            mesh1 is mesh2, adjoint_double_layer,
+            S, K
+        )
+
+        if np.any(np.isnan(S)) or np.any(np.isnan(K)):
+            raise RuntimeError("Green function returned a NaN in the interaction matrix.\n"
+                    "It could be due to overlapping panels.")
+
+        if early_dot_product: K = K.reshape((nb_collocation_points, mesh2.nb_faces))
+
+        return S, K
+
+################################
+
+class XieDelhommeau(Delhommeau):
+    """Variant of Nemoh's Green function, more accurate near the free surface.
+
+    Same arguments and methods as :class:`Delhommeau`.
+    """
+
+    fortran_core_basename = "XieDelhommeau"

capytaine/io/bemio.py

@@ -0,0 +1,141 @@
+import logging
+
+import numpy as np
+import pandas as pd
+from scipy.optimize import newton
+
+LOG = logging.getLogger(__name__)
+
+#######################
+#  Import from Bemio  #
+#######################
+
+def dataframe_from_bemio(bemio_obj, wavenumber, wavelength):
+    """Transform a :class:`bemio.data_structures.bem.HydrodynamicData` into a
+        :class:`pandas.DataFrame`.
+
+        Parameters
+        ----------
+        bemio_obj: Bemio data_stuctures.bem.HydrodynamicData class
+            Loaded NEMOH, AQWA, or WAMIT data created using `bemio.io.nemoh.read`,
+            `bemio.io.aqwa.read`, or `bemio.io.wamit.read` functions, respectively.
+        wavenumber: bool
+            If True, the coordinate 'wavenumber' will be added to the output dataset.
+        wavelength: bool
+            If True, the coordinate 'wavelength' will be added to the output dataset.
+        """
+
+
+    dofs = np.array(['Surge', 'Sway', 'Heave', 'Roll', 'Pitch', 'Yaw'])
+    for i in range(bemio_obj.body[0].num_bodies):
+        difr_dict = []
+        rad_dict = []
+
+        rho = bemio_obj.body[0].rho
+        g = bemio_obj.body[0].g
+
+        if bemio_obj.body[i].water_depth == 'infinite':
+            bemio_obj.body[i].water_depth = np.inf
+
+        if bemio_obj.body[i].bem_code == 'WAMIT': # WAMIT coefficients need to be dimensionalized
+            from_wamit = True
+
+        for omega_idx, omega in enumerate(np.sort(bemio_obj.body[i].w)):
+
+            # DiffractionProblem variable equivalents
+            for dir_idx, dir in enumerate(bemio_obj.body[i].wave_dir):
+                temp_dict = {}
+                temp_dict['body_name'] = bemio_obj.body[i].name
+                temp_dict['water_depth'] = bemio_obj.body[i].water_depth
+                temp_dict['omega'] = omega
+                temp_dict['period'] = 2*np.pi/omega
+                temp_dict['rho'] = rho
+                temp_dict['g'] = g
+                temp_dict['forward_speed'] = 0.0
+                temp_dict['wave_direction'] = np.radians(dir)
+                temp_dict['influenced_dof'] = dofs
+
+                if wavenumber or wavelength:
+                    if temp_dict['water_depth'] == np.inf or omega**2*temp_dict['water_depth']/temp_dict['g'] > 20:
+                        k = omega**2/temp_dict['g']
+                    else:
+                        k = newton(lambda x: x*np.tanh(x) - omega**2*temp_dict['water_depth']/temp_dict['g'], x0=1.0)/temp_dict['water_depth']
+
+                    if wavenumber:
+                        temp_dict['wavenumber'] = k
+
+                    if wavelength:
+                        if k == 0.0:
+                            temp_dict['wavelength'] = np.inf
+                        else:
+                            temp_dict['wavelength'] = 2*np.pi/k
+
+                Fexc = np.empty(shape=bemio_obj.body[i].ex.re[:, dir_idx, omega_idx].shape, dtype=np.complex128)
+                if from_wamit:
+                    Fexc.real = bemio_obj.body[i].ex.re[:, dir_idx, omega_idx] * rho * g
+                    Fexc.imag = bemio_obj.body[i].ex.im[:, dir_idx, omega_idx] * rho * g
+                else:
+                    Fexc.real = bemio_obj.body[i].ex.re[:, dir_idx, omega_idx]
+                    Fexc.imag = bemio_obj.body[i].ex.im[:, dir_idx, omega_idx]
+                temp_dict['diffraction_force'] = Fexc.flatten()
+
+                try:
+                    Fexc_fk = np.empty(shape=bemio_obj.body[i].ex.fk.re[:, dir_idx, omega_idx].shape, dtype=np.complex128)
+                    if from_wamit:
+                        Fexc_fk.real = bemio_obj.body[i].ex.fk.re[:, dir_idx, omega_idx] * rho * g
+                        Fexc_fk.imag = bemio_obj.body[i].ex.fk.im[:, dir_idx, omega_idx] * rho * g
+                    else:
+                        Fexc_fk.real = bemio_obj.body[i].ex.fk.re[:, dir_idx, omega_idx]
+                        Fexc_fk.imag = bemio_obj.body[i].ex.fk.im[:, dir_idx, omega_idx]
+                    temp_dict['Froude_Krylov_force'] = Fexc_fk.flatten()
+
+                except AttributeError:
+                        # LOG.warning('\tNo Froude-Krylov forces found for ' + bemio_obj.body[i].name + ' at ' + str(dir) + \
+                        #       ' degrees (omega = ' + str(omega) + '), replacing with zeros.')
+                        temp_dict['Froude_Krylov_force'] = np.zeros((bemio_obj.body[i].ex.re[:, dir_idx, omega_idx].size,), dtype=np.complex128)
+
+                difr_dict.append(temp_dict)
+
+            # RadiationProblem + Hydrostatics variable equivalents
+            for radiating_dof_idx, radiating_dof in enumerate(dofs):
+                temp_dict = {}
+                temp_dict['body_name'] = bemio_obj.body[i].name
+                temp_dict['water_depth'] = bemio_obj.body[i].water_depth
+                temp_dict['omega'] = omega
+                temp_dict['rho'] = rho
+                temp_dict['g'] = g
+                temp_dict['forward_speed'] = 0.0
+                temp_dict['wave_direction'] = 0.0
+                temp_dict['influenced_dof'] = dofs
+                temp_dict['radiating_dof'] = radiating_dof
+                temp_dict['added_mass'] = bemio_obj.body[i].am.all[radiating_dof_idx, :, omega_idx].flatten()
+                temp_dict['radiation_damping'] = bemio_obj.body[i].rd.all[radiating_dof_idx, :, omega_idx].flatten()
+
+                if from_wamit:
+                    temp_dict['added_mass'] = temp_dict['added_mass'] * rho
+                    temp_dict['radiation_damping'] = temp_dict['radiation_damping'] * rho * omega
+
+                if wavenumber or wavelength:
+                    if temp_dict['water_depth'] == np.inf or omega**2*temp_dict['water_depth']/temp_dict['g'] > 20:
+                        k = omega**2/temp_dict['g']
+                    else:
+                        k = newton(lambda x: x*np.tanh(x) - omega**2*temp_dict['water_depth']/temp_dict['g'], x0=1.0)/temp_dict['water_depth']
+
+                    if wavenumber:
+                        temp_dict['wavenumber'] = k
+
+                    if wavelength:
+                        if k == 0.0:
+                            temp_dict['wavelength'] = np.inf
+                        else:
+                            temp_dict['wavelength'] = 2*np.pi/k
+
+                rad_dict.append(temp_dict)
+
+    df = pd.concat([
+        pd.DataFrame.from_dict(difr_dict).explode(['influenced_dof', 'diffraction_force', 'Froude_Krylov_force']),
+        pd.DataFrame.from_dict(rad_dict).explode(['influenced_dof', 'added_mass', 'radiation_damping'])
+        ])
+    df = df.astype({'added_mass': np.float64, 'radiation_damping': np.float64, 'diffraction_force': np.complex128, 'Froude_Krylov_force': np.complex128})
+
+    return df