capytaine 2.1__cp312-cp312-win_amd64.whl

capytaine/bodies/bodies.py

@@ -0,0 +1,1084 @@
+"""Floating bodies to be used in radiation-diffraction problems."""
+# Copyright (C) 2017-2019 Matthieu Ancellin
+# See LICENSE file at <https://github.com/mancellin/capytaine>
+
+import logging
+import copy
+from itertools import chain, accumulate, zip_longest
+
+import numpy as np
+import xarray as xr
+
+from capytaine.tools.optional_imports import silently_import_optional_dependency
+meshio = silently_import_optional_dependency("meshio")
+
+from capytaine.meshes.geometry import Abstract3DObject, ClippableMixin, Plane, inplace_transformation
+from capytaine.meshes.meshes import Mesh
+from capytaine.meshes.symmetric import build_regular_array_of_meshes
+from capytaine.meshes.collections import CollectionOfMeshes
+from capytaine.bodies.dofs import RigidBodyDofsPlaceholder
+
+LOG = logging.getLogger(__name__)
+
+TRANSLATION_DOFS_DIRECTIONS = {"surge": (1, 0, 0), "sway": (0, 1, 0), "heave": (0, 0, 1)}
+ROTATION_DOFS_AXIS = {"roll": (1, 0, 0), "pitch": (0, 1, 0), "yaw": (0, 0, 1)}
+
+
+class FloatingBody(ClippableMixin, Abstract3DObject):
+    """A floating body described as a mesh and some degrees of freedom.
+
+    The mesh structure is stored as a Mesh from capytaine.mesh.mesh or a
+    CollectionOfMeshes from capytaine.mesh.meshes_collection.
+
+    The degrees of freedom (dofs) are stored as a dict associating a name to
+    a complex-valued array of shape (nb_faces, 3). To each face of the body
+    (as indexed in the mesh) corresponds a complex-valued 3d vector, which
+    defines the displacement of the center of the face in frequency domain.
+
+    Parameters
+    ----------
+    mesh : Mesh or CollectionOfMeshes, optional
+        the mesh describing the geometry of the floating body.
+        If none is given, a empty one is created.
+    dofs : dict, optional
+        the degrees of freedom of the body.
+        If none is given, a empty dictionary is initialized.
+    mass : float or None, optional
+        the mass of the body in kilograms.
+        Required only for some hydrostatics computation.
+        If None, the mass is implicitly assumed to be the mass of displaced water.
+    center_of_mass: 3-element array, optional
+        the position of the center of mass.
+        Required only for some hydrostatics computation.
+    name : str, optional
+        a name for the body.
+        If none is given, the one of the mesh is used.
+    """
+
+    def __init__(self, mesh=None, dofs=None, mass=None, center_of_mass=None, name=None):
+        if mesh is None:
+            self.mesh = Mesh(name="dummy_mesh")
+
+        elif meshio is not None and isinstance(mesh, meshio._mesh.Mesh):
+            from capytaine.io.meshio import load_from_meshio
+            self.mesh = load_from_meshio(mesh)
+
+        elif isinstance(mesh, Mesh) or isinstance(mesh, CollectionOfMeshes):
+            self.mesh = mesh
+
+        else:
+            raise TypeError("Unrecognized `mesh` object passed to the FloatingBody constructor.")
+
+        if name is None and mesh is None:
+            self.name = "dummy_body"
+        elif name is None:
+            self.name = self.mesh.name
+        else:
+            self.name = name
+
+        self.mass = mass
+        if center_of_mass is not None:
+            self.center_of_mass = np.asarray(center_of_mass, dtype=float)
+        else:
+            self.center_of_mass = None
+
+        if self.mesh.nb_vertices > 0 and self.mesh.nb_faces > 0:
+            self.mesh.heal_mesh()
+
+        if dofs is None:
+            self.dofs = {}
+        elif isinstance(dofs, RigidBodyDofsPlaceholder):
+            if dofs.rotation_center is not None:
+                self.rotation_center = np.asarray(dofs.rotation_center, dtype=float)
+            self.dofs = {}
+            self.add_all_rigid_body_dofs()
+        else:
+            self.dofs = dofs
+
+        LOG.info(f"New floating body: {self.__str__()}.")
+
+    @staticmethod
+    def from_meshio(mesh, name=None) -> 'FloatingBody':
+        """Create a FloatingBody from a meshio mesh object."""
+        from capytaine.io.meshio import load_from_meshio
+        return FloatingBody(mesh=load_from_meshio(mesh, name), name=name)
+
+    @staticmethod
+    def from_file(filename: str, file_format=None, name=None) -> 'FloatingBody':
+        """Create a FloatingBody from a mesh file using meshmagick."""
+        from capytaine.io.mesh_loaders import load_mesh
+        if name is None: name = filename
+        mesh = load_mesh(filename, file_format, name=f"{name}_mesh")
+        return FloatingBody(mesh, name=name)
+
+    def __lt__(self, other: 'FloatingBody') -> bool:
+        """Arbitrary order. The point is to sort together the problems involving the same body."""
+        return self.name < other.name
+
+    ##########
+    #  Dofs  #
+    ##########
+
+    @property
+    def nb_dofs(self) -> int:
+        """Number of degrees of freedom."""
+        return len(self.dofs)
+
+    def add_translation_dof(self, direction=None, name=None, amplitude=1.0) -> None:
+        """Add a new translation dof (in place).
+        If no direction is given, the code tries to infer it from the name.
+
+        Parameters
+        ----------
+        direction : array of shape (3,), optional
+            the direction of the translation
+        name : str, optional
+            a name for the degree of freedom
+        amplitude : float, optional
+            amplitude of the dof (default: 1.0 m/s)
+        """
+        if direction is None:
+            if name is not None and name.lower() in TRANSLATION_DOFS_DIRECTIONS:
+                direction = TRANSLATION_DOFS_DIRECTIONS[name.lower()]
+            else:
+                raise ValueError("A direction needs to be specified for the dof.")
+
+        if name is None:
+            name = f"dof_{self.nb_dofs}_translation"
+
+        direction = np.asarray(direction)
+        assert direction.shape == (3,)
+
+        motion = np.empty((self.mesh.nb_faces, 3))
+        motion[:, :] = direction
+        self.dofs[name] = amplitude * motion
+
+    def add_rotation_dof(self, axis=None, name=None, amplitude=1.0) -> None:
+        """Add a new rotation dof (in place).
+        If no axis is given, the code tries to infer it from the name.
+
+        Parameters
+        ----------
+        axis: Axis, optional
+            the axis of the rotation
+        name : str, optional
+            a name for the degree of freedom
+        amplitude : float, optional
+            amplitude of the dof (default: 1.0)
+        """
+        if axis is None:
+            if name is not None and name.lower() in ROTATION_DOFS_AXIS:
+                axis_direction = ROTATION_DOFS_AXIS[name.lower()]
+                for point_attr in ('rotation_center', 'center_of_mass', 'geometric_center'):
+                    if hasattr(self, point_attr) and getattr(self, point_attr) is not None:
+                        axis_point = getattr(self, point_attr)
+                        LOG.info(f"The rotation dof {name} has been initialized around the point: "
+                                 f"FloatingBody(..., name={self.name}).{point_attr} = {getattr(self, point_attr)}")
+                        break
+                else:
+                    axis_point = np.array([0, 0, 0])
+                    LOG.warning(f"The rotation dof {name} has been initialized "
+                                f"around the origin of the domain (0, 0, 0).")
+            else:
+                raise ValueError("A direction needs to be specified for the dof.")
+        else:
+            axis_point = axis.point
+            axis_direction = axis.vector
+
+        if name is None:
+            name = f"dof_{self.nb_dofs}_rotation"
+
+        if self.mesh.nb_faces == 0:
+            self.dofs[name] = np.empty((self.mesh.nb_faces, 3))
+        else:
+            motion = np.cross(axis_point - self.mesh.faces_centers, axis_direction)
+            self.dofs[name] = amplitude * motion
+
+    def add_all_rigid_body_dofs(self) -> None:
+        """Add the six degrees of freedom of rigid bodies (in place)."""
+        self.add_translation_dof(name="Surge")
+        self.add_translation_dof(name="Sway")
+        self.add_translation_dof(name="Heave")
+        self.add_rotation_dof(name="Roll")
+        self.add_rotation_dof(name="Pitch")
+        self.add_rotation_dof(name="Yaw")
+
+    def integrate_pressure(self, pressure):
+        forces = {}
+        for dof_name in self.dofs:
+            # Scalar product on each face:
+            normal_dof_amplitude_on_face = - np.sum(self.dofs[dof_name] * self.mesh.faces_normals, axis=1)
+            # The minus sign in the above line is because we want the force of the fluid on the body and not the force of the body on the fluid.
+            # Sum over all faces:
+            forces[dof_name] = np.sum(pressure * normal_dof_amplitude_on_face * self.mesh.faces_areas)
+        return forces
+
+    @inplace_transformation
+    def keep_only_dofs(self, dofs):
+        for dof in list(self.dofs.keys()):
+            if dof not in dofs:
+                del self.dofs[dof]
+
+        if hasattr(self, 'inertia_matrix'):
+            self.inertia_matrix = self.inertia_matrix.sel(radiating_dof=dofs, influenced_dof=dofs)
+        if hasattr(self, 'hydrostatic_stiffness'):
+            self.hydrostatic_stiffness = self.hydrostatic_stiffness.sel(radiating_dof=dofs, influenced_dof=dofs)
+
+        return self
+
+    def add_dofs_labels_to_vector(self, vector):
+        """Helper function turning a bare vector into a vector labelled by the name of the dofs of the body,
+        to be used for instance for the computation of RAO."""
+        return xr.DataArray(data=np.asarray(vector), dims=['influenced_dof'],
+                            coords={'influenced_dof': list(self.dofs)},
+                            )
+
+    def add_dofs_labels_to_matrix(self, matrix):
+        """Helper function turning a bare matrix into a matrix labelled by the name of the dofs of the body,
+        to be used for instance for the computation of RAO."""
+        return xr.DataArray(data=np.asarray(matrix), dims=['influenced_dof', 'radiating_dof'],
+                            coords={'influenced_dof': list(self.dofs), 'radiating_dof': list(self.dofs)},
+                            )
+
+    ###################
+    # Hydrostatics #
+    ###################
+
+    def surface_integral(self, data, **kwargs):
+        """Returns integral of given data along wet surface area."""
+        return self.mesh.surface_integral(data, **kwargs)
+
+    def waterplane_integral(self, data, **kwargs):
+        """Returns integral of given data along water plane area."""
+        return self.mesh.waterplane_integral(data, **kwargs)
+
+    @property
+    def wet_surface_area(self):
+        """Returns wet surface area."""
+        return self.mesh.wet_surface_area
+
+    @property
+    def volumes(self):
+        """Returns volumes using x, y, z components of the FloatingBody."""
+        return self.mesh.volumes
+
+    @property
+    def volume(self):
+        """Returns volume of the FloatingBody."""
+        return self.mesh.volume
+
+    def disp_mass(self, *, rho=1000):
+        return self.mesh.disp_mass(rho=rho)
+
+    @property
+    def center_of_buoyancy(self):
+        """Returns center of buoyancy of the FloatingBody."""
+        return self.mesh.center_of_buoyancy
+
+    @property
+    def waterplane_area(self):
+        """Returns water plane area of the FloatingBody."""
+        return self.mesh.waterplane_area
+
+    @property
+    def waterplane_center(self):
+        """Returns water plane center of the FloatingBody.
+
+        Note: Returns None if the FloatingBody is full submerged.
+        """
+        return self.mesh.waterplane_center
+
+    @property
+    def transversal_metacentric_radius(self):
+        """Returns transversal metacentric radius of the mesh."""
+        inertia_moment = -self.waterplane_integral(self.mesh.faces_centers[:,1]**2)
+        return inertia_moment / self.volume
+
+    @property
+    def longitudinal_metacentric_radius(self):
+        """Returns longitudinal metacentric radius of the mesh."""
+        inertia_moment = -self.waterplane_integral(self.mesh.faces_centers[:,0]**2)
+        return inertia_moment / self.volume
+
+    @property
+    def transversal_metacentric_height(self):
+        """Returns transversal metacentric height of the mesh."""
+        gb = self.center_of_mass - self.center_of_buoyancy
+        return self.transversal_metacentric_radius - gb[2]
+
+    @property
+    def longitudinal_metacentric_height(self):
+        """Returns longitudinal metacentric height of the mesh."""
+        gb = self.center_of_mass - self.center_of_buoyancy
+        return self.longitudinal_metacentric_radius - gb[2]
+
+    def dof_normals(self, dof):
+        """Returns dot product of the surface face normals and DOF"""
+        return np.sum(self.mesh.faces_normals * dof, axis=1)
+
+    def _infer_rotation_center(self):
+        """Hacky way to infer the point around which the rotation dofs are defined.
+        (Assuming all three rotation dofs are defined around the same point).
+        In the future, should be replaced by something more robust.
+        """
+        if hasattr(self, "rotation_center"):
+            return np.asarray(self.rotation_center)
+
+        else:
+            try:
+                xc1 = self.dofs["Pitch"][:, 2] + self.mesh.faces_centers[:, 0]
+                xc2 = -self.dofs["Yaw"][:, 1] + self.mesh.faces_centers[:, 0]
+                yc1 = self.dofs["Yaw"][:, 0] + self.mesh.faces_centers[:, 1]
+                yc2 = -self.dofs["Roll"][:, 2] + self.mesh.faces_centers[:, 1]
+                zc1 = -self.dofs["Pitch"][:, 0] + self.mesh.faces_centers[:, 2]
+                zc2 = self.dofs["Roll"][:, 1] + self.mesh.faces_centers[:, 2]
+
+                # All items should be identical in a given vector
+                assert np.isclose(xc1, xc1[0]).all()
+                assert np.isclose(yc1, yc1[0]).all()
+                assert np.isclose(zc1, zc1[0]).all()
+
+                # Both vector should be identical
+                assert np.allclose(xc1, xc2)
+                assert np.allclose(yc1, yc2)
+                assert np.allclose(zc1, zc2)
+
+                return np.array([xc1[0], yc1[0], zc1[0]])
+
+            except Exception as e:
+                raise ValueError(
+                        f"Failed to infer the rotation center of {self.name} to compute rigid body hydrostatics.\n"
+                        f"Possible fix: add a `rotation_center` attribute to {self.name}.\n"
+                        "Note that rigid body hydrostatic methods currently assume that the three rotation dofs have the same rotation center."
+                        ) from e
+
+    def each_hydrostatic_stiffness(self, influenced_dof_name, radiating_dof_name, *,
+                                         influenced_dof_div=0.0, rho=1000.0, g=9.81):
+        r"""
+        Return the hydrostatic stiffness for a pair of DOFs.
+
+        :math:`C_{ij} = \rho g\iint_S (\hat{n} \cdot V_j) (w_i + z D_i) dS`
+
+        where :math:`\hat{n}` is surface normal,
+
+        :math:`V_i = u_i \hat{n}_x + v_i \hat{n}_y + w_i \hat{n}_z` is DOF vector and
+
+        :math:`D_i = \nabla \cdot V_i` is the divergence of the DOF.
+
+        Parameters
+        ----------
+        influenced_dof_name : str
+            Name of influenced DOF vector of the FloatingBody
+        radiating_dof_name: str
+            Name of radiating DOF vector of the FloatingBody
+        influenced_dof_div: np.ndarray (Face_count), optional
+            Influenced DOF divergence of the FloatingBody, by default 0.0.
+        rho: float, optional
+            water density, by default 1000.0
+        g: float, optional
+            Gravity acceleration, by default 9.81
+
+        Returns
+        -------
+        hs_ij: xarray.variable
+            hydrostatic_stiffness of ith DOF and jth DOF.
+
+        Note
+        ----
+            This function computes the hydrostatic stiffness assuming :math:`D_{i} = 0`.
+            If :math:`D_i \neq 0`, input the divergence interpolated to face centers.
+
+            General integral equations are used for the rigid body modes and
+            Neumann (1994) method is used for flexible modes.
+
+        References
+        ----------
+            Newman, John Nicholas. "Wave effects on deformable bodies."Applied ocean
+            research" 16.1 (1994): 47-59.
+            http://resolver.tudelft.nl/uuid:0adff84c-43c7-43aa-8cd8-d4c44240bed8
+
+        """
+        # Newman (1994) formula is not 'complete' as recovering the rigid body
+        # terms is not possible. https://doi.org/10.1115/1.3058702.
+
+        # Alternative is to use the general equation of hydrostatic and
+        # restoring coefficient for rigid modes and use Newman equation for elastic
+        # modes.
+
+        rigid_dof_names = ("Surge", "Sway", "Heave", "Roll", "Pitch", "Yaw")
+        dof_pair = (influenced_dof_name, radiating_dof_name)
+
+        if set(dof_pair).issubset(set(rigid_dof_names)):
+            if self.center_of_mass is None:
+                raise ValueError(f"Trying to compute rigid-body hydrostatic stiffness for {self.name}, but no center of mass has been defined.\n"
+                                 f"Suggested solution: define a `center_of_mass` attribute for the FloatingBody {self.name}.")
+            mass = self.disp_mass(rho=rho) if self.mass is None else self.mass
+            xc, yc, zc = self._infer_rotation_center()
+
+            if dof_pair == ("Heave", "Heave"):
+                norm_hs_stiff = self.waterplane_area
+            elif dof_pair in [("Heave", "Roll"), ("Roll", "Heave")]:
+                norm_hs_stiff = -self.waterplane_integral(self.mesh.faces_centers[:,1] - yc)
+            elif dof_pair in [("Heave", "Pitch"), ("Pitch", "Heave")]:
+                norm_hs_stiff = self.waterplane_integral(self.mesh.faces_centers[:,0] - xc)
+            elif dof_pair == ("Roll", "Roll"):
+                norm_hs_stiff = (
+                        -self.waterplane_integral((self.mesh.faces_centers[:,1] - yc)**2)
+                        + self.volume*(self.center_of_buoyancy[2] - zc) - mass/rho*(self.center_of_mass[2] - zc)
+                )
+            elif dof_pair in [("Roll", "Pitch"), ("Pitch", "Roll")]:
+                norm_hs_stiff = self.waterplane_integral((self.mesh.faces_centers[:,0] - xc)
+                                                          * (self.mesh.faces_centers[:,1] - yc))
+            elif dof_pair == ("Roll", "Yaw"):
+                norm_hs_stiff = - self.volume*(self.center_of_buoyancy[0] - xc) + mass/rho*(self.center_of_mass[0] - xc)
+            elif dof_pair == ("Pitch", "Pitch"):
+                norm_hs_stiff = (
+                        -self.waterplane_integral((self.mesh.faces_centers[:,0] - xc)**2)
+                        + self.volume*(self.center_of_buoyancy[2] - zc) - mass/rho*(self.center_of_mass[2] - zc)
+                        )
+            elif dof_pair == ("Pitch", "Yaw"):
+                norm_hs_stiff = - self.volume*(self.center_of_buoyancy[1] - yc) + mass/rho*(self.center_of_mass[1] - yc)
+            else:
+                norm_hs_stiff = 0.0
+        else:
+            if self.mass is not None and not np.isclose(self.mass, self.disp_mass(rho=rho), rtol=1e-4):
+                raise NotImplementedError(
+                        f"Trying to compute the hydrostatic stiffness for dofs {radiating_dof_name} and {influenced_dof_name}"
+                        f"of body {self.name}, which is not neutrally buoyant (mass={self.mass}, disp_mass={self.disp_mass(rho=rho)}).\n"
+                        f"This case has not been implemented in Capytaine. You need either a single rigid body or a neutrally buoyant body."
+                        )
+
+            # Newman (1994) formula for flexible DOFs
+            influenced_dof = np.array(self.dofs[influenced_dof_name])
+            radiating_dof = np.array(self.dofs[radiating_dof_name])
+            influenced_dof_div_array = np.array(influenced_dof_div)
+
+            radiating_dof_normal = self.dof_normals(radiating_dof)
+            z_influenced_dof_div = influenced_dof[:,2] + self.mesh.faces_centers[:,2] * influenced_dof_div_array
+            norm_hs_stiff = self.surface_integral( -radiating_dof_normal * z_influenced_dof_div)
+
+        hs_stiff = rho * g * norm_hs_stiff
+
+        return xr.DataArray([[hs_stiff]],
+                            dims=['influenced_dof', 'radiating_dof'],
+                            coords={'influenced_dof': [influenced_dof_name],
+                            'radiating_dof': [radiating_dof_name]},
+                            name="hydrostatic_stiffness"
+                            )
+
+    def compute_hydrostatic_stiffness(self, *, divergence=None, rho=1000.0, g=9.81):
+        r"""
+        Compute hydrostatic stiffness matrix for all DOFs of the body.
+
+        :math:`C_{ij} = \rho g\iint_S (\hat{n} \cdot V_j) (w_i + z D_i) dS`
+
+        where :math:`\hat{n}` is surface normal,
+
+        :math:`V_i = u_i \hat{n}_x + v_i \hat{n}_y + w_i \hat{n}_z` is DOF vector and
+
+        :math:`D_i = \nabla \cdot V_i` is the divergence of the DOF.
+
+        Parameters
+        ----------
+        divergence : dict mapping a dof name to an array of shape (nb_faces) or
+                        xarray.DataArray of shape (nb_dofs × nb_faces), optional
+            Divergence of the DOFs, by default None
+        rho : float, optional
+            Water density, by default 1000.0
+        g: float, optional
+            Gravity acceleration, by default 9.81
+
+        Returns
+        -------
+        xr.DataArray
+            Matrix of hydrostatic stiffness
+
+        Note
+        ----
+            This function computes the hydrostatic stiffness assuming :math:`D_{i} = 0`.
+            If :math:`D_i \neq 0`, input the divergence interpolated to face centers.
+
+            General integral equations are used for the rigid body modes and
+            Neumann (1994) method is used for flexible modes.
+
+        References
+        ----------
+            Newman, John Nicholas. "Wave effects on deformable bodies."Applied ocean
+            research" 16.1 (1994): 47-59.
+            http://resolver.tudelft.nl/uuid:0adff84c-43c7-43aa-8cd8-d4c44240bed8
+
+        """
+        if len(self.dofs) == 0:
+            raise AttributeError("Cannot compute hydrostatics stiffness on {} since no dof has been defined.".format(self.name))
+
+        def divergence_dof(influenced_dof):
+            if divergence is None:
+                return 0.0
+            elif isinstance(divergence, dict) and influenced_dof in divergence.keys():
+                return divergence[influenced_dof]
+            elif isinstance(divergence, xr.DataArray) and influenced_dof in divergence.coords["influenced_dof"]:
+                return divergence.sel(influenced_dof=influenced_dof).values
+            else:
+                LOG.warning("Computing hydrostatic stiffness without the divergence of {}".format(influenced_dof))
+                return 0.0
+
+        hs_set =  xr.merge([
+            self.each_hydrostatic_stiffness(
+                influenced_dof_name, radiating_dof_name,
+                influenced_dof_div = divergence_dof(influenced_dof_name),
+                rho=rho, g=g
+                )
+            for radiating_dof_name in self.dofs
+            for influenced_dof_name in self.dofs
+            ])
+
+        # Reorder dofs
+        K = hs_set.hydrostatic_stiffness.sel(influenced_dof=list(self.dofs.keys()), radiating_dof=list(self.dofs.keys()))
+        return K
+
+    def compute_rigid_body_inertia(self, *, rho=1000, output_type="body_dofs"):
+        """
+        Inertia Mass matrix of the body for 6 rigid DOFs.
+
+        Parameters
+        ----------
+        rho : float, optional
+            Density of water, by default 1000.0
+        output_type : {"body_dofs", "rigid_dofs", "all_dofs"}
+            Type of DOFs for mass mat output, by default "body_dofs".
+
+        Returns
+        -------
+        xarray.DataArray
+            Inertia matrix
+
+        Raises
+        ------
+        ValueError
+            If output_type is not in {"body_dofs", "rigid_dofs", "all_dofs"}.
+        """
+        if self.center_of_mass is None:
+            raise ValueError(f"Trying to compute rigid-body inertia matrix for {self.name}, but no center of mass has been defined.\n"
+                             f"Suggested solution: define a `center_of_mass` attribute for the FloatingBody {self.name}.")
+
+        rc = self._infer_rotation_center()
+        fcs = (self.mesh.faces_centers - rc).T
+        combinations = np.array([fcs[0]**2, fcs[1]**2, fcs[2]**2, fcs[0]*fcs[1],
+                                 fcs[1]*fcs[2], fcs[2]*fcs[0]])
+        integrals = np.array([
+            [np.sum(normal_i * fcs[axis] * combination * self.mesh.faces_areas)
+            for combination in combinations]
+            for axis, normal_i in enumerate(self.mesh.faces_normals.T)])
+
+
+        inertias = np.array([
+            (integrals[0,1]   + integrals[0,2]   + integrals[1,1]/3
+             + integrals[1,2]   + integrals[2,1] + integrals[2,2]/3)/3,
+            (integrals[0,0]/3 + integrals[0,2]   + integrals[1,0]
+             + integrals[1,2]   + integrals[2,0] + integrals[2,2]/3)/3,
+            (integrals[0,0]/3 + integrals[0,1]   + integrals[1,0]
+             + integrals[1,1]/3 + integrals[2,0] + integrals[2,1]  )/3,
+            integrals[2,3],
+            integrals[0,4],
+            integrals[1,5]
+        ])
+
+        cog = self.center_of_mass - rc
+        volume = self.volume
+        volumic_inertia_matrix = np.array([
+            [ volume        , 0              , 0               ,
+              0             , volume*cog[2]  , -volume*cog[1]  ],
+            [ 0             , volume         , 0               ,
+             -volume*cog[2] , 0              , volume*cog[0]   ],
+            [ 0             , 0              , volume          ,
+              volume*cog[1] , -volume*cog[0] , 0 ]             ,
+            [ 0             , -volume*cog[2] , volume*cog[1]   ,
+              inertias[0]   , -inertias[3]   , -inertias[5]    ],
+            [ volume*cog[2] , 0              , -volume*cog[0]  ,
+             -inertias[3]   , inertias[1]    , -inertias[4]    ],
+            [-volume*cog[1] , volume*cog[0]  , 0               ,
+             -inertias[5]   , -inertias[4]   , inertias[2]     ],
+        ])
+
+        density = rho if self.mass is None else self.mass/volume
+        inertia_matrix = density * volumic_inertia_matrix
+
+        # Rigid DOFs
+        rigid_dof_names = ["Surge", "Sway", "Heave", "Roll", "Pitch", "Yaw"]
+        rigid_inertia_matrix_xr = xr.DataArray(data=np.asarray(inertia_matrix),
+                            dims=['influenced_dof', 'radiating_dof'],
+                            coords={'influenced_dof': rigid_dof_names,
+                                    'radiating_dof': rigid_dof_names},
+                            name="inertia_matrix")
+
+        # Body DOFs (Default as np.nan)
+        body_dof_names = list(self.dofs)
+        body_dof_count = len(body_dof_names)
+        other_dofs_inertia_matrix_xr = xr.DataArray(np.nan * np.zeros([body_dof_count, body_dof_count]),
+                                    dims=['influenced_dof', 'radiating_dof'],
+                                    coords={'influenced_dof': body_dof_names,
+                                            'radiating_dof': body_dof_names},
+                                    name="inertia_matrix")
+
+        total_mass_xr = xr.merge([rigid_inertia_matrix_xr, other_dofs_inertia_matrix_xr], compat="override").inertia_matrix
+
+        non_rigid_dofs = set(body_dof_names) - set(rigid_dof_names)
+
+        if output_type == "body_dofs":
+            if len(non_rigid_dofs) > 0:
+                LOG.warning(f"Non-rigid dofs: {non_rigid_dofs} are detected and \
+respective inertia coefficients are assigned as NaN.")
+
+            inertia_matrix_xr = total_mass_xr.sel(influenced_dof=body_dof_names,
+                                                  radiating_dof=body_dof_names)
+        elif output_type == "rigid_dofs":
+            inertia_matrix_xr = total_mass_xr.sel(influenced_dof=rigid_dof_names,
+                                                  radiating_dof=rigid_dof_names)
+        elif output_type == "all_dofs":
+            if len(non_rigid_dofs) > 0:
+                LOG.warning("Non-rigid dofs: {non_rigid_dofs} are detected and \
+respective inertia coefficients are assigned as NaN.")
+
+            inertia_matrix_xr = total_mass_xr
+        else:
+            raise ValueError(f"output_type should be either 'body_dofs', \
+'all_dofs' or 'rigid_dofs'. Given output_type = '{output_type}'.")
+
+        return inertia_matrix_xr
+
+
+    def compute_hydrostatics(self, *, rho=1000.0, g=9.81, divergence=None):
+        """Compute hydrostatics of the FloatingBody.
+
+        Parameters
+        ----------
+        rho : float, optional
+            Density of Water. The default is 1000.
+        g: float, optional
+            Gravity acceleration. The default is 9.81.
+        divergence : np.ndarray, optional
+            Divergence of the DOFs.
+
+        Returns
+        -------
+        hydrostatics : dict
+            All hydrostatics values of the FloatingBody.
+        """
+        if self.center_of_mass is None:
+            raise ValueError(f"Trying to compute hydrostatics for {self.name}, but no center of mass has been defined.\n"
+                             f"Suggested solution: define a `center_of_mass` attribute for the FloatingBody {self.name}.")
+
+        immersed_self = self.immersed_part()
+
+        full_mesh_vertices = self.mesh.vertices
+        coord_max = full_mesh_vertices.max(axis=0)
+        coord_min = full_mesh_vertices.min(axis=0)
+        full_length, full_breadth, depth = full_mesh_vertices.max(axis=0) - full_mesh_vertices.min(axis=0)
+
+        vertices = immersed_self.mesh.vertices
+        sub_length, sub_breadth, _ = vertices.max(axis=0) - vertices.min(axis=0)
+
+        if abs(immersed_self.waterplane_area) > 1e-10:
+            water_plane_idx = np.isclose(vertices[:,2], 0.0)
+            water_plane = vertices[water_plane_idx][:,:-1]
+            wl_length, wl_breadth = water_plane.max(axis=0) - water_plane.min(axis=0)
+        else:
+            wl_length, wl_breadth = 0.0, 0.0
+
+        hydrostatics = {}
+        hydrostatics["g"] = g
+        hydrostatics["rho"] = rho
+        hydrostatics["center_of_mass"] = self.center_of_mass
+
+        hydrostatics["wet_surface_area"] = immersed_self.wet_surface_area
+        hydrostatics["disp_volumes"] = immersed_self.volumes
+        hydrostatics["disp_volume"] = immersed_self.volume
+        hydrostatics["disp_mass"] = immersed_self.disp_mass(rho=rho)
+        hydrostatics["center_of_buoyancy"] = immersed_self.center_of_buoyancy
+        hydrostatics["waterplane_center"] = np.append(immersed_self.waterplane_center, 0.0)
+        hydrostatics["waterplane_area"] = immersed_self.waterplane_area
+        hydrostatics["transversal_metacentric_radius"] = immersed_self.transversal_metacentric_radius
+        hydrostatics["longitudinal_metacentric_radius"] = immersed_self.longitudinal_metacentric_radius
+        hydrostatics["transversal_metacentric_height"] = immersed_self.transversal_metacentric_height
+        hydrostatics["longitudinal_metacentric_height"] = immersed_self.longitudinal_metacentric_height
+        self.hydrostatic_stiffness = hydrostatics["hydrostatic_stiffness"] = immersed_self.compute_hydrostatic_stiffness(
+            divergence=divergence, rho=rho, g=g)
+
+        hydrostatics["length_overall"] = full_length
+        hydrostatics["breadth_overall"] = full_breadth
+        hydrostatics["depth"] = depth
+        hydrostatics["draught"] = np.abs(coord_min[2])
+        hydrostatics["length_at_waterline"] = wl_length
+        hydrostatics["breadth_at_waterline"] = wl_breadth
+        hydrostatics["length_overall_submerged"] = sub_length
+        hydrostatics["breadth_overall_submerged"] = sub_breadth
+        if any(dof.lower() in {"surge", "sway", "heave", "roll", "pitch", "yaw"}
+               for dof in self.dofs) > 0: # If there is at least one rigid body dof:
+            self.inertia_matrix = hydrostatics["inertia_matrix"] = self.compute_rigid_body_inertia(rho=rho)
+
+        return hydrostatics
+
+
+    ###################
+    # Transformations #
+    ###################
+
+    def __add__(self, body_to_add: 'FloatingBody') -> 'FloatingBody':
+        return self.join_bodies(body_to_add)
+
+    def join_bodies(*bodies, name=None) -> 'FloatingBody':
+        if name is None:
+            name = "+".join(body.name for body in bodies)
+        meshes = CollectionOfMeshes([body.mesh for body in bodies], name=f"{name}_mesh")
+        dofs = FloatingBody.combine_dofs(bodies)
+
+        if all(body.mass is not None for body in bodies):
+            new_mass = sum(body.mass for body in bodies)
+        else:
+            new_mass = None
+
+        if (all(body.mass is not None for body in bodies)
+                and all(body.center_of_mass is not None for body in bodies)):
+            new_cog = sum(body.mass*np.asarray(body.center_of_mass) for body in bodies)/new_mass
+        else:
+            new_cog = None
+
+        joined_bodies = FloatingBody(
+            mesh=meshes, dofs=dofs, mass=new_mass, center_of_mass=new_cog, name=name
+            )
+
+        for matrix_name in ["inertia_matrix", "hydrostatic_stiffness"]:
+            if all(hasattr(body, matrix_name) for body in bodies):
+                from scipy.linalg import block_diag
+                setattr(joined_bodies, matrix_name, joined_bodies.add_dofs_labels_to_matrix(
+                        block_diag(*[getattr(body, matrix_name) for body in bodies])
+                        ))
+
+        return joined_bodies
+
+    @staticmethod
+    def combine_dofs(bodies) -> dict:
+        """Combine the degrees of freedom of several bodies."""
+        dofs = {}
+        cum_nb_faces = accumulate(chain([0], (body.mesh.nb_faces for body in bodies)))
+        total_nb_faces = sum(body.mesh.nb_faces for body in bodies)
+        for body, nbf in zip(bodies, cum_nb_faces):
+            # nbf is the cumulative number of faces of the previous subbodies,
+            # that is the offset of the indices of the faces of the current body.
+            for name, dof in body.dofs.items():
+                new_dof = np.zeros((total_nb_faces, 3))
+                new_dof[nbf:nbf+len(dof), :] = dof
+                if '__' not in name:
+                    new_dof_name = '__'.join([body.name, name])
+                else:
+                    # The body is probably a combination of bodies already.
+                    # So for the associativity of the + operation,
+                    # it is better to keep the same name.
+                    new_dof_name = name
+                dofs[new_dof_name] = new_dof
+        return dofs
+
+    def copy(self, name=None) -> 'FloatingBody':
+        """Return a deep copy of the body.
+
+        Parameters
+        ----------
+        name : str, optional
+            a name for the new copy
+        """
+        new_body = copy.deepcopy(self)
+        if name is None:
+            new_body.name = f"copy_of_{self.name}"
+            LOG.debug(f"Copy {self.name}.")
+        else:
+            new_body.name = name
+            LOG.debug(f"Copy {self.name} under the name {name}.")
+        return new_body
+
+    def assemble_regular_array(self, distance, nb_bodies):
+        """Create an regular array of identical bodies.
+
+        Parameters
+        ----------
+        distance : float
+            Center-to-center distance between objects in the array
+        nb_bodies : couple of ints
+            Number of objects in the x and y directions.
+
+        Returns
+        -------
+        FloatingBody
+        """
+        bodies = (self.translated((i*distance, j*distance, 0), name=f"{i}_{j}") for j in range(nb_bodies[1]) for i in range(nb_bodies[0]))
+        array = FloatingBody.join_bodies(*bodies)
+        array.mesh = build_regular_array_of_meshes(self.mesh, distance, nb_bodies)
+        array.name = f"array_of_{self.name}"
+        return array
+
+    def assemble_arbitrary_array(self, locations:np.ndarray):
+
+        if not isinstance(locations, np.ndarray):
+            raise TypeError('locations must be of type np.ndarray')
+        assert locations.shape[1] == 2, 'locations must be of shape nx2, received {:}'.format(locations.shape)
+        n = locations.shape[0]
+
+        fb_list = []
+        for idx, li in enumerate(locations):
+            fb1 = self.copy()
+            fb1.translate(np.append(li,0))
+            fb1.name = 'arbitrary_array_body{:02d}'.format(idx)
+            fb_list.append(fb1)
+
+        arbitrary_array = fb_list[0].join_bodies(*fb_list[1:])
+
+        return arbitrary_array
+
+    def extract_faces(self, id_faces_to_extract, return_index=False):
+        """Create a new FloatingBody by extracting some faces from the mesh.
+        The dofs evolve accordingly.
+        """
+        if isinstance(self.mesh, CollectionOfMeshes):
+            raise NotImplementedError  # TODO
+
+        if return_index:
+            new_mesh, id_v = Mesh.extract_faces(self.mesh, id_faces_to_extract, return_index)
+        else:
+            new_mesh = Mesh.extract_faces(self.mesh, id_faces_to_extract, return_index)
+        new_body = FloatingBody(new_mesh)
+        LOG.info(f"Extract floating body from {self.name}.")
+
+        new_body.dofs = {}
+        for name, dof in self.dofs.items():
+            new_body.dofs[name] = dof[id_faces_to_extract, :]
+
+        if return_index:
+            return new_body, id_v
+        else:
+            return new_body
+
+    def sliced_by_plane(self, plane):
+        return FloatingBody(mesh=self.mesh.sliced_by_plane(plane), dofs=self.dofs, name=self.name)
+
+    def minced(self, nb_slices=(8, 8, 4)):
+        """Experimental method decomposing the mesh as a hierarchical structure.
+
+        Parameters
+        ----------
+        nb_slices: Tuple[int, int, int]
+            The number of slices in each of the x, y and z directions.
+            Only powers of 2 are supported at the moment.
+
+        Returns
+        -------
+        FloatingBody
+        """
+        minced_body = self.copy()
+
+        # Extreme points of the mesh in each directions.
+        x_min, x_max, y_min, y_max, z_min, z_max = self.mesh.axis_aligned_bbox
+        sizes = [(x_min, x_max), (y_min, y_max), (z_min, z_max)]
+
+        directions = [np.array(d) for d in [(1, 0, 0), (0, 1, 0), (0, 0, 1)]]
+
+        def _slice_positions_at_depth(i):
+            """Helper function.
+
+            Returns a list of floats as follows:
+            i=1 -> [1/2]
+            i=2 -> [1/4, 3/4]
+            i=3 -> [1/8, 3/8, 5/8, 7/8]
+                   ...
+            """
+            denominator = 2**i
+            return [numerator/denominator for numerator in range(1, denominator, 2)]
+
+        # GENERATE ALL THE PLANES THAT WILL BE USED TO MINCE THE MESH
+        planes = []
+        for direction, nb_slices_in_dir, (min_coord, max_coord) in zip(directions, nb_slices, sizes):
+            planes_in_dir = []
+
+            depth_of_treelike_structure = int(np.log2(nb_slices_in_dir))
+            for i_depth in range(1, depth_of_treelike_structure+1):
+                planes_in_dir_at_depth = []
+                for relative_position in _slice_positions_at_depth(i_depth):
+                    slice_position = (min_coord + relative_position*(max_coord-min_coord))*direction
+                    plane = Plane(normal=direction, point=slice_position)
+                    planes_in_dir_at_depth.append(plane)
+                planes_in_dir.append(planes_in_dir_at_depth)
+            planes.append(planes_in_dir)
+
+        # SLICE THE MESH
+        intermingled_x_y_z = chain.from_iterable(zip_longest(*planes))
+        for planes in intermingled_x_y_z:
+            if planes is not None:
+                for plane in planes:
+                    minced_body = minced_body.sliced_by_plane(plane)
+        return minced_body
+
+    @inplace_transformation
+    def mirror(self, plane):
+        self.mesh.mirror(plane)
+        for dof in self.dofs:
+            self.dofs[dof] -= 2 * np.outer(np.dot(self.dofs[dof], plane.normal), plane.normal)
+        for point_attr in ('geometric_center', 'rotation_center', 'center_of_mass'):
+            if point_attr in self.__dict__ and self.__dict__[point_attr] is not None:
+                point = np.array(self.__dict__[point_attr])
+                shift = - 2 * (np.dot(point, plane.normal) - plane.c) * plane.normal
+                self.__dict__[point_attr] = point + shift
+        return self
+
+    @inplace_transformation
+    def translate(self, vector, *args, **kwargs):
+        self.mesh.translate(vector, *args, **kwargs)
+        for point_attr in ('geometric_center', 'rotation_center', 'center_of_mass'):
+            if point_attr in self.__dict__ and self.__dict__[point_attr] is not None:
+                self.__dict__[point_attr] = np.array(self.__dict__[point_attr]) + vector
+        return self
+
+    @inplace_transformation
+    def rotate(self, axis, angle):
+        self.mesh.rotate(axis, angle)
+        for point_attr in ('geometric_center', 'rotation_center', 'center_of_mass'):
+            if point_attr in self.__dict__ and self.__dict__[point_attr] is not None:
+                self.__dict__[point_attr] = axis.rotate_points([self.__dict__[point_attr]], angle)[0, :]
+        for dof in self.dofs:
+            self.dofs[dof] = axis.rotate_vectors(self.dofs[dof], angle)
+        return self
+
+    @inplace_transformation
+    def clip(self, plane):
+        # Clip mesh
+        LOG.info(f"Clipping {self.name} with respect to {plane}")
+        self.mesh.clip(plane)
+
+        # Clip dofs
+        ids = self.mesh._clipping_data['faces_ids']
+        for dof in self.dofs:
+            if len(ids) > 0:
+                self.dofs[dof] = np.array(self.dofs[dof])[ids]
+            else:
+                self.dofs[dof] = np.empty((0, 3))
+        return self
+
+
+    #############
+    #  Display  #
+    #############
+
+    def __short_str__(self):
+        return (f"{self.__class__.__name__}(..., name=\"{self.name}\")")
+
+    def _optional_params_str(self):
+        items = []
+        if self.mass is not None: items.append(f"mass={self.mass}, ")
+        if self.center_of_mass is not None: items.append(f"center_of_mass={self.center_of_mass}, ")
+        return ''.join(items)
+
+    def __str__(self):
+        short_dofs = '{' + ', '.join('"{}": ...'.format(d) for d in self.dofs) + '}'
+        return (f"{self.__class__.__name__}(mesh={self.mesh.__short_str__()}, dofs={short_dofs}, {self._optional_params_str()}name=\"{self.name}\")")
+
+    def __repr__(self):
+        short_dofs = '{' + ', '.join('"{}": ...'.format(d) for d in self.dofs) + '}'
+        return (f"{self.__class__.__name__}(mesh={str(self.mesh)}, dofs={short_dofs}, {self._optional_params_str()}name=\"{self.name}\")")
+
+    def _repr_pretty_(self, p, cycle):
+        p.text(self.__str__())
+
+    def __rich_repr__(self):
+        class DofWithShortRepr:
+            def __repr__(self):
+                return '...'
+        yield "mesh", self.mesh
+        yield "dofs", {d: DofWithShortRepr() for d in self.dofs}
+        if self.mass is not None:
+            yield "mass", self.mass, None
+        if self.center_of_mass is not None:
+            yield "center_of_mass", tuple(self.center_of_mass)
+        yield "name", self.name
+
+    def show(self, **kwargs):
+        from capytaine.ui.vtk.body_viewer import FloatingBodyViewer
+        viewer = FloatingBodyViewer()
+        viewer.add_body(self, **kwargs)
+        viewer.show()
+        viewer.finalize()
+
+    def show_matplotlib(self, *args, **kwargs):
+        return self.mesh.show_matplotlib(*args, **kwargs)
+
+    def animate(self, motion, *args, **kwargs):
+        """Display a motion as a 3D animation.
+
+        Parameters
+        ==========
+        motion: dict or pd.Series or str
+            A dict or series mapping the name of the dofs to its amplitude.
+            If a single string is passed, it is assumed to be the name of a dof
+            and this dof with a unit amplitude will be displayed.
+        """
+        from capytaine.ui.vtk.animation import Animation
+        if isinstance(motion, str):
+            motion = {motion: 1.0}
+        elif isinstance(motion, xr.DataArray):
+            motion = {k: motion.sel(radiating_dof=k).data for k in motion.coords["radiating_dof"].data}
+
+        if any(dof not in self.dofs for dof in motion):
+            missing_dofs = set(motion.keys()) - set(self.dofs.keys())
+            raise ValueError(f"Trying to animate the body {self.name} using dof(s) {missing_dofs}, but no dof of this name is defined for {self.name}.")
+
+        animation = Animation(*args, **kwargs)
+        animation._add_actor(self.mesh.merged(), faces_motion=sum(motion[dof_name] * dof for dof_name, dof in self.dofs.items() if dof_name in motion))
+        return animation
+
+    @property
+    def minimal_computable_wavelength(self):
+        """For accuracy of the resolution, wavelength should not be smaller than this value."""
+        return 8*self.mesh.faces_radiuses.max()
+
+    def cluster_bodies(*bodies, name=None):
+        """
+        Builds a hierarchical clustering from a group of bodies
+
+        Parameters
+        ----------
+        bodies: list
+            a list of bodies
+        name: str, optional
+            a name for the new body
+
+        Returns
+        -------
+        FloatingBody
+            Array built from the provided bodies
+        """
+        from scipy.cluster.hierarchy import linkage, dendrogram
+        nb_buoys = len(bodies)
+
+        if any(body.center_of_buoyancy is None for body in bodies):
+            raise ValueError("The center of buoyancy of each body needs to be known for clustering")
+        buoys_positions = np.stack([body.center_of_buoyancy for body in bodies])[:,:2]
+
+        ln_matrix = linkage(buoys_positions, method='centroid', metric='euclidean')
+
+        node_list = list(bodies)  # list of nodes of the tree: the first nodes are single bodies
+
+        # Join the bodies, with an ordering consistent with the dendrogram.
+        # Done by reading the linkage matrix: its i-th row contains the labels
+        # of the two nodes that are merged to form the (n + i)-th node
+        for ii in range(len(ln_matrix)):
+            node_tag = ii + nb_buoys # the first nb_buoys tags are already taken
+            merge_left = int(ln_matrix[ii,0])
+            merge_right = int(ln_matrix[ii,1])
+            # The new node is the parent of merge_left and merge_right
+            new_node_ls = [node_list[merge_left], node_list[merge_right]]
+            new_node = FloatingBody.join_bodies(*new_node_ls, name='node_{:d}'.format(node_tag))
+            node_list.append(new_node)
+
+        # The last node is the parent of all others
+        all_buoys = new_node
+
+        if name is not None:
+            all_buoys.name = name
+
+        return all_buoys