capytaine 2.0__cp38-cp38-win_amd64.whl → 2.2__cp38-cp38-win_amd64.whl

capytaine/bodies/bodies.py

@@ -1,25 +1,25 @@
-#!/usr/bin/env python
-# coding: utf-8
 """Floating bodies to be used in radiation-diffraction problems."""
-# Copyright (C) 2017-2019 Matthieu Ancellin
-# See LICENSE file at <https://github.com/mancellin/capytaine>
+# Copyright (C) 2017-2024 Matthieu Ancellin
+# See LICENSE file at <https://github.com/capytaine/capytaine>
 
 import logging
 import copy
-from itertools import chain, accumulate, product, zip_longest
+from itertools import chain, accumulate, zip_longest
+from functools import cached_property
 
 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.collections import CollectionOfMeshes
 from capytaine.meshes.geometry import Abstract3DObject, ClippableMixin, Plane, inplace_transformation
+from capytaine.meshes.properties import connected_components, connected_components_of_waterline
 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
 
+from capytaine.tools.optional_imports import silently_import_optional_dependency
+meshio = silently_import_optional_dependency("meshio")
+
 LOG = logging.getLogger(__name__)
 
 TRANSLATION_DOFS_DIRECTIONS = {"surge": (1, 0, 0), "sway": (0, 1, 0), "heave": (0, 0, 1)}
@@ -40,8 +40,12 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
     Parameters
     ----------
     mesh : Mesh or CollectionOfMeshes, optional
-        the mesh describing the geometry of the floating body.
+        the mesh describing the geometry of the hull of the floating body.
         If none is given, a empty one is created.
+    lid_mesh : Mesh or CollectionOfMeshes or None, optional
+        a mesh of an internal lid for irregular frequencies removal.
+        Unlike the mesh of the hull, no dof is defined on the lid_mesh.
+        If none is given, none is used when solving the Boundary Integral Equation.
     dofs : dict, optional
         the degrees of freedom of the body.
         If none is given, a empty dictionary is initialized.
@@ -57,7 +61,7 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         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):
+    def __init__(self, mesh=None, dofs=None, mass=None, center_of_mass=None, name=None, *, lid_mesh=None):
         if mesh is None:
             self.mesh = Mesh(name="dummy_mesh")
 
@@ -71,6 +75,11 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         else:
             raise TypeError("Unrecognized `mesh` object passed to the FloatingBody constructor.")
 
+        if lid_mesh is not None:
+            self.lid_mesh = lid_mesh.with_normal_vector_going_down(inplace=False)
+        else:
+            self.lid_mesh = None
+
         if name is None and mesh is None:
             self.name = "dummy_body"
         elif name is None:
@@ -84,6 +93,9 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         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):
@@ -94,21 +106,19 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         else:
             self.dofs = dofs
 
-        if self.mesh.nb_vertices == 0 or self.mesh.nb_faces == 0:
-            LOG.warning(f"New floating body (with empty mesh!): {self.name}.")
-        else:
-            self.mesh.heal_mesh()
-            LOG.info(f"New floating body: {self.name}.")
+        LOG.info(f"New floating body: {self.__str__()}.")
 
     @staticmethod
     def from_meshio(mesh, name=None) -> 'FloatingBody':
-        """Create a FloatingBody from a meshio mesh object."""
+        """Create a FloatingBody from a meshio mesh object.
+        Kinda deprecated, use cpt.load_mesh instead."""
         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."""
+        """Create a FloatingBody from a mesh file using meshmagick.
+        Kinda deprecated, use cpt.load_mesh instead."""
         from capytaine.io.mesh_loaders import load_mesh
         if name is None: name = filename
         mesh = load_mesh(filename, file_format, name=f"{name}_mesh")
@@ -118,6 +128,13 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         """Arbitrary order. The point is to sort together the problems involving the same body."""
         return self.name < other.name
 
+    @cached_property
+    def mesh_including_lid(self):
+        if self.lid_mesh is not None:
+            return CollectionOfMeshes([self.mesh, self.lid_mesh])
+        else:
+            return self.mesh
+
     ##########
     #  Dofs  #
     ##########
@@ -176,7 +193,7 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
                     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"{self.name}.{point_attr} = {getattr(self, point_attr)}")
+                                 f"{self.__short_str__()}.{point_attr} = {getattr(self, point_attr)}")
                         break
                 else:
                     axis_point = np.array([0, 0, 0])
@@ -270,7 +287,7 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         """Returns volume of the FloatingBody."""
         return self.mesh.volume
 
-    def disp_mass(self, *, rho=1000):
+    def disp_mass(self, *, rho=1000.0):
         return self.mesh.disp_mass(rho=rho)
 
     @property
@@ -351,7 +368,7 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
             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` attibute to {self.name}.\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
 
@@ -444,10 +461,10 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
             else:
                 norm_hs_stiff = 0.0
         else:
-            if self.mass is not None and np.isclose(self.mass, self.disp_mass(rho), rtol=1e-4):
+            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={body.mass}, disp_mass={body.disp_mass(rho)}.\n"
+                        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."
                         )
 
@@ -515,7 +532,9 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
             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:
+            if influenced_dof.lower() in [*TRANSLATION_DOFS_DIRECTIONS, *ROTATION_DOFS_AXIS]:
+                return 0.0  # Dummy value that is not actually used afterwards.
+            elif divergence is None:
                 return 0.0
             elif isinstance(divergence, dict) and influenced_dof in divergence.keys():
                 return divergence[influenced_dof]
@@ -539,7 +558,7 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
         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"):
+    def compute_rigid_body_inertia(self, *, rho=1000.0, output_type="body_dofs"):
         """
         Inertia Mass matrix of the body for 6 rigid DOFs.
 
@@ -629,8 +648,8 @@ class FloatingBody(ClippableMixin, Abstract3DObject):
 
         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.")
+                LOG.warning(f"Non-rigid dofs {non_rigid_dofs} detected: their \
+inertia coefficients are assigned as NaN.")
 
             inertia_matrix_xr = total_mass_xr.sel(influenced_dof=body_dof_names,
                                                   radiating_dof=body_dof_names)
@@ -732,7 +751,17 @@ respective inertia coefficients are assigned as NaN.")
     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")
+        meshes = CollectionOfMeshes(
+                [body.mesh for body in bodies],
+                name=f"{name}_mesh"
+                )
+        if all(body.lid_mesh is None for body in bodies):
+            lid_meshes = None
+        else:
+            lid_meshes = CollectionOfMeshes(
+                    [body.lid_mesh for body in bodies if body.lid_mesh is not None],
+                    name=f"{name}_lid_mesh"
+                    )
         dofs = FloatingBody.combine_dofs(bodies)
 
         if all(body.mass is not None for body in bodies):
@@ -747,7 +776,8 @@ respective inertia coefficients are assigned as NaN.")
             new_cog = None
 
         joined_bodies = FloatingBody(
-            mesh=meshes, dofs=dofs, mass=new_mass, center_of_mass=new_cog, name=name
+            mesh=meshes, lid_mesh=lid_meshes, dofs=dofs,
+            mass=new_mass, center_of_mass=new_cog, name=name
             )
 
         for matrix_name in ["inertia_matrix", "hydrostatic_stiffness"]:
@@ -823,7 +853,6 @@ respective inertia coefficients are assigned as NaN.")
         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):
@@ -839,6 +868,7 @@ respective inertia coefficients are assigned as NaN.")
     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.
+        The lid_mesh, center_of_mass, mass and hydrostatics data are discarded.
         """
         if isinstance(self.mesh, CollectionOfMeshes):
             raise NotImplementedError  # TODO
@@ -860,7 +890,12 @@ respective inertia coefficients are assigned as NaN.")
             return new_body
 
     def sliced_by_plane(self, plane):
-        return FloatingBody(mesh=self.mesh.sliced_by_plane(plane), dofs=self.dofs, name=self.name)
+        """Return the same body, but replace the mesh by a set of two meshes
+        corresponding to each sides of the plane."""
+        return FloatingBody(mesh=self.mesh.sliced_by_plane(plane),
+                            lid_mesh=self.lid_mesh.sliced_by_plane(plane)
+                                        if self.lid_mesh is not None else None,
+                            dofs=self.dofs, name=self.name)
 
     def minced(self, nb_slices=(8, 8, 4)):
         """Experimental method decomposing the mesh as a hierarchical structure.
@@ -921,27 +956,35 @@ respective inertia coefficients are assigned as NaN.")
     @inplace_transformation
     def mirror(self, plane):
         self.mesh.mirror(plane)
+        if self.lid_mesh is not None:
+            self.lid_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:
-                self.__dict__[point_attr] -= 2 * (np.dot(self.__dict__[point_attr], plane.normal) - plane.c) * plane.normal
+                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)
+        if self.lid_mesh is not None:
+            self.lid_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] += vector
+                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)
+        if self.lid_mesh is not None:
+            self.lid_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)
+                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
@@ -951,6 +994,8 @@ respective inertia coefficients are assigned as NaN.")
         # Clip mesh
         LOG.info(f"Clipping {self.name} with respect to {plane}")
         self.mesh.clip(plane)
+        if self.lid_mesh is not None:
+            self.lid_mesh.clip(plane)
 
         # Clip dofs
         ids = self.mesh._clipping_data['faces_ids']
@@ -966,15 +1011,52 @@ respective inertia coefficients are assigned as NaN.")
     #  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):
-        return self.name
+        short_dofs = '{' + ', '.join('"{}": ...'.format(d) for d in self.dofs) + '}'
+
+        if self.lid_mesh is not None:
+            lid_mesh_str = self.lid_mesh.__short_str__()
+        else:
+            lid_mesh_str = str(None)
+
+        return (f"{self.__class__.__name__}(mesh={self.mesh.__short_str__()}, lid_mesh={lid_mesh_str}, "
+                f"dofs={short_dofs}, {self._optional_params_str()}name=\"{self.name}\")")
 
     def __repr__(self):
-        return (f"{self.__class__.__name__}(mesh={self.mesh.name}, "
-                f"dofs={{{', '.join(self.dofs.keys())}}}, name={self.name})")
+        short_dofs = '{' + ', '.join('"{}": ...'.format(d) for d in self.dofs) + '}'
+
+        if self.lid_mesh is not None:
+            lid_mesh_str = str(self.lid_mesh)
+        else:
+            lid_mesh_str = str(None)
+
+        return (f"{self.__class__.__name__}(mesh={str(self.mesh)}, lid_mesh={lid_mesh_str}, "
+                f"dofs={short_dofs}, {self._optional_params_str()}name=\"{self.name}\")")
 
     def _repr_pretty_(self, p, cycle):
-        p.text(self.__repr__())
+        p.text(self.__str__())
+
+    def __rich_repr__(self):
+        class DofWithShortRepr:
+            def __repr__(self):
+                return '...'
+        yield "mesh", self.mesh
+        yield "lid_mesh", self.lid_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
@@ -1013,5 +1095,91 @@ respective inertia coefficients are assigned as NaN.")
     @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()
+        if self.lid_mesh is not None:
+            return max(8*self.mesh.faces_radiuses.max(), 8*self.lid_mesh.faces_radiuses.max())
+        else:
+            return 8*self.mesh.faces_radiuses.max()
+
+    def first_irregular_frequency_estimate(self, *, g=9.81):
+        r"""Estimates the angular frequency of the lowest irregular
+        frequency.
+        This is based on the formula for the lowest irregular frequency of a
+        parallelepiped of size :math:`L \times B` and draft :math:`H`:
+
+        .. math::
+            \omega = \sqrt{
+                        \frac{\pi g \sqrt{\frac{1}{B^2} + \frac{1}{L^2}}}
+                             {\tanh\left(\pi H \sqrt{\frac{1}{B^2} + \frac{1}{L^2}} \right)}
+                     }
+
+        The formula is applied to all shapes to get an estimate that is usually
+        conservative.
+        The definition of a lid (supposed to be fully covering and horizontal)
+        is taken into account.
+        """
+        if self.lid_mesh is None:
+            draft = abs(self.mesh.vertices[:, 2].min())
+        else:
+            draft = abs(self.lid_mesh.vertices[:, 2].min())
+            if draft < 1e-6:
+                return np.inf
+
+        # Look for the x and y span of each components (e.g. for multibody) and
+        # keep the one causing the lowest irregular frequency.
+        # The draft is supposed to be same for all components.
+        omega = np.inf
+        for comp in connected_components(self.mesh):
+            for ccomp in connected_components_of_waterline(comp):
+                x_span = ccomp.vertices[:, 0].max() - ccomp.vertices[:, 0].min()
+                y_span = ccomp.vertices[:, 1].max() - ccomp.vertices[:, 1].min()
+                p = np.hypot(1/x_span, 1/y_span)
+                omega_comp = np.sqrt(np.pi*g*p/(np.tanh(np.pi*draft*p)))
+                omega = min(omega, omega_comp)
+        return omega
+
+    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
+        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

capytaine/bodies/predefined/__init__.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 # Copyright (C) 2017-2019 Matthieu Ancellin
 # See LICENSE file at <https://github.com/mancellin/capytaine>
 

capytaine/bodies/predefined/cylinders.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 """Legacy interfaces to predefined meshes"""
 # Copyright (C) 2017-2022 Matthieu Ancellin
 # See LICENSE file at <https://github.com/capytaine/capytaine>

capytaine/bodies/predefined/rectangles.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 """Legacy interfaces to predefined meshes"""
 # Copyright (C) 2017-2022 Matthieu Ancellin
 # See LICENSE file at <https://github.com/capytaine/capytaine>

capytaine/bodies/predefined/spheres.py

@@ -68,5 +68,3 @@ class Sphere(FloatingBody):
         self.radius = radius
         self.geometric_center = np.array(center, dtype=float)
         FloatingBody.__init__(self, mesh=mesh, name=name)
-
-

capytaine/green_functions/abstract_green_function.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# coding: utf-8
 """Abstract structure of a class used to compute the Green function"""
 # Copyright (C) 2017-2019 Matthieu Ancellin
 # See LICENSE file at <https://github.com/mancellin/capytaine>
@@ -12,4 +10,3 @@ class AbstractGreenFunction(ABC):
     @abstractmethod
     def evaluate(self, mesh1, mesh2, free_surface, sea_bottom, wavenumber):
         pass
-