capytaine 2.2.1__cp39-cp39-win_amd64.whl → 2.3__cp39-cp39-win_amd64.whl

capytaine/meshes/symmetric.py

@@ -10,7 +10,7 @@ import numpy as np
 
 from capytaine.meshes.meshes import Mesh
 from capytaine.meshes.collections import CollectionOfMeshes
-from capytaine.meshes.geometry import Axis, Plane, Oz_axis, inplace_transformation
+from capytaine.meshes.geometry import Axis, Plane, xOy_Plane, Oz_axis, inplace_transformation
 
 LOG = logging.getLogger(__name__)
 
@@ -89,7 +89,7 @@ class ReflectionSymmetricMesh(SymmetricMesh):
             "Only meshes with the same symmetry can be joined together."
         assert all(meshes[0].plane == mesh.plane for mesh in meshes), \
             "Only reflection symmetric meshes with the same reflection plane can be joined together."
-        half_mesh = CollectionOfMeshes([mesh.half for mesh in meshes], name=f"half_of_{name}" if name is not None else None)
+        half_mesh = meshes[0].half.join_meshes(*(mesh.half for mesh in meshes[1:]), name=f"half_of_{name}" if name is not None else None)
         return ReflectionSymmetricMesh(half_mesh, plane=meshes[0].plane, name=name)
 
     @inplace_transformation
@@ -110,6 +110,15 @@ class ReflectionSymmetricMesh(SymmetricMesh):
         CollectionOfMeshes.mirror(self, plane)
         return self
 
+    def generate_lid(self, z=0.0, faces_max_radius=None, name=None):
+        if name is None:
+            name = "lid for {}".format(self.name)
+        return ReflectionSymmetricMesh(self.half.generate_lid(z, faces_max_radius), self.plane, name=name)
+
+    def extract_lid(self, plane=xOy_Plane):
+        hull, lid = self.half.extract_lid(plane)
+        return ReflectionSymmetricMesh(hull, self.plane), ReflectionSymmetricMesh(lid, self.plane)
+
 
 class TranslationalSymmetricMesh(SymmetricMesh):
     """A mesh with a repeating pattern by translation.

capytaine/post_pro/kochin.py

@@ -1,6 +1,6 @@
 """Computation of the Kochin function."""
 # Copyright (C) 2017-2019 Matthieu Ancellin
-# See LICENSE file at <https://github.com/mancellin/capytaine>
+# See LICENSE file at <https://github.com/capytaine/capytaine>
 
 import logging
 import numpy as np
@@ -29,9 +29,9 @@ def compute_kochin(result, theta, ref_point=(0.0, 0.0)):
         LOG.warning("Kochin functions with forward speed have never been validated.")
 
     if result.sources is None:
-        raise Exception(f"""The values of the sources of {result} cannot been found.
-        They probably have not been stored by the solver because the option keep_details=True have not been set.
-        Please re-run the resolution with this option.""")
+        raise ValueError(f"""The values of the sources of {result} cannot been found.
+        They have not been stored by the solver either because the direct method has been used or the option keep_details=True have not been set.
+        Please re-run the resolution with `method='indirect'` and `keep_details=True`.""")
 
     k = result.wavenumber
     h = result.water_depth

capytaine/tools/lists_of_points.py

@@ -1,7 +1,7 @@
 import numpy as np
 from capytaine.bodies import FloatingBody
 from capytaine.post_pro.free_surfaces import FreeSurface
-from capytaine.meshes import Mesh, CollectionOfMeshes
+from capytaine.meshes.mesh_like_protocol import MeshLike
 
 
 def _normalize_points(points, keep_mesh=False):
@@ -11,7 +11,7 @@ def _normalize_points(points, keep_mesh=False):
         else:
             return points.mesh.faces_centers, (points.mesh.nb_faces,)
 
-    if isinstance(points, (Mesh, CollectionOfMeshes)):
+    if isinstance(points, MeshLike):
         if keep_mesh:
             return points, (points.nb_faces,)
         else:
@@ -41,7 +41,7 @@ def _normalize_free_surface_points(points, keep_mesh=False):
     if keep_mesh and isinstance(points, (FloatingBody, FreeSurface)):
         return points.mesh, (points.mesh.nb_faces,)
 
-    if keep_mesh and isinstance(points, (Mesh, CollectionOfMeshes)):
+    if keep_mesh and isinstance(points, MeshLike):
         return points, (points.nb_faces,)
 
     points, output_shape = _normalize_points(points, keep_mesh)

capytaine/tools/prony_decomposition.py

@@ -1,8 +1,8 @@
 """Prony decomposition: tool to approximate a function as a sum of exponentials.
 Used in particular in the finite depth Green function.
 """
-# 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
 
@@ -12,6 +12,7 @@ from scipy.optimize import curve_fit
 from scipy.linalg import toeplitz
 
 LOG = logging.getLogger(__name__)
+RNG = np.random.default_rng()
 
 
 def exponential_decomposition(X, F, m):
@@ -66,8 +67,8 @@ def exponential_decomposition(X, F, m):
 
 
 def error_exponential_decomposition(X, F, a, lamda):
-    """Compare exponential decomposition defined by the coefficients a and lamda to the reference
-    values in F.
+    """Mean square error of the exponential decomposition defined by the
+    coefficients a and lamda with respect to the reference values in F.
 
     Parameters
     ----------
@@ -92,3 +93,58 @@ def error_exponential_decomposition(X, F, a, lamda):
         return np.sum(a * np.exp(lamda*x), axis=0)
 
     return np.square(f(X) - F).mean()
+
+
+class PronyDecompositionFailure(Exception):
+    pass
+
+
+def find_best_exponential_decomposition(f, x_min, x_max, n_exp_range, *, tol=1e-4, noise_on_domain_points_std=0.01):
+    """Tries to construct an exponential decompositoin of the function f on the
+    domain [x_min, x_max] by testing the number of exponentials in n_exp_range.
+
+    Parameters
+    ----------
+    f: callable
+        The function ℝ→ℝ to be approximated.
+        Should support vectorized calls (that is passing a vector of inputs
+        and get the vector of corresponding outputs)
+    x_min, x_max: floats
+        The bounds of the domain of input in which f should be approximated
+    n_exp_range: iterable of ints
+        The decomposition sizes that will be tested
+    tol: float, optional
+        The target mean square error.
+    noise_on_domain_points_std: float, optional
+        Introduces some random variability on the points where the function is evaluated.
+        Set this parameter to zero to disable randomness.
+
+    """
+    # Try different range of evaluation points to construct the decomposition.
+    for n_exp in n_exp_range:
+
+        # f might be ill-defined at some single specific values
+        # (for the use-case of delhommeau.py, it is when x = kh exactly).
+        # Thus we slightly randomize the range of evaluation points for the Prony decomposition.
+        # This way, if one of the evaluation points hits the singular point, it will most likely not hit it again at the next iteration.
+        x_max_iter = (1 + noise_on_domain_points_std*RNG.uniform())*x_max
+
+        try:
+            # The coefficients are computed on a resolution of 4*n_exp+1 ...
+            X = np.linspace(x_min, x_max_iter, 4*n_exp+1)
+            a, lamda = exponential_decomposition(X, f(X), n_exp)
+
+            # ... and they are evaluated on a finer discretization.
+            X = np.linspace(x_min, x_max_iter, 8*n_exp+1)
+            if error_exponential_decomposition(X, f(X), a, lamda) < tol:
+                return a, lamda
+        except Exception:
+            # If something bad happened while computing the decomposition, try
+            # the next one.
+            continue
+
+    raise PronyDecompositionFailure(
+            "No suitable Prony decomposition has been found in "
+            f"[{x_min}, {x_max}] for tol={tol} "
+            f"using a number of terms in {n_exp_range}."
+            )

capytaine/tools/symbolic_multiplication.py

@@ -16,6 +16,8 @@ class SymbolicMultiplication:
     def __init__(self, symbol, value=1.0):
         self.symbol = symbol
         self.value = value
+        if hasattr(value, "shape"):
+            self.shape = value.shape  # When wrapping Numpy arrays
 
     def __format__(self, format_spec):
         return f"{self.symbol}×{self.value.__format__(format_spec)}"
@@ -40,6 +42,9 @@ class SymbolicMultiplication:
     def __radd__(self, x):
         return x + self._concretize()
 
+    def __neg__(self):
+        return SymbolicMultiplication(self.symbol, -self.value)
+
     def __mul__(self, x):
         return SymbolicMultiplication(self.symbol, self.value * x)
 
@@ -106,6 +111,13 @@ class SymbolicMultiplication:
     def reshape(self, *args):
         return SymbolicMultiplication(self.symbol, self.value.reshape(*args))
 
+    def sum(self, *args, **kwargs):
+        return SymbolicMultiplication(self.symbol, self.value.sum(*args, **kwargs))
+
+    @property
+    def T(self):
+        return SymbolicMultiplication(self.symbol, self.value.T)
+
 
 def supporting_symbolic_multiplication(f):
     """

capytaine/tools/timer.py

@@ -0,0 +1,64 @@
+"""A simple timer class used to measure the time spent in various parts of the BEM solver."""
+
+from functools import wraps
+import time
+
+class Timer:
+    """A simple timer class that can be used as context manager or as decorator using `wraps_function` method
+
+    Example
+    -------
+    timer = Timer()
+    with timer:
+        sleep(1.0)
+
+    print(timer.total)  # 1.0...
+
+    @timer.wraps_function
+    def my_function():
+        sleep(0.5)
+
+    my_function()
+    print(timer.total)  # 1.5...
+    my_function()
+    print(timer.total)  # 2.0...
+
+    print(timer.timings)  # [1.0, 0.5, 0.5]
+    """
+
+    def __init__(self, timings=None):
+        if timings is None:
+            self.timings = []
+        else:
+            self.timings = timings
+
+    def __repr__(self):
+        return f"Timer({self.timings})"
+
+    @property
+    def nb_timings(self):
+        return len(self.timings)
+
+    @property
+    def total(self):
+        return sum(self.timings)
+
+    @property
+    def mean(self):
+        if self.nb_timings == 0:
+            return float('nan')
+        else:
+            return self.total/self.nb_timings
+
+    def __enter__(self):
+        self.start_time = time.perf_counter()
+
+    def __exit__(self, *exc):
+        self.timings.append(time.perf_counter() - self.start_time)
+
+    def wraps_function(self, f):
+        @wraps(f)
+        def wrapped_f(*args, **kwargs):
+            with self:
+                return f(*args, **kwargs)
+        return wrapped_f

capytaine-2.3.dist-info/DELVEWHEEL

@@ -0,0 +1,2 @@
+Version: 1.10.1
+Arguments: ['C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-9rerwt60\\cp39-win_amd64\\build\\venv\\Scripts\\delvewheel', 'repair', '-w', 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-9rerwt60\\cp39-win_amd64\\repaired_wheel', 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-9rerwt60\\cp39-win_amd64\\built_wheel\\capytaine-2.3-cp39-cp39-win_amd64.whl', '--no-mangle-all']

{capytaine-2.2.1.dist-info → capytaine-2.3.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: capytaine
-Version: 2.2.1
+Version: 2.3
 Summary: Python BEM solver for linear potential flow, based on Nemoh
-Author-Email: Matthieu Ancellin <matthieu.ancellin@eurobios.com>
+Author-Email: Matthieu Ancellin <matthieu.ancellin@mews-labs.com>
 License:                     GNU GENERAL PUBLIC LICENSE
                                 Version 3, 29 June 2007
          
@@ -683,6 +683,7 @@ Classifier: Programming Language :: Fortran
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Topic :: Scientific/Engineering
+Project-URL: homepage, https://capytaine.org
 Project-URL: repository, https://github.com/capytaine/capytaine
 Requires-Python: >=3.8
 Requires-Dist: numpy>=1.20; python_version >= "3.9"
@@ -695,8 +696,14 @@ Provides-Extra: optional
 Requires-Dist: matplotlib; extra == "optional"
 Requires-Dist: joblib>=1.3; extra == "optional"
 Requires-Dist: meshio; extra == "optional"
+Requires-Dist: netcdf4; extra == "optional"
+Requires-Dist: vtk; extra == "optional"
+Provides-Extra: more-optional
+Requires-Dist: pygmsh; extra == "more-optional"
+Requires-Dist: gmsh; extra == "more-optional"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
+Requires-Dist: capytaine[optional]; extra == "test"
 Provides-Extra: docs
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinx-toolbox; extra == "docs"

{capytaine-2.2.1.dist-info → capytaine-2.3.dist-info}/RECORD

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 capytaine/matrices/__init__.py,sha256=BYCiuVbu4sp3Z6mdbK5uTphUTalvaLhHX1aPLljlsRA,720
-capytaine/meshes/clipper.py,sha256=Xq1SYNFTuw_9oi9qFMaudRn2YnXyuM_Lxe6I_umKrT0,19097
-capytaine/meshes/collections.py,sha256=yIFmip3Dt3UUT4jGZtTuzKmlGitxhyClkbf2R3SZW3c,11081
+capytaine/meshes/clipper.py,sha256=3C1vxe6mlAYdv0uvtvc3ZA_Lb43ks7UZmDZ1mE9ImRc,19142
+capytaine/meshes/collections.py,sha256=8El0zPaUIWbGu_hoqo_CNIv_rbuLfO77AaxNmTr3R7c,11423
 capytaine/meshes/geometry.py,sha256=QSowVTd4dva0pe4osfFZj0giaL-7Dj-T3wdVZ4k-Clg,14516
-capytaine/meshes/meshes.py,sha256=237COlvNonY-zv_y5smvrkMWaLXuBxvOHmnjIZVZvdw,32750
+capytaine/meshes/meshes.py,sha256=-avX1RpGhCp2rLyNtuC7kSBSivjpaguV_K_9x4LfUN8,33165
+capytaine/meshes/mesh_like_protocol.py,sha256=ACIwdvJO_qK6wwvbXUT8s5EoHAIUWWJNoBpDrR_3WCY,1066
 capytaine/meshes/properties.py,sha256=zNnQCTAMReiJDMguU9pPwca_Zj_NDTTRqT-uVgABI0E,11066
 capytaine/meshes/quadratures.py,sha256=j6waiQlEoRfzUsnTL2dQg9Ynq5WYkwZT7vV8KOCwN4E,3307
 capytaine/meshes/quality.py,sha256=YVS294DJCTEyB9qGXEP56h9yqxjWIl6hg8P0QI2msIo,14831
 capytaine/meshes/surface_integrals.py,sha256=7s_LOtyz2I1SFFsUE1YMoeSR-02MsocRb8AJS6hTEjc,2326
-capytaine/meshes/symmetric.py,sha256=9A5HDqbcIq3r0Gkgzgzo9lvAcppCL7fi5rlgyrLYjQg,15611
+capytaine/meshes/symmetric.py,sha256=_yQ8iRiCooFtvH6ryoOUYv0nIbutYiz5atU2rD8USIM,16089
 capytaine/meshes/__init__.py,sha256=FKeQT_I3TAb9iHNqJi0qf9HPo_O001P4fXhZQZ8Oj50,367
 capytaine/meshes/predefined/cylinders.py,sha256=r2UC8uMb60QyyUBaMEvCEkJ9EmazZvDnO-p0GsS2Us8,15160
 capytaine/meshes/predefined/rectangles.py,sha256=wX0vtY8YLMmJ3UZk2oi7q5eKakDnULCXxMhO1KC8eC8,12555
@@ -49,16 +64,17 @@ capytaine/meshes/predefined/spheres.py,sha256=1_fwCvK2sdv3VPdH8xzMeLasbIb-ZYQkT5
 capytaine/meshes/predefined/__init__.py,sha256=BQJOD_GolXloY8Lww0Orhhi0F5m838urQl_-MbsfKLI,371
 capytaine/post_pro/free_surfaces.py,sha256=QwkBHU3si7TlXu3reWFDAuWQb_HrlkeMZwDmArJpzM0,3205
 capytaine/post_pro/impedance.py,sha256=Or2rzFQDewXc0aeO1_Q_B3Sy0sR_hK6afW1VcVe6zT4,3584
-capytaine/post_pro/kochin.py,sha256=My3bdBOanWzCYeEM4jY6vJofQIFjt68NWMv6JycbonQ,1915
+capytaine/post_pro/kochin.py,sha256=xM--OknA8T9zp9m_zgSuUYyJw6tlqIMOeCEB6d375nA,1981
 capytaine/post_pro/rao.py,sha256=vyrNCCInAAsVZHsM3agsk35-PLelcMLAV25LsAUJwlQ,2353
 capytaine/post_pro/__init__.py,sha256=Q5cAAosHI_X24h6mALZvfJWGUobCxWyB4lSMHFMDX4M,280
 capytaine/tools/cache_on_disk.py,sha256=LwUaMkvd-Z46EXeVyYhGQpeNve5PVpM2qj0ESUHXYRs,938
 capytaine/tools/deprecation_handling.py,sha256=oewPgemWDwbZ9of3uPS5k_RZ4kBldHtHYvjbX2PgerY,827
-capytaine/tools/lists_of_points.py,sha256=S0nB3pA_LSxIpDALPDAI9b-bfiaNWlCEADZe9aTRfVY,1913
+capytaine/tools/lists_of_points.py,sha256=OOCZkFBsPZj25KGYAvX2BhVLNnxbR-1lT3BSoEDq5YQ,1880
 capytaine/tools/lru_cache.py,sha256=OH1J6XhXyKQGKfDhngBne_D_C2Jub3g92Y5JWWcN4ik,1758
 capytaine/tools/optional_imports.py,sha256=L2_6h1My2jjl7GHL0_hmHsjOE8hRWFrs0eiq_OIDTH8,887
-capytaine/tools/prony_decomposition.py,sha256=p7xdG8Ky3VVe7YbNr9UkC0JA_v8iDVenFfkCnFP-QQA,2786
-capytaine/tools/symbolic_multiplication.py,sha256=WRreeWbtANlZGxrFkqMc5b0Vp-TReGOtdzfhN5j2vwQ,4139
+capytaine/tools/prony_decomposition.py,sha256=_iqHEhop8oBREz0zY35WXV-UkPw1QHbQhP6L_BrtCQM,5297
+capytaine/tools/symbolic_multiplication.py,sha256=MQLsbAfQcWEn7YgcSNRhBmHMRRXY_8wA9Okt4IGaDmI,4560
+capytaine/tools/timer.py,sha256=Ch47sRiDcOF-EcVrdM7Eyv4Lch2wqf2eQpIXNgHENMY,1528
 capytaine/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 capytaine/ui/cli.py,sha256=DLgsJdmMASM70BqN7bbNQxBkiHKReJDJqgf4E9mr_yk,825
 capytaine/ui/rich.py,sha256=kxI4CVa4ycJBloEHvLpLqrEArkLT4wAdcPKhbEw2hcY,238
@@ -68,13 +84,13 @@ capytaine/ui/vtk/body_viewer.py,sha256=1WGMjHBRhyGkCFxgvJKs_dY-eL2YCCKhqqehKgIww
 capytaine/ui/vtk/helpers.py,sha256=V1_DeB6svtTlzdNzdcL7-GGj5QvCW6wpVzhXVmpVlwI,2722
 capytaine/ui/vtk/mesh_viewer.py,sha256=V6ReLbsArkVAZRX6QZdqHhyo1dStT2ql8T2AzpP8HbA,15211
 capytaine/ui/vtk/__init__.py,sha256=mtXE0si8Fc8QGneQIQNdGPPzhRLNwi4bPMUmQ9Vs1io,164
-capytaine-2.2.1.dist-info/DELVEWHEEL,sha256=jyJZ8RHzSZabqn80y8fle5rfhZ5i82yae3AMyGAWpO0,415
-capytaine-2.2.1.dist-info/entry_points.txt,sha256=R72-je8lc6ELm8ftt7lJ7f1aalnQs5BWYrGDBMexHII,53
-capytaine-2.2.1.dist-info/LICENSE,sha256=Czg9WmPaZE9ijZnDOXbqZIftiaqlnwsyV5kt6sEXHms,35821
-capytaine-2.2.1.dist-info/METADATA,sha256=mntdNUvFCH4TIl63JhG2wWpWawEFM3EUy0haUPlIyCw,45212
-capytaine-2.2.1.dist-info/RECORD,,
-capytaine-2.2.1.dist-info/WHEEL,sha256=8AdrFzOtKQ6LLJ-VyqCU3y1iN8N--fMXYqrdkeTKDn0,83
-capytaine.libs/.load-order-capytaine-2.2.1,sha256=GAsTsgRkHGMz8jIw1tqU1-FXOdyTmahlPtPnfkRAJOc,89
+capytaine-2.3.dist-info/DELVEWHEEL,sha256=_bZsGPyy8YBTzDYdjxkK2J_t4wi58f8_8qko4gwAdng,414
+capytaine-2.3.dist-info/entry_points.txt,sha256=R72-je8lc6ELm8ftt7lJ7f1aalnQs5BWYrGDBMexHII,53
+capytaine-2.3.dist-info/LICENSE,sha256=Czg9WmPaZE9ijZnDOXbqZIftiaqlnwsyV5kt6sEXHms,35821
+capytaine-2.3.dist-info/METADATA,sha256=NSFNwYHZoOfMqn7if-xXY-r9qOLAGrlbUSG8qtlahy8,45516
+capytaine-2.3.dist-info/RECORD,,
+capytaine-2.3.dist-info/WHEEL,sha256=8AdrFzOtKQ6LLJ-VyqCU3y1iN8N--fMXYqrdkeTKDn0,83
+capytaine.libs/.load-order-capytaine-2.3,sha256=1ekdUP0Ux3u3Da1tlcpgxxB3LcBoQ6M-ATaNPXVQ_zc,89
 capytaine.libs/libgcc_s_seh-1.dll,sha256=q2m46g2pAq7jvn1d0qbVW6WqyOpxQ6KtnAdh5r3gCxY,111616
 capytaine.libs/libgfortran-5.dll,sha256=wLLASxjhj_hbogJghmWeKSyi6w4L9h8xR04-iS1Ejq4,3118080
 capytaine.libs/libgomp-1.dll,sha256=yCJD_z8GQ7Hi7iXgwG2hkjFAOqf-KeE45YnavaKCpf8,280576

capytaine-2.2.1.dist-info/DELVEWHEEL

@@ -1,2 +0,0 @@
-Version: 1.9.0
-Arguments: ['C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-qolinjw3\\cp39-win_amd64\\build\\venv\\Scripts\\delvewheel', 'repair', '-w', 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-qolinjw3\\cp39-win_amd64\\repaired_wheel', 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\cibw-run-qolinjw3\\cp39-win_amd64\\built_wheel\\capytaine-2.2.1-cp39-cp39-win_amd64.whl', '--no-mangle-all']

capytaine.libs/{.load-order-capytaine-2.2.1 → .load-order-capytaine-2.3}

@@ -1,5 +1,5 @@
-libgomp-1.dll
+libquadmath-0.dll
 libgfortran-5.dll
+libgomp-1.dll
 libgcc_s_seh-1.dll
 libwinpthread-1.dll
-libquadmath-0.dll