Merge pull request #23 from Universite-Gustave-Eiffel/dev

Doc improvements

.flake8

@@ -4,3 +4,5 @@ ignore = W605, W503
 exclude =
     demo
     conf.py
+    jupyter_execute
+    venv

.gitignore

@@ -47,6 +47,7 @@ wheels/
 .installed.cfg
 *.egg
 docs/_build/
+jupyter_execute/
 
 # Unit test / coverage reports
 htmlcov/

Dockerfile.lab

@@ -8,7 +8,7 @@ COPY ./demo /root/demo/
 
 # Install elastodynamicsx and optional dependencies
 RUN pip3 install . &&\
-    pip3 install tqdm pyvista ipygany pythreejs ipyvtklink --upgrade &&\
+    pip3 install tqdm pyvista[trame] --upgrade &&\
     rm -rf /tmp/*
 
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 GeoENDGroup / Instrumentation
+Copyright (c) 2022-2024 ElastodynamiCSx developers
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

demo/README.rst

@@ -0,0 +1,64 @@
+Demos
+=====
+
+The following examples illustrate how to use ``elastodynamicsx`` to build and solve problems from begin to end. They can be run in parallel with:
+
+.. code-block:: bash
+
+  # run on 2 nodes:
+  mpiexec -n 2 python3 example.py
+
+Several examples rely on functions that are not embedded in the main .py file (models, analytical solutions): companion files can be found in the `demo/ <https://github.com/Universite-Gustave-Eiffel/elastodynamicsx/tree/main/demo>`_ folder in github.
+
+
+Time domain
+-----------
+
+| **Explicit** scheme
+|     *Wave propagation modeling*, *Spectral elements*
+
+.. nbgallery::
+   :maxdepth: 3
+   :titlesonly:
+   :glob:
+
+   weq*
+
+
+| **Implicit** scheme
+|     *Structural dynamics*
+
+.. nbgallery::
+   :maxdepth: 3
+   :titlesonly:
+   :glob:
+
+   tdsdyn*
+
+
+Frequency domain -- Helmoltz equation
+-------------------------------------
+
+.. nbgallery::
+   :maxdepth: 3
+   :titlesonly:
+   :glob:
+
+   freq*
+
+
+Eigenmodes
+----------
+
+.. nbgallery::
+   :maxdepth: 3
+   :titlesonly:
+   :glob:
+
+   eigs*
+
+
+Guided waves
+------------
+
+* *coming soon*

demo/__init__.py

@@ -1,2 +0,0 @@
-from . import *
-

demo/analyticalsolutions/analyticalsolutions.py → demo/analyticalsolutions.py

@@ -409,4 +409,5 @@ def src_t(t):
 
 
 if __name__ == "__main__" :
-    _test()
+    # _test()
+    pass

demo/eigs_3D_AluminumCube.py

@@ -1,80 +1,100 @@
-"""
-Eigenmodes
-
-Free resonances of an aluminum cube, compared against litterature data
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.15.2
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# # Resonances of an aluminum cube
+#
+# - Eigenmodes
+# - 3D
+# - Comparison with literature data
 
-Data from: Ogi, H., Sato, K., Asada, T., & Hirao, M. (2002). Complete mode
-identification for resonance ultrasound spectroscopy. The Journal of the
-Acoustical Society of America, 112(6), 2553-2557.
-"""
+# +
+import numpy as np
 
-from dolfinx import mesh, fem
+from dolfinx import mesh, fem, default_scalar_type
 from mpi4py import MPI
 from petsc4py import PETSc
-import numpy as np
 
 from elastodynamicsx.pde import material, PDE
 from elastodynamicsx.solvers import EigenmodesSolver
+# -
 
-# -----------------------------------------------------
-#                     FE domain
-# -----------------------------------------------------
-L1, L2, L3 = 11.92, 10.93, 9.86  # millimeters
-
-Nx = Ny = Nz = 6
+# ### FE domain
 
+# +
+L1, L2, L3 = 11.92, 10.93, 9.86  # Lengths, in millimeters
+Nx = Ny = Nz = 6  # Nb of elts.
 extent = [[0., 0., 0.], [L1, L2, L3]]
 domain = mesh.create_box(MPI.COMM_WORLD, extent, [Nx, Ny, Nz])
-#
-V = fem.FunctionSpace(domain, ("Lagrange", 2, (domain.geometry.dim,)))
-#
-# -----------------------------------------------------
 
+V = fem.FunctionSpace(domain, ("Lagrange", 2, (domain.geometry.dim,)))
+# -
 
-# -----------------------------------------------------
-#                 Material parameters
-# -----------------------------------------------------
-rho, C11, C44 = 2.788, 109.26, 26.72  # Aluminum. rho in g/cm3, Cij in GPa -> freq. in MHz
-lambda_ = C11 - 2*C44
+# ### Define the material law
+# Material:
+# - Aluminum
+# - isotropic elasticity
+#
+# Units:
+# - $\rho$ in g/cm3
+# - $C_{ij}$ in GPa
+# - -> frequencies in MHz
+
+# +
+rho, C11, C44 = 2.788, 109.26, 26.72
+lambda_ = C11 - 2 * C44
 mu      = C44
-rho     = fem.Constant(domain, PETSc.ScalarType(rho))
-lambda_ = fem.Constant(domain, PETSc.ScalarType(lambda_))
-mu      = fem.Constant(domain, PETSc.ScalarType(mu))
+rho     = fem.Constant(domain, default_scalar_type(rho))
+lambda_ = fem.Constant(domain, default_scalar_type(lambda_))
+mu      = fem.Constant(domain, default_scalar_type(mu))
 
-material = material(V, 'isotropic', rho, lambda_, mu)
-#
-# -----------------------------------------------------
+aluminum = material(V, 'isotropic', rho, lambda_, mu)
+# -
 
+# ### Assemble the PDE
 
-# -----------------------------------------------------
-#                       Solve
-# -----------------------------------------------------
-### PDE
-pde = PDE(V, materials=[material])
+pde = PDE(V, materials=[aluminum])
+
+# ### Solve
 
-### Initialize the solver
-eps = EigenmodesSolver(V.mesh.comm, pde.M(), None, pde.K(), nev=20)
+# ## Initialize the solver; prepare to solve for 20 eigenvalues
+M = pde.M()  # mass matrix (PETSc)
+C = None  # None to ensure no damping
+K = pde.K()  # stiffness matrix (PETSc)
+eps = EigenmodesSolver(V.mesh.comm, M, C, K, nev=20)
 
-### Run the big calculation!
+# ## Run the big calculation!
 eps.solve()
-### End of big calc.
+# ## End of big calc.
 
-### Get the result
+# +
+# ## Get the result
 # eps.printEigenvalues()
 eigenfreqs = eps.getEigenfrequencies()
 # eigenmodes = eps.getEigenmodes()
+
 eps.plot(V, slice(6,6+9), wireframe=True, factor=30)  # Avoid the first 6 rigid body modes
-#
-# -----------------------------------------------------
+# -
 
 
+# ### Compare with literature values
 # -----------------------------------------------------
-#            Compare with litterature values
-# -----------------------------------------------------
-# Data from: Ogi, H., Sato, K., Asada, T., & Hirao, M. (2002). Complete mode
-# identification for resonance ultrasound spectroscopy. The Journal of the
-# Acoustical Society of America, 112(6), 2553-2557.
+# Data from:  
+#   Ogi, H., Sato, K., Asada, T., & Hirao, M. (2002). Complete mode
+# identification for resonance ultrasound spectroscopy. *The Journal of the
+# Acoustical Society of America*, 112(6), 2553-2557.
 
+# +
 freqs_OgiEtAl_exp  = np.array([116.716, 143.783, 158.081, 166.5  , 169.523, 177.846, 183.875, 186.047,
                                190.341, 197.386, 201.133, 207.386, 209.836, 214.753, 223.548, 231.266,
                                233.538, 234.717, 250.98 , 251.256, 252.742, 256.122, 257.595, 258.118,
@@ -93,7 +113,3 @@
 print('  FE   \tOgi et al, calc.\t Ogi et al, exp. \t(kHz)')
 for fFE, fOgi_calc, fOgi_exp in zip(eigenfreqs[6:]*1e3, freqs_OgiEtAl_calc, freqs_OgiEtAl_exp):  # *1e3 to convert MHz into kHz
     print(str(round(fFE, 3)) +"\t     "+ str(round(fOgi_calc, 3)) +"\t\t     "+ str(round(fOgi_exp, 3)))
-#
-# -----------------------------------------------------
-
-