dolfinx v0.8.0

Author: pierricmora

AUTHORS

@@ -0,0 +1,3 @@
+Pierric Mora
+MassinaFengal
+mlehujeur

Dockerfile.lab

@@ -1,4 +1,4 @@
-FROM dolfinx/lab:v0.7.3
+FROM dolfinx/lab:v0.8.0
 LABEL maintainer="Pierric Mora <pierric.mora@univ-eiffel.fr>"
 LABEL description=" elastodynamics with FEniCSx/DOLFINx "
 
@@ -19,14 +19,15 @@ RUN pip3 install . &&\
 ARG PYTHON_VERSION=3.10
 
 # Clone DOLFINX_MPC source dir
-RUN git clone  --branch v0.7.0.post1 https://github.com/jorgensd/dolfinx_mpc.git
+RUN git clone  --branch v0.8.1 https://github.com/jorgensd/dolfinx_mpc.git
 
 # Install real mode
 RUN . /usr/local/bin/dolfinx-real-mode && \
     . /usr/local/dolfinx-real/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real  -DCMAKE_BUILD_TYPE=Developer -B build-dir-real dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-real && \
-    python3 -m pip install -v --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir dolfinx_mpc/python
+    python3 -m pip install -v --break-system-packages --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 # Clean repo to remove build dir from pip
 RUN rm -rf dolfinx_mpc/python/build 
@@ -36,7 +37,8 @@ RUN . /usr/local/bin/dolfinx-complex-mode && \
     . /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja  -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-complex -DCMAKE_BUILD_TYPE=Developer -B build-dir-complex dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-complex && \
-    python3 -m pip install -v --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir dolfinx_mpc/python
+    python3 -m pip install --break-system-packages -v --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 
 WORKDIR /root

Dockerfile.shell

@@ -1,4 +1,4 @@
-FROM dolfinx/dolfinx:v0.7.3
+FROM dolfinx/dolfinx:v0.8.0
 LABEL maintainer="Pierric Mora <pierric.mora@univ-eiffel.fr>"
 LABEL description=" elastodynamics with FEniCSx/DOLFINx "
 
@@ -26,14 +26,15 @@ RUN apt-get update && \
 ARG PYTHON_VERSION=3.10
 
 # Clone DOLFINX_MPC source dir
-RUN git clone  --branch v0.7.0.post1 https://github.com/jorgensd/dolfinx_mpc.git
+RUN git clone  --branch v0.8.1 https://github.com/jorgensd/dolfinx_mpc.git
 
 # Install real mode
 RUN . /usr/local/bin/dolfinx-real-mode && \
     . /usr/local/dolfinx-real/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-real  -DCMAKE_BUILD_TYPE=Developer -B build-dir-real dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-real && \
-    python3 -m pip install -v --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir dolfinx_mpc/python
+    python3 -m pip install -v --break-system-packages --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-real/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 # Clean repo to remove build dir from pip
 RUN rm -rf dolfinx_mpc/python/build 
@@ -43,7 +44,8 @@ RUN . /usr/local/bin/dolfinx-complex-mode && \
     . /usr/local/dolfinx-complex/lib/dolfinx/dolfinx.conf && \
     cmake -G Ninja  -DCMAKE_INSTALL_PREFIX=/usr/local/dolfinx-complex -DCMAKE_BUILD_TYPE=Developer -B build-dir-complex dolfinx_mpc/cpp/ && \
     ninja install -j4  -C build-dir-complex && \
-    python3 -m pip install -v --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir dolfinx_mpc/python
+    python3 -m pip install --break-system-packages -v --no-build-isolation --check-build-dependencies \
+    --target /usr/local/dolfinx-complex/lib/python${PYTHON_VERSION}/dist-packages --no-dependencies --no-cache-dir ./dolfinx_mpc/python
 
 
 WORKDIR /root

demo/eigs_3D_AluminumCube.py

@@ -36,7 +36,7 @@
 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,)))
 # -
 
 # ### Define the material law

demo/eigs_3D_ElasticBeam.py

@@ -52,7 +52,7 @@
 domain = mesh.create_box(MPI.COMM_WORLD, extent, [Nx, Ny, Nz])
 
 # create the function space
-V = fem.FunctionSpace(domain, ("Lagrange", 2, (domain.geometry.dim,)))
+V = fem.functionspace(domain, ("Lagrange", 2, (domain.geometry.dim,)))
 
 # define some tags
 tag_left, tag_top, tag_right, tag_bottom, tag_back, tag_front = 1, 2, 3, 4, 5, 6

demo/freq_2D-PSV_FullSpace.py

@@ -50,7 +50,7 @@
 domain = mesh.create_rectangle(MPI.COMM_WORLD, extent, [Nx, Ny], mesh.CellType.triangle)
 
 # create the function space
-V = fem.FunctionSpace(domain, ("Lagrange", degElement, (domain.geometry.dim,)))
+V = fem.functionspace(domain, ("Lagrange", degElement, (domain.geometry.dim,)))
 
 tag_left, tag_top, tag_right, tag_bottom = 1, 2, 3, 4
 all_tags = (tag_left, tag_top, tag_right, tag_bottom)
@@ -131,7 +131,7 @@
 u_res = fem.Function(V, name='solution')
 
 # Solve
-fdsolver.solve(omega=omega, out=u_res.vector)
+fdsolver.solve(omega=omega, out=u_res.x.petsc_vec)
 
 # Plot
 if domain.comm.rank == 0:
@@ -190,7 +190,7 @@ def cbck_storeAtPoints(i, out):
     p = None
 
 # Solve
-fdsolver.solve(omega=omegas, out=u_res.vector, callbacks=[cbck_storeAtPoints], live_plotter=p)
+fdsolver.solve(omega=omegas, out=u_res.x.petsc_vec, callbacks=[cbck_storeAtPoints], live_plotter=p)
 # -
 
 # ### Post-processing

demo/freq_2D-SH_FullSpace.py

@@ -52,7 +52,7 @@
 domain = mesh.create_rectangle(MPI.COMM_WORLD, extent, [Nx, Ny], mesh.CellType.triangle)
 
 # create the function space
-V = fem.FunctionSpace(domain, ("Lagrange", degElement))
+V = fem.functionspace(domain, ("Lagrange", degElement))
 
 tag_left, tag_top, tag_right, tag_bottom = 1, 2, 3, 4
 all_tags = (tag_left, tag_top, tag_right, tag_bottom)
@@ -136,7 +136,7 @@
 u_res = fem.Function(V, name='solution')
 
 # Solve
-fdsolver.solve(omega=omega, out=u_res.vector)
+fdsolver.solve(omega=omega, out=u_res.x.petsc_vec)
 
 # Plot
 if domain.comm.rank == 0:
@@ -193,7 +193,7 @@ def cbck_storeAtPoints(i, out):
     p = None
 
 # Solve
-fdsolver.solve(omega=omegas, out=u_res.vector, callbacks=[cbck_storeAtPoints], live_plotter=p)
+fdsolver.solve(omega=omegas, out=u_res.x.petsc_vec, callbacks=[cbck_storeAtPoints], live_plotter=p)
 # -
 
 # ### Post-processing

demo/tdsdyn_3D_ElasticBeam.py

@@ -46,7 +46,7 @@
 domain = mesh.create_box(MPI.COMM_WORLD, extent, [Nx, Ny, Nz])
 
 # create the function space
-V = fem.FunctionSpace(domain, ("Lagrange", 1, (domain.geometry.dim,)))
+V = fem.functionspace(domain, ("Lagrange", 1, (domain.geometry.dim,)))
 
 # define some tags
 tag_left, tag_top, tag_right, tag_bottom, tag_back, tag_front = 1, 2, 3, 4, 5, 6
@@ -152,7 +152,9 @@
 kwargsTScheme = dict(scheme='g-a-newmark', alpha_m=alpha_m, alpha_f=alpha_f)
 
 # Time integration: define a TimeStepper instance
-tStepper = TimeStepper.build(V, pde.m, pde.c, pde.k, pde.L, dt, bcs=bcs, **kwargsTScheme)
+tStepper = TimeStepper.build(V,
+                             pde.M_fn, pde.C_fn, pde.K_fn, pde.b_fn, dt, bcs=bcs,
+                             **kwargsTScheme)
 
 # Set the initial values
 tStepper.set_initial_condition(u0=[0, 0, 0], v0=[0, 0, 0], t0=0)
@@ -184,9 +186,19 @@
 u_n = tStepper.timescheme.u  # The displacement at time t_n
 v_n = tStepper.timescheme.v  # The velocity at time t_n
 comm = V.mesh.comm
-Energy_elastic = lambda *a: comm.allreduce(fem.assemble_scalar(fem.form(1/2 * pde.k(u_n, u_n))), op=MPI.SUM)
-Energy_kinetic = lambda *a: comm.allreduce(fem.assemble_scalar(fem.form(1/2 * pde.m(v_n, v_n))), op=MPI.SUM)
-Energy_damping = lambda *a: dt * comm.allreduce(fem.assemble_scalar(fem.form(pde.c(v_n, v_n))), op=MPI.SUM)
+
+
+def Energy_elastic():
+    return comm.allreduce(fem.assemble_scalar(fem.form(1/2 * pde.K_fn(u_n, u_n))), op=MPI.SUM)
+
+
+def Energy_kinetic():
+    return comm.allreduce(fem.assemble_scalar(fem.form(1/2 * pde.M_fn(v_n, v_n))), op=MPI.SUM)
+
+
+def Energy_damping():
+    return dt * comm.allreduce(fem.assemble_scalar(fem.form(pde.C_fn(v_n, v_n))), op=MPI.SUM)
+
 
 # -> live plotting parameters
 clim = 0.4 * L_ * B_ * H_ / (E * B_ * H_**3 / 12) * np.amax(F_0) * np.array([0, 1])

demo/weq_2D-PSV_FullSpace.py

@@ -59,7 +59,7 @@
 domain = mesh.create_rectangle(MPI.COMM_WORLD, extent, [Nx, Ny], cell_type)
 
 # create the function space
-V = fem.FunctionSpace(domain, specFE)
+V = fem.functionspace(domain, specFE)
 
 # define some tags
 tag_left, tag_top, tag_right, tag_bottom = 1, 2, 3, 4
@@ -165,7 +165,7 @@ def F_body_function(t):  # source(x) at a given time
 #  Time integration
 #     diagonal=True assumes the left hand side operator is indeed diagonal
 tStepper = TimeStepper.build(V,
-                             pde.m, pde.c, pde.k, pde.L, dt, bcs=bcs,
+                             pde.M_fn, pde.C_fn, pde.K_fn, pde.b_fn, dt, bcs=bcs,
                              scheme='leapfrog', diagonal=True)
 
 # Set the initial values

demo/weq_2D-PSV_HalfSpace_Lamb_KomatitschVilotte_BSSA1998.py

@@ -66,7 +66,7 @@
 domain, cell_tags, facet_tags = gmshio.model_to_mesh(model, comm, gmsh_model_rank, gdim=2)
 
 # Create the function space
-V = fem.FunctionSpace(domain, specFE)
+V = fem.functionspace(domain, specFE)
 
 
 def y_surf(x):
@@ -174,7 +174,7 @@ def T_N_function(t):
 #  Time integration
 #     diagonal=True assumes the left hand side operator is indeed diagonal
 tStepper = TimeStepper.build(V,
-                             pde.m, pde.c, pde.k, pde.L, dt, bcs=bcs,
+                             pde.M_fn, pde.C_fn, pde.K_fn, pde.b_fn, dt, bcs=bcs,
                              scheme='leapfrog', diagonal=True)
 
 # Set the initial values