https://github.com/FEniCS/dolfinx/pull/2763

Author: jorgensd

Changelog.md

@@ -1,20 +1,24 @@
 # Changelog
 
 ## main
+
+- Renamed `dolfinx.graph.create_adjacencylist` to `dolfinx.graph.adjacencylist`
+- Renamed `dolfinx.plot.create_vtk_mesh` to `dolfinx.plot.vtk_mesh`
 - `dolfinx.geometry.BoundingBoxTree` has been changed to `dolfinx.geometry.bb_tree`
 - `create_mesh` with Meshio has been modified. Note that you now need to pass dtype `np.int32` to the cell_data.
 - Update dolfinx petsc API. Now one needs to explicitly import `dolfinx.fem.petsc` and `dolfinx.fem.nls`, as PETSc is no longer a strict requirement. Replace `petsc4py.PETSc.ScalarType` with `dolfinx.default_scalar_type` in demos where we do not use `petsc4py` explicitly.
 
 ## v0.6.0
+
 - Remove `ipygany` and `pythreejs` as plotting backends. Using `panel`.
 - Add gif-output to [chapter2/diffusion_code] and [chapter2/hyperelasticity].
 - Replace `dolfinx.fem.Function.geometric_dimension` with `len(dolfinx.fem.Function)`
 - Improve [chapter2/ns_code2] to have better splitting scheme and density.
 - Improve mesh quality in [chapter3/em].
 - `jit_params` and `form_compiler_params` renamed to `*_options`.
 
-
 ## v0.5.0
+
 - Using new GMSH interface in DOLFINx (`dolfinx.io.gmshio`) in all demos using GMSH
 - Added a section on custom Newton-solvers, see [chapter4/newton-solver].
 - Various minor DOLFINx API updates. `dolfinx.mesh.compute_boundary_facets` -> `dolfinx.mesh.exterior_facet_indices` with slightly different functionality. Use `dolfinx.mesh.MeshTagsMetaClass.find` instead of `mt.indices[mt.values==value]`.
@@ -23,9 +27,11 @@
 - Add example of how to use `DOLFINx` in complex mode, see [chapter1/complex_mode].
 
 ## 0.4.1
+
 - No changes
 
 ## 0.4.0 (05.02.2021)
+
 - All `pyvista` plotting has been rewritten to use `ipygany` and `pythreejs` as well as using a cleaner interface.
 - `dolfinx.plot.create_vtk_topology` has been renamed to `dolfinx.plot.create_vtk_mesh` and can now be directly used as input to `pyvista.UnstructuredGrid`.
 - `dolfinx.fem.Function.compute_point_values` has been deprecated. Interpolation into a CG-1 is now the way of getting vertex values.
@@ -36,14 +42,14 @@
 - Various API changes relating to the import structure of DOLFINx
 
 ## 0.3.0 (09.09.2021)
+
 - Major improvements in [Form compiler parameters](chapter4/compiler_parameters), using pandas and seaborn for visualization of speed-ups gained using form compiler parameters.
 - API change: `dolfinx.cpp.la.scatter_forward(u.x)` -> `u.x.scatter_forward`
 - Various plotting updates due to new version of pyvista.
 - Updating of the [Hyperelasticity demo](chapter2/hyperelasticity), now using DOLFINx wrappers to create the non-linear problem
 - Internal updates due to bumping of jupyter-book versions
 - Various typos and capitalizations fixed by @mscroggs in [PR 35](https://github.com/jorgensd/dolfinx-tutorial/pull/35).
 
-
-
 ## 0.1.0 (11.05.2021)
-- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).
+
+- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).

chapter1/complex_mode.ipynb

@@ -119,8 +119,8 @@
 
 import pyvista
 pyvista.start_xvfb()
-p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.create_vtk_mesh(mesh, mesh.topology.dim))
-pyvista_cells, cell_types, geometry = dolfinx.plot.create_vtk_mesh(V)
+p_mesh = pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(mesh, mesh.topology.dim))
+pyvista_cells, cell_types, geometry = dolfinx.plot.vtk_mesh(V)
 grid = pyvista.UnstructuredGrid(pyvista_cells, cell_types, geometry)
 grid.point_data["u_real"] = uh.x.array.real
 grid.point_data["u_imag"] = uh.x.array.imag

chapter1/complex_mode.py

@@ -417,7 +417,7 @@
     "## Plotting the mesh using pyvista\n",
     "We will visualizing the mesh using [pyvista](https://docs.pyvista.org/), an interface to the VTK toolkit.\n",
     "We start by converting the mesh to a format that can be used with `pyvista`.\n",
-    "To do this we use the function `dolfinx.plot.create_vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.\n",
+    "To do this we use the function `dolfinx.plot.vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.\n",
     "We need to start a virtual framebuffer for plotting through docker containers. You can print the current backend and change it with `pyvista.set_jupyter_backend(backend)`"
    ]
   },
@@ -453,7 +453,7 @@
    "source": [
     "from dolfinx import plot\n",
     "pyvista.start_xvfb()\n",
-    "topology, cell_types, geometry = plot.create_vtk_mesh(domain, tdim)\n",
+    "topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)\n",
     "grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)"
    ]
   },
@@ -1231,7 +1231,7 @@
    "metadata": {},
    "source": [
     "## Plotting a function using pyvista\n",
-    "We want to plot the solution `uh`. As the function space used to defined the mesh is disconnected from the function space defining the mesh, we create a mesh based on the dof coordinates for the function space `V`. We use `dolfinx.plot.create_vtk_mesh` with the function space as input to create a mesh with mesh geometry based on the dof coordinates."
+    "We want to plot the solution `uh`. As the function space used to defined the mesh is disconnected from the function space defining the mesh, we create a mesh based on the dof coordinates for the function space `V`. We use `dolfinx.plot.vtk_mesh` with the function space as input to create a mesh with mesh geometry based on the dof coordinates."
    ]
   },
   {
@@ -1245,7 +1245,7 @@
    },
    "outputs": [],
    "source": [
-    "u_topology, u_cell_types, u_geometry = plot.create_vtk_mesh(V)"
+    "u_topology, u_cell_types, u_geometry = plot.vtk_mesh(V)"
    ]
   },
   {

chapter1/fundamentals_code.ipynb

@@ -223,7 +223,7 @@
 # ## Plotting the mesh using pyvista
 # We will visualizing the mesh using [pyvista](https://docs.pyvista.org/), an interface to the VTK toolkit.
 # We start by converting the mesh to a format that can be used with `pyvista`.
-# To do this we use the function `dolfinx.plot.create_vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.
+# To do this we use the function `dolfinx.plot.vtk_mesh`. The first step is to create an unstructured grid that can be used by `pyvista`.
 # We need to start a virtual framebuffer for plotting through docker containers. You can print the current backend and change it with `pyvista.set_jupyter_backend(backend)`
 
 import pyvista
@@ -232,7 +232,7 @@
 # + vscode={"languageId": "python"}
 from dolfinx import plot
 pyvista.start_xvfb()
-topology, cell_types, geometry = plot.create_vtk_mesh(domain, tdim)
+topology, cell_types, geometry = plot.vtk_mesh(domain, tdim)
 grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
 # -
 
@@ -252,10 +252,10 @@
 # -
 
 # ## Plotting a function using pyvista
-# We want to plot the solution `uh`. As the function space used to defined the mesh is disconnected from the function space defining the mesh, we create a mesh based on the dof coordinates for the function space `V`. We use `dolfinx.plot.create_vtk_mesh` with the function space as input to create a mesh with mesh geometry based on the dof coordinates.
+# We want to plot the solution `uh`. As the function space used to defined the mesh is disconnected from the function space defining the mesh, we create a mesh based on the dof coordinates for the function space `V`. We use `dolfinx.plot.vtk_mesh` with the function space as input to create a mesh with mesh geometry based on the dof coordinates.
 
 # + vscode={"languageId": "python"}
-u_topology, u_cell_types, u_geometry = plot.create_vtk_mesh(V)
+u_topology, u_cell_types, u_geometry = plot.vtk_mesh(V)
 # -
 
 # Next, we create the `pyvista.UnstructuredGrid` and add the dof-values to the mesh.

chapter1/fundamentals_code.py

@@ -1013,12 +1013,12 @@
     }
    ],
    "source": [
-    "from dolfinx.plot import create_vtk_mesh\n",
+    "from dolfinx.plot import vtk_mesh\n",
     "import pyvista\n",
     "pyvista.start_xvfb()\n",
     "\n",
     "# Extract topology from mesh and create pyvista mesh\n",
-    "topology, cell_types, x = create_vtk_mesh(V)\n",
+    "topology, cell_types, x = vtk_mesh(V)\n",
     "grid = pyvista.UnstructuredGrid(topology, cell_types, x)\n",
     "\n",
     "# Set deflection values and add it to plotter\n",
@@ -1136,7 +1136,7 @@
    ],
    "source": [
     "load_plotter = pyvista.Plotter()\n",
-    "p_grid = pyvista.UnstructuredGrid(*create_vtk_mesh(Q))\n",
+    "p_grid = pyvista.UnstructuredGrid(*vtk_mesh(Q))\n",
     "p_grid.point_data[\"p\"] = pressure.x.array.real\n",
     "warped_p = p_grid.warp_by_scalar(\"p\", factor=0.5)\n",
     "warped_p.set_active_scalars(\"p\")\n",

chapter1/membrane_code.ipynb

@@ -118,12 +118,12 @@ def on_boundary(x):
 # We first plot the deflection $u_h$ over the domain $\Omega$.
 
 # +
-from dolfinx.plot import create_vtk_mesh
+from dolfinx.plot import vtk_mesh
 import pyvista
 pyvista.start_xvfb()
 
 # Extract topology from mesh and create pyvista mesh
-topology, cell_types, x = create_vtk_mesh(V)
+topology, cell_types, x = vtk_mesh(V)
 grid = pyvista.UnstructuredGrid(topology, cell_types, x)
 
 # Set deflection values and add it to plotter
@@ -141,7 +141,7 @@ def on_boundary(x):
 # We next plot the load on the domain
 
 load_plotter = pyvista.Plotter()
-p_grid = pyvista.UnstructuredGrid(*create_vtk_mesh(Q))
+p_grid = pyvista.UnstructuredGrid(*vtk_mesh(Q))
 p_grid.point_data["p"] = pressure.x.array.real
 warped_p = p_grid.warp_by_scalar("p", factor=0.5)
 warped_p.set_active_scalars("p")

chapter1/membrane_code.py

@@ -924,7 +924,7 @@
     "import pyvista\n",
     "pyvista.start_xvfb()\n",
     "\n",
-    "grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))\n",
+    "grid = pyvista.UnstructuredGrid(*plot.vtk_mesh(V))\n",
     "grid.point_data[\"u\"] = uh.x.array.real\n",
     "grid.set_active_scalars(\"u\")\n",
     "plotter = pyvista.Plotter()\n",

chapter1/nitsche.ipynb

@@ -96,7 +96,7 @@
 import pyvista
 pyvista.start_xvfb()
 
-grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))
+grid = pyvista.UnstructuredGrid(*plot.vtk_mesh(V))
 grid.point_data["u"] = uh.x.array.real
 grid.set_active_scalars("u")
 plotter = pyvista.Plotter()

chapter1/nitsche.py

@@ -198,7 +198,7 @@
     "import matplotlib as mpl\n",
     "pyvista.start_xvfb()\n",
     "\n",
-    "grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))\n",
+    "grid = pyvista.UnstructuredGrid(*plot.vtk_mesh(V))\n",
     "\n",
     "plotter = pyvista.Plotter()\n",
     "plotter.open_gif(\"u_time.gif\", fps=10)\n",

chapter2/diffusion_code.ipynb

@@ -123,7 +123,7 @@ def initial_condition(x, a=5):
 import matplotlib as mpl
 pyvista.start_xvfb()
 
-grid = pyvista.UnstructuredGrid(*plot.create_vtk_mesh(V))
+grid = pyvista.UnstructuredGrid(*plot.vtk_mesh(V))
 
 plotter = pyvista.Plotter()
 plotter.open_gif("u_time.gif", fps=10)