update with pointcloud plotting and v0.8.0.0

.github/workflows/run_tests.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   Run-Tests:
     runs-on: ubuntu-latest
-    container: dolfinx/dolfinx:v0.7.3
+    container: dolfinx/dolfinx:nightly
     steps:
       - uses: actions/checkout@v3
 

examples/demo_bad_fe_problem.py

@@ -10,7 +10,7 @@
 
 
 mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 4, 4)
-V = dolfinx.fem.FunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1))
 v = ufl.TestFunction(V)
 
 u = dolfinx.fem.Function(V)

examples/demo_debug_plotting.py

@@ -17,13 +17,13 @@
 febug.plot_mesh(mesh, plotter=subplotter)
 
 # -- CG1 dofmap and ordering
-V = dolfinx.fem.FunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1))
 subplotter.subplot(0, 1)
 subplotter.add_title("CG1 dofmap")
 febug.plot_dofmap(V, plotter=subplotter)
 
 # -- CG2 dofmap and ordering
-V = dolfinx.fem.FunctionSpace(mesh, ("CG", 2))
+V = dolfinx.fem.functionspace(mesh, ("CG", 2))
 subplotter.subplot(0, 2)
 subplotter.add_title("CG2 dofmap")
 febug.plot_dofmap(V, plotter=subplotter)
@@ -40,7 +40,7 @@
 for e_i, e in enumerate(eles):
     subplotter.subplot(2, e_i)
     subplotter.add_title(f"{e[0]}{e[1]} space DoFs")
-    V = dolfinx.fem.FunctionSpace(mesh, e)
+    V = dolfinx.fem.functionspace(mesh, e)
     u = dolfinx.fem.Function(V)
     u.interpolate(lambda x: x[0]*x[1])
     febug.plot_function(u, plotter=subplotter)

examples/demo_ksp_monitors.py

@@ -23,7 +23,7 @@
 x = ufl.SpatialCoordinate(mesh)
 f = ufl.sin(ufl.pi*x[0])*ufl.sin(ufl.pi*x[1])*ufl.sin(ufl.pi*x[2])
 
-V = dolfinx.fem.FunctionSpace(mesh, ("Lagrange", 2))
+V = dolfinx.fem.functionspace(mesh, ("Lagrange", 2))
 u = ufl.TrialFunction(V)
 v = ufl.TestFunction(V)
 a = dolfinx.fem.form(inner(grad(u), grad(v)) * dx)

examples/demo_plotting.py

@@ -20,42 +20,42 @@
 # -- function
 subplotter.subplot(0, 1)
 subplotter.add_title("CG1")
-V = dolfinx.fem.FunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1))
 u = dolfinx.fem.Function(V)
 u.interpolate(lambda x: np.sin(np.pi*x[0])*np.sin(np.pi*x[1]))
 febug.plot_function(u, plotter=subplotter)
 
 # -- high order function
 subplotter.subplot(0, 2)
 subplotter.add_title("CG2")
-V = dolfinx.fem.FunctionSpace(mesh, ("CG", 2))
+V = dolfinx.fem.functionspace(mesh, ("CG", 2))
 u = dolfinx.fem.Function(V)
 u.interpolate(lambda x: np.sin(np.pi*x[0])*np.sin(np.pi*x[1]))
 febug.plot_function(u, plotter=subplotter)
 
 # -- vector function magnitude
 subplotter.subplot(1, 0)
 subplotter.add_title("magnitude")
-V = dolfinx.fem.VectorFunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1, (2,)))
 u = dolfinx.fem.Function(V, dtype=np.float64)
 u.interpolate(lambda x: np.stack((-x[1], x[0])))
-u_scalar = dolfinx.fem.Function(dolfinx.fem.FunctionSpace(mesh, ("CG", 1)))
+u_scalar = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", 1)))
 u_scalar.interpolate(dolfinx.fem.Expression(ufl.inner(u, u),
                      u_scalar.function_space.element.interpolation_points()))
 febug.plot_function(u_scalar, plotter=subplotter)
 
 # -- vector function
 subplotter.subplot(1, 1)
 subplotter.add_title("quiver")
-V = dolfinx.fem.VectorFunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1, (2,)))
 u = dolfinx.fem.Function(V)
 u.interpolate(lambda x: np.stack((-x[1], x[0])))
 febug.plot_quiver(u, plotter=subplotter)
 
 # -- warp
 subplotter.subplot(1, 2)
 subplotter.add_title("warp")
-V = dolfinx.fem.VectorFunctionSpace(mesh, ("CG", 1))
+V = dolfinx.fem.functionspace(mesh, ("CG", 1, (2,)))
 u = dolfinx.fem.Function(V)
 u.interpolate(lambda x: np.stack((-x[1], x[0])))
 febug.plot_warp(u, plotter=subplotter)

febug/__init__.py

@@ -4,7 +4,8 @@
                    plot_streamlines_evenly_spaced_2D,
                    plot_streamlines_from_source,
                    plot_entity_indices,
-                   plot_mesh_quality, plot_function_dofs)
+                   plot_mesh_quality, plot_function_dofs,
+                   plot_point_cloud)
 
 
 def overload_dolfinx():

febug/plot.py

@@ -19,7 +19,7 @@ def _to_pyvista_grid(mesh: dolfinx.mesh.Mesh, tdim: int,
 
 
 @_to_pyvista_grid.register
-def _(V: dolfinx.fem.FunctionSpaceBase):
+def _(V: dolfinx.fem.FunctionSpace):
     return pyvista.UnstructuredGrid(*dolfinx.plot.vtk_mesh(V))
 
 
@@ -40,7 +40,7 @@ def _(u: dolfinx.fem.Function):
     if np.iscomplexobj(dof_values):
         dof_values = dof_values.real
 
-    if V.ufl_element().degree() == 0:
+    if V.ufl_element().degree == 0:
         grid = _to_pyvista_grid(mesh, mesh.topology.dim)
         num_dofs_local = V.dofmap.index_map.size_local
         grid.cell_data[u.name] = dof_values[:num_dofs_local]
@@ -242,7 +242,7 @@ def plot_streamlines_from_source(
     return plotter
 
 
-def plot_dofmap(V: dolfinx.fem.FunctionSpaceBase, plotter: pyvista.Plotter=None):
+def plot_dofmap(V: dolfinx.fem.FunctionSpace, plotter: pyvista.Plotter=None):
     if plotter is None:
         plotter = pyvista.Plotter()
     mesh = V.mesh
@@ -354,6 +354,21 @@ def plot_entity_indices(mesh: dolfinx.mesh.Mesh, tdim: int,
     return plotter
 
 
+def plot_point_cloud(xp: np.ndarray[float],
+                     plotter: pyvista.Plotter=None):
+    if plotter is None:
+        plotter = pyvista.Plotter()
+
+    pv_point_cloud = pyvista.PolyData(xp)
+    plotter.add_mesh(pv_point_cloud)
+
+    if np.all(np.isclose(xp[:,2], 0.0)):
+        plotter.enable_parallel_projection()
+        plotter.view_xy()
+
+    return plotter
+
+
 def plot_mesh_quality(mesh: dolfinx.mesh.Mesh, tdim: int,
                       plotter: pyvista.Plotter=None,
                       quality_measure: str="scaled_jacobian",

setup.py

@@ -13,9 +13,9 @@
     print("Python 3.10 or higher required, please upgrade.")
     sys.exit(1)
 
-VERSION = "2024.0.1"
+VERSION = "0.8.0"
 
-REQUIREMENTS = ["pyvista", "fenics-dolfinx>0.7.0.dev0"]
+REQUIREMENTS = ["pyvista", "fenics-dolfinx>0.8.0"]
 
 
 class CMakeExtension(Extension):

test/test_fem.py

@@ -9,7 +9,7 @@
 
 def test_petsc_object_count_limit():
     mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 4, 4)
-    V = dolfinx.fem.FunctionSpace(mesh, ("CG", 1))
+    V = dolfinx.fem.functionspace(mesh, ("CG", 1))
     v = ufl.TestFunction(V)
 
     u = dolfinx.fem.Function(V)

test/test_nls.py

@@ -11,7 +11,7 @@
                           (lambda x: x[0]+1, False)))
 def test_singularity_finder_residual(u_lmbda_has_zero):
     mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 4, 4)
-    V = dolfinx.fem.FunctionSpace(mesh, ("CG", 1))
+    V = dolfinx.fem.functionspace(mesh, ("CG", 1))
     v = ufl.TestFunction(V)
 
     u_lmbda, has_zero = u_lmbda_has_zero

test/test_plot.py

@@ -20,14 +20,14 @@
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_function_cg(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.FunctionSpace(mesh, ("CG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", p)))
     febug.plot_function(u)
 
 
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 @pytest.mark.parametrize("p", [0, 1, 2])
 def test_plot_function_dg(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.FunctionSpace(mesh, ("DG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("DG", p)))
     febug.plot_function(u)
 
 
@@ -38,7 +38,7 @@ def test_plot_function_dg(p, mesh):
      for msh in meshes1D + meshes2D + meshes3D])
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_warp(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.VectorFunctionSpace(mesh, ("CG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", p, (mesh.geometry.dim,))))
     febug.plot_warp(u)
 
 
@@ -49,7 +49,7 @@ def test_plot_warp(p, mesh):
      for msh in meshes1D + meshes2D + meshes3D])
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_quiver(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.VectorFunctionSpace(mesh, ("CG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", p, (mesh.geometry.dim,))))
     febug.plot_quiver(u)
 
 
@@ -60,7 +60,7 @@ def test_plot_quiver(p, mesh):
      for msh in meshes1D + meshes2D + meshes3D])
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_streamlines_evenly_spaced_2D(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.VectorFunctionSpace(mesh, ("CG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", p, (mesh.geometry.dim,))))
     febug.plot_streamlines_evenly_spaced_2D(u, start_position=(0.5, 0.5, 0.0))
 
 
@@ -71,7 +71,7 @@ def test_plot_streamlines_evenly_spaced_2D(p, mesh):
      for msh in meshes1D + meshes2D + meshes3D])
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_streamlines_from_source(p, mesh):
-    u = dolfinx.fem.Function(dolfinx.fem.VectorFunctionSpace(mesh, ("CG", p)))
+    u = dolfinx.fem.Function(dolfinx.fem.functionspace(mesh, ("CG", p, (mesh.geometry.dim,))))
     pt_cloud_source = pyvista.PolyData(mesh.geometry.x)
     febug.plot_streamlines_from_source(u, pt_cloud_source, max_time=1.0)
 
@@ -89,16 +89,16 @@ def test_plot_mesh(mesh):
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 @pytest.mark.parametrize("p", [1, 2])
 def test_plot_dofmap(p, mesh):
-    V = dolfinx.fem.FunctionSpace(mesh, ("CG", p))
+    V = dolfinx.fem.functionspace(mesh, ("CG", p))
     febug.plot_dofmap(V)
 
 
-_plot_elements = [("CG", 1), ("CG", 2), ("DG", 0), ("DG", 1)]
+_plot_elements = (("CG", 1), ("CG", 2), ("DG", 0), ("DG", 1))
 
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 @pytest.mark.parametrize("e", _plot_elements)
 def test_plot_function_dofs(e, mesh):
-    V = dolfinx.fem.FunctionSpace(mesh, e)
+    V = dolfinx.fem.functionspace(mesh, e)
     u = dolfinx.fem.Function(V)
     febug.plot_function_dofs(u, fmt=".3e")
 
@@ -107,7 +107,7 @@ def test_plot_function_dofs(e, mesh):
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 @pytest.mark.parametrize("e", _plot_elements)
 def test_plot_vector_function_dofs(e, mesh, vec_dim):
-    V = dolfinx.fem.VectorFunctionSpace(mesh, e, dim=vec_dim)
+    V = dolfinx.fem.functionspace(mesh, (*e, (vec_dim,)))
     u = dolfinx.fem.Function(V)
     febug.plot_function_dofs(u, fmt=".3e")
 
@@ -125,11 +125,23 @@ def test_plot_meshtags(mesh):
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 def test_plot_mesh_quality(mesh):
     for d in range(1, mesh.topology.dim+1):
-        febug.plot_mesh_quality(mesh, d)
+        mesh.topology.create_entities(d)
+        febug.plot_mesh_quality(
+            mesh, d,
+            entities=np.arange(mesh.topology.index_map(d).size_local))
 
 
 @pytest.mark.parametrize("mesh", meshes1D + meshes2D + meshes3D)
 def test_plot_entity_indices(mesh):
     for d in range(mesh.topology.dim+1):
         mesh.topology.create_entities(d)
         febug.plot_entity_indices(mesh, d)
+
+
+@pytest.mark.parametrize("dim", [1, 2, 3])
+def test_plot_point_cloud(dim):
+    np.random.seed(1)
+    pc = np.random.rand(10, 3)
+    if dim < 3:
+        pc[:,(3-dim):] = 0.0
+    febug.plot_point_cloud(pc)