Update for DOLFINx 0.7.2 (#9)

* Update to v0.6.0

* Update for 0.7.2, switch to scikit-build-core, remove sphinx makefile

* flake8 and isort

* Definetly doesn't work with nanobind based DOLFINx

* Trigger test.

* Install scikit-build-core

.github/workflows/tests.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   build-and-test:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/dolfinx:v0.6.0-r1
+    container: ghcr.io/fenics/dolfinx/dolfinx:v0.7.2
     steps:
       - name: Checkout
         uses: actions/checkout@v3
@@ -33,12 +33,13 @@ jobs:
       
       - name: Install FEniCSx-Shells
         run: |
-          python3 -m pip install .
+          pip install scikit-build-core[pyproject] # TO REMOVE ONCE 0.8.0 RELEASED
+          python3 -m pip install --no-build-isolation --check-build-dependencies .
 
       - name: Build documentation
         run: |
           cd doc
-          make html
+          python3 -m sphinx -W -b html source/ build/html/
 
       - name: Run demos
         run: |

CMakeLists.txt

@@ -1,9 +1,8 @@
-cmake_minimum_required(VERSION 3.16)
+cmake_minimum_required(VERSION 3.18)
 
-project(fenicsx_shells VERSION "0.1.0")
+project(fenicsx_shells VERSION "0.1.0.0")
 
-set(Python_FIND_IMPLEMENTATIONS CPython)
-find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(Python COMPONENTS Interpreter Development REQUIRED)
 find_package(DOLFINX REQUIRED)
 
 # Set C++ standard before finding pybind11

README.md

@@ -12,7 +12,7 @@ numerical methods for solving a wide range of thin structural models (beams,
 plates and shells) expressed in the Unified Form Language (UFL) of the FEniCS
 Project.
 
-*FEniCSx-Shells is an experimental version targeting version v0.5.0 of the new
+*FEniCSx-Shells is an experimental version targeting version v0.7.2 of the new
 [DOLFINx solver](https://github.com/fenics/dolfinx).*
 
 The foundational aspects of the FEniCS-Shells project are described in the paper:

demo/demo_kirchhoff-love-clamped.py

@@ -41,18 +41,16 @@
 import ufl
 from dolfinx.fem import FunctionSpace, dirichletbc
 from dolfinx.fem.petsc import LinearProblem
-from dolfinx.mesh import create_unit_square, CellType
+from dolfinx.mesh import CellType, create_unit_square
 from ufl import (FacetNormal, FiniteElement, Identity, Measure, MixedElement,
                  grad, inner, sym, tr)
 
 from mpi4py import MPI
 
 # We then create a two-dimensional mesh of the mid-plane of the plate $\Omega =
-# [0, 1] \times [0, 1]$. `GhostMode.shared_facet` is required as the Form will
-# use Nédélec elements and DG-type restrictions.
+# [0, 1] \times [0, 1]$.
 
-mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, CellType.triangle,
-                          dolfinx.mesh.GhostMode.shared_facet)
+mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, CellType.triangle)
 
 # The Hellen-Herrmann-Johnson element for the Kirchhoff-Love plate problem
 # consists of:
@@ -207,19 +205,19 @@ def all_boundary(x):
 
 # +
 problem = LinearProblem(a, L, bcs=bcs, petsc_options={
-                        "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps", "ksp_view": ""})
+                        "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
 u_h = problem.solve()
 
-bb_tree = dolfinx.geometry.BoundingBoxTree(mesh, 2)
-point = np.array([0.5, 0.5, 0.0], dtype=np.float64)
-cell_candidates = dolfinx.geometry.compute_collisions(bb_tree, point)
+bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
+point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
+cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
 cells = dolfinx.geometry.compute_colliding_cells(
     mesh, cell_candidates, point)
 
 w, M = u_h.split()
 
 if len(cells) > 0:
-    value = w.eval(point, cells[0])
+    value = w.eval(point, cells.array[0])
     print(value[0])
 
 # TODO: IO?

demo/demo_reissner-mindlin-clamped-tdnns.py

@@ -43,8 +43,7 @@
 import ufl
 from dolfinx.fem import Function, FunctionSpace, dirichletbc
 from dolfinx.fem.petsc import LinearProblem
-from dolfinx.io.utils import XDMFFile
-from dolfinx.mesh import CellType, GhostMode, create_unit_square
+from dolfinx.mesh import CellType, create_unit_square
 from ufl import (FacetNormal, FiniteElement, Identity, Measure, MixedElement,
                  grad, inner, split, sym, tr)
 
@@ -53,12 +52,10 @@
 # -
 
 # We then create a two-dimensional mesh of the mid-plane of the plate $\Omega =
-# [0, 1] \times [0, 1]$. `GhostMode.shared_facet` is required as the Form will
-# use Nédélec elements and DG-type restrictions.
+# [0, 1] \times [0, 1]$.
 
 # +
-mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, CellType.triangle,
-                          GhostMode.shared_facet)
+mesh = create_unit_square(MPI.COMM_WORLD, 16, 16, CellType.triangle)
 
 # -
 
@@ -161,7 +158,8 @@ def inner_divdiv(M, theta):
     """Discrete div-div inner product"""
     n = FacetNormal(M.ufl_domain())
     M_nn = nn(M)
-    result = -inner(M, k_theta(theta))*dx + inner(M_nn("+"), ufl.jump(theta, n))*dS + inner(M_nn, ufl.dot(theta, n))*ds
+    result = -inner(M, k_theta(theta))*dx + inner(M_nn("+"),
+                                                  ufl.jump(theta, n))*dS + inner(M_nn, ufl.dot(theta, n))*ds
     return result
 
 
@@ -179,11 +177,11 @@ def gamma(theta, w):
 # Imposition of boundary conditions requires some care. We reproduce the table
 # from Pechstein and Schöberl specifying the different types of boundary condition.
 #
-# | Essential                            | Natural                              | Non-homogeneous term                                                |
-# | ------------------------------------ | ------------------------------------ | ------------------------------------------------------------------- |
-# | $w = \bar{w}$                        | $\mu(\partial_n w - \theta_n) = g_w$ | $\int_{\Gamma} g_w \tilde{w} \; \mathrm{d}s$                        |
-# | $\theta_\tau = \bar{\theta}_{\tau} $ | $m_{n\tau} = g_{\theta_\tau}$        | $\int_{\Gamma} g_{\theta_\tau} \cdot \tilde{\theta} \; \mathrm{d}s$ |
-# | $m_{nn} = \bar{m}_{nn}$              | $\theta_n = g_{\theta_n}$            | $\int_{\Gamma} g_{\theta_n} \tilde{m}_{nn} \; \mathrm{d}s$          |
+# | Essential                            | Natural                              | Non-homogeneous term                                                |  # noqa: E501
+# | ------------------------------------ | ------------------------------------ | ------------------------------------------------------------------- |  # noqa: E501
+# | $w = \bar{w}$                        | $\mu(\partial_n w - \theta_n) = g_w$ | $\int_{\Gamma} g_w \tilde{w} \; \mathrm{d}s$                        |  # noqa: E501
+# | $\theta_\tau = \bar{\theta}_{\tau} $ | $m_{n\tau} = g_{\theta_\tau}$        | $\int_{\Gamma} g_{\theta_\tau} \cdot \tilde{\theta} \; \mathrm{d}s$ |  # noqa: E501
+# | $m_{nn} = \bar{m}_{nn}$              | $\theta_n = g_{\theta_n}$            | $\int_{\Gamma} g_{\theta_n} \tilde{m}_{nn} \; \mathrm{d}s$          |  # noqa: E501
 #
 # where $\theta_{n} = \theta_n$ is the normal component of the rotation,
 # $\theta_{\tau} = \theta \cdot \tau $ is the tangential component of the
@@ -235,20 +233,14 @@ def all_boundary(x):
                         "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
 u_h = problem.solve()
 
-bb_tree = dolfinx.geometry.BoundingBoxTree(mesh, 2)
-point = np.array([0.5, 0.5, 0.0], dtype=np.float64)
-cell_candidates = dolfinx.geometry.compute_collisions(bb_tree, point)
+bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
+point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
+cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
 cells = dolfinx.geometry.compute_colliding_cells(
     mesh, cell_candidates, point)
 
 theta, w, M = u_h.split()
 
 if len(cells) > 0:
-    value = w.eval(point, cells[0])
+    value = w.eval(point, cells.array[0])
     print(value[0])
-
-with XDMFFile(MPI.COMM_WORLD, "w.xdmf", "w") as f:
-    f.write_mesh(mesh)
-    f.write_function(w)
-
-# TODO: Output of m and theta using new interpolation functions?

demo/demo_reissner-mindlin-clamped.py

@@ -44,8 +44,7 @@
 # [0, 1] \times [0, 1]$. `GhostMode.shared_facet` is required as the Form will
 # use Nédélec elements and DG-type restrictions.
 
-mesh = create_unit_square(MPI.COMM_WORLD, 32, 32, CellType.triangle,
-                          dolfinx.cpp.mesh.GhostMode.shared_facet)
+mesh = create_unit_square(MPI.COMM_WORLD, 32, 32, CellType.triangle)
 
 # The Durán-Liberman element [1] for the Reissner-Mindlin plate problem
 # consists of:
@@ -217,16 +216,16 @@ def all_boundary(x):
                         "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
 u_ = problem.solve()
 
-bb_tree = dolfinx.geometry.BoundingBoxTree(mesh, 2)
-point = np.array([0.5, 0.5, 0.0], dtype=np.float64)
-cell_candidates = dolfinx.geometry.compute_collisions(bb_tree, point)
+bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
+point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
+cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
 cells = dolfinx.geometry.compute_colliding_cells(
     mesh, cell_candidates, point)
 
 theta, w, R_gamma, p = u_.split()
 
 if len(cells) > 0:
-    value = w.eval(point, cells[0])
+    value = w.eval(point, cells.array[0])
     print(value[0])
     # NOTE: FEniCS-Shells (old dolfin) `demo/documented/reissner-mindlin-clamped`
     # gives 1.28506469462e-06 on a 32 x 32 mesh and 1.2703580973e-06 on a 64 x 64
@@ -239,9 +238,6 @@ def test_center_displacement():
     f.write_mesh(mesh)
     f.write_function(w)
 
-with XDMFFile(MPI.COMM_WORLD, "theta.xdmf", "w") as f:
-    f.write_mesh(mesh)
-    f.write_function(theta)
 # -
 
 # ## Appendix

demo/demo_reissner-mindlin-simply-supported.py

@@ -33,7 +33,6 @@
 import ufl
 from dolfinx.fem import Function, FunctionSpace, dirichletbc
 from dolfinx.fem.petsc import LinearProblem
-from dolfinx.io.utils import XDMFFile
 from dolfinx.mesh import CellType, create_unit_square
 from ufl import (FiniteElement, MixedElement, VectorElement, dx, grad, inner,
                  split, sym, tr)
@@ -44,8 +43,7 @@
 # [0, 1] \times [0, 1]$. `GhostMode.shared_facet` is required as the Form will
 # use Nédélec elements and DG-type restrictions.
 
-mesh = create_unit_square(MPI.COMM_WORLD, 32, 32, CellType.quadrilateral,
-                          dolfinx.cpp.mesh.GhostMode.shared_facet)
+mesh = create_unit_square(MPI.COMM_WORLD, 32, 32, CellType.quadrilateral)
 
 # The MITC4 element [1] for the Reissner-Mindlin plate problem
 # consists of:
@@ -233,24 +231,15 @@ def make_bc(value, V, on_boundary):
                         "ksp_type": "preonly", "pc_type": "lu", "pc_factor_mat_solver_type": "mumps"})
 u_ = problem.solve()
 
-bb_tree = dolfinx.geometry.BoundingBoxTree(mesh, 2)
-point = np.array([0.5, 0.5, 0.0], dtype=np.float64)
-cell_candidates = dolfinx.geometry.compute_collisions(bb_tree, point)
+bb_tree = dolfinx.geometry.bb_tree(mesh, 2)
+point = np.array([[0.5, 0.5, 0.0]], dtype=np.float64)
+cell_candidates = dolfinx.geometry.compute_collisions_points(bb_tree, point)
 cells = dolfinx.geometry.compute_colliding_cells(
     mesh, cell_candidates, point)
 
 theta, w, R_gamma, p = u_.split()
 
 if len(cells) > 0:
-    value = w.eval(point, cells[0])
+    value = w.eval(point, cells.array[0])
     print(value[0])
-
-
-with XDMFFile(MPI.COMM_WORLD, "w.xdmf", "w") as f:
-    f.write_mesh(mesh)
-    f.write_function(w)
-
-with XDMFFile(MPI.COMM_WORLD, "theta.xdmf", "w") as f:
-    f.write_mesh(mesh)
-    f.write_function(theta)
 # -

doc/source/conf.py

@@ -6,13 +6,12 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-import sys
 import os
+import sys
 
 sys.path.insert(0, os.path.abspath('.'))
 import jupytext_process
 
-
 jupytext_process.process()
 
 project = 'FEniCSx-Shells'

doc/source/jupytext_process.py

@@ -4,9 +4,9 @@
 #
 # SPDX-License-Identifier:    LGPL-3.0-or-later
 
-import shutil
-import pathlib
 import os
+import pathlib
+import shutil
 
 import jupytext
 

launch-container.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 CONTAINER_ENGINE="docker"
-${CONTAINER_ENGINE} run -ti -v $(pwd):/shared -w /shared dolfinx/dolfinx:v0.6.0-r1
+${CONTAINER_ENGINE} run -ti -v $(pwd):/shared -w /shared dolfinx/dolfinx:v0.7.2

pyproject.toml

@@ -1,3 +1,18 @@
 [build-system]
-requires = ["setuptools>=42", "wheel", "pybind11", "cmake"]
-build-backend = "setuptools.build_meta"
+requires = ["scikit-build-core[pyproject]", "wheel", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "fenicsx-shells"
+version = "0.1.0.dev0"
+description = "FEniCSx-Shells"
+readme = "README.md"
+requires-python = ">=3.8.0"
+license = { file = "COPYING.LESSER" }
+authors = [
+      { email = "[email protected]" },
+      { name = "Jack S. Hale" },
+]
+dependencies = [
+      "fenics-dolfinx>=0.7.2,<0.8.0",
+]