Merge pull request #1039 from jhdark/update_dolfinx_0.10

Update to use dolfinx v0.10

Author: jhdark

.github/workflows/benchmark.yml

@@ -4,7 +4,7 @@ on: [pull_request, push]
 jobs:
   benchmark:
     runs-on: ubuntu-latest
-    container: dolfinx/dolfinx:v0.9.0
+    container: dolfinx/dolfinx:v0.10.0
 
     steps:
       - name: Checkout code

.github/workflows/ci_conda.yml

@@ -3,8 +3,14 @@ on: [pull_request, push]
 
 jobs:
   run-tests:
+    name: run-tests (fenics-dolfinx v${{ matrix.dolfinx }})
     runs-on: ubuntu-latest
 
+    strategy:
+      fail-fast: false
+      matrix:
+        dolfinx: ['0.9.0', '0.10.0']
+
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
@@ -20,7 +26,7 @@ jobs:
     - name: Create Conda environment
       shell: bash -l {0}
       run: |
-        conda install -c conda-forge fenics-dolfinx=0.9.0 scifem adios4dolfinx
+        conda install -c conda-forge fenics-dolfinx=${{ matrix.dolfinx }} scifem adios4dolfinx
 
     - name: Install local package and dependencies
       shell: bash -l {0}

.github/workflows/ci_docker.yml

@@ -3,11 +3,12 @@ on: [pull_request, push]
 
 jobs:
   run-tests:
+    name: run-tests (fenics-dolfinx ${{ matrix.container_version }})
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        container_version: [v0.9.0, nightly]
+        container_version: [v0.9.0, v0.10.0, nightly]
     container: dolfinx/dolfinx:${{ matrix.container_version }}
     steps:
         - name: Checkout code

pyproject.toml

@@ -32,8 +32,8 @@ lint = ["ruff", "mypy"]
 docs = ["sphinx", "sphinx-book-theme", "sphinx-design", "matplotlib"]
 
 [project.urls]
-Homepage = "https://github.com/RemDelaporteMathurin/FESTIM"
-Issues = "https://github.com/RemDelaporteMathurin/FESTIM/issues"
+Homepage = "https://github.com/festim-dev/FESTIM"
+Issues = "https://github.com/festim-dev/FESTIM/issues"
 
 
 [tool.setuptools_scm]

src/festim/exports/average_surface.py

@@ -1,4 +1,3 @@
-from dolfinx import fem
 from scifem import assemble_scalar
 
 from festim.exports.surface_quantity import SurfaceQuantity
@@ -27,6 +26,6 @@ def compute(self, ds):
         """
 
         self.value = assemble_scalar(
-            fem.form(self.field.solution * ds(self.surface.id))
-        ) / assemble_scalar(fem.form(1 * ds(self.surface.id)))
+            self.field.solution * ds(self.surface.id)
+        ) / assemble_scalar(1 * ds(self.surface.id))
         self.data.append(self.value)

src/festim/exports/average_volume.py

@@ -1,4 +1,3 @@
-from dolfinx import fem
 from scifem import assemble_scalar
 
 from festim.exports.volume_quantity import VolumeQuantity
@@ -26,6 +25,6 @@ def compute(self, u, dx, entity_maps=None):
         subdomain, and appends it to the data list
         """
         self.value = assemble_scalar(
-            fem.form(u * dx(self.volume.id), entity_maps=entity_maps)
-        ) / assemble_scalar(fem.form(1 * dx(self.volume.id)))
+            u * dx(self.volume.id), entity_maps=entity_maps
+        ) / assemble_scalar(1 * dx(self.volume.id))
         self.data.append(self.value)

src/festim/exports/total_surface.py

@@ -1,5 +1,4 @@
 import ufl
-from dolfinx import fem
 from scifem import assemble_scalar
 
 from festim.exports.surface_quantity import SurfaceQuantity
@@ -29,7 +28,5 @@ def compute(self, ds: ufl.Measure):
         Args:
             ds (ufl.Measure): surface measure of the model
         """
-        self.value = assemble_scalar(
-            fem.form(self.field.solution * ds(self.surface.id))
-        )
+        self.value = assemble_scalar(self.field.solution * ds(self.surface.id))
         self.data.append(self.value)

src/festim/exports/total_volume.py

@@ -1,5 +1,4 @@
 import ufl
-from dolfinx import fem
 from scifem import assemble_scalar
 
 from festim.exports.volume_quantity import VolumeQuantity
@@ -31,7 +30,5 @@ def compute(self, u, dx: ufl.Measure, entity_maps=None):
             dx: volume measure of the model
             entity_maps: entity maps relating parent mesh and submesh
         """
-        self.value = assemble_scalar(
-            fem.form(u * dx(self.volume.id), entity_maps=entity_maps)
-        )
+        self.value = assemble_scalar(u * dx(self.volume.id), entity_maps=entity_maps)
         self.data.append(self.value)

src/festim/problem.py

@@ -184,7 +184,6 @@ def create_solver(self):
                     "ksp_type": "preonly",
                     "pc_type": "lu",
                     "pc_factor_mat_solver_type": linear_solver,
-                    "snes_monitor": None,
                 }
             else:
                 petsc_options = self.petsc_options

test/benchmark.py

@@ -5,6 +5,7 @@
 from petsc4py import PETSc
 
 import basix
+import dolfinx
 import numpy as np
 import tqdm.autonotebook
 from dolfinx.fem import (
@@ -17,12 +18,9 @@
     locate_dofs_geometrical,
     locate_dofs_topological,
 )
-from dolfinx.fem.petsc import (
-    NonlinearProblem,
-)
+from dolfinx.fem.petsc import NonlinearProblem
 from dolfinx.io import XDMFFile
 from dolfinx.mesh import create_mesh, locate_entities, meshtags
-from dolfinx.nls.petsc import NewtonSolver
 from test_permeation_problem import test_permeation_problem
 from ufl import (
     FacetNormal,
@@ -111,24 +109,28 @@ def siverts_law(T, S_0, E_S, pressure):
 
     dt = 1 / 20
     final_time = 50
-    num_steps = int(final_time / dt)
 
     F = dot(D * grad(u), grad(v)) * dx(1)
     F += ((u - u_n) / dt) * v * dx(1)
 
-    problem = NonlinearProblem(F, u, bcs=bcs)
-    solver = NewtonSolver(MPI.COMM_WORLD, problem)
-    solver.convergence_criterion = "incremental"
-    solver.rtol = 1e-10
-    solver.atol = 1e10
-    solver.report = True
-    ksp = solver.krylov_solver
-    opts = PETSc.Options()
-    option_prefix = ksp.getOptionsPrefix()
-    opts[f"{option_prefix}ksp_type"] = "cg"
-    opts[f"{option_prefix}pc_type"] = "gamg"
-    opts[f"{option_prefix}pc_factor_mat_solver_type"] = "mumps"
-    ksp.setFromOptions()
+    petsc_options = {
+        "snes_type": "newtonls",
+        "snes_linesearch_type": "none",
+        "snes_stol": 1e-8,
+        "snes_atol": 0,
+        "snes_rtol": 0,
+        "snes_max_it": 30,
+        "ksp_type": "cg",
+        "pc_type": "gamg",
+    }
+
+    solver = NonlinearProblem(
+        F,
+        u,
+        bcs=bcs,
+        petsc_options=petsc_options,
+        petsc_options_prefix="festim_solver",
+    )
 
     temp_dir = tempfile.TemporaryDirectory()
     mobile_xdmf = XDMFFile(
@@ -146,7 +148,7 @@ def siverts_law(T, S_0, E_S, pressure):
         progress.update(float(dt))
         t += float(dt)
 
-        solver.solve(u)
+        _ = solver.solve()
 
         mobile_xdmf.write_function(u, t)