Move to SNES solver for dolfinx>=0.10 and be ready for dolfinx-adjoint

.cspell_dict.txt

@@ -10,6 +10,7 @@ Barnafi
 Bartolucci
 basix
 bcast
+bddc
 behaviour
 bestel
 Bestel
@@ -78,16 +79,20 @@ Jilberto
 Karabelas
 Kasra
 Kluwer
+kwonlyargs
 Laszlo
 LDRB
 levelname
 libgl
 libxrender
 linalg
+linesearch
 linspace
 lmbda
 Luca
+MATIS
 Matteo
+maxstep
 mechanicsproblem
 ment
 meshtags
@@ -101,8 +106,11 @@ nabla
 ndarray
 neohookean
 Neumann
+newtonls
+newtontr
 Niederer
 Nolte
+nullspace
 numpy
 Oreste
 Orovio
@@ -130,6 +138,7 @@ SELLIER
 Severi
 Shrier
 Silvano
+snes
 Sorine
 Stefano
 stica
@@ -139,11 +148,13 @@ tomek
 Tomek
 TRAME
 transmural
+unassembled
 ureg
 Usyk
 varepsilon
 Venant
 Verlag
+vinewtonrsls
 Virag
 viscoelastic
 viscoelasticity

.github/workflows/test_package_coverage.yml

@@ -17,7 +17,6 @@ jobs:
       fail-fast: false
       matrix:
         container: [
-          "ghcr.io/fenics/dolfinx/dolfinx:v0.9.0",
           "ghcr.io/fenics/dolfinx/dolfinx:stable",
           "ghcr.io/fenics/dolfinx/dolfinx:nightly"
         ]

src/pulse/active_model.py

@@ -130,7 +130,7 @@ def S(self, C: ufl.core.expr.Expr, dev: bool = False) -> ufl.core.expr.Expr:
             Cdev = kinematics.Cdev(C)
         else:
             Cdev = C
-        return 2.0 * ufl.diff(self.strain_energy(Cdev), Cdev)
+        return 2.0 * ufl.diff(self.strain_energy(Cdev), C)
 
     def P(self, F: ufl.core.expr.Expr, dev: bool = False) -> ufl.core.expr.Expr:
         """First Piola-Kirchhoff stress tensor for the active model.

src/pulse/exceptions.py

@@ -1,10 +1,14 @@
+import logging
 import operator
 from dataclasses import dataclass
 
 from mpi4py import MPI
 
 import dolfinx
 import numpy as np
+import ufl
+
+logger = logging.getLogger(__name__)
 
 
 def check_value_greater_than(
@@ -40,6 +44,17 @@ def check_value_greater_than(
             bound,
         )
 
+    elif isinstance(f, ufl.indexed.Indexed):
+        try:
+            func, index = f.ufl_operands
+            value = func.x.array[int(index[0])]
+            return op(value, bound)
+        except Exception:
+            logger.warning(
+                "Could not extract value from ufl.indexed.Indexed. Assuming check succeeds.",
+            )
+            return True
+
     raise PulseException(  # pragma: no cover
         f"Invalid type for f: {type(f)}. Expected 'float', "
         "'dolfinx.fem.Constant', 'numpy array' or 'dolfinx.fem.Function'",