dolfinx-adjoint 0.2.0__tar.gz → 0.3.0__tar.gz

{dolfinx_adjoint-0.2.0/src/dolfinx_adjoint.egg-info → dolfinx_adjoint-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dolfinx-adjoint
-Version: 0.2.0
+Version: 0.3.0
 Summary: Automatic differentation compatible with DOLFINx
 Author-email: "Jørgen S. Dokken" <dokken@simula.no>
 License-Expression: MIT
@@ -9,6 +9,7 @@ License-File: LICENSE
 Requires-Dist: fenics-dolfinx>=0.10.0
 Requires-Dist: pyadjoint-ad>=2025.10.0
 Requires-Dist: typing_extensions; python_version < "3.11"
+Requires-Dist: packaging>=24.2
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Provides-Extra: dev
@@ -24,9 +25,9 @@ Requires-Dist: pyvista[all]>0.45; extra == "docs"
 Requires-Dist: networkx; extra == "docs"
 Requires-Dist: pygraphviz; extra == "docs"
 Provides-Extra: all
-Requires-Dist: dolfinx_adjoint[test]; extra == "all"
-Requires-Dist: dolfinx_adjoint[dev]; extra == "all"
-Requires-Dist: dolfinx_adjoint[docs]; extra == "all"
+Requires-Dist: dolfinx-adjoint[test]; extra == "all"
+Requires-Dist: dolfinx-adjoint[dev]; extra == "all"
+Requires-Dist: dolfinx-adjoint[docs]; extra == "all"
 Dynamic: license-file
 
 # DOLFINx-Adjoint
@@ -49,7 +50,7 @@ Read the [Latest Documentation here](https://scientificcomputing.github.io/dolfi
 
 ### Dependencies
 
-DOLFINx-Adjoint requires **DOLFINx** (>=0.10.0) and **pyadjoint-ad**.
+DOLFINx-Adjoint requires **DOLFINx** (>=0.11.0) and **pyadjoint-ad**.
 
 ### via pip
 
@@ -59,6 +60,14 @@ The main way to install the package is via pip:
 python3 -m pip install dolfinx-adjoint
 ```
 
+### via conda
+
+You can also install dolfinx-adjoint via conda which also comes with **DOLFINx**
+
+```bash
+conda install -c conda-forge dolfinx-adjoint
+```
+
 ### Development Install
 
 To install the latest development version directly from the repository, use:
@@ -75,15 +84,6 @@ cd dolfinx-adjoint
 python3 -m pip install -e ".[all]"
 ```
 
-### Docker
-
-A pre-built Docker image is automatically published by the CI. You can pull the nightly build which comes with DOLFINx and DOLFINx-Adjoint pre-installed:
-
-```bash
-docker run -ti ghcr.io/scientificcomputing/dolfinx-adjoint:v0.2.0
-```
-
-*(Note: Adjust the tag to the latest release or build).*
 
 ## Quick Start
 
@@ -94,6 +94,7 @@ Using `dolfinx_adjoint` is designed to be as close to standard `dolfinx` syntax
 import dolfinx
 from mpi4py import MPI
 import pyadjoint
+import ufl
 import dolfinx_adjoint
 
 # Create mesh and function space
@@ -103,16 +104,31 @@ V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1))
 # Use dolfinx_adjoint overloaded types
 # This ensures operations are tracked on the pyadjoint tape!
 f = dolfinx_adjoint.Function(V, name="Control")
+f.interpolate(lambda x: x[0] + x[1])  # Initial guess for control
 uh = dolfinx_adjoint.Function(V, name="State")
 
-# ... Define your UFL forms ...
+# Define UFL forms for a simple Poisson problem: - \Delta u = f
+u, v = ufl.TrialFunction(V), ufl.TestFunction(V)
+a = ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx
+L = f * v * ufl.dx
+
+# Set up Dirichlet boundary condition (u = 0 on boundary)
+mesh.topology.create_connectivity(mesh.topology.dim - 1, mesh.topology.dim)
+exterior_facets = dolfinx.mesh.exterior_facet_indices(mesh.topology)
+exterior_dofs = dolfinx.fem.locate_dofs_topological(V, mesh.topology.dim - 1, exterior_facets)
+bc = dolfinx.fem.dirichletbc(dolfinx.default_scalar_type(0.0), exterior_dofs, V)
 
 # Use overloaded solvers
 problem = dolfinx_adjoint.LinearProblem(a, L, u=uh, bcs=[bc])
 problem.solve()
 
+# Define a desired temperature profile 'd' and regularization parameter 'alpha'
+x = ufl.SpatialCoordinate(mesh)
+d = ufl.sin(ufl.pi * x[0]) * ufl.sin(ufl.pi * x[1])
+alpha = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(1e-6))
+
 # Assemble the objective scalar using the overloaded assembly
-J_symbolic = 0.5 * ufl.inner(uh - d, uh - d) * ufl.dx
+J_symbolic = 0.5 * ufl.inner(uh - d, uh - d) * ufl.dx + 0.5 * alpha * ufl.inner(f, f) * ufl.dx
 J = dolfinx_adjoint.assemble_scalar(J_symbolic)
 
 # Create a ReducedFunctional for optimization

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/README.md

@@ -18,7 +18,7 @@ Read the [Latest Documentation here](https://scientificcomputing.github.io/dolfi
 
 ### Dependencies
 
-DOLFINx-Adjoint requires **DOLFINx** (>=0.10.0) and **pyadjoint-ad**.
+DOLFINx-Adjoint requires **DOLFINx** (>=0.11.0) and **pyadjoint-ad**.
 
 ### via pip
 
@@ -28,6 +28,14 @@ The main way to install the package is via pip:
 python3 -m pip install dolfinx-adjoint
 ```
 
+### via conda
+
+You can also install dolfinx-adjoint via conda which also comes with **DOLFINx**
+
+```bash
+conda install -c conda-forge dolfinx-adjoint
+```
+
 ### Development Install
 
 To install the latest development version directly from the repository, use:
@@ -44,15 +52,6 @@ cd dolfinx-adjoint
 python3 -m pip install -e ".[all]"
 ```
 
-### Docker
-
-A pre-built Docker image is automatically published by the CI. You can pull the nightly build which comes with DOLFINx and DOLFINx-Adjoint pre-installed:
-
-```bash
-docker run -ti ghcr.io/scientificcomputing/dolfinx-adjoint:v0.2.0
-```
-
-*(Note: Adjust the tag to the latest release or build).*
 
 ## Quick Start
 
@@ -63,6 +62,7 @@ Using `dolfinx_adjoint` is designed to be as close to standard `dolfinx` syntax
 import dolfinx
 from mpi4py import MPI
 import pyadjoint
+import ufl
 import dolfinx_adjoint
 
 # Create mesh and function space
@@ -72,16 +72,31 @@ V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1))
 # Use dolfinx_adjoint overloaded types
 # This ensures operations are tracked on the pyadjoint tape!
 f = dolfinx_adjoint.Function(V, name="Control")
+f.interpolate(lambda x: x[0] + x[1])  # Initial guess for control
 uh = dolfinx_adjoint.Function(V, name="State")
 
-# ... Define your UFL forms ...
+# Define UFL forms for a simple Poisson problem: - \Delta u = f
+u, v = ufl.TrialFunction(V), ufl.TestFunction(V)
+a = ufl.inner(ufl.grad(u), ufl.grad(v)) * ufl.dx
+L = f * v * ufl.dx
+
+# Set up Dirichlet boundary condition (u = 0 on boundary)
+mesh.topology.create_connectivity(mesh.topology.dim - 1, mesh.topology.dim)
+exterior_facets = dolfinx.mesh.exterior_facet_indices(mesh.topology)
+exterior_dofs = dolfinx.fem.locate_dofs_topological(V, mesh.topology.dim - 1, exterior_facets)
+bc = dolfinx.fem.dirichletbc(dolfinx.default_scalar_type(0.0), exterior_dofs, V)
 
 # Use overloaded solvers
 problem = dolfinx_adjoint.LinearProblem(a, L, u=uh, bcs=[bc])
 problem.solve()
 
+# Define a desired temperature profile 'd' and regularization parameter 'alpha'
+x = ufl.SpatialCoordinate(mesh)
+d = ufl.sin(ufl.pi * x[0]) * ufl.sin(ufl.pi * x[1])
+alpha = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(1e-6))
+
 # Assemble the objective scalar using the overloaded assembly
-J_symbolic = 0.5 * ufl.inner(uh - d, uh - d) * ufl.dx
+J_symbolic = 0.5 * ufl.inner(uh - d, uh - d) * ufl.dx + 0.5 * alpha * ufl.inner(f, f) * ufl.dx
 J = dolfinx_adjoint.assemble_scalar(J_symbolic)
 
 # Create a ReducedFunctional for optimization

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61.0.0", "wheel"]
 
 [project]
 name = "dolfinx-adjoint"
-version = "0.2.0"
+version = "0.3.0"
 description = "Automatic differentation compatible with DOLFINx"
 authors = [{ name = "Jørgen S. Dokken", email = "dokken@simula.no" }]
 license = "MIT"
@@ -13,6 +13,7 @@ dependencies = [
       "fenics-dolfinx>=0.10.0",
       "pyadjoint-ad>=2025.10.0",
       "typing_extensions; python_version < '3.11'",
+      "packaging>=24.2",
 ]
 
 
@@ -28,7 +29,7 @@ docs = [
       "networkx",
       "pygraphviz"
 ]
-all = ["dolfinx_adjoint[test]", "dolfinx_adjoint[dev]", "dolfinx_adjoint[docs]"]
+all = ["dolfinx-adjoint[test]", "dolfinx-adjoint[dev]", "dolfinx-adjoint[docs]"]
 
 [tool.pytest.ini_options]
 addopts = ["--import-mode=importlib"]
@@ -91,21 +92,10 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.2.0"
+current_version = "0.3.0"
 
 
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
 search = 'version = "{current_version}"'
 replace = 'version = "{new_version}"'
-
-
-[[tool.bumpversion.files]]
-filename = "README.md"
-search = "ghcr.io/scientificcomputing/dolfinx-adjoint:v{current_version}"
-replace = "ghcr.io/scientificcomputing/dolfinx-adjoint:v{new_version}"
-
-[[tool.bumpversion.files]]
-filename = "Dockerfile"
-search = "ghcr.io/scientificcomputing/dolfinx-adjoint:v{current_version}"
-replace = "ghcr.io/scientificcomputing/dolfinx-adjoint:v{new_version}"

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/src/dolfinx_adjoint/__init__.py

@@ -7,7 +7,7 @@ import pyadjoint as _pyad
 
 from .assembly import assemble_scalar, error_norm
 from .solvers import LinearProblem, NonlinearProblem
-from .types import Constant, Function
+from .types import Constant, Function, dirichletbc
 from .types.function import assign
 
 meta = metadata("dolfinx_adjoint")
@@ -24,6 +24,7 @@ _pyad.continue_annotation()
 __all__ = [
     "Constant",
     "Function",
+    "dirichletbc",
     "LinearProblem",
     "NonlinearProblem",
     "assemble_scalar",

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/src/dolfinx_adjoint/blocks/_vector.py

@@ -41,6 +41,15 @@ def _vector(
     Returns:
         A distributed vector.
     """
+    vtype: (
+        type[dolfinx.cpp.la.Vector_float32]
+        | type[dolfinx.cpp.la.Vector_float64]
+        | type[dolfinx.cpp.la.Vector_complex64]
+        | type[dolfinx.cpp.la.Vector_complex128]
+        | type[dolfinx.cpp.la.Vector_int8]
+        | type[dolfinx.cpp.la.Vector_int32]
+        | type[dolfinx.cpp.la.Vector_int64]
+    )
     if np.issubdtype(dtype, np.float32):
         vtype = dolfinx.cpp.la.Vector_float32
     elif np.issubdtype(dtype, np.float64):
@@ -72,6 +81,8 @@ def _create_vector(L: dolfinx.fem.Form, space: dolfinx.fem.FunctionSpace) -> _Sp
     """
     # Can just take the first dofmap here, since all dof maps have the same
     # index map in mixed-topology meshes
-    dofmap = L.function_spaces[0].dofmaps(0)  # type: ignore
+
+    dofmap = L.function_spaces[0].dofmaps[0]  # type: ignore
+
     assert space._cpp_object == L.function_spaces[0], "Function space mismatch when creating vector."
     return _vector(dofmap.index_map, dofmap.index_map_bs, dtype=L.dtype, function_space=space)

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/src/dolfinx_adjoint/blocks/assembly.py

@@ -129,6 +129,7 @@ class AssembleBlock(Block):
                 form_compiler_options=self._form_compiler_options,
                 entity_maps=self._entity_maps,
             )
+
             if space is None:
                 # If space is not supplied infer it from the form
                 assert len(dform.arguments()) == 1
@@ -143,6 +144,9 @@ class AssembleBlock(Block):
             # assemble_compiled_form(compiled_adjoint, self._cached_vectors[id(space)])
             assemble_compiled_form(compiled_adjoint, vector)
             # return a vector scaled by the scalar `adj_input`
+            # Safegaurd against None seeds from PyAdjoint
+            if adj_input is None:
+                adj_input = 1.0
             vector.array[:] *= vector.x.array.dtype.type(adj_input)
             vector.scatter_forward()
 

dolfinx_adjoint-0.3.0/src/dolfinx_adjoint/blocks/dirichletbc.py

@@ -0,0 +1,42 @@
+import dolfinx
+import numpy as np
+import numpy.typing as npt
+from pyadjoint.block import Block
+
+
+class DirichletBCBlock(Block):
+    """A block representing a DirichletBC in the adjoint framework.
+
+    Args:
+        value: The value of the Dirichlet BC.
+        dofs: An array of degree-of-freedom indices in `V` where the BC should be applied.
+        V: The function space associated with the Dirichlet BC.
+        ad_block_tag: An optional tag to identify this block in the adjoint framework.
+
+    """
+
+    def __init__(
+        self,
+        value: dolfinx.fem.Function | dolfinx.fem.Constant,
+        dofs: npt.NDArray[np.int32],
+        V: dolfinx.fem.FunctionSpace | None = None,
+        ad_block_tag: str | None = None,
+    ):
+        super().__init__(ad_block_tag=ad_block_tag)
+        self._dofs = dofs
+        self._V = V
+        self.add_dependency(value)
+
+    @property
+    def dofs(self):
+        return self._dofs
+
+    @property
+    def V(self):
+        return self._V
+
+    def prepare_recompute_component(self, inputs, relevant_outputs):
+        return inputs[0] if inputs else None
+
+    def recompute_component(self, inputs, block_variable, idx, prepared):
+        return block_variable.saved_output

{dolfinx_adjoint-0.2.0 → dolfinx_adjoint-0.3.0}/src/dolfinx_adjoint/blocks/function_assigner.py

@@ -6,8 +6,7 @@ import ufl
 from pyadjoint import AdjFloat, Block, OverloadedType
 from ufl.formatting.ufl2unicode import ufl2unicode
 
-from dolfinx_adjoint.utils import function_from_vector
-
+from ..utils import function_from_vector
 from ._vector import _vector
 
 
@@ -178,15 +177,18 @@ class FunctionAssignBlock(Block):
     def recompute_component(self, inputs, block_variable, idx, prepared):
         if self.expr is None:
             prepared = inputs[0]
-        output = dolfinx.fem.Function(
-            block_variable.output.function_space, name="f{block_variable.output.name}_AssignBlockRecompute"
-        )
+
+        # We should return the exact object instance to maintain C++ memory bindings
+        # (especially for DirichletBCs), updating it in-place.
+        output = block_variable.saved_output
+
         try:
             if output.function_space == prepared.function_space:
                 output.x.array[:] = prepared.x.array[:]
         except AttributeError:
             # Handling float value
             output.x.array[:] = prepared
+
         return output
 
     def __str__(self):