Update for DOLFINx v0.11

.github/workflows/ci_conda.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        dolfinx: ['0.9.0', '0.10.0']
+        dolfinx: ['0.9.0', '0.10.0', '0.11.0']
 
     steps:
     - name: Checkout code
@@ -26,7 +26,7 @@ jobs:
     - name: Create Conda environment
       shell: bash -l {0}
       run: |
-        conda install -c conda-forge python pip fenics-dolfinx=${{ matrix.dolfinx }} scifem adios4dolfinx
+        conda install -c conda-forge python pip fenics-dolfinx=${{ matrix.dolfinx }} scifem io4dolfinx
 
     - name: Install local package and dependencies
       shell: bash -l {0}

.github/workflows/ci_docker.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        container_version: [v0.9.0, v0.10.0, nightly]
+        container_version: [v0.9.0, v0.10.0, v0.11.0, nightly]
     container: dolfinx/dolfinx:${{ matrix.container_version }}
     steps:
       - name: Checkout code
@@ -23,9 +23,9 @@ jobs:
           python -m pip install scipy  # needed in scifem, can be removed when scifem adds it to their dependencies
           python -m pip install .[test]
 
-      - name: Overload adios4dolfinx
-        if: ${{ matrix.container_version == 'nightly' }}
-        run: python3 -m pip install git+https://github.com/jorgensd/adios4dolfinx.git
+      - name: Overload io4dolfinx
+      #   if: ${{ matrix.container_version == 'nightly' }}
+        run: python3 -m pip install git+https://github.com/scientificcomputing/io4dolfinx.git
 
       - name: Run tests
         run: |

conda/recipe/meta.yaml

@@ -27,7 +27,7 @@ requirements:
     - python >={{ python_min }}
     - fenics-dolfinx >=0.9,<=0.10
     - scifem >=0.2.13
-    - adios4dolfinx
+    - io4dolfinx
     - tqdm
 
 test:

docs/environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - numpy==1.24
   - tqdm
   - scifem>=0.2.8
-  - adios4dolfinx
+  - io4dolfinx
   - sphinx-design
   - sphinxcontrib-bibtex
   - sympy

pyproject.toml

@@ -17,7 +17,7 @@ description = "Finite element simulations of hydrogen transport"
 readme = "README.md"
 requires-python = ">=3.9"
 license = "Apache-2.0"
-dependencies = ["tqdm", "scifem>=0.2.13", "adios4dolfinx"]
+dependencies = ["tqdm", "scifem>=0.2.13", "io4dolfinx"]
 classifiers = [
     "Natural Language :: English",
     "Topic :: Scientific/Engineering",

src/festim/exports/vtx.py

@@ -89,7 +89,7 @@ class VTXSpeciesExport(ExportBaseClass):
         field: Set of species to export
         subdomain: A field can be defined on multiple domains. This arguments specifies
             what subdomains we export on. If `None` we export on all domains.
-        checkpoint: If True, the export will be a checkpoint file using adios4dolfinx
+        checkpoint: If True, the export will be a checkpoint file using io4dolfinx
             and won't be readable by ParaView. Default is False.
         times: if provided, the field will be exported at these timesteps. Otherwise
             exports at all timesteps. Defaults to None.
@@ -196,7 +196,7 @@ class CustomFieldExport(ExportBaseClass):
         subdomain: The volume subdomain on which the custom
             field is evaluated. Defaults to None.
         checkpoint: If True, the export will be a checkpoint file using
-            adios4dolfinx and won't be readable by ParaView. Default is False.
+            io4dolfinx and won't be readable by ParaView. Default is False.
 
     Attributes:
         filename: The name of the output file
@@ -358,7 +358,7 @@ class ReactionRateExport(CustomFieldExport):
         subdomain: The volume subdomain on which the reaction
             rate is evaluated. Defaults to None.
         checkpoint: If True, the export will be a checkpoint file using
-            adios4dolfinx and won't be readable by ParaView. Default is False.
+            io4dolfinx and won't be readable by ParaView. Default is False.
     """
 
     def __init__(

src/festim/hydrogen_transport_problem.py

@@ -4,9 +4,9 @@
 from mpi4py import MPI
 from petsc4py import PETSc
 
-import adios4dolfinx
 import basix
 import dolfinx
+import io4dolfinx
 import numpy as np
 import numpy.typing as npt
 import tqdm.auto
@@ -450,7 +450,11 @@ def initialise_exports(self):
                         )
 
                     else:
-                        adios4dolfinx.write_mesh(export.filename, mesh=self.mesh.mesh)
+                        io4dolfinx.write_mesh(
+                            filename=export.filename,
+                            mesh=self.mesh.mesh,
+                            backend="adios2",
+                        )
 
                 elif isinstance(export, exports.CustomFieldExport):
                     export.function = fem.Function(self.V_CG_1)
@@ -1003,9 +1007,9 @@ def post_processing(self):
                 if isinstance(export, exports.VTXSpeciesExport):
                     if export._checkpoint:
                         for field in export.field:
-                            adios4dolfinx.write_function(
-                                export.filename,
-                                field.post_processing_solution,
+                            io4dolfinx.write_function(
+                                filename=export.filename,
+                                u=field.post_processing_solution,
                                 time=float(self.t),
                                 name=field.name,
                             )
@@ -1723,9 +1727,10 @@ def initialise_exports(self):
                         engine="BP5",
                     )
                 else:
-                    adios4dolfinx.write_mesh(
-                        export.filename,
+                    io4dolfinx.write_mesh(
+                        filename=export.filename,
                         mesh=functions[0].function_space.mesh,
+                        backend="adios2",
                     )
             elif isinstance(export, exports.VTXTemperatureExport):
                 assert isinstance(self.temperature_fenics, fem.Function), (
@@ -1754,6 +1759,7 @@ def initialise_exports(self):
                     output=export.function,
                     engine="BP5",
                 )
+
         # compute diffusivity function for surface fluxes
         # for the discontinuous case, we don't use D_global as in
         # HydrogenTransportProblem
@@ -1843,9 +1849,9 @@ def post_processing(self):
                                     export._subdomain
                                 ]
                             )
-                            adios4dolfinx.write_function(
-                                export.filename,
-                                post_processing_solution,
+                            io4dolfinx.write_function(
+                                filename=export.filename,
+                                u=post_processing_solution,
                                 time=float(self.t),
                                 name=species.name,
                             )

src/festim/initial_condition.py

@@ -3,8 +3,8 @@
 
 from mpi4py import MPI
 
-import adios4dolfinx
 import dolfinx
+import io4dolfinx
 import numpy as np
 import ufl
 from dolfinx import fem
@@ -247,8 +247,9 @@ def read_function_from_file(
     """Read a function from a file.
 
     note::
-        The function is read from a file using adios4dolfinx. For more information
-        see the [adios4dolfinx documentation](https://jsdokken.com/adios4dolfinx/README.html).
+        The function is read from a file using io4dolfinx. For more information
+        see the [io4dolfinx documentation](
+        scientificcomputing.github.io/io4dolfinx/README.html).
 
     Args:
         filename: the filename
@@ -261,10 +262,10 @@ def read_function_from_file(
     Returns:
         the function
     """
-    mesh_in = adios4dolfinx.read_mesh(filename, MPI.COMM_WORLD)
+    mesh_in = io4dolfinx.read_mesh(filename=filename, comm=MPI.COMM_WORLD)
     V_in = fem.functionspace(mesh_in, (family, order))
     u_in = fem.Function(V_in)
-    adios4dolfinx.read_function(
+    io4dolfinx.read_function(
         filename=filename,
         u=u_in,
         name=name,

test/test_initial_condition.py

@@ -2,8 +2,8 @@
 
 from mpi4py import MPI
 
-import adios4dolfinx
 import dolfinx
+import io4dolfinx
 import numpy as np
 import pytest
 from dolfinx import fem
@@ -159,8 +159,8 @@ def f(x):
     u_ref.interpolate(f)
     filename = tmpdir.join("initial_condition.bp")
 
-    adios4dolfinx.write_mesh(filename, mesh)
-    adios4dolfinx.write_function(filename, u_ref, name="my_function", time=0.2)
+    io4dolfinx.write_mesh(filename, mesh)
+    io4dolfinx.write_function(filename, u_ref, name="my_function", time=0.2)
 
     # create problem
     my_problem = F.HydrogenTransportProblem()
@@ -213,9 +213,9 @@ def f2(x):
     u_ref2.interpolate(f2)
     filename = tmpdir.join("initial_condition.bp")
 
-    adios4dolfinx.write_mesh(filename, mesh)
-    adios4dolfinx.write_function(filename, u_ref1, name="my_function1", time=0.2)
-    adios4dolfinx.write_function(filename, u_ref2, name="my_function2", time=0.3)
+    io4dolfinx.write_mesh(filename, mesh)
+    io4dolfinx.write_function(filename, u_ref1, name="my_function1", time=0.2)
+    io4dolfinx.write_function(filename, u_ref2, name="my_function2", time=0.3)
 
     # create problem
     my_problem = F.HydrogenTransportProblem()