VTKHDF backend for reading and writing point data (#199)

* Start working on a mesh-writer that depends on time

* Fix write (time-dependent) geometry to file

* Fix vtkhdf in topology permutation

* After hours of Gemini prompting, it turns out I need to read the VTKHDF docs more carefully, should just have turned on track_groups. Only thing Gemini in the end did for me.

* Add recursive search through groups

* Fix all vtkhdf tests

* Further work, writing meshtags

* Add reading multiple meshes

* Add write/read meshtags

* Add geometry dofmap constructor that is bulletproof

* Create vtk-hdf backend that can write point data

* Add read/write capabilities of point/cell-data

* Add test of mixed data types

* Clean up paths.

* Finsberg/vtkhdf write mesh (#200)

* Add pyvista and xdmf deps to test dependencies

* Use tmp_path

* Apply suggestions from code review

Documentation fixes and some logic simplification

Co-authored-by: Henrik Finsberg <henrikfinsberg@hotmail.com>

* Refactor vtkhdf backend (#203)

* Refactor code for getting UnstructuredGrid

* Refactor time index

* No more walrus

* Refactor single partition data

* Less indendation

* Simplifications and type hinting

* Documentation and some simplifications

* Remove stray comment

---------

Co-authored-by: Jørgen S. Dokken <dokken@simula.no>

---------

Co-authored-by: Henrik Finsberg <henrikfinsberg@hotmail.com>

Author: jorgensd

.github/workflows/test_package.yml

@@ -82,7 +82,7 @@ jobs:
       - name: Install package
         run: |
           HDF5_MPI=ON HDF5_PKGCONFIG_NAME="hdf5" python3 -m pip install h5py  --no-build-isolation --no-binary=h5py
-          python3 -m pip install  .[test,xdmf,pyvista]
+          python3 -m pip install  .[test]
 
       - name: Run tests
         run: |

.github/workflows/test_package_openmpi.yml

@@ -78,7 +78,7 @@ jobs:
       - name: Install package
         run: |
           HDF5_MPI=ON HDF5_PKGCONFIG_NAME="hdf5" python3 -m pip install h5py  --no-build-isolation --no-binary=h5py
-          python3 -m pip install  .[test,xdmf,pyvista]
+          python3 -m pip install  .[test]
       - name: Run tests
         run: |
           coverage run --rcfile=.coveragerc -m mpi4py -m pytest -xvs ./tests/

pyproject.toml

@@ -11,7 +11,14 @@ readme = "README.md"
 dependencies = ["fenics-dolfinx>=0.10.0", "packaging"]
 
 [project.optional-dependencies]
-test = ["pytest", "coverage", "ipyparallel", "adios4dolfinx[h5py]"]
+test = [
+    "pytest", 
+    "coverage", 
+    "ipyparallel", 
+    "adios4dolfinx[h5py]", 
+    "adios4dolfinx[pyvista]", 
+    "adios4dolfinx[xdmf]"
+]
 dev = ["pdbpp", "ipython", "mypy", "ruff"]
 h5py = ["h5py"]
 pyvista = ["pyvista"]

src/adios4dolfinx/__init__.py

@@ -17,9 +17,11 @@
     read_meshtags,
     read_timestamps,
     write_attributes,
+    write_cell_data,
     write_function,
     write_mesh,
     write_meshtags,
+    write_point_data,
 )
 from .original_checkpoint import write_function_on_input_mesh, write_mesh_input_order
 from .readers import (
@@ -52,9 +54,12 @@
     "write_function_on_input_mesh",
     "write_mesh_input_order",
     "write_attributes",
+    "write_data",
     "read_attributes",
     "read_function_names",
     "read_point_data",
     "read_timestamps",
     "get_backend",
+    "write_cell_data",
+    "write_point_data",
 ]

src/adios4dolfinx/backends/__init__.py

@@ -9,7 +9,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from ..structures import FunctionData, MeshData, MeshTagsData, ReadMeshData
+from ..structures import ArrayData, FunctionData, MeshData, MeshTagsData, ReadMeshData
 
 __all__ = ["FileMode", "IOBackend", "get_backend"]
 
@@ -381,6 +381,28 @@ def read_cell_data(
         """
         ...
 
+    def write_data(
+        self,
+        filename: Path | str,
+        array_data: ArrayData,
+        comm: MPI.Intracomm,
+        time: str | float | None,
+        mode: FileMode,
+        backend_args: dict[str, Any] | None,
+    ):
+        """Write a 2D-array to file.
+
+
+        Args:
+            filename: Path to file
+            array_data: Data to write to file.
+            comm: The MPI communicator to open the writer with.
+            time: The time stamp
+            mode: Append or write
+            backend_args: The backend arguments
+        """
+        ...
+
 
 def get_backend(backend: str) -> IOBackend:
     """Get backend class from backend name.

src/adios4dolfinx/backends/adios2/backend.py

@@ -9,7 +9,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from ...structures import FunctionData, MeshData, MeshTagsData, ReadMeshData
+from ...structures import ArrayData, FunctionData, MeshData, MeshTagsData, ReadMeshData
 from ...utils import check_file_exists, compute_local_range
 from .. import FileMode, ReadMode
 from .helpers import (
@@ -971,3 +971,25 @@ def read_cell_data(
         freedom within that cell.
     """
     raise NotImplementedError("The ADIOS2 backend does not support reading cell data.")
+
+
+def write_data(
+    filename: Path | str,
+    array_data: ArrayData,
+    comm: MPI.Intracomm,
+    time: str | float | None,
+    mode: FileMode,
+    backend_args: dict[str, Any] | None,
+):
+    """Write a 2D-array to file (distributed across proceses with MPI).
+
+
+    Args:
+        filename: Path to file
+        array_data: Data to write to file
+        comm: MPI communicator to open the file with.
+        time: Time stamp
+        mode: Append or write
+        backend_args: The backend arguments
+    """
+    raise NotImplementedError("ADIOS2 has not implemented this yet")

src/adios4dolfinx/backends/h5py/backend.py

@@ -17,7 +17,7 @@
 import numpy.typing as npt
 from dolfinx.graph import adjacencylist
 
-from ...structures import FunctionData, MeshData, MeshTagsData, ReadMeshData
+from ...structures import ArrayData, FunctionData, MeshData, MeshTagsData, ReadMeshData
 from ...utils import check_file_exists, compute_local_range
 from .. import FileMode, ReadMode
 
@@ -199,7 +199,9 @@ def write_mesh(
         # Write geometry data
         gdim = mesh.local_geometry.shape[1]
         geometry_dataset = geometry_group.create_dataset(
-            "Points", [mesh.num_nodes_global, gdim], dtype=mesh.local_geometry.dtype
+            "Points",
+            [mesh.num_nodes_global, gdim],
+            dtype=mesh.local_geometry.dtype,
         )
         geometry_dataset[slice(*mesh.local_geometry_pos), :] = mesh.local_geometry
 
@@ -796,3 +798,24 @@ def read_cell_data(
         freedom within that cell.
     """
     raise NotImplementedError("The h5py backend does not support reading cell data.")
+
+
+def write_data(
+    filename: Path | str,
+    array_data: ArrayData,
+    comm: MPI.Intracomm,
+    time: str | float | None,
+    mode: FileMode,
+    backend_args: dict[str, Any] | None,
+):
+    """Write a 2D-array to file (distributed across proceses with MPI).
+
+    Args:
+        filename: Path to file
+        array_data: Data to write to file
+        comm: MPI communicator to open the file with
+        time: Time-stamp for data.
+        mode: Append or write
+        backend_args: The backend arguments
+    """
+    raise NotImplementedError("H5PY has not implemented this yet")

src/adios4dolfinx/backends/pyvista/backend.py

@@ -18,14 +18,15 @@
 import basix
 import dolfinx
 
-from adios4dolfinx.structures import FunctionData, MeshData, MeshTagsData, ReadMeshData
+from adios4dolfinx.structures import ArrayData, FunctionData, MeshData, MeshTagsData, ReadMeshData
 from adios4dolfinx.utils import check_file_exists
 
 from .. import FileMode, ReadMode
 
 # Cell types can be found at
 # https://vtk.org/doc/nightly/html/vtkCellType_8h_source.html
 _first_order_vtk = {
+    1: "point",
     3: "interval",
     5: "triangle",
     9: "quadrilateral",
@@ -564,3 +565,24 @@ def read_hdf5_array(
                 Process 0 has [0, M), process 1 [M, N), process 2 [N, O) etc.
     """
     raise NotImplementedError("The Pyvista backend cannot read HDF5 arrays")
+
+
+def write_data(
+    filename: Path | str,
+    array_data: ArrayData,
+    comm: MPI.Intracomm,
+    time: str | float | None,
+    mode: FileMode,
+    backend_args: dict[str, Any] | None,
+):
+    """Write a 2D-array to file (distributed across proceses with MPI).
+
+    Args:
+        filename: Path to file
+        array_data: Data to write to file
+        comm: MPI communicator to open the file with
+        time: Time stamp
+        mode: Append or write
+        backend_args: The backend arguments
+    """
+    raise NotImplementedError("The pyvista backend does not support writing point data")