DOLFIN / FEniCS XML#

.xml read + write eager

Summary of the specification#

The legacy DOLFIN mesh format is a small XML tree: a <dolfin> root containing a <mesh> whose celltype attribute names the element (interval, triangle, tetrahedron) and whose dim gives the geometric dimension. Inside, <vertices> and <cells> declare their sizes and hold one <vertex> or one <triangle> element per entity, each with an explicit index and its coordinates or node references. Everything is indexed, 0-based and explicit.

Specification at a glance#

root	<dolfin xmlns:dolfin=”…”>
mesh element	<mesh celltype=”triangle” dim=”2”>
vertices	<vertices size=”n”> with <vertex index x y z>
cells	<cells size=”n”> with <triangle index v0 v1 v2> etc.
homogeneity	one cell type per file
status	superseded by XDMF in modern FEniCS

Read the full DOLFIN / FEniCS XML specification ↗

Reading#

import polyxios as px

mesh = px.read("model.xml")
mesh.vertices          # (n, 3)
mesh.element_types     # one type code per element

Writing#

px.write(mesh, "out.xml")
px.write(mesh, "out.xml", dim=2)

Format-specific options#

Option	Default	Effect
`dim`	`None`	On write: the geometric dimension written as `<mesh dim>`. Inferred when not given: 2 for a mesh of no solid cells whose vertices lie in the `z = 0` plane, 3 otherwise. Every vertex is written with its `z` whatever `dim` says.

Quirks worth knowing#

The cell types read and written are interval, triangle, quadrilateral, tetrahedron and hexahedron; any other celltype is refused with CodecError.
The format holds a single cell type per file. Writing a mixed mesh keeps the type of its first writable element and skips every other element with a warning; a mesh with no element of a supported type is refused.
A 2-D file’s coordinates are padded with a zero z, so the mesh is 3-D like every other one polyxios holds, and global_attrs["was_2d"] records the fact. The dim attribute follows it. The writer puts it back so long as the vertices have stayed in the plane; a mesh whose vertices have since left it is written in three with a warning. An inferred dim is 3 for a mesh of solid cells however flat it lies, DOLFIN needing its geometric dimension to be at least its topological one; a dim= given by the caller is left alone.
Only the <vertices> and <cells> are read: mesh function, mesh value collection and domain data blocks are ignored, so no attribute or tag comes back.