Meshes

When your simulation is built on a spatial mesh (e.g. a finite-element or finite-volume mesh), you can store the mesh geometry inside data.h5 using the mesh API. Meshes are kept in the /mesh group of the file and are referenced by name.

Adding a mesh

Meshes are written via a SimulationWriter. You need to supply the node coordinates and cell connectivity.

import numpy as np
from bamboost import Collection
from bamboost.core.simulation.types import CellType

coll = Collection(uid="315628DE80")
sim = coll["my-simulation"].edit()

nodes = np.array([[0, 0], [1, 0], [1, 1], [0, 1]], dtype=float)
cells = np.array([[0, 1, 2], [0, 2, 3]], dtype=np.int64)

sim.meshes.add(
    nodes=nodes,
    cells=cells,
    name="fluid",           # optional; default is "default"
    cell_type=CellType.TRIANGLE,
)

Reading a mesh

sim = coll["my-simulation"]

mesh = sim.meshes["fluid"]
coords = mesh.coordinates    # np.ndarray, shape (n_nodes, n_dim)
topo   = mesh.cells          # np.ndarray, shape (n_cells, n_nodes_per_cell)
ctype  = mesh.cell_type      # str, e.g. "triangle"

Cell types

Cell types are defined by the CellType enum and follow XDMF / ParaView conventions. Common values include TRIANGLE, QUAD, TETRA, HEX, WEDGE.

The cell type is stored as an attribute on the topology dataset and is used when exporting to XDMF for visualisation in ParaView.

Multiple meshes

You can store as many meshes as you need under different names. Series field data can reference a mesh by name (see add_field).

sim = coll["my-simulation"].edit()
sim.meshes.add(nodes=nodes_fluid, cells=cells_fluid, name="fluid")
sim.meshes.add(nodes=nodes_solid, cells=cells_solid, name="solid",
               cell_type=CellType.TETRA)

XDMF export

Once meshes and field data are stored, you can export a standard XDMF file for use in ParaView or other post-processors.

sim = coll["my-simulation"].edit()
sim.write_xdmf()

This creates a data.xdmf file next to data.h5 that links the mesh topology with the series field data.