Getting started¶

Install¶

NekMeshPy needs Python >= 3.9. Its only required dependencies are numpy>=1.21 and scipy>=1.7.

git clone https://github.com/khanhn201/NekMeshPy.git
cd NekMeshPy

Either run straight from the checkout:

PYTHONPATH=. python examples/flow_past_hemisphere.py

or install it as a library (editable, so the checkout stays the source):

pip install -e .
python examples/flow_past_hemisphere.py

Build a mesh¶

from nekmeshpy import BoundaryConditions, writer, linemesh, quadmesh, hexmesh

n_side = 6
boundary = linemesh.circle(radius=0.5, n=4*n_side, element_tag="wall")
section = quadmesh.ogrid(boundary, n_side=n_side, radial=4)
mesh = hexmesh.extrude(section, axis=(0, 0, 1), length=5.0, layers=40,
                       first_tag="inlet", last_tag="outlet")
print(hexmesh.report(mesh))

Export it¶

Tag names map to Nek BC codes at export.

VEL_BC = {"wall": ("W  ", 1), "inlet": ("v  ", 2), "outlet": ("O  ", 3)}  # (cbc, boundaryID)
TEMP_BC = {"wall": ("I  ", 1), "inlet": ("t  ", 2), "outlet": ("O  ", 3)}
BC = BoundaryConditions(velocity=VEL_BC, temperature=TEMP_BC)
writer.to_re2(mesh, "case.re2", bc=BC) # native Nek5000/NekRS binary mesh
writer.to_fld(mesh, "case.f00000")             # contains high order nodes
writer.to_vtu(mesh, "case.vtu", bc=VEL_BC) # ParaView / VisIt (XML VTK)

Visualize it¶

It is recommended to export and open the .vtu file with your favorite visualizer (Paraview/Visit) and reload the file as you mesh to the .vtu file.

Use high order nodes in Nek5000/NekRS¶

.re2 only store the linear mesh. Higher order nodes can be exported through fld file

writer.to_re2(mesh, "case.re2", bc=VEL_BC)   # topology + BCs, linear
writer.to_fld(mesh, "case.f00000")               # contains high order nodes

to_fld writes the X field — the mesh’s high-order GLL nodes. Point the solver’s .par restart at it so Nek5000/RS reads the high-order nodes:

# Nek5000/NekRS .par file
[GENERAL]
startFrom = case.f00000

Restarting a run with velocity while keeping the high-order geometry

# Nek5000 .par file
[GENERAL]
startFrom = "checkpoint1.f00000 upt,case.f00000 x"

# NekRS .par file
[GENERAL]
startFrom = "checkpoint1.f00000+u+p+t,case.f00000+x"

Examples¶

Full meshers live in examples/, run from the repo root:

python examples/circular_pipe.py
python examples/flow_past_hemisphere.py

Development¶

Optional extras of the library (declared in pyproject.toml):

install	adds	needed for
`pip install -e ".[plot]"`	matplotlib	plotting in the examples / docs
`pip install -e ".[io]"`	meshio	reading the written `.vtu` back in Python (tests, scripts)
`pip install -e ".[mesh]"`	gmsh	`examples/femoral.py` (on Linux the gmsh wheel may also want `libGLU`)
`pip install -e ".[smooth]"`	mfem (PyMFEM 4.8)	the optional TMOP smoother stage (`("tmop", {...})`, MFEM smoother)
`pip install -e ".[all]"`	matplotlib, meshio, pytest, gmsh, mfem	running every example and the whole test suite
`pip install -e ".[all,dev]"`	+ ruff, mypy	development (what the CI lint job installs)
`pip install -e ".[docs]"`	sphinx, myst-parser, furo, sphinx-copybutton, matplotlib, meshio	building the docs

pip install -e ".[all,dev]"          # once
ruff check nekmeshpy tests examples
mypy                                 # type-checks the whole nekmeshpy package
python -m pytest                     # algorithm tests

Build and view the docs¶

The build needs network access: Sphinx fetches the Python/NumPy/SciPy inventories, and the gallery loads vtk.js from a CDN when a page is opened.

pip install -e ".[docs]"                                       # once
python docs/_ext/gen_viewer_assets.py                          # gallery .vtp assets
sphinx-build -b html -n -W --keep-going docs docs/_build/html  # same flags as CI
python -m http.server -d docs/_build/html 8000                 # open http://localhost:8000