# Copyright (c) 2012-2024, OpenGeoSys Community (http://www.opengeosys.org)
# Distributed under a Modified BSD License.
# See accompanying file LICENSE.txt or
# http://www.opengeosys.org/project/license
#
from collections.abc import Collection
from itertools import pairwise
from pathlib import Path
import gmsh
import numpy as np
import pyvista as pv
def _line(
geo: gmsh.model.geo, length: float, n_edge_cells: int, structured: bool
) -> int:
geo.addPoint(0, 0, 0, tag=1)
geo.addPoint(length, 0, 0, tag=2)
line_tag = geo.addLine(1, 2, tag=1)
if structured:
geo.mesh.setTransfiniteCurve(1, n_edge_cells + 1)
geo.mesh.setTransfiniteSurface(1)
geo.mesh.setRecombine(dim=1, tag=1)
return line_tag
[docs]
def rect(
lengths: float | tuple[float, float] = 1.0,
n_edge_cells: int | tuple[int, int] = 1,
n_layers: int = 1,
structured_grid: bool = True,
order: int = 1,
mixed_elements: bool = False,
jiggle: float = 0.0,
out_name: Path | str = Path("rect.msh"),
msh_version: float | None = None,
layer_ids: list | None = None,
) -> None:
gmsh.initialize()
gmsh.option.set_number("General.Verbosity", 0)
if msh_version is not None:
gmsh.option.setNumber("Mesh.MshFileVersion", msh_version)
name = Path(out_name).stem
gmsh.model.add(name)
dx, dy = lengths if isinstance(lengths, Collection) else [lengths] * 2
nx, ny = (
n_edge_cells
if isinstance(n_edge_cells, Collection)
else [n_edge_cells] * 2
)
bottom_tag = _line(gmsh.model.geo, dx, nx, structured_grid)
right_tags = []
left_tags = []
top_tag = bottom_tag
if layer_ids is None:
layer_ids = list(range(n_layers))
assert isinstance(layer_ids, list)
for n in range(n_layers):
recombine = n % 2 if mixed_elements else structured_grid
newEntities = gmsh.model.geo.extrude(
dimTags=[(1, top_tag)],
dx=0,
dy=dy / n_layers,
dz=0,
numElements=[ny] if structured_grid else [],
recombine=recombine, # fmt: skip
)
top_tag = abs(newEntities[0][1])
plane_tag = abs(newEntities[1][1])
layer_name = f"Layer {n}" if n_layers > 1 else name
tag = layer_ids[n]
gmsh.model.addPhysicalGroup(
dim=2, tags=[plane_tag], name=layer_name, tag=tag
)
right_tags += [abs(newEntities[2][1])]
left_tags += [abs(newEntities[3][1])]
gmsh.model.addPhysicalGroup(dim=1, tags=[bottom_tag], name="bottom")
gmsh.model.addPhysicalGroup(dim=1, tags=[top_tag], name="top")
gmsh.model.addPhysicalGroup(dim=1, tags=right_tags, name="right")
gmsh.model.addPhysicalGroup(dim=1, tags=left_tags, name="left")
gmsh.model.geo.synchronize()
gmsh.option.setNumber("Mesh.SecondOrderIncomplete", 1)
if not structured_grid:
gmsh.option.setNumber("Mesh.MeshSizeMin", dy / ny)
gmsh.option.setNumber("Mesh.MeshSizeMax", dy / ny)
gmsh.model.mesh.generate(dim=2)
if jiggle > 0.0:
node_ids = gmsh.model.mesh.getNodes(dim=2)[0]
for node_id in node_ids:
offset = np.append(np.random.default_rng().random(2), 0.0)
coord, parametric_coord, _, tag = gmsh.model.mesh.get_node(node_id)
coord = np.asarray(coord) + offset * jiggle
gmsh.model.mesh.set_node(node_id, coord, parametric_coord)
gmsh.model.mesh.setOrder(order)
gmsh.write(str(out_name))
gmsh.finalize()
def _square(
geo: gmsh.model.geo,
lengths: tuple[float, float],
n_edge_cells: tuple[int, int],
structured: bool,
) -> int:
geo.addPoint(0, 0, 0, tag=1)
geo.addPoint(lengths[0], 0, 0, tag=2)
geo.addPoint(lengths[0], lengths[1], 0, tag=3)
geo.addPoint(0, lengths[1], 0, tag=4)
geo.addLine(1, 2, tag=1)
geo.addLine(2, 3, tag=2)
geo.addLine(3, 4, tag=3)
geo.addLine(4, 1, tag=4)
geo.addCurveLoop([1, 2, 3, 4], tag=1)
plane_tag = geo.addPlaneSurface([1], tag=1)
geo.mesh.setTransfiniteCurve(1, n_edge_cells[0] + 1)
geo.mesh.setTransfiniteCurve(2, n_edge_cells[1] + 1)
geo.mesh.setTransfiniteCurve(3, n_edge_cells[0] + 1)
geo.mesh.setTransfiniteCurve(4, n_edge_cells[1] + 1)
if structured:
geo.mesh.setTransfiniteSurface(1)
geo.mesh.setRecombine(dim=2, tag=1)
return plane_tag
[docs]
def cuboid(
lengths: float | tuple[float, float, float] = 1.0,
n_edge_cells: int | tuple[int, int, int] = 1,
n_layers: int = 1,
structured_grid: bool = True,
order: int = 1,
mixed_elements: bool = False,
out_name: Path = Path("unit_cube.msh"),
msh_version: float | None = None,
) -> None:
gmsh.initialize()
gmsh.option.set_number("General.Verbosity", 0)
if msh_version is not None:
gmsh.option.setNumber("Mesh.MshFileVersion", msh_version)
name = Path(out_name).stem
gmsh.model.add(name)
_lengths = lengths if isinstance(lengths, Collection) else (lengths,) * 3
_n_edge_cells = (
n_edge_cells
if isinstance(n_edge_cells, Collection)
else (n_edge_cells,) * 3
)
bottom_tag = _square(
gmsh.model.geo,
_lengths[1:],
_n_edge_cells[1:],
structured_grid and not mixed_elements,
)
dz = lengths if isinstance(lengths, float) else lengths[2]
nz = n_edge_cells if isinstance(n_edge_cells, int) else n_edge_cells[2]
front_tags = []
right_tags = []
back_tags = []
left_tags = []
top_tag = 1
for n in range(n_layers):
recombine = n % 2 if mixed_elements else structured_grid
newEntities = gmsh.model.geo.extrude(
dimTags=[(2, top_tag)],
dx=0,
dy=0,
dz=dz / n_layers,
numElements=[nz] if structured_grid else [],
recombine=recombine, # fmt: skip
)
top_tag = abs(newEntities[0][1])
vol_tag = abs(newEntities[1][1])
layer_name = f"Layer {n}" if n_layers > 1 else name
tag = -1 if n_layers > 1 else 0
gmsh.model.addPhysicalGroup(
dim=3, tags=[vol_tag], name=layer_name, tag=tag
)
front_tags += [abs(newEntities[2][1])]
right_tags += [abs(newEntities[3][1])]
back_tags += [abs(newEntities[4][1])]
left_tags += [abs(newEntities[5][1])]
gmsh.model.addPhysicalGroup(dim=2, tags=[bottom_tag], name="bottom")
gmsh.model.addPhysicalGroup(dim=2, tags=[top_tag], name="top")
gmsh.model.addPhysicalGroup(dim=2, tags=front_tags, name="front")
gmsh.model.addPhysicalGroup(dim=2, tags=right_tags, name="right")
gmsh.model.addPhysicalGroup(dim=2, tags=back_tags, name="back")
gmsh.model.addPhysicalGroup(dim=2, tags=left_tags, name="left")
gmsh.model.geo.synchronize()
gmsh.model.mesh.generate(dim=3)
gmsh.option.setNumber("Mesh.SecondOrderIncomplete", 1)
if not structured_grid:
gmsh.option.setNumber(
"Mesh.MeshSizeMin", _lengths[0] / _n_edge_cells[0]
)
gmsh.option.setNumber(
"Mesh.MeshSizeMax", _lengths[0] / _n_edge_cells[0]
)
gmsh.model.mesh.setOrder(order)
gmsh.write(str(out_name))
gmsh.finalize()
def _ordered_edges(mesh: pv.UnstructuredGrid) -> np.ndarray:
"Return edge elements ordered to form a contiguous array."
edges = mesh.extract_feature_edges()
n_cells = edges.n_cells
# shape=(n_cells, 2, 3), the 2 is for pointA and pointB
cell_pts = np.asarray([cell.points for cell in edges.cell])
ordered_cell_ids = [0]
cell_id = 0
for _ in range(n_cells):
next_id = np.argmax(
np.equal(cell_pts[cell_id, 1], cell_pts[:, 0]).all(axis=1)
)
ordered_cell_ids += [int(next_id)]
cell_id = int(next_id)
return cell_pts[ordered_cell_ids[:-1], 0]
[docs]
def remesh_with_triangles(
mesh: pv.UnstructuredGrid,
output_file: Path | str = Path() / "tri_mesh.msh",
size_factor: float = 1.0,
order: int = 1,
) -> None:
"""Discretizes a given Mesh with triangles and saves as gmsh .msh.
Requires the mesh to be 2D and to contain 'MaterialIDs in the cell data.
:param mesh: The mesh which shall be discretized with triangles
:param output_file: The full filepath to the resulting file
:param size_factor: A factor to scale the element sizes.
:param order: The element order (1=linear, 2=quadratic, ...)
"""
gmsh.initialize()
gmsh.option.set_number("General.Verbosity", 0)
gmsh.clear()
gmsh.model.add("domain")
mat_ids = np.unique(mesh["MaterialIDs"])
# gmsh requires the domain ids to start at 1
id_offset = 1 if 0 in mat_ids else 0
region_edge_points = [
_ordered_edges(mesh.threshold([m, m], "MaterialIDs")) for m in (mat_ids)
]
for point in np.vstack(region_edge_points):
gmsh.model.geo.addPoint(point[0], point[1], point[2])
region_lengths = [len(pts) for pts in region_edge_points]
region_start_tag = np.cumsum([0] + region_lengths) + 1
for tag_0, tag_1 in pairwise(region_start_tag):
for index in range(tag_0, tag_1 - 1):
gmsh.model.geo.addLine(index, index + 1)
gmsh.model.geo.addLine(tag_1 - 1, tag_0)
field = gmsh.model.mesh.field
for index, points in enumerate(region_edge_points):
mat_id = mat_ids[index] + id_offset
line_tags = range(region_start_tag[index], region_start_tag[index + 1])
gmsh.model.geo.addCurveLoop(line_tags, tag=mat_id)
gmsh.model.geo.addPlaneSurface([mat_id], tag=mat_id)
gmsh.model.addPhysicalGroup(
dim=2, tags=[mat_id], name=f"Layer {mat_id}"
)
f1, f2 = (2 * mat_id, 2 * mat_id + 1)
distances = np.linalg.norm(np.diff(points, axis=0), axis=1)
DEFAULT_SIZE = 6 # pylint: disable=C0103
min_elem_size = size_factor * np.min(distances) * DEFAULT_SIZE
max_elem_size = size_factor * np.max(distances) * DEFAULT_SIZE
field.add("Distance", f1)
field.setNumbers(f1, "CurvesList", line_tags)
field.add("Threshold", f2)
field.setNumber(f2, "IField", f1)
field.setNumber(f2, "SizeMin", min_elem_size)
field.setNumber(f2, "SizeMax", max_elem_size)
field.setNumber(f2, "DistMin", min_elem_size)
field.setNumber(f2, "DistMax", 3 * max_elem_size)
field.add("Min", tag=f2 + 1)
field.setNumbers(f2 + 1, "FieldsList", (mat_ids * 2 + 1).tolist())
field.setAsBackgroundMesh(f2 + 1)
gmsh.model.geo.removeAllDuplicates()
gmsh.model.geo.synchronize()
gmsh.option.setNumber("Mesh.SecondOrderIncomplete", 1)
gmsh.option.setNumber("Mesh.MeshSizeExtendFromBoundary", 0)
gmsh.option.setNumber("Mesh.MeshSizeFromPoints", 0)
gmsh.option.setNumber("Mesh.MeshSizeFromCurvature", 0)
gmsh.model.mesh.generate(dim=2)
gmsh.model.mesh.setOrder(order)
gmsh.write(str(output_file))
gmsh.finalize()
return
