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feat: Add resolution gradient support in the mesh generator #177

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Mar 26, 2024
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feat: Add resolution gradient support in the mesh generator #177

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2 changes: 1 addition & 1 deletion examples/fluidity/advection2d/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ $(OUT_DIR)/$(SIM_NAME).flml: $(SRC_DIR)/$(SIM_NAME).flml
$(OUT_DIR)/$(SIM_NAME).msh:
@echo "********** Building the mesh file..."
./envcheck.sh -m
pydrex-mesh -k="rectangle" -a xy $(WIDTH),$(DEPTH) $(RESOLUTION) $@
pydrex-mesh -k="rectangle" -a xy $(WIDTH),$(DEPTH) -r G:$(RESOLUTION) $@

.PHONY: clean
clean:
Expand Down
36 changes: 33 additions & 3 deletions src/pydrex/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,10 @@ def _get_args(self) -> argparse.Namespace:
class MeshGenerator(CliTool):
"""PyDRex script to generate various simple meshes.

Only rectangular (2D) meshes are currently supported.
Only rectangular (2D) meshes are currently supported. The RESOLUTION must be a comma
delimited set of directives of the form `<LOC>:<RES>` where `<LOC>` is a location
specifier, i.e. either "G" (global) or a compas direction like "N", "S", "NE", etc.,
and `<RES>` is a floating point value to be set as the resolution at that location.

"""

Expand All @@ -54,21 +57,48 @@ def __call__(self):
assert len(center) == 2

width, height = map(float, args.size.split(","))
_loc_map = {
"G": "global",
"N": "north",
"S": "south",
"E": "east",
"W": "west",
"NE": "north-east",
"NW": "north-west",
"SE": "south-east",
"SW": "south-west",
}
try:
resolution = {
_loc_map[k]: float(v)
for k, v in map(lambda s: s.split(":"), args.resolution.split(","))
}
except KeyError:
raise KeyError(
"invalid or unsupported location specified in resolution directive"
) from None
except ValueError:
raise ValueError(
"invalid resolution value. The format should be '<LOC1>:<RES1>,<LOC2>:<RES2>,...'"
) from None
_mesh.rectangle(
args.output[:-4],
(args.ref_axes[0], args.ref_axes[1]),
center,
width,
height,
args.resolution,
resolution,
)

def _get_args(self) -> argparse.Namespace:
description, epilog = self.__doc__.split(os.linesep + os.linesep, 1)
parser = argparse.ArgumentParser(description=description, epilog=epilog)
parser.add_argument("size", help="width,height[,depth] of the mesh")
parser.add_argument(
"resolution", help="base resolution of the mesh (edge length hint for gmsh)"
"-r",
"--resolution",
help="resolution for the mesh (edge length hint(s) for gmsh)",
required=True,
)
parser.add_argument("output", help="output file (.msh)")
parser.add_argument(
Expand Down
111 changes: 99 additions & 12 deletions src/pydrex/mesh.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@

@dataclass
class Model:
"""An object-oriented gmsh model API.
"""A context manager for using the gmsh model API.

>>> with Model("example_model", 2, _write_file=False) as model:
... model.point_constraints = [
Expand All @@ -32,6 +32,8 @@ class Model:

"""

# https://gitlab.onelab.info/gmsh/gmsh/-/raw/master/api/gmsh.py

name: str
dim: int
optimize_args: dict = field(default_factory=dict)
Expand All @@ -42,9 +44,15 @@ class Model:
surface_tags: list = field(default_factory=list)
physical_line_tags: list = field(default_factory=list)
physical_group_tags: list = field(default_factory=list)
mesh_info: dict = field(default_factory=dict)
_write_file: bool = True
_was_entered: bool = False

# TODO: Possible attributes worth adding, no particular order:
# - boundary/boundaries, see gm.model.getBoundary()
# - bounding_box, see gm.model.getBoundingBox()
# - wrapper method for gm.model.getClosestPoint() ? maybe we need entities for that

def __enter__(self):
# See: <https://gitlab.onelab.info/gmsh/gmsh/-/issues/1142>
gm.initialize(["-noenv"]) # Don't let gmsh mess with $PYTHONPATH and $PATH.
Expand All @@ -56,6 +64,22 @@ def __exit__(self, exc_type, exc_val, exc_tb):
gm.model.geo.synchronize()
self.add_physical_groups()
gm.model.mesh.generate(self.dim)
# Populate some mesh info for later reference.
node_tags, node_coords, _ = gm.model.mesh.getNodes()
self.mesh_info["node_tags"] = node_tags
self.mesh_info["node_coords"] = node_coords.reshape((node_tags.size, 3))
element_types, element_tags, _ = gm.model.mesh.getElements()
self.mesh_info["element_types"] = element_types
self.mesh_info["element_tags"] = element_tags
edge_tags, edge_orientations = gm.model.mesh.getAllEdges()
self.mesh_info["edge_tags"] = edge_tags
self.mesh_info["edge_orientations"] = edge_orientations
tri_face_tags, tri_face_nodes = gm.model.mesh.getAllFaces(3)
self.mesh_info["tri_face_tags"] = tri_face_tags
self.mesh_info["tri_face_nodes"] = tri_face_nodes
quad_face_tags, quad_face_nodes = gm.model.mesh.getAllFaces(4)
self.mesh_info["quad_face_tags"] = quad_face_tags
self.mesh_info["quad_face_nodes"] = quad_face_nodes
if len(self.optimize_args) > 0:
gm.model.mesh.optimize(**self.optimize_args)
_log.info(
Expand Down Expand Up @@ -111,21 +135,83 @@ def add_physical_groups(self):
)


def rectangle(name, ref_axes, center, width, height, resolution):
"""Generate a rectangular (2D) mesh."""
def rectangle(name, ref_axes, center, width, height, resolution, **kwargs):
"""Generate a rectangular (2D) mesh.

>>> rect = rectangle(
... "test_rect",
... ("x", "z"),
... center=(0, 0),
... width=1,
... height=1,
... resolution={"global": 1e-2},
... _write_file=False
... )
>>> rect.dim
2
>>> rect.name
'test_rect'
>>> rect.line_tags
[1, 2, 3, 4]
>>> rect.loop_tags
[1]
>>> [p[-1] for p in rect.point_constraints]
[0.01, 0.01, 0.01, 0.01]

>>> rect = rectangle(
... "test_rect",
... ("x", "z"),
... center=(0, 0),
... width=1,
... height=1,
... resolution={"north": 1e-2, "south": 1e-3},
... _write_file=False
... )
>>> [p[-1] for p in rect.point_constraints]
[0.001, 0.001, 0.01, 0.01]

>>> rect = rectangle(
... "test_rect",
... ("x", "z"),
... center=(0, 0),
... width=1,
... height=1,
... resolution={"north-west": 1e-3, "south-east": 1e-2},
... _write_file=False
... )
>>> rect.point_constraints[1][-1]
0.01
>>> rect.point_constraints[3][-1]
0.001
>>> rect.point_constraints[0][-1] == rect.point_constraints[2][-1]
True
>>> rect.point_constraints[0][-1]
0.0055

# TODO: Support resolution gradients like:
# resolution_gradient=(1e-2, "radial_grow") # from 1e-2 at the center to `resolution` at the edges
# resolution_gradient=(1e-2, "radial_shrink") # opposite of the above
# resolution_gradient=(1e-2, "south") # from `resolution` at the top to 1e-2 at the bottom
# resolution_gradient=(1e-2, "west")
# default should be resolution_gradient=None
"""

h, v = _geo.to_indices(*ref_axes)
center_h, center_v = center
point_constraints = np.zeros((4, 4)) # x, y, z, nearby_edge_length
# TODO: Support "center" which should trigger creation of an additional
# point_constraint that is not connected by lines but just anchors the central
# resolution constraint (assuming this is possible in gmsh).
_loc_map = {
"global": range(4),
"north": (2, 3),
"south": (0, 1),
"east": (1, 2),
"west": (0, 3),
"north-east": (2,),
"north-west": (3,),
"south-east": (1,),
"south-west": (0,),
}
for i, p in enumerate(point_constraints):
p[-1] = resolution
p[-1] = np.mean(list(resolution.values()))
for k, res in resolution.items():
if i in _loc_map[k]:
p[-1] = res
match i:
case 0:
p[h] = center_h - width / 2
Expand All @@ -140,12 +226,13 @@ def rectangle(name, ref_axes, center, width, height, resolution):
p[h] = center_h - width / 2
p[v] = center_v + height / 2

with Model(name, 2) as model:
with Model(name, 2, **kwargs) as model:
model.point_constraints = point_constraints
model.add_tags()
model.add_physical_groups()
return model


#
# def orthopiped():
# """Generate an orthopiped (3D “box”) mesh."""
# ...
Expand Down
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