I have the following code representing a .geo file for Gmsh that I want to load in FiPy for process simulation. It contains: (i) Oxide, (ii) Silicon and (iii) Gas as physical entities that needs to identified as separate meshes.
SetFactory("OpenCASCADE");
//
ns = 1e-1;
ns2 = 1e-2;
//
x1 = 0;
x2 = 1;
y1 = 0;
y2 = 0.5;
Point(1) = {x1, y1, 0, ns};
Point(2) = {x2, y1, 0, ns};
Point(3) = {x2, y2, 0, ns2};
Point(4) = {x1, y2, 0, ns2};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 1};
Curve Loop(1) = {1, 2, 3, 4};
Plane Surface(1) = {1};
Physical Surface("Oxide") = {1};
//
y1 = 0.5;
y2 = 1.0;
shiftX = 0.4;
Point(51) = {x1, y1, 0, ns2};
Point(61) = {x1+shiftX, y1, 0, ns2};
Point(71) = {x1+shiftX, y2, 0, ns2};
Point(81) = {x1, y2, 0, ns2};
Line(51) = {51, 61};
Line(61) = {61, 71};
Line(71) = {71, 81};
Line(81) = {81, 51};
Curve Loop(21) = {51, 61, 71, 81};
Plane Surface(21) = {21};
Physical Surface("Silicon") = {21};
//
Point(52) = {x2-shiftX, y1, 0, ns2};
Point(62) = {x2, y1, 0, ns2};
Point(72) = {x2, y2, 0, ns2};
Point(82) = {x2-shiftX, y2, 0, ns2};
Line(52) = {52, 62};
Line(62) = {62, 72};
Line(72) = {72, 82};
Line(82) = {82, 52};
Curve Loop(22) = {52, 62, 72, 82};
Plane Surface(22) = {22};
Physical Surface("Silicon") += {22};
//
y1 = 1.0;
y2 = 1.5;
shiftX = 0.4;
shiftY = 0.5;
Point(9) = {x1, y1, 0, ns2};
Point(91) = {x1+shiftX, y1, 0, ns2};
Point(92) = {x1+shiftX, y1-shiftY, 0, ns2};
Point(101) = {x2-shiftX, y1-shiftY, 0, ns2};
Point(102) = {x2-shiftX, y1, 0, ns2};
Point(10) = {x2, y1, 0, ns2};
Point(11) = {x2, y2, 0, ns};
Point(12) = {x1, y2, 0, ns};
Line(9) = {9, 91};
Line(91) = {91, 92};
Line(92) = {92, 101};
Line(101) = {101, 102};
Line(102) = {102, 10};
Line(10) = {10, 11};
Line(11) = {11, 12};
Line(12) = {12, 9};
Curve Loop(3) = {9, 91, 92, 101, 102, 10, 11, 12};
Plane Surface(3) = {3};
Physical Surface("Gas") = {3};
//
Is there a way to read this in FiPy and create 3 meshes with the given physical name?
Here is a refinement on the brute-force solution I initially offered:
import fipy as fp
mesh = fp.Gmsh2D('''
SetFactory("OpenCASCADE");
//
ns = 1e-1;
ns2 = 1e-2;
//
x1 = 0;
x2 = 1;
y1 = 0;
y2 = 0.5;
Point(1) = {x1, y1, 0, ns};
Point(2) = {x2, y1, 0, ns};
Point(3) = {x2, y2, 0, ns2};
Point(4) = {x1, y2, 0, ns2};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 1};
Curve Loop(1) = {1, 2, 3, 4};
Plane Surface(1) = {1};
Physical Surface("Oxide") = {1};
//
y1 = 0.5;
y2 = 1.0;
shiftX = 0.4;
Point(51) = {x1, y1, 0, ns2};
Point(61) = {x1+shiftX, y1, 0, ns2};
Point(71) = {x1+shiftX, y2, 0, ns2};
Point(81) = {x1, y2, 0, ns2};
Line(51) = {51, 61};
Line(61) = {61, 71};
Line(71) = {71, 81};
Line(81) = {81, 51};
Curve Loop(21) = {51, 61, 71, 81};
Plane Surface(21) = {21};
Physical Surface("Silicon") = {21};
//
Point(52) = {x2-shiftX, y1, 0, ns2};
Point(62) = {x2, y1, 0, ns2};
Point(72) = {x2, y2, 0, ns2};
Point(82) = {x2-shiftX, y2, 0, ns2};
Line(52) = {52, 62};
Line(62) = {62, 72};
Line(72) = {72, 82};
Line(82) = {82, 52};
Curve Loop(22) = {52, 62, 72, 82};
Plane Surface(22) = {22};
Physical Surface("Silicon") += {22};
//
y1 = 1.0;
y2 = 1.5;
shiftX = 0.4;
shiftY = 0.5;
Point(9) = {x1, y1, 0, ns2};
Point(91) = {x1+shiftX, y1, 0, ns2};
Point(92) = {x1+shiftX, y1-shiftY, 0, ns2};
Point(101) = {x2-shiftX, y1-shiftY, 0, ns2};
Point(102) = {x2-shiftX, y1, 0, ns2};
Point(10) = {x2, y1, 0, ns2};
Point(11) = {x2, y2, 0, ns};
Point(12) = {x1, y2, 0, ns};
Line(9) = {9, 91};
Line(91) = {91, 92};
Line(92) = {92, 101};
Line(101) = {101, 102};
Line(102) = {102, 10};
Line(10) = {10, 11};
Line(11) = {11, 12};
Line(12) = {12, 9};
Curve Loop(3) = {9, 91, 92, 101, 102, 10, 11, 12};
Plane Surface(3) = {3};
Physical Surface("Gas") = {3};
//''')
from fipy.meshes.mesh2D import Mesh2D
def extract_mesh(mesh, mask):
cellFaceIDs = mesh.cellFaceIDs[..., mask]
faceIDs = numerix.unique(cellFaceIDs.flatten())
facemap = numerix.zeros(mesh.faceVertexIDs.shape[1], dtype=int)
facemap[faceIDs] = faceIDs.argsort()
faceVertexIDs = mesh.faceVertexIDs[..., faceIDs]
vertIDs = numerix.unique(faceVertexIDs.flatten())
vertmap = numerix.zeros(mesh.vertexCoords.shape[1], dtype=int)
vertmap[vertIDs] = vertIDs.argsort()
return Mesh2D(mesh.vertexCoords[..., vertIDs],
vertmap[faceVertexIDs],
facemap[cellFaceIDs])
mesh_gas = extract_mesh(mesh=mesh, mask=mesh.physicalCells["Gas"])
mesh_silicon = extract_mesh(mesh=mesh, mask=mesh.physicalCells["Silicon"])
mesh_oxide = extract_mesh(mesh=mesh, mask=mesh.physicalCells["Oxide"])
The derived meshes have compact vertex and face lists and reasonable numbers of exterior faces.
nearest still won't do what you want, because the vast majority of the faces (exterior or otherwise) of the gas mesh are not anywhere near the oxide mesh. You only want the faces that are coincident. To see how complicated that is, you need about 98% of this code.
I think a much better answer is to define the boundaries you are interested in using the Gmsh GEO script, with Physical Line definitions. These can then be extracted as mesh.physicalFaces (some further work would need to be done to extract_mesh(), but I think it's tractable).