Meshing union of shapes

6 months 2 days ago #2495 by dfoiles
Hello everyone,

I am trying to create a mesh of a nanorod in water. I am intending for the nanorod to be a cylinder with two hemispherical endcaps inside a larger cylinder of water inside a larger cylinder of PML. However, when I run my script, I get an error. I have determined that the problem is when I try to add the endcaps of the nanorod to its main cylindrical body. Specifically, I get the error

File "<string>", line 2
SyntaxError: (unicode error) 'unicodeescape' codec can't decode bytes in position 1-2: malformed \N character escape
Start Findpoints

at which point, Netgen will hang permanently. I would really appreciate it if you could help me figure out why I am getting this error.

Thank you

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Thank you

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6 months 2 days ago - 6 months 2 days ago #2501 by matthiash

you can just add the whole sphere to the cylinder. It seems the mesher has problems identifiying the edge of the cylinder with the one of the hemisphere.
from ngsolve import *
from netgen.csg import *

def Nanorod(aeff,ratio):

	geo = CSGeometry()

	radius = aeff*(2/(3*ratio-1))**(1/3)
	length = 2 * radius * ratio 
	cyl_length = length/2 - radius

	physical_space = length + 100
	domain = physical_space + 150

	sphere1 = Sphere(Pnt(0,-cyl_length,0),radius)
	sphere2 = Sphere(Pnt(0,cyl_length,0),radius)

	cyl1 = Cylinder(Pnt(0,-2*cyl_length,0),Pnt(0,2*cyl_length,0),radius)
	cyl2 = Cylinder(Pnt(0,-2*physical_space,0),Pnt(0,2*physical_space,0),radius+100)
	cyl3 = Cylinder(Pnt(0,-2*domain,0),Pnt(0,2*domain,0),radius+200).bc('outer')

	box2 = OrthoBrick(Pnt(-physical_space,-physical_space,-physical_space),Pnt(physical_space,physical_space,physical_space)) 
	box3 = OrthoBrick(Pnt(-domain,-domain,-domain),Pnt(domain,domain,domain)).bc('outer')

	plane1 = Plane(Pnt(0,-cyl_length,0),Vec(0,-1,0))
	plane2 = Plane(Pnt(0,cyl_length,0),Vec(0,1,0))

	middle = cyl1*plane1*plane2

	AuNP = (middle+sphere1+sphere2).mat('gold')
	water = (cyl2*box2 - AuNP).mat('water')
	pmldom = (cyl3*box3 - water).mat('pml')


	ngmesh = geo.GenerateMesh()

	mesh = Mesh(ngmesh)
	return mesh

mesh = Nanorod(40,1.6)

The following user(s) said Thank You: dfoiles

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6 months 2 days ago #2503 by dfoiles
That did the trick. Thank you very much for your help and quick reply.

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