def Nanorod(aeff, ratio, mt_length):
geo = CSGeometry()
if ratio == 1:
return Nanosphere(aeff, mt_length)
if mt_length == 0:
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
#Endcaps
sphere1 = Sphere(Pnt(0, -cyl_length, 0), radius)
sphere2 = Sphere(Pnt(0, cyl_length, 0), radius)
#Water
sphere3 = Sphere(Pnt(0, 0, 0), physical_space)
#PML
sphere4 = Sphere(Pnt(0, 0, 0), domain).bc('outer')
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')
plane1 = Plane(Pnt(0, -cyl_length, 0), Vec(0, -1, 0))
plane2 = Plane(Pnt(0, cyl_length, 0), Vec(0, 1, 0))
plane3 = Plane(Pnt(0, -physical_space, 0), Vec(0, -1, 0))
plane4 = Plane(Pnt(0, physical_space, 0), Vec(0, 1, 0))
plane5 = Plane(Pnt(0, -domain, 0), Vec(0, -1, 0))
plane6 = Plane(Pnt(0, domain, 0), Vec(0, 1, 0))
middle = cyl1 * plane1 * plane2
AuNP = (middle + sphere1 + sphere2).mat('gold')
water = (cyl2 * plane3 * plane4 - AuNP).mat('water')
pmldom = (cyl3 * plane5 * plane6 - cyl2 * plane3 * plane4).mat('pml')
geo.Add(AuNP)
geo.Add(water)
geo.Add(pmldom)
else:
radius = aeff * (2 / (3 * ratio - 1))**(1 / 3)
length = 2 * radius * ratio
cyl_length = length / 2 - radius
particle = radius + mt_length
physical_space = length + mt_length + 100
domain = physical_space + 150
#Nanoparticle
cyl1 = Cylinder(Pnt(0, -1, 0), Pnt(0, 1, 0), radius)
#Microtubules
cyl2 = Cylinder(Pnt(0, -1, 0), Pnt(0, 1, 0), particle)
#Water
cyl3 = Cylinder(Pnt(0, -1, 0), Pnt(0, 1, 0), particle + 100)
#PML
cyl4 = Cylinder(Pnt(0, -2, 0), Pnt(0, 2, 0),
particle + 150).bc('outer')
#Nanoparticle endcaps
sphere1 = Sphere(Pnt(0, -cyl_length, 0), radius)
sphere2 = Sphere(Pnt(0, cyl_length, 0), radius)
#Microtubule endcaps
sphere3 = Sphere(Pnt(0, -cyl_length, 0), particle)
sphere4 = Sphere(Pnt(0, cyl_length, 0), particle)
#Endcap cut-offs
plane1 = Plane(Pnt(0, -cyl_length, 0), Vec(0, -1, 0))
plane2 = Plane(Pnt(0, cyl_length, 0), Vec(0, 1, 0))
plane3 = Plane(Pnt(0, -physical_space, 0), Vec(0, -1, 0))
plane4 = Plane(Pnt(0, physical_space, 0), Vec(0, 1, 0))
plane5 = Plane(Pnt(0, -domain, 0), Vec(0, -1, 0))
plane6 = Plane(Pnt(0, domain, 0), Vec(0, 1, 0))
middle = cyl1 * plane1 * plane2
AuNP = (middle + sphere1 + sphere2).mat('gold')
mt_middle = ((cyl2 - cyl1) * plane1 * plane2).mat('mt_mid')
endcap1_mt = (sphere3 - plane1) - sphere1
endcap2_mt = (sphere4 - plane2) - sphere2
mt_endcaps = (endcap1_mt + endcap2_mt).mat('mt_end')
total_body = AuNP + endcap1_mt + endcap2_mt + mt_middle
water = (cyl3 * plane3 * plane4 - total_body).mat('water')
pmldom = ((cyl4 - cyl3) * plane5 * plane6 -
(water + total_body)).mat('pml')
geo.Add(AuNP)
geo.Add(mt_endcaps)
geo.Add(mt_middle)
geo.Add(water)
geo.Add(pmldom)
ngmesh = geo.GenerateMesh()
mesh = Mesh(ngmesh)
p = pml.BrickRadial((-domain, -domain, -domain), (domain, domain, domain),
alpha=1J)
mesh.SetPML(p, 'pml')
return mesh, radius, length
def Nanosphere(particle, mt_length, physical_space, domain, mt_model="radial"):
# physical_space = particle + mt_length + 150
# domain = physical_space + 200
particle /= 100
mt_length /= 100
physical_space /= 100
domain /= 100
geo = CSGeometry()
if mt_length == 0:
sphere1 = Sphere(Pnt(0, 0, 0), particle)
sphere2 = Sphere(Pnt(0, 0, 0), physical_space)
sphere3 = Sphere(Pnt(0, 0, 0), domain).bc('outer')
AuNP = sphere1.mat('gold')
water = (sphere2 - sphere1).mat('water')
pmldom = (sphere3 - sphere2).mat('pml')
geo.Add(AuNP)
geo.Add(water)
geo.Add(pmldom, maxh=.7)
else:
if mt_model == "radial":
sphere1 = Sphere(Pnt(0, 0, 0), particle)
sphere2 = Sphere(Pnt(0, 0, 0), particle + mt_length)
sphere3 = Sphere(Pnt(0, 0, 0), physical_space)
sphere4 = Sphere(Pnt(0, 0, 0), domain).bc('outer')
AuNP = sphere1.mat('gold')
mt = (sphere2 - sphere1).mat('mt_sphere')
water = (sphere3 - sphere2).mat('water')
pmldom = (sphere4 - sphere3).mat('pml')
geo.Add(AuNP)
geo.Add(mt)
geo.Add(water)
geo.Add(pmldom)
else:
mt_radius = .125 # 12.5 nm
sphere1 = Sphere(Pnt(0, 0, 0), particle)
sphere2 = Sphere(Pnt(0, 0, 0), physical_space)
sphere3 = Sphere(Pnt(0, 0, 0), domain).bc('outer')
cyl1 = Cylinder(Pnt(0, 0, 0), Pnt(0, 0, 1), mt_radius)
cyl2 = Cylinder(Pnt(0, 0, 0), Pnt(0, 1, 0), mt_radius)
cyl3 = Cylinder(Pnt(0, 0, 0), Pnt(1, 0, 0), mt_radius)
plane1 = Plane(Pnt(0, 0, mt_length + particle), Vec(0, 0, 1))
plane2 = Plane(Pnt(0, 0, -(mt_length + particle)), Vec(0, 0, -1))
plane3 = Plane(Pnt(0, mt_length + particle, 0), Vec(0, 1, 0))
plane4 = Plane(Pnt(0, -(mt_length + particle), 0), Vec(0, -1, 0))
plane5 = Plane(Pnt(mt_length + particle, 0, 0), Vec(1, 0, 0))
plane6 = Plane(Pnt(-(mt_length + particle), 0, 0), Vec(-1, 0, 0))
mt1 = ((plane2 * cyl1 * plane1) - sphere1).mat("mt_cyl")
mt2 = ((plane3 * cyl2 * plane4) - sphere1).mat("mt_cyl")
mt3 = ((plane5 * cyl3 * plane6) - sphere1).mat("mt_cyl")
AuNP = sphere1.mat("gold")
water = ((((sphere2 - mt1) - mt2) - mt3) - AuNP).mat("water")
pmldom = (sphere3 - sphere2).mat("pml")
geo.Add(AuNP)
geo.Add(mt1)
geo.Add(mt2)
geo.Add(mt3)
geo.Add(water)
geo.Add(pmldom, maxh=1)
ngmesh = geo.GenerateMesh(maxh=2)
mesh = Mesh(ngmesh)
p = pml.Radial(origin=(0, 0, 0), rad=domain)
mesh.SetPML(p, 'pml')
return mesh, particle, particle
