def setUp(self):
prefix = "examples/SimpleTrap/SimpleTrap"
self.ele = Electrodes.from_trap(open("%s.ele" % prefix), scale=40e-6)
self.tri = Mesh.from_electrodes(self.ele)
self.tri.triangulate(opts="qQ")
self.job = Configuration.select(self.tri, "RF").next()
s, n = .1, 2 * 10
self.grid = Grid(center=(0, 0, 1.5), step=(s, s, s), shape=(n, n, n))
def main():
prefix = "examples/system_to_3d/rfjunction"
scale = 40e-6
fname = "/home/rjordens/work/nist/qc-tools/trunk/bin/rfjunction_gaps.gds"
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s %(name)s %(processName)s[%(process)s] "
"%(filename)s:%(funcName)s() %(levelname)s: %(message)s",
filename="%s.log" % prefix,
filemode="w")
sh = logging.StreamHandler()
sh.setLevel(logging.INFO)
sh.setFormatter(
logging.Formatter("%(processName)s[%(process)s] "
"%(filename)s:%(funcName)s(): %(message)s"))
logging.getLogger().addHandler(sh)
fil = open(fname)
s = from_gds(fil, scale)
if False:
p = system_to_polygons(s)
#check_validity(p)
#p = remove_overlaps(p)
## p = add_gaps(p, .1)
ele = Electrodes.from_polygons(p)
else:
ele = Electrodes.from_system(s)
# ele.cleanup()
ele.extrude(-.1)
mesh = Mesh.from_electrodes(ele)
mesh.triangulate(opts="Q")
mesh.areas_from_constraints(
Sphere(center=np.array([0, 0, 1.]), radius=3, inside=.2, outside=20.))
mesh.triangulate(opts="qQ", new=False)
mesh.to_vtk(prefix)
sim = Simulation(mesh)
#sel = list(sim.select(potentials=[], fields=["r"]))
sel = list(sim.select(potentials=[".*"], fields=["r.*"]))
n, s = 2 * 40, .05
grid = Grid(center=(0, 0, 1.5), step=(s, s, s), shape=(n, n, n))
pool = Pool(4)
c = pool.map(run_job, ((sim, grid, prefix, job) for job in sel))
print([i[0] for i in sel])
print(np.array(c) * 4 * np.pi * epsilon_0 * scale)
Result.view(prefix, "r")
class SimpletrapNewCase(unittest.TestCase):
"""simple trap triangulation and bem simulation"""
def setUp(self):
prefix = "examples/SimpleTrap/SimpleTrap"
self.ele = Electrodes.from_trap(open("%s.ele" % prefix), scale=40e-6)
self.tri = Mesh.from_electrodes(self.ele)
self.tri.triangulate(opts="qQ")
self.job = Configuration.select(self.tri, "RF").next()
s, n = .1, 2 * 10
self.grid = Grid(center=(0, 0, 1.5), step=(s, s, s), shape=(n, n, n))
def assertBetween(self, a, b, c):
self.assertGreaterEqual(a, b)
self.assertLess(a, c)
def test_triangulation(self):
self.assertBetween(self.tri.points.shape[0], 60, 90)
self.assertEqual(self.tri.points.shape[1], 3)
self.assertBetween(self.tri.triangles.shape[0], 40, 70)
self.assertEqual(self.tri.triangles.shape[1], 3)
def test_select(self):
self.assertEqual(self.job.name, "RF")
self.assertEqual(self.tri.keys().index("RF"),
self.job.potentials.argmax())
def test_grid(self):
self.assertEqual(self.grid.to_points().shape, (20**3, 3))
def test_adapt(self):
self.job.adapt_mesh(triangles=2e2)
self.assertBetween(self.job.mesh.points.shape[0], 180, 220)
self.job.adapt_mesh(triangles=1e3)
self.assertBetween(self.job.mesh.points.shape[0], 700, 1100)
def test_simulate(self):
# refine twice adaptively with increasing number of triangles
self.job.adapt_mesh(triangles=5e2)
self.job.adapt_mesh(triangles=1e3)
# solve for charges, get potentials and fields
result = self.job.simulate(self.grid)
def test_simulate_no_fmm(self):
# refine twice adaptively with increasing number of triangles
self.job.adapt_mesh(triangles=5e2)
self.job.adapt_mesh(triangles=1e3)
# solve for charges, get potentials and fields
result = self.job.simulate(self.grid, num_lev=1)
def evaluate(prefix, electrodes):
logging.basicConfig(
level=logging.DEBUG,
format="%(asctime)s %(name)s %(processName)s[%(process)s] "
"%(filename)s:%(funcName)s() %(levelname)s: %(message)s",
filename="%s.log" % prefix,
filemode="w")
sh = logging.StreamHandler()
sh.setLevel(logging.INFO)
sh.setFormatter(
logging.Formatter("%(processName)s[%(process)s] "
"%(filename)s:%(funcName)s(): %(message)s"))
logging.getLogger().addHandler(sh)
n, s = 2 * 10, .1 # FIXME: parametrize
grid = Grid(center=(0, 0, 1.5), step=(s, s, s), shape=(n, n, n))
pool = Pool()
c = map(run_job,
((grid, prefix, (e, True, True, True)) for e in electrodes))
for e in electrodes:
Result.view(prefix, e + "_new")
result = job.simulate(grid, field=job.name == "RF", num_lev=1)
result.to_vtk(prefix)
print("finished job %s" % job.name)
return job.collect_charges()
# set .1 max area within 3
mesh.areas_from_constraints(
Sphere(center=np.array([0, 0, 1.]), radius=2, inside=.2, outside=10.))
# retriangulate quality and quiet with areas
mesh.triangulate(opts="qQ", new=False)
# save base mesh to vtk
mesh.to_vtk(prefix)
# grid to evalute potential and fields at
n, s = 2 * 10, .1
grid = Grid(center=(0, 0, 1.5), step=(s, s, s), shape=(n, n, n))
# generate electrode potential configurations to simulate
# use regexps to match electrode names
jobs = list(Configuration.select(mesh, "DC.*", "RF"))
# run the different electrodes on the parallel pool
#pmap = Pool().map # parallel map
pmap = map # serial map
list(pmap(run_job, ((job, grid, prefix) for job in jobs)))
# isocontour plot of the RF pseudopotential radially
result = Result.from_vtk(prefix, "RF")
p = result.pseudo_potential
x = grid.to_mgrid()[:, p.shape[0] // 2]
p = p[p.shape[0] // 2]
fig, ax = plt.subplots()
ax.set_aspect("equal")