def makeGrid(shape, N):
rmax = 2.0 # line length
agrid, pts = [], []
for th in np.linspace(0, np.pi, N, endpoint=True):
lats = []
for ph in np.linspace(0, 2 * np.pi, N, endpoint=True):
p = np.array([sin(th) * cos(ph), sin(th) * sin(ph), cos(th)]) * rmax
intersections = shape.intersectWithLine([0, 0, 0], p)
if len(intersections):
value = mag(intersections[0])
lats.append(value - rbias)
pts.append(intersections[0])
else:
lats.append(rmax - rbias)
pts.append(p)
agrid.append(lats)
agrid = np.array(agrid)
actor = Points(pts, c="k", alpha=0.4, r=1)
return agrid, actor
def FinalizeSolutionStep(self):
super().FinalizeSolutionStep()
if self.timestep > 1.5:
if self.timestep == 2:
self.a_mesh = vedo.load(
f'./vtk_output/VISUALIZE_HROM_0_{self.timestep}.vtk'
).tomesh(fill=True, shrink=1)
displs = self.a_mesh.getPointArray("DISPLACEMENT")
if self.timestep > 2:
b_mesh = vedo.load(
f'./vtk_output/VISUALIZE_HROM_0_{self.timestep}.vtk'
).tomesh(fill=True, shrink=1)
newpoints = b_mesh.points()
displs = b_mesh.getPointArray("DISPLACEMENT")
self.a_mesh.points(newpoints + displs)
self.a_mesh.pointColors(vedo.mag(displs),
cmap='jet',
vmin=0,
vmax=0.009).addScalarBar()
self.a_mesh.show(axes=1, viewup='z')
self.timestep += 1
# Create the springs out of N links
link = [None] * N
for k in range(N):
p0 = bob[k].pos()
p1 = bob[k + 1].pos()
link[k] = Spring(p0, p1, thickness=0.015, r=R / 3, c="gray")
plt += link[k]
# Create some auxiliary variables
x_dot_m = np.zeros(N + 1)
y_dot_m = np.zeros(N + 1)
dij = np.zeros(N + 1) # array with distances to previous bob
dij_m = np.zeros(N + 1)
for k in range(1, N + 1):
dij[k] = mag([bob_x[k] - bob_x[k - 1], bob_y[k] - bob_y[k - 1]])
fctr = lambda x: (x - 1) / x
Dt *= np.sqrt(1 / g)
Dt2 = Dt / 2 # Midpoint time step
DiaSq = (2 * R)**2 # Diameter of bob squared
printc("Press ESC to exit.", c="red", invert=1)
while True:
bob_x_m = list(map((lambda x, dx: x + Dt2 * dx), bob_x,
x_dot)) # midpoint variables
bob_y_m = list(map((lambda y, dy: y + Dt2 * dy), bob_y, y_dot))
for k in range(1, N + 1):
factor = fctr(dij[k])
pz = pavg * np.cos(theta)
poslist.append((x, y, z))
plist.append((px, py, pz))
mlist.append(mass)
rlist.append(Ratom)
pos = np.array(poslist)
poscircle = pos
p = np.array(plist)
m = np.array(mlist)
m.shape = (Natoms, 1)
radius = np.array(rlist)
r = pos - pos[:, np.newaxis] # all pairs of atom-to-atom vectors
ds = (p / m) * (dt / 2.0)
if "False" not in np.less_equal(mag(ds), radius).tolist():
pos = pos + (p / mass) * (dt / 2.0) # initial half-step
pb = ProgressBar(0, Nsteps, c=1)
for i in pb.range():
# Update all positions
ds = mag((p / m) * (dt / 2.0))
if "False" not in np.less_equal(ds, radius).tolist():
pos = pos + (p / m) * dt
r = pos - pos[:, np.newaxis] # all pairs of atom-to-atom vectors
rmag = np.sqrt(np.sum(np.square(r), -1)) # atom-to-atom scalar distances
hit = np.less_equal(rmag, radius + radius[:, None]) - np.identity(Natoms)
hitlist = np.sort(np.nonzero(
hit.flat)[0]).tolist() # i,j encoded as i*Natoms+j
#############################################################
shape = load(datadir + 'apple.ply').normalize().pos(x0).lineWidth(0.1)
show(shape, at=0, N=2, axes=dict(zxGrid=False))
############################################################
# cast rays from the center and find intersections
agrid, pts = [], []
for th in np.linspace(0, np.pi, N, endpoint=False):
lats = []
for ph in np.linspace(0, 2 * np.pi, N, endpoint=False):
p = spher2cart(rmax, th, ph)
intersections = shape.intersectWithLine([0, 0, 0], p)
if len(intersections):
value = mag(intersections[0])
lats.append(value)
pts.append(intersections[0])
else:
lats.append(rmax)
pts.append(p)
agrid.append(lats)
agrid = np.array(agrid)
grid = pyshtools.SHGrid.from_array(agrid)
clm = grid.expand()
grid_reco = clm.expand(lmax=lmax) # cut "high frequency" components
#############################################################
# interpolate to a finer grid
agrid_reco = grid_reco.to_array()
