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bridge_dynamics_2.py
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bridge_dynamics_2.py
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import numpy as np
import matplotlib.pyplot as plt
import re
from scipy.interpolate import griddata
from scipy.interpolate import RegularGridInterpolator
from scipy import interpolate
from scipy.integrate import quad
import pickle
target_folder = 'comsol_results/capillary_bridge_dynamics/sketch_2/'
comsol_filename = target_folder + 'velocity_field.txt'
comsol_npy_filename = target_folder + 'velocity_field.npy'
interpolators_filename = target_folder + 'interps.pkl'
# comsol_data = np.loadtxt(comsol_filename, skiprows=9)
# np.save(comsol_npy_filename, comsol_data)
comsol_data = np.load(comsol_npy_filename)
r = comsol_data[:,0]
z = comsol_data[:,1]
line = open(comsol_filename, "r").readlines()[8]
regex1 = re.compile('''@ t=(.+?) ''', re.DOTALL)
res = regex1.findall(line)
ts = np.array(sorted([float(x) for x in list(set(res))]))
def get_field_for_t(t):
index = np.where(ts == t)[0][0]
#u,w
u = comsol_data[:, 2 + index * 3]
w = comsol_data[:, 2 + index * 3 + 1]
return u,w
def get_field_interp_for_timenode(t):
u,w = get_field_for_t(t)
# position = np.argmax(ts > t)
x = r
y = z
Ex_raw = u
Ey_raw = w
xi = np.array(sorted(list(set(list(x)))))
yi = np.array(sorted(list(set(list(y)))))
X, Y = np.meshgrid(xi, yi)
Ex = griddata((x, y), Ex_raw, (X, Y), method='linear')
Ey = griddata((x, y), Ey_raw, (X, Y), method='linear')
# plt.pcolor(X,Y,Ey)
# plt.colorbar()
# plt.show()
# plt.plot(xi, Ey[0,:], color='C0')
# plt.show()
Ex_interp = RegularGridInterpolator(points=[xi, yi], values=Ex.T, method='linear', fill_value=None,
bounds_error=False)
Ey_interp = RegularGridInterpolator(points=[xi, yi], values=Ey.T, method='linear', fill_value=None,
bounds_error=False)
return Ex_interp, Ey_interp
def precompute_interps():
print('Precomputing interpolators.')
interp_list = [get_field_interp_for_timenode(t) for t in ts]
with open(interpolators_filename, 'wb') as f:
pickle.dump(interp_list, f)
def load_interps():
with open(interpolators_filename, 'rb') as f:
interp_list = pickle.load(f)
return interp_list
# precompute_interps()
interp_list = load_interps()
def get_interface_line_for_timenode(t):
index = np.where(ts == t)[0][0]
dom = comsol_data[:, 2 + index * 3 + 2]
ri = np.array(sorted(list(set(list(r)))))
zi = np.array(sorted(list(set(list(z)))))
R, Z = np.meshgrid(ri, zi)
dom_grid = griddata((r, z), dom, (R, Z), method='linear')
interface_rs = []
for z_index, z_here in enumerate(zi):
if np.any(dom_grid[z_index, :] > 1):
r_index = np.argmax(dom_grid[z_index, :] > 1)
else:
r_index = -1
interface_rs.append(ri[r_index])
interface_rs = np.array(interface_rs)
plt.plot(interface_rs, zi, '-', label='{0}'.format(t), color='black')
# get_interface_line_for_timenode(ts[70])
# get_interface_line_for_timenode(ts[100])
# plt.legend()
# plt.show()
def sample_field_interp(points, Ex_interp, Ey_interp):
return np.stack((Ex_interp(points), Ey_interp(points))).T
def field_at_arbitrary_point(r0,z0,t0, precomputed=True):
right_time_index = np.argmax(ts > t0)
left_time_index = right_time_index - 1
t1 = ts[left_time_index]
t2 = ts[right_time_index]
point = np.array([r0, z0])
if not precomputed:
Ex_interp, Ey_interp = get_field_interp_for_timenode(t1)
u1, w1 = sample_field_interp(point, Ex_interp, Ey_interp)[0]
Ex_interp, Ey_interp = get_field_interp_for_timenode(t2)
u2, w2 = sample_field_interp(point, Ex_interp, Ey_interp)[0]
else:
a = interp_list[left_time_index][0](point)
b = interp_list[left_time_index][1](point)
u1, w1 = sample_field_interp(point, interp_list[left_time_index][0], interp_list[left_time_index][1])[0]
u2, w2 = sample_field_interp(point, interp_list[right_time_index][0], interp_list[right_time_index][1])[0]
u_interp = interpolate.interp1d([t1, t2], [u1, u2])([t0])[0]
w_interp = interpolate.interp1d([t1, t2], [w1, w2])([t0])[0]
return u_interp, w_interp
# u_here, w_here = field_at_arbitrary_point(10, 50, ts[70])
# get_interface_line_for_timenode(ts[70])
# plt.show()
# get_field_interp_for_timenode(ts[0])
# ws = []
# for r_here in np.array(sorted(list(set(list(r))))):
# u_here, w_here = field_at_arbitrary_point(r_here, 50.4, ts[0])
# ws.append(np.copy(w_here))
# plt.plot(np.array(sorted(list(set(list(r))))), ws, color='C1')
# plt.show()
# pos = np.array([6.74, 50.098])
positions = []
rs = np.array(sorted(list(set(list(r)))))
for r_here in rs[:250]:
positions.append([r_here, 50.005])
positions = np.array(positions)
pos_list = [positions]
# tss = np.logspace(-7, np.log10(ts[100]), num=100)
tss = ts
t_list = [tss[0]]
volume_list = [0]
for i in range(tss.shape[0]-1):
for j in range(positions.shape[0]):
u_here, w_here = field_at_arbitrary_point(positions[j, 0], positions[j, 1], tss[i])
positions[j, :] += np.array([u_here, w_here])*1e6*(tss[i+1]-tss[i])
t_list.append(tss[i+1])
pos_list.append(np.copy(positions))
print(i)
print(tss[i])
f_interp = lambda rr: np.interp(rr, positions[:, 0], positions[:, 1])
def f_volume(rr):
return f_interp(rr)*2*np.pi*rr
tip = np.argmax(positions[:, 1])
tipr = positions[tip, 0]
tipz = positions[tip, 1]
volume = np.pi*tipr**2*np.max(positions[:, 1]) - quad(f_volume, 0, tipr)[0]
print('Volume: {0}'.format(volume))
volume_list.append(volume)
if i > 130:
break
if i % 50 == 0:
fig = plt.figure(1)
u, w = get_field_for_t(ts[i+1])
xi = np.array(sorted(list(set(list(r)))))
yi = np.array(sorted(list(set(list(z)))))
R, Z = np.meshgrid(xi, yi)
Ey = griddata((r, z), w, (R, Z), method='linear')
plt.pcolor(R,Z,Ey, cmap='seismic', vmin=-1*np.max(np.abs(Ey)), vmax=np.max(np.abs(Ey)))
plt.colorbar()
get_interface_line_for_timenode(ts[i+1])
plt.plot(positions[:, 0], positions[:, 1], '-', color='green')
plt.scatter(tipr, tipz, color='yellow')
plt.xlim(0, 3)
plt.ylim(50, 50.03)
fig.savefig('comsol_results/capillary_bridge_dynamics/figures/frame{0:08d}.png'.format(i))
# plt.show()
plt.close('all')
for i in range(len(volume_list)):
if volume_list[i] > 0:
plt.loglog(1/tss[i], volume_list[i], 'o-', color='black')
plt.grid(b=True, which='major', color='#666666', linestyle='-')
plt.xlabel('Inverse time $1/ \\tau $, 1/s')
plt.ylabel('Transfer volume, fL')
plt.show()
# # pos_list = np.array(pos_list)
# for positions in pos_list:
# plt.plot(positions[:,0], positions[:,1], '-')
# get_interface_line_for_timenode(ts[0])
# get_interface_line_for_timenode(ts[100])
# plt.show()
print(1)