def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=16):
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 30)) * 0.0003
return -np.exp(-0.5 * (x * x + y * y)) * center + (x + 8) * gradient
source_functions = {
'G': source_G,
}
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
def nucleation_3D(writer, args, R=20):
raise NotImplementedError("Needs some work")
params = {
"A": 3.4,
"B": 13.5,
"k2": 1.0,
"k-2": 0.1,
"k5": 0.9,
"D_G": 1.0,
"D_X": 1.0,
"D_Y": 1.95,
"density_G": 1.0,
"density_X": 0.0002,
"density_Y": 0.043,
"base-density": 9.0,
"viscosity": 0.3,
"speed-of-sound": 1.0,
}
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
z = y
x, y, z = np.meshgrid(x, y, z, indexing='ij')
def source_G(t):
center = np.exp(-0.3 * (t - 6)**2) * 10
return -np.exp(-0.5 * (x * x + y * y + z * z)) * center
source_functions = {
'G': source_G,
}
# We need some noise to break spherical symmetry
noise_scale = 1e-4
G = bl_noise(x.shape) * noise_scale
X = bl_noise(x.shape) * noise_scale
Y = bl_noise(x.shape) * noise_scale
flow = [
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale
]
fluid_model_g = FluidModelG(
G,
X,
Y,
flow,
dx,
dt=args.dt,
params=params,
source_functions=source_functions,
)
flow_particle_origins = []
for _ in range(1000):
flow_particle_origins.append([np.random.rand() * s for s in x.shape])
flow_particles = tf.constant(flow_particle_origins, dtype='float64')
flow_streaks = 0 * x[:, :, 0]
print("Rendering 'Nucleation and Motion in G gradient in 3D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
for _ in range(20):
indices = tf.cast(flow_particles, 'int32')
for index in indices.numpy():
flow_streaks[index[0], index[1]] += 0.15 / args.oversampling
dx = tf.gather_nd(fluid_model_g.u, indices)
dy = tf.gather_nd(fluid_model_g.v, indices)
dz = tf.gather_nd(fluid_model_g.w, indices)
flow_particles = (flow_particles +
tf.stack([dx, dy, dz], axis=1) * 400) % x.shape
if n % args.oversampling == 0:
rgb = [
tf.reduce_mean(
(7 * fluid_model_g.G)**2, axis=2) + flow_streaks,
tf.reduce_mean((4 * fluid_model_g.Y)**2, axis=2),
tf.reduce_mean((2 * fluid_model_g.X)**2, axis=2),
]
frame = make_video_frame(rgb)
writer.append_data(frame)
flow_streaks *= 0
flow_particles = tf.constant(flow_particle_origins,
dtype='float64')
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=30):
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 30)) * 0.0003
#x = np.linspace(-40, 40, 500)
triangle = 10 * signal.sawtooth(40 * np.pi * 1 / 1400 * x + 0,
0.5) + 10
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
#u = x/5
#return -(
# #np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
# np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
#) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
return -(
#np.exp(-0.5*((x-D)**2+y*y)) * nucleator +
#(u*u - 1) * potential
#np.exp(-0.5*((x-15)**2+y*y)) * center + (u*u - 1) * gradient #+ (x+8) * gradient
#np.exp(-0.5*((x-15)**2 + y*y)) + np.exp(-0.5*((x+15)**2 + y*y)) * center - (u*u + 5) * gradient
np.exp(-0.5 *
((x - 12)**2 + y * y)) + np.exp(-0.5 *
((x + 12)**2 + y * y))
) * center + triangle * gradient # BJD - note minus sign maybe in wrong w.r.t. (u*u - 1) --- 22.12.2020
source_functions = {
'G': source_G,
}
"""
def source_X(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-(1/18)*(t-10)**2)
#gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center #+ (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
source_functions = {
'X': source_X,
}
"""
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=16):
c1 = 0 # BJD added this on 20.11.2020
dx = 2*R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
#return -(
# np.exp(-0.5*((x-25)**2 + y*y)) + np.exp(-0.5*((x+25)**2 + y*y))
#) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
#return (
if x < 50:
return -(
np.exp(-0.5*((x-25)**2 + y*y)) # + np.exp(-0.5*((x+25)**2 + y*y))
) * center #+ (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
else :
return -(
np.exp(-0.5*((x-25)**2 + y*y)) + np.exp(-0.5*((x+25)**2 + y*y))
) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
#return -(
# np.exp( -0.5*( (x - 50)**2 + y*y ) ) +
# np.exp( -0.5*( (x + 50)**2 + y*y ) )
#) * center + (x+8) * gradient # BJD altered for 2 seeds 29.11.2020
"""
def source_G(t):
amount = np.exp(-0.5*(t-5)**2)
return (
np.exp(-0.5*((x-D)**2+y*y)) * weights[0] +
np.exp(-0.5*((x+D)**2+y*y)) * weights[1]
) * amount
"""
source_functions = {
'G': source_G,
}
flow = [0*x, 0*x]
fluid_model_g = FluidModelG(
x*0,
x*0,
x*0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
#c1 = 0
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6*(-fluid_model_g.G + max_G) / (max_G - min_G),
5*(fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#========================BJD added 18.11.2020===================================================
if n == 100:
print("n = ", n)
break
#if n == 4:
# X_array = [
# 0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
# ] # BJD put this in 18.11.2020
# print("Array of X: ", X_array) # ***** BJD inserted this line 18.11.2020 *****
c1 = c1 + 1
print("H E L L O")
y1 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array5/X.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
y2 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array5/Y.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
y3 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array5/G.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
row1 = y1[214] # choose row 214 of 2D array = (426,240)
row2 = y2[214] # choose row 214 of 2D array = (426,240)
row3 = y3[214] # choose row 214 of 2D array = (426,240)
#t = linspace(0, 2*math.pi, 400)
#a = sin(t)
#b = cos(t)
#c = a + b
print(row1)
fig, pp = plt.subplots( nrows=1, ncols=1 ) # create figure & 1 axis
#fig, ax = plt.subplots( nrows=1, ncols=1 ) # create figure & 1 axis
#ax.plot([0,1,2], [10,20,3])
#pp.plot(t, a, 'r') # plotting t, a separately - BJD new plotting code 21.11.2020
#pp.plot(t, b, 'b') # plotting t, b separately - BJD new plotting code 21.11.2020
#pp.plot(t, c, 'g') # plotting t, c separately - BJD new plotting code 21.11.2020
# https://stackoverflow.com/questions/22276066/how-to-plot-multiple-functions-on-the-same-figure-in-matplotlib
pp.plot(row1, 'r') # plotting t, a separately - BJD new plotting code 21.11.2020
pp.plot(row2, 'b') # plotting t, b separately - BJD new plotting code 21.11.2020
pp.plot(row3, 'g') # plotting t, c separately - BJD new plotting code 21.11.2020
#pp.plot(row1) # BJD previous working plot code 21.11.2020
#pp.show()
#plt.savefig('test2.png')
#plt.savefig('test2.pdf')
plt.title('X, Y, G potential vs 1D space - time = ' + str(c1))
plt.xlabel("1D spacial units")
plt.ylabel("X, Y, G pot. - concentration per unit vol")
#fig.savefig('test2.png') # save the figure to file
plt.legend(["X", "Y", "G"]) # BJD legend added 21.11.2020
fig.savefig('/home/brendan/software/tf2-model-g/plots/1D_video7/1D_video_XYG_' + str(c1) + '.png')
plt.close(fig) # close the figure window
#plt.savefig('test2_' + str(c1) + '.png')
#===========================================================================
#for i in xrange(10):
#with io.open("file_" + str(i) + ".dat", 'w', encoding='utf-8') as f:
#with io.open("file_" + str(c1) + ".txt", 'w', encoding='utf-8') as f:
#f.write(str(func(c1))
#for number in range(1, 11):
#filename = 'a%d.txt' % number
#data = read_data(filename)
#for c1 in xrange(10):
"""
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=30):
dx = 2*R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
"""
for item in array:
if item >= 3:
print("yes")
else:
print("no")
"""
#"""
#return (
#for item in x:
# if item < 0:
#if np.all(a == 0):
#if np.all(x < 0): # might work!
# if x.all() < 0:
#if np.where(x < 0):
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y))
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x+8)**2 + y*y))
) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
#else:
# return -(
# np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y))
# ) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
#"""
source_functions = {
'G': source_G,
}
flow = [0*x, 0*x]
fluid_model_g = FluidModelG(
x*0,
x*0,
x*0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6*(-fluid_model_g.G + max_G) / (max_G - min_G),
5*(fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=30):
c1 = 0 # BJD added this on 20.11.2020
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 30)) * 0.0003
return -(np.exp(-0.5 * ((x - 25)**2 + y * y)) + np.exp(-0.5 * (
(x + 25)**2 + y * y))) * center + (
x + 8
) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
"""
def source_G(t):
amount = np.exp(-0.5*(t-5)**2)
return (
np.exp(-0.5*((x-D)**2+y*y)) * weights[0] +
np.exp(-0.5*((x+D)**2+y*y)) * weights[1]
) * amount
"""
source_functions = {
'G': source_G,
}
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
#c1 = 0
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#========================BJD added 18.11.2020===================================================
if n == 150:
print("n = ", n)
break
#if n == 4:
# X_array = [
# 0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
# ] # BJD put this in 18.11.2020
# print("Array of X: ", X_array) # ***** BJD inserted this line 18.11.2020 *****
c1 = c1 + 1
print("H E L L O")
x1 = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/array9/X.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
x2 = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/array9/Y.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
x3 = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/array9/G.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#ndArray[ : , column_index] # @ https://thispointer.com/python-numpy-select-rows-columns-by-index-from-a-2d-ndarray-multi-dimension/
column1 = x1[:, 120] # choose row 214 of 2D array = (426,240)
column2 = x2[:, 120] # choose row 214 of 2D array = (426,240)
column3 = x3[:, 120] # choose row 214 of 2D array = (426,240)
#t = linspace(0, 2*math.pi, 400)
#a = sin(t)
#b = cos(t)
#c = a + b
print(column1)
fig, pp = plt.subplots(nrows=1, ncols=1) # create figure & 1 axis
#axes = pp.add_axes([0.1,0.1,0.8,0.8])
#-------------------
#a= plt.figure()
#axes= a.add_axes([0.1,0.1,0.8,0.8])
# adding axes
#x= np.arange(0,11)
#axes.plot(x,x**3, marker='*')
#axes.set_xlim([0,250])
#axes.set_ylim([-3,2])
#plt.show()
#------------------
#fig, ax = plt.subplots( nrows=1, ncols=1 ) # create figure & 1 axis
#ax.plot([0,1,2], [10,20,3])
#pp.plot(t, a, 'r') # plotting t, a separately - BJD new plotting code 21.11.2020
#pp.plot(t, b, 'b') # plotting t, b separately - BJD new plotting code 21.11.2020
#pp.plot(t, c, 'g') # plotting t, c separately - BJD new plotting code 21.11.2020
# https://stackoverflow.com/questions/22276066/how-to-plot-multiple-functions-on-the-same-figure-in-matplotlib
#row1 = range(-3, 2)
#row2 = range(-3, 2)
#row3 = range(-3, 2)
#y = range(-3, 2)
pp.plot(
column1, 'r'
) # plotting t, a separately - BJD new plotting code 21.11.2020
pp.plot(
column2, 'b'
) # plotting t, b separately - BJD new plotting code 21.11.2020
pp.plot(
column3, 'g'
) # plotting t, c separately - BJD new plotting code 21.11.2020
#axes.set_xlim([0,250])
#axes.set_ylim([-3,2])
#pp.set_xlim([0,250])
pp.set_ylim(
[-4, 4]) # ******* BJD this one works! 1.12.2020 ***********
#pp.plot(row1) # BJD previous working plot code 21.11.2020
#pp.show()
#plt.savefig('test2.png')
#plt.savefig('test2.pdf')
plt.title('X, Y, G potential vs 1D space - time = ' + str(c1))
plt.xlabel("1D spacial units")
plt.ylabel("X, Y, G pot. - concentration per unit vol")
#fig.savefig('test2.png') # save the figure to file
plt.legend(["X", "Y", "G"]) # BJD legend added 21.11.2020
fig.savefig(
'/home/brendan/software/tf2-model-g/plots/1D_video16/1D_video_XYG_'
+ str(c1) + '.png')
plt.close(fig) # close the figure window
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=50): # was R=30 BJD 4.1.2021
dx = 2*R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
#def trapezoid_signal(x, width=2., slope=1., amp=1., offs=0):
def trapezoid_signal(x, width=2., slope=1., amp=10., offs=1):
#a = 10 * slope*width*signal.sawtooth(2 * np.pi * 1/10* x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width - 1, width=0.5)/4.
a[a>amp/2.] = amp/2.
a[a<-amp/2.] = -amp/2.
return a + amp/2. + offs
#x = np.linspace(100, -100, 1000)
#plt.plot(t,trapezoid_signal(x, width=2, slope=2, amp=1.), label="width=2, slope=2, amp=1")
#plt.plot(x,trapezoid_signal(x, width=4, slope=1, amp=0.6), label="width=4, slope=1, amp=0.6")
#plt.plot(x,trapezoid_signal(x, width=10, slope=5, amp=20), label="width=10, slope=3, amp=20")
#plt.legend( loc=(0.25,1.015))
#plt.show()
def source_G(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
#x = np.linspace(-40, 40, 500)
#triangle = 10 * signal.sawtooth(40 * np.pi * 1/1400 * x + 0, 0.5) + 10
#triangle = 10 * signal.sawtooth(2 * np.pi * 1/70 * x + 0.001, 0.5) + 10 # BJD: last used here 28.12.2020
#trapezoid = trapezoid_signal(x, width=30, slope=10, amp=30)
trapezoid = trapezoid_signal(x, width=40, slope=10, amp=50)
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
#u = x/5
#return -(
# #np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
# np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
#) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
return -(
#np.exp(-0.5*((x-D)**2+y*y)) * nucleator +
#(u*u - 1) * potential
#np.exp(-0.5*((x-15)**2+y*y)) * center + (u*u - 1) * gradient #+ (x+8) * gradient
#np.exp(-0.5*((x-15)**2 + y*y)) + np.exp(-0.5*((x+15)**2 + y*y)) * center - (u*u + 5) * gradient
#np.exp(-0.5*((x-12)**2 + y*y)) + np.exp(-0.5*((x+12)**2 + y*y))
#) * center + triangle * gradient # BJD - note minus sign maybe in wrong w.r.t. (u*u - 1) --- 22.12.2020
np.exp(-0.5*((x-25)**2 + (y-15)**2)) + np.exp(-0.5*((x+50)**2 + (y+15)**2))
) * center + trapezoid * gradient # BJD - note minus sign maybe in wrong w.r.t. (u*u - 1) --- 22.12.2020
source_functions = {
'G': source_G,
}
"""
def source_X(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-(1/18)*(t-10)**2)
#gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center #+ (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
source_functions = {
'X': source_X,
}
"""
flow = [0*x, 0*x]
fluid_model_g = FluidModelG(
x*0,
x*0,
x*0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6*(-fluid_model_g.G + max_G) / (max_G - min_G),
5*(fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
def nucleation_and_motion_in_G_gradient_fluid_2D(writer,
args,
R=60
): # was R=30 BJD 4.1.2021
#c1 = 0 # BJD added this on 20.11.2020
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
#def trapezoid_signal(x, width=2., slope=1., amp=1., offs=0):
def trapezoid_signal(x, width=2., slope=1., amp=10., offs=1):
#a = 10 * slope*width*signal.sawtooth(2 * np.pi * 1/10* x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
a = slope * width * signal.sawtooth(
2 * np.pi * 1 / 10 * x / width - 0.8, width=0.5) / 4.
a[a > amp / 2.] = amp / 2.
a[a < -amp / 2.] = -amp / 2.
return a + amp / 2. + offs
#...........................................
"""
#def piecewise_function(x, list(map(f, x)), 'b-')
def f(x):
#b = x
#list(map(lambda x: -2.*x if x<0. else x, -x))
x[x < 0.] = -2.*x
x[x > 0.] = -x
#if x < 0:
#return 0
return x
#elif :
#else :
#x[x > 0.] = -x
#return t * t - 100
#return -x
#return -x
#x = np.arange(-100, 100, 1)
#plt.plot(t, map(f, t), 'b-')
#plt.plot(x, list(map(f, x)), 'b-') # for python3
#plt.show()
"""
def f(x):
#return -3*x/10 #+ 20
neg = x < 0
neg2 = np.logical_and(
x >= 0, x < 4.7
) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
neg3 = x >= 4.7
return neg * (-x / 5 + 1) + neg2 * (
50 * signal.square(2 * np.pi / 10 * x)) + neg3 * 1
def f2(x):
#return -3*x/10 #+ 20
neg4 = x < 0
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
neg5 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg4 * (-x / 5 + 1) + neg5 * 1
def f3(x):
#return -3*x/10 #+ 20
#neg = x < 0
#neg6 = np.logical_and(y >= -10, y <= 10)
#neg7 = np.logical_and(y < -10, y > 10)
neg6 = np.logical_and(y >= -10, y <= 10)
neg7 = np.logical_or(y < -10, y > 10)
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
#neg3 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg6 * f2(x) + neg7 * f(x)
#...........................................
#x = np.linspace(100, -100, 1000)
#plt.plot(t,trapezoid_signal(x, width=2, slope=2, amp=1.), label="width=2, slope=2, amp=1")
#plt.plot(x,trapezoid_signal(x, width=4, slope=1, amp=0.6), label="width=4, slope=1, amp=0.6")
#plt.plot(x,trapezoid_signal(x, width=10, slope=5, amp=20), label="width=10, slope=3, amp=20")
#plt.legend( loc=(0.25,1.015))
#plt.show()
"""
def composite_triangle(x):
#x = np.arange(1, 11)
y = np.array([100, 10, 300, 20, 500, 60, 700, 80, 900, 100])
return y
"""
def source_G(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 30)) * 0.0003
#potential = 0.015 * (np.tanh(t-25) + 1)
#x = np.linspace(-40, 40, 500)
#triangle = 10 * signal.sawtooth(40 * np.pi * 1/1400 * x + 0, 0.5) + 10
#triangle = 10 * signal.sawtooth(2 * np.pi * 1/70 * x + 0.001, 0.5) + 10 # BJD: last used here 28.12.2020
#trapezoid = trapezoid_signal(x, width=40, slope=5, amp=50)
#piecewise = f(x)
piecewise_choice = f3(x)
#piecewise_1 = list(map(f, x))
#trapezoid = trapezoid_signal(x, width=40, slope=10, amp=50)
#composite = composite_triangle(x)
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
#u = x/25
#u = x/10
return -(
# #np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5 *
((x + 50)**2 + y * y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center + piecewise_choice * gradient # piecewise function test 5.2.2021
#return -(
#np.exp( -0.5*( (x+25)**2 + y*y ) )
# x * y * ( x**2 - y**2 ) / ( x**2 + y**2 )
#) * center #+ (u*u + 1) * gradient #+ (x+8) * potential
#np.exp(-0.5*((x-D)**2+y*y)) * nucleator +
#(u*u - 1) * potential
#np.exp(-0.5*((x-15)**2+y*y)) * center + (u*u - 1) * gradient #+ (x+8) * gradient
#np.exp(-0.5*((x-15)**2 + y*y)) + np.exp(-0.5*((x+15)**2 + y*y)) * center - (u*u + 5) * gradient
#np.exp(-0.5*((x-12)**2 + y*y)) + np.exp(-0.5*((x+12)**2 + y*y))
#) * center + triangle * gradient # BJD - note minus sign maybe in wrong w.r.t. (u*u - 1) --- 22.12.2020
#np.exp(-0.5*((x-15)**2 + (y-25)**2)) + np.exp(-0.5*((x-15)**2 + (y+25)**2)) +
#np.exp(-0.5*((x+55)**2 + (y)**2))
#) * center + trapezoid * gradient # 3 particles for de Broglie diffraction --- 5.2.2021
"""
u = x / R
return (
np.exp(-0.5*((x-D)**2+y*y)) * nucleator +
(u*u - 1) * potential
)
"""
"""
def trapezoid_signal(x, width=2., slope=1., amp=10., offs=1):
a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width - 1, width=0.5)/4.
a[a>amp/2.] = amp/2.
a[a<-amp/2.] = -amp/2.
return a + amp/2. + offs
def source_G(t):
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
trapezoid = trapezoid_signal(x, width=30, slope=10, amp=30)
return -(
np.exp(-0.5*((x-12)**2 + (y-5)**2)) + np.exp(-0.5*((x+32)**2 + (y+5)**2))
) * center + trapezoid * gradient # 2 particles colliding one stationary
"""
source_functions = {
'G': source_G,
}
"""
def source_X(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-(1/18)*(t-10)**2)
#gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center #+ (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
source_functions = {
'X': source_X,
}
"""
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
#x*0 # BJD 28.1.2021 --- added
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#-------------------------BJD 28.1.2021----rough code at present-----------------------------------------
"""
if n == 200:
print("n = ", n)
break
#c1 = c1 + 1
print("H E L L O")
#y1 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#y2 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
c1 = c1 + 1
# Set up grid and test data
#nx, ny = 256, 1024
nx, ny = 240, 426
#(426,240)
x1 = range(nx)
y1 = range(ny)
#data = numpy.random.random((nx, ny))
U = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array25/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
V = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array25/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
# BJD 28.1.2021: u and v are saved as arrays in fluid_model_g.py as fllows:
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/u.txt", self.u)
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/v.txt", self.v)
#data = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array12/Y.txt")
#hf = plt.figure(figsize=(10,10))
#ha = hf.add_subplot(111, projection='3d')
#ha = hf.add_subplot(111, projection='2d')
X1, Y1 = np.meshgrid(x1, y1) # `plot_surface` expects `x` and `y` data to be 2D
#ha.plot_surface(X, Y, data)
#ha.plot_surface(X, Y, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.plot_surface(X.T, Y.T, data)
#surf = ha.plot_surface(X1, Y1, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.set_zlim(-1, 3)
#hf.colorbar(surf, shrink=0.5, aspect=10)
#hf = plt.figure(figsize=(10,10))
"""
"""
fig, hf = plt.subplots(figsize=(10,10))
#ax3.set_title("pivot='tip'; scales with x view")
hf.set_title("pivot='tip'; scales with x view" + str(c1))
M = np.hypot(U, V)
Q = hf.quiver(X1, Y1, U, V, M, units='x', pivot='tip', width=0.022,
scale=1 / 0.15)
qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$1 \frac{m}{s}$', labelpos='E',
coordinates='figure')
hf.scatter(X1, Y1, color='0.5', s=1)
"""
"""
fig, hf = plt.subplots(figsize=(10,10))
hf.set_title("Model G fluid velocity vector field - every 5th arrow, time = " + str(c1))
#Q = hf.quiver(X1[::10, ::10], Y1[::10, ::10], U[::10, ::10], V[::10, ::10],
#pivot='mid', units='inches')
#M = np.hypot(U, V)
Q = hf.quiver(X1[::5, ::5], Y1[::5, ::5], U[::5, ::5], V[::5, ::5], units='width',
pivot='mid', scale=0.1, headwidth=7)#pivot='mid', units='inches')#, scale=1)#, scale=5)
#qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$\frac{distance}{time}$', labelpos='E',
#coordinates='figure')
qk = hf.quiverkey(Q, 0.9, 0.9, 0.1, r'$\frac{distance}{time}$', labelpos='E',
coordinates='figure')#, color='b')
hf.scatter(X1[::5, ::5], Y1[::5, ::5], color='r', s=5)
#plt.show()
#plt.title('Y potential in 2D space - time = ' + str(c1))
#plt.xlabel("x spacial units")
#plt.ylabel("y spacial units")
#plt.zlabel("X, Y, G pot. - concentration per unit vol")
#fig.savefig('test2.png') # save the figure to file
#plt.legend(["X", "Y", "G"]) # BJD legend added 21.11.2020
#plt.show()
plt.savefig('/home/brendan/software/tf2-model-g/plots/2D_video31/2D_video_velocity_' + str(c1) + '.png')
#plt.close(hf) # close the figure window
#y3 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array10/G.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#column1 = y1[120] # choose column 120 of 2D array = (426,240)
#column2 = y2[120] # choose column 120 of 2D array = (426,240)
#column3 = y3[120] # choose column 120 of 2D array = (426,240)
#row1 = y1[214] # choose row 214 of 2D array = (426,240)
#row2 = y2[214] # choose row 214 of 2D array = (426,240)
#row3 = y3[214] # choose row 214 of 2D array = (426,240)
#x, y = np.meshgrid(x, y, indexing='ij')
#X, Y = np.meshgrid(np.arange(0, 2 * np.pi, .2), np.arange(0, 2 * np.pi, .2))
#U = np.gradient(fluid_model_g.G,1)
#V = np.gradient(fluid_model_g.G,2)
#U = np.cos(X)
#V = np.sin(Y)
#np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array13/X.txt", np.gradient(fluid_model_g.G,1))
# sphinx_gallery_thumbnail_number = 3
"""
"""
def nucleation_3D(animated=False, N=128, R=20):
params = {
"A": 3.4,
"B": 13.5,
"k2": 1.0,
"k-2": 0.1,
"k5": 0.9,
"D_G": 1.0,
"D_X": 1.0,
"D_Y": 1.95,
"density_G": 1.0,
"density_X": 0.0002,
"density_Y": 0.043,
"base-density": 20.0,
"viscosity": 0.4,
"speed-of-sound": 1.0,
}
x = np.linspace(-R, R, N)
dx = x[1] - x[0]
x, y, z = np.meshgrid(x, x, x, indexing='ij')
def source_G(t):
center = np.exp(-0.5 * (t - 5)**2) * 10
return -np.exp(-0.5 * (x * x + y * y + z * z)) * center
source_functions = {
'G': source_G,
}
# We need some noise to break spherical symmetry
noise_scale = 1e-4
G = bl_noise(x.shape) * noise_scale
X = bl_noise(x.shape) * noise_scale
Y = bl_noise(x.shape) * noise_scale
flow = [
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale
]
dt = 0.2 * dx
fluid_model_g = FluidModelG(
G,
X,
Y,
flow,
dx,
dt=dt,
params=params,
source_functions=source_functions,
)
if animated:
def get_data():
G, X, Y, (u, v, w) = fluid_model_g.numpy()
x_scale = 0.1
y_scale = 0.1
return (
G[N // 2, N // 2],
X[N // 2, N // 2] * x_scale,
Y[N // 2, N // 2] * y_scale,
u[N // 2, N // 2],
v[N // 2, N // 2],
w[N // 2, N // 2],
)
G, X, Y, u, v, w = get_data()
plots = []
plots.extend(pylab.plot(z[0, 0], G))
plots.extend(pylab.plot(z[0, 0], X))
plots.extend(pylab.plot(z[0, 0], Y))
plots.extend(pylab.plot(z[0, 0], u))
plots.extend(pylab.plot(z[0, 0], v))
pylab.ylim(-0.1, 0.1)
def update(frame):
fluid_model_g.step()
G, X, Y, u, v, w = get_data()
print(fluid_model_g.t, abs(G).max(), abs(u).max())
plots[0].set_ydata(G)
plots[1].set_ydata(X)
plots[2].set_ydata(Y)
plots[3].set_ydata(u)
plots[4].set_ydata(v)
plots[4].set_ydata(w)
return plots
FuncAnimation(pylab.gcf(),
update,
frames=range(100),
init_func=lambda: plots,
blit=True,
repeat=True,
interval=20)
pylab.show()
else:
from datetime import datetime
from pathlib import Path
start = datetime.now()
num_steps = int(1.0 / dt)
print("Starting simulation {} steps at a time".format(num_steps))
path = Path("/tmp/model_g")
path.mkdir(exist_ok=True)
while True:
for _ in range(num_steps):
fluid_model_g.step()
print("Saving a snapshot into {}".format(path))
G, X, Y, (u, v, w) = fluid_model_g.numpy()
np.save(path / 'G.npy', G)
np.save(path / 'X.npy', X)
np.save(path / 'Y.npy', Y)
np.save(path / 'u.npy', u)
np.save(path / 'v.npy', v)
np.save(path / 'w.npy', w)
print("Saved everything")
wall_clock_time = (datetime.now() - start).total_seconds()
print("t={}, wall clock time={} s, efficiency={}".format(
fluid_model_g.t, wall_clock_time,
fluid_model_g.t / wall_clock_time))
print("max|G|={}, max|u|={}".format(abs(G).max(), abs(u).max()))
def nucleation_and_motion_in_G_gradient_2D(N=128, R=16):
params = {
"A": 3.42,
"B": 13.5,
"k2": 1.0,
"k-2": 0.1,
"k5": 0.9,
"D_G": 1.0,
"D_X": 1.0,
"D_Y": 1.95,
"density_G": 2.0,
"density_X": 1.0,
"density_Y": 1.5,
"base-density": 35.0,
"viscosity": 0.4,
"speed-of-sound": 1.0,
}
x = np.linspace(-R, R, N)
dx = x[1] - x[0]
x, y = np.meshgrid(x, x, indexing='ij')
def source_G(t):
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 40)) * 0.0005
return -np.exp(-0.5 * (x * x + y * y)) * center + (x + 8) * gradient
source_functions = {
'G': source_G,
}
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
flow,
dx,
dt=0.25 * dx,
params=params,
source_functions=source_functions,
)
times = []
locs = []
def get_data():
G, X, Y, (u, v) = fluid_model_g.numpy()
loc = l2_location(X, x, y)
times.append(fluid_model_g.t)
locs.append(loc[0])
print("t={}\tL2 location: {}".format(fluid_model_g.t, tuple(loc)))
x_scale = 0.1
y_scale = 0.1
return (
G[:, N // 2],
X[:, N // 2] * x_scale,
Y[:, N // 2] * y_scale,
u[:, N // 2],
v[:, N // 2],
)
G, X, Y, u, v = get_data()
plots = []
plots.extend(pylab.plot(x[:, 0], G))
plots.extend(pylab.plot(x[:, 0], X))
plots.extend(pylab.plot(x[:, 0], Y))
plots.extend(pylab.plot(x[:, 0], u))
plots.extend(pylab.plot(x[:, 0], v))
pylab.ylim(-0.1, 0.1)
def update(frame):
for _ in range(20):
fluid_model_g.step()
G, X, Y, u, v = get_data()
plots[0].set_ydata(G)
plots[1].set_ydata(X)
plots[2].set_ydata(Y)
plots[3].set_ydata(u)
plots[4].set_ydata(v)
return plots
FuncAnimation(pylab.gcf(),
update,
frames=range(100),
init_func=lambda: plots,
blit=True,
repeat=True,
interval=20)
pylab.show()
G, X, Y, (u, v) = fluid_model_g.numpy()
pylab.imshow(X)
pylab.show()
pylab.plot(times, locs)
pylab.show()
def nucleation_3D(writer, args, R=12):
# raise NotImplementedError("Needs some work")
params = {
"A": 3.4,
"B": 13.5,
"k2": 1.0,
"k-2": 0.1,
"k5": 0.9,
"D_G": 1.0,
"D_X": 1.0,
"D_Y": 1.95,
"density_G": 1.0,
"density_X": 0.0002,
"density_Y": 0.043,
"base-density": 9.0,
"viscosity": 0.3,
"speed-of-sound": 1.0,
}
c1 = 0 # BJD added this on 22.4.2021
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
z = y
x, y, z = np.meshgrid(x, y, z, indexing='ij')
def source_G(t):
center = np.exp(-0.3 * (t - 6)**2) * 10
return -np.exp(-0.5 * (x * x + y * y + z * z)) * center
source_functions = {
'G': source_G,
}
# We need some noise to break spherical symmetry
noise_scale = 1e-4
G = bl_noise(x.shape) * noise_scale
X = bl_noise(x.shape) * noise_scale
Y = bl_noise(x.shape) * noise_scale
flow = [
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale,
bl_noise(x.shape) * noise_scale
]
fluid_model_g = FluidModelG(
G,
X,
Y,
flow,
dx,
dt=args.dt,
params=params,
source_functions=source_functions,
)
flow_particle_origins = []
for _ in range(1000):
flow_particle_origins.append([np.random.rand() * s for s in x.shape])
flow_particles = tf.constant(flow_particle_origins, dtype='float64')
flow_streaks = 0 * x[:, :, 0]
print("Rendering 'Nucleation and Motion in G gradient in 3D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
for _ in range(20):
indices = tf.cast(flow_particles, 'int32')
for index in indices.numpy():
flow_streaks[index[0], index[1]] += 0.15 / args.oversampling
dx = tf.gather_nd(fluid_model_g.u, indices)
dy = tf.gather_nd(fluid_model_g.v, indices)
dz = tf.gather_nd(fluid_model_g.w, indices)
flow_particles = (flow_particles +
tf.stack([dx, dy, dz], axis=1) * 400) % x.shape
if n % args.oversampling == 0:
rgb = [
tf.reduce_mean(
(7 * fluid_model_g.G)**2, axis=2) + flow_streaks,
tf.reduce_mean((4 * fluid_model_g.Y)**2, axis=2),
tf.reduce_mean((2 * fluid_model_g.X)**2, axis=2),
]
frame = make_video_frame(rgb)
writer.append_data(frame)
flow_streaks *= 0
flow_particles = tf.constant(flow_particle_origins,
dtype='float64')
#=====================BJD 20.4.2021==========================================
#-------------------------BJD 22.4.2021----rough code at present-----------------------------------------
if n == 200:
print("n = ", n)
break
#c1 = c1 + 1
print("H E L L O")
#y1 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#y2 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
c1 = c1 + 1
# Set up grid and test data
#nx, ny = 256, 1024
nx, ny, nz = 240, 426, 426
#nx, ny = 426, 240 # changed round to check!
#(426,240)
x1 = range(nx)
y1 = range(ny)
z1 = range(nz)
#data = numpy.random.random((nx, ny))
U = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/quiver3D_array31/u.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
V = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/quiver3D_array31/v.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
W = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/quiver3D_array31/w.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
# BJD 28.1.2021: u and v are saved as arrays in fluid_model_g.py as fllows:
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/u.txt", self.u)
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/v.txt", self.v)
#data = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array12/Y.txt")
#hf = plt.figure(figsize=(10,10))
#ha = hf.add_subplot(111, projection='3d')
#ha = hf.add_subplot(111, projection='2d')
X1, Y1, Z1 = np.meshgrid(
x1, y1, z1) # `plot_surface` expects `x` and `y` data to be 2D
#x, y, z = np.meshgrid(np.arange(-0.8, 1, 0.2),
# np.arange(-0.8, 1, 0.2),
# np.arange(-0.8, 1, 0.8))
#ha.plot_surface(X, Y, data)
#ha.plot_surface(X, Y, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.plot_surface(X.T, Y.T, data)
#surf = ha.plot_surface(X1, Y1, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.set_zlim(-1, 3)
#hf.colorbar(surf, shrink=0.5, aspect=10)
#hf = plt.figure(figsize=(10,10))
"""
fig, hf = plt.subplots(figsize=(10,10))
#ax3.set_title("pivot='tip'; scales with x view")
hf.set_title("pivot='tip'; scales with x view" + str(c1))
M = np.hypot(U, V)
Q = hf.quiver(X1, Y1, U, V, M, units='x', pivot='tip', width=0.022,
scale=1 / 0.15)
qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$1 \frac{m}{s}$', labelpos='E',
coordinates='figure')
hf.scatter(X1, Y1, color='0.5', s=1)
# Below, from Color_Quiver_Plot.py 17.4.2021 - BJD
color = np.sqrt(((dx-n)/2)*2 + ((dy-n)/2)*2)
ax2.quiver(X, Y, dx, dy, color)
ax2.xaxis.set_ticks([])
ax2.yaxis.set_ticks([])
ax2.set_aspect('equal')
ax2.set_title('gradient')
plt.tight_layout()
plt.show()
#also arrow head 17.4.2021 BJD:
Q = hf.quiver(X1[::10, ::10], Y1[::10, ::10], U[::10, ::10], V[::10, ::10], units='width',
pivot='mid', scale=0.005)#pivot='mid', units='inches')#, scale=1)#, scale=5)
"""
#fig, hf = plt.subplots(figsize=(10,10))
fig = plt.figure(figsize=(10, 10))
ax = fig.gca(projection='3d')
ax.set_title(
"pivot='mid'; every 10th arrow; units='velocity vector' time="
+ str(c1))
#Q = ax.quiver(X1[::10, ::10], Y1[::10, ::10], Z1[::10, ::10], U[::10, ::10],
# V[::10, ::10], W[::10, ::10], pivot='mid', units='inches')
Q = ax.quiver(X1[::10, ::10, ::10],
Y1[::10, ::10, ::10],
Z1[::10, ::10, ::10],
U[::10, ::10, ::10],
V[::10, ::10, ::10],
W[::10, ::10, ::10],
pivot='mid',
units='inches')
#hf.set_title("pivot='mid'; every 10th arrow; units='velocity vector' time=" + str(c1))
#Q = hf.quiver(X1[::10, ::10], Y1[::10, ::10], U[::10, ::10], V[::10, ::10], pivot='mid',
#units='inches')
#q = ax.quiver(x, y, z, u, v, w, length=0.1, cmap='Reds', lw=2)
#q.set_array(np.random.rand(np.prod(x.shape)))
Q.set_array(np.random.rand(np.prod(
x.shape))) # may need this? BJD 22.4.2021
#plt.show()
#qk = ax.quiverkey(Q, 0.9, 0.9, 5, r'$1 \frac{m}{s}$', labelpos='E',
#coordinates='figure')
#Q = hf.quiver(X1[::10, ::10], Y1[::10, ::10], U[::10, ::10], V[::10, ::10], units='width',
#pivot='mid', scale=0.1, headwidth=7)
#ax1.quiver(X, Y, u, v, color, alpha = 0.8) # from Color_Quiver_Plot.py
#qk = hf.quiverkey(Q, 0.9, 0.9, 5, r'$1 \frac{m}{s}$', labelpos='E',
#coordinates='figure')
#hf.scatter(X1[::10, ::10], Y1[::10, ::10], color='r', s=5)
#hf.scatter(X1[::10, ::10], Y1[::10, ::10], color='c', alpha = 0.8)
#hf.scatter(X1[::10, ::10], Y1[::10, ::10], color='c', s=0)
#ax.scatter(X1[::10, ::10], Y1[::10, ::10], Z1[::10, ::10], color='c', s=0)
ax.scatter(X1[::10, ::10, ::10],
Y1[::10, ::10, ::10],
Z1[::10, ::10, ::10],
color='c',
s=0)
plt.tight_layout()
plt.savefig(
'/home/brendan/software/tf2-model-g/plots/3D_video37/3D_video_velocity_'
+ str(c1) + '.png')
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=16):
c1 = 0 # BJD added this on 20.11.2020
dx = 2*R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
"""
def source_G(t):
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient # BJD original 29.11.2020
#return -(
# np.exp( -0.5*( (x - 50)**2 + y*y ) ) +
# np.exp( -0.5*( (x + 50)**2 + y*y ) )
#) * center + (x+8) * gradient # BJD altered for 2 seeds 29.11.2020
def source_G(t):
amount = np.exp(-0.5*(t-5)**2)
return (
np.exp(-0.5*((x-D)**2+y*y)) * weights[0] +
np.exp(-0.5*((x+D)**2+y*y)) * weights[1]
) * amount
source_functions = {
'G': source_G,
}
"""
def source_X(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-(1/18)*(t-10)**2)
gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center + (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
source_functions = {
'X': source_X,
}
flow = [0*x, 0*x]
fluid_model_g = FluidModelG(
x*0,
x*0,
x*0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
#c1 = 0
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6*(-fluid_model_g.G + max_G) / (max_G - min_G),
5*(fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#========================BJD added 18.11.2020===================================================
if n == 200:
print("n = ", n)
break
c1 = c1 + 1
# Set up grid and test data
#nx, ny = 256, 1024
nx, ny = 240, 426
#(426,240)
x1 = range(nx)
y1 = range(ny)
#data = numpy.random.random((nx, ny))
data = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array12/Y.txt")
hf = plt.figure(figsize=(10,10))
ha = hf.add_subplot(111, projection='3d')
X1, Y1 = np.meshgrid(x1, y1) # `plot_surface` expects `x` and `y` data to be 2D
#ha.plot_surface(X, Y, data)
#ha.plot_surface(X, Y, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.plot_surface(X.T, Y.T, data)
surf = ha.plot_surface(X1, Y1, data, rstride=1, cstride=1, cmap=cm.coolwarm,
linewidth=0, antialiased=False)
ha.set_zlim(-1, 3)
hf.colorbar(surf, shrink=0.5, aspect=10)
plt.title('Y potential in 2D space - time = ' + str(c1))
plt.xlabel("x spacial units")
plt.ylabel("y spacial units")
#plt.zlabel("X, Y, G pot. - concentration per unit vol")
#fig.savefig('test2.png') # save the figure to file
#plt.legend(["X", "Y", "G"]) # BJD legend added 21.11.2020
#plt.show()
hf.savefig('/home/brendan/software/tf2-model-g/plots/3D_video19/3D_video_XYG_' + str(c1) + '.png')
plt.close(hf) # close the figure window
"""
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=8): # was R=60, 30 and 15 -BJD 14.1.2021
c1 = 0 # BJD added this on 20.11.2020
dx = 2*R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
#def trapezoid_signal(x, width=2., slope=1., amp=1., offs=0):
def trapezoid_signal(x, width=2., slope=1., amp=10., offs=1):
#a = 10 * slope*width*signal.sawtooth(2 * np.pi * 1/10* x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width - 1, width=0.5)/4.
a[a>amp/2.] = amp/2.
a[a<-amp/2.] = -amp/2.
return a + amp/2. + offs
def f(x):
#return -3*x/10 #+ 20
neg = x < 0
neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
neg3 = x >= 4.7
return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
def f2(x):
#return -3*x/10 #+ 20
neg4 = x < 0
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
neg5 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg4 * (-x/5 + 1) + neg5 * 1
def f3(x):
#return -3*x/10 #+ 20
#neg = x < 0
#neg6 = np.logical_and(y >= -10, y <= 10)
#neg7 = np.logical_and(y < -10, y > 10)
neg6 = np.logical_and(y >= -5, y <= 5)
neg7 = np.logical_or(y < -5, y > 5)
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
#neg3 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg6 * f2(x) + neg7 * f(x)
#...........................................
def source_G(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-0.5*(t-5)**2) * 10
gradient = (1+np.tanh(t-30)) * 0.0003
#potential = 0.015 * (np.tanh(t-25) + 1)
#x = np.linspace(-40, 40, 500)
#triangle = 10 * signal.sawtooth(40 * np.pi * 1/1400 * x + 0, 0.5) + 10
#triangle = 10 * signal.sawtooth(2 * np.pi * 1/70 * x + 0.001, 0.5) + 10 # BJD: last used here 28.12.2020
#trapezoid = trapezoid_signal(x, width=40, slope=5, amp=50)
#piecewise = f(x)
piecewise_choice = f3(x)
#piecewise_1 = list(map(f, x))
#trapezoid = trapezoid_signal(x, width=40, slope=10, amp=50)
#composite = composite_triangle(x)
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
#u = x/25
#u = x/10
return -(
np.exp(-0.5*( (x)**2 + y*y) ) #+ np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
#np.exp(-0.5*((x+50)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center # + piecewise_choice * gradient # piecewise function --- G gap in G wall 13.3.2021
#......................................................
source_functions = {
'G': source_G,
}
flow = [0*x, 0*x]
fluid_model_g = FluidModelG(
x*0,
x*0,
x*0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6*(-fluid_model_g.G + max_G) / (max_G - min_G),
5*(fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#-------------------------BJD 28.1.2021----rough code at present-----------------------------------------
if n == 600:
print("n = ", n)
break
#c1 = c1 + 1
#print("H E L L O")
#y1 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#y2 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
c1 = c1 + 1
# Set up grid and test data
#nx, ny = 256, 1024
#nx, ny = 240, 426
#nx, ny = 426, 240 # changed round to check!
nx, ny = 240, 426
#(426,240)
x1 = range(nx)
y1 = range(ny)
#data = numpy.random.random((nx, ny))
U = np.loadtxt("/home/brendan/runs/tf2-model-g_1/tf2-model-g/arrays/quiver_array30/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
V = np.loadtxt("/home/brendan/runs/tf2-model-g_1/tf2-model-g/arrays/quiver_array30/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
# BJD 28.1.2021: u and v are saved as arrays in fluid_model_g.py as fllows:
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/u.txt", self.u)
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/v.txt", self.v)
#data = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array12/Y.txt")
#hf = plt.figure(figsize=(10,10))
#ha = hf.add_subplot(111, projection='3d')
#ha = hf.add_subplot(111, projection='2d')
X1, Y1 = np.meshgrid(x1, y1) # `plot_surface` expects `x` and `y` data to be 2D
#ha.plot_surface(X, Y, data)
#ha.plot_surface(X, Y, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.plot_surface(X.T, Y.T, data)
#surf = ha.plot_surface(X1, Y1, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.set_zlim(-1, 3)
#hf.colorbar(surf, shrink=0.5, aspect=10)
#hf = plt.figure(figsize=(10,10))
"""
fig, hf = plt.subplots(figsize=(10,10))
#ax3.set_title("pivot='tip'; scales with x view")
hf.set_title("pivot='tip'; scales with x view" + str(c1))
M = np.hypot(U, V)
Q = hf.quiver(X1, Y1, U, V, M, units='x', pivot='tip', width=0.022,
scale=1 / 0.15)
qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$1 \frac{m}{s}$', labelpos='E',
coordinates='figure')
hf.scatter(X1, Y1, color='0.5', s=1)
"""
fig, hf = plt.subplots(figsize=(10,10))
hf.set_title("pivot='mid'; every 1th arrow; units='velocity vector'" + str(c1))
Q = hf.quiver(X1[::5, ::5], Y1[::5, ::5], U[::5, ::5], V[::5, ::5],
pivot='mid', units='inches')
qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$1 \frac{m}{s}$', labelpos='E',
coordinates='figure')
hf.scatter(X1[::5, ::5], Y1[::5, ::5], color='r', s=5)
plt.savefig('/home/brendan/runs/tf2-model-g_1/tf2-model-g/plots/2D_video36/2D_video_velocity_' + str(c1) + '.png')
def nucleation_and_motion_in_G_gradient_fluid_2D(writer,
args,
R=16
): # was R=30 BJD 4.1.2021
c1 = 0 # BJD added this on 20.11.2020
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
#def trapezoid_signal(x, width=2., slope=1., amp=1., offs=0):
def trapezoid_signal(x, width=2., slope=1., amp=10., offs=1):
#a = 10 * slope*width*signal.sawtooth(2 * np.pi * 1/10* x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
#a = slope * width * signal.sawtooth(2 * np.pi * 1/10 * x/width, width=0.5)/4.
a = slope * width * signal.sawtooth(
2 * np.pi * 1 / 10 * x / width - 0.8, width=0.5) / 4.
a[a > amp / 2.] = amp / 2.
a[a < -amp / 2.] = -amp / 2.
return a + amp / 2. + offs
def f(x):
#return -3*x/10 #+ 20
neg = x < 0
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
neg2 = np.logical_and(x >= 0, x < 29.5)
#neg3 = x >= 4.7
neg3 = x >= 29.5
return neg * (-3 * x / 10 + 1) + neg2 * (
20 * signal.square(2 * np.pi / 60 * x)) + neg3 * 1
#return neg * 1 + neg2 * (10 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
def f2(x):
#return -3*x/10 #+ 20
neg4 = x < 0
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
neg5 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg4 * (-x / 5 + 1) + neg5 * 1
def f3(x):
#return -3*x/10 #+ 20
#neg = x < 0
#neg6 = np.logical_and(y >= -10, y <= 10)
#neg7 = np.logical_and(y < -10, y > 10)
neg6 = np.logical_and(y >= -10, y <= 10)
neg7 = np.logical_or(y < -10, y > 10)
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
#neg3 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg6 * f2(x) + neg7 * f(x)
def f4(x):
neg8 = x <= 0
#return neg8 * (-x/5 + 1)
return neg8 * (-3 * x / 10 + 1)
def f5(x):
neg9 = x > 0
#return neg9 * (x/5 + 1)
return neg9 * (3 * x / 10 + 1)
def f6(x):
neg10 = y >= 0
neg11 = y < 0
#neg10 = np.logical_and(y >= -10, y <= 10)
#neg11 = np.logical_or(y < -10, y > 10)
#neg2 = np.logical_and(x >= 0, x < 4.7) #c[a & b] x >= 0 and x < 20 c[a & b] np.logical_and(x > -2, x < 2)
#neg3 = x >= 4.7
#neg3 = x >= 0
#return neg * (-x/5 + 1) + neg2 * (50 * signal.square(2 * np.pi /10 * x)) + neg3 * 1
return neg10 * f4(x) + neg11 * f5(x)
#...........................................
def source_G(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-0.5 * (t - 5)**2) * 10
#gradient = (1+np.tanh(t-30)) * 0.0003
gradient2 = 0.0006
#potential = 0.015 * (np.tanh(t-25) + 1)
#x = np.linspace(-40, 40, 500)
#triangle = 10 * signal.sawtooth(40 * np.pi * 1/1400 * x + 0, 0.5) + 10
#triangle = 10 * signal.sawtooth(2 * np.pi * 1/70 * x + 0.001, 0.5) + 10 # BJD: last used here 28.12.2020
#trapezoid = trapezoid_signal(x, width=40, slope=5, amp=50)
#piecewise = f6(x)
#piecewise_choice = f3(x)
piecewise = f6(x)
#trapezoid = trapezoid_signal(x, width=40, slope=10, amp=50)
#composite = composite_triangle(x)
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
#u = x/25
#u = x/10
return -(
# #np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5 * ((x)**2 + y * y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center + piecewise * gradient2 # piecewise function test 5.2.2021
#return -(
#np.exp( -0.5*( (x+25)**2 + y*y ) )
# x * y * ( x**2 - y**2 ) / ( x**2 + y**2 )
#) * center #+ (u*u + 1) * gradient #+ (x+8) * potential
#np.exp(-0.5*((x-D)**2+y*y)) * nucleator +
#(u*u - 1) * potential
#np.exp(-0.5*((x-15)**2+y*y)) * center + (u*u - 1) * gradient #+ (x+8) * gradient
#np.exp(-0.5*((x-15)**2 + y*y)) + np.exp(-0.5*((x+15)**2 + y*y)) * center - (u*u + 5) * gradient
#np.exp(-0.5*((x-12)**2 + y*y)) + np.exp(-0.5*((x+12)**2 + y*y))
#) * center + triangle * gradient # BJD - note minus sign maybe in wrong w.r.t. (u*u - 1) --- 22.12.2020
#np.exp(-0.5*((x-15)**2 + (y-25)**2)) + np.exp(-0.5*((x-15)**2 + (y+25)**2)) +
#np.exp(-0.5*((x+55)**2 + (y)**2))
#) * center + trapezoid * gradient # 3 particles for de Broglie diffraction --- 5.2.2021
#......................................................
source_functions = {
'G': source_G,
}
"""
def source_X(t):
#center = np.exp(-0.5*(t-5)**2) * 10
center = np.exp(-(1/18)*(t-10)**2)
#gradient = (1+np.tanh(t-30)) * 0.0003
#gradient = ( (t/3) - 8 ) * 0.0003 # (1+np.tanh(t-30)) * 0.0003
#print("x = ", x)
#return -np.exp(-0.5*(x*x+y*y))* center + (x+8) * gradient
return -(
#np.exp(-0.5*((x-8)**2 + y*y)) + np.exp(-0.5*((x+8)**2 + y*y)) # 2 particles 16 units apart
np.exp(-0.5*((x)**2 + y*y)) #+ np.exp(-0.5*((x)**2 + y*y))
) * center #+ (x+8) * gradient # BJD 2.2.2020 --- try gradient for half of plot!!
source_functions = {
'X': source_X,
}
"""
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
#x*0 # BJD 28.1.2021 --- added
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#-------------------------BJD 28.1.2021----rough code at present-----------------------------------------
if n == 400:
print("n = ", n)
break
#c1 = c1 + 1
print("H E L L O")
#y1 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/u.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#y2 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array14/v.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
c1 = c1 + 1
# Set up grid and test data
#nx, ny = 256, 1024
nx, ny = 240, 426 # original 10.10.2021
#nx, ny = 426, 240 # BJD changed here 10.10.2021
#ny, nx = 240, 426 # BJD changed here 10.10.2021
#(426,240)
x1 = range(nx)
y1 = range(ny)
#x1 = range(ny) #BJD changed here 10.10.2021
#y1 = range(nx) #BJD changed here 10.10.2021
#data = numpy.random.random((nx, ny))
# swapped U and V around - BJD 3.9.2021
U = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/quiver_array38/v.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
V = np.loadtxt(
"/home/brendan/software/tf2-model-g/arrays/quiver_array38/u.txt"
) #, delimiter=" :-) ", usecols=(120)) # (426, 240)
# swapped U and V around - BJD 2.9.2021
#U = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array37/del_X_dy.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#V = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/quiver_array37/del_X_dx.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
# BJD 28.1.2021: u and v are saved as arrays in fluid_model_g.py as fllows:
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/u.txt", self.u)
# np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array18/v.txt", self.v)
N = np.sqrt(
U**2 +
V**2) # there may be a faster numpy "normalize" function
U1, V1 = U / N, V / N
#F = 0.001 # normalisation factor
F = 0.004
U1 *= F
V1 *= F
#data = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array12/Y.txt")
#hf = plt.figure(figsize=(10,10))
#ha = hf.add_subplot(111, projection='3d')
#ha = hf.add_subplot(111, projection='2d')
X1, Y1 = np.meshgrid(
x1, y1) # `plot_surface` expects `x` and `y` data to be 2D
#ha.plot_surface(X, Y, data)
#ha.plot_surface(X, Y, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.plot_surface(X.T, Y.T, data)
#surf = ha.plot_surface(X1, Y1, data, rstride=1, cstride=1, cmap=cm.coolwarm,
# linewidth=0, antialiased=False)
#ha.set_zlim(-1, 3)
#hf.colorbar(surf, shrink=0.5, aspect=10)
#hf = plt.figure(figsize=(10,10))
"""
fig, hf = plt.subplots(figsize=(10,10))
#ax3.set_title("pivot='tip'; scales with x view")
hf.set_title("pivot='tip'; scales with x view" + str(c1))
M = np.hypot(U, V)
Q = hf.quiver(X1, Y1, U, V, M, units='x', pivot='tip', width=0.022,
scale=1 / 0.15)
qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$1 \frac{m}{s}$', labelpos='E',
coordinates='figure')
hf.scatter(X1, Y1, color='0.5', s=1)
"""
#fig, hf = plt.subplots(figsize=(10,10)) #original 10.10.2021
#fig, hf = plt.subplots(figsize=(10, 5.63), dpi=80) # BJD changed here 10.10.2021
fig, hf = plt.subplots(
figsize=(5.63, 10)) #, dpi=80) # BJD changed here 10.10.2021
# 5.633802816901408, 10 inches
#figure(figsize=(8, 6), dpi=80)
#hf.set_title("Model G fluid - diffusive flux vector of X - every 10th arrow, time = " + str(c1))
hf.set_title(
"Model G fluid - velocity vector field - every 10th arrow, time = "
+ str(c1))
#Q = hf.quiver(X1[::10, ::10], Y1[::10, ::10], U[::10, ::10], V[::10, ::10],
#pivot='mid', units='inches')
#M = np.hypot(U, V)
#Q = hf.quiver(X1[::7, ::7], Y1[::7, ::7], U1[::7, ::7], V1[::7, ::7], units='width',
Q = hf.quiver(
X1[::10, ::10],
Y1[::10, ::10],
U1[::10, ::10],
V1[::10, ::10],
units='width',
pivot='mid',
scale=0.1,
headwidth=5
) #pivot='mid', units='inches')#, scale=1)#, scale=5)
#qk = hf.quiverkey(Q, 0.9, 0.9, 1, r'$\frac{distance}{time}$', labelpos='E',
#coordinates='figure')
#qk = hf.quiverkey(Q, 0.9, 0.9, 0.1, r'$2d \ vector \ plot$', labelpos='E',
qk = hf.quiverkey(Q,
0.9,
0.9,
0.1,
r'$distance/time$',
labelpos='E',
coordinates='figure') #, color='b')
hf.scatter(X1[::10, ::10], Y1[::10, ::10], color='c', s=0)
#hf.scatter(Y1[::10, ::10], X1[::10, ::10], color='c', s=0) # BJD changed Y1 and X1 around - 10.10.2021
#plt.show()
#plt.title('Y potential in 2D space - time = ' + str(c1))
#plt.xlabel("x spacial units")
#plt.ylabel("y spacial units")
#plt.zlabel("X, Y, G pot. - concentration per unit vol")
#fig.savefig('test2.png') # save the figure to file
#plt.legend(["X", "Y", "G"]) # BJD legend added 21.11.2020
#plt.show()
plt.savefig(
'/home/brendan/software/tf2-model-g/plots/2D_video56/2D_video_velocity_'
+ str(c1) + '.png')
#plt.close(hf) # close the figure window
#y3 = np.loadtxt("/home/brendan/software/tf2-model-g/arrays/array10/G.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
#column1 = y1[120] # choose column 120 of 2D array = (426,240)
#column2 = y2[120] # choose column 120 of 2D array = (426,240)
#column3 = y3[120] # choose column 120 of 2D array = (426,240)
#row1 = y1[214] # choose row 214 of 2D array = (426,240)
#row2 = y2[214] # choose row 214 of 2D array = (426,240)
#row3 = y3[214] # choose row 214 of 2D array = (426,240)
#x, y = np.meshgrid(x, y, indexing='ij')
#X, Y = np.meshgrid(np.arange(0, 2 * np.pi, .2), np.arange(0, 2 * np.pi, .2))
#U = np.gradient(fluid_model_g.G,1)
#V = np.gradient(fluid_model_g.G,2)
#U = np.cos(X)
#V = np.sin(Y)
#np.savetxt("/home/brendan/software/tf2-model-g/arrays/quiver_array13/X.txt", np.gradient(fluid_model_g.G,1))
# sphinx_gallery_thumbnail_number = 3
"""
def nucleation_and_motion_in_G_gradient_fluid_2D(writer, args, R=16):
dx = 2 * R / args.height
x = (np.arange(args.width) - args.width // 2) * dx
y = (np.arange(args.height) - args.height // 2) * dx
x, y = np.meshgrid(x, y, indexing='ij')
def source_G(t):
center = np.exp(-0.5 * (t - 5)**2) * 10
gradient = (1 + np.tanh(t - 30)) * 0.0003
return -np.exp(-0.5 * (x * x + y * y)) * center + (x + 8) * gradient
source_functions = {
'G': source_G,
}
flow = [0 * x, 0 * x]
fluid_model_g = FluidModelG(
x * 0,
x * 0,
x * 0,
flow,
dx,
dt=args.dt,
params=args.model_params,
source_functions=source_functions,
)
print("Rendering 'Nucleation and Motion in G gradient in 2D'")
print("Lattice constant dx = {}, time step dt = {}".format(
fluid_model_g.dx, fluid_model_g.dt))
min_G = -4.672736908320116
max_G = 0.028719261862332906
min_X = -3.8935243721220334
max_X = 1.2854028081816122
min_Y = -0.7454193158963579
max_Y = 4.20524950766914
#c1 = 0
for n in progressbar.progressbar(range(args.num_frames)):
fluid_model_g.step()
if n % args.oversampling == 0:
rgb = [
6 * (-fluid_model_g.G + max_G) / (max_G - min_G),
5 * (fluid_model_g.Y - min_Y) / (max_Y - min_Y),
0.7 * (fluid_model_g.X - min_X) / (max_X - min_X),
]
zero_line = 1 - tf.exp(-600 * fluid_model_g.Y**2)
frame = make_video_frame([c * zero_line for c in rgb])
writer.append_data(frame)
#===========================================================================
#if n == 4:
# X_array = [
# 0.7*(fluid_model_g.X - min_X) / (max_X - min_X),
# ] # BJD put this in 18.11.2020
# print("Array of X: ", X_array) # ***** BJD inserted this line 18.11.2020 *****
"""
print("H E L L O")
y1 = np.loadtxt("test.txt") #, delimiter=" :-) ", usecols=(120)) # (426, 240)
row1 = y1[120]
print(row1)
pp.plot(row1)
pp.show()
"""
#==============================BJD 18.11.2020=============================================
#for i in xrange(10):
#with io.open("file_" + str(i) + ".dat", 'w', encoding='utf-8') as f:
#with io.open("file_" + str(c1) + ".txt", 'w', encoding='utf-8') as f:
#f.write(str(func(c1))
#for number in range(1, 11):
#filename = 'a%d.txt' % number
#data = read_data(filename)
#for c1 in xrange(10):
for c1 in 10:
print("H E L L O")
y1 = np.loadtxt(
"file_" + str(c1) + ".txt",
'r') #, delimiter=" :-) ", usecols=(120)) # (426, 240)
row1 = y1[120]
print(row1)
pp.plot(row1)
pp.show()