def admitant_2d_matrix_element_bm(mesh, row_idx, col_idx, z0, k, coupling_sign):
n, ns = mesh.normals[row_idx], mesh.normals[col_idx]
r = mesh.centers[row_idx]
corners, admittance = mesh.corners[col_idx], mesh.admittances[col_idx]
singular = row_idx == col_idx
if singular:
element_vector = corners[1] - corners[0]
length = np.sqrt(element_vector.dot(element_vector))
lk2 = length * k / 2
return (
+(z0 * admittance * np.pi * length * k / 8)
* (+hankel2(0, lk2) * struve(-1, lk2) + hankel2(1, lk2) * struve(0, lk2))
- coupling_sign
* fixed_quad(regularized_hypersingular_bm_part, 0, lk2)[0]
/ 2
+ coupling_sign * 2j / (np.pi * k * length)
+ (1 - coupling_sign * z0 * admittance) / 2
)
else:
def integral_function(rs):
return (
hs_2d(ns, k, r, rs)
- 1j * k * z0 * admittance * g_2d(k, r, rs)
+ coupling_sign * z0 * admittance * h_2d(n, k, r, rs)
+ coupling_sign * 1j / k * hypersingular(k, r, rs, n, ns)
)
return line_integral(integral_function, corners[0], corners[1], singular)
def radimp(wf, dia):
"""calculatio radiation impedance for each frequency"""
if not wf > 0:
return 0
if dia > 0:
if _rad_calc == 'NONE':
return 0 # simple open end impedance
else:
s = dia*dia*np.pi/4.0
k = wf/_c0
x = k*dia
re = _rhoc0/s*(1 - special.jn(1, x)/x*2) # 1st order bessel function.
im = _rhoc0/s*special.struve(1, x)/x*2 # 1st order struve function.
if _rad_calc == 'BAFFLE':
zr = re + im*1j
elif _rad_calc == 'PIPE':
# real is about 0.5 times and imaginary is 0.7 times when without frange.
zr = 0.5*re + 0.7*im*1j
return zr
else:
return np.inf # closed end
def randFunc(x, sdev):
functions = [
np.sin(x),
np.cos(x),
special.gammaln(x),
np.sqrt(x),
np.log(x),
np.log10(x),
special.erf(x),
np.square(x),
special.struve(np.random.uniform(0, 2), x),
special.rgamma(x)
]
index = np.random.randint(0, int(len(functions)))
choice = functions[index] / max(functions[index])
choice = (choice**2)**0.5
choice *= np.random.uniform(0, 150)
choice += 10
for k in range(len(x)):
devSN = np.random.normal(0, sdev)
choice[k] += devSN
return (choice)
def G_int_sp(x_in):
"""Special function solution of G(x) (Coulomb integral)
Defined in Eq. (17b) Mares and Chuang, J. Appl. Phys. 74, 1388 (1993)
Keyword arguments:
x_in -- Normalized 2|ze-zh|/lambda
"""
G = x_in*(sp.pi/2.0*(sps.struve(1,x_in)-sps.y1(x_in))-1)
G[x_in <= 1.0E-8] = 1.0
return G
def _create_plot_component():
x = linspace(-2.0, 10.0, 100)
pd = ArrayPlotData(x=x)
# Create some line plots of some of the data
plot = Plot(pd, padding=50, border_visible=True, overlay_border=True)
plot.legend.visible = True
# Extend the plot's list of drawing layers
ndx = plot.draw_order.index("plot")
plot.draw_order[ndx:ndx] = ["bessel", "sine", "struve"]
# Draw struve
for i in range(3):
y_name = "struve" + str(i)
pd.set_data(y_name, struve(i, x))
renderer = plot.plot(("x", y_name),
color="blue",
name=y_name,
line_width=2)[0]
renderer.draw_layer = "struve"
renderer.unified_draw = True
# Draw bessels
for i in range(3):
y_name = "bessel" + str(i)
pd.set_data(y_name, jn(i, x))
renderer = plot.plot(("x", y_name),
color="green",
name=y_name,
line_width=2)[0]
renderer.draw_layer = "bessel"
renderer.unified_draw = True
# Draw sines
for i in range(3):
y_name = "sine" + str(i)
pd.set_data(y_name, sin(x * (i + 1) / 1.5))
renderer = plot.plot(("x", y_name),
color="red",
name=y_name,
line_width=2)[0]
renderer.draw_layer = "sine"
renderer.unified_draw = True
# Attach some tools to the plot
plot.tools.append(PanTool(plot))
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
return plot
def Hv_zeros(order, n):
"""
Calculates the first 20 zeros of the Struve function of arbitrary order
:param order: order of the Struve function
:param n: number of zeros returned (max 20)
"""
# x-vector - use only positive part, Struve functions are
# even (if order is odd) or odd( if order is even)
x = np.arange(0., 70., 0.0001)
H = struve(order, x)
xi = zero_crossings(x, H)
xi[0] = 0.
return xi[1:n + 1]
def keldysh_interaction(radius, radius_0, ep12):
"""
Keldysh Interaction.
:param radius: Distance from centre
:param radius_0: Scale distance corresponding to inherent screening.
:param ep12: average of top and bottome dielectric constants.
:return: interaction
"""
term_arg = (radius / radius_0) * ep12
struve_term = spec.struve(0, term_arg)
bessel_term = spec.y0(term_arg)
interaction = keldysh_prefactor / radius_0 * (struve_term - bessel_term)
return interaction
def misc_flatspectrum_plots(self):
""" Miscilanous plots for the flat spectrum paper """
self.logger.debug("Entering misc_flatspectrum_plots")
# Plot piston resistance and reactance functions
from scipy.special import j1, struve
x = arange(0, 15, 0.001)
r1 = lambda x: 1 - 2 * j1(x) / x
x1 = lambda x: 2 * struve(1, x) / x
plot(x, r1(x), label="$R_{1}\left(x)\\right)$")
plot(x, x1(x), linestyle="--", color="black", label="$X_{1}\left(x)\\right)$")
xlim([0, 13])
annotate("$R_{1}(x)$", xy=(10, r1(10)), xycoords="data", xytext=(10.5, r1(10.5) - 0.2),
arrowprops=dict(arrowstyle="->"))
annotate("$X_{1}(x)$", xy=(5, x1(5)), xycoords="data", xytext=(6, x1(6) + 0.2),
arrowprops=dict(arrowstyle="->"))
grid(True)
savefig("Analysis/Images/piston_impedance_functions.eps")
# Plot the piston resisance for a 100mm piston
cla()
a = 0.055
c = 340
p0 = 1.2250
f = arange(100, 10000, 0.01)
k = 2 * pi * f / c
Rr = p0 * c * pi * a ** 2 * r1(2 * k * a)
normalized_Rr = 10 * log10(Rr) - 10 * log10(Rr[-1])
semilogx(f, normalized_Rr)
ax = gca()
ax.set_xticks([16, 20, 25, 31.5, 40, 50, 63, 80, 100, 125,
160, 200, 250, 315, 400, 500, 630, 800, 1000, 1250, 1600, 2000, 2500, 3150,
4000, 5000, 6300, 8000, 1000, 12500])
ax.set_xticklabels([16, 20, 25, 31.5, 40, 50, 63, 80, 100, 125,
160, 200, 250, 315, 400, 500, 630, 800, 1000, 1250, 1600, 2000, 2500, 3150,
4000, 5000, 6300, 8000, 1000, 12500])
xlim(100, 5000)
for label in ax.get_xticklabels():
label.set_rotation('vertical')
grid(True)
subplots_adjust(left=0.15, right=0.97, top=0.97, bottom=0.15)
xlabel("Frequency Hz")
ylabel("dB re $R_{1}(2ka) = 1$")
savefig("Analysis/Images/piston_resistance_100mm.eps")
def kernel_fn(r: float) -> float:
"""
Args:
r: distance from center, expressed in terms of grid position
Returns:
value of U(r)
"""
alpha = 1.0
r0 = 10
# TODO Fix this value to r -> 0
if r == 0:
return -2 * alpha / r0
H0 = special.yn(0, r / r0)
Y0 = special.struve(0, r / r0)
return alpha / r0 * (H0 - Y0)
def _create_plot_component():
x = linspace(-2.0, 10.0, 100)
pd = ArrayPlotData(x = x)
# Create some line plots of some of the data
plot = Plot(pd, padding=50, border_visible=True, overlay_border=True)
plot.legend.visible = True
# Extend the plot's list of drawing layers
ndx = plot.draw_order.index("plot")
plot.draw_order[ndx:ndx] = ["bessel", "sine", "struve"]
# Draw struve
for i in range(3):
y_name = "struve" + str(i)
pd.set_data(y_name, struve(i, x))
renderer = plot.plot(("x", y_name), color="blue", name=y_name, line_width=2)[0]
renderer.set(draw_layer = "struve", unified_draw=True)
# Draw bessels
for i in range(3):
y_name = "bessel" + str(i)
pd.set_data(y_name, jn(i,x))
renderer = plot.plot(("x", y_name), color="green", name=y_name, line_width=2)[0]
renderer.set(draw_layer = "bessel", unified_draw=True)
# Draw sines
for i in range(3):
y_name = "sine" + str(i)
pd.set_data(y_name, sin(x * (i+1) / 1.5))
renderer = plot.plot(("x", y_name), color="red", name=y_name, line_width=2)[0]
renderer.set(draw_layer="sine", unified_draw=True)
# Attach some tools to the plot
plot.tools.append(PanTool(plot))
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
return plot
def randFunc(x,sdev):
tempDM = x/np.amax(x)
functions = [
special.gammaln(tempDM),
np.sqrt(tempDM), np.log(tempDM), np.log10(tempDM),
special.erf(tempDM), np.square(tempDM),
special.struve(np.random.uniform(0,2),tempDM)
#special.rgamma(x)
]
randVar = np.random.uniform(0,1)
combProb = 1/2
if randVar < combProb:
indices = np.random.randint(0, len(functions), 2)
distA = functions[indices[0]]
distB = functions[indices[1]]
choice = np.concatenate((distA, distB))
choice = np.random.choice(choice, size = len(tempDM), replace = False)
else:
indices = np.random.randint(0, int(len(functions)))
choice = functions[indices]
choice /= np.amax(choice)
choice = (choice**2)**0.5
choice *= np.random.uniform(2, 32)
choice += 8
for k in range(len(tempDM)):
devSN = np.random.normal(0,sdev)
choice[k] += devSN
fig2 = plt.figure()
ax2 = fig2.add_subplot(111)
ax2.scatter(x, choice)
ax2.set_title(indices)
return(choice)
def true_func(x): return struve(0, x) - y0(x)
from scipy.special import struve, y0, yn from fast_interp import FunctionGenerator as FG def protect(F): def new_func(x): if isinstance(x, np.ndarray): dtype = type(F(1)) sel = x > 1e-10 out = np.zeros(x.shape, dtype=dtype) out[sel] = F(x[sel]) else: out = 0.0 if x < 1e-10 else F(x) return out return new_func H0 = FG(lambda x: struve( 0, x), 1e-10, 10) H1 = FG(lambda x: struve(-1, x), 1e-10, 10) H2 = FG(lambda x: struve(-2, x), 1e-10, 10) H3 = FG(lambda x: struve(-3, x), 1e-10, 10) Y0 = FG(lambda x: y0(x), 1e-10, 10) Y1 = FG(lambda x: yn(1, x), 1e-10, 10) Y2 = FG(lambda x: yn(2, x), 1e-10, 10) """ Test how to do biharmonic FMM using cloud of points... """ def random3(N): a1 = np.random.rand(N)-0.5 a2 = np.random.rand(N)-0.5 a3 = np.random.rand(N)-0.5
def X(x): return struve(1, x) / x
def chi(omega, r_mouth): """Reactive part of impedance""" return struve(1, omega * r_mouth) / omega / r_mouth
import numpy as np
from scipy import special
from matplotlib import pyplot as plt
tempDM = np.linspace(0.001, 10, 10000) # X-vals to evaluate the distributions over
functions = np.array([ # Possible distributions that noise can follow
special.gammaln(tempDM), np.sqrt(tempDM), np.log(tempDM),
-special.gammaln(tempDM), -np.sqrt(tempDM), -np.log(tempDM),
special.erf(tempDM), np.square(tempDM),
-special.erf(tempDM), -np.square(tempDM),
special.struve(0,tempDM), special.struve(1,tempDM), special.struve(2,tempDM),
-special.struve(0,tempDM), -special.struve(1,tempDM), -special.struve(2,tempDM),
[np.random.uniform(0, 5)]*len(tempDM), tempDM, -tempDM, special.rgamma(tempDM)
])
def generation(numPoints, upperDM):
"""Randomly pick shapes for noise to follow. With probability of multiple, different,
distributions (as well as their inverted counterparts) to be convolved with each other and
form unpredictable shapes.
Keyword arguments:
numPoints -- the number of points that the noise/fake signal will have
upperDM -- the highest DM for the data (w.r.t. 0), to be multiplied by the normalised plot in the end
"""
np.random.seed() # As random seeds are used at some points this just ensure it is reset every time
convProb = 3/4 # Probability of convolution of a signal taking place
def base_gf(x):
Y = y0(x)
H = struve(0, x)
return 0.25 * (H - Y)
def GF(x):
Y = yn(1, x)
S3 = struve(-3, x)
S2 = struve(-2, x)
return (x * (Y - S3) - 4 * S2) / x**2
def __init__(self,
N,
vb,
cb,
epsilon,
r0=33.875,
shift=0.5,
spin_orbit=True,
cutoff=np.inf):
if spin_orbit:
self.model = tbmodels.Model.from_wannier_files(
hr_file='TB-Models/MoS2_hr.dat',
wsvec_file='TB-Models/MoS2_wsvec.dat',
xyz_file='TB-Models/MoS2_centres.xyz',
win_file='TB-Models/MoS2.win')
else:
self.model = tbmodels.Model.from_wannier_files(
hr_file='TB-Models/wann_hr.dat',
wsvec_file='TB-Models/wann_wsvec.dat',
xyz_file='TB-Models/wann_centres.xyz',
win_file='TB-Models/wann.win')
self.k1 = self.model.reciprocal_lattice[0]
self.k2 = self.model.reciprocal_lattice[1]
self.a1 = self.model.uc[0]
self.a2 = self.model.uc[1]
self.norb = self.model.hamilton([0., 0., 0.]).shape[0]
self.cutoff = cutoff
self.epsilon = epsilon #
self.r0 = r0 / epsilon
self.shift = shift # scissor operator
self.N = N # k-points grid
self.vb = vb # valence bands
self.cb = cb # conduction bands
self.nv = len(self.vb)
self.nc = len(self.cb)
self.E = np.zeros((N, N, self.norb))
self.K = np.zeros((N, N, 3))
self.D = np.zeros((N, N, self.norb, self.norb), dtype=np.complex)
self.H = np.zeros((N, N, self.norb, self.norb), dtype=np.complex)
for i, j in product(range(N), range(N)):
self.H[i, j] = self.model.hamilton([i / N, j / N, 0])
e, d = np.linalg.eigh(self.H[i, j])
self.E[i, j] = e
self.D[i, j] = d
self.K[i, j] = i * self.k1 / N + j * self.k2 / N
R = np.zeros((N, N, 3))
for i, j in product(range(N), range(N)):
R[i, j] = self.a1 * (i - N / 2) + self.a2 * (j - N / 2)
self.R = R
WR = np.zeros((N, N))
VR = np.zeros((N, N))
for i, j in product(range(N), range(N)):
radius = np.linalg.norm(R[i, j])
if radius != 0:
WR[i, j] = Hartree * Bohr * np.pi / (
2 * self.epsilon * self.r0) * (
struve(0, radius / self.r0) - yn(0, radius / self.r0))
VR[i, j] = Hartree * Bohr / radius
else:
WR[i, j] = 0
VR[i, j] = 0
WR = np.fft.fftshift(WR)
self.W = np.fft.fft2(WR) / N**2
VR = np.fft.fftshift(VR)
self.V = np.fft.fft2(VR) / N**2
self.gap = self.E[:, :, cb[0]] - self.E[:, :, vb[-1]] + shift
self.Egap = np.min(self.gap)
self.weight = np.ones((self.N, self.N))
self.weight[self.gap > (self.Egap + self.cutoff)] = 0
self.indexes = []
for kx, ky in product(range(self.N), range(self.N)):
if self.weight[kx, ky] == 1:
for i, j in product(self.cb, self.vb):
self.indexes.append((kx, ky, i, j))
self.NH = len(self.indexes)
print('Exciton Hamiltonian size: ' + str(self.NH) + ' K-space size: ' +
str(int(np.sum(self.weight))))
R = np.fft.fftshift(self.R, axes=(0, 1))
HR = np.fft.ifft2(self.H, axes=(0, 1))
dx = np.fft.fft2(1j * R[:, :, 0, None, None] * HR, axes=(0, 1))
dy = np.fft.fft2(1j * R[:, :, 1, None, None] * HR, axes=(0, 1))
for i, j in product(range(N), range(N)):
dx[i, j] = np.linalg.multi_dot(
[self.D[i, j].T.conj(), dx[i, j], self.D[i, j]])
dy[i, j] = np.linalg.multi_dot(
[self.D[i, j].T.conj(), dy[i, j], self.D[i, j]])
self.dx = dx
self.dy = dy
def _init_values_struve(self):
temp_values = np.arange(0, 20, 0.002)
self.value_map = special.struve(1, temp_values)
c_max = np.amax(self.value_map)
np.multiply(self.value_map, 1.0 / c_max, out=self.value_map)
self.value_map = np.concatenate((self.value_map, self.value_map[::-1]))
def G(a, gamma):
if abs(gamma) < 1.0e-9:
return 1.0
else:
x = 2 * abs(gamma) / a
return x * (np.pi / 2 * (sp.struve(1, x) - sp.y1(x)) - 1)
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import matplotlib.pyplot as plt
from scipy import special
import numpy as np
fig = plt.figure()
ax = fig.gca(projection='3d')
X = np.arange(-5, 5, 0.25)
Y = np.arange(-5, 5, 0.25)
X, Y = np.meshgrid(X, Y)
R = np.sqrt(X**2 + Y**2)
Z = special.struve(0, R)
surf = ax.plot_surface(X,
Y,
Z,
rstride=1,
cstride=1,
cmap=cm.coolwarm,
linewidth=0,
antialiased=False)
ax.set_zlim(None, None)
ax.zaxis.set_major_locator(LinearLocator(10))
ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))
fig.colorbar(surf, shrink=0.5, aspect=5)
plt.show()
def misc_flatspectrum_plots(self):
""" Miscilanous plots for the flat spectrum paper """
self.logger.debug("Entering misc_flatspectrum_plots")
# Plot piston resistance and reactance functions
from scipy.special import j1, struve
x = arange(0, 15, 0.001)
r1 = lambda x: 1 - 2 * j1(x) / x
x1 = lambda x: 2 * struve(1, x) / x
plot(x, r1(x), label="$R_{1}\left(x)\\right)$")
plot(x,
x1(x),
linestyle="--",
color="black",
label="$X_{1}\left(x)\\right)$")
xlim([0, 13])
annotate("$R_{1}(x)$",
xy=(10, r1(10)),
xycoords="data",
xytext=(10.5, r1(10.5) - 0.2),
arrowprops=dict(arrowstyle="->"))
annotate("$X_{1}(x)$",
xy=(5, x1(5)),
xycoords="data",
xytext=(6, x1(6) + 0.2),
arrowprops=dict(arrowstyle="->"))
grid(True)
savefig("Analysis/Images/piston_impedance_functions.eps")
# Plot the piston resisance for a 100mm piston
cla()
a = 0.055
c = 340
p0 = 1.2250
f = arange(100, 10000, 0.01)
k = 2 * pi * f / c
Rr = p0 * c * pi * a**2 * r1(2 * k * a)
normalized_Rr = 10 * log10(Rr) - 10 * log10(Rr[-1])
semilogx(f, normalized_Rr)
ax = gca()
ax.set_xticks([
16, 20, 25, 31.5, 40, 50, 63, 80, 100, 125, 160, 200, 250, 315,
400, 500, 630, 800, 1000, 1250, 1600, 2000, 2500, 3150, 4000, 5000,
6300, 8000, 1000, 12500
])
ax.set_xticklabels([
16, 20, 25, 31.5, 40, 50, 63, 80, 100, 125, 160, 200, 250, 315,
400, 500, 630, 800, 1000, 1250, 1600, 2000, 2500, 3150, 4000, 5000,
6300, 8000, 1000, 12500
])
xlim(100, 5000)
for label in ax.get_xticklabels():
label.set_rotation('vertical')
grid(True)
subplots_adjust(left=0.15, right=0.97, top=0.97, bottom=0.15)
xlabel("Frequency Hz")
ylabel("dB re $R_{1}(2ka) = 1$")
savefig("Analysis/Images/piston_resistance_100mm.eps")