def D_prec(R0, phi0, epsilon, sig, z):
D565, grad565 = sp.pbdv(-0.565, -((R0 - z)/sig))
D1565, grad1565 = sp.pbdv(-1.565, -((R0 - z)/sig))
frontfac = ((np.exp( (-(R0 - z)**2)/(4.0*(sig**2))) * (sig**0.565))/(1.0 + 0.012*R0))*phi0
bracfac = 11.26*D565/sig + ((0.157 + 11.26*epsilon)/R0)*D1565
return frontfac * bracfac * toGray
def D_prec(R0, phi0, epsilon, sig, z):
D565, grad565 = sp.pbdv(-0.565, -((R0 - z) / sig))
D1565, grad1565 = sp.pbdv(-1.565, -((R0 - z) / sig))
frontfac = ((np.exp((-(R0 - z)**2) / (4.0 * (sig**2))) * (sig**0.565)) /
(1.0 + 0.012 * R0)) * phi0
bracfac = 11.26 * D565 / sig + ((0.157 + 11.26 * epsilon) / R0) * D1565
return frontfac * bracfac * toGray
def _expected_E_FW_acen(eobs_sq, sig_eobs_sq):
''' First moment of the expected E distribution i.e. <E>'''
from math import sqrt, pi, exp
CROSSOVER1 = -12.5
CROSSOVER2 = 18
x = (eobs_sq - sig_eobs_sq**2) / sig_eobs_sq
xsqr = x**2
if x < CROSSOVER1: # Large negative argument: asymptotic approximation
e_xpct = sqrt(-pi * sig_eobs_sq / x) * (
(-916620705 + xsqr * (91891800 + xsqr *
(-11531520 + xsqr *
(1935360 + xsqr *
(-491520 + xsqr * 262144))))) /
(-495452160 + xsqr * (55050240 + xsqr *
(-7864320 + xsqr *
(1572864 + xsqr *
(-524288 + xsqr * 524288))))))
elif x > CROSSOVER2: # Large positive argument: asymptotic approximation
e_xpct = sqrt(sig_eobs_sq) * ((-45045 + 32 * xsqr *
(-315 + 8 * xsqr *
(-15 - 16 * xsqr + 128 * xsqr**2))) /
(32768 * x**7.5))
else:
from scipy.special import pbdv, erfc # parabolic cylinder function D, complementary error function
e_xpct = (
sqrt(sig_eobs_sq / 2) * exp(-xsqr / 4) * pbdv(-1.5, -x)[0]
/ # Scipy parabolic cylinder function returns value *and* derivative
erfc(-x / sqrt(2)))
return e_xpct
def cal_bragg_straggle(E, z, straggle):
"""
Calculates the Bragg peak based on the Bortfeld equation considering range straggling.
This uses parabolic cylinder function, which is a fit to the Gaussian convolution with non-straggled curve (Bortfeld).
:param E: scalar. Initial beam energy in MeV.
:param z: a numpy array of positions to calculate the dose. The unit is centimeter.
:param straggle: scalar. Initial energy sigma in MeV.
:return: (dose, index of bragg peak: the maximum value of the dose vector)
"""
p = 1.77 # Unitless
alpha = 2.2e-3 # Unitless
g = 0.6 # Unitless
beta = 0.012 # 1 / cm
phiIN = 0.0001 # Primary fluence
# phiIN = 0.1
rho = 1.00 # gm / cm3(Mass density of the medium)
R = alpha * E**p # cm(Range, neglecting straggling)
sigmamono = 0.012 * (
R**0.935
) # 2nd March, remember to test with or without brackets same result.
sigmaEzero = straggle
sigmatotal = np.sqrt(sigmamono**2 + (sigmaEzero**2) * (alpha**2) * (p**2) *
(E**(2 * p - 2)))
eta = (R - z) * 1. / sigmatotal
epsilon = 0.0
# print 'eta = ', eta
pdd = []
denom = np.sqrt(2 * np.pi) * rho * p * (alpha**(1 / p)) * (1 + beta * R)
for zd in eta:
para1 = pbdv(-1 / p, -zd)[0]
para2 = pbdv(-1 / p - 1, -zd)[0]
numerator = phiIN * (np.exp(-(zd**2) / 4) *
(sigmatotal**(1 / p)) * gamma(1 / p))
add1 = 1. / sigmatotal * para1
add2 = (beta / p + g * beta + epsilon / R) * para2
pdd_zd = (numerator / denom) * (add1 + add2)
pdd.append(pdd_zd)
pdd = np.array(pdd)
dose_nostraggle, _ = cal_bragg_nostraggle(E=E, z=z)
nan_index = np.argwhere(~np.isfinite(pdd))
pdd[nan_index] = dose_nostraggle[nan_index]
return pdd, np.argmax(pdd)
def D(R0, phi0, epsilon, sig, z):
"""
This is the very specialised equation for water only. It's equation 28/29 in the paper
"""
if z < (R0 - 10*sig):
fac = (phi0)/(1.0 + 0.012*R0)
term1 = 17.93*((R0 - z)**-0.435)
term2 = ((0.444 + 31.7*epsilon)/R0)*((R0-z)**0.565)
return fac*(term1 + term2) * toGray
elif z < (R0 + 5*sig):
D565, grad565 = sp.pbdv(-0.565, -((R0 - z)/sig))
D1565, grad1565 = sp.pbdv(-1.565, -((R0 - z)/sig))
frontfac = ((np.exp( (-(R0 - z)**2)/(4.0*(sig**2))) * (sig**0.565))/(1.0 + 0.012*R0))*phi0
bracfac = 11.26*D565/sig + ((0.157 + 11.26*epsilon)/R0)*D1565
return frontfac * bracfac * toGray
else:
return 0.0
def D(R0, phi0, epsilon, sig, z):
"""
This is the very specialised equation for water only. It's equation 28/29 in the paper
"""
if z < (R0 - 10 * sig):
fac = (phi0) / (1.0 + 0.012 * R0)
term1 = 17.93 * ((R0 - z)**-0.435)
term2 = ((0.444 + 31.7 * epsilon) / R0) * ((R0 - z)**0.565)
return fac * (term1 + term2) * toGray
elif z < (R0 + 5 * sig):
D565, grad565 = sp.pbdv(-0.565, -((R0 - z) / sig))
D1565, grad1565 = sp.pbdv(-1.565, -((R0 - z) / sig))
frontfac = ((np.exp((-(R0 - z)**2) / (4.0 * (sig**2))) *
(sig**0.565)) / (1.0 + 0.012 * R0)) * phi0
bracfac = 11.26 * D565 / sig + ((0.157 + 11.26 * epsilon) / R0) * D1565
return frontfac * bracfac * toGray
else:
return 0.0
def _expected_E_FW_cen(eobs_sq, sig_eobs_sq):
''' First moment of the expected E distribution i.e. <E>'''
CROSSOVER1 = -17.5
CROSSOVER2 = 17.5
from math import pi, sqrt
x = sig_eobs_sq / 2 - eobs_sq / sig_eobs_sq
xsqr = x**2
if x < CROSSOVER1:
pcd_ratio = ((1024 * sqrt(pi) * (-x)**6.5) /
(3465 + xsqr * (840 + xsqr * (384 + xsqr * 1024))))
elif x > CROSSOVER2:
pcd_ratio = ((3440640 + xsqr * (-491520 + xsqr *
(98304 + xsqr *
(-32768 + xsqr * 32768)))) /
(675675 + xsqr * (-110880 + xsqr *
(26880 + xsqr *
(-12288 + xsqr * 32768))))) / sqrt(x)
else:
from scipy.special import pbdv
pcd_ratio = pbdv(-1, x)[0] / pbdv(-0.5, x)[0]
e_xpct = sqrt(sig_eobs_sq / pi) * pcd_ratio
return e_xpct
def _expected_Esq_FW_cen(eobs_sq, sig_eobs_sq):
''' Second moment of the expected E distribution, i.e. <E**2> '''
CROSSOVER1 = -17.5
CROSSOVER2 = 17.5
x = sig_eobs_sq / 2 - eobs_sq / sig_eobs_sq
xsqr = x**2
if x < CROSSOVER1:
pcd_ratio = ((45045 + xsqr * (10080 + xsqr *
(3840 + xsqr * (4096 - xsqr * 32768)))) /
(x * (55440 + xsqr * (13440 + xsqr *
(6144 + xsqr * 16384)))))
elif x > CROSSOVER2:
pcd_ratio = ((11486475 + xsqr * (-1441440 + xsqr *
(241920 + xsqr *
(-61440 + xsqr * 32768)))) /
(x * (675675 + xsqr * (-110880 + xsqr *
(26880 + xsqr *
(-12288 + xsqr * 32768))))))
else:
from scipy.special import pbdv
pcd_ratio = pbdv(-1.5, x)[0] / pbdv(-0.5, x)[0]
esq_xpct = sig_eobs_sq * pcd_ratio / 2
return esq_xpct
def calcAutoconversionIntegral(muChi,sigmaChi,muNcn,sigmaNcn,rhoChiNcn,alpha,beta):
"""Calculate the Khairoutdinov-Kogan autoconversion rate,
upscaled over a single normal-lognormal PDF."""
from scipy.special import gamma, pbdv
from math import sqrt, exp, pi
sC = muChi/sigmaChi + rhoChiNcn*sigmaNcn*beta
# sC = muChi/sigmaChi - rhoChiNcn*sigmaNcn*beta
(parabCylFnc, parabCylDer) = pbdv(-alpha-1,-sC)
# (parabCylFnc, parabCylDer) = pbdv(-alpha-1,sC)
analyticIntegral = (1/sqrt(2*pi))*(sigmaChi**alpha) \
*exp(muNcn*beta + 0.5*(sigmaNcn*beta)**2 - 0.25*sC**2) \
*gamma(alpha+1)*parabCylFnc
# pdb.set_trace()
return analyticIntegral
def pcfd(v, x):
return sc.pbdv(v, x)[0]
def pcfd(v, x):
return sc.pbdv(v, x)[0]
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.pbdv(0, R)
Z = Z[0]
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 write_report(self, data, interaction, dimensions, density, temperature):
"""Genertes a report in a *.txt file"""
if interaction == 1:
if not os.path.exists("ideal_gas"):
os.mkdir("ideal_gas")
f_report = open("ideal_gas/report_{0}d_{1}.txt".format(dimensions,
datetime.now()), "w")
f_plot = open("ideal_gas/plot_{0}d.cvs".format(dimensions,
density), "a")
avg_temp = self.calculate_average(data, "T")
avg_pres = self.calculate_average(data, "P")
avg_density = avg_pres/avg_temp
error_density = (abs(density-avg_density)/density)*100
f_report.write("REPORT " + str(datetime.now()) + "\n" +
"-----------------------------------------" + "\n" +
"CONFIGURATION:" + "\n" +
"Interaction -> Ideal Gas" + "\n"
"Dimensions -> " + str(dimensions) + "\n"
"Steps = " + str(MEASUREMENT_STEPS) + "\n" +
"Density = " + str(density) + "\n" +
"Temperature = " + str(temperature) + "\n" +
"-----------------------------------------" + "\n" +
"SIMULATION RESULTS:" + "\n" +
"Temperature (Average) = " + str(avg_temp) + "\n" +
"Pressure (Average) = " + str(avg_pres) + "\n" +
"Density (Average) = " + str(avg_density) + "\n"+
"Density Error (%) = "+ str(error_density))
f_plot.write("{0}, {1}, {2} , {3}, {4}\n".format(avg_temp, avg_pres,
avg_density, density, error_density))
if interaction == 2:
if not os.path.exists("lennard_jones"):
os.mkdir("lennard_jones")
f_report = open("lennard_jones/report_{0}d_{1}.txt".format(dimensions,
datetime.now()), "w")
f_plot = open("lennard_jones/plot_{0}d.cvs".format(dimensions,
density), "a")
#kinetic_energy = self.calculate_average(data, "K")
potential_energy = self.calculate_average(data, "V")
total_energy = self.calculate_average(data, "E")
avg_temp = self.calculate_average(data, "T")
avg_pres = self.calculate_average(data, "P")
hermite = ((pbdv(1/2., -(2/avg_temp)**(1/2.))[0])*2**(1/4.)*
np.e**(.5/avg_temp))
B2 = (2/3.)*np.pi*(2*np.pi)**(1/2.)*(1/avg_temp)**(1/4.)*hermite
virial_pres = density*avg_temp*(1 + density*B2)
error_pres = (abs(virial_pres - avg_pres)/virial_pres)*100
f_report.write("REPORT " + str(datetime.now()) + "\n" +
"-----------------------------------------" + "\n" +
"CONFIGURATION:" + "\n" +
"Interaction -> Lennard-Jones" + "\n" +
"Dimensions -> " + str(dimensions) + "\n" +
"Steps = " + str(MEASUREMENT_STEPS) + "\n" +
"Density = " + str(density) + "\n" +
"Temperature = " + str(temperature) + "\n" +
"-----------------------------------------" + "\n" +
"SIMULATION RESULTS:" + "\n" +
"Temperature (Average) = " + str(avg_temp) + "\n" +
"Second Virial Coefficient = " + str(B2) + "\n" +
"Pressure (Average) = " + str(avg_pres) + "\n" +
"Pressure (Virial) = " + str(virial_pres) + "\n" +
"Pressure Error (%) = " + str(error_pres) + "\n" +
"\n" +
#"Kinetic energy average = " + str(kinetic_energy) + "\n" +
"Potential energy average = " + str(potential_energy)+"\n"+
"Total energy average = " + str(total_energy) + "\n")
f_plot.write("{0}, {1}, {2} , {3}, {4}\n".format(density, avg_temp,
avg_pres, virial_pres, error_pres))
if interaction == 3:
if not os.path.exists("pedestrian"):
os.mkdir("pedestrian")
f_report=open("pedestrian/report_{0}d_{1}.txt".format(dimensions,
datetime.now()), "w")
f_plot=open("pedestrian/plot_{0}d.cvs".format(dimensions,
density), "a")
kinetic_energy = self.calculate_average(data, "K")
potential_energy = self.calculate_average(data, "V")
total_energy = self.calculate_average(data, "E")
avg_temp = self.calculate_average(data, "T")
avg_pres = self.calculate_average(data, "P")
B2 = 0.
virial_pres = 1.
error_pres = (abs(virial_pres - avg_pres)/virial_pres)*100
f_report.write("REPORT " + str(datetime.now()) + "\n" +
"-----------------------------------------" + "\n" +
"CONFIGURATION:" + "\n" +
"Interaction -> Pedestrian" + "\n" +
"Dimensions -> " + str(dimensions) + "\n" +
"Steps = " + str(MEASUREMENT_STEPS) + "\n" +
"Density = " + str(density) + "\n" +
"Temperature = " + str(temperature) + "\n" +
"-----------------------------------------" + "\n" +
"SIMULATION RESULTS:" + "\n" +
"Temperature (Average) = " + str(avg_temp) + "\n" +
"Second Virial Coefficient = " + str(B2) + "\n" +
"Pressure (Average) = " + str(avg_pres) + "\n" +
"Pressure (Virial) = " + str(virial_pres) + "\n" +
"Pressure Error (%) = " + str(error_pres) + "\n" +
"\n" +
"Kinetic energy average = " + str(kinetic_energy) + "\n" +
"Potential energy average = " + str(potential_energy)+"\n"+
"Total energy average = " + str(total_energy) + "\n")
f_plot.write("{0}, {1}, {2} , {3}, {4}\n".format(density, avg_temp,
avg_pres, virial_pres, error_pres))
f_report.close()
f_plot.close()
