def get_density_profiles(mainpath, desired_list):
#determine the location of the period
datalist = []
path_maindensity = os.path.join(mainpath, 'density.dat')
data = np.loadtxt(path_maindensity)
fAmin = np.min(data[:, 1])
cs = CubicSpline(data[:, 0], data[:, 1] - fAmin)
x = np.linspace(np.min(data[:, 0]), np.max(data[:, 0]), 1000)
roots = cs.roots()
loc = np.where((roots > np.min(data[:, 0]))
& (roots < np.max(data[:, 0])))[0]
domain_min = np.min(roots[loc[1]])
domain_max = np.max(roots[loc[3]])
loc = np.where((data[:, 0] > domain_min) & (data[:, 0] < domain_max))[0]
data_domain = data[loc, :]
data_domain[:, 0] = data_domain[:, 0] - np.min(data_domain[:, 0])
cs = CubicSpline(data_domain[:, 0] / np.max(data_domain[:, 0]),
data_domain[:, 1])
integral = 1 #cs.integrate(0,1)
x = np.linspace(0, 1, 10000)
y = cs(x) / integral
datalist.append(np.vstack((x, y)).transpose())
path_data = os.path.join(mainpath, 'density_chain0.dat')
all_data = np.loadtxt(path_data)
loc = np.where((all_data[:, 0] > domain_min)
& (all_data[:, 0] < domain_max))[0]
data = all_data[loc, :]
data[:, 0] = data[:, 0] - np.min(data[:, 0])
shape = np.shape(data)
for i in range(1, shape[1]):
if i in desired_list:
cs = CubicSpline(data[:, 0] / np.max(data[:, 0]), data[:, i])
integral = cs.integrate(0, 1)
x = np.linspace(0, 1, 10000)
y = cs(x) / integral
datalist.append(np.vstack((x, y)).transpose())
return datalist
color = ['tab:blue','tab:orange','tab:red','tab:olive','tab:brown']
path = '/home/tquah/Projects/positions/backboneposition_LAM_lowchi/Bottlebrush/density_chain0.dat'
data = np.loadtxt(path)
shape = np.shape(data)
plt.close('all')
plt.figure()
for i in range(1,shape[1]):
if i<shape[1]-2:
cs = CubicSpline(data[:,0]/np.max(data[:,0]),data[:,i])
integral = cs.integrate(0,1)
x = np.linspace(0,1,1000)
y = cs(x)/integral
plt.plot(x,y,label = str(i))
# plt.legend()
path = '/home/tquah/Projects/positions/backboneposition_LAM_lowchi/linear/density_chain0.dat'
data = np.loadtxt(path)
shape = np.shape(data)
# plt.close('all')
# plt.figure()
for i in range(1,shape[1]):
if i<shape[1]:
# print(integrand1(E1))
# plt.plot(E1,integrand1(E1),color='r')
# plt.scatter(E1,a0_final*np.exp(-11.604*E1/T)*E1,alpha=.01,c='b')
# plt.yscale('log')
# plt.show()
# intg = integrate.romberg(integrand1,min(energyList),max(energyList),divmax=40)
# intg1 = integrate.quad(integrand1,min(energyList),max(energyList),limit=200)
intg2 = 0
for ind,elem in enumerate(E1):
if ind < len(E1):
intg2 += a0_final[ind]*np.exp(-11.604*E1[ind]/T)*E1[ind]*dE
intg3 = integrand1.integrate(min(E1),max(E1))
# intg4 = integrate.cumtrapz(a0_final*np.exp(-11.604*E1/T)*E1,E1)[-1]
# intg5 = integrate.trapz(a0_final*np.exp(-11.604*E1/T)*E1,E1)
intg6 = integrate.simps(a0_final*np.exp(-11.604*E1/T)*E1,E1)
intg7 = np.trapz(a0_final*np.exp(-11.604*E1/T)*E1,E1)
# rate = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg
# rate1 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg1[0]
rate2 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg2
rate3 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg3
# rate4 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg4
# rate5 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg5
rate6 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg6
rate7 = rxnRateCONST * mu**(-.5) * T**(-1.5) * intg7
class Density:
alt_models = {
'photon': 'fit_models/Alt_photon_pol3_model.txt',
'muon': 'fit_models/Alt_muon_pol3_model.txt'
}
eff_photon = 0.0001
eff_muon = 0.5
__xmin__ = 1e-24 # km
__xmax__ = 1e4 # km
def __init__(self):
self.alt = R.TF1('Alt_muon', Alt.fitexpr, Density.__xmin__,
Density.__xmax__)
def set_shower(self, mass_number, energy_eV, altitude_km):
self.A = mass_number
self.E = energy_eV
self.H = altitude_km
x = np.logspace(np.log10(Density.__xmin__), np.log10(Density.__xmax__),
10000)
for i in range(4):
self.alt.SetParameter(
i,
Coefficients.get(i, Density.alt_models['photon'], self.A,
self.E, self.H))
y1 = np.zeros(x.size)
y2 = np.zeros(x.size)
for i in range(x.size):
y1[i] = self.alt.Eval(x[i])
y2[i] = x[i] * y1[i]
y2 = 2. * np.pi * 1e10 * y2
self.photon = CubicSpline(x, y1)
self.photon2 = CubicSpline(x, y2)
y3 = np.zeros(x.size)
for i in range(x.size):
y3[i] = self.photon2.integrate(0., x[i])
self.N_photons = y3[-1]
y3 = y3 / y3[-1]
cut = -1
while (y3[cut] == 1.):
cut -= 1
cut += 2
self.photon_cdf = CubicSpline(y3[:cut], x[:cut])
for i in range(4):
self.alt.SetParameter(
i,
Coefficients.get(i, Density.alt_models['muon'], self.A, self.E,
self.H))
y1 = np.zeros(x.size)
y2 = np.zeros(x.size)
for i in range(x.size):
y1[i] = self.alt.Eval(x[i])
y2[i] = x[i] * y1[i]
y2 = 2. * np.pi * 1e10 * y2
self.muon = CubicSpline(x, y1)
self.muon2 = CubicSpline(x, y2)
y3 = np.zeros(x.size)
for i in range(x.size):
y3[i] = self.muon2.integrate(0., x[i])
self.N_muons = y3[-1]
y3 = y3 / y3[-1]
cut = -1
while (y3[cut] == 1.):
cut -= 1
cut += 2
self.muon_cdf = CubicSpline(y3[:cut], x[:cut])
def densm(alt, d0, xm, tz, zn3, tn3, tgn3, zn2, tn2, tgn2, gsurf, re):
rgas = 831.4
densm_tmp = d0
tz_tmp = tz
mn3, mn2 = len(zn3), len(zn2)
if alt > zn2[0]:
if xm == 0:
densm_tmp = tz
return densm_tmp, tz_tmp
else:
densm_tmp = d0
return densm_tmp, tz_tmp
# stratosphere/mesosphere temperature
if alt > zn2[mn2 - 1]:
z = alt
else:
z = zn2[mn2 - 1]
mn = mn2
xs, ys = [np.zeros(mn) for i in range(2)]
z1, z2 = zn2[0], zn2[mn - 1]
t1, t2 = tn2[0], tn2[mn - 1]
zg, zgdif = zeta(z, z1, re), zeta(z2, z1, re)
# set up spline nodes
for k in range(mn):
xs[k] = zeta(zn2[k], z1, re) / zgdif
ys[k] = 1 / tn2[k]
yd1 = -tgn2[0] / t1**2 * zgdif
yd2 = -tgn2[1] / t2**2 * zgdif * ((re + z2) / (re + z1))**2
# calculate spline coefficients
cs = CubicSpline(xs, ys, bc_type=((1, yd1), (1, yd2)))
x = zg / zgdif
y = cs(x)
# temperature at altitude
tz_tmp = 1 / y
if xm != 0:
# calaculate stratosphere/mesospehere density
glb = gsurf / (1 + z1 / re)**2
gamm = xm * glb * zgdif / rgas
# Integrate temperature profile
yi = cs.integrate(xs[0], x)
expl = gamm * yi
if expl > 50:
expl = 50
# Density at altitude
densm_tmp = densm_tmp * (t1 / tz_tmp) * np.exp(-expl)
if alt > zn3[0]:
if xm == 0:
densm_tmp = tz_tmp
return densm_tmp, tz_tmp
else:
return densm_tmp, tz_tmp
# troposhere/stratosphere temperature
z = alt
mn = mn3
xs, ys = [np.zeros(mn) for i in range(2)]
z1, z2 = zn3[0], zn3[mn - 1]
t1, t2 = tn3[0], tn3[mn - 1]
zg, zgdif = zeta(z, z1, re), zeta(z2, z1, re)
# set up spline nodes
for k in range(mn):
xs[k] = zeta(zn3[k], z1, re) / zgdif
ys[k] = 1 / tn3[k]
yd1 = -tgn3[0] / t1**2 * zgdif
yd2 = -tgn3[1] / t2**2 * zgdif * ((re + z2) / (re + z1))**2
# calculate spline coefficients
cs = CubicSpline(xs, ys, bc_type=((1, yd1), (1, yd2)))
x = zg / zgdif
y = cs(x)
# temperature at altitude
tz_tmp = 1 / y
if xm != 0:
# calaculate tropospheric / stratosphere density
glb = gsurf / (1 + z1 / re)**2
gamm = xm * glb * zgdif / rgas
# Integrate temperature profile
yi = cs.integrate(xs[0], x)
expl = gamm * yi
if expl > 50: expl = 50
# Density at altitude
densm_tmp = densm_tmp * (t1 / tz_tmp) * np.exp(-expl)
if xm == 0:
densm_tmp = tz_tmp
return densm_tmp, tz_tmp
else:
return densm_tmp, tz_tmp
def densu(alt, dlb, tinf, tlb, xm, alpha, tz, zlb, s2, zn1, tn1, tgn1, gsurf,
re):
'''
Calculate Temperature and Density Profiles for MSIS models
'''
rgas = 831.4
densu_tmp = 1
mn1 = len(zn1)
# joining altitudes of Bates and spline
za = zn1[0]
if alt > za:
z = alt
else:
z = za
# geopotential altitude difference from ZLB
zg2 = zeta(z, zlb, re)
# Bates temperature
tt = tinf - (tinf - tlb) * np.exp(-s2 * zg2)
ta = tz = tt
densu_tmp = tz_tmp = tz
if alt < za:
# calculate temperature below ZA
# temperature gradient at ZA from Bates profile
dta = (tinf - ta) * s2 * ((re + zlb) / (re + za))**2
tgn1[0], tn1[0] = dta, ta
if alt > zn1[mn1 - 1]:
z = alt
else:
z = zn1[mn1 - 1]
mn = mn1
xs, ys = [np.zeros(mn) for i in range(2)]
z1, z2 = zn1[0], zn1[mn - 1]
t1, t2 = tn1[0], tn1[mn - 1]
# geopotental difference from z1
zg, zgdif = zeta(z, z1, re), zeta(z2, z1, re)
# set up spline nodes
for k in range(mn):
xs[k] = zeta(zn1[k], z1, re) / zgdif
ys[k] = 1 / tn1[k]
# end node derivatives
yd1 = -tgn1[0] / t1**2 * zgdif
yd2 = -tgn1[1] / t2**2 * zgdif * ((re + z2) / (re + z1))**2
# calculate spline coefficients
cs = CubicSpline(xs, ys, bc_type=((1, yd1), (1, yd2)))
x = zg / zgdif
y = cs(x)
# temperature at altitude
tz_tmp = 1 / y
densu_tmp = tz_tmp
if xm == 0: return densu_tmp, tz_tmp
# calculate density above za
glb = gsurf / (1 + zlb / re)**2
gamma = xm * glb / (s2 * rgas * tinf)
expl = np.exp(-s2 * gamma * zg2)
if expl > 50: expl = 50
if tt <= 0: expl = 50
# density at altitude
densa = dlb * (tlb / tt)**(1 + alpha + gamma) * expl
densu_tmp = densa
if alt >= za: return densu_tmp, tz_tmp
# calculate density below za
glb = gsurf / (1 + z1 / re)**2
gamm = xm * glb * zgdif / rgas
# integrate spline temperatures
yi = cs.integrate(xs[0], x)
expl = gamm * yi
if expl > 50: expl = 50
if tz_tmp <= 0: expl = 50
# density at altitude
densu_tmp = densu_tmp * (t1 / tz_tmp)**(1 + alpha) * np.exp(-expl)
return densu_tmp, tz_tmp
#!/usr/bin/env python3
from scipy.interpolate import CubicSpline
import numpy as np
x = np.arange(21) * np.pi / 5.0
y = np.sin(x)
y[0] = 0.01
y[-1] = y[0]
xq = np.linspace(min(x), max(x), 101)
cs_not_a_knot = CubicSpline(x, y, bc_type='not-a-knot')
cs_clamped = CubicSpline(x, y, bc_type='clamped')
cs_natural = CubicSpline(x, y, bc_type='natural')
cs_periodic = CubicSpline(x, y, bc_type='periodic')
yq_knot = cs_not_a_knot(xq)
yq_clamped = cs_clamped(xq)
yq_natural = cs_natural(xq)
yq_period = cs_periodic(xq)
ofl = open('cubicSplineInterpolation.txt', 'w')
for i in range(len(xq)):
ofl.write("%e, %e, %e, %e, %e\n" %
(xq[i], yq_knot[i], yq_clamped[i], yq_natural[i], yq_period[i]))
ofl.close()
print(cs_not_a_knot.integrate(0, 1))
print(cs_natural.integrate(max(x), 0))
print(cs_clamped.integrate(4.08, 6))
print(cs_periodic.integrate(3.99, max(x)))
print(cs_periodic.integrate(3.007729, 2.541008))
