def get_dens(self):
"""Gets estimated layer density from user.
Could make this a calc from xtal struct in future...
"""
user_alert('Layer Density:\nUsed solely to convert thicknesses in '
'ug/cm^2 to Angstroms; has no effect on the results.')
rho = get_nums('Approximate density (g/cm^3):', 25, 0)
return rho
def setup_vars(self):
"""Get element data"""
# Get element data from tables or calculation
# Electron shell e.g. K, L1, M1, N1
self.shell = self.get_shell()
with open('atomic_data.txt', 'r') as data_file:
for row in data_file:
data = row.split("\t")
if int(data[0]) == 0:
cols = data
if self.z == int(data[0]):
# Element Mass
self.mass = float(data[cols.index('Mass')])
edge = float(data[cols.index(self.shell)])
# Absorption Edge [KeV]
self.edge = edge if edge > 0.0 else 50000.0
# Coster-Kronig Coefficients
# self.ck = float(
# data[cols.index(get_options('ck (c12, c13, c23):',
# ('c12', 'c13', 'c23'),
# casesen = 'Lower'
# ))])
xray = float(data[cols.index(self.line)])
# X-Ray Emmision Line Energy [KeV]
if xray > 0.0:
self.xray = xray
else:
50000.0
user_alert('X-Ray emmision line not valid for'
'element %s\n X-Ray energy set to 50MeV.'
'\nPlease select another line to prevent'
'anomalous calculations!' %self.name)
# Fluorescence Yields
self.omega = self.get_omega()
# Number of electrons in the ionized shell.
self.znl = self.get_znl()
# JUMP Ratios
self.rjump = self.get_rjump()
# EFFective Fluorescence YieLD
self.effyld = self.get_effyld()
# TRaNSition PROBability of line after shell ionization
self.trnsprob = self.get_trnsprob()
def user_input(self, volt):
z, name = get_options('Please enter Element Symbol:',
'els', count=True)
# make sure the selected line is valid
while True:
line = get_options('Please enter Element X-Ray Line '
'(Ka, Lg2, etc.):', 'lines')
xray = get_data(z, line)
if xray > 0:
break
user_alert('Invalid line for this element; try again:')
opt = self.get_opt()
if volt is None:
volt = get_nums('Accelerating voltage for this element?:',
50, 0)
return name, line, z, volt, opt
def Mac(el1, el2):
"""Calculation of Mass the Absorption Coefficient of an impinging X-Ray
from el1 on el2.
This calc needs to be checked. See above refs"""
if el1.z == 5 and el2.z == 40:
""" B xray interacting with Zr ??? weird"""
xmu = 8270.0
iflag = 2
ie = ""
cutoff = 0
xray = el1.xray
z = el2.z
mass = el2.mass
# calculate 'c' parameter
if xray > get_data(z, 'K'):
if z < 6:
c = -2.87536e-4 + 1.808599e-3 * z
else:
c = (5.253e-3 +
1.33257e-3 * z +
-7.5937e-5 * z**2 +
1.69357e-6 * z**3 +
-1.3975e-8 * z**4)
elif xray < get_data(z, 'L3'):
c = (-9.24e-5 +
1.41478e-4 * z +
-5.24999e-6 * z**2 +
9.85296e-8 * z**3 +
-9.07306e-10 * z**4 +
3.19254e-12 * z**5)
if xray > get_data(z, 'L1'):
c = c
elif xray > get_data(z, 'L2'):
c = c * 0.858
else:
c = c*(0.8933 - z*8.29e-3 + z**2*6.38e-5)
elif xray > get_data(z, 'M1'):
if z < 30:
c = (1.889757e-2 +
-1.8517159e-3 * z +
6.9602789e-5 * z**2 +
-1.1641145e-6 * z**3 +
7.2773258e-9 * z**4)
else:
c = (3.0039e-3 +
-1.73663566e-4 * z +
4.0424792e-6 * z**2 +
-4.0585911e-8 * z**3 +
1.497763e-10 * z**4)
elif xray > get_data(z, 'M5'):
c1 = (7.7708e-5 +
-7.83544e-6 * z +
2.209365e-7 * z**2 +
-1.29086e-9 * z**3)
c2 = (1.406 +
0.0162 * z +
-6.561e-4 * z**2 +
4.865e-6 * z**3)
c3 = (0.584 +
0.01955 * z +
-1.285e-4 * z**2)
c4 = (1.082 +
1.366e-3 * z)
c5 = (1.6442 +
-0.0480 * z +
4.0664e-4 * z**2)
if xray > get_data(z, 'M2'):
c = c1*c2*c3
elif xray > get_data(z, 'M3'):
c = c1*c2*c4
elif xray > get_data(z, 'M4'):
c = c1*c2*0.95
else: # M5
ie = 'M5'
c = c1*c2*c5
else:
c = 1.08*(4.3156e-3 +
-1.4653e-4 * z +
1.707073e-6 * z**2 +
-6.69827e-9 * z**3)
if xray < get_data(z, 'N1'):
cutoff = ((0.252*z - 31.1812)*z + 1042.)/1000.0
ie = 'N1'
# calculate 'n' parameter
if xray > get_data(z, 'K'):
if z < 6:
n = (3.34745 +
0.02652873 * z +
-0.01273815 * z**2)
else:
n = (3.112 +
-0.0121 * z)
elif xray > get_data(z, 'L3'):
n = (2.7575 +
1.889e-3 * z +
-4.982e-5 * z**2)
elif xray > get_data(z, 'M1'):
n = (0.5385 +
0.084597 * z +
-1.08246e-3 * z**2 +
4.4509e-6 * z**3)
elif xray > get_data(z, 'M5'):
n = 3.0 - 0.004*z
else:
n = 0.3736 + 0.02401*z
# calculate 'a' parameter
if xray > get_data(z, 'K'):
if z < 6:
a = (24.4545 +
155.6055 * z +
-14.15422 * z**2)
else:
a = (47.0 * z +
6.52 * z**2 +
-0.152624 * z**3)
elif xray > get_data(z, 'L3'):
a = (17.8096 * z +
0.067429 * z**2 +
0.01253775 * z**3 +
-1.16286e-4 * z**4)
elif xray > get_data(z, 'M1'):
a = (10.2575657 * z +
-0.822863477 * z**2 +
2.63199611e-2 * z**3 +
-1.8641019e-4 * z**4)
elif xray > get_data(z, 'M5'):
a = (4.62 * z +
-0.04 * z**2)
else:
a = (19.64 * z +
-0.61239 * z**2 +
5.39309e-3 * z**3)
# calculate 'b' parameter
if xray > get_data(z, 'K'):
if z < 6:
b = -103. + 18.2*z
else:
b = 0.
elif xray > get_data(z, 'L3'):
b = 0.
elif xray > get_data(z, 'M1'):
if z < 61:
b = (5.654 * z +
-0.536839169 * z**2 +
0.018972278 * z**3 +
-1.683474e-4 * z**4)
else:
b = (-1232.4022 * z +
51.114164 * z**2 +
-0.699473097 * z**3 +
3.1779619e-3 * z**4)
elif xray > get_data(z, 'M5'):
b = (2.51 +
(-0.052) * z +
3.78e-4 * z**2) * get_data(z, 'M4') * 1000.
else:
b = -113. + 4.5*z
if xray > get_data(z, 'N1'):
qq = (-xray*1000.+b)/a
if qq > 88.:
qq = 88.
elif qq < -88.:
qq = -88.
xmu = c * z**4 / mass * ((12.397 / xray)**n) * (1. - np.exp(qq))
if xmu < 0.0:
mess = '!!! negative mac !!!'
else:
xmu = (((12.397 / xray)**n) * c * z**4 / mass * (xray - cutoff) /
(1.08 * get_data(z, 'N1')))
if xray < 1.1 * cutoff:
mess = '!!! Ec<1.1xcutoff !!!'
elif xray - cutoff < 0.02 and xray - cutoff > -0.005:
mess = '!!! close to edge !!!'
else:
mess = 'Good!!'
if ie == 'M5':
mess += '!!!M4>Ec>M5 edge & Zab<70!!!'
if el2.mass >= 70:
mess = 'Good!!'
if ie == 'N1':
mess += '!!! Ec below M5 edge !!!'
if xmu < 0.0 and ie == 'N1':
mess = '!!!neg. mac & Ec<M5edge!!!'
user_alert(mess + '\nemiter=%s %s; absorber=%s; mu=%.4g'
% (el1.name, el1.line, el2.name, xmu))
if xmu <= 0.0:
xmu1 = xmu
xmu = get_nums('MAC is negative; Enter a value for this MAC :')
user_alert('emiter=%s %s; absorber=%s;'
'mu changed from %.4g to %.4g'
% (el1.name, el1.line, el2.name, xmu1, xmu))
return xmu
