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 get_volts(self):
"""Get accelerating voltages"""
volts = []
while True:
volts.append(get_nums('Accelerating Voltage [KeV]?:', 60, 0))
reply = yes_no('Add another voltage?(Y/N):')
if reply is False:
break
return volts
def fixlayer(self):
"""Get fixed values for thickness and composition"""
# Get Thickness (layers not sub - sub has "infinite" thickness)
if not self.fix:
self.thick = 0.0
return False
self.units = get_options('+Enter fixed thicknesses in Angstroms (a)'
'or ug/cm**2 (u), (def=a):', ('A', 'U'), 'A')
if self.units == 'A':
label = 'Angstroms'
if self.units == 'U':
label = 'ug/cm**2'
self.thick = get_nums('Fixed thickness [%s]:' % label,
10e5, 0, 0)
self.thick = self.thick/1.0e6 # g/cm**2
if self.units == 'A':
self.thick = self.thick*self.rho/100. # cm
# Get Composition
if len(self.els) == 1:
# fraction in layer is one if only 1 element
self.els[0] = 1.0
else:
reply = get_options('Enter the fixed composition %s by '
'weight fractions (w) or by atomic '
'formula (def=a) :', ('W', 'A'), 'A')
for i in range(0, len(self.els)):
if reply == 'W':
for j in range(0, self.els):
self.els[j].wtfrac = get_nums(
'Weight fraction concentration'
'of element %s:' % self.els[j], 1.0, 0.0,
default=1, zeroval=1.0e-9)
elif reply == 'A':
self.els[j].atform = get_nums(
'Atomic Formula of element %s '
'(i.e 1 for Si in SiO2):' % self.els[j], 100)
if reply == 'A':
wtfracs = wtfract([el.name for el in self.els],
[el.atform for el in self.els])
for x, _ in enumerate(wtfracs):
self.els[x].wtfrac = wtfracs[x]
def new_std(self):
how = get_options('Input %s standard composition in wt. %% (w) '
'or atomic formula(a) (def=a):' % self.name,
('W', 'A'), 'A')
while True:
count = 0
while True:
count += 1
print "Element %d in %s" % (count, self.name)
name = get_options('Element Symbol:', 'els')
line = get_options('Lowest Excited X-Ray Line:', 'lines')
self.els.append(AtomicElement(name, line))
if how.upper() == 'W':
self.els[-1].wtfract = get_nums('Weight Fraction:', 1)
else:
self.els[-1].atform = get_nums('Atomic Formula:', 100)
print ("Entered so far: %s"
% ' '.join([el.name for el in self.els]))
if not yes_no("Add another element? (Y/N)"):
break
if how.upper() == 'A':
wtfracs = wtfract(self.els, [el.atform for el in self.els])
for x, _ in enumerate(wtfracs):
self.els[x].wtfrac = wtfracs[x]
print ('%s compound standard: els, weight fractions:'
% self.name)
print "\t".join([self.els[x].name for x
in range(0, len(self.els))])
print "\t".join([str(round(el.wtfrac, 5)) for el in self.els])
if yes_no("Is this correct?\n(restarts if no)(Y/N):", False):
break
data = ""
for i in range(0, len(self.els)):
data += "\t%s\t%s\t%s" % (self.els[i].name,
self.els[i].line,
self.els[i].wtfrac)
towrite = "%s%s\n" % (self.name, data)
with open('empastds.txt', 'a') as myfile:
myfile.write(towrite)
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 macstd(self, el1, el2, macchang, caller):
"""controls calculation of mass absorption coefficients
for compound standards."""
xmu = mac(el1, el2)
if macchang == 'Y':
mess = ('+MAC for %s %s in %s is %.4g\nChange to:(def.=current)'
% (el1.name, el1.line, el2.name, xmu))
if caller == 'B':
mess = mess + 'XRF, Compd. Stnd.:'
if caller == 'C':
mess = mess + 'Compound Standard:'
if caller == 'P':
mess = mess + 'Pure Element Stnd:'
if caller == 'F':
mess = mess + 'Addl. XRF, Sample:'
xmu = get_nums(mess, 10e10, 0, xmu)
print '+Changed to %.4g' % xmu
return xmu
def get_valences(self):
"""input of valences when one element is analyzed by stoichiometry
May want to make this a selection in gui version...
"""
for lar, el in self:
if el.opt == 'S':
lar.stoich = el
else:
lar.stoich = 0
for lar, el in self:
i = self.layers.index(lar)
if lar.fix:
continue
if lar.stoich == 0:
continue
if el.valence == -1:
el.valence = get_nums('Enter valence for layer %d element %s:'
% (i, el.name), 20, 0)
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
def get_toa(self):
"""get take-off angle from user"""
return get_nums('Enter take-off angle (default=40 degrees):',
90, 0, 40)
