def xray_scattering_lengths(self, condition, energy=8.048):
vh, vt = self.conditions[condition]
h_density = calculate_density(self.hf, vh)
t_density = calculate_density(self.tf, vt)
h_sld = pt.xray_sld(self.hf, density=h_density, energy=energy)
t_sld = pt.xray_sld(self.tf, density=t_density, energy=energy)
h_scatlen = complex(*h_sld[0:2]) * vh / 1e6
t_scatlen = complex(*t_sld[0:2]) * vt / 1e6
return h_scatlen, t_scatlen
def calculate(self):
try:
formula = pt.formula(self.ui.chemical_formula.text(), )
except (pyparsing.ParseException, TypeError, ValueError):
return
density = self.ui.mass_density.value()
molecular_volume = self.ui.molecular_volume.value()
neutron_wavelength = self.ui.neutron_wavelength.value()
xray_energy = self.ui.xray_energy.value()
if self.ui.use_volume.isChecked():
density = formula.molecular_mass / formula.volume(
a=molecular_volume, b=1, c=1)
self.ui.mass_density.setValue(density)
elif self.ui.use_density.isChecked():
volume = formula.mass / density / \
pt.constants.avogadro_number * 1e24
self.ui.molecular_volume.setValue(volume)
real, imag, mu = pt.neutron_sld(formula,
density=density,
wavelength=neutron_wavelength)
self.ui.neutron_SLD.setText('%.6g' % real + ' + ' + '%.6g' % imag +
'j')
real, imag = pt.xray_sld(formula, density=density, energy=xray_energy)
self.ui.xray_SLD.setText('%.6g' % real + ' + ' + '%.6g' % imag + 'j')
def test():
from periodictable.constants import avogadro_number
# Beta casein results checked against Duncan McGillivray's spreadsheet
# beta casein 23561.9 23880.9 30872.9 1.27 12614 11.55 1.68 2.75
s = Sequence("beta casein", beta_casein)
assert abs(s.Dmass-23880.9) < 0.1
#print "density",s.mass/avogadro_number/s.cell_volume*1e24
assert abs(s.mass/avogadro_number/s.cell_volume*1e24 - 1.267) < 0.01
assert abs(s.Dsld-2.75) < 0.01
# Check that X-ray sld is independent of isotope
H = isotope_substitution(s.formula, pt.T, pt.H)
D = isotope_substitution(s.formula, pt.T, pt.D)
Hsld, Dsld = pt.xray_sld(H, wavelength=1.54), pt.xray_sld(D, wavelength=1.54)
#print Hsld, Dsld
assert abs(Hsld[0]-Dsld[0]) < 1e-10
def test():
from periodictable.constants import avogadro_number
# Beta casein results checked against Duncan McGillivray's spreadsheet
# beta casein 23561.9 23880.9 30872.9 1.27 12614 11.55 1.68 2.75
s = Sequence("beta casein", beta_casein)
assert abs(s.D.mass-23880.9) < 0.1
#print "density",s.mass/avogadro_number/s.cell_volume*1e24
assert abs(s.natural.mass/avogadro_number/s.cell_volume*1e24 - 1.267) < 0.01
assert abs(s.D_sld-2.75) < 0.01
# Check that X-ray sld is independent of isotope
H = isotope_substitution(s.formula, pt.T, pt.H)
D = isotope_substitution(s.formula, pt.T, pt.D)
H_sld, D_sld = pt.xray_sld(H,wavelength=1.54), pt.xray_sld(D,wavelength=1.54)
#print H_sld, D_sld
assert abs(H_sld[0] - D_sld[0]) < 1e-10
def get_iron_oxide(wavelength):
oxide = pt.formula("Fe2O3")
dens = 5.24
rho, mu = pt.xray_sld(oxide,
density=dens,
wavelength=wavelength / angstrom)
return ba.MaterialBySLD("Fe203", rho * 1e-6, mu * 1e-6)
def get_si(wavelength):
si = pt.formula("Si")
dens = pt.Si.density
rho, mu = pt.xray_sld(si,
density=pt.Si.density,
wavelength=wavelength / angstrom)
return ba.MaterialBySLD("si", rho * 1e-6, mu * 1e-6)
def get_iron_oxide(self, wavelength):
oxide = pt.formula("Fe2O3")
dens = 5.24
rho, mu = pt.xray_sld(oxide, density=dens, wavelength=wavelength / angstrom)
rho *= 1e-6
mu *= 1e-6
print("MaterialLibrary > wavelength:{0} formula:{1} density:{2} rho:{3} mu:{4}".format(wavelength, oxide,
dens, rho, mu))
return ba.MaterialBySLD("Fe203", rho, mu)
def get_si(self, wavelength):
si = pt.formula("Si")
dens = pt.Si.density
rho, mu = pt.xray_sld(si, density=pt.Si.density, wavelength=wavelength / angstrom)
rho *= 1e-6
mu *= 1e-6
print("MaterialLibrary > wavelength:{0} formula:{1} density:{2} rho:{3} mu:{4}".format(wavelength, si,
dens, rho, mu))
return ba.MaterialBySLD("si", rho, mu)
def calculate(self):
try:
formula = pt.formula(self.ui.chemical_formula.text())
except (pyparsing.ParseException, TypeError, ValueError, KeyError):
# a problem was experience during parsing of the formula.
return
if not len(formula.atoms):
return
density = self.ui.mass_density.value()
molecular_volume = self.ui.molecular_volume.value()
neutron_wavelength = self.ui.neutron_wavelength.value()
xray_energy = self.ui.xray_energy.value()
if self.ui.use_volume.isChecked():
density = formula.molecular_mass / formula.volume(
a=molecular_volume, b=1, c=1)
self.ui.mass_density.setValue(density)
elif self.ui.use_density.isChecked():
try:
volume = (formula.mass / density /
pt.constants.avogadro_number * 1e24)
except ZeroDivisionError:
volume = np.nan
self.ui.molecular_volume.setValue(volume)
try:
real, imag, mu = pt.neutron_sld(formula,
density=density,
wavelength=neutron_wavelength)
self.ui.neutron_SLD.setText("%.6g" % real + " + " + "%.6g" % imag +
"j")
except Exception:
self.ui.neutron_SLD.setText("NaN")
try:
real, imag = pt.xray_sld(formula,
density=density,
energy=xray_energy)
self.ui.xray_SLD.setText("%.6g" % real + " + " + "%.6g" % imag +
"j")
except Exception:
self.ui.xray_SLD.setText("NaN")
def fasta_table():
rows = []
rows += [v for k, v in sorted(AMINO_ACID_CODES.items())]
rows += [v for k, v in sorted(NUCLEIC_ACID_COMPONENTS.items())]
rows += [Sequence("beta casein", beta_casein)]
print("%20s %7s %7s %7s %5s %5s %5s %5s %5s %5s" %
("name", "M(H2O)", "M(D2O)", "volume", "den", "#el", "xray", "nH2O",
"nD2O", "%D2O match"))
for v in rows:
protons = sum(num * el.number for el, num in v.formula.atoms.items())
electrons = protons - v.charge
Xsld = pt.xray_sld(v.formula, wavelength=pt.Cu.K_alpha)
print("%20s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f" %
(v.name, v.Hmass, v.Dmass, v.cell_volume, v.formula.density,
electrons, Xsld[0], v.Hsld, v.Dsld, v.D2Omatch))
def fasta_table():
rows = []
rows += [v for k, v in sorted(AMINO_ACID_CODES.items())]
rows += [v for k, v in sorted(NUCLEIC_ACID_COMPONENTS.items())]
rows += [Sequence("beta casein", beta_casein)]
print("%20s %7s %7s %7s %5s %5s %5s %5s %5s %5s"
% ("name", "M(H2O)", "M(D2O)", "volume",
"den", "#el", "xray", "nH2O", "nD2O", "%D2O match"))
for v in rows:
protons = sum(num*el.number for el, num in v.formula.atoms.items())
electrons = protons - v.charge
Xsld = pt.xray_sld(v.formula, wavelength=pt.Cu.K_alpha)
print("%20s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f"%(
v.name, v.Hmass, v.Dmass, v.cell_volume, v.formula.density,
electrons, Xsld[0], v.Hsld, v.Dsld, v.D2Omatch))
def calculate(self):
try:
formula = pt.formula(self.ui.chemical_formula.text(),)
except (pyparsing.ParseException, TypeError, ValueError):
return
density = self.ui.mass_density.value()
molecular_volume = self.ui.molecular_volume.value()
neutron_wavelength = self.ui.neutron_wavelength.value()
xray_energy = self.ui.xray_energy.value()
if self.ui.use_volume.isChecked():
density = formula.molecular_mass / formula.volume(
a=molecular_volume,
b=1,
c=1)
self.ui.mass_density.setValue(density)
elif self.ui.use_density.isChecked():
volume = formula.mass / density / \
pt.constants.avogadro_number * 1e24
self.ui.molecular_volume.setValue(volume)
real, imag, mu = pt.neutron_sld(formula,
density=density,
wavelength=neutron_wavelength)
self.ui.neutron_SLD.setText(
'%.6g' %
real +
' + ' +
'%.6g' %
imag +
'j')
real, imag = pt.xray_sld(formula,
density=density,
energy=xray_energy)
self.ui.xray_SLD.setText('%.6g' % real + ' + ' + '%.6g' % imag + 'j')
def cgi_call():
form = cgi.FieldStorage()
#print >>sys.stderr, form
#print >>sys.stderr, "sample",form.getfirst('sample')
#print >>sys.stderr, "mass",form.getfirst('mass')
# Parse inputs
errors = {};
calculate = form.getfirst('calculate','all')
if calculate not in ('scattering','activation','all'):
errors['calculate'] = "calculate should be one of 'scattering', 'activation' or 'all'"
try: chem = formula(form.getfirst('sample'))
except: errors['sample'] = error()
try: fluence = float(form.getfirst('flux',100000))
except: errors['flux'] = error()
try: fast_ratio = float(form.getfirst('fast','0'))
except: errors['fast'] = error()
try: Cd_ratio = float(form.getfirst('Cd','0'))
except: errors['Cd'] = error()
try: exposure = parse_hours(form.getfirst('exposure','1'))
except: errors['exposure'] = error()
try:
mass_str = form.getfirst('mass','1')
if mass_str.endswith('kg'):
mass = 1000*float(mass_str[:-2])
elif mass_str.endswith('mg'):
mass = 0.001*float(mass_str[:-2])
elif mass_str.endswith('ug'):
mass = 1e-6*float(mass_str[:-2])
elif mass_str.endswith('g'):
mass = float(mass_str[:-1])
else:
mass = float(mass_str)
except: errors['mass'] = error()
try: density_type,density_value = parse_density(form.getfirst('density','0'))
except: errors['density'] = error()
try:
#print >>sys.stderr,form.getlist('rest[]')
rest_times = [parse_rest(v) for v in form.getlist('rest[]')]
if not rest_times: rest_times = [0,1,24,360]
except: errors['rest'] = error()
try: decay_level = float(form.getfirst('decay','0.001'))
except: errors['decay'] = error()
try: thickness = float(form.getfirst('thickness', '1'))
except: errors['thickness'] = error()
try:
wavelength_str = form.getfirst('wavelength','1').strip()
if wavelength_str.endswith('meV'):
wavelength = nsf.neutron_wavelength(float(wavelength_str[:-3]))
elif wavelength_str.endswith('m/s'):
wavelength = nsf.neutron_wavelength_from_velocity(float(wavelength_str[:-3]))
elif wavelength_str.endswith('Ang'):
wavelength = float(wavelength_str[:-3])
else:
wavelength = float(wavelength_str)
#print >>sys.stderr,wavelength_str
except: errors['wavelength'] = error()
try:
xray_source = form.getfirst('xray','Cu Ka').strip()
if xray_source.endswith('Ka'):
xray_wavelength = elements.symbol(xray_source[:-2].strip()).K_alpha
elif xray_source.endswith('keV'):
xray_wavelength = xsf.xray_wavelength(float(xray_source[:-3]))
elif xray_source.endswith('Ang'):
xray_wavelength = float(xray_source[:-3])
elif xray_source[0].isalpha():
xray_wavelength = elements.symbol(xray_source).K_alpha
else:
xray_wavelength = float(xray_source)
#print >>sys.stderr,"xray",xray_source,xray_wavelength
except: errors['xray'] = error()
try:
abundance_source = form.getfirst('abundance','IAEA')
if abundance_source == "NIST":
abundance = activation.NIST2001_isotopic_abundance
elif abundance_source == "IAEA":
abundance = activation.IAEA1987_isotopic_abundance
else:
raise ValueError("abundance should be NIST or IAEA")
except: errors['abundance'] = error()
if errors: return {'success':False, 'error':'invalid request', 'detail':errors}
# Fill in defaults
#print >>sys.stderr,density_type,density_value,chem.density
if density_type == 'default' or density_value == 0:
# default to a density of 1
if chem.density is None: chem.density = 1
elif density_type == 'volume':
chem.density = chem.molecular_mass/density_value
elif density_type == 'natural':
# if density is given, assume it is for natural abundance
chem.natural_density = density_value
elif density_type == 'isotope':
chem.density = density_value
else:
raise ValueError("unknown density type %r"%density_type)
result = {'success': True}
result['sample'] = {
'formula': str(chem),
'mass': mass,
'density': chem.density,
'thickness': thickness,
'natural_density': chem.natural_density,
}
# Run calculations
if calculate in ('activation', 'all'):
try:
env = activation.ActivationEnvironment(fluence=fluence,fast_ratio=fast_ratio, Cd_ratio=Cd_ratio)
sample = activation.Sample(chem, mass=mass)
sample.calculate_activation(env,exposure=exposure,rest_times=rest_times,abundance=abundance)
decay_time = sample.decay_time(decay_level)
total = [0]*len(sample.rest_times)
rows = []
for el,activity_el in activation.sorted_activity(sample.activity.items()):
total = [t+a for t,a in zip(total,activity_el)]
rows.append({'isotope':el.isotope,'reaction':el.reaction,'product':el.daughter,
'halflife':el.Thalf_str,'comments':el.comments,'levels':activity_el})
result['activation'] = {
'flux': fluence,
'fast': fast_ratio,
'Cd': Cd_ratio,
'exposure': exposure,
'rest': rest_times,
'activity': rows,
'total': total,
'decay_level': decay_level,
'decay_time': decay_time,
}
#print >>sys.stderr,result
except:
result['activation'] = {"error": error()}
#nsf_sears.replace_neutron_data()
if calculate in ('scattering', 'all'):
try:
sld,xs,penetration = neutron_scattering(chem, wavelength=wavelength)
result['scattering'] = {
'neutron': {
'wavelength': wavelength,
'energy': nsf.neutron_energy(wavelength),
'velocity': nsf.VELOCITY_FACTOR/wavelength,
},
'xs': {'coh': xs[0], 'abs': xs[1], 'incoh': xs[2]},
'sld': {'real': sld[0], 'imag': sld[1], 'incoh': sld[2]},
'penetration': penetration,
'transmission': 100*exp(-thickness/penetration),
}
except:
missing = [str(el) for el in chem.atoms if not el.neutron.has_sld()]
if any(missing):
msg = "missing neutron cross sections for "+", ".join(missing)
else:
msg = error()
result['scattering'] = {'error': msg }
try:
xsld = xray_sld(chem, wavelength=xray_wavelength)
result['xray_scattering'] = {
'xray': {
'wavelength': xray_wavelength,
'energy': xsf.xray_energy(xray_wavelength),
},
'sld': {'real': xsld[0], 'imag': xsld[1]},
}
except:
result['xray_scattering'] = {'error': error()}
return result
fPt = formula("Pt")
fNiFe = formula("Ni80Fe20",density=0.8*Ni.density+0.2*Fe.density)
fFePt = formula("Fe55Pt45",density=0.55*Fe.density+0.45*Pt.density)
# Note: we have been given the Cu K-alpha SLD of the glass substrate
# but the formula itself was not provided. The common glass
# preparations below do not come close to matching the given SLD
# unless density is lowered to about 1.85. Since most glass has
# a density in [2.2, 2.5], none of these formulas can be used, and we
# will restrict ourselves to an approximate SLD provided by the grower.
#fglass = formula("SiO2",density=2.2)
#fglass = mix_by_weight('SiO2',75,'Na2O',15,'CaO',10,density=2.52)
#fglass = mix_by_weight('SiO2',73,'B2O3',10,'Na2O',8,'K2O',8,'CaO',1,density=2.2)
glass_sld = 15,0.5
# Bulk SLD
cap.rho.value, cap.irho.value = xray_sld(fPt, wavelength=Cu.K_alpha)
NiFe.rho.value, NiFe.irho.value = xray_sld(fNiFe, wavelength=Cu.K_alpha)
FePt.rho.value, FePt.irho.value = xray_sld(fFePt, wavelength=Cu.K_alpha)
seed.rho.value, seed.irho.value = xray_sld(fFePt, wavelength=Cu.K_alpha)
glass.rho.value,glass.irho_value = glass_sld
# Expected thickness/interface
Lseed.thickness.value = 15
LFePt.thickness.value = 200
LNiFe.thickness.value = 500
Lcap.thickness.value = 25
for i,L in enumerate(sample[1:-2]):
L.interface.value = 10
# Fit parameters
#probe.theta_offset.dev(0.01) # accurate to 0.01 degrees
fPt = formula("Pt")
fNiFe = formula("Ni80Fe20", density=0.8 * Ni.density + 0.2 * Fe.density)
fFePt = formula("Fe55Pt45", density=0.55 * Fe.density + 0.45 * Pt.density)
# Note: we have been given the Cu K-alpha SLD of the glass substrate
# but the formula itself was not provided. The common glass
# preparations below do not come close to matching the given SLD
# unless density is lowered to about 1.85. Since most glass has
# a density in [2.2, 2.5], none of these formulas can be used, and we
# will restrict ourselves to an approximate SLD provided by the grower.
#fglass = formula("SiO2",density=2.2)
#fglass = mix_by_weight('SiO2',75,'Na2O',15,'CaO',10,density=2.52)
#fglass = mix_by_weight('SiO2',73,'B2O3',10,'Na2O',8,'K2O',8,'CaO',1,density=2.2)
glass_sld = 15, 0.5
# Bulk SLD
cap.rho.value, cap.irho.value = xray_sld(fPt, wavelength=Cu.K_alpha)
NiFe.rho.value, NiFe.irho.value = xray_sld(fNiFe, wavelength=Cu.K_alpha)
FePt.rho.value, FePt.irho.value = xray_sld(fFePt, wavelength=Cu.K_alpha)
seed.rho.value, seed.irho.value = xray_sld(fFePt, wavelength=Cu.K_alpha)
glass.rho.value, glass.irho_value = glass_sld
# Expected thickness/interface
Lseed.thickness.value = 15
LFePt.thickness.value = 200
LNiFe.thickness.value = 500
Lcap.thickness.value = 25
for i, L in enumerate(sample[1:-2]):
L.interface.value = 10
# Fit parameters
#probe.theta_offset.dev(0.01) # accurate to 0.01 degrees