def _neutron_transmission_depth(material, wavelength):
"""
Calculate the penetration depth for a material with a given neutron
wavelength
Parameters
----------
material : pt.Formula
wavelength : float
neutron wavelength in Angstrom
"""
import periodictable as pt
return 10.0 * pt.neutron_scattering(material, wavelength=wavelength)[-1]
def test():
H, He, D, O = elements.H, elements.He, elements.D, elements.O
assert H.neutron.absorption == 0.3326
assert H.neutron.total == 82.02
assert H.neutron.incoherent == 80.26
assert H.neutron.coherent == 1.7568
assert elements.Ru[101].neutron.bp == None
assert H[1].nuclear_spin == '1/2'
assert H[2].nuclear_spin == '1'
assert not H[6].neutron.has_sld()
assert He[3].neutron.b_c_i == -1.48
assert He[3].neutron.bm_i == -5.925
Nb = elements.Nb
assert Nb.neutron.absorption == Nb[93].neutron.absorption
# Check that b_c values match abundance-weighted values
# Note: Currently they do not for match within 5% for Ar,V,Sm or Gd
for el in elements:
if not hasattr(el, 'neutron'): continue
b_c = 0
complete = True
for iso in el:
if iso.neutron != None:
if iso.neutron.b_c == None:
complete = False
else:
b_c += iso.neutron.b_c * iso.neutron.abundance / 100.
if complete and b_c != 0 and abs((b_c - el.neutron.b_c) / b_c) > 0.05:
err = abs((b_c - el.neutron.b_c) / b_c)
## Printing suppressed for the release version
#print("%2s %.3f % 7.3f % 7.3f"%(el.symbol,err,b_c,el.neutron.b_c))
# Check neutron_sld and neutron_xs against NIST calculator
# Note that we are using different tables, so a general comparison with
# NIST numbers is not possible, but ^30Si and ^18O are the same in both.
M = formula('Si[30]O[18]2', density=2.2)
sld, xs, depth = neutron_scattering(M, wavelength=4.75)
sld2 = neutron_sld(M, wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
#_summarize(M)
#_summarize(formula('O2',density=1.14))
# Alan's numbers:
assert abs(sld[0] - 3.27) < 0.01
assert abs(sld[1] - 0) < 0.01
#assert abs(xs[2] - 0.00292) < 0.00001 # TODO fix test
assert abs(xs[1] - 0.00569) < 0.00001
#assert abs(depth - 4.329) < 0.001 # TODO fix test
# Cu/Mo K-alpha = 1.89e-5 + 2.45e-7i / 1.87e-5 + 5.16e-8i
Ni, Si = elements.Ni, elements.Si
# Make sure molecular calculation corresponds to direct calculation
sld = neutron_sld('Si', density=Si.density, wavelength=4.75)
sld2 = Si.neutron.sld(wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
sld, _, _ = Si.neutron.scattering(wavelength=4.75)
sld2 = Si.neutron.sld(wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
sld, xs, depth = neutron_scattering('Si',
density=Si.density,
wavelength=4.75)
sld2, xs2, depth2 = Si.neutron.scattering(wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
assert all(abs(v - w) < 1e-10 for v, w in zip(xs, xs2))
assert abs(depth - depth2) < 1e-14
# incoherent cross sections for Ni[62] used to be negative
sld, xs, depth = neutron_scattering('Ni[62]',
density=Ni[62].density,
wavelength=4.75)
assert sld[2] == 0 and xs[2] == 0
sld, xs, depth = Ni[62].neutron.scattering(wavelength=4.75)
assert sld[2] == 0 and xs[2] == 0
assert Ni[62].neutron.sld()[2] == 0
# Test call from periodictable
sld, xs, depth = periodictable.neutron_scattering('H2O',
density=1,
wavelength=4.75)
sld2, xs2, depth2 = neutron_scattering('H2O', density=1, wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
assert all(abs(v - w) < 1e-10 for v, w in zip(xs, xs2))
assert depth == depth2
sld = periodictable.neutron_sld('H2O', density=1, wavelength=4.75)
assert all(abs(v - w) < 1e-10 for v, w in zip(sld, sld2))
# Check empty formula
sld, xs, depth = neutron_scattering('', density=0, wavelength=4.75)
assert all(v == 0 for v in sld)
assert all(v == 0 for v in xs)
assert np.isinf(depth)
# Check density == 0 works
sld, xs, depth = neutron_scattering('Si', density=0, wavelength=4.75)
assert all(v == 0 for v in sld)
assert all(v == 0 for v in xs)
assert np.isinf(depth)
# Test natural density
D2O_density = (2 * D.mass + O.mass) / (2 * H.mass + O.mass)
sld, xs, depth = neutron_scattering('D2O',
natural_density=1,
wavelength=4.75)
sld2, xs2, depth2 = neutron_scattering('D2O',
density=D2O_density,
wavelength=4.75)
assert all(abs(v - w) < 1e-14 for v, w in zip(sld, sld2))
assert all(abs(v - w) < 1e-14 for v, w in zip(xs, xs2))
assert abs(depth - depth2) < 1e-14
# Test that sld depends on density not on the size of the unit cell
D2O_density = (2 * D.mass + O.mass) / (2 * H.mass + O.mass)
sld, xs, depth = neutron_scattering('D2O',
natural_density=1,
wavelength=4.75)
sld2, xs2, depth2 = neutron_scattering('2D2O',
natural_density=1,
wavelength=4.75)
assert all(abs(v - w) < 1e-14 for v, w in zip(sld, sld2))
assert all(abs(v - w) < 1e-14 for v, w in zip(xs, xs2))
assert abs(depth - depth2) < 1e-14
# Test energy <=> velocity <=> wavelength
assert abs(
nsf.neutron_wavelength_from_velocity(2200) -
1.7981972618436388) < 1e-14
assert abs(nsf.neutron_wavelength(25) - 1.8) < 0.1
assert abs(nsf.neutron_energy(nsf.neutron_wavelength(25)) - 25) < 1e-14
# Confirm scattering functions accept energy and wavelength
sld, xs, depth = neutron_scattering('H2O', density=1, wavelength=4.75)
sld2, xs2, depth2 = neutron_scattering('H2O',
density=1,
energy=nsf.neutron_energy(4.75))
assert all(abs(v - w) < 1e-14 for v, w in zip(sld, sld2))
assert all(abs(v - w) < 1e-14 for v, w in zip(xs, xs2))
assert abs(depth - depth2) < 1e-14
def test():
H,He,D,O = elements.H,elements.He,elements.D,elements.O
assert H.neutron.absorption == 0.3326
assert H.neutron.total == 82.02
assert H.neutron.incoherent == 80.26
assert H.neutron.coherent == 1.7568
assert elements.Ru[101].neutron.bp == None
assert H[1].nuclear_spin == '1/2'
assert H[2].nuclear_spin == '1'
assert not H[6].neutron.has_sld()
assert He[3].neutron.b_c_i == -1.48
assert He[3].neutron.bm_i == -5.925
Nb = elements.Nb
assert Nb.neutron.absorption == Nb[93].neutron.absorption
# Check that b_c values match abundance-weighted values
# Note: Currently they do not for match within 5% for Ar,V,Sm or Gd
for el in elements:
if not hasattr(el,'neutron'): continue
b_c = 0
complete = True
for iso in el:
if iso.neutron != None:
if iso.neutron.b_c == None:
complete = False
else:
b_c += iso.neutron.b_c*iso.neutron.abundance/100.
if complete and b_c != 0 and abs((b_c-el.neutron.b_c)/b_c) > 0.05:
err = abs((b_c-el.neutron.b_c)/b_c)
## Printing suppressed for the release version
#print("%2s %.3f % 7.3f % 7.3f"%(el.symbol,err,b_c,el.neutron.b_c))
# Check neutron_sld and neutron_xs against NIST calculator
# Note that we are using different tables, so a general comparison with
# NIST numbers is not possible, but ^30Si and ^18O are the same in both.
M = formula('Si[30]O[18]2',density=2.2)
sld,xs,depth = neutron_scattering(M,wavelength=4.75)
sld2 = neutron_sld(M,wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
#_summarize(M)
#_summarize(formula('O2',density=1.14))
# Alan's numbers:
assert abs(sld[0] - 3.27) < 0.01
assert abs(sld[1] - 0) < 0.01
#assert abs(xs[2] - 0.00292) < 0.00001 # TODO fix test
assert abs(xs[1] - 0.00569) < 0.00001
#assert abs(depth - 4.329) < 0.001 # TODO fix test
# Cu/Mo K-alpha = 1.89e-5 + 2.45e-7i / 1.87e-5 + 5.16e-8i
Ni,Si = elements.Ni, elements.Si
# Make sure molecular calculation corresponds to direct calculation
sld = neutron_sld('Si',density=Si.density,wavelength=4.75)
sld2 = Si.neutron.sld(wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
sld,_,_ = Si.neutron.scattering(wavelength=4.75)
sld2 = Si.neutron.sld(wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
sld,xs,depth = neutron_scattering('Si',density=Si.density,wavelength=4.75)
sld2,xs2,depth2 = Si.neutron.scattering(wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
assert all(abs(v-w)<1e-10 for v,w in zip(xs,xs2))
assert abs(depth-depth2) < 1e-14
# incoherent cross sections for Ni[62] used to be negative
sld,xs,depth = neutron_scattering('Ni[62]',density=Ni[62].density,
wavelength=4.75)
assert sld[2] == 0 and xs[2] == 0
sld,xs,depth = Ni[62].neutron.scattering(wavelength=4.75)
assert sld[2] == 0 and xs[2] == 0
assert Ni[62].neutron.sld()[2] == 0
# Test call from periodictable
sld,xs,depth = periodictable.neutron_scattering('H2O',density=1,wavelength=4.75)
sld2,xs2,depth2 = neutron_scattering('H2O',density=1,wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
assert all(abs(v-w)<1e-10 for v,w in zip(xs,xs2))
assert depth==depth2
sld = periodictable.neutron_sld('H2O',density=1,wavelength=4.75)
assert all(abs(v-w)<1e-10 for v,w in zip(sld,sld2))
# Check empty formula
sld,xs,depth = neutron_scattering('',density=0,wavelength=4.75)
assert all(v == 0 for v in sld)
assert all(v == 0 for v in xs)
assert numpy.isinf(depth)
# Check density == 0 works
sld,xs,depth = neutron_scattering('Si',density=0,wavelength=4.75)
assert all(v == 0 for v in sld)
assert all(v == 0 for v in xs)
assert numpy.isinf(depth)
# Test natural density
D2O_density = (2*D.mass + O.mass)/(2*H.mass + O.mass)
sld,xs,depth = neutron_scattering('D2O',natural_density=1,wavelength=4.75)
sld2,xs2,depth2 = neutron_scattering('D2O',density=D2O_density,wavelength=4.75)
assert all(abs(v-w)<1e-14 for v,w in zip(sld,sld2))
assert all(abs(v-w)<1e-14 for v,w in zip(xs,xs2))
assert abs(depth-depth2)<1e-14
# Test that sld depends on density not on the size of the unit cell
D2O_density = (2*D.mass + O.mass)/(2*H.mass + O.mass)
sld,xs,depth = neutron_scattering('D2O',natural_density=1,wavelength=4.75)
sld2,xs2,depth2 = neutron_scattering('2D2O',natural_density=1,wavelength=4.75)
assert all(abs(v-w)<1e-14 for v,w in zip(sld,sld2))
assert all(abs(v-w)<1e-14 for v,w in zip(xs,xs2))
assert abs(depth-depth2)<1e-14
# Test energy <=> velocity <=> wavelength
assert abs(nsf.neutron_wavelength_from_velocity(2200) - 1.7981972618436388) < 1e-14
assert abs(nsf.neutron_wavelength(25) - 1.8) < 0.1
assert abs(nsf.neutron_energy(nsf.neutron_wavelength(25)) - 25) < 1e-14
# Confirm scattering functions accept energy and wavelength
sld,xs,depth = neutron_scattering('H2O',density=1,wavelength=4.75)
sld2,xs2,depth2 = neutron_scattering('H2O',density=1,energy=nsf.neutron_energy(4.75))
assert all(abs(v-w)<1e-14 for v,w in zip(sld,sld2))
assert all(abs(v-w)<1e-14 for v,w in zip(xs,xs2))
assert abs(depth-depth2)<1e-14
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