def __init__(self,
name,
formula,
cell_volume=None,
density=None,
charge=0):
# Fill in density or cell_volume.
M = pt.formula(formula, natural_density=density)
if cell_volume is not None:
M.density = 1e24 * M.molecular_mass / cell_volume if cell_volume > 0 else 0
#print name, M.molecular_mass, cell_volume, M.density
else:
cell_volume = 1e24 * M.molecular_mass / M.density
Hnatural = isotope_substitution(M, pt.T, pt.H)
H = isotope_substitution(M, pt.T, pt.H[1])
D = isotope_substitution(M, pt.T, pt.D)
self.name = name
self.formula = M
self.cell_volume = cell_volume
self.sld = pt.neutron_sld(Hnatural, wavelength=5)[0]
self.Hsld = pt.neutron_sld(H, wavelength=5)[0]
self.Dsld = pt.neutron_sld(D, wavelength=5)[0]
self.mass, self.Hmass, self.Dmass = Hnatural.mass, H.mass, D.mass
self.D2Omatch = D2Omatch(self.sld, self.Dsld)
self.charge = charge
self.Hnatural = Hnatural
def __init__(self,
name,
formula,
cell_volume=None,
natural_density=None,
charge=0):
M = pt.formula(formula, natural_density=natural_density)
# Fill in density or cell_volume
if cell_volume is not None:
M.density = 1e24 * M.molecular_mass / cell_volume if cell_volume > 0 else 0
else:
cell_volume = 1e24 * M.molecular_mass / M.density
self.cell_volume = cell_volume
self.name = name
self.formula = M
self.natural = isotope_substitution(M, pt.T, pt.H)
self.H = isotope_substitution(M, pt.T, pt.H[1])
self.D = isotope_substitution(M, pt.T, pt.D)
self.sld = pt.neutron_sld(self.natural, wavelength=5)[0]
self.H_sld = pt.neutron_sld(self.H, wavelength=5)[0]
self.D_sld = pt.neutron_sld(self.D, wavelength=5)[0]
self.D2Omatch = D2Omatch(self.H_sld, self.D_sld)
self.charge = charge
def test():
# Regression test: make sure neutron sld is an isotope property
# Note: it is important that this test be run separately
D2O = periodictable.formula('D2O',density=20./18)
D2O_coh,D2O_abs,D2O_inc = periodictable.neutron_sld(D2O)
D2O_coh2,D2O_abs2,D2O_inc2 = periodictable.neutron_sld(D2O)
H2O = periodictable.formula('H2O',density=1)
H2O_coh,H2O_abs,H2O_inc = periodictable.neutron_sld(H2O)
assert D2O_coh == D2O_coh2
assert D2O_coh != H2O_coh
def test():
# Regression test: make sure neutron sld is an isotope property
# Note: it is important that this test be run separately
D2O = periodictable.formula('D2O', density=20. / 18)
D2O_coh, D2O_abs, D2O_inc = periodictable.neutron_sld(D2O)
D2O_coh2, D2O_abs2, D2O_inc2 = periodictable.neutron_sld(D2O)
H2O = periodictable.formula('H2O', density=1)
H2O_coh, H2O_abs, H2O_inc = periodictable.neutron_sld(H2O)
assert D2O_coh == D2O_coh2
assert D2O_coh != H2O_coh
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 __init__(self, name, formula, cell_volume=None, density=None, charge=0):
# Fill in density or cell_volume
M = pt.formula(formula, natural_density=density)
if cell_volume != None:
M.density = 1e24*M.molecular_mass/cell_volume if cell_volume>0 else 0
#print name, M.molecular_mass, cell_volume, M.density
else:
cell_volume = 1e24*M.molecular_mass/M.density
Hnatural = isotope_substitution(M, pt.T, pt.H)
H = isotope_substitution(M, pt.T, pt.H[1])
D = isotope_substitution(M, pt.T, pt.D)
self.name = name
self.formula = M
self.cell_volume = cell_volume
self.sld = pt.neutron_sld(Hnatural, wavelength=5)[0]
self.Hsld = pt.neutron_sld(H, wavelength=5)[0]
self.Dsld = pt.neutron_sld(D, wavelength=5)[0]
self.mass, self.Hmass, self.Dmass = Hnatural.mass, H.mass, D.mass
self.D2Omatch = D2Omatch(self.Hsld, self.Dsld)
self.charge = charge
def neutron_scattering_lengths(self,
condition,
vf_d_solvent=1,
neutron_wavelength=1.8):
vh, vt = self.conditions[condition]
hf = exchange_protons_formula(self.hf, self.head_exchangable,
vf_d_solvent)
tf = exchange_protons_formula(self.tf, self.tail_exchangable,
vf_d_solvent)
h_density = calculate_density(hf, vh)
t_density = calculate_density(tf, vt)
h_sld = pt.neutron_sld(hf,
density=h_density,
wavelength=neutron_wavelength)
t_sld = pt.neutron_sld(tf,
density=t_density,
wavelength=neutron_wavelength)
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, 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 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():
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
if type is None:
if filename.endswith('.fna'):
type = 'dna'
elif filename.endswith('.ffn'):
type = 'dna'
elif filename.endswith('.faa'):
type = 'aa'
elif filename.endswith('.frn'):
type = 'rna'
else:
type = 'aa'
return type
# Water density at 20C; neutron wavelength doesn't matter (use 5 A).
H2O_SLD = pt.neutron_sld(pt.formula("[email protected]"), wavelength=5)[0]
D2O_SLD = pt.neutron_sld(pt.formula("[email protected]"), wavelength=5)[0]
def D2Omatch(Hsld, Dsld):
"""
Find the D2O% concentration of solvent such that neutron SLD of the
material matches the neutron SLD of the solvent.
*Hsld*, *Dsld* are the SLDs for the hydrogenated and deuterated forms
of the material respectively, where *D* includes all the labile protons
swapped for deuterons. Water SLD is calculated at 20 C.
Note that the resulting percentage is only meaningful between
0% to 100%. Beyond 100% you will need an additional constrast agent
in the 100% D2O solvent to increase the SLD enough to match.
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 _guess_type_from_filename(filename, type):
if type is None:
if filename.endswith('.fna'):
type = 'dna'
elif filename.endswith('.ffn'):
type = 'dna'
elif filename.endswith('.faa'):
type = 'aa'
elif filename.endswith('.frn'):
type = 'rna'
else:
type = 'aa'
return type
# Water density at 20C; neutron wavelength doesn't matter (use 5 A).
H2O_SLD = pt.neutron_sld(pt.formula("[email protected]"), wavelength=5)[0]
D2O_SLD = pt.neutron_sld(pt.formula("[email protected]"), wavelength=5)[0]
def D2Omatch(Hsld, Dsld):
"""
Find the D2O% concentration of solvent such that neutron SLD of the
material matches the neutron SLD of the solvent.
*Hsld*, *Dsld* are the SLDs for the hydrogenated and deuterated forms
of the material respectively, where *D* includes all the labile protons
swapped for deuterons. Water SLD is calculated at 20 C.
Note that the resulting percentage is only meaningful between
0% to 100%. Beyond 100% you will need an additional constrast agent
in the 100% D2O solvent to increase the SLD enough to match.
"""
# SLD(%Dsample + (1-%)Hsample) = SLD(%D2O + (1-%)H2O)
