def test_contrast_matching():
from periodictable import fasta
# Test constrast match holds for varying volume fractions (no labile)
SiO2 = formula("[email protected]")
match, sld_real = nsf.D2O_match(SiO2)
sld_0p0 = nsf.D2O_sld(SiO2, volume_fraction=0.0, D2O_fraction=match)
sld_0p7 = nsf.D2O_sld(SiO2, volume_fraction=0.7, D2O_fraction=match)
sld_1p0 = nsf.D2O_sld(SiO2, volume_fraction=1.0, D2O_fraction=match)
assert np.isclose(sld_0p0[0], sld_real, 1e-14)
assert np.isclose(sld_0p7[0], sld_real, 1e-14)
assert np.isclose(sld_1p0[0], sld_real, 1e-14)
assert not np.isclose(sld_1p0[0], sld_1p0[1], 1e-14)
mol = fasta.LIPIDS["cholesteral"].labile_formula
match, sld_real = nsf.D2O_match(mol)
sld_0p7 = nsf.D2O_sld(mol, volume_fraction=0.7, D2O_fraction=match)
assert np.isclose(sld_0p7[0], sld_real, 1e-14)
# Test that labile hydrogens are being subsituted in contrast match
# Note that D2O mixture is formed from pure D2O and pure water with
# natural H:D ratios.
mol = formula("C3H4H[1][email protected]") # alanine
sld_0p7 = nsf.D2O_sld(mol, volume_fraction=1., D2O_fraction=0.7)
sld_0p7_direct = nsf.neutron_sld("[email protected]")
#print(sld_0p7)
#print(sld_0p7_direct)
assert np.isclose(sld_0p7[0], sld_0p7_direct[0], 1e-14)
assert np.isclose(sld_0p7[1], sld_0p7_direct[1], 1e-14)
def molecule_table():
# Table of scattering length densities for various molecules
print("SLDS for some molecules")
for molecule,density in [('SiO2',2.2),('B4C',2.52)]:
atoms = formula(molecule).atoms
rho,mu,inc = neutron_sld(atoms,density,wavelength=4.75)
print("%s(%g g/cm**3) rho=%.4g mu=%.4g inc=%.4g"
%(molecule,density,rho,mu,inc))
def molecule_table():
# Table of scattering length densities for various molecules
print("SLDS for some molecules")
for molecule, density in [('SiO2', 2.2), ('B4C', 2.52)]:
atoms = formula(molecule).atoms
rho, mu, inc = neutron_sld(atoms, density, wavelength=4.75)
print("%s(%g g/cm**3) rho=%.4g mu=%.4g inc=%.4g" %
(molecule, density, rho, mu, inc))
def test_composite():
from periodictable.nsf import neutron_composite_sld
calc = neutron_composite_sld([formula(s) for s in ('HSO4', 'H2O', 'CCl4')],
wavelength=4.75)
sld = calc(np.array([3, 1, 2]), density=1.2)
sld2 = neutron_sld('3HSO4+1H2O+2CCl4', density=1.2, wavelength=4.75)
#print(sld)
#print(sld2)
assert all(abs(v - w) < 1e-14 for v, w in zip(sld, sld2))
def test_composite():
from periodictable.nsf import neutron_composite_sld
calc = neutron_composite_sld([formula(s) for s in ('HSO4','H2O','CCl4')],
wavelength=4.75)
sld = calc(numpy.array([3,1,2]),density=1.2)
sld2 = neutron_sld('3HSO4+1H2O+2CCl4',density=1.2,wavelength=4.75)
#print(sld)
#print(sld2)
assert all(abs(v-w)<1e-14 for v,w in zip(sld,sld2))
def _summarize(M):
from periodictable.nsf import neutron_sld, neutron_xs
sld = neutron_sld(M,wavelength=4.75)
xs = neutron_xs(M,wavelength=4.75)
print("%s sld %s"%(M,sld))
print("%s xs %s 1/e %s"%(M,xs,1/sum(xs)))
#return
for el in list(M.atoms.keys()):
print("%s density %s"%(el,el.density))
print("%s sld %s"%(el,el.neutron.sld(wavelength=4.75)))
print("%s xs"%el + " %.15g %.15g %.15g"%el.neutron.xs(wavelength=4.75))
print("%s 1/e %s"%(el,1./sum(el.neutron.xs(wavelength=4.75))))
def _summarize(M):
from periodictable.nsf import neutron_sld, neutron_xs
sld = neutron_sld(M, wavelength=4.75)
xs = neutron_xs(M, wavelength=4.75)
print M, "sld", sld
print M, "xs", xs, "1/e", 1 / sum(xs)
#return
for el in M.atoms.keys():
print el, "density", el.density
print el, "sld", el.neutron.sld(wavelength=4.75)
print el, "xs", "%.15g %.15g %.15g" % el.neutron.xs(wavelength=4.75)
print el, "1/e", 1. / sum(el.neutron.xs(wavelength=4.75))
def _summarize(M):
from periodictable.nsf import neutron_sld, neutron_xs
sld = neutron_sld(M,wavelength=4.75)
xs = neutron_xs(M,wavelength=4.75)
print M,"sld",sld
print M,"xs",xs,"1/e",1/sum(xs)
#return
for el in M.atoms.keys():
print el,"density",el.density
print el,"sld",el.neutron.sld(wavelength=4.75)
print el,"xs","%.15g %.15g %.15g"%el.neutron.xs(wavelength=4.75)
print el,"1/e",1./sum(el.neutron.xs(wavelength=4.75))
def capacity(self):
"""
Calculate capacity [micro Ah]
The charge packing refers, for instance, to the maximum x in Li_x:Si.
To test: Li_15 Si_4 -> 3579 mAh
:param electrode: electrode composition [string]
:param radius: electrode radius [cm]
:param thickness: electrode thickness [nm]
:param packing: charge packing
:param valence_change: change in oxidation state of the carrier
"""
N_a = 6.022 * 10**23
# Charge unit in Coulombs
q = 1.602 * 10**(-19)
electrode_material = pt.formula(self.cleaned_data['material_formula'])
density = self.cleaned_data['electrode_density']
if density is None:
density = electrode_material.density # g/cm^3
if density is None:
return None
atomic_weight = electrode_material.mass # g/mol
volume = 3.1416 * self.cleaned_data[
'electrode_radius']**2 * self.cleaned_data[
'electrode_thickness'] / 10**7
# Amp*hour = Coulombs/sec * 3600 sec = 3600 Coulombs
capacity_per_gram = self.cleaned_data[
'ion_packing'] * q * self.cleaned_data[
'valence_change'] / 3600 / atomic_weight * N_a * 1000
capacity = volume * density * capacity_per_gram
# Scattering length density
# sld, imaginary sld, incoherent
sld, im_sld, incoh = nsf.neutron_sld(
compound=self.cleaned_data['material_formula'],
wavelength=6.0,
density=density)
# Return value in muAh
return dict(capacity='%6.3g' % capacity,
sld='%6.3f' % sld,
im_sld='%6.6f' % im_sld,
incoherent='%6.3f' % incoh,
density=density,
c_over_3='%6.3g' % (capacity / 3.0),
c_over_5='%6.3g' % (capacity / 5.0))
def _summarize(M):
from periodictable.nsf import neutron_sld, neutron_xs
sld = neutron_sld(M, wavelength=4.75)
xs = neutron_xs(M, wavelength=4.75)
print("%s sld %s" % (M, sld))
print("%s xs %s 1/e %s" % (M, xs, 1 / sum(xs)))
#return
for el in list(M.atoms.keys()):
print("%s density %s" % (el, el.density))
print("%s sld %s" % (el, el.neutron.sld(wavelength=4.75)))
print("%s xs" % el +
" %.15g %.15g %.15g" % el.neutron.xs(wavelength=4.75))
print("%s 1/e %s" % (el, 1. / sum(el.neutron.xs(wavelength=4.75))))
def calculate_sld(self, compound, neutron_wavelength, xray_wavelength):
wavelength_n = neutron_wavelength
wavelength_x = xray_wavelength
density = compound.density
n_real, n_imag, n_incoh = self._r(
neutron_sld(compound, density=density, wavelength=wavelength_n))
x_real, x_imag = self._r(
xray_sld(compound, density=density, wavelength=wavelength_x))
self.ui.lE_SLD_neutron_real.setText(f"{n_real}")
self.ui.lE_SLD_neutron_imag.setText(f"{n_imag}")
self.ui.lE_SLD_neutron_incoh.setText(f"{n_incoh}")
self.ui.lE_SLD_xray_real.setText(f"{x_real}")
self.ui.lE_SLD_xray_imag.setText(f"{x_imag}")
def time_composite():
from periodictable.nsf import neutron_composite_sld
import time
calc = neutron_composite_sld([formula(s) for s in 'HSO4','H2O','CCl4'],
wavelength=4.75)
q = numpy.array([3,1,2])
N = 1000
bits = [formula(s) for s in 'HSO4','H2O','CCl4']
tic = time.time()
for i in range(N):
sld = calc(q,density=1.2)
toc = time.time()-tic
print "composite %.1f us"%(toc/N*1e6)
tic = time.time()
for i in range(N):
sld = neutron_sld(q[0]*bits[0]+q[1]*bits[1]+q[2]*bits[2],
density=1.2,wavelength=4.75)
toc = time.time()-tic
print "direct %.1f us"%(toc/N*1e6)
def time_composite():
from periodictable.nsf import neutron_composite_sld
import time
calc = neutron_composite_sld([formula(s) for s in ('HSO4','H2O','CCl4')],
wavelength=4.75)
q = numpy.array([3,1,2])
N = 1000
bits = [formula(s) for s in ('HSO4','H2O','CCl4')]
tic = time.time()
for i in range(N):
sld = calc(q,density=1.2)
toc = time.time()-tic
print("composite %.1f us"%(toc/N*1e6))
tic = time.time()
for i in range(N):
sld = neutron_sld(q[0]*bits[0]+q[1]*bits[1]+q[2]*bits[2],
density=1.2,wavelength=4.75)
toc = time.time()-tic
print("direct %.1f us"%(toc/N*1e6))
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 read(self, path):
"""
Load data file
:param path: file path
:return: MagSLD
:raise RuntimeError: when the file can't be opened
"""
pos_x = np.zeros(0)
pos_y = np.zeros(0)
pos_z = np.zeros(0)
sld_n = np.zeros(0)
sld_mx = np.zeros(0)
sld_my = np.zeros(0)
sld_mz = np.zeros(0)
vol_pix = np.zeros(0)
pix_symbol = np.zeros(0)
x_line = []
y_line = []
z_line = []
x_lines = []
y_lines = []
z_lines = []
try:
input_f = open(path, 'rb')
buff = decode(input_f.read())
lines = buff.split('\n')
input_f.close()
num = 0
for line in lines:
try:
# check if line starts with "ATOM"
if line[0:6].strip().count('ATM') > 0 or \
line[0:6].strip() == 'ATOM':
# define fields of interest
atom_name = line[12:16].strip()
try:
float(line[12])
atom_name = atom_name[1].upper()
except Exception:
if len(atom_name) == 4:
atom_name = atom_name[0].upper()
elif line[12] != ' ':
atom_name = atom_name[0].upper() + \
atom_name[1].lower()
else:
atom_name = atom_name[0].upper()
_pos_x = float(line[30:38].strip())
_pos_y = float(line[38:46].strip())
_pos_z = float(line[46:54].strip())
pos_x = np.append(pos_x, _pos_x)
pos_y = np.append(pos_y, _pos_y)
pos_z = np.append(pos_z, _pos_z)
try:
val = nsf.neutron_sld(atom_name)[0]
# sld in Ang^-2 unit
val *= 1.0e-6
sld_n = np.append(sld_n, val)
atom = formula(atom_name)
# cm to A units
vol = 1.0e+24 * atom.mass / atom.density / NA
vol_pix = np.append(vol_pix, vol)
except Exception:
logger.error("Error: set the sld of %s to zero" %
atom_name)
sld_n = np.append(sld_n, 0.0)
sld_mx = np.append(sld_mx, 0)
sld_my = np.append(sld_my, 0)
sld_mz = np.append(sld_mz, 0)
pix_symbol = np.append(pix_symbol, atom_name)
elif line[0:6].strip().count('CONECT') > 0:
toks = line.split()
num = int(toks[1]) - 1
val_list = []
for val in toks[2:]:
try:
int_val = int(val)
except Exception:
break
if int_val == 0:
break
val_list.append(int_val)
#need val_list ordered
for val in val_list:
index = val - 1
if (pos_x[index], pos_x[num]) in x_line and \
(pos_y[index], pos_y[num]) in y_line and \
(pos_z[index], pos_z[num]) in z_line:
continue
x_line.append((pos_x[num], pos_x[index]))
y_line.append((pos_y[num], pos_y[index]))
z_line.append((pos_z[num], pos_z[index]))
if len(x_line) > 0:
x_lines.append(x_line)
y_lines.append(y_line)
z_lines.append(z_line)
except Exception as exc:
logger.error(exc)
output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
output.set_conect_lines(x_line, y_line, z_line)
output.filename = os.path.basename(path)
output.set_pix_type('atom')
output.set_pixel_symbols(pix_symbol)
output.set_nodes()
output.set_pixel_volumes(vol_pix)
output.sld_unit = '1/A^(2)'
return output
except Exception:
raise RuntimeError("%s is not a sld file" % path)
def read(self, path):
"""
Load data file
:param path: file path
:return: MagSLD
:raise RuntimeError: when the file can't be opened
"""
pos_x = np.zeros(0)
pos_y = np.zeros(0)
pos_z = np.zeros(0)
sld_n = np.zeros(0)
sld_mx = np.zeros(0)
sld_my = np.zeros(0)
sld_mz = np.zeros(0)
vol_pix = np.zeros(0)
pix_symbol = np.zeros(0)
x_line = []
y_line = []
z_line = []
x_lines = []
y_lines = []
z_lines = []
try:
input_f = open(path, 'rb')
buff = input_f.read()
lines = buff.split('\n')
input_f.close()
num = 0
for line in lines:
try:
# check if line starts with "ATOM"
if line[0:6].strip().count('ATM') > 0 or \
line[0:6].strip() == 'ATOM':
# define fields of interest
atom_name = line[12:16].strip()
try:
float(line[12])
atom_name = atom_name[1].upper()
except:
if len(atom_name) == 4:
atom_name = atom_name[0].upper()
elif line[12] != ' ':
atom_name = atom_name[0].upper() + \
atom_name[1].lower()
else:
atom_name = atom_name[0].upper()
_pos_x = float(line[30:38].strip())
_pos_y = float(line[38:46].strip())
_pos_z = float(line[46:54].strip())
pos_x = np.append(pos_x, _pos_x)
pos_y = np.append(pos_y, _pos_y)
pos_z = np.append(pos_z, _pos_z)
try:
val = nsf.neutron_sld(atom_name)[0]
# sld in Ang^-2 unit
val *= 1.0e-6
sld_n = np.append(sld_n, val)
atom = formula(atom_name)
# cm to A units
vol = 1.0e+24 * atom.mass / atom.density / NA
vol_pix = np.append(vol_pix, vol)
except:
print("Error: set the sld of %s to zero"% atom_name)
sld_n = np.append(sld_n, 0.0)
sld_mx = np.append(sld_mx, 0)
sld_my = np.append(sld_my, 0)
sld_mz = np.append(sld_mz, 0)
pix_symbol = np.append(pix_symbol, atom_name)
elif line[0:6].strip().count('CONECT') > 0:
toks = line.split()
num = int(toks[1]) - 1
val_list = []
for val in toks[2:]:
try:
int_val = int(val)
except:
break
if int_val == 0:
break
val_list.append(int_val)
#need val_list ordered
for val in val_list:
index = val - 1
if (pos_x[index], pos_x[num]) in x_line and \
(pos_y[index], pos_y[num]) in y_line and \
(pos_z[index], pos_z[num]) in z_line:
continue
x_line.append((pos_x[num], pos_x[index]))
y_line.append((pos_y[num], pos_y[index]))
z_line.append((pos_z[num], pos_z[index]))
if len(x_line) > 0:
x_lines.append(x_line)
y_lines.append(y_line)
z_lines.append(z_line)
except:
logger.error(sys.exc_value)
output = MagSLD(pos_x, pos_y, pos_z, sld_n, sld_mx, sld_my, sld_mz)
output.set_conect_lines(x_line, y_line, z_line)
output.filename = os.path.basename(path)
output.set_pix_type('atom')
output.set_pixel_symbols(pix_symbol)
output.set_nodes()
output.set_pixel_volumes(vol_pix)
output.sld_unit = '1/A^(2)'
return output
except:
raise RuntimeError, "%s is not a sld file" % path
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
