def debye_waller_factors(self,
miller_index=None,
miller_indices=None,
u_iso=None,
b_iso=None,
u_cart=None,
b_cart=None,
u_cif=None,
u_star=None,
exp_arg_limit=50,
truncate_exp_arg=False):
assert [miller_index, miller_indices].count(None) == 1
assert [u_iso, b_iso, u_cart, b_cart, u_cif, u_star].count(None) == 5
from cctbx import adptbx
h = miller_index
if (h is None): h = miller_indices
if (u_iso is not None):
b_iso = adptbx.u_as_b(u_iso)
if (b_iso is not None):
return adptbx.debye_waller_factor_b_iso(
self.stol_sq(h),
b_iso, exp_arg_limit, truncate_exp_arg)
if (b_cart is not None):
u_cart = adptbx.b_as_u(b_cart)
if (u_cart is not None):
u_star = adptbx.u_cart_as_u_star(self, u_cart)
if (u_cif is not None):
u_star = adptbx.u_cif_as_u_star(self, u_cif)
assert u_star is not None
return adptbx.debye_waller_factor_u_star(
h, u_star, exp_arg_limit, truncate_exp_arg)
def debye_waller_factors(self,
miller_index=None,
miller_indices=None,
u_iso=None,
b_iso=None,
u_cart=None,
b_cart=None,
u_cif=None,
u_star=None,
exp_arg_limit=50,
truncate_exp_arg=False):
assert [miller_index, miller_indices].count(None) == 1
assert [u_iso, b_iso, u_cart, b_cart, u_cif, u_star].count(None) == 5
from cctbx import adptbx
h = miller_index
if (h is None): h = miller_indices
if (u_iso is not None):
b_iso = adptbx.u_as_b(u_iso)
if (b_iso is not None):
return adptbx.debye_waller_factor_b_iso(
self.stol_sq(h),
b_iso, exp_arg_limit, truncate_exp_arg)
if (b_cart is not None):
u_cart = adptbx.b_as_u(b_cart)
if (u_cart is not None):
u_star = adptbx.u_cart_as_u_star(self, u_cart)
if (u_cif is not None):
u_star = adptbx.u_cif_as_u_star(self, u_cif)
assert u_star is not None
return adptbx.debye_waller_factor_u_star(
h, u_star, exp_arg_limit, truncate_exp_arg)
def exercise_interface():
episq = 8 * (math.pi**2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3, 4, 9, 2, 1, 7)
assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100))
for fw, bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)),
2.3)
for fw, bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(fc.u_cart_minus_u_iso,
[uii - fc.u_iso for uii in u[:3]] + list(u[3:]))
f = adptbx.factor_u_star_u_iso(unit_cell=uc,
u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_star_minus_u_iso,
adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(unit_cell=uc,
u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_cif_minus_u_iso,
adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(unit_cell=uc,
beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.beta_minus_u_iso,
adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3),
math.exp(-2.3 * 0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3),
math.exp(-2.3 * episq * 0.25))
assert approx_equal(
adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq))
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star)
assert approx_equal(
dw,
adptbx.debye_waller_factor_beta((1, 2, 3),
adptbx.u_star_as_beta(u_star)))
assert approx_equal(
dw,
adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3),
adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(
dw,
adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3),
adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1, 2, 3, 3, -4, 5, 4, 5, 6)
v = (198, 18, 1020, 116, 447, 269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(
adptbx.eigensystem(u).values(),
(14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try:
s.vectors(4)
except RuntimeError, e:
assert str(e).endswith("Index out of range.")
def exercise_interface():
episq = 8*(math.pi**2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3*episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3,4,9, 2,1,7)
assert approx_equal(adptbx.u_as_b(u), [x*episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5,4,7,80,110,100))
for fw,bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3)
for fw,bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(
fc.u_cart_minus_u_iso,
[uii-fc.u_iso for uii in u[:3]]+list(u[3:]))
f = adptbx.factor_u_star_u_iso(
unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.u_star_minus_u_iso,
adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(
unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.u_cif_minus_u_iso,
adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(
unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.beta_minus_u_iso,
adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25,2.3),
math.exp(-2.3*0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25,2.3),
math.exp(-2.3*episq*0.25))
assert approx_equal(adptbx.debye_waller_factor_b_iso(uc, (1,2,3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1,2,3), 2.3/episq))
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1,2,3), u_star)
assert approx_equal(dw, adptbx.debye_waller_factor_beta((1,2,3),
adptbx.u_star_as_beta(u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1,2,3),
adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1,2,3),
adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1,2,3, 3,-4,5, 4,5,6)
v = (198,18,1020,116,447,269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(adptbx.eigensystem(u).values(),
(14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try: s.vectors(4)
except RuntimeError, e: assert str(e).endswith("Index out of range.")
else: raise Exception_expected
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0)
assert approx_equal(uf, (3.0810418, 4.7950710, 9.3400030,
1.7461615, 1.1659954, 6.4800706))
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3)
assert approx_equal(uf, (2.7430890, 1.0378360, 2.1559895,
0.6193215, -0.3921632, 1.2846854))
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3)
assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(u).values(),
(14.2792015, 2.9369144, -1.2161159))
assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(uf).values(),
(3, 2.9369144, 0))
uf = adptbx.eigenvalue_filtering(up)
assert approx_equal(uf, up)
def exercise_interface():
episq = 8 * (math.pi ** 2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3, 4, 9, 2, 1, 7)
assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100))
for fw, bw in (
(adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif),
):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3)
for fw, bw in (
(adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso),
):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(fc.u_cart_minus_u_iso, [uii - fc.u_iso for uii in u[:3]] + list(u[3:]))
f = adptbx.factor_u_star_u_iso(unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_star_minus_u_iso, adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_cif_minus_u_iso, adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.beta_minus_u_iso, adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3), math.exp(-2.3 * 0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3), math.exp(-2.3 * episq * 0.25))
assert approx_equal(
adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq),
)
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star)
assert approx_equal(dw, adptbx.debye_waller_factor_beta((1, 2, 3), adptbx.u_star_as_beta(u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3), adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3), adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1, 2, 3, 3, -4, 5, 4, 5, 6)
v = (198, 18, 1020, 116, 447, 269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(adptbx.eigensystem(u).values(), (14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try:
s.vectors(4)
except RuntimeError, e:
assert str(e).endswith("Index out of range.")
