def __init__(self,
xray_structure,
obs_,
exti=None,
connectivity_table=None):
if exti is None:
exti = xray.dummy_extinction_correction()
adopt_init_args(self, locals())
assert obs_.fo_sq.anomalous_flag()
assert not (obs_.twin_fractions and obs_.merohedral_components)
xray_structure = xray_structure.deep_copy_scatterers()
for sc in xray_structure.scatterers():
f = xray.scatterer_flags()
f.set_use_u_aniso(sc.flags.use_u_aniso())
f.set_use_u_iso(sc.flags.use_u_iso())
f.set_use_fp_fdp(True)
sc.flags = f
twin_fractions = ()
it = xray.twin_component(sgtbx.rot_mx((-1, 0, 0, 0, -1, 0, 0, 0, -1)),
0.2, True)
twin_components = (it, )
obs = observations.customized_copy(obs_, twin_fractions,
twin_components)
# reparameterisation needs all fractions
twin_fractions += twin_components
if connectivity_table is None:
connectivity_table = smtbx.utils.connectivity_table(xray_structure)
reparametrisation = constraints.reparametrisation(
xray_structure, [],
connectivity_table,
twin_fractions=twin_fractions,
extinction=exti)
normal_eqns = least_squares.crystallographic_ls(obs, reparametrisation)
cycles = normal_eqns_solving.naive_iterations(normal_eqns,
n_max_iterations=10,
gradient_threshold=1e-7,
step_threshold=1e-4)
self.flack_x = it.value
self.sigma_x = math.sqrt(
normal_eqns.covariance_matrix(
jacobian_transpose=reparametrisation.
jacobian_transpose_matching(
reparametrisation.mapping_to_grad_fc_independent_scalars))
[0])
def __init__(self, xray_structure, obs_, exti=None, connectivity_table=None):
if exti is None:
exti = xray.dummy_extinction_correction()
adopt_init_args(self, locals())
assert obs_.fo_sq.anomalous_flag()
xray_structure = xray_structure.deep_copy_scatterers()
flags = xray_structure.scatterer_flags()
for sc in xray_structure.scatterers():
f = xray.scatterer_flags()
f.set_use_u_aniso(sc.flags.use_u_aniso())
f.set_use_u_iso(sc.flags.use_u_iso())
f.set_use_fp_fdp(True)
sc.flags = f
twin_fractions = obs_.twin_fractions
twin_components = obs_.merohedral_components
for tw in twin_fractions: tw.grad = False
for tc in twin_components: tc.grad = False
it = xray.twin_component(sgtbx.rot_mx((-1,0,0,0,-1,0,0,0,-1)), 0.2, True)
twin_components += (it,)
obs = observations.customized_copy(obs_, twin_fractions, twin_components)
# reparameterisation needs all fractions
twin_fractions += twin_components
if connectivity_table is None:
connectivity_table = smtbx.utils.connectivity_table(xray_structure)
reparametrisation = constraints.reparametrisation(
xray_structure, [], connectivity_table,
twin_fractions=twin_fractions,
extinction=exti
)
normal_eqns = least_squares.crystallographic_ls(obs,
reparametrisation)
cycles = normal_eqns_solving.naive_iterations(
normal_eqns, n_max_iterations=10,
gradient_threshold=1e-7,
step_threshold=1e-4)
self.flack_x = it.value
self.sigma_x = math.sqrt(normal_eqns.covariance_matrix(
jacobian_transpose=reparametrisation.jacobian_transpose_matching(
reparametrisation.mapping_to_grad_fc_independent_scalars))[0])
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11, 11, 13, 90, 90, 120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(
0.4, True), ))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert (measured_scale_indices[measured_cnt] == bn)
measured_cnt = measured_cnt + 1
assert (measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, 6, 9))
itr = obs.iterator(2)
assert (itr.next().h == (1, -6, -8))
# this is supposed to fail for now until somebody re-implements
# mixed HKLF 5 + merohedral twinning in a meaningful way...
try:
obs = observations.customized_copy(
obs,
twin_fractions=(xray.twin_fraction(0.7, True), ),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1, 0, 0, 0, -1, 0, 0, 0, -1)), 0.25, True), ))
itr = obs.iterator(0)
assert (itr.has_next())
assert (itr.next().h == (1, 6, -9))
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, -6, 9))
assert (itr.next().h == (-1, 6, 9))
assert (itr.next().h == (1, -6, -9))
assert (not itr.has_next())
ts = 1 - obs.ref_twin_components[0].value
ps = 1 - obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts * ps
nv = next(itr)
assert nv.scale == obs.ref_twin_components[0].value * ps
except RuntimeError as e:
pass
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11,11,13,90,90,120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(
scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(0.4,True),))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert(measured_scale_indices[measured_cnt]==bn)
measured_cnt = measured_cnt+1
assert(measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,6,9))
itr = obs.iterator(2)
assert(itr.next().h==(1,-6,-8))
obs = observations.customized_copy(obs,
twin_fractions=(xray.twin_fraction(0.7,True),),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1,0,0,0,-1,0,0,0,-1)), 0.25, True),))
itr = obs.iterator(0)
assert(itr.has_next())
assert(itr.next().h==(1,6,-9))
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,-6,9))
assert(itr.next().h==(-1,6,9))
assert(itr.next().h==(1,-6,-9))
assert(not itr.has_next())
ts = 1-obs.ref_twin_components[0].value
ps = 1-obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts*ps
nv = itr.next()
assert nv.scale == obs.ref_twin_components[0].value*ps
def exercise(self):
xs0 = self.structure
xs = xs0.deep_copy_scatterers()
xs.shake_sites_in_place(rms_difference=0.15)
xs.shake_adp()
for sc in xs.scatterers():
sc.flags.set_use_u_iso(False).set_use_u_aniso(True)
sc.flags.set_grad_site(True).set_grad_u_aniso(True)
connectivity_table = smtbx.utils.connectivity_table(xs)
if self.twin_fractions[0] < 0.5:
twin_fractions = self.twin_fractions.deep_copy() + 0.1
else:
twin_fractions = self.twin_fractions.deep_copy() - 0.1
twin_components = tuple(
[xray.twin_component(law, fraction, grad=True)
for law, fraction in zip(self.twin_laws, twin_fractions)])
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=connectivity_table,
twin_fractions=twin_components)
obs = self.fo_sq.as_xray_observations(twin_components=twin_components)
normal_eqns = least_squares.crystallographic_ls(
obs, reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.atomic_number_weighting)
cycles = normal_eqns_solving.naive_iterations(
normal_eqns,
n_max_iterations=10,
track_all=True)
assert approx_equal(
[twin.value for twin in normal_eqns.twin_fractions],
self.twin_fractions, eps=1e-2)
assert approx_equal(normal_eqns.objective(), 0, eps=1e-5)
assert normal_eqns.n_parameters == 64
# now with fixed twin fraction
xs.shake_sites_in_place(rms_difference=0.15)
xs.shake_adp()
twin_components = tuple(
[xray.twin_component(law, fraction, grad=False)
for law, fraction in zip(self.twin_laws, twin_fractions)])
#change the twin_components of the observations...
obs = observations.customized_copy(obs, twin_components=twin_components)
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=connectivity_table,
twin_fractions=twin_components)
normal_eqns = least_squares.crystallographic_ls(
obs, reparametrisation,
weighting_scheme=least_squares.unit_weighting(),
origin_fixing_restraints_type=
origin_fixing_restraints.atomic_number_weighting)
cycles = normal_eqns_solving.naive_iterations(
normal_eqns,
n_max_iterations=10,
track_all=True)
assert approx_equal(
[twin.value for twin in normal_eqns.twin_fractions],
twin_fractions)
assert normal_eqns.objective() != 0 # since the twin fraction is not refined
assert normal_eqns.n_parameters == 63