def __init__(self, site, u_iso, u_star, occupancy, fp, fdp):
self.site = site
self.u_iso = u_iso
self.u_star = u_star
self.flags = xray.scatterer_flags()
self.flags.set_use_u(
iso=(u_iso is not None),
aniso=(u_star is not None))
self.occupancy = occupancy
self.fp = fp
self.fdp = fdp
def __init__(self, site, u_iso, u_star, occupancy, fp, fdp):
self.site = site
self.u_iso = u_iso
self.u_star = u_star
self.flags = xray.scatterer_flags()
self.flags.set_use_u(
iso=(u_iso is not None),
aniso=(u_star is not None))
self.occupancy = occupancy
self.fp = fp
self.fdp = fdp
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])