def exercise(xray_structure, anomalous_flag, max_n_indices, out):
xray_structure.show_summary(f=out).show_scatterers(f=out)
miller_set = miller.build_set(
crystal_symmetry=xray_structure,
anomalous_flag=anomalous_flag,
d_min=max(1,
min(xray_structure.unit_cell().parameters()[:3]) / 2.5))
n_indices = miller_set.indices().size()
if (n_indices > max_n_indices):
miller_set = miller_set.select(
flex.random_size_t(size=max_n_indices) % n_indices)
sf = structure_factors(xray_structure=xray_structure,
miller_set=miller_set)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure, algorithm="direct",
cos_sin_table=False).f_calc()
f_calc.show_summary(f=out)
assert approx_equal(sf.fs(), f_calc.data())
f_obs = miller_set.array(data=flex.abs(sf.fs()))
noise_fin = compare_analytical_and_finite(f_obs=f_obs,
xray_structure=xray_structure,
gradients_should_be_zero=True,
eps=1.e-5,
out=out)
compare_analytical_and_finite(f_obs=f_obs.customized_copy(
data=f_obs.data() * (flex.random_double(size=f_obs.size()) + 0.5)),
xray_structure=xray_structure,
gradients_should_be_zero=False,
eps=max(1.e-5, noise_fin),
out=out)
def exercise(
space_group_info,
use_u_aniso,
anomalous_flag,
max_n_indices=5,
verbose=0):
if (not verbose):
out = StringIO()
else:
out = sys.stdout
for n_scatterers in xrange(3,3+1):
for i_trial in xrange(1):
xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["const"]*n_scatterers,
volume_per_atom=100,
general_positions_only=True,
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso = use_u_aniso,
use_u_iso = (not use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
xray_structure.show_summary(f=out).show_scatterers(f=out)
miller_set = miller.build_set(
crystal_symmetry=xray_structure,
anomalous_flag=anomalous_flag,
d_min=max(1, min(xray_structure.unit_cell().parameters()[:3])/2.5))
n_indices = miller_set.indices().size()
if (n_indices > max_n_indices):
miller_set = miller_set.select(
flex.random_size_t(size=max_n_indices) % n_indices)
sf = structure_factors(
xray_structure=xray_structure,
miller_set=miller_set)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure,
algorithm="direct",
cos_sin_table=False).f_calc()
f_calc.show_summary(f=out)
assert approx_equal(sf.fs(), f_calc.data())
f_obs = miller_set.array(data=flex.abs(sf.fs()))
compare_analytical_and_finite(
f_obs=f_obs,
xray_structure=xray_structure,
out=out)
compare_analytical_and_finite(
f_obs=f_obs.customized_copy(
data=f_obs.data()*(flex.random_double(size=f_obs.size())+0.5)),
xray_structure=xray_structure,
out=out)
def exercise(space_group_info,
use_u_aniso,
anomalous_flag,
max_n_indices=5,
verbose=0):
if (not verbose):
out = StringIO()
else:
out = sys.stdout
for n_scatterers in xrange(3, 3 + 1):
for i_trial in xrange(1):
xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["const"] * n_scatterers,
volume_per_atom=100,
general_positions_only=True,
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso=use_u_aniso,
use_u_iso=(not use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
xray_structure.show_summary(f=out).show_scatterers(f=out)
miller_set = miller.build_set(
crystal_symmetry=xray_structure,
anomalous_flag=anomalous_flag,
d_min=max(
1,
min(xray_structure.unit_cell().parameters()[:3]) / 2.5))
n_indices = miller_set.indices().size()
if (n_indices > max_n_indices):
miller_set = miller_set.select(
flex.random_size_t(size=max_n_indices) % n_indices)
sf = structure_factors(xray_structure=xray_structure,
miller_set=miller_set)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure,
algorithm="direct",
cos_sin_table=False).f_calc()
f_calc.show_summary(f=out)
assert approx_equal(sf.fs(), f_calc.data())
f_obs = miller_set.array(data=flex.abs(sf.fs()))
compare_analytical_and_finite(f_obs=f_obs,
xray_structure=xray_structure,
out=out)
compare_analytical_and_finite(f_obs=f_obs.customized_copy(
data=f_obs.data() *
(flex.random_double(size=f_obs.size()) + 0.5)),
xray_structure=xray_structure,
out=out)
def exercise(
xray_structure,
anomalous_flag,
max_n_indices,
out):
xray_structure.show_summary(f=out).show_scatterers(f=out)
miller_set = miller.build_set(
crystal_symmetry=xray_structure,
anomalous_flag=anomalous_flag,
d_min=max(1, min(xray_structure.unit_cell().parameters()[:3])/2.5))
n_indices = miller_set.indices().size()
if (n_indices > max_n_indices):
miller_set = miller_set.select(
flex.random_size_t(size=max_n_indices) % n_indices)
sf = structure_factors(
xray_structure=xray_structure,
miller_set=miller_set)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure,
algorithm="direct",
cos_sin_table=False).f_calc()
f_calc.show_summary(f=out)
assert approx_equal(sf.fs(), f_calc.data())
f_obs = miller_set.array(data=flex.abs(sf.fs()))
noise_fin = compare_analytical_and_finite(
f_obs=f_obs,
xray_structure=xray_structure,
gradients_should_be_zero=True,
eps=1.e-5,
out=out)
compare_analytical_and_finite(
f_obs=f_obs.customized_copy(
data=f_obs.data()*(flex.random_double(size=f_obs.size())+0.5)),
xray_structure=xray_structure,
gradients_should_be_zero=False,
eps=max(1.e-5, noise_fin),
out=out)
def random_elements(size, choices=["O", "Mg", "Si", "Ca"]):
return flex.select(sequence=choices,
permutation=flex.random_size_t(size=size) %
len(choices))
def random_elements(size, choices=["O", "Mg", "Si", "Ca"]):
return flex.select(
sequence=choices,
permutation=flex.random_size_t(size=size) % len(choices))
