def optimize(self):
rsos = list(self.reciprocal_space_objects.values())
for i in range(len(rsos)-1):
h_i = rsos[i].indices
for j in range(i+1, len(rsos)):
h_j = rsos[j].indices
if (flex.order(h_i, h_j) == 0):
rsos[j].indices = h_i
def optimize(self):
rsos = self.reciprocal_space_objects.values()
for i in xrange(len(rsos)-1):
h_i = rsos[i].indices
for j in xrange(i+1, len(rsos)):
h_j = rsos[j].indices
if (flex.order(h_i, h_j) == 0):
rsos[j].indices = h_i
def exercise(space_group_info,
anomalous_flag,
use_u_aniso,
n_elements=3,
d_min=3.,
verbose=0):
structure_z = random_structure.xray_structure(
space_group_info,
elements=("Se", ) * n_elements,
volume_per_atom=200,
random_f_prime_d_min=1.0,
random_f_double_prime=anomalous_flag,
random_u_iso=True,
use_u_aniso=use_u_aniso,
random_occupancy=True)
check_weight_without_occupancy(structure_z)
f_z = structure_z.structure_factors(anomalous_flag=anomalous_flag,
d_min=d_min,
algorithm="direct").f_calc()
f_abs_z = abs(f_z)
f_rad_z = f_z.phases()
f_deg_z = f_z.phases(deg=True)
hl_z = generate_random_hl(miller_set=f_z)
hl_z_rad = hl_z.phase_integrals()
if (0 or verbose):
structure_z.show_summary().show_scatterers()
print("n_special_positions:", \
structure_z.special_position_indices().size())
z2p_op = structure_z.space_group().z2p_op()
z2p_op = sgtbx.change_of_basis_op(z2p_op.c() + sgtbx.tr_vec(
(2, -1, 3), 12).new_denominator(z2p_op.c().t().den()))
for change_hand in [False, True]:
if (change_hand):
z2p_op = z2p_op * sgtbx.change_of_basis_op("-x,-y,-z")
structure_p = structure_z.change_basis(z2p_op)
check_weight_without_occupancy(structure_p)
check_site_symmetry_table(structure_z, z2p_op, structure_p)
if (0 or verbose):
structure_p.show_summary().show_scatterers()
print("n_special_positions:", \
structure_p.special_position_indices().size())
assert tuple(structure_p.special_position_indices()) \
== tuple(structure_z.special_position_indices())
structure_pz = structure_p.change_basis(z2p_op.inverse())
check_weight_without_occupancy(structure_pz)
check_site_symmetry_table(structure_p, z2p_op.inverse(), structure_pz)
assert structure_pz.unit_cell().is_similar_to(structure_z.unit_cell())
assert structure_pz.space_group() == structure_z.space_group()
f_pz = f_z.structure_factors_from_scatterers(
xray_structure=structure_pz, algorithm="direct").f_calc()
f_abs_pz = abs(f_pz)
f_rad_pz = f_pz.phases()
f_deg_pz = f_pz.phases(deg=True)
c = flex.linear_correlation(f_abs_z.data(), f_abs_pz.data())
assert c.is_well_defined()
if (0 or verbose):
print("correlation:", c.coefficient())
assert c.coefficient() > 0.999
f_p_cb = f_z.change_basis(z2p_op)
f_abs_p_cb = f_abs_z.change_basis(z2p_op)
f_rad_p_cb = f_rad_z.change_basis(z2p_op, deg=False)
f_deg_p_cb = f_deg_z.change_basis(z2p_op, deg=True)
hl_p_cb = hl_z.change_basis(z2p_op)
hl_p_cb_rad = hl_p_cb.phase_integrals()
assert approx_equal(
hl_z_rad.change_basis(z2p_op).data(), hl_p_cb_rad.data())
assert f_abs_p_cb.indices().all_eq(f_p_cb.indices())
if (not change_hand):
o = flex.order(f_abs_p_cb.indices(), f_abs_z.indices())
else:
o = flex.order(-f_abs_p_cb.indices(), f_abs_z.indices())
if (f_abs_z.space_group().n_ltr() == 1):
assert o == 0
else:
assert o != 0
f_pz = f_p_cb.change_basis(z2p_op.inverse())
f_abs_pz = f_abs_p_cb.change_basis(z2p_op.inverse())
f_rad_pz = f_rad_p_cb.change_basis(z2p_op.inverse(), deg=False)
f_deg_pz = f_deg_p_cb.change_basis(z2p_op.inverse(), deg=True)
hl_pz = hl_p_cb.change_basis(z2p_op.inverse())
hl_pz_rad = hl_pz.phase_integrals()
assert approx_equal(hl_z_rad.data(), hl_pz_rad.data())
for i, o in zip(hl_z.data(), hl_pz.data()):
assert approx_equal(i, o)
assert approx_equal(flex.max(flex.abs(f_pz.data() - f_z.data())), 0)
assert flex.order(f_abs_pz.indices(), f_abs_z.indices()) == 0
assert f_abs_pz.indices().all_eq(f_pz.indices())
assert approx_equal(
flex.max(
scitbx.math.phase_error(phi1=f_rad_pz.data(),
phi2=f_rad_z.data())), 0)
assert approx_equal(
flex.max(
scitbx.math.phase_error(phi1=f_deg_pz.data(),
phi2=f_deg_z.data(),
deg=True)), 0)
assert approx_equal(f_deg_pz.data(), f_rad_pz.data() * (180 / math.pi))
f_p_sf = f_p_cb.structure_factors_from_scatterers(
xray_structure=structure_p, algorithm="direct").f_calc()
det = abs(z2p_op.c().r().determinant())
assert approx_equal(
flex.max(flex.abs(f_p_sf.data() * complex(det) - f_p_cb.data())),
0)
f_abs_p_sf = abs(f_p_sf)
f_rad_p_sf = f_p_sf.phases()
f_deg_p_sf = f_p_sf.phases(deg=True)
assert approx_equal(
flex.max(
scitbx.math.phase_error(phi1=f_rad_p_sf.data(),
phi2=f_rad_p_cb.data())), 0)
assert approx_equal(
flex.max(
scitbx.math.phase_error(phi1=f_deg_p_sf.data(),
phi2=f_deg_p_cb.data(),
deg=True)), 0)
c = flex.linear_correlation(f_abs_p_sf.data(), f_abs_p_cb.data())
assert c.is_well_defined()
if (0 or verbose):
print("correlation:", c.coefficient())
assert c.coefficient() > 0.999
def exercise(
space_group_info,
anomalous_flag,
use_u_aniso,
n_elements=3,
d_min=3.,
verbose=0):
structure_z = random_structure.xray_structure(
space_group_info,
elements=("Se",)*n_elements,
volume_per_atom=200,
random_f_prime_d_min=1.0,
random_f_double_prime=anomalous_flag,
random_u_iso=True,
use_u_aniso=use_u_aniso,
random_occupancy=True)
check_weight_without_occupancy(structure_z)
f_z = structure_z.structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct").f_calc()
f_abs_z = abs(f_z)
f_rad_z = f_z.phases()
f_deg_z = f_z.phases(deg=True)
hl_z = generate_random_hl(miller_set=f_z)
hl_z_rad = hl_z.phase_integrals()
if (0 or verbose):
structure_z.show_summary().show_scatterers()
print "n_special_positions:", \
structure_z.special_position_indices().size()
z2p_op = structure_z.space_group().z2p_op()
z2p_op = sgtbx.change_of_basis_op(
z2p_op.c()
+ sgtbx.tr_vec((2,-1,3), 12).new_denominator(z2p_op.c().t().den()))
for change_hand in [False, True]:
if (change_hand):
z2p_op = z2p_op * sgtbx.change_of_basis_op("-x,-y,-z")
structure_p = structure_z.change_basis(z2p_op)
check_weight_without_occupancy(structure_p)
check_site_symmetry_table(structure_z, z2p_op, structure_p)
if (0 or verbose):
structure_p.show_summary().show_scatterers()
print "n_special_positions:", \
structure_p.special_position_indices().size()
assert tuple(structure_p.special_position_indices()) \
== tuple(structure_z.special_position_indices())
structure_pz = structure_p.change_basis(z2p_op.inverse())
check_weight_without_occupancy(structure_pz)
check_site_symmetry_table(structure_p, z2p_op.inverse(), structure_pz)
assert structure_pz.unit_cell().is_similar_to(structure_z.unit_cell())
assert structure_pz.space_group() == structure_z.space_group()
f_pz = f_z.structure_factors_from_scatterers(
xray_structure=structure_pz,
algorithm="direct").f_calc()
f_abs_pz = abs(f_pz)
f_rad_pz = f_pz.phases()
f_deg_pz = f_pz.phases(deg=True)
c = flex.linear_correlation(f_abs_z.data(), f_abs_pz.data())
assert c.is_well_defined()
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999
f_p_cb = f_z.change_basis(z2p_op)
f_abs_p_cb = f_abs_z.change_basis(z2p_op)
f_rad_p_cb = f_rad_z.change_basis(z2p_op, deg=False)
f_deg_p_cb = f_deg_z.change_basis(z2p_op, deg=True)
hl_p_cb = hl_z.change_basis(z2p_op)
hl_p_cb_rad = hl_p_cb.phase_integrals()
assert approx_equal(
hl_z_rad.change_basis(z2p_op).data(), hl_p_cb_rad.data())
assert f_abs_p_cb.indices().all_eq(f_p_cb.indices())
if (not change_hand):
o = flex.order(f_abs_p_cb.indices(), f_abs_z.indices())
else:
o = flex.order(-f_abs_p_cb.indices(), f_abs_z.indices())
if (f_abs_z.space_group().n_ltr() == 1):
assert o == 0
else:
assert o != 0
f_pz = f_p_cb.change_basis(z2p_op.inverse())
f_abs_pz = f_abs_p_cb.change_basis(z2p_op.inverse())
f_rad_pz = f_rad_p_cb.change_basis(z2p_op.inverse(), deg=False)
f_deg_pz = f_deg_p_cb.change_basis(z2p_op.inverse(), deg=True)
hl_pz = hl_p_cb.change_basis(z2p_op.inverse())
hl_pz_rad = hl_pz.phase_integrals()
assert approx_equal(hl_z_rad.data(), hl_pz_rad.data())
for i,o in zip(hl_z.data(), hl_pz.data()):
assert approx_equal(i, o)
assert approx_equal(
flex.max(flex.abs(f_pz.data() - f_z.data())), 0)
assert flex.order(f_abs_pz.indices(), f_abs_z.indices()) == 0
assert f_abs_pz.indices().all_eq(f_pz.indices())
assert approx_equal(flex.max(scitbx.math.phase_error(
phi1=f_rad_pz.data(), phi2=f_rad_z.data())), 0)
assert approx_equal(flex.max(scitbx.math.phase_error(
phi1=f_deg_pz.data(), phi2=f_deg_z.data(), deg=True)), 0)
assert approx_equal(f_deg_pz.data(), f_rad_pz.data()*(180/math.pi))
f_p_sf = f_p_cb.structure_factors_from_scatterers(
xray_structure=structure_p,
algorithm="direct").f_calc()
det = abs(z2p_op.c().r().determinant())
assert approx_equal(
flex.max(flex.abs(f_p_sf.data()*complex(det) - f_p_cb.data())), 0)
f_abs_p_sf = abs(f_p_sf)
f_rad_p_sf = f_p_sf.phases()
f_deg_p_sf = f_p_sf.phases(deg=True)
assert approx_equal(flex.max(scitbx.math.phase_error(
phi1=f_rad_p_sf.data(), phi2=f_rad_p_cb.data())), 0)
assert approx_equal(flex.max(scitbx.math.phase_error(
phi1=f_deg_p_sf.data(), phi2=f_deg_p_cb.data(), deg=True)), 0)
c = flex.linear_correlation(f_abs_p_sf.data(), f_abs_p_cb.data())
assert c.is_well_defined()
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999
def exercise(
space_group_info,
use_primitive_setting,
anomalous_flag,
use_u_aniso,
n_elements=3,
d_min=3.,
verbose=0):
if (use_primitive_setting):
space_group_info = space_group_info.primitive_setting()
structure = random_structure.xray_structure(
space_group_info,
elements=("Se",)*n_elements,
volume_per_atom=200,
random_f_prime_d_min=1.0,
random_f_double_prime=anomalous_flag,
random_u_iso=True,
use_u_aniso=use_u_aniso,
random_occupancy=True)
if (0 or verbose):
structure.show_summary().show_scatterers()
print "n_special_positions:", \
structure.special_position_indices().size()
structure_p1 = structure.expand_to_p1()
assert structure_p1.scatterers()[0].label == "Se1"
assert structure_p1.scatterers()[-1].label == ("Se%d" % n_elements)
structure_p1 = structure.expand_to_p1(append_number_to_labels=True)
if (0 or verbose):
structure_p1.show_summary().show_scatterers()
l,i = structure_p1.scatterers()[0].label.split("_")
assert l == "Se1"
assert int(i) == 0
l,i = structure_p1.scatterers()[-1].label.split("_")
assert l == ("Se%d" % n_elements)
assert int(i) \
== structure.site_symmetry_table().get(n_elements-1).multiplicity()-1
assert structure_p1.special_position_indices().size() == 0
f_calc = structure.structure_factors(
anomalous_flag=anomalous_flag, d_min=d_min, algorithm="direct").f_calc()
miller_set_p1 = miller.set.expand_to_p1(f_calc)
f_calc_p1 = f_calc.expand_to_p1()
assert flex.order(miller_set_p1.indices(), f_calc_p1.indices()) == 0
amplitudes = abs(f_calc)
amplitudes_p1 = amplitudes.expand_to_p1()
assert flex.order(miller_set_p1.indices(), amplitudes_p1.indices()) == 0
c = flex.linear_correlation(abs(f_calc_p1).data(), amplitudes_p1.data())
assert c.is_well_defined()
assert c.n() > 20
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999
for phase_deg in (False, True):
phases = f_calc.arg(phase_deg)
phases_p1 = phases.expand_to_p1(phase_deg)
assert flex.order(miller_set_p1.indices(), phases_p1.indices()) == 0
f_calc_p1_phases = f_calc_p1.arg(phase_deg)
for i,phase in enumerate(f_calc_p1_phases.data()):
e = scitbx.math.phase_error(phase, phases_p1.data()[i], deg=phase_deg)
assert e < 1.e-6
ctrl_amplitudes_p1 = abs(miller_set_p1.structure_factors_from_scatterers(
xray_structure=structure_p1,
algorithm="direct").f_calc())
c = flex.linear_correlation(amplitudes_p1.data(), ctrl_amplitudes_p1.data())
assert c.is_well_defined()
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999
def exercise(space_group_info,
use_primitive_setting,
anomalous_flag,
use_u_aniso,
n_elements=3,
d_min=3.,
verbose=0):
if (use_primitive_setting):
space_group_info = space_group_info.primitive_setting()
structure = random_structure.xray_structure(
space_group_info,
elements=("Se", ) * n_elements,
volume_per_atom=200,
random_f_prime_d_min=1.0,
random_f_double_prime=anomalous_flag,
random_u_iso=True,
use_u_aniso=use_u_aniso,
random_occupancy=True)
if (0 or verbose):
structure.show_summary().show_scatterers()
print "n_special_positions:", \
structure.special_position_indices().size()
structure_p1 = structure.expand_to_p1()
assert structure_p1.scatterers()[0].label == "Se1"
assert structure_p1.scatterers()[-1].label == ("Se%d" % n_elements)
structure_p1 = structure.expand_to_p1(append_number_to_labels=True)
if (0 or verbose):
structure_p1.show_summary().show_scatterers()
l, i = structure_p1.scatterers()[0].label.split("_")
assert l == "Se1"
assert int(i) == 0
l, i = structure_p1.scatterers()[-1].label.split("_")
assert l == ("Se%d" % n_elements)
assert int(i) \
== structure.site_symmetry_table().get(n_elements-1).multiplicity()-1
assert structure_p1.special_position_indices().size() == 0
f_calc = structure.structure_factors(anomalous_flag=anomalous_flag,
d_min=d_min,
algorithm="direct").f_calc()
miller_set_p1 = miller.set.expand_to_p1(f_calc)
f_calc_p1 = f_calc.expand_to_p1()
assert flex.order(miller_set_p1.indices(), f_calc_p1.indices()) == 0
amplitudes = abs(f_calc)
amplitudes_p1 = amplitudes.expand_to_p1()
assert flex.order(miller_set_p1.indices(), amplitudes_p1.indices()) == 0
c = flex.linear_correlation(abs(f_calc_p1).data(), amplitudes_p1.data())
assert c.is_well_defined()
assert c.n() > 20
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999
for phase_deg in (False, True):
phases = f_calc.arg(phase_deg)
phases_p1 = phases.expand_to_p1(phase_deg)
assert flex.order(miller_set_p1.indices(), phases_p1.indices()) == 0
f_calc_p1_phases = f_calc_p1.arg(phase_deg)
for i, phase in enumerate(f_calc_p1_phases.data()):
e = scitbx.math.phase_error(phase,
phases_p1.data()[i],
deg=phase_deg)
assert e < 1.e-6
ctrl_amplitudes_p1 = abs(
miller_set_p1.structure_factors_from_scatterers(
xray_structure=structure_p1, algorithm="direct").f_calc())
c = flex.linear_correlation(amplitudes_p1.data(),
ctrl_amplitudes_p1.data())
assert c.is_well_defined()
if (0 or verbose):
print "correlation:", c.coefficient()
assert c.coefficient() > 0.999