def exercise_covariance():
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
(5.01,5.01,5.47,90,90,120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1/2.,1/2.,1/3.)),
xray.scatterer("O", (0.197,-0.197,0.83333))]))
uc = xs.unit_cell()
flags = xs.scatterer_flags()
for f in flags:
f.set_grad_site(True)
xs.set_scatterer_flags(flags)
cov = flex.double((1e-8,1e-9,2e-9,3e-9,4e-9,5e-9,
2e-8,1e-9,2e-9,3e-9,4e-9,
3e-8,1e-9,2e-9,3e-9,
2e-8,1e-9,2e-9,
3e-8,1e-9,
4e-8))
param_map = xs.parameter_map()
assert approx_equal(cov,
covariance.extract_covariance_matrix_for_sites(flex.size_t([0,1]), cov, param_map))
cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map)
O = matrix.sqr(uc.orthogonalization_matrix())
for i in range(param_map.n_scatterers):
cov_i = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov, param_map)
cov_i_cart = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov_cart, param_map)
assert approx_equal(
O * matrix.sym(sym_mat3=cov_i) * O.transpose(),
matrix.sym(sym_mat3=cov_i_cart).as_mat3())
for f in flags: f.set_grads(False)
flags[0].set_grad_u_aniso(True)
flags[0].set_use_u_aniso(True)
flags[1].set_grad_u_iso(True)
flags[1].set_use_u_iso(True)
xs.set_scatterer_flags(flags)
param_map = xs.parameter_map()
cov = flex.double(7*7, 0)
cov.reshape(flex.grid(7,7))
cov.matrix_diagonal_set_in_place(flex.double([i for i in range(7)]))
cov = cov.matrix_symmetric_as_packed_u()
assert approx_equal([i for i in range(6)],
covariance.extract_covariance_matrix_for_u_aniso(
0, cov, param_map).matrix_packed_u_diagonal())
assert covariance.variance_for_u_iso(1, cov, param_map) == 6
try: covariance.variance_for_u_iso(0, cov, param_map)
except RuntimeError: pass
else: raise Exception_expected
try: covariance.extract_covariance_matrix_for_u_aniso(1, cov, param_map)
except RuntimeError: pass
else: raise Exception_expected
approx_equal(covariance.extract_covariance_matrix_for_sites(
flex.size_t([1]), cov, param_map), (0,0,0,0,0,0))
def exercise_covariance():
xs = xray.structure(crystal_symmetry=crystal.symmetry(
(5.01, 5.01, 5.47, 90, 90, 120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1 / 2., 1 / 2., 1 / 3.)),
xray.scatterer("O", (0.197, -0.197, 0.83333))
]))
uc = xs.unit_cell()
flags = xs.scatterer_flags()
for f in flags:
f.set_grad_site(True)
xs.set_scatterer_flags(flags)
cov = flex.double(
(1e-8, 1e-9, 2e-9, 3e-9, 4e-9, 5e-9, 2e-8, 1e-9, 2e-9, 3e-9, 4e-9,
3e-8, 1e-9, 2e-9, 3e-9, 2e-8, 1e-9, 2e-9, 3e-8, 1e-9, 4e-8))
param_map = xs.parameter_map()
assert approx_equal(
cov,
covariance.extract_covariance_matrix_for_sites(flex.size_t([0, 1]),
cov, param_map))
cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map)
O = matrix.sqr(uc.orthogonalization_matrix())
for i in range(param_map.n_scatterers):
cov_i = covariance.extract_covariance_matrix_for_sites(
flex.size_t([i]), cov, param_map)
cov_i_cart = covariance.extract_covariance_matrix_for_sites(
flex.size_t([i]), cov_cart, param_map)
assert approx_equal(O * matrix.sym(sym_mat3=cov_i) * O.transpose(),
matrix.sym(sym_mat3=cov_i_cart).as_mat3())
for f in flags:
f.set_grads(False)
flags[0].set_grad_u_aniso(True)
flags[0].set_use_u_aniso(True)
flags[1].set_grad_u_iso(True)
flags[1].set_use_u_iso(True)
xs.set_scatterer_flags(flags)
param_map = xs.parameter_map()
cov = flex.double(7 * 7, 0)
cov.reshape(flex.grid(7, 7))
cov.matrix_diagonal_set_in_place(flex.double([i for i in range(7)]))
cov = cov.matrix_symmetric_as_packed_u()
assert approx_equal([i for i in range(6)],
covariance.extract_covariance_matrix_for_u_aniso(
0, cov, param_map).matrix_packed_u_diagonal())
assert covariance.variance_for_u_iso(1, cov, param_map) == 6
try:
covariance.variance_for_u_iso(0, cov, param_map)
except RuntimeError:
pass
else:
raise Exception_expected
try:
covariance.extract_covariance_matrix_for_u_aniso(1, cov, param_map)
except RuntimeError:
pass
else:
raise Exception_expected
approx_equal(
covariance.extract_covariance_matrix_for_sites(flex.size_t([1]), cov,
param_map),
(0, 0, 0, 0, 0, 0))
def __init__(self,
xray_structure,
covariance_matrix=None,
cell_covariance_matrix=None):
crystal_symmetry_as_cif_block.__init__(
self,
xray_structure.crystal_symmetry(),
cell_covariance_matrix=cell_covariance_matrix)
scatterers = xray_structure.scatterers()
uc = xray_structure.unit_cell()
if covariance_matrix is not None:
param_map = xray_structure.parameter_map()
covariance_diagonal = covariance_matrix.matrix_packed_u_diagonal()
u_star_to_u_cif_linear_map_pow2 = flex.pow2(
flex.double(uc.u_star_to_u_cif_linear_map()))
u_star_to_u_iso_linear_form = matrix.row(
uc.u_star_to_u_iso_linear_form())
fmt = "%.6f"
# _atom_site_* loop
atom_site_loop = model.loop(
header=('_atom_site_label', '_atom_site_type_symbol',
'_atom_site_fract_x', '_atom_site_fract_y',
'_atom_site_fract_z', '_atom_site_U_iso_or_equiv',
'_atom_site_adp_type', '_atom_site_occupancy'))
for i_seq, sc in enumerate(scatterers):
# site
if covariance_matrix is not None and sc.flags.grad_site():
site = []
for i in range(3):
idx = param_map[i_seq].site
if idx > -1:
var = covariance_diagonal[idx + i]
else:
var = 0
if var > 0:
site.append(
format_float_with_su(sc.site[i], math.sqrt(var)))
else:
site.append(fmt % sc.site[i])
else:
site = [fmt % sc.site[i] for i in range(3)]
# u_eq
if (covariance_matrix is not None
and (sc.flags.grad_u_iso() or sc.flags.grad_u_aniso())):
if sc.flags.grad_u_iso():
u_iso_or_equiv = format_float_with_su(
sc.u_iso,
math.sqrt(
covariance.variance_for_u_iso(
i_seq, covariance_matrix, param_map)))
else:
cov = covariance.extract_covariance_matrix_for_u_aniso(
i_seq, covariance_matrix,
param_map).matrix_packed_u_as_symmetric()
var = (u_star_to_u_iso_linear_form *
matrix.sqr(cov)).dot(u_star_to_u_iso_linear_form)
u_iso_or_equiv = format_float_with_su(
sc.u_iso_or_equiv(uc), math.sqrt(var))
else:
u_iso_or_equiv = fmt % sc.u_iso_or_equiv(uc)
if sc.flags.use_u_aniso():
adp_type = 'Uani'
else:
adp_type = 'Uiso'
atom_site_loop.add_row(
(sc.label, sc.scattering_type, site[0], site[1], site[2],
u_iso_or_equiv, adp_type, fmt % sc.occupancy))
self.cif_block.add_loop(atom_site_loop)
# _atom_site_aniso_* loop
aniso_scatterers = scatterers.select(scatterers.extract_use_u_aniso())
if aniso_scatterers.size():
labels = list(scatterers.extract_labels())
aniso_loop = model.loop(
header=('_atom_site_aniso_label', '_atom_site_aniso_U_11',
'_atom_site_aniso_U_22', '_atom_site_aniso_U_33',
'_atom_site_aniso_U_12', '_atom_site_aniso_U_13',
'_atom_site_aniso_U_23'))
for sc in aniso_scatterers:
u_cif = adptbx.u_star_as_u_cif(uc, sc.u_star)
if covariance_matrix is not None:
row = [sc.label]
idx = param_map[labels.index(sc.label)].u_aniso
if idx > -1:
var = covariance_diagonal[
idx:idx + 6] * u_star_to_u_cif_linear_map_pow2
for i in range(6):
if var[i] > 0:
row.append(
format_float_with_su(
u_cif[i], math.sqrt(var[i])))
else:
row.append(fmt % u_cif[i])
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
aniso_loop.add_row(row)
self.cif_block.add_loop(aniso_loop)
self.cif_block.add_loop(atom_type_cif_loop(xray_structure))
def __init__(self, xray_structure, covariance_matrix=None, cell_covariance_matrix=None):
crystal_symmetry_as_cif_block.__init__(
self, xray_structure.crystal_symmetry(), cell_covariance_matrix=cell_covariance_matrix
)
scatterers = xray_structure.scatterers()
uc = xray_structure.unit_cell()
if covariance_matrix is not None:
param_map = xray_structure.parameter_map()
covariance_diagonal = covariance_matrix.matrix_packed_u_diagonal()
u_star_to_u_cif_linear_map_pow2 = flex.pow2(flex.double(uc.u_star_to_u_cif_linear_map()))
u_star_to_u_iso_linear_form = matrix.row(uc.u_star_to_u_iso_linear_form())
fmt = "%.6f"
# _atom_site_* loop
atom_site_loop = model.loop(
header=(
"_atom_site_label",
"_atom_site_type_symbol",
"_atom_site_fract_x",
"_atom_site_fract_y",
"_atom_site_fract_z",
"_atom_site_U_iso_or_equiv",
"_atom_site_adp_type",
"_atom_site_occupancy",
)
)
for i_seq, sc in enumerate(scatterers):
site = occu = u_iso_or_equiv = None
# site
if covariance_matrix is not None:
params = param_map[i_seq]
if sc.flags.grad_site() and params.site >= 0:
site = []
for i in range(3):
site.append(format_float_with_su(sc.site[i], math.sqrt(covariance_diagonal[params.site + i])))
# occupancy
if sc.flags.grad_occupancy() and params.occupancy >= 0:
occu = format_float_with_su(sc.occupancy, math.sqrt(covariance_diagonal[params.occupancy]))
# Uiso/eq
if sc.flags.grad_u_iso() or sc.flags.grad_u_aniso():
if sc.flags.grad_u_iso():
u_iso_or_equiv = format_float_with_su(
sc.u_iso, math.sqrt(covariance.variance_for_u_iso(i_seq, covariance_matrix, param_map))
)
else:
cov = covariance.extract_covariance_matrix_for_u_aniso(
i_seq, covariance_matrix, param_map
).matrix_packed_u_as_symmetric()
var = (u_star_to_u_iso_linear_form * matrix.sqr(cov)).dot(u_star_to_u_iso_linear_form)
u_iso_or_equiv = format_float_with_su(sc.u_iso_or_equiv(uc), math.sqrt(var))
if site is None:
site = [fmt % sc.site[i] for i in range(3)]
if occu is None:
occu = fmt % sc.occupancy
if u_iso_or_equiv is None:
u_iso_or_equiv = fmt % sc.u_iso_or_equiv(uc)
if sc.flags.use_u_aniso():
adp_type = "Uani"
else:
adp_type = "Uiso"
atom_site_loop.add_row(
(sc.label, sc.scattering_type, site[0], site[1], site[2], u_iso_or_equiv, adp_type, occu)
)
self.cif_block.add_loop(atom_site_loop)
# _atom_site_aniso_* loop
aniso_scatterers = scatterers.select(scatterers.extract_use_u_aniso())
if aniso_scatterers.size():
labels = list(scatterers.extract_labels())
aniso_loop = model.loop(
header=(
"_atom_site_aniso_label",
"_atom_site_aniso_U_11",
"_atom_site_aniso_U_22",
"_atom_site_aniso_U_33",
"_atom_site_aniso_U_12",
"_atom_site_aniso_U_13",
"_atom_site_aniso_U_23",
)
)
for sc in aniso_scatterers:
u_cif = adptbx.u_star_as_u_cif(uc, sc.u_star)
if covariance_matrix is not None:
row = [sc.label]
idx = param_map[labels.index(sc.label)].u_aniso
if idx > -1:
var = covariance_diagonal[idx : idx + 6] * u_star_to_u_cif_linear_map_pow2
for i in range(6):
if var[i] > 0:
row.append(format_float_with_su(u_cif[i], math.sqrt(var[i])))
else:
row.append(fmt % u_cif[i])
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
else:
row = [sc.label] + [fmt % u_cif[i] for i in range(6)]
aniso_loop.add_row(row)
self.cif_block.add_loop(aniso_loop)
self.cif_block.add_loop(atom_type_cif_loop(xray_structure))
