def exercise_lbfgs(test_case, use_geo, out, d_min=2):
sites_cart, geo_manager = cctbx.geometry_restraints.manager.\
construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=flex.vec3_double(test_case.sites),
edge_list_bonds=test_case.bonds,
edge_list_angles=test_case.angles())
scatterers = flex.xray_scatterer(sites_cart.size(),
xray.scatterer(scattering_type="C", b=20))
for sc, lbl in zip(scatterers, test_case.labels):
sc.label = lbl
structure = xray.structure(crystal_symmetry=geo_manager.crystal_symmetry,
scatterers=scatterers)
structure.set_sites_cart(sites_cart=sites_cart)
f_calc = structure.structure_factors(d_min=d_min,
anomalous_flag=False).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
if (use_geo):
axis = matrix.col(flex.random_double_point_on_sphere())
rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(axis=axis,
angle=25,
deg=True)
trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0
structure.apply_rigid_body_shift(rot=rot, trans=trans)
geo_manager.energies_sites(sites_cart=structure.sites_cart()).show(
f=out)
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
geometry_restraints_manager=geo_manager,
gradients_method="fd",
real_space_target_weight=1,
real_space_gradients_delta=d_min / 3)
geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out)
else:
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
unit_cell=structure.unit_cell(),
gradients_method="fd",
real_space_gradients_delta=d_min / 3)
rmsd_start = sites_cart.rms_difference(structure.sites_cart())
rmsd_final = sites_cart.rms_difference(minimized.sites_cart)
print("RMSD start, final:", rmsd_start, rmsd_final, file=out)
if (use_geo):
assert rmsd_start >= 1 - 1e-6
assert rmsd_final < 0.2
def show_f_g(label, f, g):
print(label, "f, |g|:", f, flex.mean_sq(g)**0.5, file=out)
show_f_g(label="start", f=minimized.f_start, g=minimized.g_start)
show_f_g(label="final", f=minimized.f_final, g=minimized.g_final)
assert minimized.f_final <= minimized.f_start
return minimized
def exercise_lbfgs(test_case, use_geo, out, d_min=2):
sites_cart, geo_manager = cctbx.geometry_restraints.manager.construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=flex.vec3_double(test_case.sites),
edge_list_bonds=test_case.bonds,
edge_list_angles=test_case.angles())
scatterers = flex.xray_scatterer(
sites_cart.size(), xray.scatterer(scattering_type="C", b=20))
for sc,lbl in zip(scatterers, test_case.labels):
sc.label = lbl
structure = xray.structure(
crystal_symmetry=geo_manager.crystal_symmetry,
scatterers=scatterers)
structure.set_sites_cart(sites_cart=sites_cart)
f_calc = structure.structure_factors(
d_min=d_min, anomalous_flag=False).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
if (use_geo):
axis = matrix.col(flex.random_double_point_on_sphere())
rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(
axis=axis, angle=25, deg=True)
trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0
structure.apply_rigid_body_shift(rot=rot, trans=trans)
geo_manager.energies_sites(sites_cart=structure.sites_cart()).show(f=out)
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
geometry_restraints_manager=geo_manager,
real_space_target_weight=1,
real_space_gradients_delta=d_min/3)
geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out)
else:
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
unit_cell=structure.unit_cell(),
real_space_gradients_delta=d_min/3)
rmsd_start = sites_cart.rms_difference(structure.sites_cart())
rmsd_final = sites_cart.rms_difference(minimized.sites_cart)
print >> out, "RMSD start, final:", rmsd_start, rmsd_final
if (use_geo):
assert rmsd_start >= 1-1e-6
assert rmsd_final < 0.2
def show_f_g(label, f, g):
print >> out, label, "f, |g|:", f, flex.mean_sq(g)**0.5
show_f_g(label="start", f=minimized.f_start, g=minimized.g_start)
show_f_g(label="final", f=minimized.f_final, g=minimized.g_final)
assert minimized.f_final <= minimized.f_start
return minimized
def exercise_subtract_continuous_allowed_origin_shifts(space_group_info,
use_niggli_cell,
n_elements=3):
structure = random_structure.xray_structure(space_group_info,
elements=["Si"] * n_elements,
volume_per_atom=300,
min_distance=3.,
general_positions_only=False)
if (use_niggli_cell):
structure = structure.niggli_cell()
f_obs = abs(
structure.structure_factors(d_min=3, algorithm="direct").f_calc())
assert f_obs.indices().size() >= 10
transl = matrix.col(flex.random_double_point_on_sphere()) * 2.345
transl_no_cont = matrix.col(
structure.subtract_continuous_allowed_origin_shifts(
translation_cart=transl))
transl_cont = transl - transl_no_cont
structure_transl = structure.apply_shift(
shift=structure.unit_cell().fractionalize(transl_cont),
recompute_site_symmetries=True)
f_transl = abs(
f_obs.structure_factors_from_scatterers(
xray_structure=structure_transl, algorithm="direct").f_calc())
assert approx_equal(f_transl.data(), f_obs.data())
def exercise_subtract_continuous_allowed_origin_shifts(
space_group_info,
use_niggli_cell,
n_elements=3):
structure = random_structure.xray_structure(
space_group_info,
elements=["Si"]*n_elements,
volume_per_atom=300,
min_distance=3.,
general_positions_only=False)
if (use_niggli_cell):
structure = structure.niggli_cell()
f_obs = abs(structure.structure_factors(
d_min=3, algorithm="direct").f_calc())
assert f_obs.indices().size() >= 10
transl = matrix.col(flex.random_double_point_on_sphere()) * 2.345
transl_no_cont = matrix.col(
structure.subtract_continuous_allowed_origin_shifts(
translation_cart=transl))
transl_cont = transl - transl_no_cont
structure_transl = structure.apply_shift(
shift=structure.unit_cell().fractionalize(transl_cont),
recompute_site_symmetries=True)
f_transl = abs(f_obs.structure_factors_from_scatterers(
xray_structure=structure_transl, algorithm="direct").f_calc())
assert approx_equal(f_transl.data(), f_obs.data())
