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))