def __init__(self, xray_structure, n_real=None, grid_step=None):
assert [n_real, grid_step].count(None) == 1
self.xray_structure = xray_structure
if (n_real is None):
a_cell, b_cell, c_cell = xray_structure.unit_cell().parameters(
)[:3]
nx,ny,nz = \
int(a_cell/grid_step),int(b_cell/grid_step),int(c_cell/grid_step)
else:
nx, ny, nz = n_real[0], n_real[1], n_real[2]
#u_base = flex.min_default(xray_structure.extract_u_iso_or_u_equiv(),0)
u_base = xray_structure.min_u_cart_eigenvalue()
self.sampled_model_density = ext.sampled_model_density(
unit_cell=xray_structure.unit_cell(),
scatterers=xray_structure.scatterers(),
scattering_type_registry=xray_structure.scattering_type_registry(),
fft_n_real=(nx, ny, nz),
fft_m_real=(nx, ny, nz),
u_base=u_base,
wing_cutoff=1.e-6,
exp_table_one_over_step_size=-1000,
force_complex=False,
sampled_density_must_be_positive=False,
tolerance_positive_definite=1.e-5)
assert approx_equal(self.sampled_model_density.u_extra(), 0.0)
def __init__(self, xray_structure,
n_real = None,
grid_step = None):
assert [n_real, grid_step].count(None) == 1
self.xray_structure = xray_structure
if(n_real is None):
a_cell, b_cell, c_cell = xray_structure.unit_cell().parameters()[:3]
nx,ny,nz = \
int(a_cell/grid_step),int(b_cell/grid_step),int(c_cell/grid_step)
else:
nx,ny,nz = n_real[0],n_real[1],n_real[2]
#u_base = flex.min_default(xray_structure.extract_u_iso_or_u_equiv(),0)
u_base = xray_structure.min_u_cart_eigenvalue()
self.sampled_model_density = ext.sampled_model_density(
unit_cell = xray_structure.unit_cell(),
scatterers = xray_structure.scatterers(),
scattering_type_registry = xray_structure.scattering_type_registry(),
fft_n_real = (nx,ny,nz),
fft_m_real = (nx,ny,nz),
u_base = u_base,
wing_cutoff = 1.e-6,
exp_table_one_over_step_size = -1000,
force_complex = False,
sampled_density_must_be_positive = False,
tolerance_positive_definite = 1.e-5)
assert approx_equal(self.sampled_model_density.u_extra(), 0.0)
def __init__(self, manager, xray_structure, miller_set, algorithm="fft"):
scattering_type_registry = xray_structure.scattering_type_registry()
if (len(scattering_type_registry.unassigned_types()) > 0):
self.show_unknown_scatterers(registry=scattering_type_registry)
time_all = user_plus_sys_time()
managed_calculation_base.__init__(self,
manager,
xray_structure,
miller_set,
algorithm="fft")
assert miller_set.d_min() > manager.d_min() * (1 - 1e-6)
manager.setup_fft() # before timing
time_sampling = user_plus_sys_time()
sampled_density = ext.sampled_model_density(
unit_cell=xray_structure.unit_cell(),
scatterers=xray_structure.scatterers(),
scattering_type_registry=scattering_type_registry,
fft_n_real=manager.rfft().n_real(),
fft_m_real=manager.rfft().m_real(),
u_base=manager.u_base(),
wing_cutoff=manager.wing_cutoff(),
exp_table_one_over_step_size=manager.exp_table_one_over_step_size(
),
force_complex=manager.force_complex(),
sampled_density_must_be_positive=manager.
sampled_density_must_be_positive(),
tolerance_positive_definite=manager.tolerance_positive_definite())
time_sampling = time_sampling.elapsed()
time_fft = user_plus_sys_time()
if (not sampled_density.anomalous_flag()):
sf_map = manager.rfft().forward(sampled_density.real_map())
collect_conj = True
else:
sf_map = manager.cfft().backward(sampled_density.complex_map())
collect_conj = False
time_fft = time_fft.elapsed()
time_from_map = user_plus_sys_time()
self._f_calc_data = maptbx.structure_factors.from_map(
space_group=miller_set.space_group(),
anomalous_flag=sampled_density.anomalous_flag(),
miller_indices=miller_set.indices(),
complex_map=sf_map,
conjugate_flag=collect_conj).data()
time_from_map = time_from_map.elapsed()
time_apply_u_extra = user_plus_sys_time()
sampled_density.eliminate_u_extra_and_normalize(
miller_set.indices(), self._f_calc_data)
time_apply_u_extra = time_apply_u_extra.elapsed()
introspection.virtual_memory_info().update_max()
manager.estimate_time_fft.register(
n_scatterers=xray_structure.scatterers().size(),
n_miller_indices=miller_set.indices().size(),
time_sampling=time_sampling,
time_fft=time_fft,
time_from_or_to_map=time_from_map,
time_apply_u_extra=time_apply_u_extra)
global_counters.from_scatterers_fft.process(time_all.elapsed())
def __init__(self, manager,
xray_structure,
miller_set,
algorithm="fft"):
time_all = user_plus_sys_time()
managed_calculation_base.__init__(self,
manager, xray_structure, miller_set, algorithm="fft")
assert miller_set.d_min() > manager.d_min() * (1-1e-6)
manager.setup_fft() # before timing
time_sampling = user_plus_sys_time()
sampled_density = ext.sampled_model_density(
unit_cell=xray_structure.unit_cell(),
scatterers=xray_structure.scatterers(),
scattering_type_registry=xray_structure.scattering_type_registry(),
fft_n_real=manager.rfft().n_real(),
fft_m_real=manager.rfft().m_real(),
u_base=manager.u_base(),
wing_cutoff=manager.wing_cutoff(),
exp_table_one_over_step_size=manager.exp_table_one_over_step_size(),
force_complex=manager.force_complex(),
sampled_density_must_be_positive=
manager.sampled_density_must_be_positive(),
tolerance_positive_definite=manager.tolerance_positive_definite())
time_sampling = time_sampling.elapsed()
time_fft = user_plus_sys_time()
if (not sampled_density.anomalous_flag()):
sf_map = manager.rfft().forward(sampled_density.real_map())
collect_conj = True
else:
sf_map = manager.cfft().backward(sampled_density.complex_map())
collect_conj = False
time_fft = time_fft.elapsed()
time_from_map = user_plus_sys_time()
self._f_calc_data = maptbx.structure_factors.from_map(
space_group=miller_set.space_group(),
anomalous_flag=sampled_density.anomalous_flag(),
miller_indices=miller_set.indices(),
complex_map=sf_map,
conjugate_flag=collect_conj).data()
time_from_map = time_from_map.elapsed()
time_apply_u_extra = user_plus_sys_time()
sampled_density.eliminate_u_extra_and_normalize(
miller_set.indices(),
self._f_calc_data)
time_apply_u_extra = time_apply_u_extra.elapsed()
introspection.virtual_memory_info().update_max()
manager.estimate_time_fft.register(
n_scatterers=xray_structure.scatterers().size(),
n_miller_indices=miller_set.indices().size(),
time_sampling=time_sampling,
time_fft=time_fft,
time_from_or_to_map=time_from_map,
time_apply_u_extra=time_apply_u_extra)
global_counters.from_scatterers_fft.process(time_all.elapsed())
