def __init__(self,
xray_structure,
miller_set,
manager=None,
cos_sin_table=False,
algorithm="direct"):
"""Evaluate structure factors via direct calculations
:type xray_structure: cctbx.xray.structure
:param xray_structure: the X-ray structure to evaluate the structure factors of
:type miller_set: cctbx.miller.set
:param miller_set: the set of miller indices to evaluate the structure factors at
:type manager: cctbx.xray.structure_factors.manager
:param manager: ? (TODO: doc)
:type algorithm: string
:param algorithm: the name of the evaluation method, either \
"direct", "use_alt_parallel"
:type cos_sin_table: boolean
:param cos_sin_table: If set to 'True' a precalculated cos_sin_table is used \
instead of actual trigonometric functions. Using a manager overrides this \
setting with the one specified in the manager.
:rtype: cctbx.xray.structure_factors.from_scatterers_direct
:retruns: an instance `e` of `cctbx.xray.structure_factors.from_scatterers_direct` \
providing the evaluated structure factors as `e.f_calc()`
"""
time_all = user_plus_sys_time()
managed_calculation_base.__init__(self,
manager,
xray_structure,
miller_set,
algorithm="direct")
if hasattr(algorithm, "use_alt_parallel"):
#enumeration of indices() is fast compared to direct summation
from cctbx.xray.structure_factors.from_scatterers_direct_parallel import pprocess
pprocess(self, algorithm)
return
timer = user_plus_sys_time()
if (manager is not None):
cos_sin_table = manager.cos_sin_table()
if (cos_sin_table == True):
cos_sin_table = default_cos_sin_table
elif (cos_sin_table == False):
cos_sin_table = None
if (cos_sin_table is None):
self._results = ext.structure_factors_direct(
self._miller_set.unit_cell(), self._miller_set.space_group(),
self._miller_set.indices(), self._xray_structure.scatterers(),
self._xray_structure.scattering_type_registry())
else:
self._results = ext.structure_factors_direct(
cos_sin_table, self._miller_set.unit_cell(),
self._miller_set.space_group(), self._miller_set.indices(),
self._xray_structure.scatterers(),
self._xray_structure.scattering_type_registry())
if (manager is not None):
manager.estimate_time_direct.register(
xray_structure.scatterers().size() *
miller_set.indices().size(), timer.elapsed())
global_counters.from_scatterers_direct.process(time_all.elapsed())
def __init__(self, xray_structure,
miller_set,
manager=None,
cos_sin_table=False,
algorithm="direct"):
"""Evaluate structure factors via direct calculations
:type xray_structure: cctbx.xray.structure
:param xray_structure: the X-ray structure to evaluate the structure factors of
:type miller_set: cctbx.miller.set
:param miller_set: the set of miller indices to evaluate the structure factors at
:type manager: cctbx.xray.structure_factors.manager
:param manager: ? (TODO: doc)
:type algorithm: string
:param algorithm: the name of the evaluation method, either \
"direct", "use_alt_parallel"
:type cos_sin_table: boolean
:param cos_sin_table: If set to 'True' a precalculated cos_sin_table is used \
instead of actual trigonometric functions. Using a manager overrides this \
setting with the one specified in the manager.
:rtype: cctbx.xray.structure_factors.from_scatterers_direct
:retruns: an instance `e` of `cctbx.xray.structure_factors.from_scatterers_direct` \
providing the evaluated structure factors as `e.f_calc()`
"""
time_all = user_plus_sys_time()
managed_calculation_base.__init__(self,
manager, xray_structure, miller_set, algorithm="direct")
if hasattr(algorithm,"use_alt_parallel"):
#enumeration of indices() is fast compared to direct summation
from cctbx.xray.structure_factors.from_scatterers_direct_parallel import pprocess
pprocess(self,algorithm)
return
timer = user_plus_sys_time()
if (manager is not None):
cos_sin_table = manager.cos_sin_table()
if (cos_sin_table == True):
cos_sin_table = default_cos_sin_table
elif (cos_sin_table == False):
cos_sin_table = None
if (cos_sin_table is None):
self._results = ext.structure_factors_direct(
self._miller_set.unit_cell(),
self._miller_set.space_group(),
self._miller_set.indices(),
self._xray_structure.scatterers(),
self._xray_structure.scattering_type_registry())
else:
self._results = ext.structure_factors_direct(
cos_sin_table,
self._miller_set.unit_cell(),
self._miller_set.space_group(),
self._miller_set.indices(),
self._xray_structure.scatterers(),
self._xray_structure.scattering_type_registry())
if (manager is not None):
manager.estimate_time_direct.register(
xray_structure.scatterers().size() * miller_set.indices().size(),
timer.elapsed())
global_counters.from_scatterers_direct.process(time_all.elapsed())
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())
