def __init__(self, manager,
xray_structure,
u_iso_refinable_params,
miller_set,
d_target_d_f_calc,
n_parameters):
time_all = time_apply_u_extra = user_plus_sys_time()
gradients_base.__init__(self,
manager, xray_structure, miller_set, algorithm="fft")
self._d_target_d_f_calc = d_target_d_f_calc
manager.setup_fft() # before timing
time_apply_u_extra = user_plus_sys_time()
self._results = ext.fast_gradients(
unit_cell=xray_structure.unit_cell(),
scatterers=xray_structure.scatterers(),
scattering_type_registry=xray_structure.scattering_type_registry(),
u_base=manager.u_base(),
wing_cutoff=manager.wing_cutoff(),
exp_table_one_over_step_size=manager.exp_table_one_over_step_size(),
tolerance_positive_definite=manager.tolerance_positive_definite())
coeff = self._gradient_map_coeff()
time_apply_u_extra = time_apply_u_extra.elapsed()
time_from_or_to_map = user_plus_sys_time()
coeff_map = self._gradient_map_coeff_to_map(coeff)
time_from_or_to_map = time_from_or_to_map.elapsed()
time_fft = user_plus_sys_time()
if (not coeff.anomalous_flag()):
gradient_map = manager.rfft().backward(coeff_map.complex_map())
else:
gradient_map = manager.cfft().backward(coeff_map.complex_map())
time_fft = time_fft.elapsed()
time_sampling = user_plus_sys_time()
self._results.sampling(
scatterers=xray_structure.scatterers(),
u_iso_refinable_params=u_iso_refinable_params,
scattering_type_registry=xray_structure.scattering_type_registry(),
site_symmetry_table=xray_structure.site_symmetry_table(),
ft_d_target_d_f_calc=gradient_map,
n_parameters=n_parameters,
sampled_density_must_be_positive=
manager.sampled_density_must_be_positive())
time_sampling = time_sampling.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_or_to_map,
time_apply_u_extra=time_apply_u_extra)
self.d_target_d_site_frac_was_used = False
self.d_target_d_u_star_was_used = False
global_counters.gradients_fft.process(time_all.elapsed())
def __init__(self, manager, xray_structure, u_iso_refinable_params,
miller_set, d_target_d_f_calc, n_parameters):
time_all = time_apply_u_extra = user_plus_sys_time()
gradients_base.__init__(self,
manager,
xray_structure,
miller_set,
algorithm="fft")
self._d_target_d_f_calc = d_target_d_f_calc
manager.setup_fft() # before timing
time_apply_u_extra = user_plus_sys_time()
self._results = ext.fast_gradients(
unit_cell=xray_structure.unit_cell(),
scatterers=xray_structure.scatterers(),
scattering_type_registry=xray_structure.scattering_type_registry(),
u_base=manager.u_base(),
wing_cutoff=manager.wing_cutoff(),
exp_table_one_over_step_size=manager.exp_table_one_over_step_size(
),
tolerance_positive_definite=manager.tolerance_positive_definite())
coeff = self._gradient_map_coeff()
time_apply_u_extra = time_apply_u_extra.elapsed()
time_from_or_to_map = user_plus_sys_time()
coeff_map = self._gradient_map_coeff_to_map(coeff)
time_from_or_to_map = time_from_or_to_map.elapsed()
time_fft = user_plus_sys_time()
if (not coeff.anomalous_flag()):
gradient_map = manager.rfft().backward(coeff_map.complex_map())
else:
gradient_map = manager.cfft().backward(coeff_map.complex_map())
time_fft = time_fft.elapsed()
time_sampling = user_plus_sys_time()
self._results.sampling(
scatterers=xray_structure.scatterers(),
u_iso_refinable_params=u_iso_refinable_params,
scattering_type_registry=xray_structure.scattering_type_registry(),
site_symmetry_table=xray_structure.site_symmetry_table(),
ft_d_target_d_f_calc=gradient_map,
n_parameters=n_parameters,
sampled_density_must_be_positive=manager.
sampled_density_must_be_positive())
time_sampling = time_sampling.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_or_to_map,
time_apply_u_extra=time_apply_u_extra)
self.d_target_d_site_frac_was_used = False
self.d_target_d_u_star_was_used = False
global_counters.gradients_fft.process(time_all.elapsed())
def __init__(self, xray_structure,
u_iso_refinable_params,
miller_set,
d_target_d_f_calc,
n_parameters,
manager=None,
cos_sin_table=False):
time_all = user_plus_sys_time()
gradients_base.__init__(self,
manager, xray_structure, miller_set, algorithm="direct")
self._d_target_d_f_calc = d_target_d_f_calc
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_gradients_direct(
self._miller_set.unit_cell(),
self._miller_set.space_group(),
self._miller_set.indices(),
self._xray_structure.scatterers(),
u_iso_refinable_params,
self._xray_structure.scattering_type_registry(),
self._xray_structure.site_symmetry_table(),
d_target_d_f_calc,
n_parameters)
else:
self._results = ext.structure_factors_gradients_direct(
cos_sin_table,
self._miller_set.unit_cell(),
self._miller_set.space_group(),
self._miller_set.indices(),
self._xray_structure.scatterers(),
u_iso_refinable_params,
self._xray_structure.scattering_type_registry(),
self._xray_structure.site_symmetry_table(),
d_target_d_f_calc,
n_parameters)
if (manager is not None):
manager.estimate_time_direct.register(
xray_structure.scatterers().size() * miller_set.indices().size(),
timer.elapsed())
self.d_target_d_site_cart_was_used = False
self.d_target_d_u_cart_was_used = False
global_counters.gradients_direct.process(time_all.elapsed())
def __init__(self,
xray_structure,
u_iso_refinable_params,
miller_set,
d_target_d_f_calc,
n_parameters,
manager=None,
cos_sin_table=False):
time_all = user_plus_sys_time()
gradients_base.__init__(self,
manager,
xray_structure,
miller_set,
algorithm="direct")
self._d_target_d_f_calc = d_target_d_f_calc
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_gradients_direct(
self._miller_set.unit_cell(), self._miller_set.space_group(),
self._miller_set.indices(), self._xray_structure.scatterers(),
u_iso_refinable_params,
self._xray_structure.scattering_type_registry(),
self._xray_structure.site_symmetry_table(), d_target_d_f_calc,
n_parameters)
else:
self._results = ext.structure_factors_gradients_direct(
cos_sin_table, self._miller_set.unit_cell(),
self._miller_set.space_group(), self._miller_set.indices(),
self._xray_structure.scatterers(), u_iso_refinable_params,
self._xray_structure.scattering_type_registry(),
self._xray_structure.site_symmetry_table(), d_target_d_f_calc,
n_parameters)
if (manager is not None):
manager.estimate_time_direct.register(
xray_structure.scatterers().size() *
miller_set.indices().size(), timer.elapsed())
self.d_target_d_site_cart_was_used = False
self.d_target_d_u_cart_was_used = False
global_counters.gradients_direct.process(time_all.elapsed())