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())
Exemple #2
0
 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())
Exemple #4
0
 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())