cctbx.xray.minimization module

cctbx.xray.minimization.add_gradients(scatterers, xray_gradients, site_gradients=None, u_iso_gradients=None, u_aniso_gradients=None, occupancy_gradients=None)
class cctbx.xray.minimization.lbfgs(target_functor, xray_structure, occupancy_penalty=None, lbfgs_termination_params=None, lbfgs_core_params=None, correct_special_position_tolerance=0.01, cos_sin_table=True, structure_factor_algorithm=None, verbose=0)

Bases: object

A minimisation of a function of the free parameters of a X-ray structure, relying on the LBFGS algorithm.

That function is represented by a functor object f which should abide to the following interface

  • B{f.f_obs()}

  • B{f(f_calc, compute_derivatives)}

in the manner of cctbx.xray.target_functors.least_squares_residual or cctbx.xray.target_functors.intensity_correlation

apply_shifts()
callback_after_step(minimizer)
compute_functional_and_gradients()
compute_target(compute_gradients)
class cctbx.xray.minimization.occupancy_penalty_exp(penalty_factor=1, penalty_scale=100, min_functional=1e-10)

Bases: object

functional(occupancy)
gradient(occupancy)