def __init__(self,
fmodels,
constrained_groups_selections,
selections,
par_initial,
max_number_of_iterations):
adopt_init_args(self, locals())
self.fmodels.create_target_functors()
self.fmodels.prepare_target_functors_for_minimization()
from phenix.refinement import weight_xray_chem
self.weights = weight_xray_chem.weights(wx = 1,
wx_scale = 1,
angle_x = None,
wn = 1,
wn_scale = 1,
angle_n = None,
w = 0,
wxn = 1) # XXX
self.par_min = self.par_initial.deep_copy()
self.x = self.pack(self.par_min)
self.n = self.x.size()
self.minimizer = lbfgs.run(
target_evaluator = self,
termination_params = lbfgs.termination_parameters(
max_iterations = max_number_of_iterations),
exception_handling_params = lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True,
ignore_line_search_failed_step_at_upper_bound = True))
self.compute_functional_and_gradients()
del self.x
def __init__(self,
fmodels,
constrained_groups_selections,
selections,
par_initial,
max_number_of_iterations):
adopt_init_args(self, locals())
self.fmodels.create_target_functors()
self.fmodels.prepare_target_functors_for_minimization()
from phenix.refinement import weight_xray_chem
self.weights = weight_xray_chem.weights(wx = 1,
wx_scale = 1,
angle_x = None,
wn = 1,
wn_scale = 1,
angle_n = None,
w = 0,
wxn = 1) # XXX
self.par_min = self.par_initial.deep_copy()
self.x = self.pack(self.par_min)
self.n = self.x.size()
self.minimizer = lbfgs.run(
target_evaluator = self,
termination_params = lbfgs.termination_parameters(
max_iterations = max_number_of_iterations),
exception_handling_params = lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True,
ignore_line_search_failed_step_at_upper_bound = True))
self.compute_functional_and_gradients()
del self.x
def __init__(self, fmodels,
restraints_manager = None,
model = None,
is_neutron_scat_table = None,
target_weights = None,
tan_b_iso_max = None,
refine_xyz = False,
refine_adp = False,
lbfgs_termination_params = None,
use_fortran = False,
verbose = 0,
correct_special_position_tolerance = 1.0,
iso_restraints = None,
h_params = None,
qblib_params = None,
macro_cycle = None,
u_min = adptbx.b_as_u(-5.0),
u_max = adptbx.b_as_u(999.99),
collect_monitor = True,
log = None):
timer = user_plus_sys_time()
adopt_init_args(self, locals())
self.f=None
self.xray_structure = self.fmodels.fmodel_xray().xray_structure
self.fmodels.create_target_functors()
self.fmodels.prepare_target_functors_for_minimization()
if(self.refine_adp and fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
self.weights = None
# QBLIB INSERT
self.qblib_params = qblib_params
if(self.qblib_params is not None and self.qblib_params.qblib):
self.macro = macro_cycle
self.qblib_cycle_count = 0
self.tmp_XYZ = None
self.XYZ_diff_curr=None
# QBLIB END
self.correct_special_position_tolerance = correct_special_position_tolerance
if(refine_xyz and target_weights is not None):
self.weights = target_weights.xyz_weights_result
elif(refine_adp and target_weights is not None):
self.weights = target_weights.adp_weights_result
else:
from phenix.refinement import weight_xray_chem
self.weights = weight_xray_chem.weights(wx = 1,
wx_scale = 1,
angle_x = None,
wn = 1,
wn_scale = 1,
angle_n = None,
w = 0,
wxn = 1)
if(self.collect_monitor):
self.monitor = monitor(
weights = self.weights,
fmodels = fmodels,
model = model,
iso_restraints = iso_restraints,
refine_xyz = refine_xyz,
refine_adp = refine_adp,
refine_occ = False)
if(self.collect_monitor): self.monitor.collect()
self.neutron_refinement = (self.fmodels.fmodel_n is not None)
self.x = flex.double(self.xray_structure.n_parameters(), 0)
self._scatterers_start = self.xray_structure.scatterers()
self.minimizer = scitbx.lbfgs.run(
target_evaluator = self,
termination_params = lbfgs_termination_params,
use_fortran = use_fortran,
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True))
self.apply_shifts()
del self._scatterers_start
self.compute_target(compute_gradients = False,u_iso_refinable_params = None)
if(self.refine_adp and self.fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
if(self.collect_monitor):
self.monitor.collect(iter = self.minimizer.iter(),
nfun = self.minimizer.nfun())
self.fmodels.create_target_functors()
# QBLIB INSERT
if(self.qblib_params is not None and self.qblib_params.qblib):
print >>self.qblib_params.qblib_log,'{:-^80}'.format("")
print >>self.qblib_params.qblib_log
def __init__(self, fmodels,
restraints_manager = None,
model = None,
is_neutron_scat_table = None,
target_weights = None,
refine_xyz = False,
refine_adp = False,
lbfgs_termination_params = None,
use_fortran = False,
verbose = 0,
correct_special_position_tolerance = 1.0,
iso_restraints = None,
h_params = None,
qblib_params = None,
macro_cycle = None,
u_min = adptbx.b_as_u(-5.0),
u_max = adptbx.b_as_u(999.99),
collect_monitor = True,
log = None):
timer = user_plus_sys_time()
adopt_init_args(self, locals())
self.f=None
self.xray_structure = self.fmodels.fmodel_xray().xray_structure
self.fmodels.create_target_functors()
self.fmodels.prepare_target_functors_for_minimization()
if(self.refine_adp and fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
self.weights = None
# QBLIB INSERT
self.qblib_params = qblib_params
if(self.qblib_params is not None and self.qblib_params.qblib):
self.macro = macro_cycle
self.qblib_cycle_count = 0
self.tmp_XYZ = None
self.XYZ_diff_curr=None
# QBLIB END
self.correct_special_position_tolerance = correct_special_position_tolerance
if(refine_xyz and target_weights is not None):
self.weights = target_weights.xyz_weights_result
elif(refine_adp and target_weights is not None):
self.weights = target_weights.adp_weights_result
else:
from phenix.refinement import weight_xray_chem
self.weights = weight_xray_chem.weights(wx = 1,
wx_scale = 1,
angle_x = None,
wn = 1,
wn_scale = 1,
angle_n = None,
w = 0,
wxn = 1)
if(self.collect_monitor):
self.monitor = monitor(
weights = self.weights,
fmodels = fmodels,
model = model,
iso_restraints = iso_restraints,
refine_xyz = refine_xyz,
refine_adp = refine_adp,
refine_occ = False)
if(self.collect_monitor): self.monitor.collect()
self.neutron_refinement = (self.fmodels.fmodel_n is not None)
self.x = flex.double(self.xray_structure.n_parameters(), 0)
self.riding_h_manager = self.model.riding_h_manager
self._scatterers_start = self.xray_structure.scatterers()
#lbfgs_core_params = scitbx.lbfgs.core_parameters(
# stpmin = 1.e-9,
# stpmax = adptbx.b_as_u(10))
self.minimizer = scitbx.lbfgs.run(
target_evaluator = self,
termination_params = lbfgs_termination_params,
use_fortran = use_fortran,
# core_params = lbfgs_core_params,
# gradient_only=True,
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True))
self.apply_shifts()
del self._scatterers_start
self.compute_target(compute_gradients = False,u_iso_refinable_params = None)
if(self.refine_adp and self.fmodels.fmodel_neutron() is None):
self.xray_structure.tidy_us()
self.fmodels.update_xray_structure(
xray_structure = self.xray_structure,
update_f_calc = True)
if(self.collect_monitor):
self.monitor.collect(iter = self.minimizer.iter(),
nfun = self.minimizer.nfun())
self.fmodels.create_target_functors()
# QBLIB INSERT
if(self.qblib_params is not None and self.qblib_params.qblib):
print('{:-^80}'.format(""), file=self.qblib_params.qblib_log)
print(file=self.qblib_params.qblib_log)
