def run_00():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 100,
volume_per_atom=50.0,
random_u_iso=True)
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group, reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(
xrs.unit_cell(), adptbx.random_u_cart(u_scale=1, u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start = adptbx.u_as_b(
adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
b_cart_start = [
b_cart_start[0] - tr, b_cart_start[1] - tr, b_cart_start[2] - tr,
b_cart_start[3], b_cart_start[4], b_cart_start[5]
]
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
F = xrs.structure_factors(d_min=2.0).f_calc()
u_star = adptbx.u_cart_as_u_star(F.unit_cell(),
adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data=flex.abs(fc.data() * fbc))
t0 = time.time()
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices(),
adp_constraint_matrix=adp_constraints.gradient_sum_matrix())
time_aniso_u_scaler += (time.time() - t0)
b_cart_final = adptbx.u_as_b(
adptbx.u_star_as_u_cart(
f_obs.unit_cell(),
adp_constraints.all_params(tuple(obj.u_star_independent))))
#
obj = bulk_solvent.aniso_u_scaler(f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices())
b_cart_final2 = adptbx.u_as_b(
adptbx.u_star_as_u_cart(f_obs.unit_cell(), tuple(obj.u_star)))
#
assert approx_equal(b_cart_final, b_cart_final2)
#print "Output b_cart:", " ".join(["%8.4f"%i for i in b_cart_final])
assert approx_equal(b_cart_start, b_cart_final, 1.e-4)
print("Time (aniso_u_scaler only): %6.4f" % time_aniso_u_scaler)
def run_00():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*100,
volume_per_atom = 50.0,
random_u_iso = True)
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group,
reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(),
adptbx.random_u_cart(u_scale=1,u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start=adptbx.u_as_b(adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
b_cart_start = [b_cart_start[0]-tr,b_cart_start[1]-tr,b_cart_start[2]-tr,
b_cart_start[3],b_cart_start[4],b_cart_start[5]]
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
F = xrs.structure_factors(d_min = 2.0).f_calc()
u_star = adptbx.u_cart_as_u_star(
F.unit_cell(), adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data = flex.abs(fc.data()*fbc))
t0 = time.time()
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = flex.abs(fc.data()),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
adp_constraint_matrix = adp_constraints.gradient_sum_matrix())
time_aniso_u_scaler += (time.time()-t0)
b_cart_final = adptbx.u_as_b(adptbx.u_star_as_u_cart(f_obs.unit_cell(),
adp_constraints.all_params(tuple(obj.u_star_independent))))
#
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = flex.abs(fc.data()),
f_obs = f_obs.data(),
miller_indices = f_obs.indices())
b_cart_final2 = adptbx.u_as_b(adptbx.u_star_as_u_cart(f_obs.unit_cell(),
tuple(obj.u_star)))
#
assert approx_equal(b_cart_final, b_cart_final2)
#print "Output b_cart:", " ".join(["%8.4f"%i for i in b_cart_final])
assert approx_equal(b_cart_start, b_cart_final, 1.e-4)
print "Time (aniso_u_scaler only): %6.4f"%time_aniso_u_scaler
def run_02():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol=symbol)
xrs = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 100,
volume_per_atom=50.0,
random_u_iso=True)
xrs.scattering_type_registry(table="wk1995")
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group, reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(
xrs.unit_cell(), adptbx.random_u_cart(u_scale=1, u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start = adptbx.u_as_b(
adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
b_cart_start = [
b_cart_start[0] - tr, b_cart_start[1] - tr, b_cart_start[2] - tr,
b_cart_start[3], b_cart_start[4], b_cart_start[5]
]
tr = (b_cart_start[0] + b_cart_start[1] + b_cart_start[2]) / 3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
reg = xrs.scattering_type_registry(table="wk1995", d_min=1 / 12)
f_000 = reg.sum_of_scattering_factors_at_diffraction_angle_0()
F = xrs.structure_factors(d_min=2.0).f_calc()
i = F.indices()
i.append([0, 0, 0])
d = F.data()
d.append(f_000)
F = F.customized_copy(indices=i, data=d)
u_star = adptbx.u_cart_as_u_star(F.unit_cell(),
adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data=flex.abs(fc.data() * fbc))
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
obj = bulk_solvent.aniso_u_scaler(f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices(),
unit_cell=f_obs.unit_cell())
a = obj.a
####
#print "Input a :", " ".join(["%7.3f"%i for i in a])
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), a, f_obs.unit_cell())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data()*overall_anisotropic_scale)
f_obs = abs(fc)
f_obs = f_obs.customized_copy(data=f_obs.data() *
overall_anisotropic_scale)
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
t0 = time.time()
obj = bulk_solvent.aniso_u_scaler(f_model_abs=flex.abs(fc.data()),
f_obs=f_obs.data(),
miller_indices=f_obs.indices(),
unit_cell=f_obs.unit_cell())
time_aniso_u_scaler += (time.time() - t0)
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), obj.a, f_obs.unit_cell())
assert approx_equal(
bulk_solvent.r_factor(f_obs.data(),
fc.data() * overall_anisotropic_scale), 0.0,
1.e-2) # XXX seems to be low
#print "Output a:", " ".join(["%7.3f"%i for i in obj.a])
assert approx_equal(a, obj.a, 1.e-4) # XXX can it be smaller?
assert overall_anisotropic_scale[len(overall_anisotropic_scale) -
1] == 1
print("Time (aniso_u_scaler only): %6.4f" % time_aniso_u_scaler)
def anisotropic_scaling(self, r_start):
r_expanal, r_poly, r_expmin = None, None, None
k_anisotropic_expanal, k_anisotropic_poly, \
k_anisotropic_expmin = None, None, None
scale_matrix_expanal, scale_matrix_poly, scale_matrix_expmin = None, None, None
sel = self.selection_work.data()
f_model_abs = flex.abs(
self.core.f_model_no_aniso_scale.data().select(sel))
f_obs = self.f_obs.data().select(sel)
mi = self.f_obs.indices().select(sel)
uc = self.f_obs.unit_cell()
mi_all = self.f_obs.indices()
# try exp_anal
if (self.try_expanal):
obj = bulk_solvent.aniso_u_scaler(
f_model_abs=f_model_abs,
f_obs=f_obs,
miller_indices=mi,
adp_constraint_matrix=self.adp_constraints.gradient_sum_matrix(
))
u_star = self.adp_constraints.all_params(
tuple(obj.u_star_independent))
scale_matrix_expanal = adptbx.u_as_b(
adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expanal = ext.k_anisotropic(mi_all, u_star)
r_expanal = self.try_scale(k_anisotropic=k_anisotropic_expanal)
if (self.verbose):
print >> self.log, " r_expanal: %6.4f" % r_expanal
# try poly
if (self.try_poly):
obj = bulk_solvent.aniso_u_scaler(f_model_abs=f_model_abs,
f_obs=f_obs,
miller_indices=mi,
unit_cell=uc)
scale_matrix_poly = obj.a
k_anisotropic_poly = ext.k_anisotropic(mi_all, obj.a, uc)
r_poly = self.try_scale(k_anisotropic=k_anisotropic_poly)
if (self.verbose):
print >> self.log, " r_poly : %6.4f" % r_poly
# pre-analyze
force_to_use_expmin = False
if (k_anisotropic_poly is not None and self.auto and r_poly < r_expanal
and (k_anisotropic_poly <= 0).count(True) > 0):
force_to_use_expmin = True
self.try_expmin = True
# try expmin
if (self.try_expmin):
zero = self.f_obs.select(sel).customized_copy(
data=flex.complex_double(f_obs.size(), 0))
fm = mmtbx.f_model.manager_kbu(
f_obs=self.f_obs.select(sel),
f_calc=self.core.f_model_no_aniso_scale.select(sel),
f_masks=[zero],
f_part1=zero,
f_part2=zero,
ss=self.ss)
obj = kbu_refinery.tgc(
f_obs=self.f_obs.select(sel),
f_calc=self.core.f_model_no_aniso_scale.select(sel),
f_masks=[zero],
ss=self.ss,
k_sols=[
0,
],
b_sols=[
0,
],
u_star=[0, 0, 0, 0, 0, 0])
obj.minimize_u()
u_star = obj.kbu.u_star()
scale_matrix_expmin = adptbx.u_as_b(
adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expmin = ext.k_anisotropic(mi_all, u_star)
r_expmin = self.try_scale(k_anisotropic=k_anisotropic_expmin)
if (self.verbose):
print >> self.log, " r_expmin : %6.4f" % r_expmin
if (force_to_use_expmin):
self.core = self.core.update(
k_anisotropic=k_anisotropic_expmin)
if (self.verbose):
self.format_scale_matrix(m=scale_matrix_expmin)
return
# select best
r = [(r_expanal, k_anisotropic_expanal, scale_matrix_expanal),
(r_poly, k_anisotropic_poly, scale_matrix_poly),
(r_expmin, k_anisotropic_expmin, scale_matrix_expmin)]
r_best = r_start
k_anisotropic_best = None
scale_matrix_best = None
for result in r:
r_factor, k_anisotropic, scale_matrix = result
if (r_factor is not None and r_factor < r_best):
r_best = r_factor
k_anisotropic_best = k_anisotropic.deep_copy()
scale_matrix_best = scale_matrix[:]
if (scale_matrix_best is None):
if (self.verbose):
print >> self.log, " result rejected due to r-factor increase"
else:
self.scale_matrices = scale_matrix_best
self.core = self.core.update(k_anisotropic=k_anisotropic_best)
r_aniso = self.r_factor()
if (self.verbose):
self.format_scale_matrix()
print >> self.log, " r_final : %6.4f" % r_aniso
def run_02():
time_aniso_u_scaler = 0
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
#print symbol, "-"*50
space_group_info = sgtbx.space_group_info(symbol = symbol)
xrs = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*100,
volume_per_atom = 50.0,
random_u_iso = True)
xrs.scattering_type_registry(table = "wk1995")
# XXX ad a method to adptbx to do this
point_group = sgtbx.space_group_info(
symbol=symbol).group().build_derived_point_group()
adp_constraints = sgtbx.tensor_rank_2_constraints(
space_group=point_group,
reciprocal_space=True)
u_star = adptbx.u_cart_as_u_star(xrs.unit_cell(),
adptbx.random_u_cart(u_scale=1,u_min=0.1))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
b_cart_start=adptbx.u_as_b(adptbx.u_star_as_u_cart(xrs.unit_cell(), u_star))
#
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
b_cart_start = [b_cart_start[0]-tr,b_cart_start[1]-tr,b_cart_start[2]-tr,
b_cart_start[3],b_cart_start[4],b_cart_start[5]]
tr = (b_cart_start[0]+b_cart_start[1]+b_cart_start[2])/3
#
#print "Input b_cart :", " ".join(["%8.4f"%i for i in b_cart_start]), "tr:", tr
reg = xrs.scattering_type_registry(table="wk1995", d_min=1/12)
f_000 = reg.sum_of_scattering_factors_at_diffraction_angle_0()
F = xrs.structure_factors(d_min = 2.0).f_calc()
i = F.indices()
i.append([0,0,0])
d = F.data()
d.append(f_000)
F = F.customized_copy(indices = i, data = d)
u_star = adptbx.u_cart_as_u_star(
F.unit_cell(), adptbx.b_as_u(b_cart_start))
fbc = mmtbx.f_model.ext.k_anisotropic(F.indices(), u_star)
fc = F.structure_factors_from_scatterers(xray_structure=xrs).f_calc()
f_obs = F.customized_copy(data = flex.abs(fc.data()*fbc))
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
obj = bulk_solvent.aniso_u_scaler(
f_model = fc.data(),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
unit_cell = f_obs.unit_cell())
a = obj.a
####
#print "Input a :", " ".join(["%7.3f"%i for i in a])
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), a, f_obs.unit_cell())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data()*overall_anisotropic_scale)
f_obs = abs(fc)
f_obs = f_obs.customized_copy(data = f_obs.data() * overall_anisotropic_scale)
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
#print bulk_solvent.r_factor(f_obs.data(), fmodel.f_model().data())
t0 = time.time()
obj = bulk_solvent.aniso_u_scaler(
f_model = fc.data(),
f_obs = f_obs.data(),
miller_indices = f_obs.indices(),
unit_cell = f_obs.unit_cell())
time_aniso_u_scaler += (time.time()-t0)
overall_anisotropic_scale = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), obj.a, f_obs.unit_cell())
assert approx_equal(bulk_solvent.r_factor(f_obs.data(),
fc.data()*overall_anisotropic_scale), 0.0, 1.e-2) # XXX seems to be low
#print "Output a:", " ".join(["%7.3f"%i for i in obj.a])
assert approx_equal(a, obj.a, 1.e-4) # XXX can it be smaller?
assert overall_anisotropic_scale[len(overall_anisotropic_scale)-1]==1
print "Time (aniso_u_scaler only): %6.4f"%time_aniso_u_scaler
def anisotropic_scaling(self, r_start):
r_expanal, r_poly, r_expmin = None,None,None
k_anisotropic_expanal, k_anisotropic_poly, \
k_anisotropic_expmin = None, None, None
scale_matrix_expanal, scale_matrix_poly, scale_matrix_expmin= None,None,None
sel = self.selection_work.data()
f_model_abs = flex.abs(self.core.f_model_no_aniso_scale.data().select(sel))
f_obs = self.f_obs.data().select(sel)
mi = self.f_obs.indices().select(sel)
uc = self.f_obs.unit_cell()
mi_all = self.f_obs.indices()
# try exp_anal
if(self.try_expanal):
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = f_model_abs,
f_obs = f_obs,
miller_indices = mi,
adp_constraint_matrix = self.adp_constraints.gradient_sum_matrix())
u_star = self.adp_constraints.all_params(tuple(obj.u_star_independent))
scale_matrix_expanal = adptbx.u_as_b(adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expanal = ext.k_anisotropic(mi_all, u_star)
r_expanal = self.try_scale(k_anisotropic = k_anisotropic_expanal)
if(self.verbose):
print >> self.log, " r_expanal: %6.4f"%r_expanal
# try poly
if(self.try_poly):
obj = bulk_solvent.aniso_u_scaler(
f_model_abs = f_model_abs,
f_obs = f_obs,
miller_indices = mi,
unit_cell = uc)
scale_matrix_poly = obj.a
k_anisotropic_poly = ext.k_anisotropic(mi_all, obj.a, uc)
r_poly = self.try_scale(k_anisotropic = k_anisotropic_poly)
if(self.verbose):
print >> self.log, " r_poly : %6.4f"%r_poly
# pre-analyze
force_to_use_expmin=False
if(k_anisotropic_poly is not None and self.auto and r_poly<r_expanal and
(k_anisotropic_poly<=0).count(True)>0):
force_to_use_expmin = True
self.try_expmin = True
# try expmin
if(self.try_expmin):
zero = self.f_obs.select(sel).customized_copy(data =
flex.complex_double(f_obs.size(), 0))
fm = mmtbx.f_model.manager_kbu(
f_obs = self.f_obs.select(sel),
f_calc = self.core.f_model_no_aniso_scale.select(sel),
f_masks = [zero],
f_part1 = zero,
f_part2 = zero,
ss = self.ss)
obj = kbu_refinery.tgc(
f_obs = self.f_obs.select(sel),
f_calc = self.core.f_model_no_aniso_scale.select(sel),
f_masks = [zero],
ss = self.ss,
k_sols = [0,],
b_sols = [0,],
u_star = [0,0,0,0,0,0])
obj.minimize_u()
u_star = obj.kbu.u_star()
scale_matrix_expmin = adptbx.u_as_b(adptbx.u_star_as_u_cart(uc, u_star))
k_anisotropic_expmin = ext.k_anisotropic(mi_all, u_star)
r_expmin = self.try_scale(k_anisotropic = k_anisotropic_expmin)
if(self.verbose): print >> self.log, " r_expmin : %6.4f"%r_expmin
if(force_to_use_expmin):
self.core = self.core.update(k_anisotropic = k_anisotropic_expmin)
if(self.verbose):
self.format_scale_matrix(m=scale_matrix_expmin)
return
# select best
r = [(r_expanal, k_anisotropic_expanal, scale_matrix_expanal),
(r_poly, k_anisotropic_poly, scale_matrix_poly),
(r_expmin, k_anisotropic_expmin, scale_matrix_expmin)]
r_best = r_start
k_anisotropic_best = None
scale_matrix_best = None
for result in r:
r_factor, k_anisotropic, scale_matrix = result
if(r_factor is not None and r_factor < r_best):
r_best = r_factor
k_anisotropic_best = k_anisotropic.deep_copy()
scale_matrix_best = scale_matrix[:]
if(scale_matrix_best is None):
if(self.verbose):
print >> self.log, " result rejected due to r-factor increase"
else:
self.scale_matrices = scale_matrix_best
self.core = self.core.update(k_anisotropic = k_anisotropic_best)
r_aniso = self.r_factor()
if(self.verbose):
self.format_scale_matrix()
print >> self.log, " r_final : %6.4f"%r_aniso