def exercise_tensor_constraints_core(crystal_symmetry):
from cctbx import crystal
from cctbx import adptbx
from scitbx import matrix
site_symmetry = crystal.special_position_settings(
crystal_symmetry).site_symmetry(site=(0, 0, 0))
unit_cell = crystal_symmetry.unit_cell()
group = crystal_symmetry.space_group()
assert site_symmetry.n_matrices() == group.order_p()
for reciprocal_space in [False, True]:
c_tensor_constraints = sgtbx.tensor_rank_2_constraints(
space_group=group,
reciprocal_space=reciprocal_space).row_echelon_form()
p_tensor_constraints = python_tensor_constraints(
self=group, reciprocal_space=reciprocal_space)
assert c_tensor_constraints.all_eq(p_tensor_constraints)
adp_constraints = group.adp_constraints()
u_cart_p1 = adptbx.random_u_cart()
u_star_p1 = adptbx.u_cart_as_u_star(unit_cell, u_cart_p1)
u_star = site_symmetry.average_u_star(u_star_p1)
f = unit_cell.volume()**(2 / 3.)
assert approx_equal(
list(matrix.col(group.average_u_star(u_star=u_star_p1)) * f),
list(matrix.col(u_star) * f))
independent_params = adp_constraints.independent_params(u_star)
assert adp_constraints.n_independent_params() == len(independent_params)
assert adp_constraints.n_independent_params() \
+ adp_constraints.n_dependent_params() == 6
u_star_vfy = adp_constraints.all_params(independent_params)
u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star)
u_cart_vfy = adptbx.u_star_as_u_cart(unit_cell, list(u_star_vfy))
assert approx_equal(u_cart_vfy, u_cart)
def exercise_derivatives(space_group_info, out):
crystal_symmetry = space_group_info.any_compatible_crystal_symmetry(
volume=1000)
space_group = space_group_info.group()
adp_constraints = space_group.adp_constraints()
m = adp_constraints.row_echelon_form()
print >> out, matrix.rec(m, (m.size()//6, 6)).mathematica_form(
one_row_per_line=True)
print >> out, list(adp_constraints.independent_indices)
u_cart_p1 = adptbx.random_u_cart()
u_star_p1 = adptbx.u_cart_as_u_star(crystal_symmetry.unit_cell(), u_cart_p1)
u_star = space_group.average_u_star(u_star_p1)
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry, d_min=3, anomalous_flag=False)
for h in miller_set.indices():
grads_fin = d_dw_d_u_star_finite(h=h, u_star=u_star)
print >> out, "grads_fin:", list(grads_fin)
grads_ana = d_dw_d_u_star_analytical(h=h, u_star=u_star)
print >> out, "grads_ana:", list(grads_ana)
compare_derivatives(grads_ana, grads_fin)
curvs_fin = d2_dw_d_u_star_d_u_star_finite(h=h, u_star=u_star)
print >> out, "curvs_fin:", list(curvs_fin)
curvs_ana = d2_dw_d_u_star_d_u_star_analytical(h=h, u_star=u_star)
print >> out, "curvs_ana:", list(curvs_ana)
compare_derivatives(curvs_ana, curvs_fin)
#
u_indep = adp_constraints.independent_params(u_star)
grads_indep_fin = d_dw_d_u_indep_finite(
adp_constraints=adp_constraints, h=h, u_indep=u_indep)
print >> out, "grads_indep_fin:", list(grads_indep_fin)
grads_indep_ana = flex.double(adp_constraints.independent_gradients(
all_gradients=list(grads_ana)))
print >> out, "grads_indep_ana:", list(grads_indep_ana)
compare_derivatives(grads_indep_ana, grads_indep_fin)
curvs_indep_fin = d2_dw_d_u_indep_d_u_indep_finite(
adp_constraints=adp_constraints, h=h, u_indep=u_indep)
print >> out, "curvs_indep_fin:", list(curvs_indep_fin)
curvs_indep_ana = adp_constraints.independent_curvatures(
all_curvatures=curvs_ana)
print >> out, "curvs_indep_ana:", list(curvs_indep_ana)
compare_derivatives(curvs_indep_ana, curvs_indep_fin)
#
curvs_indep_mm = None
if (str(space_group_info) == "P 1 2 1"):
assert list(adp_constraints.independent_indices) == [0,1,2,4]
curvs_indep_mm = p2_curv(h, u_star)
elif (str(space_group_info) == "P 4"):
assert list(adp_constraints.independent_indices) == [1,2]
curvs_indep_mm = p4_curv(h, u_star)
elif (str(space_group_info) in ["P 3", "P 6"]):
assert list(adp_constraints.independent_indices) == [2,3]
curvs_indep_mm = p3_curv(h, u_star)
elif (str(space_group_info) == "P 2 3"):
assert list(adp_constraints.independent_indices) == [2]
curvs_indep_mm = p23_curv(h, u_star)
if (curvs_indep_mm is not None):
curvs_indep_mm = flex.double(
curvs_indep_mm).matrix_symmetric_as_packed_u()
print >> out, "curvs_indep_mm:", list(curvs_indep_mm)
compare_derivatives(curvs_indep_ana, curvs_indep_mm)
def exercise_tensor_constraints_core(crystal_symmetry):
from cctbx import crystal
from cctbx import adptbx
from scitbx import matrix
site_symmetry = crystal.special_position_settings(
crystal_symmetry).site_symmetry(site=(0,0,0))
unit_cell = crystal_symmetry.unit_cell()
group = crystal_symmetry.space_group()
assert site_symmetry.n_matrices() == group.order_p()
for reciprocal_space in [False, True]:
c_tensor_constraints = sgtbx.tensor_rank_2_constraints(
space_group=group,
reciprocal_space=reciprocal_space).row_echelon_form()
p_tensor_constraints = python_tensor_constraints(
self=group, reciprocal_space=reciprocal_space)
assert c_tensor_constraints.all_eq(p_tensor_constraints)
adp_constraints = group.adp_constraints()
u_cart_p1 = adptbx.random_u_cart()
u_star_p1 = adptbx.u_cart_as_u_star(unit_cell, u_cart_p1)
u_star = site_symmetry.average_u_star(u_star_p1)
f = unit_cell.volume()**(2/3.)
assert approx_equal(
list(matrix.col(group.average_u_star(u_star=u_star_p1))*f),
list(matrix.col(u_star)*f))
independent_params = adp_constraints.independent_params(u_star)
assert adp_constraints.n_independent_params() == len(independent_params)
assert adp_constraints.n_independent_params() \
+ adp_constraints.n_dependent_params() == 6
u_star_vfy = adp_constraints.all_params(independent_params)
u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star)
u_cart_vfy = adptbx.u_star_as_u_cart(unit_cell, list(u_star_vfy))
assert approx_equal(u_cart_vfy, u_cart)
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 ru(crystal_symmetry, u_scale=1, u_min=0.1):
from cctbx import sgtbx
symbol = crystal_symmetry.space_group().type().lookup_symbol()
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(crystal_symmetry.unit_cell(),
adptbx.random_u_cart(u_scale=u_scale,u_min=u_min))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
r = flex.sym_mat3_double()
r.append(adptbx.u_star_as_u_cart(crystal_symmetry.unit_cell(), u_star))
return r
def ru(crystal_symmetry, u_scale=1, u_min=0.1):
from cctbx import sgtbx
symbol = crystal_symmetry.space_group().type().lookup_symbol()
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(
crystal_symmetry.unit_cell(),
adptbx.random_u_cart(u_scale=u_scale, u_min=u_min))
u_indep = adp_constraints.independent_params(all_params=u_star)
u_star = adp_constraints.all_params(independent_params=u_indep)
r = flex.sym_mat3_double()
r.append(adptbx.u_star_as_u_cart(crystal_symmetry.unit_cell(), u_star))
return r
def __init__(self):
sgi = sgtbx.space_group_info("Hall: %s" % self.hall)
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
xs = xray.structure(crystal.special_position_settings(cs))
for i, sc in enumerate(self.scatterers()):
sc.flags.set_use_u_iso(False).set_use_u_aniso(True)\
.set_grad_u_aniso(True)
xs.add_scatterer(sc)
site_symm = xs.site_symmetry_table().get(i)
u_cart = adptbx.random_u_cart(u_scale=self.random_u_cart_scale)
u_star = adptbx.u_cart_as_u_star(cs.unit_cell(), u_cart)
xs.scatterers()[-1].u_star = site_symm.average_u_star(u_star)
self.xray_structure = xs
mi = cs.build_miller_set(d_min=0.5, anomalous_flag=False)
ma = mi.structure_factors_from_scatterers(xs, algorithm="direct").f_calc()
self.fo_sq = ma.norm().customized_copy(
sigmas=flex.double(ma.size(), 1.))
def __init__(self):
sgi = sgtbx.space_group_info("Hall: %s" % self.hall)
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
xs = xray.structure(crystal.special_position_settings(cs))
for i, sc in enumerate(self.scatterers()):
sc.flags.set_use_u_iso(False).set_use_u_aniso(True)\
.set_grad_u_aniso(True)
xs.add_scatterer(sc)
site_symm = xs.site_symmetry_table().get(i)
u_cart = adptbx.random_u_cart(u_scale=self.random_u_cart_scale)
u_star = adptbx.u_cart_as_u_star(cs.unit_cell(), u_cart)
xs.scatterers()[-1].u_star = site_symm.average_u_star(u_star)
self.xray_structure = xs
mi = cs.build_miller_set(d_min=0.5, anomalous_flag=False)
ma = mi.structure_factors_from_scatterers(xs, algorithm="direct").f_calc()
self.fo_sq = ma.norm().customized_copy(
sigmas=flex.double(ma.size(), 1.))
def exercise_02_b_cart_sym_constr(d_min = 2.0, tolerance = 1.e-6):
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
space_group_info = sgtbx.space_group_info(symbol = symbol)
xray_structure = get_xray_structure_random(space_group_info)
sg = xray_structure.space_group()
uc = xray_structure.unit_cell()
u_cart_p1 = adptbx.random_u_cart(u_scale=5, u_min=5)
u_star_p1 = adptbx.u_cart_as_u_star(uc, u_cart_p1)
b_cart_1 = adptbx.u_star_as_u_cart(uc, u_star_p1)
b_cart_2 = adptbx.u_star_as_u_cart(uc, sg.average_u_star(u_star = u_star_p1))
for b_cart in (b_cart_1, b_cart_2):
f_obs, r_free_flags = \
get_f_obs_freer(d_min = d_min,
k_sol = 0,
b_sol = 0,
b_cart = b_cart,
xray_structure = xray_structure)
fmodel = mmtbx.f_model.manager(
r_free_flags = r_free_flags,
f_obs = f_obs,
xray_structure = xray_structure)
for flag in (True, False):
params = bss.master_params.extract()
params.bulk_solvent = False
params.anisotropic_scaling = True
params.k_sol_b_sol_grid_search = False
params.minimization_k_sol_b_sol = False
params.minimization_b_cart = True
params.symmetry_constraints_on_b_cart = flag
params.max_iterations = 50
params.min_iterations = 50
result = bss.bulk_solvent_and_scales(
fmodel_kbu = fmodel.fmodel_kbu(), params = params)
if(flag == False and approx_equal(b_cart, b_cart_1, out=None)):
assert approx_equal(result.b_cart(), b_cart, tolerance)
if(flag == True and approx_equal(b_cart, b_cart_2, out=None)):
assert approx_equal(result.b_cart(), b_cart, tolerance)
if(flag == False and approx_equal(b_cart, b_cart_2, out=None)):
assert approx_equal(result.b_cart(), b_cart, tolerance)
if(flag == True and approx_equal(b_cart, b_cart_1, out=None)):
for u2, ufm in zip(b_cart_2, result.b_cart()):
if(abs(u2) < 1.e-6): assert approx_equal(ufm, 0.0, tolerance)
def exercise_02_b_cart_sym_constr(d_min=2.0, tolerance=1.e-6):
for symbol in sgtbx.bravais_types.acentric + sgtbx.bravais_types.centric:
space_group_info = sgtbx.space_group_info(symbol=symbol)
xray_structure = get_xray_structure_random(space_group_info)
sg = xray_structure.space_group()
uc = xray_structure.unit_cell()
u_cart_p1 = adptbx.random_u_cart(u_scale=5, u_min=5)
u_star_p1 = adptbx.u_cart_as_u_star(uc, u_cart_p1)
b_cart_1 = adptbx.u_star_as_u_cart(uc, u_star_p1)
b_cart_2 = adptbx.u_star_as_u_cart(uc,
sg.average_u_star(u_star=u_star_p1))
for b_cart in (b_cart_1, b_cart_2):
f_obs, r_free_flags = \
get_f_obs_freer(d_min = d_min,
k_sol = 0,
b_sol = 0,
b_cart = b_cart,
xray_structure = xray_structure)
fmodel = mmtbx.f_model.manager(r_free_flags=r_free_flags,
f_obs=f_obs,
xray_structure=xray_structure)
flag = True
params = bss.master_params.extract()
params.number_of_macro_cycles = 3
params.bulk_solvent = False
params.anisotropic_scaling = True
params.k_sol_b_sol_grid_search = False
params.minimization_k_sol_b_sol = False
params.minimization_b_cart = True
params.symmetry_constraints_on_b_cart = flag
params.max_iterations = 50
params.min_iterations = 50
result = bss.bulk_solvent_and_scales(
fmodel_kbu=fmodel.fmodel_kbu(), params=params)
if (flag == True and approx_equal(b_cart, b_cart_2, out=None)):
assert approx_equal(result.b_cart(), b_cart, tolerance)
if (flag == True and approx_equal(b_cart, b_cart_1, out=None)):
for u2, ufm in zip(b_cart_2, result.b_cart()):
if (abs(u2) < 1.e-6):
assert approx_equal(ufm, 0.0, tolerance)
def exercise(small=1.e-9):
for symbol in ["P 1"]:
space_group_info = sgtbx.space_group_info(symbol=symbol)
random_xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=["N"] * 10,
volume_per_atom=50.0,
random_u_iso=False,
u_iso=adptbx.b_as_u(20.0))
sg = random_xray_structure.space_group()
uc = random_xray_structure.unit_cell()
print(symbol, uc)
print()
sys.stdout.flush()
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
counter += 1
r = random.random()
if (r < 0.333):
m = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
n = adptbx.random_u_cart(u_scale=20. * random.random(),
u_min=0)
while 1:
for ind in range(6):
r = random.random()
m = flex.double(m)
if (r > 0.5):
m[ind] = n[ind]
m = list(m)
if (adptbx.is_positive_definite(m, 0)
and adptbx.is_positive_definite(n, 0)):
break
elif (r >= 0.333 and r < 0.66):
m, n = branch_3_mn()
else:
m, n = branch_2_mn(0)
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
m = factor(list(m), i)
n = factor(list(n), i)
qq = tools.common(n, m, small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if (qq.branch_0()): branch_0 += 1
if (qq.branch_1()): branch_1 += 1
if (qq.branch_1_1()): branch_1_1 += 1
if (qq.branch_1_2()): branch_1_2 += 1
if (qq.branch_1_2_1()): branch_1_2_1 += 1
if (qq.branch_1_2_2()): branch_1_2_2 += 1
if (qq.branch_1_2_3()): branch_1_2_3 += 1
if (qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if (qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print("." * 30, symbol)
print("i= ", i, "out of ", trials)
print("branch_0 = ", branch_0)
print("branch_1 = ", branch_1)
print("branch_1_1 = ", branch_1_1)
print("branch_1_2 = ", branch_1_2)
print("branch_1_2_1 = ", branch_1_2_1)
print("branch_1_2_2 = ", branch_1_2_2)
print("branch_1_2_3 = ", branch_1_2_3)
print("branch_1_2_3_1 = ", branch_1_2_3_1)
print("branch_1_2_3_2 = ", branch_1_2_3_2)
sys.stdout.flush()
def build_scatterers(self,
elements,
sites_frac=None,
grid=None,
t_centre_of_inversion=None):
existing_sites = [scatterer.site for scatterer in self.scatterers()]
if (sites_frac is None):
all_sites = random_sites(
special_position_settings=self,
existing_sites=existing_sites,
n_new=len(elements),
min_hetero_distance=self.min_distance,
general_positions_only=self.general_positions_only,
grid=grid,
t_centre_of_inversion=t_centre_of_inversion)
else:
assert len(sites_frac) == len(elements)
all_sites = existing_sites + list(sites_frac)
assert len(all_sites) <= self.n_scatterers
sf_dict = {}
for element in elements:
if (not sf_dict.has_key(element)):
sf_dict[element] = eltbx.xray_scattering.best_approximation(element)
fp = 0
fdp = 0
n_existing = self.scatterers().size()
i_label = n_existing
for element,site in zip(elements, all_sites[n_existing:]):
i_label += 1
scatterer = xray.scatterer(
label=element + str(i_label),
scattering_type=element,
site=site)
site_symmetry = scatterer.apply_symmetry(
self.unit_cell(),
self.space_group(),
self.min_distance_sym_equiv())
if (self.random_f_prime_d_min):
f0 = sf_dict[element].at_d_star_sq(1./self.random_f_prime_d_min**2)
assert f0 > 0
fp = -f0 * random.random() * self.random_f_prime_scale
if (self.random_f_double_prime):
f0 = sf_dict[element].at_d_star_sq(0)
fdp = f0 * random.random() * self.random_f_double_prime_scale
scatterer.fp = fp
scatterer.fdp = fdp
if (self.use_u_iso_):
scatterer.flags.set_use_u_iso_only()
u_iso = self.u_iso
if (not u_iso and self.random_u_iso):
u_iso = random.random() * self.random_u_iso_scale \
+ self.random_u_iso_min
scatterer.u_iso = u_iso
if (self.use_u_aniso):
scatterer.flags.set_use_u_aniso_only()
run_away_counter = 0
while 1:
run_away_counter += 1
assert run_away_counter < 100
u_cart = adptbx.random_u_cart(u_scale=self.random_u_cart_scale)
scatterer.u_star = site_symmetry.average_u_star(
adptbx.u_cart_as_u_star(
self.unit_cell(), u_cart))
u_cart = adptbx.u_star_as_u_cart(self.unit_cell(), scatterer.u_star)
eigenvalues = adptbx.eigenvalues(u_cart)
if (min(eigenvalues) > 0.001):
break
if (self.random_occupancy):
scatterer.occupancy = self.random_occupancy_min \
+ (1-self.random_occupancy_min)*random.random()
self.add_scatterer(scatterer)
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 exercise(space_group_info,
n_elements=10,
table="wk1995",
d_min=2.0,
k_sol=0.35,
b_sol=45.0,
b_cart=None,
quick=False,
verbose=0):
xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=(("O", "N", "C") * (n_elements // 3 + 1))[:n_elements],
volume_per_atom=100,
min_distance=1.5,
general_positions_only=True,
random_u_iso=False,
random_occupancy=False)
xray_structure.scattering_type_registry(table=table)
sg = xray_structure.space_group()
uc = xray_structure.unit_cell()
u_cart_1 = adptbx.random_u_cart(u_scale=5, u_min=5)
u_star_1 = adptbx.u_cart_as_u_star(uc, u_cart_1)
b_cart = adptbx.u_star_as_u_cart(uc, sg.average_u_star(u_star=u_star_1))
for anomalous_flag in [False, True]:
scatterers = xray_structure.scatterers()
if (anomalous_flag):
assert scatterers.size() >= 7
for i in [1, 7]:
scatterers[i].fp = -0.2
scatterers[i].fdp = 5
have_non_zero_fdp = True
else:
for i in [1, 7]:
scatterers[i].fp = 0
scatterers[i].fdp = 0
have_non_zero_fdp = False
f_obs = abs(
xray_structure.structure_factors(
d_min=d_min,
anomalous_flag=anomalous_flag,
cos_sin_table=sfg_params.cos_sin_table,
algorithm=sfg_params.algorithm).f_calc())
f_obs_comp = f_obs.structure_factors_from_scatterers(
xray_structure=xray_structure,
algorithm=sfg_params.algorithm,
cos_sin_table=sfg_params.cos_sin_table).f_calc()
f_obs = abs(f_obs_comp)
flags = f_obs.generate_r_free_flags(fraction=0.1, max_free=99999999)
#flags = flags.array(data = flex.bool(f_obs.data().size(), False))
xrs = xray_structure.deep_copy_scatterers()
xrs.shake_sites_in_place(rms_difference=0.3)
for target in mmtbx.refinement.targets.target_names:
if target == "mli": continue
if (quick):
if (target not in ["ls_wunit_k1", "ml", "mlhl", "ml_sad"]):
continue
if (target == "mlhl"):
if (have_non_zero_fdp): continue # XXX gradients not correct!
experimental_phases = generate_random_hl(miller_set=f_obs)
else:
experimental_phases = None
if (target == "ml_sad"
and (not anomalous_flag
or mmtbx.refinement.targets.phaser is None)):
continue
print(" ", target)
xray.set_scatterer_grad_flags(scatterers=xrs.scatterers(),
site=True)
ss = 1. / flex.pow2(f_obs.d_spacings().data()) / 4.
u_star = adptbx.u_cart_as_u_star(f_obs.unit_cell(),
adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), u_star)
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
fmodel = mmtbx.f_model.manager(
xray_structure=xrs,
f_obs=f_obs,
r_free_flags=flags,
target_name=target,
abcd=experimental_phases,
sf_and_grads_accuracy_params=sfg_params,
k_mask=k_mask,
k_anisotropic=k_anisotropic,
mask_params=masks.mask_master_params.extract())
fmodel.update_xray_structure(xray_structure=xrs,
update_f_calc=True,
update_f_mask=True)
xray.set_scatterer_grad_flags(
scatterers=fmodel.xray_structure.scatterers(), site=True)
fmodel.update_xray_structure(update_f_calc=True)
t_f = fmodel.target_functor()
t_f.prepare_for_minimization()
gs = t_f(compute_gradients=True).d_target_d_site_cart().as_double()
gfd = finite_differences_site(target_functor=t_f)
cc = flex.linear_correlation(gs, gfd).coefficient()
if (0 or verbose):
print("ana:", list(gs))
print("fin:", list(gfd))
print("rat:", [f / a for a, f in zip(gs, gfd)])
print(target, "corr:", cc, space_group_info)
print()
diff = gs - gfd
diff /= max(1, flex.max(flex.abs(gfd)))
tolerance = 1.2e-5
assert approx_equal(abs(flex.min(diff)), 0.0, tolerance)
assert approx_equal(abs(flex.mean(diff)), 0.0, tolerance)
assert approx_equal(abs(flex.max(diff)), 0.0, tolerance)
assert approx_equal(cc, 1.0, tolerance)
fmodel.model_error_ml()
def build_scatterers(self,
elements,
sites_frac=None,
grid=None,
t_centre_of_inversion=None):
existing_sites = [scatterer.site for scatterer in self.scatterers()]
if (sites_frac is None):
all_sites = random_sites(
special_position_settings=self,
existing_sites=existing_sites,
n_new=len(elements),
min_hetero_distance=self.min_distance,
general_positions_only=self.general_positions_only,
grid=grid,
t_centre_of_inversion=t_centre_of_inversion)
else:
assert len(sites_frac) == len(elements)
all_sites = existing_sites + list(sites_frac)
assert len(all_sites) <= self.n_scatterers
sf_dict = {}
for element in elements:
if (not sf_dict.has_key(element)):
sf_dict[element] = eltbx.xray_scattering.best_approximation(
element)
fp = 0
fdp = 0
n_existing = self.scatterers().size()
i_label = n_existing
for element, site in zip(elements, all_sites[n_existing:]):
i_label += 1
scatterer = xray.scatterer(label=element + str(i_label),
scattering_type=element,
site=site)
site_symmetry = scatterer.apply_symmetry(
self.unit_cell(), self.space_group(),
self.min_distance_sym_equiv())
if (self.random_f_prime_d_min):
f0 = sf_dict[element].at_d_star_sq(
1. / self.random_f_prime_d_min**2)
assert f0 > 0
fp = -f0 * random.random() * self.random_f_prime_scale
if (self.random_f_double_prime):
f0 = sf_dict[element].at_d_star_sq(0)
fdp = f0 * random.random() * self.random_f_double_prime_scale
scatterer.fp = fp
scatterer.fdp = fdp
if (self.use_u_iso_):
scatterer.flags.set_use_u_iso_only()
u_iso = self.u_iso
if (not u_iso and self.random_u_iso):
u_iso = random.random() * self.random_u_iso_scale \
+ self.random_u_iso_min
scatterer.u_iso = u_iso
if (self.use_u_aniso):
scatterer.flags.set_use_u_aniso_only()
run_away_counter = 0
while 1:
run_away_counter += 1
assert run_away_counter < 100
u_cart = adptbx.random_u_cart(
u_scale=self.random_u_cart_scale)
scatterer.u_star = site_symmetry.average_u_star(
adptbx.u_cart_as_u_star(self.unit_cell(), u_cart))
u_cart = adptbx.u_star_as_u_cart(self.unit_cell(),
scatterer.u_star)
eigenvalues = adptbx.eigenvalues(u_cart)
if (min(eigenvalues) > 0.001):
break
if (self.random_occupancy):
scatterer.occupancy = self.random_occupancy_min \
+ (1-self.random_occupancy_min)*random.random()
self.add_scatterer(scatterer)
def random_aniso_adp(space_group, unit_cell, u_scale=2, u_min=0):
return adptbx.u_star_as_u_cart(unit_cell, space_group.average_u_star(
u_star = adptbx.u_cart_as_u_star(unit_cell, adptbx.random_u_cart(
u_scale=u_scale, u_min=u_min))))
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 exercise(space_group_info,
n_elements = 10,
table = "wk1995",
d_min = 2.0,
k_sol = 0.35,
b_sol = 45.0,
b_cart = None,
quick=False,
verbose=0):
xray_structure = random_structure.xray_structure(
space_group_info = space_group_info,
elements =(("O","N","C")*(n_elements//3+1))[:n_elements],
volume_per_atom = 100,
min_distance = 1.5,
general_positions_only = True,
random_u_iso = False,
random_occupancy = False)
xray_structure.scattering_type_registry(table = table)
sg = xray_structure.space_group()
uc = xray_structure.unit_cell()
u_cart_1 = adptbx.random_u_cart(u_scale=5, u_min=5)
u_star_1 = adptbx.u_cart_as_u_star(uc, u_cart_1)
b_cart = adptbx.u_star_as_u_cart(uc, sg.average_u_star(u_star = u_star_1))
for anomalous_flag in [False, True]:
scatterers = xray_structure.scatterers()
if (anomalous_flag):
assert scatterers.size() >= 7
for i in [1,7]:
scatterers[i].fp = -0.2
scatterers[i].fdp = 5
have_non_zero_fdp = True
else:
for i in [1,7]:
scatterers[i].fp = 0
scatterers[i].fdp = 0
have_non_zero_fdp = False
f_obs = abs(xray_structure.structure_factors(
d_min = d_min,
anomalous_flag = anomalous_flag,
cos_sin_table = sfg_params.cos_sin_table,
algorithm = sfg_params.algorithm).f_calc())
f_obs_comp = f_obs.structure_factors_from_scatterers(
xray_structure = xray_structure,
algorithm = sfg_params.algorithm,
cos_sin_table = sfg_params.cos_sin_table).f_calc()
f_obs = abs(f_obs_comp)
flags = f_obs.generate_r_free_flags(fraction = 0.1,
max_free = 99999999)
#flags = flags.array(data = flex.bool(f_obs.data().size(), False))
xrs = xray_structure.deep_copy_scatterers()
xrs.shake_sites_in_place(rms_difference=0.3)
for target in mmtbx.refinement.targets.target_names:
if (quick):
if (target not in ["ls_wunit_k1", "ml", "mlhl", "ml_sad"]):
continue
if (target == "mlhl"):
if (have_non_zero_fdp): continue # XXX gradients not correct!
experimental_phases = generate_random_hl(miller_set=f_obs)
else:
experimental_phases = None
if (target == "ml_sad"
and (not anomalous_flag or mmtbx.refinement.targets.phaser is None)):
continue
print " ",target
xray.set_scatterer_grad_flags(
scatterers = xrs.scatterers(),
site = True)
ss = 1./flex.pow2(f_obs.d_spacings().data()) / 4.
u_star = adptbx.u_cart_as_u_star(
f_obs.unit_cell(), adptbx.b_as_u(b_cart))
k_anisotropic = mmtbx.f_model.ext.k_anisotropic(
f_obs.indices(), u_star)
k_mask = mmtbx.f_model.ext.k_mask(ss, k_sol, b_sol)
fmodel = mmtbx.f_model.manager(
xray_structure = xrs,
f_obs = f_obs,
r_free_flags = flags,
target_name = target,
abcd = experimental_phases,
sf_and_grads_accuracy_params = sfg_params,
k_mask = k_mask,
k_anisotropic = k_anisotropic,
mask_params = masks.mask_master_params.extract())
fmodel.update_xray_structure(
xray_structure=xrs,
update_f_calc=True,
update_f_mask=True)
xray.set_scatterer_grad_flags(
scatterers=fmodel.xray_structure.scatterers(),
site=True)
fmodel.update_xray_structure(update_f_calc=True)
t_f = fmodel.target_functor()
t_f.prepare_for_minimization()
gs = t_f(compute_gradients=True).d_target_d_site_cart().as_double()
gfd = finite_differences_site(target_functor=t_f)
cc = flex.linear_correlation(gs, gfd).coefficient()
if (0 or verbose):
print "ana:", list(gs)
print "fin:", list(gfd)
print "rat:", [f/a for a,f in zip(gs,gfd)]
print target, "corr:", cc, space_group_info
print
diff = gs - gfd
diff /= max(1, flex.max(flex.abs(gfd)))
tolerance = 1.2e-5
assert approx_equal(abs(flex.min(diff) ), 0.0, tolerance)
assert approx_equal(abs(flex.mean(diff)), 0.0, tolerance)
assert approx_equal(abs(flex.max(diff) ), 0.0, tolerance)
assert approx_equal(cc, 1.0, tolerance)
fmodel.model_error_ml()
def random_aniso_adp(space_group, unit_cell, u_scale=2, u_min=0):
return adptbx.u_star_as_u_cart(
unit_cell,
space_group.average_u_star(u_star=adptbx.u_cart_as_u_star(
unit_cell, adptbx.random_u_cart(u_scale=u_scale, u_min=u_min))))
def exercise(small = 1.e-9):
for symbol in ["P 1"]:
space_group_info = sgtbx.space_group_info(symbol = symbol)
random_xray_structure = random_structure.xray_structure(
space_group_info = space_group_info,
elements = ["N"]*10,
volume_per_atom = 50.0,
random_u_iso = False,
u_iso = adptbx.b_as_u(20.0))
sg = random_xray_structure.space_group()
uc = random_xray_structure.unit_cell()
print symbol, uc
print
sys.stdout.flush()
counter = 0
trials = 100000
i = 0
branch_0 = 0
branch_1 = 0
branch_1_1 = 0
branch_1_2 = 0
branch_1_2_1 = 0
branch_1_2_2 = 0
branch_1_2_3 = 0
branch_1_2_3_1 = 0
branch_1_2_3_2 = 0
while i < trials:
i += 1
counter += 1
r = random.random()
if(r < 0.333):
m = adptbx.random_u_cart(u_scale=20.*random.random(), u_min=0)
n = adptbx.random_u_cart(u_scale=20.*random.random(), u_min=0)
while 1:
for ind in xrange(6):
r = random.random()
m = flex.double(m)
if(r > 0.5):
m[ind] = n[ind]
m = list(m)
if(adptbx.is_positive_definite(m,0) and
adptbx.is_positive_definite(n,0)): break
elif(r>=0.333 and r<0.66):
m,n = branch_3_mn()
else:
m,n = branch_2_mn(0)
m_dc = copy.deepcopy(m)
n_dc = copy.deepcopy(n)
m = factor(list(m), i)
n = factor(list(n), i)
qq = tools.common(n,m,small)
#assert approx_equal(m,m_dc)
#assert approx_equal(n,n_dc)
if(qq.branch_0() ): branch_0 += 1
if(qq.branch_1() ): branch_1 += 1
if(qq.branch_1_1() ): branch_1_1 += 1
if(qq.branch_1_2() ): branch_1_2 += 1
if(qq.branch_1_2_1() ): branch_1_2_1 += 1
if(qq.branch_1_2_2() ): branch_1_2_2 += 1
if(qq.branch_1_2_3() ): branch_1_2_3 += 1
if(qq.branch_1_2_3_1()): branch_1_2_3_1 += 1
if(qq.branch_1_2_3_2()): branch_1_2_3_2 += 1
if (counter >= 10000):
counter = 0
print "."*30, symbol
print "i= ", i, "out of ", trials
print "branch_0 = ", branch_0
print "branch_1 = ", branch_1
print "branch_1_1 = ", branch_1_1
print "branch_1_2 = ", branch_1_2
print "branch_1_2_1 = ", branch_1_2_1
print "branch_1_2_2 = ", branch_1_2_2
print "branch_1_2_3 = ", branch_1_2_3
print "branch_1_2_3_1 = ", branch_1_2_3_1
print "branch_1_2_3_2 = ", branch_1_2_3_2
sys.stdout.flush()
def exercise_negative_parameters(verbose=0):
structure_default = xray.structure(
crystal_symmetry = crystal.symmetry(
unit_cell=((10,13,17,75,80,85)),
space_group_symbol="P 1"),
scatterers=flex.xray_scatterer([
xray.scatterer(label="C", site=(0,0,0), u=0.25)]))
negative_gaussian = eltbx.xray_scattering.gaussian((1,2), (2,3), -4)
for i_trial in xrange(7):
structure = structure_default.deep_copy_scatterers()
scatterer = structure.scatterers()[0]
if (i_trial == 1):
scatterer.occupancy *= -1
elif (i_trial == 2):
structure.scattering_type_registry(custom_dict={"C": negative_gaussian})
elif (i_trial == 3):
scatterer.u_iso *= -1
elif (i_trial == 4):
u_cart = adptbx.random_u_cart(u_scale=1, u_min=-1.1)
assert max(adptbx.eigenvalues(u_cart)) < 0
u_star = adptbx.u_cart_as_u_star(structure.unit_cell(), u_cart)
scatterer.u_star = u_star
scatterer.flags.set_use_u_aniso_only()
elif (i_trial == 5):
scatterer.fp = -10
elif (i_trial == 6):
scatterer.fp = -3
f_direct = structure.structure_factors(
d_min=1, algorithm="direct", cos_sin_table=False).f_calc()
f_fft = structure.structure_factors(
d_min=1, algorithm="fft",
quality_factor=1.e8, wing_cutoff=1.e-10).f_calc()
if (i_trial == 2):
assert negative_gaussian.at_d_star_sq(f_fft.d_star_sq().data()).all_lt(0)
if (i_trial in [5,6]):
f = structure.scattering_type_registry().gaussian_not_optional(
scattering_type="C").at_d_star_sq(f_fft.d_star_sq().data())
if (i_trial == 5):
assert flex.max(f) + scatterer.fp < 0
else:
assert flex.max(f) + scatterer.fp > 0
assert flex.min(f) + scatterer.fp < 0
cc = flex.linear_correlation(
abs(f_direct).data(),
abs(f_fft).data()).coefficient()
if (cc < 0.999):
raise AssertionError("i_trial=%d, correlation=%.6g" % (i_trial, cc))
elif (0 or verbose):
print "correlation=%.6g" % cc
#
# very simple test of gradient calculations with negative parameters
structure_factor_gradients = \
cctbx.xray.structure_factors.gradients(
miller_set=f_direct,
cos_sin_table=False)
target_functor = xray.target_functors.intensity_correlation(
f_obs=abs(f_direct))
target_result = target_functor(f_fft, True)
xray.set_scatterer_grad_flags(scatterers = structure.scatterers(),
site = True,
u_iso = True,
u_aniso = True,
occupancy = True,
fp = True,
fdp = True)
for algorithm in ["direct", "fft"]:
grads = structure_factor_gradients(
xray_structure=structure,
u_iso_refinable_params=None,
miller_set=f_direct,
d_target_d_f_calc=target_result.derivatives(),
n_parameters = structure.n_parameters(),
algorithm=algorithm).packed()
def exercise_negative_parameters(verbose=0):
structure_default = xray.structure(
crystal_symmetry=crystal.symmetry(unit_cell=((10, 13, 17, 75, 80, 85)),
space_group_symbol="P 1"),
scatterers=flex.xray_scatterer(
[xray.scatterer(label="C", site=(0, 0, 0), u=0.25)]))
negative_gaussian = eltbx.xray_scattering.gaussian((1, 2), (2, 3), -4)
for i_trial in range(7):
structure = structure_default.deep_copy_scatterers()
scatterer = structure.scatterers()[0]
if (i_trial == 1):
scatterer.occupancy *= -1
elif (i_trial == 2):
structure.scattering_type_registry(
custom_dict={"C": negative_gaussian})
elif (i_trial == 3):
scatterer.u_iso *= -1
elif (i_trial == 4):
u_cart = adptbx.random_u_cart(u_scale=1, u_min=-1.1)
assert max(adptbx.eigenvalues(u_cart)) < 0
u_star = adptbx.u_cart_as_u_star(structure.unit_cell(), u_cart)
scatterer.u_star = u_star
scatterer.flags.set_use_u_aniso_only()
elif (i_trial == 5):
scatterer.fp = -10
elif (i_trial == 6):
scatterer.fp = -3
f_direct = structure.structure_factors(d_min=1,
algorithm="direct",
cos_sin_table=False).f_calc()
f_fft = structure.structure_factors(d_min=1,
algorithm="fft",
quality_factor=1.e8,
wing_cutoff=1.e-10).f_calc()
if (i_trial == 2):
assert negative_gaussian.at_d_star_sq(
f_fft.d_star_sq().data()).all_lt(0)
if (i_trial in [5, 6]):
f = structure.scattering_type_registry().gaussian_not_optional(
scattering_type="C").at_d_star_sq(f_fft.d_star_sq().data())
if (i_trial == 5):
assert flex.max(f) + scatterer.fp < 0
else:
assert flex.max(f) + scatterer.fp > 0
assert flex.min(f) + scatterer.fp < 0
cc = flex.linear_correlation(abs(f_direct).data(),
abs(f_fft).data()).coefficient()
if (cc < 0.999):
raise AssertionError("i_trial=%d, correlation=%.6g" %
(i_trial, cc))
elif (0 or verbose):
print("correlation=%.6g" % cc)
#
# very simple test of gradient calculations with negative parameters
structure_factor_gradients = \
cctbx.xray.structure_factors.gradients(
miller_set=f_direct,
cos_sin_table=False)
target_functor = xray.target_functors.intensity_correlation(
f_obs=abs(f_direct))
target_result = target_functor(f_fft, True)
xray.set_scatterer_grad_flags(scatterers=structure.scatterers(),
site=True,
u_iso=True,
u_aniso=True,
occupancy=True,
fp=True,
fdp=True)
for algorithm in ["direct", "fft"]:
grads = structure_factor_gradients(
xray_structure=structure,
u_iso_refinable_params=None,
miller_set=f_direct,
d_target_d_f_calc=target_result.derivatives(),
n_parameters=structure.n_parameters(),
algorithm=algorithm).packed()
