def calc_factor_in_front_of_density_for_fm_perp(
self, hkl, space_group_symop: SpaceGroupSymopL, cell: Cell,
atom_site_susceptibility: AtomSiteSusceptibilityL, h_loc,
chi_iso_ferro: float = 0., chi_iso_antiferro: float = 0.,
flag_two_channel: bool = False):
"""Calculate factor in front of density for FM_perp.
Arguments
---------
- hkl
- space_group_symop
- ...
"""
v_hkl_2d_i, v_ferro, v_antiferro = \
self.calc_factor_in_front_of_density_for_fm(
hkl, space_group_symop, cell, atom_site_susceptibility, h_loc,
chi_iso_ferro=chi_iso_ferro,
chi_iso_antiferro=chi_iso_antiferro,
flag_two_channel=flag_two_channel)
k_hkl_1, k_hkl_2, k_hkl_3 = cell.calc_k_loc(*hkl)
na = numpy.newaxis
v_hkl_perp_2d_i = calc_moment_perp(
(k_hkl_1[:, na], k_hkl_2[:, na], k_hkl_3[:, na]), v_hkl_2d_i)
v_perp_ferro = calc_moment_perp(
(k_hkl_1[:, na], k_hkl_2[:, na], k_hkl_3[:, na]), v_ferro)
v_perp_antiferro = calc_moment_perp(
(k_hkl_1[:, na], k_hkl_2[:, na], k_hkl_3[:, na]), v_antiferro)
return v_hkl_perp_2d_i, v_perp_ferro, v_perp_antiferro
def temp_func(l_par):
for name, parameter in zip(l_name, l_par):
if name[0][0] == "atom_site_susceptibility":
atom_site_susceptibility.set_variable_by_name(name, parameter)
elif name[0][0] == "mem_parameters":
mem_parameters.set_variable_by_name(name, parameter)
chi_iso_f = mem_parameters.chi_ferro
chi_iso_af = mem_parameters.chi_antiferro
atom_site_susceptibility.apply_chi_iso_constraint(cell)
atom_site_susceptibility.apply_moment_iso_constraint(cell)
atom_site_susceptibility.apply_space_group_constraint(
atom_site, space_group)
l_chi_sq = []
l_der_chi_sq, l_der_chi_sq_f, l_der_chi_sq_a = [], [], []
# FIXME: add flag for orbital magnetic moment
for diffrn, f_nucl, fr_e, fr_s, e_up, h_loc, k_hkl, phase_3d, \
chi_perp_ferro, chi_perp_aferro in \
zip(l_diffrn, l_f_nucl, l_fr_e, l_fr_s, l_e_up, l_h_loc, l_k_hkl,
l_phase_3d, l_chi_perp_ferro, l_chi_perp_antiferro):
moment_2d, moment_ferro, moment_antiferro = \
density_point.calc_moment_2d(
space_group_symop, cell, atom_site_susceptibility, h_loc,
chi_iso_ferro=1., chi_iso_antiferro=1.,
flag_two_channel=flag_two_channel)
f_m = calc_fm_by_density(mult_i, den_i, np, volume, moment_2d,
phase_3d)
f_m_perp = calc_moment_perp(k_hkl, f_m)
# # correction on orbital moment
# diffrn_refln = diffrn.diffrn_refln
# setup = diffrn.setup
# field = setup.field
# ind_h = diffrn_refln.numpy_index_h
# ind_k = diffrn_refln.numpy_index_k
# ind_l = diffrn_refln.numpy_index_l
# chi_m = crystal.calc_susceptibility_moment_tensor(
# ind_h, ind_k, ind_l, flag_only_orbital=True)
# sft_ij = chi_m[:9]
# sftm_ij = chi_m[9:]
# fm_orb_perp_loc = calc_fm_perp_loc(e_up, field, k_hkl, sft_ij,
# sftm_ij)
# add ferro and anti_ferro
f_m_perp_sum = (f_m_perp[0] + chi_iso_f * chi_perp_ferro[0] +
chi_iso_af * chi_perp_aferro[0],
f_m_perp[1] + chi_iso_f * chi_perp_ferro[1] +
chi_iso_af * chi_perp_aferro[1],
f_m_perp[2] + chi_iso_f * chi_perp_ferro[2] +
chi_iso_af * chi_perp_aferro[2])
fr_m, delta_fr_m = diffrn.calc_fr(cell,
f_nucl,
f_m_perp_sum,
delta_f_m_perp=f_m_perp)
delta_fr_m_f = delta_fr_m
delta_fr_m_a = delta_fr_m
diffrn.diffrn_refln.numpy_fr_calc = fr_m
chi_sq, der_chi_sq = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m)
der_chi_sq_f = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m_f)[1]
der_chi_sq_a = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m_a)[1]
l_chi_sq.append(chi_sq)
l_der_chi_sq.append(der_chi_sq)
l_der_chi_sq_f.append(der_chi_sq_f)
l_der_chi_sq_a.append(der_chi_sq_a)
return sum(l_chi_sq)
def refine_susceptibility(crystal: Crystal,
l_diffrn: List[Diffrn],
density_point: DensityPointL,
mem_parameters: MEMParameters,
disp: bool = True,
d_info: dict = None) -> (float, float):
"""
Refinement of susceptibility.
Parameters
----------
crystal : Crystal
DESCRIPTION.
l_diffrn : TYPE
DESCRIPTION.
density_point : DensityPointL
DESCRIPTION.
chi_iso_ferro : float, optional
DESCRIPTION. The default is 0..
chi_iso_antiferro : float, optional
DESCRIPTION. The default is 0..
flag_ferro : bool, optional
DESCRIPTION. The default is True.
flag_antiferro : bool, optional
DESCRIPTION. The default is True.
disp : bool, optional
DESCRIPTION. The default is True.
Returns
-------
float
Chi_iso_ferro.
float
Chi_iso_antiferro.
"""
flag_info = d_info is not None
if flag_info:
d_info_keys = d_info.keys()
if "stop" not in d_info_keys:
d_info["stop"] = False
if "print" not in d_info_keys:
d_info["print"] = ""
crystal.apply_constraints()
flag_two_channel = mem_parameters.method == "2channel"
cell = crystal.cell
space_group = crystal.space_group
atom_site = crystal.atom_site
space_group_symop = space_group.full_space_group_symop
atom_site_susceptibility = crystal.atom_site_susceptibility
# l_magnetic_labes = atom_site_susceptibility.label
volume = density_point.volume_unit_cell
np = density_point.number_unit_cell
den_i = density_point.numpy_density
den_ferro_i = density_point.numpy_density_ferro
den_antiferro_i = density_point.numpy_density_antiferro
mult_i = density_point.numpy_multiplicity
l_f_nucl, l_fr_e, l_fr_s, l_e_up, l_h_loc = [], [], [], [], []
l_k_hkl, l_phase_3d = [], []
l_chi_perp_ferro, l_chi_perp_antiferro = [], []
total_peaks = 0
for diffrn in l_diffrn:
diffrn_orient_matrix = diffrn.diffrn_orient_matrix
u_matrix = diffrn_orient_matrix.u
e_up = calc_e_up_loc(0., 0., 0., u_matrix)
setup = diffrn.setup
field = float(setup.field)
h_loc = (field * e_up[0], field * e_up[1], field * e_up[2])
diffrn_refln = diffrn.diffrn_refln
index_h = numpy.array(diffrn_refln.index_h, dtype=int)
index_k = numpy.array(diffrn_refln.index_k, dtype=int)
index_l = numpy.array(diffrn_refln.index_l, dtype=int)
total_peaks += index_h.size
hkl = (index_h, index_k, index_l)
fr_e = numpy.array(diffrn_refln.fr, dtype=float)
fr_s = numpy.array(diffrn_refln.fr_sigma, dtype=float)
f_nucl = crystal.calc_f_nucl(*hkl)
k_hkl = cell.calc_k_loc(*hkl)
phase_3d = density_point.calc_phase_3d(hkl, space_group_symop)
moment_2d, chi_2d_ferro, chi_2d_antiferro = \
density_point.calc_moment_2d(
space_group_symop, cell, atom_site_susceptibility, h_loc,
chi_iso_ferro=1., chi_iso_antiferro=1.,
flag_two_channel=flag_two_channel)
chi_ferro = calc_fm_by_density(mult_i, den_ferro_i, np, volume,
chi_2d_ferro, phase_3d)
chi_perp_ferro = calc_moment_perp(k_hkl, chi_ferro)
chi_aferro = calc_fm_by_density(mult_i, den_antiferro_i, np, volume,
chi_2d_antiferro, phase_3d)
chi_perp_aferro = calc_moment_perp(k_hkl, chi_aferro)
l_f_nucl.append(f_nucl)
l_fr_e.append(fr_e)
l_fr_s.append(fr_s)
l_e_up.append(e_up)
l_h_loc.append(h_loc)
l_k_hkl.append(k_hkl)
l_phase_3d.append(phase_3d)
l_chi_perp_ferro.append(chi_perp_ferro)
l_chi_perp_antiferro.append(chi_perp_aferro)
l_name_1 = atom_site_susceptibility.get_variable_names()
l_par_1_0 = [
atom_site_susceptibility.get_variable_by_name(name)
for name in l_name_1
]
l_name_2 = mem_parameters.get_variable_names()
l_par_2_0 = [
mem_parameters.get_variable_by_name(name) for name in l_name_2
]
l_name = l_name_1 + l_name_2
l_par_0 = l_par_1_0 + l_par_2_0
def temp_func(l_par):
for name, parameter in zip(l_name, l_par):
if name[0][0] == "atom_site_susceptibility":
atom_site_susceptibility.set_variable_by_name(name, parameter)
elif name[0][0] == "mem_parameters":
mem_parameters.set_variable_by_name(name, parameter)
chi_iso_f = mem_parameters.chi_ferro
chi_iso_af = mem_parameters.chi_antiferro
atom_site_susceptibility.apply_chi_iso_constraint(cell)
atom_site_susceptibility.apply_moment_iso_constraint(cell)
atom_site_susceptibility.apply_space_group_constraint(
atom_site, space_group)
l_chi_sq = []
l_der_chi_sq, l_der_chi_sq_f, l_der_chi_sq_a = [], [], []
# FIXME: add flag for orbital magnetic moment
for diffrn, f_nucl, fr_e, fr_s, e_up, h_loc, k_hkl, phase_3d, \
chi_perp_ferro, chi_perp_aferro in \
zip(l_diffrn, l_f_nucl, l_fr_e, l_fr_s, l_e_up, l_h_loc, l_k_hkl,
l_phase_3d, l_chi_perp_ferro, l_chi_perp_antiferro):
moment_2d, moment_ferro, moment_antiferro = \
density_point.calc_moment_2d(
space_group_symop, cell, atom_site_susceptibility, h_loc,
chi_iso_ferro=1., chi_iso_antiferro=1.,
flag_two_channel=flag_two_channel)
f_m = calc_fm_by_density(mult_i, den_i, np, volume, moment_2d,
phase_3d)
f_m_perp = calc_moment_perp(k_hkl, f_m)
# # correction on orbital moment
# diffrn_refln = diffrn.diffrn_refln
# setup = diffrn.setup
# field = setup.field
# ind_h = diffrn_refln.numpy_index_h
# ind_k = diffrn_refln.numpy_index_k
# ind_l = diffrn_refln.numpy_index_l
# chi_m = crystal.calc_susceptibility_moment_tensor(
# ind_h, ind_k, ind_l, flag_only_orbital=True)
# sft_ij = chi_m[:9]
# sftm_ij = chi_m[9:]
# fm_orb_perp_loc = calc_fm_perp_loc(e_up, field, k_hkl, sft_ij,
# sftm_ij)
# add ferro and anti_ferro
f_m_perp_sum = (f_m_perp[0] + chi_iso_f * chi_perp_ferro[0] +
chi_iso_af * chi_perp_aferro[0],
f_m_perp[1] + chi_iso_f * chi_perp_ferro[1] +
chi_iso_af * chi_perp_aferro[1],
f_m_perp[2] + chi_iso_f * chi_perp_ferro[2] +
chi_iso_af * chi_perp_aferro[2])
fr_m, delta_fr_m = diffrn.calc_fr(cell,
f_nucl,
f_m_perp_sum,
delta_f_m_perp=f_m_perp)
delta_fr_m_f = delta_fr_m
delta_fr_m_a = delta_fr_m
diffrn.diffrn_refln.numpy_fr_calc = fr_m
chi_sq, der_chi_sq = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m)
der_chi_sq_f = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m_f)[1]
der_chi_sq_a = calc_chi_sq(fr_e, fr_s, fr_m, delta_fr_m_a)[1]
l_chi_sq.append(chi_sq)
l_der_chi_sq.append(der_chi_sq)
l_der_chi_sq_f.append(der_chi_sq_f)
l_der_chi_sq_a.append(der_chi_sq_a)
return sum(l_chi_sq)
chi_sq = temp_func(l_par_0)
print(f"Chi_sq before optimization {chi_sq/total_peaks:.5f}. ",
end="\r")
if flag_info:
d_info["print"] = \
f"Chi_sq/n before optimization {chi_sq/total_peaks:.5f}."
res = scipy.optimize.minimize(
temp_func,
l_par_0,
method="BFGS",
callback=lambda x: func_temp(x, param_name=l_name, d_info=d_info),
options={"eps": 0.001})
l_param = res.x
chi_sq_new = res.fun
hess_inv = res["hess_inv"]
sigma = (abs(numpy.diag(hess_inv)))**0.5
print(f"Chi_sq after optimization {chi_sq_new/total_peaks:.5f}. ",
end="\r")
if flag_info:
d_info["print"] = \
f"Chi_sq/n after optimization {chi_sq_new/total_peaks:.5f}."
for name, parameter, sig in zip(l_name, l_param, sigma):
name_sig = name[:-1] + ((f"{name[-1][0]:}_sigma", name[-1][1]), )
if name[0][0] == "atom_site_susceptibility":
atom_site_susceptibility.set_variable_by_name(name, parameter)
atom_site_susceptibility.set_variable_by_name(name_sig, sig)
elif name[0][0] == "mem_parameters":
mem_parameters.set_variable_by_name(name, parameter)
mem_parameters.set_variable_by_name(name_sig, sig)
for diffrn in l_diffrn:
diffrn.diffrn_refln.numpy_to_items()
chi_sq, points = diffrn.diffrn_refln.calc_chi_sq_points()
refine_ls = RefineLs(goodness_of_fit_all=chi_sq / points,
number_reflns=points)
diffrn.add_items([refine_ls])
def calc_fr(self):
"""Calculate Flip Ratios for diffraction experiments."""
crystal = self.crystals()[0] # FIXME:
l_diffrn = self.experiments() # FIXME:
density_point = self.density_point
mem_parameters = self.mem_parameters
chi_iso_ferro = mem_parameters.chi_ferro
chi_iso_antiferro = mem_parameters.chi_antiferro
flag_two_channel = mem_parameters.method == "2channel"
cell = crystal.cell
space_group = crystal.space_group
space_group_symop = space_group.full_space_group_symop
atom_site_susceptibility = crystal.atom_site_susceptibility
# FIXME: temporary solution of calculation rbs_i if it's not defined
density_point.calc_rbs_i(space_group_symop,
points_a=mem_parameters.points_a,
points_b=mem_parameters.points_b,
points_c=mem_parameters.points_c)
total_peaks = 0
den_i = numpy.array(density_point.density, dtype=float)
den_ferro_i = numpy.array(density_point.density_ferro, dtype=float)
den_antiferro_i = numpy.array(density_point.density_antiferro,
dtype=float)
mult_i = numpy.array(density_point.multiplicity, dtype=int)
volume = cell.volume
n_points = mult_i.sum()
for diffrn in l_diffrn:
diffrn_orient_matrix = diffrn.diffrn_orient_matrix
e_up = diffrn_orient_matrix.calc_e_up()
setup = diffrn.setup
field = float(setup.field)
h_loc = (field * e_up[0], field * e_up[1], field * e_up[2])
diffrn_refln = diffrn.diffrn_refln
index_h = numpy.array(diffrn_refln.index_h, dtype=int)
index_k = numpy.array(diffrn_refln.index_k, dtype=int)
index_l = numpy.array(diffrn_refln.index_l, dtype=int)
total_peaks += index_h.size
hkl = (index_h, index_k, index_l)
f_nucl = crystal.calc_f_nucl(*hkl)
k_hkl = cell.calc_k_loc(*hkl)
phase_3d = density_point.calc_phase_3d(hkl, space_group_symop)
moment_2d, chi_2d_ferro, chi_2d_antiferro = \
density_point.calc_moment_2d(
space_group_symop, cell, atom_site_susceptibility, h_loc,
chi_iso_ferro=1., chi_iso_antiferro=1.,
flag_two_channel=flag_two_channel)
chi_ferro = calc_fm_by_density(mult_i, den_ferro_i, n_points,
volume, chi_2d_ferro, phase_3d)
chi_perp_ferro = calc_moment_perp(k_hkl, chi_ferro)
chi_aferro = calc_fm_by_density(mult_i, den_antiferro_i, n_points,
volume, chi_2d_antiferro, phase_3d)
chi_perp_aferro = calc_moment_perp(k_hkl, chi_aferro)
f_m = calc_fm_by_density(mult_i, den_i, n_points, volume,
moment_2d, phase_3d)
f_m_perp = calc_moment_perp(k_hkl, f_m)
f_m_perp_sum = (f_m_perp[0] + chi_iso_ferro * chi_perp_ferro[0] +
chi_iso_antiferro * chi_perp_aferro[0],
f_m_perp[1] + chi_iso_ferro * chi_perp_ferro[1] +
chi_iso_antiferro * chi_perp_aferro[1],
f_m_perp[2] + chi_iso_ferro * chi_perp_ferro[2] +
chi_iso_antiferro * chi_perp_aferro[2])
fr_m, delta_fr_m = diffrn.calc_fr(cell,
f_nucl,
f_m_perp_sum,
delta_f_m_perp=f_m_perp)
diffrn.diffrn_refln.numpy_fr_calc = fr_m
for diffrn in l_diffrn:
diffrn.diffrn_refln.numpy_to_items()
chi_sq, points = diffrn.diffrn_refln.calc_chi_sq_points()
refine_ls = RefineLs(goodness_of_fit_all=chi_sq / points,
number_reflns=points)
diffrn.add_items([refine_ls])