def test_FeMn_nonzero():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
chi_sq, n_points = rhochi.calc_chi_sq()
assert chi_sq < 5112.6
assert int(n_points) == 1091
def test_f_mag():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "1.0.2_URu0.96Rh0.04Si2.mcif")
globaln = cryspy.file_to_globaln(f_name)
mag_cif = globaln.mag_crystal_5yOhtAoR
index_hkl = numpy.array(
[[1, 2, 0, 1, 0, 3, 2, 2, 4],
[0, 0, 0, 1, 1, 0, 0, 1, 0],
[1, 0, 2, 0, 1, 1, 2, 1, 0]], dtype=int)
space_group_symop_magn_operation = mag_cif.space_group_symop_magn_operation
space_group_symop_magn_centering = mag_cif.space_group_symop_magn_centering
cell = mag_cif.cell
atom_site = mag_cif.atom_site
try:
atom_site_aniso = mag_cif.atom_site_aniso
except AttributeError as e:
atom_site_aniso = None
atom_site_scat = mag_cif.atom_site_scat
atom_site_scat.load_atom_type_scat_by_atom_site(atom_site)
atom_site_moment = mag_cif.atom_site_moment
flag_derivatives = False
flag_only_orbital= False
f_mag, dder = calc_f_mag(index_hkl, space_group_symop_magn_operation,
space_group_symop_magn_centering, cell, atom_site,
atom_site_aniso, atom_site_scat, atom_site_moment,
flag_derivatives=flag_derivatives, flag_only_orbital=flag_only_orbital)
def test_UNPD_PbSo4():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
chi_sq, n_points = rhochi.calc_chi_sq()
assert chi_sq < 4427.6
assert int(n_points) == 756
def test_refine_mcif():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "pd_test.rcif")
rhochi = cryspy.file_to_globaln(f_name)
chi_sq, n_points = rhochi.calc_chi_sq()
assert chi_sq < 3036.0
assert int(n_points) == 4901
def test_calc_FR_2channel():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
mem = cryspy.file_to_globaln(f_name)
mem.calc_fr()
diffrn = mem.diffrn_exp_mnbite
refine_ls = diffrn.refine_ls
def test_wrong_cif():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "wrong_cif.rcif")
globaln = cryspy.file_to_globaln(f_name)
assert globaln.data_Tb2Ti2O7.geom_angle[0].label is None
assert globaln.data_tb2ti2o7.atom_type[
"TI"].scat_length_neutron.real == -0.3438
assert globaln.data_global.journal.name_full == "Journal Name"
def test_refine():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
rhochi.refine()
chi_sq, n_points = rhochi.calc_chi_sq()
assert chi_sq < 429.1
assert int(n_points) == 142
def test_estimate_fm():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
l_estimation = rhochi.estimate_f_mag_for_diffrn()
estim = l_estimation[0]
l_f_m = estim.f_m
l_f_m_sigma = estim.f_m_sigma
def test_calc_FR_tensorMEM():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
mem = cryspy.file_to_globaln(f_name)
mem.calc_fr()
diffrn = mem.diffrn_exp_mnbite
refine_ls = diffrn.refine_ls
mem.create_prior_density()
def test_refine_mcif():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "pd_test.rcif")
rhochi = cryspy.file_to_globaln(f_name)
d_out = cryspy.rhochi_no_refinement(rhochi)
chi_sq = d_out["chi_sq"]
n_points = d_out["n_points"]
assert chi_sq < 3036.0
assert int(n_points) == 4901
def test_FeMn_nonzero():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
d_out = cryspy.rhochi_no_refinement(rhochi)
chi_sq = d_out["chi_sq"]
n_points = d_out["n_points"]
assert chi_sq < 5112.6
assert int(n_points) == 1091
def test_UNPD_PbSo4():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
d_out = cryspy.rhochi_no_refinement(rhochi)
chi_sq = d_out["chi_sq"]
n_points = d_out["n_points"]
# chi_sq, n_points = rhochi.calc_chi_sq()
assert chi_sq < 55600.9
assert int(n_points) == 25553
def test_calc_FR_2channel():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
mem = cryspy.file_to_globaln(f_name)
mem.calc_fr()
diffrn = mem.diffrn_exp_mnbite
refine_ls = diffrn.refine_ls
assert refine_ls.goodness_of_fit_all < 0.986
assert refine_ls.number_reflns == 142
def test_refine():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
cryspy.rhochi_run(rhochi)
d_out = cryspy.rhochi_no_refinement(rhochi)
chi_sq = d_out["chi_sq"]
n_points = d_out["n_points"]
assert chi_sq < 429.1
assert int(n_points) == 142
def test_calc_FR_tensorMEM():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
mem = cryspy.file_to_globaln(f_name)
mem.calc_fr()
diffrn = mem.diffrn_exp_mnbite
refine_ls = diffrn.refine_ls
assert refine_ls.goodness_of_fit_all < 4.99
assert refine_ls.number_reflns == 142
mem.create_prior_density()
def test_estimate_fm():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
l_estimation = cryspy.calc_f_mag_for_diffrn(rhochi)
estim = l_estimation[0]
l_f_m = estim.f_m
l_f_m_sigma = estim.f_m_sigma
assert abs(float(l_f_m[0]) - (-0.7881)) < 0.001
assert abs(float(l_f_m[1]) - (-0.2003)) < 0.001
assert abs(float(l_f_m[2]) - (0.68611)) < 0.001
assert abs(float(l_f_m[3]) - (0.41953)) < 0.001
assert abs(float(l_f_m_sigma[0]) - 0.16078) < 0.001
assert abs(float(l_f_m_sigma[1]) - 0.14083) < 0.001
assert abs(float(l_f_m_sigma[2]) - 0.47949) < 0.001
assert abs(float(l_f_m_sigma[3]) - 0.34928) < 0.001
import numpy
from cryspy import file_to_globaln
from cryspy.A_functions_base.function_1_matrices import calc_chi_sq
f_name = "main.rcif"
mem_obj = file_to_globaln(f_name)
mem_obj.calc_fr()
density_point = mem_obj.density_point
diffrn = mem_obj.diffrn_exp_mnbite
diffrn_refln = diffrn.diffrn_refln
# Analytical Derivatives
fr_e = numpy.array(diffrn_refln.fr, dtype=float)
fr_s = numpy.array(diffrn_refln.fr_sigma, dtype=float)
crystal = mem_obj.crystals()[0]
l_diffrn = mem_obj.experiments()
mem_parameters = mem_obj.mem_parameters
density_point.volume_unit_cell = crystal.cell.volume
density_point.number_unit_cell = \
mem_parameters.points_a * mem_parameters.points_b * \
mem_parameters.points_c
chi_iso_ferro = mem_parameters.chi_ferro
def test_FeMn_zero():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
chi_sq, n_points = rhochi.calc_chi_sq()
def test_UNPD_PbSo4():
dir = os.path.dirname(__file__)
f_name = os.path.join(dir, "main.rcif")
rhochi = cryspy.file_to_globaln(f_name)
rhochi.refine()
chi_sq, n_points = rhochi.calc_chi_sq()
