elif _type == 'repr':
np.fill_diagonal(_ellipsoid, _T)
# The mathematics of this transformation can be found on pp. 206 in Giacovazzo
_X_ijk = np.matmul(_V, np.matmul(_ellipsoid, np.transpose(_V)))
_X_abc = np.matmul(
structure.ABC_Mbt_IJK,
np.matmul(_X_ijk, np.transpose(structure.ABC_Mbt_IJK)))
_X_o = np.linalg.inv(np.matmul(oMa, np.matmul(_X_abc, oMa))) * _scale
_magnetic_atom_U_index = cf[_blockname][
'_atom_site_aniso_label'].index(atom)
cf[_blockname]['_atom_site_aniso_U_11'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[0, 0])
cf[_blockname]['_atom_site_aniso_U_22'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[1, 1])
cf[_blockname]['_atom_site_aniso_U_33'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[2, 2])
cf[_blockname]['_atom_site_aniso_U_23'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[1, 2])
cf[_blockname]['_atom_site_aniso_U_13'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[0, 2])
cf[_blockname]['_atom_site_aniso_U_12'][
_magnetic_atom_U_index] = '{:<7.5f}'.format(_X_o[0, 1])
_outname = _cifname[:-4] + '_magn.cif'
outfile = open(_outname, 'w')
outfile.write(cf.WriteOut())
outfile.close()
subprocess.Popen(['mercury', '{}'.format(_outname)])
def finalise_parameters(self, file_name, index, current_temp):
#Finalises the CIF with important parameters such as beamline parameters
cif = ReadCif(file_name)
try:
data_block = cif[str(index + 1)]
except TypeError as error:
os.remove(file_name)
self.logger.info(f'Cif empty due to poor refinement - {error}')
else:
self.C = data_block['_diffrn_reflns_number']
self.A = data_block['_diffrn_reflns_theta_min']
self.B = data_block['_diffrn_reflns_theta_max']
beamline = self.cfg['User_Parameters_Full_Pipeline'][
'Experiment_Configuration']['beamline']
if beamline != '':
data_block['_computing_data_collection'] = self.cfg[
'Instrument_Parameters'][beamline + '_data_collection']
data_block['_exptl_absorp_correction_type'] = self.cfg[
'Instrument_Parameters'][beamline + '_absorp_correction']
data_block['_diffrn_radiation_wavelength'] = self.cfg[
'User_Parameters_Full_Pipeline'][
'Experiment_Configuration']['wavelength']
data_block['_diffrn_radiation_type'] = self.cfg[
'Instrument_Parameters'][beamline + '_radiation_type']
data_block['_diffrn_source'] = self.cfg[
'Instrument_Parameters'][beamline + '_radiation_type']
data_block['_diffrn_measurement_device_type'] = self.cfg[
'Instrument_Parameters'][beamline + '_detector']
data_block['_diffrn_measurement_method'] = self.cfg[
'Instrument_Parameters'][beamline + '_measurement_method']
data_block['_computing_cell_refinement'] = self.cfg[
'Instrument_Parameters'][beamline + '_cell_refinement']
data_block['_computing_data_reduction'] = self.cfg[
'Instrument_Parameters'][beamline + '_cell_refinement']
data_block['_computing_structure_solution'] = self.cfg[
'Instrument_Parameters'][beamline + '_structure_soln']
data_block['_diffrn_radiation_monochromator'] = self.cfg[
'Instrument_Parameters'][beamline + '_monochromator']
data_block['_diffrn_radiation_source'] = self.cfg[
'Instrument_Parameters'][beamline + '_source']
data_block['_chemical_formula_moiety'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'chemical_formula']
data_block['_exptl_crystal_colour'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'crystal_colour']
data_block['_exptl_crystal_description'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'crystal_habit']
data_block['_cell_measurement_temperature'] = current_temp
data_block['_diffrn_ambient_temperature'] = current_temp
data_block['_exptl_crystal_size_max'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'max_crystal_dimension']
data_block['_exptl_crystal_size_mid'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'middle_crystal_dimension']
data_block['_exptl_crystal_size_min'] = self.cfg[
'User_Parameters_Full_Pipeline']['Crystal_Descriptions'][
'min_crystal_dimension']
data_block['_cell_measurement_reflns_used'] = self.C
data_block['_cell_measurement_theta_min'] = self.A
data_block['_cell_measurement_theta_max'] = self.B
with open('edited.cif', 'w') as updated:
updated.write(cif.WriteOut())
os.rename('edited.cif', file_name)