示例#1
0
        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)])
示例#2
0
    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)