# HG changeset patch # User muon-spectroscopy-computational-project # Date 1699976109 0 # Node ID edf7f8ccf4af855dcaa1910ddedfe1c7eccc99c1 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735 diff -r 000000000000 -r edf7f8ccf4af larch_feff.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/larch_feff.py Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,165 @@ +import json +import re +import shutil +import sys +from pathlib import Path + +from larch.xafs.feffrunner import feff6l + +from pymatgen.io.cif import CifParser +from pymatgen.io.feff import Atoms, Header, Potential + + +def get_path_labels(paths_file): + is_meta = True + count = 0 + a_path = {} + all_paths = {} + with open(paths_file) as datfile: + dat_lines = datfile.readlines() + for a_line in dat_lines: + count += 1 + if re.match("-{15}", a_line.strip()) is not None: + is_meta = False + elif not is_meta: + if re.match(r"\s*\d*\s{4}\d*\s{3}", a_line) is not None: + if a_path: + all_paths[a_path["index"]] = a_path + line_data = a_line.split() + a_path = { + "index": line_data[0], + "nleg": line_data[1], + "degeneracy": line_data[2], + } + elif ( + re.match(r"\s{6}x\s{11}y\s{5}", a_line) is None + ): # ignore the intermediate headings + line_data = a_line.split() + if "label" not in a_path: + a_path["label"] = line_data[4].replace("'", "") + else: + a_path["label"] += "." + line_data[4].replace("'", "") + if a_path and "index" in a_path: + all_paths[a_path["index"]] = a_path + return all_paths + + +def main(structure_file: str, file_format: dict): + crystal_f = Path(structure_file) + feff_dir = "feff" + feff_inp = "feff.inp" + header_inp = "header" + atoms_inp = "atoms" + potential_inp = "potential" + path = Path(feff_dir, feff_inp) + path.parent.mkdir(parents=True, exist_ok=True) + + if file_format["format"] == "cif": + print(f"Parsing {crystal_f.name} and saving to {path}") + cif_parser = CifParser(crystal_f) + structures = cif_parser.get_structures() + length = len(structures) + if length != 1: + raise ValueError( + f"Execpted single structure in cif file but found {length}" + ) + try: + aborsbing_atom = int(file_format["absorbing_atom"]) + except ValueError: + # aborsbing_atom can be int or chemical symbol + aborsbing_atom = file_format["absorbing_atom"] + + feff_header = Header(structures[0]) + potential = Potential(structures[0], aborsbing_atom) + atoms = Atoms(structures[0], aborsbing_atom, file_format["radius"]) + # if len(atoms.struct.sites) < len(potential.): + + # print(atoms.as_dict()) + feff_header.write_file(header_inp) + potential.write_file(potential_inp) + atoms.write_file(atoms_inp) + with open(path, "w") as feff_inp_file: + with open(header_inp) as f: + header_text = f.read() + print(header_text) + feff_inp_file.write(header_text + "\n") + with open(potential_inp) as f: + potential_text = f.readlines() + print(*potential_text) + feff_inp_file.writelines(potential_text + ["\n"]) + with open(atoms_inp) as f: + atoms_text = f.readlines() + print(*atoms_text) + feff_inp_file.writelines(atoms_text + ["\n"]) + if len(atoms_text) <= len(potential_text): + print( + "WARNING: Every potential in the structure must be represented" + " by at least one atom, consider increasing the radius" + ) + else: + print(f"Copying {crystal_f.name} to {path}") + shutil.copy(crystal_f, path) + + feff6l(folder=feff_dir, feffinp=feff_inp) + + feff_files = "files.dat" + input_file = Path(feff_dir, feff_files) + # the .dat data is stored in fixed width strings + comma_positions = [13, 21, 32, 41, 48, 61] + paths_data = [] + # get the list of paths info to assign labels to paths + try: + paths_info = get_path_labels(Path(feff_dir, "paths.dat")) + except FileNotFoundError as err: + raise FileNotFoundError( + "paths.dat does not exist, which implies FEFF failed to run" + ) from err + + print("Reading from: " + str(input_file)) + with open(input_file) as datfile: + # Read until we find the line at the end of the header + line = datfile.readline() + while not re.match("-+", line.strip()): + line = datfile.readline() + + # Build headers + line = datfile.readline() + header = "" + start = 0 + for end in comma_positions: + header += line[start:end] + "," + start = end + header += f" {'label':30s}, {'select':6s}\n" + paths_data.append(header) + + # Read data + line = datfile.readline() + while line: + data = "" + start = 0 + for end in comma_positions[:-1]: + data += line[start:end] + "," + start = end + + # Last column needs padding to align + data += line[start:-1] + " ," + + # Add label and select column + path_id = int(data[5:9]) + try: + label = paths_info[str(path_id)]["label"] + f".{path_id}" + except KeyError as err: + msg = f"{path_id} not in {paths_info.keys()}" + raise KeyError(msg) from err + data += f" {label:30s}, {0:6d}\n" + paths_data.append(data) + line = datfile.readline() + + with open("out.csv", "w") as out: + out.writelines(paths_data) + + +if __name__ == "__main__": + structure_file = sys.argv[1] + input_values = json.load(open(sys.argv[2], "r", encoding="utf-8")) + main(structure_file, input_values["format"]) diff -r 000000000000 -r edf7f8ccf4af larch_feff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/larch_feff.xml Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,103 @@ + + generate FEFF paths from XAFS data + + + 0.9.71 + + 0 + + + 10.1088/1742-6596/430/1/012007 + + + + + + xraylarch + matplotlib + zip + + + + + + + + + + + + + + + + + + + + + + + + + + + + + format["format"]=="cif" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @TOOL_CITATION@ + 10.1107/S0909049505012719 + 10.1016/j.commatsci.2012.10.028 + + \ No newline at end of file diff -r 000000000000 -r edf7f8ccf4af test-data/1564889.cif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1564889.cif Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,1650 @@ +#------------------------------------------------------------------------------ +#$Date: 2021-10-09 01:09:41 +0300 (Sat, 09 Oct 2021) $ +#$Revision: 269866 $ +#$URL: file:///home/coder/svn-repositories/cod/cif/1/56/48/1564889.cif $ +#------------------------------------------------------------------------------ +# +# This file is available in the Crystallography Open Database (COD), +# http://www.crystallography.net/ +# +# All data on this site have been placed in the public domain by the +# contributors. +# +data_1564889 +loop_ +_publ_author_name +'Ma, KeYuan' +'Lef\`evre, Robin' +'Li, Qingtian' +'Lago, Jorge' +'Blacque, Olivier' +'Yang, Wanli' +'von Rohr, Fabian O.' +_publ_section_title +; + Synthetic control over polymorph formation in the d-band semiconductor + system FeS2 +; +_journal_name_full 'Chemical Science' +_journal_paper_doi 10.1039/D1SC03026D +_journal_year 2021 +_chemical_formula_moiety 'Fe S2' +_chemical_formula_sum 'Fe S2' +_chemical_formula_weight 119.97 +_chemical_name_systematic Marcasite +_space_group_crystal_system orthorhombic +_space_group_IT_number 58 +_space_group_name_Hall '-P 2 2n' +_space_group_name_H-M_alt 'P n n m' +_atom_sites_solution_primary dual +_audit_creation_date 2018-05-07 +_audit_creation_method +; +Olex2 1.2 +(compiled 2018.04.26 svn.r3504 for OlexSys, GUI svn.r5492) +; +_audit_update_record +; +2021-02-24 deposited with the CCDC. 2021-09-20 downloaded from the CCDC. +; +_cell_angle_alpha 90 +_cell_angle_beta 90 +_cell_angle_gamma 90 +_cell_formula_units_Z 2 +_cell_length_a 4.4474(4) +_cell_length_b 5.4287(4) +_cell_length_c 3.3852(3) +_cell_measurement_reflns_used 884 +_cell_measurement_temperature 160(1) +_cell_measurement_theta_max 32.6 +_cell_measurement_theta_min 5.9 +_cell_volume 81.731(12) +_computing_cell_refinement 'CrysAlisPro 1.171.39.13a (Rigaku OD, 2015)' +_computing_data_collection 'CrysAlisPro 1.171.39.13a (Rigaku OD, 2015)' +_computing_data_reduction 'CrysAlisPro 1.171.39.13a (Rigaku OD, 2015)' +_computing_molecular_graphics 'Olex2 (Dolomanov et al., 2009)' +_computing_publication_material 'Olex2 (Dolomanov et al., 2009)' +_computing_structure_refinement 'ShelXL (Sheldrick, 2015b)' +_computing_structure_solution 'ShelXT (Sheldrick, 2015a)' +_diffrn_ambient_environment N~2~ +_diffrn_ambient_temperature 160(1) +_diffrn_detector 'CCD plate' +_diffrn_detector_type 'Pilatus 200K' +_diffrn_measured_fraction_theta_full 0.978 +_diffrn_measured_fraction_theta_max 0.982 +_diffrn_measurement_details +; +List of Runs (angles in degrees, time in seconds): + + # Type Start End Width t~exp~ \w \q \k \f Frames +#-------------------------------------------------------------------------- + 1 \w -27.00 22.00 0.50 0.40 -- -10.35 -99.00-120.00 98 + 2 \w -20.00 67.00 0.50 0.40 -- -10.35 38.00 150.00 174 + 3 \w -23.00 64.00 0.50 0.40 -- -10.35 51.00 61.00 174 + 4 \w -68.00 18.00 0.50 0.40 -- 9.10 -38.00 -60.00 172 + 5 \w -27.00 20.00 0.50 0.40 -- -10.35 -99.00 120.00 94 + 6 \w -20.00 69.00 0.50 0.40 -- -10.35 19.00-120.00 178 +; +_diffrn_measurement_device 'four-circle diffractometer' +_diffrn_measurement_device_type 'XtaLAB Synergy, Dualflex, Pilatus 200K' +_diffrn_measurement_method '\w scans' +_diffrn_orient_matrix_type +'CrysAlisPro convention (1999,Acta A55,543-557)' +_diffrn_orient_matrix_UB_11 0.0324086000 +_diffrn_orient_matrix_UB_12 0.1195180000 +_diffrn_orient_matrix_UB_13 -0.1285090000 +_diffrn_orient_matrix_UB_21 -0.1184482000 +_diffrn_orient_matrix_UB_22 0.0643839000 +_diffrn_orient_matrix_UB_23 0.0259992000 +_diffrn_orient_matrix_UB_31 0.0446231000 +_diffrn_orient_matrix_UB_32 0.0840167000 +_diffrn_orient_matrix_UB_33 0.1631699000 +_diffrn_radiation_monochromator mirror +_diffrn_radiation_probe x-ray +_diffrn_radiation_type MoK\a +_diffrn_radiation_wavelength 0.71073 +_diffrn_reflns_av_R_equivalents 0.0582 +_diffrn_reflns_av_unetI/netI 0.0244 +_diffrn_reflns_Laue_measured_fraction_full 0.978 +_diffrn_reflns_Laue_measured_fraction_max 0.982 +_diffrn_reflns_limit_h_max 5 +_diffrn_reflns_limit_h_min -5 +_diffrn_reflns_limit_k_max 7 +_diffrn_reflns_limit_k_min -7 +_diffrn_reflns_limit_l_max 4 +_diffrn_reflns_limit_l_min -4 +_diffrn_reflns_number 979 +_diffrn_reflns_point_group_measured_fraction_full 0.978 +_diffrn_reflns_point_group_measured_fraction_max 0.982 +_diffrn_reflns_theta_full 25.242 +_diffrn_reflns_theta_max 27.866 +_diffrn_reflns_theta_min 5.929 +_diffrn_source 'micro-focus sealed X-ray tube' +_diffrn_source_type 'PhotonJet (Mo) X-ray Source' +_exptl_absorpt_coefficient_mu 11.144 +_exptl_absorpt_correction_T_max 0.883 +_exptl_absorpt_correction_T_min 0.505 +_exptl_absorpt_correction_type analytical +_exptl_absorpt_process_details +; +CrysAlisPro 1.171.39.13a (Rigaku Oxford Diffraction, 2015) +Analytical numeric absorption correction using a multifaceted crystal +model based on expressions derived by R.C. Clark & J.S. Reid. +(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897) +Empirical absorption correction using spherical harmonics, + implemented in SCALE3 ABSPACK scaling algorithm. +; +_exptl_crystal_colour black +_exptl_crystal_density_diffrn 4.875 +_exptl_crystal_description plate +_exptl_crystal_F_000 116 +_exptl_crystal_recrystallization_method 'Hydrothermal method' +_exptl_crystal_size_max 0.09 +_exptl_crystal_size_mid 0.06 +_exptl_crystal_size_min 0.015 +_refine_diff_density_max 1.840 +_refine_diff_density_min -0.930 +_refine_diff_density_rms 0.256 +_refine_ls_extinction_coef 0.26(3) +_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^ +_refine_ls_extinction_method 'SHELXL-2018/3 (Sheldrick, 2018)' +_refine_ls_goodness_of_fit_ref 1.187 +_refine_ls_hydrogen_treatment undef +_refine_ls_matrix_type full +_refine_ls_number_parameters 12 +_refine_ls_number_reflns 112 +_refine_ls_number_restraints 0 +_refine_ls_restrained_S_all 1.187 +_refine_ls_R_factor_all 0.0266 +_refine_ls_R_factor_gt 0.0253 +_refine_ls_shift/su_max 0.000 +_refine_ls_shift/su_mean 0.000 +_refine_ls_structure_factor_coef Fsqd +_refine_ls_weighting_details +'w=1/[\s^2^(Fo^2^)+(0.0350P)^2^+0.2064P] where P=(Fo^2^+2Fc^2^)/3' +_refine_ls_weighting_scheme calc +_refine_ls_wR_factor_gt 0.0631 +_refine_ls_wR_factor_ref 0.0638 +_reflns_Friedel_coverage 0.000 +_reflns_number_gt 105 +_reflns_number_total 112 +_reflns_threshold_expression 'I > 2\s(I)' +_cod_data_source_file d1sc03026d2.cif +_cod_data_source_block kma0205 +_cod_database_code 1564889 +_shelx_shelxl_version_number 2018/3 +_shelx_space_group_comment +; +The symmetry employed for this shelxl refinement is uniquely defined +by the following loop, which should always be used as a source of +symmetry information in preference to the above space-group names. +They are only intended as comments. +; +_shelx_estimated_absorpt_t_max 0.851 +_shelx_estimated_absorpt_t_min 0.434 +_shelx_res_file +; +TITL exp_202_a.res in Pnnm + new.res + created by SHELXL-2018/3 at 13:53:49 on 04-May-2018 +CELL 0.71073 4.4474 5.4287 3.3852 90 90 90 +ZERR 2 0.0004 0.0004 0.0003 0 0 0 +LATT 1 +SYMM -X,-Y,+Z +SYMM 0.5+X,0.5-Y,0.5-Z +SYMM 0.5-X,0.5+Y,0.5-Z +SFAC Fe S +UNIT 2 4 + +L.S. 8 0 0 +PLAN 20 +SIZE 0.015 0.06 0.09 +TEMP -113.1(10) +list 4 +fmap 2 53 +acta +SHEL 100 0.76 +OMIT 0 2 0 +OMIT 0 6 0 +REM +REM +REM + +WGHT 0.035000 0.206400 +EXTI 0.256184 +FVAR 3.97198 +FE1 1 0.000000 0.000000 0.000000 10.25000 0.00313 0.00347 = + 0.00316 0.00000 0.00000 0.00016 +S1 2 0.199942 0.378036 0.000000 10.50000 0.00320 0.00358 = + 0.00371 0.00000 0.00000 -0.00005 +HKLF 4 + + + + +REM exp_202_a.res in Pnnm +REM wR2 = 0.0638, GooF = S = 1.187, Restrained GooF = 1.187 for all data +REM R1 = 0.0253 for 105 Fo > 4sig(Fo) and 0.0266 for all 112 data +REM 12 parameters refined using 0 restraints + +END + +WGHT 0.0350 0.2067 + +REM Highest difference peak 1.840, deepest hole -0.930, 1-sigma level 0.256 +Q1 1 0.0000 0.5000 0.0000 10.25000 0.05 1.84 +Q2 1 0.1984 0.1378 0.0000 10.50000 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2714.65 294.491 3 + -4 1 3 1997.78 279.828 5 + -4 -1 -3 2181.89 333.762 2 + -4 1 -3 2435.99 374.045 6 + -4 -1 3 2517.87 307.207 1 + -4 1 3 2618.11 270.527 1 + 4 -2 3 6606.96 503.520 3 + -4 -2 3 6280.71 533.234 5 + -4 -2 -3 5983.19 612.862 2 + -4 2 -3 7069.73 663.160 6 + -4 -2 -3 6947.75 587.069 6 + -4 -2 3 5993.60 508.905 1 + -4 -3 3 7230.98 575.401 5 + 4 3 3 6331.14 526.440 4 + -4 -3 -3 5672.71 610.604 2 + -4 3 -3 7128.63 673.838 6 + 4 -3 3 7036.08 524.219 3 + -4 -3 3 5932.15 519.151 1 + 0 0 4 26548.8 1217.24 5 + 0 0 -4 24554.7 1007.19 2 + 0 -1 4 23.7014 51.5407 5 + 0 1 4-26.0330 56.6111 5 + 0 -1 -4-16.6688 20.9279 2 + 0 -1 4 83.1586 46.6916 6 + 0 2 4 6617.24 529.260 5 + 0 2 4 5639.65 328.553 4 + 0 -2 4 6323.75 487.553 1 + 0 -2 -4 5123.94 438.564 2 + 0 3 4-21.0683 52.9077 5 + 0 3 4 38.2679 27.7490 4 + 0 -3 -4 74.7450 62.5659 2 + 0 -3 4 49.6500 53.9892 1 + 0 4 4 393.499 103.367 4 + 0 -4 -4 228.393 101.740 2 + 1 0 4 21.8496 38.7949 5 + -1 0 4 25.4706 55.3880 5 + -1 0 4 48.3790 45.2727 1 + -1 0 -4-31.0503 43.5850 2 + 1 0 -4 13.3934 29.1250 2 + -1 0 -4 44.1604 48.0153 6 + 1 1 4 2644.88 319.435 5 + -1 1 4 2752.98 353.760 5 + -1 -1 4 2640.83 286.221 1 + -1 -1 -4 2299.53 275.108 2 + -1 1 -4 2842.82 330.018 6 + 1 -1 -4 2015.37 243.277 2 + -1 -1 4 2293.52 306.006 5 + 1 2 4 7454.54 524.125 5 + -1 2 4 7643.49 589.101 5 + 1 2 4 7479.97 419.149 4 + -1 2 4 5943.15 346.817 4 + -1 -2 -4 5988.62 497.680 2 + -1 2 -4 7324.33 537.564 6 + 1 -2 -4 6455.91 487.877 2 + -1 -2 4 5999.28 490.460 1 + -1 -2 4 5668.18 522.225 5 + -1 3 4 6806.94 542.049 5 + 1 3 4 6490.09 421.512 4 + -1 3 4 6433.80 415.197 4 + -1 -3 -4 6441.80 557.142 2 + -1 3 -4 6090.15 467.184 6 + 1 -3 -4 6377.44 526.031 2 + -1 -3 4 7045.97 559.964 1 + 1 4 4 53.2862 38.7052 4 + -1 -4 -4 183.226 93.9461 2 + -1 4 4 212.786 77.1603 4 + -1 -4 4 55.3532 49.2040 1 + 1 -4 -4 139.814 78.5418 2 + 2 0 4 19.9929 35.5108 5 + -2 0 4 54.1169 67.9501 5 + -2 0 -4 39.0335 42.4513 2 + -2 0 4 50.6465 51.9268 1 + -2 0 -4 27.4615 59.7249 6 + 2 -1 -4 1224.55 194.640 2 + -2 -1 4 1086.46 215.024 5 + -2 1 4 1288.07 242.823 5 + -2 1 4 1192.91 173.432 1 + -2 -1 -4 911.164 188.064 2 + -2 1 -4 1313.57 247.775 6 + -2 -1 -4 1266.84 236.478 6 + -2 -1 4 902.956 171.640 1 + 2 -2 -4 3333.45 360.121 2 + -2 2 4 4008.48 428.501 5 + 2 2 4 3972.24 331.200 4 + -2 -2 -4 3882.41 422.736 2 + -2 -2 4 4547.72 411.874 1 + -2 2 -4 3606.52 398.569 6 + 2 -3 -4 1494.94 250.763 2 + -2 -3 4 1182.53 234.334 5 + 2 3 4 1100.89 178.784 4 + -2 -3 -4 1231.91 249.977 2 + -2 -3 4 1261.24 224.312 1 + -2 3 -4 1232.25 213.248 6 + -3 0 -4 44.3090 39.3607 2 + -3 0 4 56.8950 41.2643 1 + -3 -1 4 11888.9 793.034 5 + -3 -1 4 11127.8 694.215 1 + -3 -1 -4 11556.3 764.862 2 + -3 1 -4 12371.3 874.620 6 + -3 -1 -4 11308.0 813.683 6 + -3 -2 4 2030.09 305.414 5 + -3 2 4 1814.92 285.868 5 + -3 -2 4 2016.64 281.721 1 + -3 -2 -4 2021.50 322.023 2 + -3 2 -4 2179.97 329.481 6 + 0 0 0 0.00 0.00 0 +; +_shelx_hkl_checksum 82444 +_olex2_submission_special_instructions 'No special instructions were received' +_oxdiff_exptl_absorpt_empirical_details +; +Empirical correction (ABSPACK) includes: +- Absorption correction using spherical harmonics +- Frame scaling +- Detector area scaling +; +_oxdiff_exptl_absorpt_empirical_full_max 1.455 +_oxdiff_exptl_absorpt_empirical_full_min 0.766 +loop_ +_space_group_symop_operation_xyz +'x, y, z' +'-x, -y, z' +'x+1/2, -y+1/2, -z+1/2' +'-x+1/2, y+1/2, -z+1/2' +'-x, -y, -z' +'x, y, -z' +'-x-1/2, y-1/2, z-1/2' +'x-1/2, -y-1/2, z-1/2' +loop_ +_atom_site_label +_atom_site_type_symbol +_atom_site_fract_x +_atom_site_fract_y +_atom_site_fract_z +_atom_site_U_iso_or_equiv +_atom_site_adp_type +_atom_site_occupancy +_atom_site_site_symmetry_order +_atom_site_calc_flag +_atom_site_refinement_flags_posn +_atom_site_refinement_flags_adp +_atom_site_refinement_flags_occupancy +_atom_site_disorder_assembly +_atom_site_disorder_group +Fe1 Fe 0.000000 0.000000 0.000000 0.0033(5) Uani 1 4 d S T P . . +S1 S 0.1999(3) 0.37804(19) 0.000000 0.0035(5) Uani 1 2 d S T P . . +loop_ +_atom_site_aniso_label +_atom_site_aniso_U_11 +_atom_site_aniso_U_22 +_atom_site_aniso_U_33 +_atom_site_aniso_U_23 +_atom_site_aniso_U_13 +_atom_site_aniso_U_12 +Fe1 0.0031(7) 0.0035(6) 0.0032(7) 0.000 0.000 0.0002(3) +S1 0.0032(7) 0.0036(7) 0.0037(7) 0.000 0.000 -0.0001(4) +loop_ +_atom_type_symbol +_atom_type_description +_atom_type_scat_dispersion_real +_atom_type_scat_dispersion_imag +_atom_type_scat_source +Fe Fe 0.3463 0.8444 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' +S S 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' +loop_ +_exptl_crystal_face_index_h +_exptl_crystal_face_index_k +_exptl_crystal_face_index_l +_exptl_crystal_face_perp_dist +-5 1 -3 0.0031 +-1 5 -1 0.0272 +1 -5 1 0.0272 +5 -1 0 0.0289 +6 1 3 0.0089 +-2 1 5 0.0316 +3 5 -1 0.0263 +-4 -5 -2 0.0255 +5 -1 3 0.0101 +loop_ +_geom_angle_atom_site_label_1 +_geom_angle_atom_site_label_2 +_geom_angle_atom_site_label_3 +_geom_angle +_geom_angle_site_symmetry_1 +_geom_angle_site_symmetry_3 +_geom_angle_publ_flag +S1 Fe1 S1 180.0 5 . ? +S1 Fe1 S1 91.957(18) . 7_655 ? +S1 Fe1 S1 91.956(18) 5 3_454 ? +S1 Fe1 S1 88.043(18) . 3_454 ? +S1 Fe1 S1 82.70(4) 3_454 7_655 ? +S1 Fe1 S1 88.043(18) . 3_455 ? +S1 Fe1 S1 82.70(4) 7_656 3_455 ? +S1 Fe1 S1 97.30(4) 3_454 3_455 ? +S1 Fe1 S1 180.0 7_656 3_454 ? +S1 Fe1 S1 91.957(18) . 7_656 ? +S1 Fe1 S1 97.30(4) 7_656 7_655 ? +S1 Fe1 S1 91.957(18) 5 3_455 ? +S1 Fe1 S1 180.0 3_455 7_655 ? +S1 Fe1 S1 88.044(18) 5 7_656 ? +S1 Fe1 S1 88.043(18) 5 7_655 ? +Fe1 S1 Fe1 97.30(4) 3 3_554 ? +Fe1 S1 Fe1 120.31(3) . 3_554 ? +Fe1 S1 Fe1 120.31(3) . 3 ? +S1 S1 Fe1 107.42(5) 5_565 3_554 ? +S1 S1 Fe1 107.42(5) 5_565 3 ? +S1 S1 Fe1 103.24(7) 5_565 . ? +loop_ +_geom_bond_atom_site_label_1 +_geom_bond_atom_site_label_2 +_geom_bond_distance +_geom_bond_site_symmetry_2 +_geom_bond_publ_flag +Fe1 S1 2.2366(11) 5 ? +Fe1 S1 2.2548(8) 7_655 ? +Fe1 S1 2.2548(8) 7_656 ? +Fe1 S1 2.2366(11) . ? +Fe1 S1 2.2548(8) 3_455 ? +Fe1 S1 2.2548(8) 3_454 ? +S1 S1 2.217(2) 5_565 ? \ No newline at end of file diff -r 000000000000 -r edf7f8ccf4af test-data/[CSV_summary_of_1564889.cif].csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/[CSV_summary_of_1564889.cif].csv Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,9 @@ + file , sig2 , amp ratio, deg , nlegs, r effective, label , select + feff0001.dat, 0.00000, 100.000 , 2.000, 2 , 2.2366 , S.Fe.1 , 0 + feff0002.dat, 0.00000, 100.000 , 4.000, 2 , 2.2549 , S.Fe.2 , 0 + feff0003.dat, 0.00000, 17.561 , 2.000, 2 , 3.3852 , Fe.Fe.3 , 0 + feff0004.dat, 0.00000, 16.957 , 2.000, 2 , 3.4915 , S.Fe.4 , 0 + feff0005.dat, 0.00000, 31.275 , 4.000, 2 , 3.6045 , S.Fe.5 , 0 + feff0006.dat, 0.00000, 7.146 , 8.000, 3 , 3.8064 , S.S.Fe.6 , 0 + feff0007.dat, 0.00000, 7.214 , 8.000, 3 , 3.8606 , S.S.Fe.7 , 0 + feff0008.dat, 0.00000, 50.180 , 8.000, 2 , 3.8958 , Fe.Fe.8 , 0 diff -r 000000000000 -r edf7f8ccf4af test-data/[CSV_summary_of_test.inp].csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/[CSV_summary_of_test.inp].csv Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,95 @@ + file , sig2 , amp ratio, deg , nlegs, r effective, label , select + feff0001.dat, 0.00000, 100.000 , 1.000, 2 , 1.9149 , C.Rh.1 , 0 + feff0002.dat, 0.00000, 91.295 , 1.000, 2 , 1.9854 , C.Rh.2 , 0 + feff0003.dat, 0.00000, 83.637 , 1.000, 2 , 2.0550 , C.Rh.3 , 0 + feff0004.dat, 0.00000, 79.929 , 1.000, 2 , 2.0917 , C.Rh.4 , 0 + feff0005.dat, 0.00000, 89.367 , 1.000, 2 , 2.7050 , Rh.Rh.5 , 0 + feff0006.dat, 0.00000, 86.941 , 1.000, 2 , 2.7337 , Rh.Rh.6 , 0 + feff0007.dat, 0.00000, 81.971 , 1.000, 2 , 2.7957 , Rh.Rh.7 , 0 + feff0008.dat, 0.00000, 37.159 , 1.000, 2 , 3.0163 , O.Rh.8 , 0 + feff0009.dat, 0.00000, 100.000 , 2.000, 3 , 3.0167 , O.C.Rh.9 , 0 + feff0010.dat, 0.00000, 76.145 , 1.000, 4 , 3.0170 , C.O.C.Rh.10 , 0 + feff0011.dat, 0.00000, 32.597 , 1.000, 2 , 3.0220 , O.Rh.11 , 0 + feff0012.dat, 0.00000, 29.179 , 1.000, 2 , 3.1366 , O.Rh.12 , 0 + feff0013.dat, 0.00000, 25.921 , 2.000, 3 , 3.1653 , O.C.Rh.13 , 0 + feff0014.dat, 0.00000, 27.950 , 1.000, 2 , 3.1819 , O.Rh.14 , 0 + feff0015.dat, 0.00000, 58.926 , 2.000, 3 , 3.2132 , O.C.Rh.15 , 0 + feff0016.dat, 0.00000, 32.939 , 1.000, 4 , 3.2445 , C.O.C.Rh.16 , 0 + feff0017.dat, 0.00000, 21.901 , 2.000, 3 , 3.2875 , O.C.Rh.17 , 0 + feff0018.dat, 0.00000, 7.728 , 1.000, 4 , 3.3087 , C.O.C.Rh.18 , 0 + feff0019.dat, 0.00000, 5.677 , 2.000, 3 , 3.3214 , Rh.C.Rh.19 , 0 + feff0020.dat, 0.00000, 5.763 , 2.000, 3 , 3.3260 , Rh.C.Rh.20 , 0 + feff0021.dat, 0.00000, 6.231 , 1.000, 4 , 3.4384 , C.O.C.Rh.21 , 0 + feff0023.dat, 0.00000, 16.232 , 1.000, 2 , 3.5372 , C.Rh.23 , 0 + feff0024.dat, 0.00000, 3.728 , 2.000, 3 , 3.5425 , C.C.Rh.24 , 0 + feff0025.dat, 0.00000, 15.819 , 1.000, 2 , 3.5671 , C.Rh.25 , 0 + feff0026.dat, 0.00000, 3.312 , 2.000, 3 , 3.5939 , C.C.Rh.26 , 0 + feff0027.dat, 0.00000, 4.223 , 2.000, 3 , 3.6181 , C.C.Rh.27 , 0 + feff0029.dat, 0.00000, 14.227 , 1.000, 2 , 3.6920 , C.Rh.29 , 0 + feff0030.dat, 0.00000, 11.517 , 2.000, 3 , 3.8220 , C.C.Rh.30 , 0 + feff0031.dat, 0.00000, 4.455 , 1.000, 4 , 3.8297 , C.Rh.C.Rh.31 , 0 + feff0032.dat, 0.00000, 12.091 , 1.000, 2 , 3.8888 , C.Rh.32 , 0 + feff0033.dat, 0.00000, 15.264 , 2.000, 4 , 3.9003 , C.Rh.C.Rh.33 , 0 + feff0034.dat, 0.00000, 14.184 , 1.000, 2 , 3.9535 , O.Rh.34 , 0 + feff0035.dat, 0.00000, 3.684 , 1.000, 4 , 3.9708 , C.Rh.C.Rh.35 , 0 + feff0036.dat, 0.00000, 10.240 , 1.000, 4 , 3.9783 , O.C.O.Rh.36 , 0 + feff0037.dat, 0.00000, 32.052 , 2.000, 5 , 3.9787 , O.C.O.C.Rh.37 , 0 + feff0038.dat, 0.00000, 25.210 , 1.000, 6 , 3.9790 , C.O.C.O.C.Rh.38 , 0 + feff0039.dat, 0.00000, 11.124 , 1.000, 2 , 3.9920 , C.Rh.39 , 0 + feff0040.dat, 0.00000, 13.715 , 1.000, 2 , 3.9945 , O.Rh.40 , 0 + feff0041.dat, 0.00000, 8.332 , 2.000, 3 , 4.0838 , C.Rh.Rh.41 , 0 + feff0042.dat, 0.00000, 3.048 , 2.000, 3 , 4.0890 , Rh.Rh.Rh.42 , 0 + feff0043.dat, 0.00000, 3.260 , 2.000, 3 , 4.1013 , Rh.Rh.Rh.43 , 0 + feff0044.dat, 0.00000, 3.073 , 1.000, 4 , 4.1100 , C.Rh.C.Rh.44 , 0 + feff0045.dat, 0.00000, 7.914 , 2.000, 3 , 4.1209 , C.Rh.Rh.45 , 0 + feff0046.dat, 0.00000, 3.206 , 2.000, 3 , 4.1223 , Rh.Rh.Rh.46 , 0 + feff0047.dat, 0.00000, 2.799 , 1.000, 4 , 4.1834 , C.Rh.C.Rh.47 , 0 + feff0048.dat, 0.00000, 7.874 , 2.000, 3 , 4.1912 , C.Rh.Rh.48 , 0 + feff0050.dat, 0.00000, 8.949 , 1.000, 2 , 4.2696 , C.Rh.50 , 0 + feff0051.dat, 0.00000, 10.748 , 1.000, 2 , 4.3002 , O.Rh.51 , 0 + feff0052.dat, 0.00000, 10.714 , 1.000, 2 , 4.3043 , O.Rh.52 , 0 + feff0053.dat, 0.00000, 10.621 , 1.000, 2 , 4.3155 , O.Rh.53 , 0 + feff0054.dat, 0.00000, 7.182 , 2.000, 3 , 4.3251 , C.Rh.Rh.54 , 0 + feff0055.dat, 0.00000, 5.235 , 1.000, 4 , 4.3347 , O.C.O.Rh.55 , 0 + feff0057.dat, 0.00000, 3.558 , 1.000, 4 , 4.3452 , O.C.O.Rh.57 , 0 + feff0058.dat, 0.00000, 8.350 , 1.000, 2 , 4.3603 , C.Rh.58 , 0 + feff0059.dat, 0.00000, 12.514 , 2.000, 5 , 4.3660 , O.C.O.C.Rh.59 , 0 + feff0060.dat, 0.00000, 16.294 , 2.000, 3 , 4.3787 , C.Rh.Rh.60 , 0 + feff0062.dat, 0.00000, 7.648 , 1.000, 6 , 4.3972 , C.O.C.O.C.Rh.62 , 0 + feff0063.dat, 0.00000, 6.643 , 2.000, 3 , 4.4001 , C.Rh.Rh.63 , 0 + feff0064.dat, 0.00000, 13.337 , 2.000, 3 , 4.4055 , O.C.Rh.64 , 0 + feff0066.dat, 0.00000, 5.926 , 2.000, 3 , 4.4541 , C.Rh.Rh.66 , 0 + feff0068.dat, 0.00000, 9.336 , 1.000, 2 , 4.4832 , O.Rh.68 , 0 + feff0069.dat, 0.00000, 7.222 , 1.000, 4 , 4.4878 , Rh.C.Rh.Rh.69 , 0 + feff0070.dat, 0.00000, 4.653 , 2.000, 5 , 4.4886 , O.C.O.C.Rh.70 , 0 + feff0071.dat, 0.00000, 12.751 , 2.000, 3 , 4.4927 , C.Rh.Rh.71 , 0 + feff0072.dat, 0.00000, 5.932 , 1.000, 4 , 4.4955 , C.O.C.Rh.72 , 0 + feff0078.dat, 0.00000, 3.284 , 2.000, 3 , 4.5615 , O.C.Rh.78 , 0 + feff0079.dat, 0.00000, 2.902 , 2.000, 3 , 4.5732 , C.C.Rh.79 , 0 + feff0080.dat, 0.00000, 3.436 , 2.000, 3 , 4.6064 , Rh.C.Rh.80 , 0 + feff0081.dat, 0.00000, 4.653 , 1.000, 4 , 4.6251 , Rh.C.Rh.Rh.81 , 0 + feff0082.dat, 0.00000, 6.854 , 2.000, 3 , 4.6311 , O.C.Rh.82 , 0 + feff0083.dat, 0.00000, 6.727 , 1.000, 2 , 4.6507 , C.Rh.83 , 0 + feff0084.dat, 0.00000, 8.204 , 1.000, 2 , 4.6551 , O.Rh.84 , 0 + feff0085.dat, 0.00000, 2.780 , 2.000, 3 , 4.6567 , C.C.Rh.85 , 0 + feff0087.dat, 0.00000, 3.264 , 2.000, 3 , 4.6645 , Rh.C.Rh.87 , 0 + feff0088.dat, 0.00000, 6.619 , 1.000, 2 , 4.6730 , C.Rh.88 , 0 + feff0089.dat, 0.00000, 3.068 , 2.000, 4 , 4.6823 , Rh.C.C.Rh.89 , 0 + feff0091.dat, 0.00000, 18.587 , 2.000, 3 , 4.7211 , C.Rh.Rh.91 , 0 + feff0092.dat, 0.00000, 13.756 , 1.000, 4 , 4.7692 , Rh.C.Rh.Rh.92 , 0 + feff0094.dat, 0.00000, 6.951 , 2.000, 3 , 4.7831 , C.O.Rh.94 , 0 + feff0095.dat, 0.00000, 6.102 , 2.000, 3 , 4.7842 , C.Rh.Rh.95 , 0 + feff0098.dat, 0.00000, 10.393 , 2.000, 4 , 4.7967 , C.Rh.Rh.Rh.98 , 0 + feff0099.dat, 0.00000, 2.759 , 2.000, 5 , 4.8110 , O.C.O.C.Rh.99 , 0 + feff0102.dat, 0.00000, 7.049 , 1.000, 2 , 4.8622 , O.Rh.102 , 0 + feff0104.dat, 0.00000, 6.792 , 1.000, 2 , 4.9136 , O.Rh.104 , 0 + feff0105.dat, 0.00000, 5.690 , 2.000, 3 , 4.9161 , C.O.Rh.105 , 0 + feff0107.dat, 0.00000, 11.074 , 2.000, 3 , 4.9167 , O.C.Rh.107 , 0 + feff0108.dat, 0.00000, 10.137 , 2.000, 4 , 4.9368 , C.Rh.O.Rh.108 , 0 + feff0109.dat, 0.00000, 5.170 , 1.000, 6 , 4.9403 , O.C.O.C.O.Rh.109 , 0 + feff0110.dat, 0.00000, 16.546 , 2.000, 7 , 4.9407 , O.C.O.C.O.C.Rh.110 , 0 + feff0111.dat, 0.00000, 13.280 , 1.000, 8 , 4.9410 , C.O.C.O.C.O.C.Rh.111 , 0 + feff0112.dat, 0.00000, 3.562 , 2.000, 3 , 4.9549 , O.Rh.Rh.112 , 0 + feff0113.dat, 0.00000, 5.689 , 2.000, 4 , 4.9593 , O.C.Rh.Rh.113 , 0 + feff0114.dat, 0.00000, 5.096 , 1.000, 4 , 4.9712 , C.O.C.Rh.114 , 0 + feff0115.dat, 0.00000, 6.492 , 1.000, 2 , 4.9766 , O.Rh.115 , 0 diff -r 000000000000 -r edf7f8ccf4af test-data/[FEFF_input_of_1564889.cif].txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/[FEFF_input_of_1564889.cif].txt Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,52 @@ +* This FEFF.inp file generated by pymatgen +TITLE comment: None given +TITLE Source: +TITLE Structure Summary: Fe2 S4 +TITLE Reduced formula: FeS2 +TITLE space group: (Pnnm), space number: (58) +TITLE abc: 3.385200 4.447400 5.428700 +TITLE angles: 90.000000 90.000000 90.000000 +TITLE sites: 6 +* 1 Fe 0.000000 0.000000 0.000000 +* 2 Fe 0.500000 0.500000 0.500000 +* 3 S 0.000000 0.199900 0.378040 +* 4 S 0.000000 0.800100 0.621960 +* 5 S 0.500000 0.699900 0.121960 +* 6 S 0.500000 0.300100 0.878040 + +POTENTIALS + *ipot Z tag lmax1 lmax2 xnatph(stoichometry) spinph +******- **- ****- ******- ******- ********************** ******** + 0 26 Fe -1 -1 0.0001 0 + 1 26 Fe -1 -1 2 0 + 2 16 S -1 -1 4 0 + +ATOMS + * x y z ipot Atom Distance Number +**********- ********- ******- ****** ****** ********** ******** + 0 0 0 0 Fe 0 0 + -0.889035 -2.05227 -0 2 S 2.23656 4 + 0.889035 2.05227 0 2 S 2.23656 22 + -1.33466 0.662084 -1.6926 2 S 2.2549 6 + -1.33466 0.662084 1.6926 2 S 2.2549 8 + 1.33466 -0.662084 -1.6926 2 S 2.2549 11 + 1.33466 -0.662084 1.6926 2 S 2.2549 13 + 0 0 -3.3852 1 Fe 3.3852 18 + 0 0 3.3852 1 Fe 3.3852 19 + -0.889035 3.37643 0 2 S 3.49152 9 + 0.889035 -3.37643 -0 2 S 3.49152 15 + -3.11273 -0.662084 -1.6926 2 S 3.60449 1 + -3.11273 -0.662084 1.6926 2 S 3.60449 3 + 3.11273 0.662084 -1.6926 2 S 3.60449 16 + 3.11273 0.662084 1.6926 2 S 3.60449 20 + -2.2237 -2.71435 -1.6926 1 Fe 3.89582 2 + -2.2237 -2.71435 1.6926 1 Fe 3.89582 5 + -2.2237 2.71435 -1.6926 1 Fe 3.89582 7 + -2.2237 2.71435 1.6926 1 Fe 3.89582 10 + 2.2237 -2.71435 -1.6926 1 Fe 3.89582 12 + 2.2237 -2.71435 1.6926 1 Fe 3.89582 14 + 2.2237 2.71435 -1.6926 1 Fe 3.89582 17 + 2.2237 2.71435 1.6926 1 Fe 3.89582 21 +END + + diff -r 000000000000 -r edf7f8ccf4af test-data/test.inp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.inp Tue Nov 14 15:35:09 2023 +0000 @@ -0,0 +1,204 @@ + * This feff6 file was generated by Demeter 0.9.25 + * Demeter written by and copyright (c) Bruce Ravel, 2006-2016 + + * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- + * title = Rh4 (C O)12 + * title = Wei, C.H. + * title = Structural analyses of tetracobalt dodecacarbonyl and tetrarhodium + * title = dodecacarbonyl. crystallographic treatments of a disordered structure and + * title = a twinned composite + * space = P 1 21/c 1 + * a = 9.24000 b = 12.02000 c = 17.74000 + * alpha = 90.00000 beta = 90.01000 gamma = 90.00000 + * rmax = 8.00000 core = Rh2 + # polarization = 0 0 0 + * shift = 0 0 0 + * atoms + * # el. x y z tag + * Rh 0.80300 0.12960 0.11700 Rh2 + * O 0.32670 0.09340 0.15840 O10 + * O 0.47530 0.42690 0.24520 O11 + * O 0.64010 0.15120 0.97000 O7 + * C 0.80890 0.35860 0.30760 C2 + * O 0.99670 0.08910 0.25960 O5 + * C 0.98250 0.12050 0.04890 C6 + * O 0.72440 0.60230 0.15200 O3 + * Rh 0.72980 0.25550 0.24390 Rh4 + * O 0.06690 0.11270 0.01760 O6 + * C 0.40570 0.15010 0.13420 C10 + * C 0.88320 0.15360 0.21520 C5 + * C 0.83230 0.37670 0.00980 C1 + * O 0.73780 0.87010 0.12710 O9 + * C 0.56420 0.35920 0.22170 C11 + * C 0.03540 0.36270 0.14590 C4 + * Rh 0.82980 0.35370 0.11720 Rh1 + * Rh 0.56000 0.25930 0.11900 Rh3 + * C 0.77150 0.51620 0.13940 C3 + * C 0.64400 0.15530 0.31920 C8 + * O 0.38340 0.40770 0.02090 O12 + * O 0.87610 0.36940 0.94120 O1 + * O 0.12820 0.37820 0.16300 O4 + * O 0.89300 0.39590 0.35940 O2 + * C 0.46010 0.35540 0.06580 C12 + * C 0.64700 0.16520 0.04390 C7 + * O 0.57470 0.12500 0.36390 O8 + * C 0.73760 0.96320 0.11150 C9 + * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- + + * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- + * total mu*x=1: 112.246 microns, unit edge step: 136.115 microns + * specific gravity: 2.521 + * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- + * normalization correction: 0.00020 ang^2 + * --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*-- + + TITLE Rh4 (C O)12 + TITLE Wei, C.H. + TITLE Structural analyses of tetracobalt dodecacarbonyl and tetrarhodium + TITLE dodecacarbonyl. crystallographic treatments of a disordered structure and + TITLE a twinned composite + + HOLE 1 1.0 * FYI: (Rh K edge @ 23220 eV, second number is S0^2) + * mphase,mpath,mfeff,mchi + CONTROL 1 1 1 1 + PRINT 1 0 0 0 + + RMAX 5.0 + *POLARIZATION 0 0 0 + + POTENTIALS + * ipot Z tag + 0 45 Rh + 1 45 Rh + 2 8 O + 3 6 C + + + ATOMS * this list contains 124 atoms + * x y z ipot tag distance + 0.00000 0.00000 0.00000 0 Rh2 0.00000 + -0.74105 0.28848 -1.74194 3 C5.1 1.91487 + 1.44144 0.42791 1.29654 3 C7.1 1.98542 + -1.65858 -0.10938 1.20838 3 C6.1 2.05500 + 0.60430 -2.00013 0.09746 3 C9.1 2.09170 + -0.24763 2.69368 -0.00350 1 Rh1.1 2.70504 + 2.24532 1.55899 -0.03587 1 Rh3.1 2.73372 + 0.67637 1.51332 -2.25132 1 Rh4.1 2.79572 + -2.43844 -0.20314 1.76378 2 O6.1 3.01632 + 1.50520 0.25963 2.60752 2 O7.1 3.02195 + -1.78979 -0.48681 -2.52941 2 O5.1 3.13660 + 0.60245 -3.11919 -0.17928 2 O9.1 3.18189 + -0.27073 2.97014 1.90178 3 C1.1 3.53720 + -2.14738 2.80186 -0.51231 3 C4.1 3.56709 + 3.67105 0.24641 -0.30577 3 C10.1 3.69200 + 1.46916 0.30891 -3.58728 3 C8.1 3.88876 + -1.20212 -2.91245 2.38801 2 O6.2 3.95349 + 2.20651 2.75979 -1.85776 3 C11.1 3.99205 + -2.80896 -2.80907 -0.41817 2 O2.1 3.99450 + 3.16840 2.71412 0.90774 3 C12.1 4.26956 + -0.67544 2.88240 3.11881 2 O1.1 4.30016 + 2.57149 -2.43645 -2.44502 2 O11.1 4.30430 + -3.00485 2.98817 -0.81552 2 O4.1 4.31548 + -0.05452 2.75258 -3.38123 3 C2.1 4.36032 + 4.40101 -0.43512 -0.73520 2 O10.1 4.48316 + -1.98198 -3.00620 2.94341 3 C6.2 4.65072 + -0.83160 -0.30651 4.56997 2 O2.2 4.65512 + 0.29106 4.64693 -0.39743 3 C3.1 4.67297 + 2.10949 -0.05529 -4.38037 2 O8.1 4.86217 + -4.83899 -0.43512 -0.73359 2 O10.2 4.91358 + -0.63571 -3.02183 -3.90269 2 O4.2 4.97660 + -3.58604 -3.25742 -1.33697 3 C2.2 5.02573 + 3.02795 3.57355 -2.27480 2 O11.2 5.20705 + 3.87710 3.34276 1.70414 2 O12.1 5.39538 + -0.83160 3.20093 -4.30003 2 O2.3 5.42474 + -0.05452 0.14184 5.48877 3 C2.3 5.49087 + -1.49318 -3.20814 -4.20589 3 C4.2 5.49648 + 3.39293 -3.25021 -2.86205 3 C11.2 5.50156 + 4.09424 -3.37522 1.54267 2 O7.2 5.52582 + -5.56895 0.24641 -0.30416 3 C10.2 5.58269 + 1.19843 -2.68046 4.88539 2 O10.3 5.69983 + 0.72626 5.68185 -0.62103 2 O3.1 5.76165 + 2.10949 2.94971 4.48963 2 O8.2 5.77126 + -0.67544 0.01202 -5.75119 2 O1.2 5.79073 + 1.92839 -3.36199 4.45595 3 C10.3 5.90569 + -4.24486 -1.11546 4.05433 3 C9.2 5.97500 + -4.36682 -0.32815 -4.09718 2 O3.2 5.99697 + -3.93162 -1.36307 -4.32078 3 C3.2 5.99873 + 1.46916 2.58550 5.28272 3 C8.2 6.06221 + -4.24301 0.00361 4.33107 2 O9.2 6.06311 + 4.15800 -3.54350 2.85364 3 C7.2 6.16349 + -1.85077 5.52319 -2.18879 2 O5.2 6.22268 + 1.72234 5.56165 2.44605 2 O12.2 6.31519 + -3.64056 -3.11558 4.15180 1 Rh2.1 6.34018 + -5.14576 -3.37522 1.54428 2 O7.3 6.34474 + 4.87318 -0.32815 -4.09879 2 O3.3 6.37618 + 0.72626 -6.33815 -0.62103 2 O3.4 6.40978 + 4.99514 -1.11546 4.05272 3 C9.3 6.52842 + -5.36290 3.34276 1.70575 2 O12.3 6.54555 + 4.99699 0.00361 4.32946 2 O9.3 6.61167 + 5.65396 -3.25742 -1.33858 3 C2.4 6.66107 + -3.39293 -3.31632 -4.71470 1 Rh1.2 6.68867 + -4.31693 -4.49668 -2.46688 1 Rh4.2 6.70384 + -6.07160 2.71412 0.90935 3 C12.2 6.71250 + -2.96512 -5.99798 1.03299 2 O1.3 6.77014 + -2.96512 6.02202 1.03299 2 O1.4 6.79144 + 0.67637 1.38110 6.61868 1 Rh4.3 6.79498 + -5.08200 -3.54350 2.85525 3 C7.3 6.82170 + -4.24301 2.89081 -4.53893 2 O9.4 6.85286 + 3.48995 5.95471 -0.33944 2 O8.3 6.91039 + 1.19843 5.57488 -3.98461 2 O10.4 6.95648 + 1.50520 2.63478 -6.26248 2 O7.4 6.95891 + 2.43104 -3.29588 -5.62755 3 C12.3 6.96004 + 6.23515 2.98817 -0.81713 2 O4.3 6.96233 + -0.27073 -0.07573 -6.96822 3 C1.2 6.97389 + 5.30838 -1.36307 -4.32239 3 C3.3 6.97996 + 3.48995 -6.06529 -0.33944 2 O8.4 7.00591 + 6.80156 -0.20314 1.76217 2 O6.3 7.02907 + 6.43104 -2.80907 -0.41979 2 O2.4 7.03032 + -2.89951 -5.72152 -2.97627 3 C5.2 7.07115 + 2.43104 -5.82970 3.24245 3 C12.4 7.09992 + -1.85077 -6.49681 -2.18879 2 O5.3 7.10104 + 4.92307 -4.49668 -2.46849 1 Rh4.4 7.10987 + 3.35412 -4.67458 4.18605 1 Rh3.2 7.11511 + 1.72234 -6.45835 2.44605 2 O12.4 7.11757 + 4.13028 -5.70109 -1.13253 3 C8.3 7.13051 + 1.72234 -2.66724 -6.42395 2 O12.5 7.16574 + -6.99468 1.55899 -0.03426 1 Rh3.3 7.16639 + -3.36983 5.93427 2.25002 3 C1.3 7.18568 + -4.36682 3.22256 4.77282 2 O3.5 7.22730 + -5.84707 -3.25021 -2.86044 3 C11.3 7.27559 + 3.35412 -4.45101 -4.68395 1 Rh3.4 7.28017 + 3.02795 -0.67913 6.59520 2 O11.3 7.28879 + -3.36983 -6.08573 2.25002 3 C1.4 7.31125 + 4.99699 2.89081 -4.54054 2 O9.5 7.34460 + 2.20651 0.13462 7.01224 3 C11.4 7.35243 + -3.93162 4.25748 4.54922 3 C3.4 7.36744 + 0.29106 -7.37307 -0.39743 3 C3.5 7.38951 + -2.89951 -3.40406 5.89373 3 C5.3 7.39803 + 2.43104 6.19030 3.24245 3 C12.5 7.39887 + -1.78979 3.38123 6.34059 2 O5.4 7.40534 + -1.85077 -2.62877 6.68121 2 O5.5 7.41447 + -6.66851 -2.43645 -2.44341 2 O11.4 7.50837 + 1.92839 -5.76359 -4.41405 3 C10.4 7.51142 + -6.21205 3.57355 -2.27318 2 O11.5 7.51846 + 4.87318 3.22256 4.77121 2 O3.6 7.54302 + -2.89951 6.29848 -2.97627 3 C5.4 7.54561 + -4.24486 4.00987 -4.81567 3 C9.4 7.56892 + -0.74105 2.60594 7.12806 3 C5.5 7.62557 + 4.13028 6.31891 -1.13253 3 C8.4 7.63351 + 5.59944 -3.11558 4.15018 1 Rh2.2 7.63444 + 7.09262 2.80186 -0.51392 3 C4.3 7.64329 + 1.19843 -6.44512 -3.98461 2 O10.5 7.67157 + 7.58142 -0.10938 1.20677 3 C6.3 7.67764 + -1.49318 -5.91745 4.66411 3 C4.4 7.68112 + -5.10972 -5.70109 -1.13092 3 C8.5 7.73890 + -0.63571 5.91624 4.96731 2 O4.4 7.75115 + -7.03349 2.75979 -1.85615 3 C11.5 7.78021 + -1.49318 6.10255 4.66411 3 C4.5 7.82462 + 7.45021 -0.48681 -2.53102 2 O5.6 7.88345 + -0.63571 -6.10376 4.96731 2 O4.5 7.89520 + 1.92839 6.25641 -4.41405 3 C10.5 7.89590 + -3.39293 -5.80927 4.15530 1 Rh1.3 7.90734 + -7.79856 0.42791 1.29815 3 C7.4 7.91744 + + END