Mercurial > repos > muon-spectroscopy-computational-project > larch_feff
changeset 0:edf7f8ccf4af draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 5be486890442dedfb327289d597e1c8110240735
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Tue, 14 Nov 2023 15:35:09 +0000 |
| parents | |
| children | 8ee2cc3374fe |
| files | larch_feff.py larch_feff.xml test-data/1564889.cif test-data/[CSV_summary_of_1564889.cif].csv test-data/[CSV_summary_of_test.inp].csv test-data/[FEFF_input_of_1564889.cif].txt test-data/test.inp |
| diffstat | 7 files changed, 2278 insertions(+), 0 deletions(-) [+] |
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--- /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"])
--- /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 @@ +<tool id="larch_feff" name="Larch FEFF" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05" license="MIT"> + <description>generate FEFF paths from XAFS data</description> + <macros> + <!-- version of underlying tool (PEP 440) --> + <token name="@TOOL_VERSION@">0.9.71</token> + <!-- version of this tool wrapper (integer) --> + <token name="@WRAPPER_VERSION@">0</token> + <!-- citation should be updated with every underlying tool version --> + <!-- typical fields to update are version, month, year, and doi --> + <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token> + </macros> + <creator> + <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin" identifier="https://orcid.org/0000-0002-6279-7823"/> + </creator> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">xraylarch</requirement> + <requirement type="package" version="3.5.2">matplotlib</requirement> + <requirement type="package" version="3.0">zip</requirement> + </requirements> + <required_files> + <include type="literal" path="larch_feff.py"/> + </required_files> + <command detect_errors="exit_code"><![CDATA[ + python '${__tool_directory__}/larch_feff.py' '$format.structure_file' '$inputs' + && zip -r out.zip feff + ]]></command> + <configfiles> + <inputs name="inputs"/> + </configfiles> + <inputs> + <conditional name="format"> + <param name="format" type="select" display="radio" label="Structure file format"> + <option value="feff" selected="true">FEFF input</option> + <option value="cif">CIF</option> + </param> + <when value="feff"> + <param name="structure_file" type="data" format="inp" label="Crystal structure file" help="Crystal structure file to be used for fitting, already in FEFF .inp format."/> + </when> + <when value="cif"> + <param name="structure_file" type="data" format="cif" label="Crystal structure file" help="Crystal structure file to be used for fitting, in CIF format."/> + <param name="absorbing_atom" type="text" value="0" label="Absorbing atom" help="Either the chemical symbol or index of the absorbing atom within the structure."/> + <param name="radius" type="float" value="4.0" label="Radius" help="Atoms within this distance of the absorbing atom will be included in the FEFF calculation. Note that this must include at least one atom for each unique potential identified in the strucutre. Larger radii will lead to more potential scattering paths."/> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_csv" format="feff" from_work_dir="out.csv" label="CSV summary of ${format.structure_file.name}"/> + <data name="out_dir" format="zip" from_work_dir="out.zip" label="FEFF paths of ${format.structure_file.name}"/> + <data name="feff_inp" format="inp" from_work_dir="feff/feff.inp" label="FEFF input of ${format.structure_file.name}"> + <filter>format["format"]=="cif"</filter> + </data> + </outputs> + <tests> + <!-- Test FEFF input --> + <test expect_num_outputs="2"> + <conditional name="format"> + <param name="format" value="feff"/> + <param name="structure_file" value="test.inp"/> + </conditional> + <output name="out_csv" file="[CSV_summary_of_test.inp].csv"/> + <output name="out_dir"> + <assert_contents> + <has_size value="276800" delta="100"/> + </assert_contents> + </output> + </test> + <!-- Test CIF input --> + <test expect_num_outputs="3"> + <conditional name="format"> + <param name="format" value="cif"/> + <param name="structure_file" value="1564889.cif"/> + </conditional> + <output name="feff_inp" file="[FEFF_input_of_1564889.cif].txt"/> + <output name="out_csv" file="[CSV_summary_of_1564889.cif].csv"/> + <output name="out_dir"> + <assert_contents> + <has_size value="85700" delta="100"/> + </assert_contents> + </output> + </test> + <!-- Test CIF input failure with low radius --> + <test expect_failure="true"> + <conditional name="format"> + <param name="format" value="cif"/> + <param name="structure_file" value="1564889.cif"/> + <param name="absorbing_atom" value="S"/> + <param name="radius" value="0.1"/> + </conditional> + </test> + </tests> + <help><![CDATA[ + Runs a FEFF6 calculation to find potential scattering paths in the provided structure. + + If a ``cif`` file is used, the formatted FEFF ``inp`` file will be produced as an output that can be used again in the future. + Be aware that the choice of Absorbing atom and Radius will affect the success of the calculation, as all unique potentials must be represented in the final structure. + It is also possible that the ``cif`` file itself is not suitable, for example chemical symbols denoting ions (e.g. ``Fe2+``) are not supported. + ]]></help> + <citations> + <citation type="doi">@TOOL_CITATION@</citation> + <citation type="doi">10.1107/S0909049505012719</citation> + <citation type="doi">10.1016/j.commatsci.2012.10.028</citation> + </citations> +</tool> \ No newline at end of file
--- /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 <olex2.extras> +REM <HklSrc "%.\\new.hkl"> +REM </olex2.extras> + +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 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1828.98 169.956 3 + -3 1 3 1935.71 200.906 1 + -3 -1 -3 1262.20 235.801 2 + -3 -1 3 1861.42 159.382 4 + -3 -1 -3 1529.49 213.639 4 + -3 -1 3 1754.41 170.921 2 + -3 -1 3 2041.13 198.929 3 + -3 1 3 2017.33 181.529 6 + -3 1 -3 1517.66 270.826 6 + -3 -1 -3 1233.06 232.735 6 + -3 -1 3 1689.09 217.288 1 + -3 -2 3 6806.20 508.885 5 + 3 2 3 5207.13 427.256 4 + -3 2 3 6848.93 379.671 1 + -3 -2 -3 4926.39 515.967 2 + -3 2 -3 5012.46 516.825 6 + -3 2 3 7106.29 419.465 6 + 3 -2 3 5003.03 397.223 3 + 3 -2 -3 6857.27 391.141 3 + -3 -2 3 5193.16 426.959 1 + -3 -3 3 1762.86 248.437 1 + 3 -3 -3 1862.91 291.210 2 + 3 3 3 1507.27 227.263 4 + -3 -3 -3 1239.43 259.351 2 + 3 -3 3 1783.22 228.192 3 + -3 3 -3 1470.85 270.195 6 + -3 -3 3 1697.02 250.014 5 + 3 -4 -3 22082.9 1138.23 2 + 3 4 3 16140.8 907.207 4 + -3 -4 -3 16912.7 1051.24 2 + -3 4 -3 19562.4 1101.17 6 + 3 -4 3 15147.6 809.574 3 + -3 -4 3 20893.9 1015.65 5 + -4 0 3 136.872 70.1652 5 + 4 0 3-16.8623 36.6893 3 + -4 0 3 156.982 73.9192 1 + -4 0 -3 117.379 104.213 6 + -4 -1 3 2288.53 302.121 5 + 4 -1 3 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
--- /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
--- /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
--- /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 + +
--- /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