# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1709552612 0
# Node ID 8ee2cc3374fe82ed77e67732b610f89b025e22cc
# Parent edf7f8ccf4af855dcaa1910ddedfe1c7eccc99c1
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_feff commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
diff -r edf7f8ccf4af -r 8ee2cc3374fe larch_feff.py
--- a/larch_feff.py Tue Nov 14 15:35:09 2023 +0000
+++ b/larch_feff.py Mon Mar 04 11:43:32 2024 +0000
@@ -5,9 +5,10 @@
from pathlib import Path
from larch.xafs.feffrunner import feff6l
+from larch.xrd import cif2feff
+from pymatgen.core import Species
from pymatgen.io.cif import CifParser
-from pymatgen.io.feff import Atoms, Header, Potential
def get_path_labels(paths_file):
@@ -48,54 +49,54 @@
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}")
+
+ # Parse the cif file here... but only so that we can extract the
+ # chemical symbols present in the crystal
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}"
+ f"Expected 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.):
+ # cif2feffinp below will take the absorber to be a chemical symbol,
+ # while this tool should support integer site index or chemical symbol
+ # of site (string). Hence convert any integer input to the relevant
+ # chemical symbol string.
+ try:
+ absorbing_atom_int = int(file_format["absorbing_atom"])
+ specie = structures[0][absorbing_atom_int].specie
+ if isinstance(specie, Species):
+ absorbing_atom = str(specie.element)
+ else:
+ absorbing_atom = str(specie)
+ except ValueError:
+ absorbing_atom = file_format["absorbing_atom"]
- # print(atoms.as_dict())
- feff_header.write_file(header_inp)
- potential.write_file(potential_inp)
- atoms.write_file(atoms_inp)
+ # NOTE: Here the first site listed in the cif file with the species
+ # 'absorbing_atom' is selected as the absorbing atom.
+ # NOTE: This generates output for FEFF6 via the 'version8' flag
+ inp_data = cif2feff.cif2feffinp(
+ crystal_f,
+ absorber=absorbing_atom,
+ edge=None,
+ cluster_size=file_format["radius"],
+ absorber_site=1,
+ site_index=None,
+ extra_titles=None,
+ with_h=False,
+ version8=False,
+ )
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"
- )
+ feff_inp_file.write(inp_data + "\n")
+ print(inp_data + "\n")
+
else:
print(f"Copying {crystal_f.name} to {path}")
shutil.copy(crystal_f, path)
diff -r edf7f8ccf4af -r 8ee2cc3374fe larch_feff.xml
--- a/larch_feff.xml Tue Nov 14 15:35:09 2023 +0000
+++ b/larch_feff.xml Mon Mar 04 11:43:32 2024 +0000
@@ -2,7 +2,7 @@
generate FEFF paths from XAFS data
- 0.9.71
+ 0.9.74
0
@@ -51,7 +51,7 @@
-
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@@ -64,7 +64,7 @@
-
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@@ -74,11 +74,151 @@
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diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/1627088.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1627088.cif Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,256 @@
+#######################################################################
+#
+# This file contains crystal structure data downloaded from the
+# Cambridge Structural Database (CSD) hosted by the Cambridge
+# Crystallographic Data Centre (CCDC) in cooperation with FIZ Karlsruhe.
+#
+# Please note that these data are only for research purposes or private use.
+# For detailed information please see under Terms & Conditions.
+# Full information about CCDC and FIZ Karlsruhe data access policies and
+# citation guidelines are available at http://www.ccdc.cam.ac.uk/access/V1
+#
+# Audit and citation data items may have been added by FIZ Karlsruhe.
+# Please retain this information to preserve the provenance of
+# this file and to allow appropriate attribution of the data.
+#
+#######################################################################
+
+data_64918-ICSD
+_database_code_depnum_ccdc_archive 'CCDC 1627088'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1103/PhysRev.17.571 1921
+_audit_update_record
+;
+2022-01-11 deposited with the CCDC. 2024-01-29 downloaded from the CCDC.
+;
+_database_code_ICSD 64918
+_audit_creation_date 1998-06-26
+_chemical_name_common Palladium
+_chemical_formula_structural Pd
+_chemical_formula_sum Pd1
+_chemical_name_structure_type fcc(ccp)#Cu
+_exptl_crystal_density_diffrn 11.46
+_cell_length_a 3.95
+_cell_length_b 3.95
+_cell_length_c 3.95
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 90.
+_cell_volume 61.62
+_cell_formula_units_Z 4
+_space_group_name_H-M_alt 'F m -3 m'
+_space_group_IT_number 225
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 'z, y, -x'
+2 'y, x, -z'
+3 'x, z, -y'
+4 'z, x, -y'
+5 'y, z, -x'
+6 'x, y, -z'
+7 'z, -y, x'
+8 'y, -x, z'
+9 'x, -z, y'
+10 'z, -x, y'
+11 'y, -z, x'
+12 'x, -y, z'
+13 '-z, y, x'
+14 '-y, x, z'
+15 '-x, z, y'
+16 '-z, x, y'
+17 '-y, z, x'
+18 '-x, y, z'
+19 '-z, -y, -x'
+20 '-y, -x, -z'
+21 '-x, -z, -y'
+22 '-z, -x, -y'
+23 '-y, -z, -x'
+24 '-x, -y, -z'
+25 '-z, -y, x'
+26 '-y, -x, z'
+27 '-x, -z, y'
+28 '-z, -x, y'
+29 '-y, -z, x'
+30 '-x, -y, z'
+31 '-z, y, -x'
+32 '-y, x, -z'
+33 '-x, z, -y'
+34 '-z, x, -y'
+35 '-y, z, -x'
+36 '-x, y, -z'
+37 'z, -y, -x'
+38 'y, -x, -z'
+39 'x, -z, -y'
+40 'z, -x, -y'
+41 'y, -z, -x'
+42 'x, -y, -z'
+43 'z, y, x'
+44 'y, x, z'
+45 'x, z, y'
+46 'z, x, y'
+47 'y, z, x'
+48 'x, y, z'
+49 'z, y+1/2, -x+1/2'
+50 'y, x+1/2, -z+1/2'
+51 'x, z+1/2, -y+1/2'
+52 'z, x+1/2, -y+1/2'
+53 'y, z+1/2, -x+1/2'
+54 'x, y+1/2, -z+1/2'
+55 'z, -y+1/2, x+1/2'
+56 'y, -x+1/2, z+1/2'
+57 'x, -z+1/2, y+1/2'
+58 'z, -x+1/2, y+1/2'
+59 'y, -z+1/2, x+1/2'
+60 'x, -y+1/2, z+1/2'
+61 '-z, y+1/2, x+1/2'
+62 '-y, x+1/2, z+1/2'
+63 '-x, z+1/2, y+1/2'
+64 '-z, x+1/2, y+1/2'
+65 '-y, z+1/2, x+1/2'
+66 '-x, y+1/2, z+1/2'
+67 '-z, -y+1/2, -x+1/2'
+68 '-y, -x+1/2, -z+1/2'
+69 '-x, -z+1/2, -y+1/2'
+70 '-z, -x+1/2, -y+1/2'
+71 '-y, -z+1/2, -x+1/2'
+72 '-x, -y+1/2, -z+1/2'
+73 '-z, -y+1/2, x+1/2'
+74 '-y, -x+1/2, z+1/2'
+75 '-x, -z+1/2, y+1/2'
+76 '-z, -x+1/2, y+1/2'
+77 '-y, -z+1/2, x+1/2'
+78 '-x, -y+1/2, z+1/2'
+79 '-z, y+1/2, -x+1/2'
+80 '-y, x+1/2, -z+1/2'
+81 '-x, z+1/2, -y+1/2'
+82 '-z, x+1/2, -y+1/2'
+83 '-y, z+1/2, -x+1/2'
+84 '-x, y+1/2, -z+1/2'
+85 'z, -y+1/2, -x+1/2'
+86 'y, -x+1/2, -z+1/2'
+87 'x, -z+1/2, -y+1/2'
+88 'z, -x+1/2, -y+1/2'
+89 'y, -z+1/2, -x+1/2'
+90 'x, -y+1/2, -z+1/2'
+91 'z, y+1/2, x+1/2'
+92 'y, x+1/2, z+1/2'
+93 'x, z+1/2, y+1/2'
+94 'z, x+1/2, y+1/2'
+95 'y, z+1/2, x+1/2'
+96 'x, y+1/2, z+1/2'
+97 'z+1/2, y, -x+1/2'
+98 'y+1/2, x, -z+1/2'
+99 'x+1/2, z, -y+1/2'
+100 'z+1/2, x, -y+1/2'
+101 'y+1/2, z, -x+1/2'
+102 'x+1/2, y, -z+1/2'
+103 'z+1/2, -y, x+1/2'
+104 'y+1/2, -x, z+1/2'
+105 'x+1/2, -z, y+1/2'
+106 'z+1/2, -x, y+1/2'
+107 'y+1/2, -z, x+1/2'
+108 'x+1/2, -y, z+1/2'
+109 '-z+1/2, y, x+1/2'
+110 '-y+1/2, x, z+1/2'
+111 '-x+1/2, z, y+1/2'
+112 '-z+1/2, x, y+1/2'
+113 '-y+1/2, z, x+1/2'
+114 '-x+1/2, y, z+1/2'
+115 '-z+1/2, -y, -x+1/2'
+116 '-y+1/2, -x, -z+1/2'
+117 '-x+1/2, -z, -y+1/2'
+118 '-z+1/2, -x, -y+1/2'
+119 '-y+1/2, -z, -x+1/2'
+120 '-x+1/2, -y, -z+1/2'
+121 '-z+1/2, -y, x+1/2'
+122 '-y+1/2, -x, z+1/2'
+123 '-x+1/2, -z, y+1/2'
+124 '-z+1/2, -x, y+1/2'
+125 '-y+1/2, -z, x+1/2'
+126 '-x+1/2, -y, z+1/2'
+127 '-z+1/2, y, -x+1/2'
+128 '-y+1/2, x, -z+1/2'
+129 '-x+1/2, z, -y+1/2'
+130 '-z+1/2, x, -y+1/2'
+131 '-y+1/2, z, -x+1/2'
+132 '-x+1/2, y, -z+1/2'
+133 'z+1/2, -y, -x+1/2'
+134 'y+1/2, -x, -z+1/2'
+135 'x+1/2, -z, -y+1/2'
+136 'z+1/2, -x, -y+1/2'
+137 'y+1/2, -z, -x+1/2'
+138 'x+1/2, -y, -z+1/2'
+139 'z+1/2, y, x+1/2'
+140 'y+1/2, x, z+1/2'
+141 'x+1/2, z, y+1/2'
+142 'z+1/2, x, y+1/2'
+143 'y+1/2, z, x+1/2'
+144 'x+1/2, y, z+1/2'
+145 'z+1/2, y+1/2, -x'
+146 'y+1/2, x+1/2, -z'
+147 'x+1/2, z+1/2, -y'
+148 'z+1/2, x+1/2, -y'
+149 'y+1/2, z+1/2, -x'
+150 'x+1/2, y+1/2, -z'
+151 'z+1/2, -y+1/2, x'
+152 'y+1/2, -x+1/2, z'
+153 'x+1/2, -z+1/2, y'
+154 'z+1/2, -x+1/2, y'
+155 'y+1/2, -z+1/2, x'
+156 'x+1/2, -y+1/2, z'
+157 '-z+1/2, y+1/2, x'
+158 '-y+1/2, x+1/2, z'
+159 '-x+1/2, z+1/2, y'
+160 '-z+1/2, x+1/2, y'
+161 '-y+1/2, z+1/2, x'
+162 '-x+1/2, y+1/2, z'
+163 '-z+1/2, -y+1/2, -x'
+164 '-y+1/2, -x+1/2, -z'
+165 '-x+1/2, -z+1/2, -y'
+166 '-z+1/2, -x+1/2, -y'
+167 '-y+1/2, -z+1/2, -x'
+168 '-x+1/2, -y+1/2, -z'
+169 '-z+1/2, -y+1/2, x'
+170 '-y+1/2, -x+1/2, z'
+171 '-x+1/2, -z+1/2, y'
+172 '-z+1/2, -x+1/2, y'
+173 '-y+1/2, -z+1/2, x'
+174 '-x+1/2, -y+1/2, z'
+175 '-z+1/2, y+1/2, -x'
+176 '-y+1/2, x+1/2, -z'
+177 '-x+1/2, z+1/2, -y'
+178 '-z+1/2, x+1/2, -y'
+179 '-y+1/2, z+1/2, -x'
+180 '-x+1/2, y+1/2, -z'
+181 'z+1/2, -y+1/2, -x'
+182 'y+1/2, -x+1/2, -z'
+183 'x+1/2, -z+1/2, -y'
+184 'z+1/2, -x+1/2, -y'
+185 'y+1/2, -z+1/2, -x'
+186 'x+1/2, -y+1/2, -z'
+187 'z+1/2, y+1/2, x'
+188 'y+1/2, x+1/2, z'
+189 'x+1/2, z+1/2, y'
+190 'z+1/2, x+1/2, y'
+191 'y+1/2, z+1/2, x'
+192 'x+1/2, y+1/2, z'
+loop_
+_atom_type_symbol
+_atom_type_oxidation_number
+Pd0+ 0
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Pd1 Pd0+ 4 a 0 0 0 . 1.
+#End of TTdata_64918-ICSD
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/1627088_modified.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1627088_modified.cif Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,255 @@
+#######################################################################
+#
+# This file contains crystal structure data downloaded from the
+# Cambridge Structural Database (CSD) hosted by the Cambridge
+# Crystallographic Data Centre (CCDC) in cooperation with FIZ Karlsruhe.
+#
+# Please note that these data are only for research purposes or private use.
+# For detailed information please see under Terms & Conditions.
+# Full information about CCDC and FIZ Karlsruhe data access policies and
+# citation guidelines are available at http://www.ccdc.cam.ac.uk/access/V1
+#
+# Audit and citation data items may have been added by FIZ Karlsruhe.
+# Please retain this information to preserve the provenance of
+# this file and to allow appropriate attribution of the data.
+#
+#######################################################################
+
+data_64918-ICSD
+_database_code_depnum_ccdc_archive 'CCDC 1627088'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1103/PhysRev.17.571 1921
+_audit_update_record
+;
+2022-01-11 deposited with the CCDC. 2024-01-29 downloaded from the CCDC.
+;
+_database_code_ICSD 64918
+_audit_creation_date 1998-06-26
+_chemical_name_common Palladium
+_chemical_formula_structural Pd
+_chemical_formula_sum Pd1
+_chemical_name_structure_type fcc(ccp)#Cu
+_exptl_crystal_density_diffrn 11.46
+_cell_length_a 3.95
+_cell_length_b 3.95
+_cell_length_c 3.95
+_cell_angle_alpha 90.
+_cell_angle_beta 90.
+_cell_angle_gamma 90.
+_cell_volume 61.62
+_cell_formula_units_Z 4
+_space_group_name_H-M_alt 'F m -3 m'
+_space_group_IT_number 225
+loop_
+_space_group_symop_id
+_space_group_symop_operation_xyz
+1 'z, y, -x'
+2 'y, x, -z'
+3 'x, z, -y'
+4 'z, x, -y'
+5 'y, z, -x'
+6 'x, y, -z'
+7 'z, -y, x'
+8 'y, -x, z'
+9 'x, -z, y'
+10 'z, -x, y'
+11 'y, -z, x'
+12 'x, -y, z'
+13 '-z, y, x'
+14 '-y, x, z'
+15 '-x, z, y'
+16 '-z, x, y'
+17 '-y, z, x'
+18 '-x, y, z'
+19 '-z, -y, -x'
+20 '-y, -x, -z'
+21 '-x, -z, -y'
+22 '-z, -x, -y'
+23 '-y, -z, -x'
+24 '-x, -y, -z'
+25 '-z, -y, x'
+26 '-y, -x, z'
+27 '-x, -z, y'
+28 '-z, -x, y'
+29 '-y, -z, x'
+30 '-x, -y, z'
+31 '-z, y, -x'
+32 '-y, x, -z'
+33 '-x, z, -y'
+34 '-z, x, -y'
+35 '-y, z, -x'
+36 '-x, y, -z'
+37 'z, -y, -x'
+38 'y, -x, -z'
+39 'x, -z, -y'
+40 'z, -x, -y'
+41 'y, -z, -x'
+42 'x, -y, -z'
+43 'z, y, x'
+44 'y, x, z'
+45 'x, z, y'
+46 'z, x, y'
+47 'y, z, x'
+48 'x, y, z'
+49 'z, y+1/2, -x+1/2'
+50 'y, x+1/2, -z+1/2'
+51 'x, z+1/2, -y+1/2'
+52 'z, x+1/2, -y+1/2'
+53 'y, z+1/2, -x+1/2'
+54 'x, y+1/2, -z+1/2'
+55 'z, -y+1/2, x+1/2'
+56 'y, -x+1/2, z+1/2'
+57 'x, -z+1/2, y+1/2'
+58 'z, -x+1/2, y+1/2'
+59 'y, -z+1/2, x+1/2'
+60 'x, -y+1/2, z+1/2'
+61 '-z, y+1/2, x+1/2'
+62 '-y, x+1/2, z+1/2'
+63 '-x, z+1/2, y+1/2'
+64 '-z, x+1/2, y+1/2'
+65 '-y, z+1/2, x+1/2'
+66 '-x, y+1/2, z+1/2'
+67 '-z, -y+1/2, -x+1/2'
+68 '-y, -x+1/2, -z+1/2'
+69 '-x, -z+1/2, -y+1/2'
+70 '-z, -x+1/2, -y+1/2'
+71 '-y, -z+1/2, -x+1/2'
+72 '-x, -y+1/2, -z+1/2'
+73 '-z, -y+1/2, x+1/2'
+74 '-y, -x+1/2, z+1/2'
+75 '-x, -z+1/2, y+1/2'
+76 '-z, -x+1/2, y+1/2'
+77 '-y, -z+1/2, x+1/2'
+78 '-x, -y+1/2, z+1/2'
+79 '-z, y+1/2, -x+1/2'
+80 '-y, x+1/2, -z+1/2'
+81 '-x, z+1/2, -y+1/2'
+82 '-z, x+1/2, -y+1/2'
+83 '-y, z+1/2, -x+1/2'
+84 '-x, y+1/2, -z+1/2'
+85 'z, -y+1/2, -x+1/2'
+86 'y, -x+1/2, -z+1/2'
+87 'x, -z+1/2, -y+1/2'
+88 'z, -x+1/2, -y+1/2'
+89 'y, -z+1/2, -x+1/2'
+90 'x, -y+1/2, -z+1/2'
+91 'z, y+1/2, x+1/2'
+92 'y, x+1/2, z+1/2'
+93 'x, z+1/2, y+1/2'
+94 'z, x+1/2, y+1/2'
+95 'y, z+1/2, x+1/2'
+96 'x, y+1/2, z+1/2'
+97 'z+1/2, y, -x+1/2'
+98 'y+1/2, x, -z+1/2'
+99 'x+1/2, z, -y+1/2'
+100 'z+1/2, x, -y+1/2'
+101 'y+1/2, z, -x+1/2'
+102 'x+1/2, y, -z+1/2'
+103 'z+1/2, -y, x+1/2'
+104 'y+1/2, -x, z+1/2'
+105 'x+1/2, -z, y+1/2'
+106 'z+1/2, -x, y+1/2'
+107 'y+1/2, -z, x+1/2'
+108 'x+1/2, -y, z+1/2'
+109 '-z+1/2, y, x+1/2'
+110 '-y+1/2, x, z+1/2'
+111 '-x+1/2, z, y+1/2'
+112 '-z+1/2, x, y+1/2'
+113 '-y+1/2, z, x+1/2'
+114 '-x+1/2, y, z+1/2'
+115 '-z+1/2, -y, -x+1/2'
+116 '-y+1/2, -x, -z+1/2'
+117 '-x+1/2, -z, -y+1/2'
+118 '-z+1/2, -x, -y+1/2'
+119 '-y+1/2, -z, -x+1/2'
+120 '-x+1/2, -y, -z+1/2'
+121 '-z+1/2, -y, x+1/2'
+122 '-y+1/2, -x, z+1/2'
+123 '-x+1/2, -z, y+1/2'
+124 '-z+1/2, -x, y+1/2'
+125 '-y+1/2, -z, x+1/2'
+126 '-x+1/2, -y, z+1/2'
+127 '-z+1/2, y, -x+1/2'
+128 '-y+1/2, x, -z+1/2'
+129 '-x+1/2, z, -y+1/2'
+130 '-z+1/2, x, -y+1/2'
+131 '-y+1/2, z, -x+1/2'
+132 '-x+1/2, y, -z+1/2'
+133 'z+1/2, -y, -x+1/2'
+134 'y+1/2, -x, -z+1/2'
+135 'x+1/2, -z, -y+1/2'
+136 'z+1/2, -x, -y+1/2'
+137 'y+1/2, -z, -x+1/2'
+138 'x+1/2, -y, -z+1/2'
+139 'z+1/2, y, x+1/2'
+140 'y+1/2, x, z+1/2'
+141 'x+1/2, z, y+1/2'
+142 'z+1/2, x, y+1/2'
+143 'y+1/2, z, x+1/2'
+144 'x+1/2, y, z+1/2'
+145 'z+1/2, y+1/2, -x'
+146 'y+1/2, x+1/2, -z'
+147 'x+1/2, z+1/2, -y'
+148 'z+1/2, x+1/2, -y'
+149 'y+1/2, z+1/2, -x'
+150 'x+1/2, y+1/2, -z'
+151 'z+1/2, -y+1/2, x'
+152 'y+1/2, -x+1/2, z'
+153 'x+1/2, -z+1/2, y'
+154 'z+1/2, -x+1/2, y'
+155 'y+1/2, -z+1/2, x'
+156 'x+1/2, -y+1/2, z'
+157 '-z+1/2, y+1/2, x'
+158 '-y+1/2, x+1/2, z'
+159 '-x+1/2, z+1/2, y'
+160 '-z+1/2, x+1/2, y'
+161 '-y+1/2, z+1/2, x'
+162 '-x+1/2, y+1/2, z'
+163 '-z+1/2, -y+1/2, -x'
+164 '-y+1/2, -x+1/2, -z'
+165 '-x+1/2, -z+1/2, -y'
+166 '-z+1/2, -x+1/2, -y'
+167 '-y+1/2, -z+1/2, -x'
+168 '-x+1/2, -y+1/2, -z'
+169 '-z+1/2, -y+1/2, x'
+170 '-y+1/2, -x+1/2, z'
+171 '-x+1/2, -z+1/2, y'
+172 '-z+1/2, -x+1/2, y'
+173 '-y+1/2, -z+1/2, x'
+174 '-x+1/2, -y+1/2, z'
+175 '-z+1/2, y+1/2, -x'
+176 '-y+1/2, x+1/2, -z'
+177 '-x+1/2, z+1/2, -y'
+178 '-z+1/2, x+1/2, -y'
+179 '-y+1/2, z+1/2, -x'
+180 '-x+1/2, y+1/2, -z'
+181 'z+1/2, -y+1/2, -x'
+182 'y+1/2, -x+1/2, -z'
+183 'x+1/2, -z+1/2, -y'
+184 'z+1/2, -x+1/2, -y'
+185 'y+1/2, -z+1/2, -x'
+186 'x+1/2, -y+1/2, -z'
+187 'z+1/2, y+1/2, x'
+188 'y+1/2, x+1/2, z'
+189 'x+1/2, z+1/2, y'
+190 'z+1/2, x+1/2, y'
+191 'y+1/2, z+1/2, x'
+192 'x+1/2, y+1/2, z'
+loop_
+_atom_type_symbol
+Pd
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_symmetry_multiplicity
+_atom_site_Wyckoff_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_B_iso_or_equiv
+_atom_site_occupancy
+Pd1 Pd 4 a 0 0 0 . 1.
+#End of TTdata_64918-ICSD
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/1667441.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1667441.cif Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,68 @@
+#######################################################################
+#
+# This file contains crystal structure data downloaded from the
+# Cambridge Structural Database (CSD) hosted by the Cambridge
+# Crystallographic Data Centre (CCDC) in cooperation with FIZ Karlsruhe.
+#
+# Please note that these data are only for research purposes or private use.
+# For detailed information please see under Terms & Conditions.
+# Full information about CCDC and FIZ Karlsruhe data access policies and
+# citation guidelines are available at http://www.ccdc.cam.ac.uk/access/V1
+#
+# Audit and citation data items may have been added by FIZ Karlsruhe.
+# Please retain this information to preserve the provenance of
+# this file and to allow appropriate attribution of the data.
+#
+#######################################################################
+
+data_150259-ICSD
+_database_code_depnum_ccdc_archive 'CCDC 1667441'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1006/jssc.2001.9440 2002
+_audit_update_record
+;
+2018-02-27 deposited with the CCDC. 2024-02-15 downloaded from the CCDC.
+;
+_database_code_ICSD 150259
+_chemical_name_systematic 'Lanthanum Manganate'
+_chemical_formula_sum 'La1 Mn1 O3'
+_cell_length_a 5.486
+_cell_length_b 7.761
+_cell_length_c 5.487
+_cell_angle_alpha 90
+_cell_angle_beta 90
+_cell_angle_gamma 90.01
+_cell_volume 233.62
+_cell_formula_units_Z 4
+_symmetry_space_group_name_H-M 'I 1 1 2/b'
+_symmetry_Int_Tables_number 15
+_symmetry_cell_setting monoclinic
+_refine_ls_R_factor_all 0.03
+loop_
+_symmetry_equiv_pos_site_id
+_symmetry_equiv_pos_as_xyz
+1 '-x, -y+1/2, z'
+2 'x, y+1/2, -z'
+3 '-x, -y, -z'
+4 'x, y, z'
+5 '-x+1/2, -y, z+1/2'
+6 'x+1/2, y, -z+1/2'
+7 '-x+1/2, -y+1/2, -z+1/2'
+8 '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
+La1 La3+ 0 0.25 0.5052
+Mn1 Mn3+ 0 0 0
+O1 O2- 0 0.25 0.0015
+O2 O2- 0.2682 0.0015 0.2427
+
+#End of data_150259-ICSD
+
+
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/AMS_Cu.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/AMS_Cu.cif Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,227 @@
+data_global
+_chemical_name_mineral 'Copper'
+loop_
+_publ_author_name
+'Wyckoff R W G'
+_journal_name_full 'Crystal Structures'
+_journal_volume 1
+_journal_year 1963
+_journal_page_first 7
+_journal_page_last 83
+_publ_section_title
+;
+ Second edition. Interscience Publishers, New York, New York
+ Cubic closest packed, ccp, structure
+;
+_database_code_amcsd 0011145
+_chemical_formula_sum 'Cu'
+_cell_length_a 3.61496
+_cell_length_b 3.61496
+_cell_length_c 3.61496
+_cell_angle_alpha 90
+_cell_angle_beta 90
+_cell_angle_gamma 90
+_cell_volume 47.240
+_exptl_crystal_density_diffrn 8.935
+_symmetry_space_group_name_H-M 'F m 3 m'
+loop_
+_space_group_symop_operation_xyz
+ 'x,y,z'
+ 'x,1/2+y,1/2+z'
+ '1/2+x,y,1/2+z'
+ '1/2+x,1/2+y,z'
+ 'z,-x,y'
+ 'z,1/2-x,1/2+y'
+ '1/2+z,-x,1/2+y'
+ '1/2+z,1/2-x,y'
+ '-y,z,-x'
+ '-y,1/2+z,1/2-x'
+ '1/2-y,z,1/2-x'
+ '1/2-y,1/2+z,-x'
+ 'x,-y,z'
+ 'x,1/2-y,1/2+z'
+ '1/2+x,-y,1/2+z'
+ '1/2+x,1/2-y,z'
+ '-z,x,-y'
+ '-z,1/2+x,1/2-y'
+ '1/2-z,x,1/2-y'
+ '1/2-z,1/2+x,-y'
+ 'y,-z,x'
+ 'y,1/2-z,1/2+x'
+ '1/2+y,-z,1/2+x'
+ '1/2+y,1/2-z,x'
+ '-x,y,-z'
+ '-x,1/2+y,1/2-z'
+ '1/2-x,y,1/2-z'
+ '1/2-x,1/2+y,-z'
+ 'x,-z,-y'
+ 'x,1/2-z,1/2-y'
+ '1/2+x,-z,1/2-y'
+ '1/2+x,1/2-z,-y'
+ '-z,y,x'
+ '-z,1/2+y,1/2+x'
+ '1/2-z,y,1/2+x'
+ '1/2-z,1/2+y,x'
+ 'y,-x,-z'
+ 'y,1/2-x,1/2-z'
+ '1/2+y,-x,1/2-z'
+ '1/2+y,1/2-x,-z'
+ '-x,z,y'
+ '-x,1/2+z,1/2+y'
+ '1/2-x,z,1/2+y'
+ '1/2-x,1/2+z,y'
+ 'z,-y,-x'
+ 'z,1/2-y,1/2-x'
+ '1/2+z,-y,1/2-x'
+ '1/2+z,1/2-y,-x'
+ '-y,x,z'
+ '-y,1/2+x,1/2+z'
+ '1/2-y,x,1/2+z'
+ '1/2-y,1/2+x,z'
+ 'x,z,y'
+ 'x,1/2+z,1/2+y'
+ '1/2+x,z,1/2+y'
+ '1/2+x,1/2+z,y'
+ '-z,-y,-x'
+ '-z,1/2-y,1/2-x'
+ '1/2-z,-y,1/2-x'
+ '1/2-z,1/2-y,-x'
+ 'y,x,z'
+ 'y,1/2+x,1/2+z'
+ '1/2+y,x,1/2+z'
+ '1/2+y,1/2+x,z'
+ '-x,-z,-y'
+ '-x,1/2-z,1/2-y'
+ '1/2-x,-z,1/2-y'
+ '1/2-x,1/2-z,-y'
+ 'z,y,x'
+ 'z,1/2+y,1/2+x'
+ '1/2+z,y,1/2+x'
+ '1/2+z,1/2+y,x'
+ '-y,-x,-z'
+ '-y,1/2-x,1/2-z'
+ '1/2-y,-x,1/2-z'
+ '1/2-y,1/2-x,-z'
+ 'z,x,-y'
+ 'z,1/2+x,1/2-y'
+ '1/2+z,x,1/2-y'
+ '1/2+z,1/2+x,-y'
+ '-y,-z,x'
+ '-y,1/2-z,1/2+x'
+ '1/2-y,-z,1/2+x'
+ '1/2-y,1/2-z,x'
+ 'x,y,-z'
+ 'x,1/2+y,1/2-z'
+ '1/2+x,y,1/2-z'
+ '1/2+x,1/2+y,-z'
+ '-z,-x,y'
+ '-z,1/2-x,1/2+y'
+ '1/2-z,-x,1/2+y'
+ '1/2-z,1/2-x,y'
+ 'y,z,-x'
+ 'y,1/2+z,1/2-x'
+ '1/2+y,z,1/2-x'
+ '1/2+y,1/2+z,-x'
+ '-x,-y,z'
+ '-x,1/2-y,1/2+z'
+ '1/2-x,-y,1/2+z'
+ '1/2-x,1/2-y,z'
+ '-z,x,y'
+ '-z,1/2+x,1/2+y'
+ '1/2-z,x,1/2+y'
+ '1/2-z,1/2+x,y'
+ 'y,-z,-x'
+ 'y,1/2-z,1/2-x'
+ '1/2+y,-z,1/2-x'
+ '1/2+y,1/2-z,-x'
+ '-x,y,z'
+ '-x,1/2+y,1/2+z'
+ '1/2-x,y,1/2+z'
+ '1/2-x,1/2+y,z'
+ 'z,-x,-y'
+ 'z,1/2-x,1/2-y'
+ '1/2+z,-x,1/2-y'
+ '1/2+z,1/2-x,-y'
+ '-y,z,x'
+ '-y,1/2+z,1/2+x'
+ '1/2-y,z,1/2+x'
+ '1/2-y,1/2+z,x'
+ 'x,-y,-z'
+ 'x,1/2-y,1/2-z'
+ '1/2+x,-y,1/2-z'
+ '1/2+x,1/2-y,-z'
+ '-x,z,-y'
+ '-x,1/2+z,1/2-y'
+ '1/2-x,z,1/2-y'
+ '1/2-x,1/2+z,-y'
+ 'z,-y,x'
+ 'z,1/2-y,1/2+x'
+ '1/2+z,-y,1/2+x'
+ '1/2+z,1/2-y,x'
+ '-y,x,-z'
+ '-y,1/2+x,1/2-z'
+ '1/2-y,x,1/2-z'
+ '1/2-y,1/2+x,-z'
+ 'x,-z,y'
+ 'x,1/2-z,1/2+y'
+ '1/2+x,-z,1/2+y'
+ '1/2+x,1/2-z,y'
+ '-z,y,-x'
+ '-z,1/2+y,1/2-x'
+ '1/2-z,y,1/2-x'
+ '1/2-z,1/2+y,-x'
+ 'y,-x,z'
+ 'y,1/2-x,1/2+z'
+ '1/2+y,-x,1/2+z'
+ '1/2+y,1/2-x,z'
+ '-x,-z,y'
+ '-x,1/2-z,1/2+y'
+ '1/2-x,-z,1/2+y'
+ '1/2-x,1/2-z,y'
+ 'z,y,-x'
+ 'z,1/2+y,1/2-x'
+ '1/2+z,y,1/2-x'
+ '1/2+z,1/2+y,-x'
+ '-y,-x,z'
+ '-y,1/2-x,1/2+z'
+ '1/2-y,-x,1/2+z'
+ '1/2-y,1/2-x,z'
+ 'x,z,-y'
+ 'x,1/2+z,1/2-y'
+ '1/2+x,z,1/2-y'
+ '1/2+x,1/2+z,-y'
+ '-z,-y,x'
+ '-z,1/2-y,1/2+x'
+ '1/2-z,-y,1/2+x'
+ '1/2-z,1/2-y,x'
+ 'y,x,-z'
+ 'y,1/2+x,1/2-z'
+ '1/2+y,x,1/2-z'
+ '1/2+y,1/2+x,-z'
+ '-z,-x,-y'
+ '-z,1/2-x,1/2-y'
+ '1/2-z,-x,1/2-y'
+ '1/2-z,1/2-x,-y'
+ 'y,z,x'
+ 'y,1/2+z,1/2+x'
+ '1/2+y,z,1/2+x'
+ '1/2+y,1/2+z,x'
+ '-x,-y,-z'
+ '-x,1/2-y,1/2-z'
+ '1/2-x,-y,1/2-z'
+ '1/2-x,1/2-y,-z'
+ 'z,x,y'
+ 'z,1/2+x,1/2+y'
+ '1/2+z,x,1/2+y'
+ '1/2+z,1/2+x,y'
+ '-y,-z,-x'
+ '-y,1/2-z,1/2-x'
+ '1/2-y,-z,1/2-x'
+ '1/2-y,1/2-z,-x'
+loop_
+_atom_site_label
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+Cu 0.00000 0.00000 0.00000
+
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[CSV_summary_of_1564889.cif].csv
--- a/test-data/[CSV_summary_of_1564889.cif].csv Tue Nov 14 15:35:09 2023 +0000
+++ b/test-data/[CSV_summary_of_1564889.cif].csv Mon Mar 04 11:43:32 2024 +0000
@@ -3,7 +3,9 @@
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
+ feff0005.dat, 0.00000, 31.274 , 4.000, 2 , 3.6045 , S.Fe.5 , 0
+ feff0006.dat, 0.00000, 7.145 , 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
+ feff0009.dat, 0.00000, 7.793 , 8.000, 3 , 3.9475 , Fe.S.Fe.9 , 0
+ feff0010.dat, 0.00000, 8.508 , 4.000, 3 , 3.9725 , S.S.Fe.10 , 0
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[CSV_summary_of_1627088.cif].csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[CSV_summary_of_1627088.cif].csv Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,6 @@
+ file , sig2 , amp ratio, deg , nlegs, r effective, label , select
+ feff0001.dat, 0.00000, 100.000 , 12.000, 2 , 2.7931 , Pd.Pd.1 , 0
+ feff0002.dat, 0.00000, 18.733 , 6.000, 2 , 3.9500 , Pd.Pd.2 , 0
+ feff0003.dat, 0.00000, 8.554 , 48.000, 3 , 4.1896 , Pd.Pd.Pd.3 , 0
+ feff0004.dat, 0.00000, 5.107 , 48.000, 3 , 4.7681 , Pd.Pd.Pd.4 , 0
+ feff0005.dat, 0.00000, 39.601 , 24.000, 2 , 4.8377 , Pd.Pd.5 , 0
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[CSV_summary_of_1667441.cif].csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[CSV_summary_of_1667441.cif].csv Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,27 @@
+ file , sig2 , amp ratio, deg , nlegs, r effective, label , select
+ feff0001.dat, 0.00000, 100.000 , 6.000, 2 , 1.9398 , O.Mn.1 , 0
+ feff0002.dat, 0.00000, 18.050 , 24.000, 3 , 3.3113 , O.O.Mn.2 , 0
+ feff0003.dat, 0.00000, 58.072 , 8.000, 2 , 3.3596 , La.Mn.3 , 0
+ feff0004.dat, 0.00000, 13.482 , 4.000, 2 , 3.8795 , Mn.Mn.4 , 0
+ feff0005.dat, 0.00000, 6.737 , 2.000, 2 , 3.8805 , Mn.Mn.5 , 0
+ feff0006.dat, 0.00000, 16.691 , 6.000, 3 , 3.8795 , O.O.Mn.6 , 0
+ feff0007.dat, 0.00000, 37.767 , 8.000, 3 , 3.8795 , Mn.O.Mn.7 , 0
+ feff0008.dat, 0.00000, 18.868 , 4.000, 3 , 3.8805 , Mn.O.Mn.8 , 0
+ feff0009.dat, 0.00000, 16.817 , 6.000, 4 , 3.8795 , O.Mn.O.Mn.9 , 0
+ feff0010.dat, 0.00000, 5.806 , 6.000, 4 , 3.8795 , O.Mn.O.Mn.10 , 0
+ feff0011.dat, 0.00000, 26.483 , 4.000, 4 , 3.8795 , O.Mn.O.Mn.11 , 0
+ feff0012.dat, 0.00000, 13.227 , 2.000, 4 , 3.8805 , O.Mn.O.Mn.12 , 0
+ feff0014.dat, 0.00000, 19.067 , 44.000, 3 , 4.0214 , La.O.Mn.14 , 0
+ feff0015.dat, 0.00000, 18.592 , 8.000, 2 , 4.3371 , O.Mn.15 , 0
+ feff0016.dat, 0.00000, 27.876 , 12.000, 2 , 4.3379 , O.Mn.16 , 0
+ feff0017.dat, 0.00000, 9.288 , 4.000, 2 , 4.3385 , O.Mn.17 , 0
+ feff0018.dat, 0.00000, 9.216 , 8.000, 3 , 4.5105 , O.O.Mn.18 , 0
+ feff0019.dat, 0.00000, 18.433 , 16.000, 3 , 4.5100 , O.O.Mn.19 , 0
+ feff0020.dat, 0.00000, 18.424 , 16.000, 3 , 4.5107 , O.O.Mn.20 , 0
+ feff0021.dat, 0.00000, 9.212 , 8.000, 3 , 4.5113 , O.O.Mn.21 , 0
+ feff0022.dat, 0.00000, 4.622 , 16.000, 4 , 4.6834 , O.O.O.Mn.22 , 0
+ feff0023.dat, 0.00000, 11.758 , 20.000, 4 , 4.6828 , O.O.O.Mn.23 , 0
+ feff0024.dat, 0.00000, 4.617 , 12.000, 4 , 4.6838 , O.La.O.Mn.24 , 0
+ feff0025.dat, 0.00000, 7.031 , 8.000, 4 , 4.6828 , O.O.O.Mn.25 , 0
+ feff0026.dat, 0.00000, 10.542 , 12.000, 4 , 4.6837 , O.O.O.Mn.26 , 0
+ feff0029.dat, 0.00000, 3.514 , 4.000, 4 , 4.6840 , O.O.O.Mn.29 , 0
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[CSV_summary_of_AMS_Cu.cif].csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[CSV_summary_of_AMS_Cu.cif].csv Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,8 @@
+ file , sig2 , amp ratio, deg , nlegs, r effective, label , select
+ feff0001.dat, 0.00000, 100.000 , 12.000, 2 , 2.5562 , Cu.Cu.1 , 0
+ feff0002.dat, 0.00000, 22.972 , 6.000, 2 , 3.6150 , Cu.Cu.2 , 0
+ feff0003.dat, 0.00000, 10.554 , 48.000, 3 , 3.8342 , Cu.Cu.Cu.3 , 0
+ feff0004.dat, 0.00000, 8.445 , 48.000, 3 , 4.3636 , Cu.Cu.Cu.4 , 0
+ feff0005.dat, 0.00000, 55.345 , 24.000, 2 , 4.4274 , Cu.Cu.5 , 0
+ feff0006.dat, 0.00000, 10.643 , 48.000, 3 , 4.7699 , Cu.Cu.Cu.6 , 0
+ feff0007.dat, 0.00000, 21.223 , 96.000, 3 , 4.7699 , Cu.Cu.Cu.7 , 0
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[FEFF_input_of_1564889.cif].txt
--- a/test-data/[FEFF_input_of_1564889.cif].txt Tue Nov 14 15:35:09 2023 +0000
+++ b/test-data/[FEFF_input_of_1564889.cif].txt Mon Mar 04 11:43:32 2024 +0000
@@ -1,52 +1,60 @@
-* 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
+*** feff input generated by xraylarch cif2feff using pymatgen ***
+TITLE Formula: FeS2
+TITLE SpaceGroup: Pnnm
+TITLE # sites: 6
+* crystallographics sites: note that these sites may not be unique!
+* using absorber at site 1 in the list below
+* selected as absorber="Fe", absorber_site=1
+* index X Y Z species
+* 1 0.000000 0.000000 0.000000 Fe <- absorber
+* 2 0.500000 0.500000 0.500000 Fe
+* 3 0.000000 0.199900 0.378040 S
+* 4 0.000000 0.800100 0.621960 S
+* 5 0.500000 0.699900 0.121960 S
+* 6 0.500000 0.300100 0.878040 S
+*
-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
+
+HOLE 1 1.0 * Fe K edge, around 7112 eV (2nd number is S02)
+CONTROL 1 1 1 0 * phase, paths, feff, chi
+PRINT 1 0 0 0
+RMAX 4.00
+
+EXCHANGE 0
+
+* POLARIZATION 0 0 0
+
+POTENTIALS
+* IPOT Z Tag
+ 0 26 Fe
+ 1 16 S
+ 2 26 Fe
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
+* x y z ipot tag distance site_info
+ 0.00000 0.00000 0.00000 0 Fe 0.00000 * Fe_1
+ -0.88904 -2.05227 -0.00000 1 S 2.23656 * S_4
+ 0.88904 2.05227 0.00000 1 S 2.23656 * S_3
+ -1.33466 0.66208 -1.69260 1 S 2.25490 * S_5
+ -1.33466 0.66208 1.69260 1 S 2.25490 * S_5
+ 1.33466 -0.66208 -1.69260 1 S 2.25490 * S_6
+ 1.33466 -0.66208 1.69260 1 S 2.25490 * S_6
+ 0.00000 0.00000 -3.38520 2 Fe 3.38520 * Fe_1
+ 0.00000 0.00000 3.38520 2 Fe 3.38520 * Fe_1
+ -0.88904 3.37643 0.00000 1 S 3.49152 * S_4
+ 0.88904 -3.37643 -0.00000 1 S 3.49152 * S_3
+ -3.11274 -0.66208 1.69260 1 S 3.60449 * S_6
+ -3.11274 -0.66208 -1.69260 1 S 3.60449 * S_6
+ 3.11274 0.66208 -1.69260 1 S 3.60449 * S_5
+ 3.11274 0.66208 1.69260 1 S 3.60449 * S_5
+ -2.22370 2.71435 -1.69260 2 Fe 3.89582 * Fe_2
+ -2.22370 2.71435 1.69260 2 Fe 3.89582 * Fe_2
+ 2.22370 -2.71435 -1.69260 2 Fe 3.89582 * Fe_2
+ 2.22370 -2.71435 1.69260 2 Fe 3.89582 * Fe_2
+ -2.22370 -2.71435 1.69260 2 Fe 3.89582 * Fe_2
+ 2.22370 2.71435 -1.69260 2 Fe 3.89582 * Fe_2
+ -2.22370 -2.71435 -1.69260 2 Fe 3.89582 * Fe_2
+ 2.22370 2.71435 1.69260 2 Fe 3.89582 * Fe_2
+* END
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[FEFF_input_of_1627088.cif].txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[FEFF_input_of_1627088.cif].txt Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,74 @@
+*** feff input generated by xraylarch cif2feff using pymatgen ***
+TITLE Formula: Pd
+TITLE SpaceGroup: Fm-3m
+TITLE # sites: 1
+* crystallographics sites: note that these sites may not be unique!
+* using absorber at site 1 in the list below
+* selected as absorber="Pd", absorber_site=1
+* index X Y Z species
+* 1 0.000000 0.000000 0.000000 Pd0 <- absorber
+*
+
+
+HOLE 1 1.0 * Pd K edge, around 24350 eV (2nd number is S02)
+CONTROL 1 1 1 0 * phase, paths, feff, chi
+PRINT 1 0 0 0
+RMAX 5.00
+
+EXCHANGE 0
+
+* POLARIZATION 0 0 0
+
+POTENTIALS
+* IPOT Z Tag
+ 0 46 Pd
+ 1 46 Pd
+
+ATOMS
+* x y z ipot tag distance site_info
+ 0.00000 0.00000 0.00000 0 Pd 0.00000 * Pd_1
+ -1.97500 0.00000 1.97500 1 Pd 2.79307 * Pd0+_1
+ -1.97500 1.97500 0.00000 1 Pd 2.79307 * Pd0+_1
+ -0.00000 -1.97500 1.97500 1 Pd 2.79307 * Pd0+_1
+ 1.97500 -1.97500 0.00000 1 Pd 2.79307 * Pd0+_1
+ 0.00000 1.97500 -1.97500 1 Pd 2.79307 * Pd0+_1
+ 1.97500 0.00000 -1.97500 1 Pd 2.79307 * Pd0+_1
+ -1.97500 -1.97500 -0.00000 1 Pd 2.79307 * Pd0+_1
+ -1.97500 0.00000 -1.97500 1 Pd 2.79307 * Pd0+_1
+ -0.00000 -1.97500 -1.97500 1 Pd 2.79307 * Pd0+_1
+ 0.00000 1.97500 1.97500 1 Pd 2.79307 * Pd0+_1
+ 1.97500 0.00000 1.97500 1 Pd 2.79307 * Pd0+_1
+ 1.97500 1.97500 0.00000 1 Pd 2.79307 * Pd0+_1
+ -3.95000 0.00000 -0.00000 1 Pd 3.95000 * Pd0+_1
+ 3.95000 0.00000 0.00000 1 Pd 3.95000 * Pd0+_1
+ -0.00000 -3.95000 -0.00000 1 Pd 3.95000 * Pd0+_1
+ -0.00000 0.00000 -3.95000 1 Pd 3.95000 * Pd0+_1
+ 0.00000 0.00000 3.95000 1 Pd 3.95000 * Pd0+_1
+ 0.00000 3.95000 0.00000 1 Pd 3.95000 * Pd0+_1
+ -3.95000 1.97500 1.97500 1 Pd 4.83774 * Pd0+_1
+ 3.95000 -1.97500 -1.97500 1 Pd 4.83774 * Pd0+_1
+ -3.95000 -1.97500 -1.97500 1 Pd 4.83774 * Pd0+_1
+ -3.95000 -1.97500 1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 -3.95000 1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 -1.97500 3.95000 1 Pd 4.83774 * Pd0+_1
+ -3.95000 1.97500 -1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 1.97500 -3.95000 1 Pd 4.83774 * Pd0+_1
+ -1.97500 3.95000 -1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 1.97500 3.95000 1 Pd 4.83774 * Pd0+_1
+ -1.97500 3.95000 1.97500 1 Pd 4.83774 * Pd0+_1
+ 1.97500 -3.95000 -1.97500 1 Pd 4.83774 * Pd0+_1
+ 1.97500 -1.97500 -3.95000 1 Pd 4.83774 * Pd0+_1
+ 1.97500 -3.95000 1.97500 1 Pd 4.83774 * Pd0+_1
+ 1.97500 -1.97500 3.95000 1 Pd 4.83774 * Pd0+_1
+ 3.95000 -1.97500 1.97500 1 Pd 4.83774 * Pd0+_1
+ 1.97500 1.97500 -3.95000 1 Pd 4.83774 * Pd0+_1
+ 1.97500 3.95000 -1.97500 1 Pd 4.83774 * Pd0+_1
+ 3.95000 1.97500 -1.97500 1 Pd 4.83774 * Pd0+_1
+ 3.95000 1.97500 1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 -3.95000 -1.97500 1 Pd 4.83774 * Pd0+_1
+ -1.97500 -1.97500 -3.95000 1 Pd 4.83774 * Pd0+_1
+ 1.97500 1.97500 3.95000 1 Pd 4.83774 * Pd0+_1
+ 1.97500 3.95000 1.97500 1 Pd 4.83774 * Pd0+_1
+
+* END
+
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[FEFF_input_of_1627088_modified.cif].txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[FEFF_input_of_1627088_modified.cif].txt Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,74 @@
+*** feff input generated by xraylarch cif2feff using pymatgen ***
+TITLE Formula: Pd
+TITLE SpaceGroup: Fm-3m
+TITLE # sites: 1
+* crystallographics sites: note that these sites may not be unique!
+* using absorber at site 1 in the list below
+* selected as absorber="Pd", absorber_site=1
+* index X Y Z species
+* 1 0.000000 0.000000 0.000000 Pd <- absorber
+*
+
+
+HOLE 1 1.0 * Pd K edge, around 24350 eV (2nd number is S02)
+CONTROL 1 1 1 0 * phase, paths, feff, chi
+PRINT 1 0 0 0
+RMAX 5.00
+
+EXCHANGE 0
+
+* POLARIZATION 0 0 0
+
+POTENTIALS
+* IPOT Z Tag
+ 0 46 Pd
+ 1 46 Pd
+
+ATOMS
+* x y z ipot tag distance site_info
+ 0.00000 0.00000 0.00000 0 Pd 0.00000 * Pd_1
+ -1.97500 0.00000 1.97500 1 Pd 2.79307 * Pd_1
+ -1.97500 1.97500 0.00000 1 Pd 2.79307 * Pd_1
+ -0.00000 -1.97500 1.97500 1 Pd 2.79307 * Pd_1
+ 1.97500 -1.97500 0.00000 1 Pd 2.79307 * Pd_1
+ 0.00000 1.97500 -1.97500 1 Pd 2.79307 * Pd_1
+ 1.97500 0.00000 -1.97500 1 Pd 2.79307 * Pd_1
+ -1.97500 -1.97500 -0.00000 1 Pd 2.79307 * Pd_1
+ -1.97500 0.00000 -1.97500 1 Pd 2.79307 * Pd_1
+ -0.00000 -1.97500 -1.97500 1 Pd 2.79307 * Pd_1
+ 0.00000 1.97500 1.97500 1 Pd 2.79307 * Pd_1
+ 1.97500 0.00000 1.97500 1 Pd 2.79307 * Pd_1
+ 1.97500 1.97500 0.00000 1 Pd 2.79307 * Pd_1
+ -3.95000 0.00000 -0.00000 1 Pd 3.95000 * Pd_1
+ 3.95000 0.00000 0.00000 1 Pd 3.95000 * Pd_1
+ -0.00000 -3.95000 -0.00000 1 Pd 3.95000 * Pd_1
+ -0.00000 0.00000 -3.95000 1 Pd 3.95000 * Pd_1
+ 0.00000 0.00000 3.95000 1 Pd 3.95000 * Pd_1
+ 0.00000 3.95000 0.00000 1 Pd 3.95000 * Pd_1
+ -3.95000 1.97500 1.97500 1 Pd 4.83774 * Pd_1
+ 3.95000 -1.97500 -1.97500 1 Pd 4.83774 * Pd_1
+ -3.95000 -1.97500 -1.97500 1 Pd 4.83774 * Pd_1
+ -3.95000 -1.97500 1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 -3.95000 1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 -1.97500 3.95000 1 Pd 4.83774 * Pd_1
+ -3.95000 1.97500 -1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 1.97500 -3.95000 1 Pd 4.83774 * Pd_1
+ -1.97500 3.95000 -1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 1.97500 3.95000 1 Pd 4.83774 * Pd_1
+ -1.97500 3.95000 1.97500 1 Pd 4.83774 * Pd_1
+ 1.97500 -3.95000 -1.97500 1 Pd 4.83774 * Pd_1
+ 1.97500 -1.97500 -3.95000 1 Pd 4.83774 * Pd_1
+ 1.97500 -3.95000 1.97500 1 Pd 4.83774 * Pd_1
+ 1.97500 -1.97500 3.95000 1 Pd 4.83774 * Pd_1
+ 3.95000 -1.97500 1.97500 1 Pd 4.83774 * Pd_1
+ 1.97500 1.97500 -3.95000 1 Pd 4.83774 * Pd_1
+ 1.97500 3.95000 -1.97500 1 Pd 4.83774 * Pd_1
+ 3.95000 1.97500 -1.97500 1 Pd 4.83774 * Pd_1
+ 3.95000 1.97500 1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 -3.95000 -1.97500 1 Pd 4.83774 * Pd_1
+ -1.97500 -1.97500 -3.95000 1 Pd 4.83774 * Pd_1
+ 1.97500 1.97500 3.95000 1 Pd 4.83774 * Pd_1
+ 1.97500 3.95000 1.97500 1 Pd 4.83774 * Pd_1
+
+* END
+
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[FEFF_input_of_1667441.cif].txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[FEFF_input_of_1667441.cif].txt Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,82 @@
+*** feff input generated by xraylarch cif2feff using pymatgen ***
+TITLE Formula: LaMnO3
+TITLE SpaceGroup: Pm-3m
+TITLE # sites: 5
+* crystallographics sites: note that these sites may not be unique!
+* using absorber at site 2 in the list below
+* selected as absorber="Mn", absorber_site=1
+* index X Y Z species
+* 1 0.500000 0.500000 0.500000 La
+* 2 0.000000 0.000000 0.000000 Mn <- absorber
+* 3 1.000000 0.000000 0.500000 O
+* 4 1.000000 0.500000 0.000000 O
+* 5 0.500000 0.000000 0.000000 O
+*
+
+
+HOLE 1 1.0 * Mn K edge, around 6539 eV (2nd number is S02)
+CONTROL 1 1 1 0 * phase, paths, feff, chi
+PRINT 1 0 0 0
+RMAX 5.00
+
+EXCHANGE 0
+
+* POLARIZATION 0 0 0
+
+POTENTIALS
+* IPOT Z Tag
+ 0 25 Mn
+ 1 8 O
+ 2 57 La
+ 3 25 Mn
+
+ATOMS
+* x y z ipot tag distance site_info
+ 0.00000 0.00000 0.00000 0 Mn 0.00000 * Mn_2
+ -1.37150 0.00000 -1.37175 1 O 1.93977 * O_5
+ -1.37150 0.00000 1.37175 1 O 1.93977 * O_4
+ 1.37150 0.00000 -1.37175 1 O 1.93977 * O_4
+ 1.37150 0.00000 1.37175 1 O 1.93977 * O_5
+ -0.00034 1.94025 0.00000 1 O 1.94025 * O_3
+ 0.00034 -1.94025 -0.00000 1 O 1.94025 * O_3
+ 2.74266 1.94025 -0.00000 2 La 3.35958 * La_1
+ -2.74266 -1.94025 -0.00000 2 La 3.35958 * La_1
+ 2.74334 -1.94025 -0.00000 2 La 3.36013 * La_1
+ -2.74334 1.94025 -0.00000 2 La 3.36013 * La_1
+ -0.00034 1.94025 -2.74350 2 La 3.36026 * La_1
+ -0.00034 1.94025 2.74350 2 La 3.36026 * La_1
+ 0.00034 -1.94025 -2.74350 2 La 3.36026 * La_1
+ 0.00034 -1.94025 2.74350 2 La 3.36026 * La_1
+ -2.74300 0.00000 -2.74350 3 Mn 3.87954 * Mn_2
+ -2.74300 0.00000 2.74350 3 Mn 3.87954 * Mn_2
+ 2.74300 0.00000 -2.74350 3 Mn 3.87954 * Mn_2
+ 2.74300 0.00000 2.74350 3 Mn 3.87954 * Mn_2
+ -0.00068 3.88050 0.00000 3 Mn 3.88050 * Mn_2
+ 0.00068 -3.88050 -0.00000 3 Mn 3.88050 * Mn_2
+ -4.11450 0.00000 -1.37175 1 O 4.33714 * O_4
+ -4.11450 0.00000 1.37175 1 O 4.33714 * O_5
+ 4.11450 0.00000 -1.37175 1 O 4.33714 * O_5
+ 4.11450 0.00000 1.37175 1 O 4.33714 * O_4
+ -2.74266 -1.94025 -2.74350 1 O 4.33746 * O_3
+ -2.74266 -1.94025 2.74350 1 O 4.33746 * O_3
+ 2.74266 1.94025 -2.74350 1 O 4.33746 * O_3
+ 2.74266 1.94025 2.74350 1 O 4.33746 * O_3
+ -1.37150 0.00000 -4.11525 1 O 4.33778 * O_4
+ -1.37150 0.00000 4.11525 1 O 4.33778 * O_5
+ 1.37150 0.00000 -4.11525 1 O 4.33778 * O_5
+ 1.37150 0.00000 4.11525 1 O 4.33778 * O_4
+ -2.74334 1.94025 -2.74350 1 O 4.33789 * O_3
+ -2.74334 1.94025 2.74350 1 O 4.33789 * O_3
+ 2.74334 -1.94025 -2.74350 1 O 4.33789 * O_3
+ 2.74334 -1.94025 2.74350 1 O 4.33789 * O_3
+ -1.37082 -3.88050 -1.37175 1 O 4.33810 * O_5
+ -1.37082 -3.88050 1.37175 1 O 4.33810 * O_4
+ 1.37082 3.88050 -1.37175 1 O 4.33810 * O_4
+ 1.37082 3.88050 1.37175 1 O 4.33810 * O_5
+ -1.37218 3.88050 -1.37175 1 O 4.33853 * O_5
+ -1.37218 3.88050 1.37175 1 O 4.33853 * O_4
+ 1.37218 -3.88050 -1.37175 1 O 4.33853 * O_4
+ 1.37218 -3.88050 1.37175 1 O 4.33853 * O_5
+
+* END
+
diff -r edf7f8ccf4af -r 8ee2cc3374fe test-data/[FEFF_input_of_AMS_Cu.cif].txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/[FEFF_input_of_AMS_Cu.cif].txt Mon Mar 04 11:43:32 2024 +0000
@@ -0,0 +1,74 @@
+*** feff input generated by xraylarch cif2feff using pymatgen ***
+TITLE Formula: Cu
+TITLE SpaceGroup: Fm-3m
+TITLE # sites: 1
+* crystallographics sites: note that these sites may not be unique!
+* using absorber at site 1 in the list below
+* selected as absorber="Cu", absorber_site=1
+* index X Y Z species
+* 1 0.000000 0.000000 0.000000 Cu <- absorber
+*
+
+
+HOLE 1 1.0 * Cu K edge, around 8979 eV (2nd number is S02)
+CONTROL 1 1 1 0 * phase, paths, feff, chi
+PRINT 1 0 0 0
+RMAX 5.00
+
+EXCHANGE 0
+
+* POLARIZATION 0 0 0
+
+POTENTIALS
+* IPOT Z Tag
+ 0 29 Cu
+ 1 29 Cu
+
+ATOMS
+* x y z ipot tag distance site_info
+ 0.00000 0.00000 0.00000 0 Cu 0.00000 * Cu_1
+ -1.80748 1.80748 0.00000 1 Cu 2.55616 * Cu_1
+ 1.80748 -1.80748 0.00000 1 Cu 2.55616 * Cu_1
+ -1.80748 -1.80748 0.00000 1 Cu 2.55616 * Cu_1
+ -1.80748 0.00000 -1.80748 1 Cu 2.55616 * Cu_1
+ -1.80748 0.00000 1.80748 1 Cu 2.55616 * Cu_1
+ -0.00000 -1.80748 -1.80748 1 Cu 2.55616 * Cu_1
+ -0.00000 -1.80748 1.80748 1 Cu 2.55616 * Cu_1
+ 0.00000 1.80748 -1.80748 1 Cu 2.55616 * Cu_1
+ 1.80748 0.00000 -1.80748 1 Cu 2.55616 * Cu_1
+ 0.00000 1.80748 1.80748 1 Cu 2.55616 * Cu_1
+ 1.80748 0.00000 1.80748 1 Cu 2.55616 * Cu_1
+ 1.80748 1.80748 0.00000 1 Cu 2.55616 * Cu_1
+ -3.61496 0.00000 0.00000 1 Cu 3.61496 * Cu_1
+ 3.61496 0.00000 0.00000 1 Cu 3.61496 * Cu_1
+ -0.00000 -3.61496 0.00000 1 Cu 3.61496 * Cu_1
+ -0.00000 0.00000 -3.61496 1 Cu 3.61496 * Cu_1
+ 0.00000 0.00000 3.61496 1 Cu 3.61496 * Cu_1
+ 0.00000 3.61496 0.00000 1 Cu 3.61496 * Cu_1
+ -3.61496 1.80748 -1.80748 1 Cu 4.42740 * Cu_1
+ -3.61496 1.80748 1.80748 1 Cu 4.42740 * Cu_1
+ 3.61496 -1.80748 -1.80748 1 Cu 4.42740 * Cu_1
+ 3.61496 -1.80748 1.80748 1 Cu 4.42740 * Cu_1
+ -3.61496 -1.80748 -1.80748 1 Cu 4.42740 * Cu_1
+ -1.80748 -3.61496 -1.80748 1 Cu 4.42740 * Cu_1
+ -1.80748 -1.80748 -3.61496 1 Cu 4.42740 * Cu_1
+ -3.61496 -1.80748 1.80748 1 Cu 4.42740 * Cu_1
+ -1.80748 -3.61496 1.80748 1 Cu 4.42740 * Cu_1
+ -1.80748 -1.80748 3.61496 1 Cu 4.42740 * Cu_1
+ -1.80748 1.80748 -3.61496 1 Cu 4.42740 * Cu_1
+ -1.80748 3.61496 -1.80748 1 Cu 4.42740 * Cu_1
+ -1.80748 1.80748 3.61496 1 Cu 4.42740 * Cu_1
+ -1.80748 3.61496 1.80748 1 Cu 4.42740 * Cu_1
+ 1.80748 -3.61496 -1.80748 1 Cu 4.42740 * Cu_1
+ 1.80748 -1.80748 -3.61496 1 Cu 4.42740 * Cu_1
+ 1.80748 -3.61496 1.80748 1 Cu 4.42740 * Cu_1
+ 1.80748 -1.80748 3.61496 1 Cu 4.42740 * Cu_1
+ 1.80748 1.80748 -3.61496 1 Cu 4.42740 * Cu_1
+ 1.80748 3.61496 -1.80748 1 Cu 4.42740 * Cu_1
+ 3.61496 1.80748 -1.80748 1 Cu 4.42740 * Cu_1
+ 1.80748 1.80748 3.61496 1 Cu 4.42740 * Cu_1
+ 1.80748 3.61496 1.80748 1 Cu 4.42740 * Cu_1
+ 3.61496 1.80748 1.80748 1 Cu 4.42740 * Cu_1
+
+* END
+