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Bug fix: change CifWriter to save only the element symbol, and not the entire species string #3071

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kamronald wants to merge 3 commits into from
+7 −2
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Bug fix: change CifWriter to save only the element symbol, and not the entire species string #3071

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bec8149
Update CifWriter
kamronald Jun 15, 2023
c35d764
Update CifWriter to save species with oxi state
kamronald Jun 16, 2023
324a675
Merge branch 'master' into fix_cif_writer
janosh Aug 18, 2023
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9 changes: 7 additions & 2 deletions pymatgen/io/cif.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

from __future__ import annotations

import copy
import math
import os
import re
Expand Down Expand Up @@ -1355,7 +1356,9 @@ def __init__(
if symprec is None:
for site in struct:
for sp, occu in sorted(site.species.items()):
atom_site_type_symbol.append(str(sp))
sp_no_prop = copy.deepcopy(sp)
sp_no_prop._properties = {}
atom_site_type_symbol.append(str(sp_no_prop))
atom_site_symmetry_multiplicity.append("1")
atom_site_fract_x.append(format_str.format(site.a))
atom_site_fract_y.append(format_str.format(site.b))
Expand Down Expand Up @@ -1403,7 +1406,9 @@ def __init__(
),
):
for sp, occu in site.species.items():
atom_site_type_symbol.append(str(sp))
sp_no_prop = copy.deepcopy(sp)
sp_no_prop._properties = {}
atom_site_type_symbol.append(str(sp_no_prop))
atom_site_symmetry_multiplicity.append(f"{mult}")
atom_site_fract_x.append(format_str.format(site.a))
atom_site_fract_y.append(format_str.format(site.b))
Expand Down