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Transition metal oxidation state proposed fixes #35

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66ddc86
initial patch for oxidation state
Zhaoli2042 Jun 12, 2026
d2dcbc3
remove backup files
Zhaoli2042 Jun 12, 2026
9b72eca
remove backup files for properties.py
Zhaoli2042 Jun 12, 2026
6f2f3cf
Restore old-YARP property values for 5d/4d transition metals
Zhaoli2042 Jun 12, 2026
d98ae57
Patches A-D to align Lewis search with old-YARP patched behavior
Zhaoli2042 Jun 12, 2026
154d454
Revert w_rad default from -0.01 to +0.1 to match old patched YARP
Zhaoli2042 Jun 19, 2026
9ebc8be
Patch F: conditional seed-BEM re-pool (organic-only)
Zhaoli2042 Jun 19, 2026
2f7049d
Drop patch B: revert min_opt=False,min_win=0.5 back to min_opt=True
Zhaoli2042 Jun 19, 2026
3d05e4a
Add zhao-patches documentation
Zhaoli2042 Jun 19, 2026
2772b84
Update docs with corpus-wide rerun results
Zhaoli2042 Jun 21, 2026
d1a1b42
Add section 8: characterize the 10 YARP errors
Zhaoli2042 Jun 21, 2026
4dc2424
Add section 9: spot-check + 78% impossible-OS reduction headline
Zhaoli2042 Jun 21, 2026
5229887
Correct over-max headline: apples-to-apples is +0.3%, not -78%
Zhaoli2042 Jun 21, 2026
5032732
Add regenerated dial plots + per-metal OS bar comparison
Zhaoli2042 Jun 21, 2026
ee63aa9
Clarify 3 patch annotations after audit
Zhaoli2042 Jun 23, 2026
c97dc4d
Add slim bench bundle to zhao-patches-doc/
Zhaoli2042 Jun 23, 2026
0672596
Merge branch 'master' into zhao-final-20260619
erm42 Jun 25, 2026
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43 changes: 31 additions & 12 deletions yarp/util/properties.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,11 @@
'li': 1, 'be': 2, 'b': 3, 'c': 4, 'n': 5, 'o': 6, 'f': 7, 'ne': 8,
'na': 1, 'mg': 2, 'al': 3, 'si': 4, 'p': 5, 's': 6, 'cl': 7, 'ar': 8,
'k': 1, 'ca': 2, 'sc': 3, 'ti': 4, 'v': 5, 'cr': 6, 'mn': 7, 'fe': 8, 'co': 9, 'ni': 10, 'cu': 11, 'zn': 12, 'ga': 3, 'ge': 4, 'as': 5, 'se': 6, 'br': 7, 'kr': 8,
'rb': 1, 'sr': 2, 'y': None, 'zr': None, 'nb': None, 'mo': None, 'tc': None, 'ru': 8, 'rh': 9, 'pd': 10, 'ag': None, 'cd': None, 'in': 3, 'sn': 4, 'sb': 5, 'te': 6, 'i': 7, 'xe': 8,
'cs': 1, 'ba': 2, 'la': None, 'hf': None, 'ta': None, 'w': None, 're': None, 'os': None, 'ir': 9, 'pt': None, 'au': 11, 'hg': None, 'tl': 3, 'pb': 4, 'bi': 5, 'po': 6, 'at': 7, 'rn': 8}
# 2026-06-12 ZL: restored from old YARP — many TM entries had
# been replaced with None upstream, which broke valence-based
# OS extraction for those metals.
'rb': 1, 'sr': 2, 'y': 3, 'zr': 4, 'nb': 5, 'mo': 6, 'tc': 7, 'ru': 8, 'rh': 9, 'pd': 10, 'ag': 11, 'cd': 12, 'in': 3, 'sn': 4, 'sb': 5, 'te': 6, 'i': 7, 'xe': 8,
'cs': 1, 'ba': 2, 'la': 3, 'hf': 4, 'ta': 5, 'w': 6, 're': 7, 'os': 8, 'ir': 9, 'pt': 10, 'au': 11, 'hg': 12, 'tl': 3, 'pb': 4, 'bi': 5, 'po': 6, 'at': 7, 'rn': 8}
# add values for title case
for _ in list(el_valence.keys()):
el_valence[_.title()] = el_valence[_]
Expand All @@ -32,9 +35,12 @@
el_n_deficient = {'h': 2, 'he': 2,
'li': 2, 'be': 0, 'b': 8, 'c': 8, 'n': 8, 'o': 8, 'f': 8, 'ne': 8,
'na': 0, 'mg': 0, 'al': 8, 'si': 8, 'p': 8, 's': 8, 'cl': 8, 'ar': 8,
'k': 0, 'ca': 0, 'sc': 0, 'ti': 0, 'v': 0, 'cr': 0, 'mn': 0, 'fe': 5, 'co': 6, 'ni': 1, 'cu': 0, 'zn': 10, 'ga': 8, 'ge': 8, 'as': 8, 'se': 8, 'br': 8, 'kr': 8,
'rb': 0, 'sr': 0, 'y': None, 'zr': None, 'nb': None, 'mo': None, 'tc': None, 'ru': 5, 'rh': 6, 'pd': 7, 'ag': None, 'cd': None, 'in': 8, 'sn': 8, 'sb': 8, 'te': 8, 'i': 8, 'xe': 8,
'cs': 0, 'ba': 0, 'la': None, 'hf': None, 'ta': None, 'w': None, 're': None, 'os': None, 'ir': 2, 'pt': None, 'au': 1, 'hg': None, 'tl': 8, 'pb': 8, 'bi': 8, 'po': 8, 'at': 8, 'rn': 8}
# 2026-06-12 ZL: restored from old YARP. Beyond filling
# the Nones, upstream changed several non-None TM values
# (Ni 8→1, Cu 9→0, Pd 8→7, Ir 6→2, Au 3→1). Reverted those.
'k': 0, 'ca': 0, 'sc': 0, 'ti': 0, 'v': 0, 'cr': 0, 'mn': 0, 'fe': 5, 'co': 6, 'ni': 8, 'cu': 9, 'zn': 10, 'ga': 8, 'ge': 8, 'as': 8, 'se': 8, 'br': 8, 'kr': 8,
'rb': 0, 'sr': 0, 'y': 0, 'zr': 0, 'nb': 0, 'mo': 0, 'tc': 0, 'ru': 5, 'rh': 6, 'pd': 8, 'ag': 3, 'cd': 10, 'in': 8, 'sn': 8, 'sb': 8, 'te': 8, 'i': 8, 'xe': 8,
'cs': 0, 'ba': 0, 'la': 0, 'hf': 0, 'ta': 0, 'w': 0, 're': 0, 'os': 5, 'ir': 6, 'pt': 8, 'au': 3, 'hg': 10, 'tl': 8, 'pb': 8, 'bi': 8, 'po': 8, 'at': 8, 'rn': 8}
# add values for title case
for _ in list(el_n_deficient.keys()):
el_n_deficient[_.title()] = el_n_deficient[_]
Expand All @@ -45,8 +51,10 @@
'li': 2, 'be': 0, 'b': 8, 'c': 8, 'n': 8, 'o': 8, 'f': 8, 'ne': 8,
'na': 0, 'mg': 0, 'al': 8, 'si': 8, 'p': 8, 's': 8, 'cl': 8, 'ar': 8,
'k': 1000, 'ca': 1000, 'sc': 1000, 'ti': 1000, 'v': 1000, 'cr': 1000, 'mn': 1000, 'fe': 1000, 'co': 1000, 'ni': 1000, 'cu': 1000, 'zn': 1000, 'ga': 8, 'ge': 8, 'as': 8, 'se': 8, 'br': 8, 'kr': 8,
'rb': 0, 'sr': 0, 'y': None, 'zr': None, 'nb': None, 'mo': None, 'tc': None, 'ru': 1000, 'rh': 1000, 'pd': 1000, 'ag': None, 'cd': None, 'in': 8, 'sn': 8, 'sb': 8, 'te': 8, 'i': 8, 'xe': 8,
'cs': 0, 'ba': 0, 'la': None, 'hf': None, 'ta': None, 'w': None, 're': None, 'os': None, 'ir': 1000, 'pt': None, 'au': 1000, 'hg': None, 'tl': 8, 'pb': 8, 'bi': 8, 'po': 8, 'at': 8, 'rn': 8}
# 2026-06-12 ZL: restored from old YARP — None entries
# filled in. All 4d/5d TMs use the 1000 sentinel as before.
'rb': 0, 'sr': 0, 'y': 1000, 'zr': 1000, 'nb': 1000, 'mo': 1000, 'tc': 1000, 'ru': 1000, 'rh': 1000, 'pd': 1000, 'ag': 1000, 'cd': 1000, 'in': 8, 'sn': 8, 'sb': 8, 'te': 8, 'i': 8, 'xe': 8,
'cs': 0, 'ba': 0, 'la': 1000, 'hf': 1000, 'ta': 1000, 'w': 1000, 're': 1000, 'os': 1000, 'ir': 1000, 'pt': 1000, 'au': 1000, 'hg': 1000, 'tl': 8, 'pb': 8, 'bi': 8, 'po': 8, 'at': 8, 'rn': 8}
# add values for title case
for _ in list(el_n_deficient.keys()):
el_n_expand_octet[_.title()] = el_n_deficient[_]
Expand All @@ -55,9 +63,11 @@
el_expand_octet = {'h': False, 'he': False,
'li': False, 'be': False, 'b': False, 'c': False, 'n': False, 'o': False, 'f': False, 'ne': False,
'na': False, 'mg': False, 'al': True, 'si': True, 'p': True, 's': True, 'cl': True, 'ar': True,
'k': False, 'ca': False, 'sc': False, 'ti': False, 'v': True, 'cr': True, 'mn': True, 'fe': True, 'co': True, 'ni': True, 'cu': True, 'zn': True, 'ga': True, 'ge': True, 'as': True, 'se': True, 'br': True, 'kr': True,
'rb': False, 'sr': False, 'y': None, 'zr': None, 'nb': None, 'mo': None, 'tc': None, 'ru': True, 'rh': True, 'pd': True, 'ag': None, 'cd': None, 'in': True, 'sn': True, 'sb': True, 'te': True, 'i': True, 'xe': True,
'cs': False, 'ba': False, 'la': None, 'hf': None, 'ta': None, 'w': None, 're': None, 'os': None, 'ir': True, 'pt': None, 'au': True, 'hg': None, 'tl': True, 'pb': True, 'bi': True, 'po': True, 'at': True, 'rn': True}
# 2026-06-12 ZL: restored from old YARP. Also Ti reverted
# from False→True (upstream changed it; we restored).
'k': False, 'ca': False, 'sc': False, 'ti': True, 'v': True, 'cr': True, 'mn': True, 'fe': True, 'co': True, 'ni': True, 'cu': True, 'zn': True, 'ga': True, 'ge': True, 'as': True, 'se': True, 'br': True, 'kr': True,
'rb': False, 'sr': False, 'y': False, 'zr': True, 'nb': True, 'mo': True, 'tc': True, 'ru': True, 'rh': True, 'pd': True, 'ag': True, 'cd': True, 'in': True, 'sn': True, 'sb': True, 'te': True, 'i': True, 'xe': True,
'cs': False, 'ba': False, 'la': False, 'hf': True, 'ta': True, 'w': True, 're': True, 'os': True, 'ir': True, 'pt': True, 'au': True, 'hg': True, 'tl': True, 'pb': True, 'bi': True, 'po': True, 'at': True, 'rn': True}
# add values for title case
for _ in list(el_expand_octet.keys()):
el_expand_octet[_.title()] = el_expand_octet[_]
Expand All @@ -76,11 +86,16 @@
el_en[_.title()] = el_en[_]

# Polarizability ordering (for determining lewis structure)
# 2026-06-12 ZL: 5d+6p row (Cs..Rn) restored from old YARP. Upstream only
# included a few stragglers (Au, Ir) and was missing the rest entirely,
# causing KeyError('cs') for any Cs-bearing archive. Also dropped a duplicate
# `"rh": 66` key that survived in the new dict literal.
el_pol = {"h": 4.5, "he": 1.38,
"li": 164.0, "be": 377, "b": 20.5, "c": 11.3, "n": 7.4, "o": 5.3, "f": 3.74, "ne": 2.66,
"na": 163.0, "mg": 71.2, "al": 57.8, "si": 37.3, "p": 25.0, "s": 19.4, "cl": 14.6, "ar": 11.1,
"k": 290.0, "ca": 161.0, "sc": 97.0, "ti": 100.0, "v": 87.0, "cr": 83.0, "mn": 68.0, "fe": 62.0, "co": 55, "ni": 49, "cu": 47.0, "zn": 38.7, "ga": 50.0, "ge": 40.0, "as": 30.0, "se": 29.0, "br": 21.0, "kr": 16.8,
"rb": 320.0, "sr": 197.0, "y": 162, "zr": 112.0, "nb": 98.0, "mo": 87.0, "tc": 79.0, "ru": 72.0, "rh": 66, "pd": 26.1, "ag": 55, "cd": 46.0, "in": 65.0, "sn": 53.0, "sb": 43.0, "te": 28.0, "i": 32.9, "xe": 27.3, "au": 36, "rh": 66, "ir": 54}
"rb": 320.0, "sr": 197.0, "y": 162, "zr": 112.0, "nb": 98.0, "mo": 87.0, "tc": 79.0, "ru": 72.0, "rh": 66, "pd": 26.1, "ag": 55, "cd": 46.0, "in": 65.0, "sn": 53.0, "sb": 43.0, "te": 28.0, "i": 32.9, "xe": 27.3,
"cs": 401.0, "ba": 272.0, "la": 215.0, "hf": 103.0, "ta": 74.0, "w": 68.0, "re": 62.0, "os": 57.0, "ir": 54.0, "pt": 48.0, "au": 36.0, "hg": 33.9, "tl": 50.0, "pb": 47.0, "bi": 48.0, "po": 44.0, "at": 42.0, "rn": 35.0}
# add values for title case
for _ in list(el_pol.keys()):
el_pol[_.title()] = el_pol[_]
Expand Down Expand Up @@ -150,6 +165,10 @@
el_max_valence[_.lower()] = el_max_valence[_]

# In several places transition metals need to be easily identified, so this set is imported for that purpose.
# 5d transition metals (La, Hf, Ta, W, Re, Os, Pt, Hg) added 2026-05-21 ZL —
# without them adjust_metals() never dative-izes Cp on 5d centers, which
# inflates the +6 oxidation-state bin in dial plots for Hf/W/Re/Os/Ir/Pt.
el_metals = {'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn',
'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'Au', 'Ir'}
'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd',
'La', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg'}
el_metals.update({_.lower() for _ in el_metals})
27 changes: 25 additions & 2 deletions yarp/yarpecule/lewis/bem_score.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,17 @@


def bmat_score(bond_mat, elements, rings,
w_def=-1, w_exp=0.1, w_formal=0.1, w_aro=-24, w_rad=-0.01,
# Patch w_rad (2026-06-19 ZL): default reverted from -0.01 to +0.1
# to match old patched YARP convention. Note: this revert is
# COSMETIC, not a behavior change. The new bmat_score computes
# `rad_env = +pol/(100+pol)` internally; old YARP find_lewis
# passed `rad_env = -0.1 * pol/(100+pol)` from outside. The
# `w_rad * rad_env` product is algebraically identical between
# the two: new (-0.01)*(+pol/(100+pol)) == old (+0.1)*(-0.1*pol/(100+pol)).
# Empirical bisection (only-B/w_rad-only branch) confirmed zero
# chemistry impact on a 144-archive stratified TM sample.
# Reverted only to keep w_rad > 0 by downstream convention.
w_def=-1, w_exp=0.1, w_formal=0.1, w_aro=-24, w_rad=0.1,
factor=0.0, verbose=False):
"""
Score function used to rank candidate Lewis Structures during and after the exploration. The `find_lewis()` algorithm uses a few
Expand Down Expand Up @@ -547,12 +557,21 @@ def adjust_metals(bond_mats, adj_mat, elements):
continue
# type X - covalent bonds
elif b[con, con] % 2 != 0:
# GUARD (2026-05-22 ZL): only form X if metal has electrons
# to spend. Otherwise leave the partner radical and treat
# the bond as dative-like to avoid negative diagonals
# (which produce impossible high oxidation states).
if b[m_ind, m_ind] < 1:
continue
b[con, con] += -1
b[m_ind, m_ind] += -1
b[con, m_ind] += 1
b[m_ind, con] += 1
# type Z - covalent bond, empty p orbital, using two electrons from the metal
else:
# GUARD (2026-05-22 ZL): Z bond needs 2 electrons from metal.
if b[m_ind, m_ind] < 2:
continue
b[m_ind, m_ind] += -2
b[con, m_ind] += 1
b[m_ind, con] += 1
Expand All @@ -562,7 +581,11 @@ def adjust_metals(bond_mats, adj_mat, elements):
for m_ind in m_inds:
for con in return_connections(m_ind, adj_mat, inds=m_inds):
count = 0
while electrons[m_ind] < 12 and electrons[con] < 12 and b[con, con] > 0:
# GUARD (2026-05-22 ZL): also require b[m_ind, m_ind] > 0 so
# both partners have an electron to contribute to the M-M bond
# (prevents metal diagonal going negative).
while (electrons[m_ind] < 12 and electrons[con] < 12
and b[con, con] > 0 and b[m_ind, m_ind] > 0):
b[m_ind, m_ind] += -1
b[con, con] += -1
b[m_ind, con] += 1
Expand Down
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