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#3333 - Adding missing elements and test to fix the current workflow #3575

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Merged
AlexanderSavelyev merged 3 commits into from
Apr 2, 2026
Merged

#3333 - Adding missing elements and test to fix the current workflow #3575

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e94e395
Issue #3333: Adding missing elements, fixing issues and problems that…
NikolaiBalabanov Apr 2, 2026
8bcaed9
Merge remote-tracking branch 'origin/master' into 3333-Adding-missing…
NikolaiBalabanov Apr 2, 2026
a96293e
Issue #3333: Refactor element tests to consolidate group and period c…
NikolaiBalabanov Apr 2, 2026
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204 changes: 132 additions & 72 deletions core/indigo-core/molecule/src/elements.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -177,15 +177,15 @@ void Element::_initAllPeriodic()
INIT(Md, 7, 3);
INIT(No, 7, 3);
INIT(Lr, 7, 3);
INIT(Rf, 7, 3);
INIT(Db, 7, 3);
INIT(Sg, 7, 3);
INIT(Bh, 7, 3);
INIT(Hs, 7, 3);
INIT(Mt, 7, 3);
INIT(Ds, 7, 3);
INIT(Rg, 7, 3);
INIT(Cn, 7, 3);
INIT(Rf, 7, 4);
INIT(Db, 7, 5);
INIT(Sg, 7, 6);
INIT(Bh, 7, 7);
INIT(Hs, 7, 8);
INIT(Mt, 7, 8);
INIT(Ds, 7, 8);
INIT(Rg, 7, 1);
INIT(Cn, 7, 2);
INIT(Nh, 7, 3);
INIT(Fl, 7, 4);
INIT(Mc, 7, 5);
Expand Down Expand Up @@ -1244,7 +1244,7 @@ void Element::_initAromatic()
_element_parameters.at(i).can_be_aromatic = true;
for (i = ELEM_In; i <= ELEM_I; i++)
_element_parameters.at(i).can_be_aromatic = true;
for (i = ELEM_Tl; i <= ELEM_Bi; i++)
for (i = ELEM_Tl; i <= ELEM_At; i++)
_element_parameters.at(i).can_be_aromatic = true;
}

Expand All @@ -1267,71 +1267,131 @@ double Element::_getRelativeIsotopicMass(int element, int isotope) const
int Element::getNumOuterElectrons(int element)
{
// clang-format off
constexpr std::array<int, 59> outerElements{
0, // Pseudo-element
1, // H
2, // H3
1, // Li
2, // Be
3, // B
4, // C
5, // N
6, // O
7, // F
8, // Ne
1, // Na
2, // Mg
3, // Al
4, // Si
5, // P
6, // S
7, // Cl
8, // Ar
1, // K
2, // Ca
3, // Sc
4, // Ti
5, // V
6, // Cr
7, // Mn
8, // Fe
9, // Co
10, // Ni
1, // Cu
2, // Zn
3, // Ga
4, // Ge
5, // As
6, // Se
7, // Br
8, // Kr
1, // Rb
2, // Sr
3, // Y
4, // Zr
5, // Nb
6, // Mo
7, // Tc
8, // Ru
9, // Rh
10, // Pd
1, // Ag,
2, // Cd
3, // In
4, // Sn
5, // Sb
6, // Te
7, // I
8, // Xe
1, // Cs
2, // Ba
3, // La
4 // Ce
constexpr std::array<int, 119> outerElements{
0, // [0] Pseudo-element
1, // [1] H
2, // [2] He
1, // [3] Li
2, // [4] Be
3, // [5] B
4, // [6] C
5, // [7] N
6, // [8] O
7, // [9] F
8, // [10] Ne
1, // [11] Na
2, // [12] Mg
3, // [13] Al
4, // [14] Si
5, // [15] P
6, // [16] S
7, // [17] Cl
8, // [18] Ar
1, // [19] K
2, // [20] Ca
3, // [21] Sc
4, // [22] Ti
5, // [23] V
6, // [24] Cr
7, // [25] Mn
8, // [26] Fe
9, // [27] Co
10, // [28] Ni
1, // [29] Cu
2, // [30] Zn
3, // [31] Ga
4, // [32] Ge
5, // [33] As
6, // [34] Se
7, // [35] Br
8, // [36] Kr
1, // [37] Rb
2, // [38] Sr
3, // [39] Y
4, // [40] Zr
5, // [41] Nb
6, // [42] Mo
7, // [43] Tc
8, // [44] Ru
9, // [45] Rh
10, // [46] Pd
1, // [47] Ag
2, // [48] Cd
3, // [49] In
4, // [50] Sn
5, // [51] Sb
6, // [52] Te
7, // [53] I
8, // [54] Xe
1, // [55] Cs
2, // [56] Ba
3, // [57] La
4, // [58] Ce (4f1 5d1 6s2)
5, // [59] Pr (4f3 6s2)
6, // [60] Nd (4f4 6s2)
7, // [61] Pm (4f5 6s2)
8, // [62] Sm (4f6 6s2)
9, // [63] Eu (4f7 6s2)
10, // [64] Gd (4f7 5d1 6s2)
11, // [65] Tb (4f9 6s2)
12, // [66] Dy (4f10 6s2)
13, // [67] Ho (4f11 6s2)
14, // [68] Er (4f12 6s2)
15, // [69] Tm (4f13 6s2)
2, // [70] Yb (4f14 6s2, f14 core)
3, // [71] Lu (4f14 5d1 6s2, f14 core)
4, // [72] Hf
5, // [73] Ta
6, // [74] W
7, // [75] Re
8, // [76] Os
9, // [77] Ir
10, // [78] Pt (5d9 6s1)
1, // [79] Au (5d10 6s1, d10 core)
2, // [80] Hg
3, // [81] Tl
4, // [82] Pb
5, // [83] Bi
6, // [84] Po
7, // [85] At
8, // [86] Rn
1, // [87] Fr
2, // [88] Ra
3, // [89] Ac (6d1 7s2)
4, // [90] Th (6d2 7s2)
5, // [91] Pa (5f2 6d1 7s2)
6, // [92] U (5f3 6d1 7s2)
7, // [93] Np (5f4 6d1 7s2)
8, // [94] Pu (5f6 7s2)
9, // [95] Am (5f7 7s2)
10, // [96] Cm (5f7 6d1 7s2)
11, // [97] Bk (5f9 7s2)
12, // [98] Cf (5f10 7s2)
13, // [99] Es (5f11 7s2)
14, // [100] Fm (5f12 7s2)
15, // [101] Md (5f13 7s2)
2, // [102] No (5f14 7s2, f14 core)
3, // [103] Lr (5f14 7s2 7p1, f14 core)
4, // [104] Rf
5, // [105] Db
6, // [106] Sg
7, // [107] Bh
8, // [108] Hs
9, // [109] Mt
10, // [110] Ds
1, // [111] Rg (homolog of Au)
2, // [112] Cn (homolog of Hg)
3, // [113] Nh
4, // [114] Fl
5, // [115] Mc
6, // [116] Lv
7, // [117] Ts
8 // [118] Og
};
// clang-format on
if (element > static_cast<int>(outerElements.size()))
if (element < 0 || element >= static_cast<int>(outerElements.size()))
{
throw Error("outerElements are currently filled only for elements up to lantanoids");
throw Error("element number %d out of valid range for outer electrons", element);
}
return outerElements[element];
}
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