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Organic Chemistry Example#1

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paulflang wants to merge 4 commits into
mainfrom
chem
Open

Organic Chemistry Example#1
paulflang wants to merge 4 commits into
mainfrom
chem

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This Draft PR adds the organic chemistry example. Current Problem is that fails to produce some expected species.

@paulflang paulflang mentioned this pull request Jun 10, 2026
@paulflang paulflang marked this pull request as ready for review June 15, 2026 03:17
Comment thread src/netgen.rs
Comment on lines +455 to +465
let (r#1, r#2) = bond_c [] in (H_dot [r#1], H_dot [r#2])
let (r#1, r#2) = bond_c [] in (H_dot [r#1], CH3_dot [r#2])
let (r#1, r#2) = bond_c [] in (H_dot [r#1], Halo_dot [r#2, F []])
let (r#1, r#2) = bond_c [] in (H_dot [r#1], Halo_dot [r#2, Cl []])
let (r#1, r#2) = bond_c [] in (CH3_dot [r#1], CH3_dot [r#2])
let (r#1, r#2) = bond_c [] in (CH3_dot [r#1], Halo_dot [r#2, F []])
let (r#1, r#2) = bond_c [] in (CH3_dot [r#1], Halo_dot [r#2, Cl []])
let (r#1, r#2) = bond_c [] in (Halo_dot [r#1, F []], Halo_dot [r#2, F []])
let (r#1, r#2) = bond_c [] in (Halo_dot [r#1, F []], Halo_dot [r#2, Cl []])
let (r#1, r#2) = bond_c [] in (Halo_dot [r#1, Cl []], Halo_dot [r#2, F []])
let (r#1, r#2) = bond_c [] in (Halo_dot [r#1, Cl []], Halo_dot [r#2, Cl []])"#]];

@paulflang paulflang Jun 15, 2026

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We have 4 different species that can appear in a bond_c. If there is no symmetry, we should have $4 \cdot 4=16$ species; if there is, we should have $4(4+1)/2=10$ species. We have $11$. Is this expected?

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