Theory · 1 methods

Charges

What CAPS computes, as it computes it: the equation, its symbols with CAPS's defaults, when to use the method, the source file, the tests that check it, and any departure from the cited method.

Adjusting computed charges

After a charge method: atoms equivalent in the bond graph share their mean charge, every charge can be scaled, and the total brought to a chosen value — evenly, or in proportion to each atom's |q| so small charges barely move.

$$q_i \leftarrow q_i + \frac{Q - \sum_j q_j}{N}\quad\text{or}\quad q_i + (Q - \textstyle\sum_j q_j)\,\frac{|q_i|}{\sum_j |q_j|}$$

classes from the element and the neighbours' classes, refined until stable (Morgan's extended connectivity); Q defaults to the formal charge × s

Symbol	Meaning	In CAPS
s	scale factor	—
Q	target total charge	e
N	atoms	—

When to use it

Symmetric groups that a method left unequal, charge-scaled ions (the electronic continuum correction, s ≈ 0.75–0.8), a fragment's small residual charge before building a polymer from it.

Source: core/src/charges.cpp
Tested by: tests/test_qeq.cpp Charges.AverageScaleNeutralise (methanol's methyl hydrogens one class and one charge, the total kept by averaging, × 0.8, neutralised evenly and ∝ |q|)
Departure from the reference: averaging uses the bond graph only: atoms alike in 3D but not in connectivity are not merged