[us-commits] [ehb54/ultrascan3] 3f27d1: Implement the published metal and ion volumes

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3f27d1bad3fefc85e8505c6e9393c80873e3f480
      https://github.com/ehb54/ultrascan3/commit/3f27d1bad3fefc85e8505c6e9393c80873e3f480
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_psv.h
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/perceiver/tests/psv.cpp
    M us_somo/develop/src/us_hydrodyn_psv.cpp

  Log Message:
  -----------
  Implement the published metal and ion volumes

The engine reported "no volume increment for this element" for every metal.
That was wrong: Durchschlag and Zipper tabulate them, and the values had
already been extracted into the Python prototype and then never carried across
to the C++ implementation.

Table 2 supplies atomic volumes for a metal bonded into a complex, such as a
haem iron or B12's cobalt. Table 3 supplies aqueous volumes for free monatomic
ions, including iron at -32.3 and -55.1 for the divalent and trivalent forms.
Those ion values already contain the ionisation contribution, so
electrostriction is not charged a second time on top of them, and a test
asserts an isolated magnesium comes out at exactly its tabulated value with no
electrostriction term.

The trivalent iron value of -55.1 is -0.99 mL/g, the same sign and order as the
figure quoted from another compilation. Negative because electrostriction
draws water inward around the ion more than the bare ion displaces.

The effect on haem is real but small: its partial specific volume moves from
24.3% low to 23.0% low. Iron is about a percent of a 616 dalton molecule, so it
was never going to close that gap. The bulk of the error is most likely the
porphyrin itself, four fused pyrrole rings and a heavily conjugated macrocycle,
which is not what Traube-style additivity was built for.

Refs ehb54/ultrascan-tickets#980

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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