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[fix.fields.sigma.D8+] the crate was never an isovalue problem, it was a box problem
Third attempt, and the first one that is about the molecule. A clean-context
computational chemist took the second one apart and the measurement confirms
them; this is my own change from this morning being retracted, for the second
time today, on better evidence.
1. iso = 0.05 MLP, hand-tuned on aspirin. Measured: clipped the grid wall on
all four molecules tried, INCLUDING aspirin. Rendered as a gold crate.
2. iso = 97th percentile of |field|. Never clips. Also a function of `pad`,
a RENDERING constant — measured on aspirin, pad 3->10 A moves it
25.5 -> 3.4 kcal/mol, a 7.6x swing with the physics IDENTICAL. I replaced
an arbitrary constant with a HIDDEN one carrying more leverage and printed
it as a measurement. It also selects the highest-|V| voxels, which are
always interior: 84-94% of the enclosed volume sits inside the vdW
surface, where nothing binds and where the softened Coulomb has the wrong
sign anyway.
3. This. The contour is FIXED in physical units and the BOX adapts.
The reframe is the finding: an adaptive RULER destroys comparison, an adaptive
BOX costs nothing. When a picture clips, widen the frame — do not move the
ruler and call the result measured.
Verified after the change:
aspirin / retinoic acid / benzene mep iso 10.00 pad 4.0 closes
same three mlp iso 0.25 pad 4.0 closes
acetate -1, choline +1 mep iso 10.00 pad 12.0 DOES NOT CLOSE
That last row is the part worth keeping. A charged ligand's monopole does not
decay fast enough to close inside any usable box, so the honest answer is not a
cleverer isovalue — it is to say so. `contour_closes_in_box: false` and the
wall value ride on the response, and the panel prints "open surface (field is
27.761 at the box edge)". Three-valued, as ever: closed, open, or refused —
never a flat face drawn as if it were chemistry.
Two more from the same review, both measured before I believed them:
- MEP and QM MEP were contoured in their own bare units, kcal/mol against
Ha/e, so toggling between two renderings of the SAME physical quantity moved
the contour from 18 to 31.4 kcal/mol without saying so. One unit on screen
now, converted at the isovalue by cubeScale.
- MLP is one-signed for most drug-like molecules (aspirin 99.9% positive,
ibuprofen 100%). Calling it "diverging" and drawing a negative lobe that does
not exist is a claim about the molecule. `single_signed` is measured per
response and the readout says "no negative lobe exists" instead of implying
one is hiding below the contour.
The isoLock/re-fit machinery from three commits ago is deleted. It was the
right instinct — hold the ruler still — applied to a ruler that should never
have been derived from the box in the first place. A fixed contour is
comparable by construction and needs no lock.
NEXT: the same review measured that /surface/mep_at has no cost gate and no
basis whitelist, that the physics daemon's SCF has no watchdog at all (the
36-minute fix landed on one of two daemons), and that STO-3G inverts the HOMO
ordering of a substituted-benzene series — nitrobenzene comes out more
electron-rich than benzene. Those are next.1 parent 8f32bac commit da29404
2 files changed
Lines changed: 127 additions & 96 deletions
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