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@rykerfish rykerfish commented Feb 10, 2026

This is changing sqrtMdotW to respect the prefactor argument since it was ignoring it before.

To test it, I'm generating the same random samples by seeding libMobility and making sure they match with/without the prefactor. This way of testing now works for all solvers except PSE, which will require deeper changes in UAMMD. As far as I can tell, PSE pulls its seeds from the System module in UAMMD (e.g. here), which is currently seeded randomly (and amusingly).

Two questions for you @RaulPPelaez :

  1. Should I change UAMMD to be able to be seeded directly to support this way of testing the prefactor, and so that seeding actually works as indicated in general?
  2. When thinking about tests, I noticed Mdot has no prefactor argument, presumably since it doesn't have a prefactor in the usual Langevin equation. Are we fine letting Mdot go without a prefactor? It could theoretically be useful in things like time integrators to put the different constants in front of the $MF$ terms.

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@RaulPPelaez
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In general the prefactor I do not like, we are putting a lot of interface pressure in multiplying by a constant. As we just saw, this functionality, which realistically spares the launching of a near-instant kernel, is bug inducing more than anything -.-
I say lets leave Mdot as is.
Do not worry about PSE, you are right that it is fundamentally more difficult to do this test there. If you can think of a different test do that instead, cant think of anything right now though.

@rykerfish rykerfish marked this pull request as ready for review February 10, 2026 21:57
@rykerfish rykerfish merged commit 3fef370 into main Feb 10, 2026
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@rykerfish rykerfish deleted the prefactor_bugfix branch February 10, 2026 22:14
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