From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Jun 30 2015 - 10:43:40 CDT
I'm attempting some kludgy hacks to track heat exchange with the reservoir
during Langevin dynamics. Essentially what this corresponds to is tracking
the change in kinetic energy before and after the Langevin friction (the
scaling of the velociites at the initlal and half time steps) and Langevin
noise (the random force added at the initial and half time steps).
My best guess at this point is that I will need to add variables in the
langevinVelocitiesBBK1 and langevinVelocitiesBBK2 functions in Sequencer.C
- However, I have been warned that kinetic energy is computed via a
"reduction" call in Controller.C (scare quotes added bc I barely know what
that means) and that this might complicate things.
Are integration and reporting separated enough that this is a very
difficult thing to accomplish?
-- Brian Radak Postdoctoral Scholar University of Chicago Department of Biochemistry & Molecular Biology Gordon Center for Integrative Science, W323A 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 e-mail: radak_at_uchicago.edu
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