CV File external engine#626
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dwhswenson wants to merge 67 commits into
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Instead of just writing "0.0" for each frame.
Still needs a little more to do the correct shooting as expected
Based on initial ipynb tests to play with it
Removed cv_file.engine_command -- users can subclass if wanted
jhprinz
reviewed
Nov 6, 2016
| # explanation for the strange i=i is because lambdas are annoying | ||
| # when defined in loops: http://stackoverflow.com/questions/938429 | ||
| cvs = [paths.FunctionCV(self.cv_names[i], | ||
| lambda s, i=i: s.xyz.flatten()[i]) |
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Question: Just to clarify -- each column corresponds to a new CV right? There might be cases (especially for performance) where you want to use several columns together as one CV.
jhprinz
reviewed
Nov 6, 2016
| self.cv = {cv.name: cv for cv in cvs} | ||
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| self.shape = (n_atoms, n_spatial) | ||
| self.velocities = np.zeros(self.shape) # HACK |
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This could be a good use-case for a ConfigurationSnapshot called Configuration :) Just an idea.
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This is a little "engine" that allows us use the OPS analysis tools for an engine that just outputs some reduced set of CVs. Obviously, it would be very hard to run sampling with this (you would need a way to get from the reduced space of your CVs into the full space for your starting frames; OPS will only know how to write the CVs), but that's not the goal.
The goal here was to make it easy to analyze output from a simulation without needing to have an OPS version of the CV. (The idea came out a question that Gerhard Hummer asked me at the Lorentz Center workshop.)
NOTE: This is based on the ExternalEngine, and so it requires that #144 be merged first. Therefore, I'm marking it "onhold" and with a 1.x milestone.