Post equilibrium analysis #43
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…st-eq Conflicts: MCMC/MCMC-flow/project.py
Deleting Workspace from repo so changes can be pulled
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let's add .txt to the .gitignore and remove this file.
| peakx = max(x) | ||
| peaky = max(y) |
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I think first and second peaks are more information rich in rdf. The max of bin_centers is always going to be the last value in the list (largest distance) and max of rdf doesn't give us a correct estimation of the first peak.
Previously I used scipy.signal.find_peaks from scipy package to find the peak.
@chrisjonesBSU Feel free to correct me if I'm wrong.
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I agree. We should use some kind of peak finding algorithm or tool. RDFs often have more than 1 peak, so just finding the max y value may not provide enough information.
| import numpy as np | ||
| os.makedirs(os.path.join(job.ws, "analysis/rdf")) | ||
| gsdfile = job.fn('trajectory_1.gsd') | ||
| rdf = rdf(gsdfile, start=-30) |
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Please apply this change to the rdf function in utils.py
rdf.compute((box,points), reset=False)
The default value for reset is True, which means if you are computing rdf from multiple snapshots, freud doesn't accumulate the computated values from different snapshots. When reset is True, the result rdf is only from last snapshot.
This is a pull request working on step 3 of issue #40. So far I have just added the RDF code to the project.py file but it still needs work and testing. Just wanted to get a PR started.