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Path density for alanine dipeptide TPS example#511

Merged
jhprinz merged 23 commits into
openpathsampling:masterfrom
dwhswenson:path_density
Jul 7, 2016
Merged

Path density for alanine dipeptide TPS example#511
jhprinz merged 23 commits into
openpathsampling:masterfrom
dwhswenson:path_density

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@dwhswenson

@dwhswenson dwhswenson commented Jul 1, 2016 •
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Fixes some problems in the path density histogram and adds a plot to the example notebook

  • Fix path histogram for sequential points in the same cell
  • Test for sequential points in same cell in path histogram
  • Simplify plotting of path density histograms
  • Add PathDensityHistogram to alanine_dipeptide_tps_analysis.ipynb
  • Tests and docstrings for plotting

@dwhswenson dwhswenson added this to the 1.0 milestone Jul 1, 2016
@dwhswenson dwhswenson self-assigned this Jul 1, 2016
dwhswenson added 18 commits July 1, 2016 16:18
@dwhswenson
Add plotting function for 2D histograms
8a9ed7f
@dwhswenson
Progress on improving the plotting
530c5da
@dwhswenson
Fixed but in making path dens; & added vis
11cb999
@dwhswenson
Decent lookup path density, plus trajs on top!
fbd55ca 
Still need to do some significant cleanup before this will be ready to
merge.
@dwhswenson
Starting on cleanup of histogram plotting
5e78e94
@dwhswenson
That's the path histogram plotting I want
53bf319 
Now I just have to add tests and do some cleanup
@dwhswenson
Cleanup
d170141
@dwhswenson
Cleared outputs
e386708
@dwhswenson
Merge remote-tracking branch 'upstream/master' into path_density
de090d1
@dwhswenson
Reran the analysis, miscellaneous cleanup
a593874
@dwhswenson
Start tests for VoxelLookupFunction
9921555
@dwhswenson
tests for df_2d
7531734
@dwhswenson
Finish VoxelLookup tests
9864fe4
@dwhswenson
Tests for map_to_float_bins
49e553f
@dwhswenson
Start tests for histogram plotting
f1ce163
@dwhswenson
Tests for HistPlot2D setup stuff
e633846
@dwhswenson
docstrings
318af0a
@dwhswenson
Cleanup tutorial_path_histogram
27a69c1
@dwhswenson dwhswenson changed the title [WIP] Path density for alanine dipeptide TPS example Path density for alanine dipeptide TPS example Jul 5, 2016
@dwhswenson

dwhswenson commented Jul 5, 2016

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Ready for review and merge! Left the outputs on the AD_tps_analysis clean, rather than cause more errors. But you can see the path densities in earlier versions, and I'll be adding one to the paper soon.

@dwhswenson dwhswenson assigned jhprinz and unassigned dwhswenson Jul 5, 2016
@jhprinz

jhprinz commented Jul 7, 2016

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The notebooks look good. Not sure if I completely got the HistogramPlotter, but seems to work as expected. Will merge.

@jhprinz jhprinz merged commit 28c7991 into openpathsampling:master Jul 7, 2016
@dwhswenson dwhswenson mentioned this pull request Aug 24, 2016
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@dwhswenson dwhswenson deleted the path_density branch March 15, 2018 14:22
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