S-shooting by singraber · Pull Request #787 · openpathsampling/openpathsampling

singraber · 2018-06-23T11:19:17Z

Added S-shooting method to OPS, includes example and tests.

Developed as part of E-CAM ESDW in Leiden in August 2017 and finished on a sunny day in June 2018 in Vienna.

Link to the gitlab repository:
https://gitlab.e-cam2020.eu/singraber/S-Shooting

- Class SShootingSimulation added. - Class SShootingAnalysis added. - Class NonCanonicalSequentialMover added. - Class NonCanonicalSequentialMoveChange added. - Class DoubleWell added. - Class OverdampedLangevinIntegrator added. - Example IPython notebook sshooting-example.ipynb added. - Nosetests for all classes added.

dwhswenson · 2019-07-19T14:12:32Z

Please note that we have changed to the OPS license from LGPL (2.1 or later) to MIT. For any pull request to OPS that was started while the license was still LGPL, I need an explicit confirmation that you approve of the license change. Please add a comment with something like "The changes in this pull request are licensed under the MIT license."

… into s_shooting

singraber · 2020-07-20T17:57:39Z

Updating with the master introduced some inconsistencies, I will fix this... also:

The changes in this pull request are licensed under the MIT license.

dwhswenson · 2020-12-26T09:14:29Z

@singraber : Before I do a full review on this, could you do the following?

git pull to bring in the conflict fixes I made
Move the toy engine stuff you've added (PES and integrator) into the core files (intergrators.py, pes.py). The double-well PES seems frequently desired (although I use the version in OpenMMTools) and I was about to write an overdamped Langevin integrator for a tutorial I'm putting together; would rather just take yours!
Please refactor to re-use as much as possible from the reactive flux PR, which is now merged. In particular, the various NonCanonical things are already in place, I think.

Thanks!

dwhswenson · 2021-01-28T15:08:18Z

@singraber : Pinging again on this, since I think Christoph just said S-Shooting is in OPS... This needs some minor cleanup before I do the full review, but should be pretty straightforward! See #787 (comment) above for what needs to be done.

… into s_shooting

codecov · 2021-01-29T15:34:31Z

Codecov Report

Merging #787 (2094df0) into master (1279f23) will increase coverage by 1.50%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #787      +/-   ##
==========================================
+ Coverage   80.25%   81.76%   +1.50%     
==========================================
  Files         136      142       +6     
  Lines       14449    15604    +1155     
==========================================
+ Hits        11596    12758    +1162     
+ Misses       2853     2846       -7

Impacted Files	Coverage Δ
openpathsampling/movechange.py	`76.12% <ø> (+1.36%)`	⬆️
openpathsampling/pathmover.py	`84.33% <ø> (+0.47%)`	⬆️
openpathsampling/__init__.py	`100.00% <100.00%> (ø)`
openpathsampling/analysis/sshooting_analysis.py	`100.00% <100.00%> (ø)`
openpathsampling/engines/toy/__init__.py	`100.00% <100.00%> (ø)`
openpathsampling/engines/toy/integrators.py	`93.65% <100.00%> (+2.53%)`	⬆️
openpathsampling/engines/toy/pes.py	`93.33% <100.00%> (+1.02%)`	⬆️
openpathsampling/pathsimulators/__init__.py	`100.00% <100.00%> (ø)`
...pathsampling/pathsimulators/sshooting_simulator.py	`100.00% <100.00%> (ø)`
openpathsampling/engines/topology.py	`59.01% <0.00%> (-40.99%)`	⬇️
... and 90 more

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singraber · 2021-01-29T16:48:09Z

@dwhswenson Sorry for the delay, thanks for pinging! I integrated the toys from S-shooting into the main files and reused the NonCanonical stuff from the ReactiveFlux code. The example seems to run fine and I fixed a problem with the tests. The toy tests are now also merged into the test_toy_dynamics.py file. I think it's ready for reviewing...

dwhswenson

Looks pretty good -- minor changes, all in the tests. The main things are:

We're now using pytest, so please don't add tests based on nose. I tried to give guidance on how to change. Most are straightforward: just directly use Python assert statements. For assert_almost_equal or anything involving arrays, use tools in numpy.testing.
A couple of to_dict/from_dict methods weren't covered. Suggestions show how I normally do that (by testing consistency in a to_dict-from_dict-to_dict cycle).

dwhswenson

After the changes I made in the last few commits, I approve this, but probably worth allowing some time for someone else to look over my changes. No requirement that those get reviewed before merge, but I'll give some time for @sroet or @singraber to look over the changes in 9825397, 53261df, and 2094df0 before I merge.

I will leave this open for at least 24 hours, merging no earlier than Tue 14 Dec 06:00 GMT (01:00 my local).

sroet · 2021-12-14T10:01:25Z

No requirement that those get reviewed before merge, but I'll give some time for @sroet or @singraber to look over the changes in 9825397, 53261df, and 2094df0 before I merge.

Looked over them and those commits look good to me

Merge branch 'master' of github.com:openpathsampling/openpathsampling…

d439c6a

… into s_shooting

Minor changes for Python 3 compatibility

37851ed

dwhswenson added this to the 1.4 milestone Aug 12, 2020

dwhswenson added the feature label Sep 26, 2020

dwhswenson self-requested a review October 12, 2020 15:44

dwhswenson mentioned this pull request Dec 23, 2020

Fix: OPS hangs when external engine errors/exits unexpectedly #913

Merged

dwhswenson modified the milestones: 1.4, 1.5 Dec 23, 2020

Merge branch 'master' into s_shooting

f0c5be2

singraber added 3 commits January 29, 2021 13:35

Integrated S-shooting toys, reuse code from RF

a867fde

Merge branch 'master' of github.com:openpathsampling/openpathsampling…

7971c34

… into s_shooting

Fixed tests, S-shooting tests in test_toy_dynamic

a9685b1

Fixed S-shooting tests not running

5818a37

dwhswenson requested changes Mar 2, 2021

View reviewed changes

dwhswenson modified the milestones: 1.5, 1.6 Jun 18, 2021

sroet mentioned this pull request Dec 10, 2021

Actually check for CVDefinedVolume.lambda_max == "inf" #1092

Merged

dwhswenson added 3 commits December 12, 2021 23:00

Switch S-Shooting tests to pytest

9825397

serialization tests; update some old test PEP8

53261df

Update openpathsampling/tests/test_sshooting_analysis.py

2094df0

dwhswenson approved these changes Dec 13, 2021

View reviewed changes

dwhswenson merged commit 523442e into openpathsampling:master Dec 14, 2021

sroet mentioned this pull request Dec 20, 2021

make a missed string into a rawstring #1096

Merged

dwhswenson mentioned this pull request Jan 4, 2024

Release 1.6.0 #1138

Merged

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singraber commented Jun 23, 2018

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