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Unit tests for Bias and Umbrella, umbrella sampling over n windows #7

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merged 9 commits into from
Dec 7, 2021
Merged

Unit tests for Bias and Umbrella, umbrella sampling over n windows #7

merged 9 commits into from
Dec 7, 2021

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tristan-j-wood
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@tristan-j-wood tristan-j-wood commented Dec 2, 2021 •
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Tests the harmonic bias with image and grad functions. Tests umbrella sampling with n windows. Added warning if >1 configurations are identical in US. Umbrella sampling over n windows with bias potential. Fits a Gaussian and plots the data.

@tristan-j-wood tristan-j-wood changed the title Unit tests for bias.py and umbrella.py Unit tests for Bias and Umbrella, umbrella sampling over n windows Dec 2, 2021
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t-young31 commented Dec 2, 2021 •
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Needs a rebase, also, do we want to try and run GAP on CI? I can envision licencing problems..

Pushed one commit just to make the tests work on my laptop 👍

@tristan-j-wood
Umbrella sampling over n windows
d09be20 
Run umbrella sampling simulations over n windows with a chosen bias. Fits Gaussians and plots data. Included updates to doc strings in bias.py
@tristan-j-wood
Unit tests for bias.py and umbrella.py
8e15613 
Tests the harmonic bias with image and grad functions. Tests umbrella sampling with n windows. Added warning if >1 configurations are identical in US
tristan-j-wood and others added 2 commits December 3, 2021 14:42
t-young31
t-young31 reviewed Dec 5, 2021
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@tristan-j-wood
Updates on comments on PR for US
82b169f 
Updates on PR comments on umbrella, bias and tests for both
t-young31
t-young31 reviewed Dec 6, 2021
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tristan-j-wood commented Dec 7, 2021
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This looks good overall. I think the separation of the gaussian functions and reference setting makes sense, as well as everything in a sampling class. The input of the function is slightly confusing to me so could be clearer what is expected from the user

@t-young31 t-young31 merged commit 3e1fea1 into duartegroup:main Dec 7, 2021
@tanoury1 tanoury1 mentioned this pull request Mar 12, 2024
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