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Add surface wetting module #96

Merged
merged 77 commits into from
Nov 28, 2023
Merged

Add surface wetting module #96

merged 77 commits into from
Nov 28, 2023

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chrisjonesBSU
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This is still a work in progress, but begins a surface wetting module that we've discussed before. We can use this as a place to discuss the design choices we'll have to make.

@chrisjonesBSU chrisjonesBSU removed the WIP Work in progress label Nov 27, 2023
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codecov bot commented Nov 28, 2023

Codecov Report

Merging #96 (0c8d139) into main (531cd82) will increase coverage by 0.15%.
The diff coverage is 95.23%.

❗ Current head 0c8d139 differs from pull request most recent head c8105bc. Consider uploading reports for the commit c8105bc to get more accurate results

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@@            Coverage Diff             @@
##             main      #96      +/-   ##
==========================================
+ Coverage   93.87%   94.02%   +0.15%     
==========================================
  Files          20       23       +3     
  Lines        1550     1724     +174     
==========================================
+ Hits         1455     1621     +166     
- Misses         95      103       +8     
Files Coverage Δ
flowermd/base/molecule.py 96.58% <ø> (ø)
flowermd/base/simulation.py 91.44% <ø> (ø)
flowermd/base/system.py 91.90% <100.00%> (+0.38%) ⬆️
flowermd/library/surfaces.py 100.00% <100.00%> (ø)
flowermd/modules/surface_wetting/__init__.py 100.00% <100.00%> (ø)
flowermd/modules/welding/__init__.py 100.00% <ø> (ø)
flowermd/modules/welding/utils.py 100.00% <ø> (ø)
flowermd/modules/welding/welding.py 100.00% <ø> (ø)
flowermd/modules/surface_wetting/utils.py 95.31% <95.31%> (ø)
...lowermd/modules/surface_wetting/surface_wetting.py 94.11% <94.11%> (ø)

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@chrisjonesBSU
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The tutorial looks good! Just one suggestion, I think we should try to use the same formatting we have in pre-commit in the tutorial code snippets.

For example:

graphene = Graphene(x_repeat=20, y_repeat=20, n_layers=1,
                    base_units=droplet_system.reference_values)
graphene.apply_forcefield(force_field=OPLS_AA(), remove_charges=True,
                          auto_scale=False, r_cut=2.5)

Should become

graphene = Graphene(
    x_repeat=20,
    y_repeat=20,
    n_layers=1,
    base_units=droplet_system.reference_values
)

graphene.apply_forcefield(
    force_field=OPLS_AA(),
    remove_charges=True,
    auto_scale=False,
    r_cut=2.5
)

I think it is easier to read and following along this way.

@marjanalbooyeh marjanalbooyeh merged commit 6e2c173 into main Nov 28, 2023
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@chrisjonesBSU chrisjonesBSU deleted the surface-wetting branch June 20, 2024 15:14
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Add Wetting Module
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