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Add surface wetting module#96

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marjanalbooyeh merged 77 commits intomaincmelab/flowerMD:mainfrom surface-wettingcmelab/flowerMD:surface-wettingCopy head branch name to clipboardNov 28, 2023

+1,566-51

Commits

Commits on Oct 12, 2023

• droplet sim class

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• Merge branch 'main' of github.com:cmelab/flowerMD into surface-wetting

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Commits on Nov 14, 2023

• Merge branch 'main' of github.com:cmelab/flowerMD into surface-wetting

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• Merge pull request #90 from chrisjonesBSU/surface-wetting

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• graphene inherits from Molecule

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• complete doc stringsin Graphene, fix inconsistencies in doc strings of molecule.py

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• Merge pull request #93 from chrisjonesBSU/fix-surface

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Commits on Nov 15, 2023

• update class interface and add methods for surface snapshot and ff

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• use droplet ref values to get surface snapshot and ff

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• get r_cut from droplet lj forcce

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• update run_droplet params

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• add function for combining lj forces

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• Merge remote-tracking branch 'origin' into surface-wetting

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• fix formatting

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• fix formatting

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• Merge remote-tracking branch 'origin/surface-wetting' into surface-wetting

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• add methods for combining bond, angle and dihedrals

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• move module files into separate directories

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Commits on Nov 20, 2023

• fix lj combine

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• update combine forces utils

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• update comment

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• start combining snapshots

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• get wetting box, update positions

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• set snapshot pairs, bonds, angles, dihedrals

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• adjust particle positions

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• update box

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• add to surface particles

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Commits on Nov 21, 2023

• fix imports, fix spacing value in Graphene

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• load snapshot from gsd file, scale gap and box_height, fix np.concatenate calls

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• fix grabbing LJ params from surface FF, clean up setting new params

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• change z_shift, add properties

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• set integrate group for WettingSimulation

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• fix surface positioning

  marjanalbooyeh

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• change interface class name

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• add placeholder for wetting tests

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• move surface snap and ff to its class

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• add droplet sim tests

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• fixes to the fix_surfaces functionality

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• add tests

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• fix setting integrate group for surface

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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Commits on Nov 22, 2023

• improve tests

  marjanalbooyeh

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• rename properties

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• change graphene to inherit from system

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• move apply_FF params outisde of init, add test to apply a FF

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Commits on Nov 27, 2023

• Merge branch 'main' into surface-wetting

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• fix some unit test errors

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• fix docstring type for kT

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• set the ref values in apply_forcefield if there is none

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• add shrink density parameter to run_droplet;add docstring

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• add droplet unit test

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• skip problematic tests for now

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• complete interfacebuilder tests

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• add wetting sim test

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• use npisclose in test

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Commits on Nov 28, 2023

• use predefined ref values

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• fixed skipped tests by setting base_units=dict() when creating the system

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• beginning of a surface wetting tutorial

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• add surface_wetting to the docs

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• update docstrings

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• Merge branch 'surface-wetting' of github.com:cmelab/flowerMD into surface-wetting

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• add description to tutorial

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• fix cells, add warnings, add visualization

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• fix cells

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• add more details to tutorial

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• add 2 sentences about the surface wetting module

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