Refactoring hoomd polymers #8

marjanalbooyeh · 2023-05-04T17:09:31Z

This PR refactors the base classes in the repository with the goal of making the whole framework flexible and reusable.

Currently, the bulk of refactoring is going to happen on Molecule and System classes.

Make LJ chain class more flexible, add unit tests

…e molecule classes instead of system class

hoomd_polymers/base/molecule.py

chrisjonesBSU and others added 27 commits April 18, 2023 14:29

make LJ_Chain class more flexible

7961888

add tests for LJ chain class

b6152b9

update doc strings

5b10090

clean up exception

ceefb12

Merge pull request #7 from chrisjonesBSU/cg/sims

ae1486b

Make LJ chain class more flexible, add unit tests

add bead spring forcefield class

9264ac0

move forces into method

0a732f9

Merge branch 'cg/sims' into add/mol_generator

493256f

add build and generate methods to molecule class

c9539fc

add to_snapshot func

0204c87

fix to_hoomd_snapshot

8025b8e

Convert all classes to new structure

9cf267f

trying out new class structure

8c36b35

trying out a new approach, where repeat molecules are generated in th…

7dee0f8

…e molecule classes instead of system class

moving specific classes over to library

e5ab460

finish CoPolymer class, move polymers.py to library

30755e0

fix length in CoPolymer class

2ff69d9

fix pekk_meta class, remove print statements

33ac17d

move things around a bit

2f37f82

fix imports with new structure of repo

e454f04

import system classes

9ab4757

add gmso to env files

e1ff15b

Update base classes.

32433b4

Add a sample run script.

73106a6

Fix cirucular dependency.

b635c60

Identify bonded and non-bonded interactions.

20e1f7b

Update forcefield validation.

57d9be1

chrisjonesBSU reviewed May 9, 2023

View reviewed changes

hoomd_polymers/base/molecule.py Outdated Show resolved Hide resolved

marjanalbooyeh and others added 2 commits May 9, 2023 11:24

Fix Molecule generate method.

46d30a8

add coarse grain method to Molecule class, update env files

481edde

marjanalbooyeh added 23 commits August 9, 2023 15:44

change base_units default type to dict.

5f8d900

remove if condition from hoomd ff and snapshot.

eb30e17

add missing return for mass.

21dbffc

add unit test with updated ref values.

21a340a

add simulation unit test.

9b8fe8e

compare updated snapshot epsilon and gmso epsilon.

f027542

set reference values when auto_scale=False.

50ded54

fix test names and parameters.

72c51fa

remove extra test files.

4f02a08

change fixture system.

0f8df64

add simulation unit tests.

de857b0

organize files.

446bb23

sort imports.

2d1e466

Polymers unit tests.

034ac2a

remove extra files.

4c58454

sort test imports.

e8e27d9

add unit tests for forcefields in library.

3ad9f8e

arrange test files.

2ee293f

fix formatting.

a78a7be

unit tests for weld and tensile.

090504f

code formatting and style.

e7c02a6

run pre-commit.

b6ece0b

create first tutorial.

a14b22f

chrisjonesBSU marked this pull request as ready for review August 20, 2023 01:27

chrisjonesBSU and others added 5 commits August 21, 2023 12:54

pin to latest hoomd v3

2e8a573

add test to run weld sim

220475a

move apply forcefield if condition.

de3358b

fill test_ff.xml

63f0ec7

change title style.

db47b4a

marjanalbooyeh merged commit ba82d6a into cmelab:refactor Aug 22, 2023

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Refactoring hoomd polymers #8

Refactoring hoomd polymers #8

marjanalbooyeh commented May 4, 2023

Refactoring hoomd polymers #8

Refactoring hoomd polymers #8

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marjanalbooyeh commented May 4, 2023