Code

Refactor#10

Code

Merged

chrisjonesBSU merged 182 commits intomaincmelab/flowerMD:mainfrom refactorcmelab/flowerMD:refactorCopy head branch name to clipboardAug 24, 2023

+8,322-1,635

Commits

Commits on Apr 20, 2023

• add bead spring forcefield class

  chrisjonesBSU

  committed
  9264ac0

Commits on Apr 21, 2023

• move forces into method

  chrisjonesBSU

  committed
  0a732f9

• Merge branch 'cg/sims' into add/mol_generator

  chrisjonesBSU

  committed
  493256f

• add build and generate methods to molecule class

  chrisjonesBSU

  committed
  c9539fc

• add to_snapshot func

  chrisjonesBSU

  committed
  0204c87

Commits on Apr 22, 2023

• fix to_hoomd_snapshot

  chrisjonesBSU

  committed
  8025b8e

Commits on Apr 24, 2023

• Convert all classes to new structure

  chrisjonesBSU

  committed
  9cf267f

• trying out new class structure

  chrisjonesBSU

  committed
  8c36b35

Commits on Apr 25, 2023

• trying out a new approach, where repeat molecules are generated in the molecule classes instead of system class

  chrisjonesBSU

  committed
  7dee0f8

• moving specific classes over to library

  chrisjonesBSU

  committed
  e5ab460

Commits on Apr 26, 2023

• finish CoPolymer class, move polymers.py to library

  chrisjonesBSU

  committed
  30755e0

• fix length in CoPolymer class

  chrisjonesBSU

  committed
  2ff69d9

• fix pekk_meta class, remove print statements

  chrisjonesBSU

  committed
  33ac17d

Commits on Apr 28, 2023

• move things around a bit

  chrisjonesBSU

  committed
  2f37f82

• fix imports with new structure of repo

  chrisjonesBSU

  committed
  e454f04

• import system classes

  chrisjonesBSU

  committed
  9ab4757

• add gmso to env files

  chrisjonesBSU

  committed
  e1ff15b

Commits on May 2, 2023

• Update base classes.

  

  Marjan

  authored and

  Marjan

  committed
  32433b4

Commits on May 4, 2023

• Add a sample run script.

  

  Marjan

  authored and

  Marjan

  committed
  73106a6

• Fix cirucular dependency.

  

  Marjan

  authored and

  Marjan

  committed
  b635c60

Commits on May 8, 2023

• Identify bonded and non-bonded interactions.

  

  Marjan

  authored and

  Marjan

  committed
  20e1f7b

• Update forcefield validation.

  

  Marjan

  authored and

  Marjan

  committed
  57d9be1

Commits on May 9, 2023

• Fix Molecule generate method.

  marjanalbooyeh

  committed
  46d30a8

• add coarse grain method to Molecule class, update env files

  chrisjonesBSU

  committed
  481edde

Commits on May 17, 2023

• Get topology information from first molecule.

  marjanalbooyeh

  committed
  af64bd5

Commits on May 31, 2023

• install gmso from conda forge now that changes are merged, remove nohoomd env file

  chrisjonesBSU

  committed
  3da21d9

• change atom_type to atom_type.name when populating topology info

  chrisjonesBSU

  committed
  7fcf88b

• import System from base.py; add atom type fix to impropers

  chrisjonesBSU

  committed
  c181565

• remove old forcefield, molecule and system py files

  chrisjonesBSU

  committed
  3a31666

Commits on Jun 1, 2023

• changes to fix CoPolymer class

  chrisjonesBSU

  committed
  13fd027

• Add comment for getting topology info after applying ff.

  marjanalbooyeh

  committed
  9346a83

• Update atom_type name in topology information.

  marjanalbooyeh

  committed
  b7c0bf6

Commits on Jun 2, 2023

• Merge branch 'main' of github.com:chrisjonesBSU/hoomd-polymers into mol-generator

  chrisjonesBSU

  committed
  ff1e78d

• add PEKK to polymer library

  chrisjonesBSU

  committed
  f11aa44

• add force_field param to CoPolymer

  chrisjonesBSU

  committed
  e3136d2

Commits on Jun 6, 2023

• organize project directories.

  

  Marjan

  authored and

  Marjan

  committed
  622995e

• Add exceptions classes.

  

  Marjan

  authored and

  Marjan

  committed
  7d615c6

• Add __init__ files.

  

  Marjan

  authored and

  Marjan

  committed
  a416869

• Update validate_hoomd_ff.

  

  Marjan

  authored and

  Marjan

  committed
  5ed6904

• Fix bugs in system class.

  

  Marjan

  authored and

  Marjan

  committed
  d70d7f3

• Add remove_hydrogens arg to validate_hoomd_ff method.

  

  Marjan

  authored and

  Marjan

  committed
  5fa2ac2

• Rename forcefield utils file.

  

  Marjan

  authored and

  Marjan

  committed
  e1fa173

• Handle remove_hydrogen=True case.

  

  Marjan

  authored and

  Marjan

  committed
  a759cb1

• Convert particles set to list.

  

  Marjan

  authored and

  Marjan

  committed
  5a5c723

Commits on Jun 7, 2023

• Remove bond direction from topology information.

  

  Marjan

  authored and

  Marjan

  committed
  46f30a9

• Add missing bond potential exception.

  

  Marjan

  authored and

  Marjan

  committed
  b9758d6

• Validate hoomd bond potentials.

  

  Marjan

  authored and

  Marjan

  committed
  cd167d3

• Add a method to identify h in connections.

  

  Marjan

  authored and

  Marjan

  committed
  8b5f7e6

• Avoid having repetetive angles.

  

  Marjan

  authored and

  Marjan

  committed
  0239ceb

• Add missing angle potential exception.

  

  Marjan

  authored and

  Marjan

  committed
  e04c032

• Validate hoomd angle potentials.

  

  Marjan

  authored and

  Marjan

  committed
  8a091a6

• Avoid adding repeated dihedral in topology information.

  

  Marjan

  authored and

  Marjan

  committed
  6e5bea5

• Refactor exception classes.

  

  Marjan

  authored and

  Marjan

  committed
  de61632

• Validate hoomd dihedral potentials.

  

  Marjan

  authored and

  Marjan

  committed
  767c742

• Refactor molecule class.

  

  Marjan

  authored and

  Marjan

  committed
  7d518cf

• Add missing coulomb force exception.

  

  Marjan

  authored and

  Marjan

  committed
  3f160e2

• Validate hoomd Coulombic forces.

  

  Marjan

  authored and

  Marjan

  committed
  7041ee0

Commits on Jun 8, 2023

• Sort imports.

  

  Marjan

  authored and

  Marjan

  committed
  d0ad54f

• Accept different types for molecules and forcefield.

  

  Marjan

  authored and

  Marjan

  committed
  33a797d

• Updated abstractmethods for system.

  

  Marjan

  authored and

  Marjan

  committed
  9749590

• sort imports.

  

  Marjan

  authored and

  Marjan

  committed
  6009882

Commits on Jun 9, 2023

• Remove test particle charge.

  

  Marjan

  authored and

  Marjan

  committed
  4508dbb

• Refactoring base classes.

  

  Marjan

  authored and

  Marjan

  committed
  c64e011

Commits on Jun 13, 2023

• Organizing system class.

  

  Marjan

  authored and

  Marjan

  committed
  61e95f8

• Add Pack and Lattice to base system.

  

  Marjan

  authored and

  Marjan

  committed
  19f3919

• Organize imports.

  

  Marjan

  authored and

  Marjan

  committed
  a3f1fd6

• Delete repeated classes from system in library.

  

  Marjan

  authored and

  Marjan

  committed
  7790e8c

• Temporary run script.

  

  Marjan

  authored and

  Marjan

  committed
  546a3e7

Commits on Jun 16, 2023

• fix imports, _build_system func returns mb Compound, remove description attribute from molecules

  chrisjonesBSU

  committed
  9824002

• move attributes above super func in Pack and Lattice; add condition to handle list of Molecule classes passed to system

  chrisjonesBSU

  committed
  1bc3258

Commits on Jun 20, 2023

• update apply_forcefield and properties that return snapshot and hoomd force list

  chrisjonesBSU

  committed
  9b4f8c6

Commits on Jun 21, 2023

• Allow molecule to be loaded from smiles, file or mb Compound.

  

  Marjan

  authored and

  Marjan

  committed
  c7347f4

• add remove hydrogens method

  chrisjonesBSU

  committed
  59cea18

• Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polymers into mol-generator

  chrisjonesBSU

  committed
  c24a363

• add ref setters, move things around a bit

  chrisjonesBSU

  committed
  bd692d4

• Merge new changes, update molecule and ff_utils.

  

  Marjan

  authored and

  Marjan

  committed
  fff44c3

• Remove type hints.

  

  Marjan

  authored and

  Marjan

  committed
  615958d

• Check string type in check_return_iterable.

  

  Marjan

  authored and

  Marjan

  committed
  8c97a11

• Add assign_name func.

  

  Marjan

  authored and

  Marjan

  committed
  7456c71

• Handle different versions of molecules.

  

  Marjan

  authored and

  Marjan

  committed
  fd37120

• Fix bug.

  

  Marjan

  authored and

  Marjan

  committed
  df071f0

Commits on Jun 22, 2023

• Collect ff from input.

  marjanalbooyeh

  committed
  f424742

• Apply gmso ff.

  marjanalbooyeh

  committed
  dc69bd3

• Convert xml to gmso ff.

  marjanalbooyeh

  committed
  2f0b404

• Complete init method.

  

  Marjan

  authored and

  Marjan

  committed
  235d087

• Move Simulation class to base.

  

  Marjan

  authored and

  Marjan

  committed
  797710d

• Add units to reference values in system.

  

  Marjan

  authored and

  Marjan

  committed
  717f33d

• add unit error exceptions.

  

  Marjan

  authored and

  Marjan

  committed
  dfbcf26

• organize imports.

  

  Marjan

  authored and

  Marjan

  committed
  6fb0338

• add units to simulations reference values.

  

  Marjan

  authored and

  Marjan

  committed
  a238e38

Commits on Jun 23, 2023

• fix import, fix param names in polymers.py, move name += 1 line below FF dict addition

  chrisjonesBSU

  committed
  a457842

Commits on Jun 26, 2023

• add oplsaa.xml file

  chrisjonesBSU

  committed
  853bb11

Commits on Jun 27, 2023

• define a couple parameters in gmso.apply

  chrisjonesBSU

  committed
  ce747b0

Commits on Jul 6, 2023

• some small formatting fixes

  chrisjonesBSU

  committed
  0137c9e

• simplify things; set init params for remove_hydrogens, remove_charges, scale_chargers; do all of these in _apply_forcefield

  chrisjonesBSU

  committed
  c9f9f2d

Commits on Jul 9, 2023

• rerun toplogy stuff after coarse-graining. Remove hydrogen related attrs

  chrisjonesBSU

  committed
  4287c83

• Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polymers into mol-generator

  chrisjonesBSU

  committed
  1ce25ec

Commits on Jul 10, 2023

• add remove charges logic

  chrisjonesBSU

  committed
  d40dc11

Commits on Jul 11, 2023

• Adding predefined FF classes.

  marjanalb

  committed
  0e1e936

• Forcefield exception.

  marjanalb

  committed
  fbd9b1d

• Allow system to use gmso ff from provided forcefields.

  marjanalb

  committed
  0bbb620

Commits on Jul 31, 2023

• Add forcefield class.

  marjanalb

  committed
  59c865c

Commits on Aug 1, 2023

• Add base molecule tests.

  marjanalbooyeh

  committed
  29f71bc

• Fix num_mols.

  marjanalbooyeh

  committed
  0139f0f

• Add new fixtures to base_test.

  marjanalbooyeh

  committed
  8355589

• Update MissingPotentialError msg.

  marjanalbooyeh

  committed
  c31c4dc

• Check required potentials.

  marjanalbooyeh

  committed
  829a23e

• Add n_particles and n_bonds properties.

  marjanalbooyeh

  committed
  d8fc8b1

• Add some tests for polymer class.

  marjanalbooyeh

  committed
  3ab78f0

Commits on Aug 3, 2023

• Check equal lengths and num mols Polymer and Copolymer class.

  marjanalbooyeh

  committed
  bd0eb20

• Add Polymer and Copolymer unit tests.

  marjanalbooyeh

  committed
  a9adcb0

Commits on Aug 4, 2023

• Remove unused variables.

  marjanalbooyeh

  committed
  773509a

• Check site.element is not None.

  marjanalbooyeh

  committed
  438dc2a

• Remove mapping from coarse grain method.

  marjanalbooyeh

  committed
  03c9d17

• Add coarse grain tests.

  marjanalbooyeh

  committed
  7ab43e7

• Add new smiles.

  marjanalbooyeh

  committed
  0a3a3f5

• Move molecule and ff xmls to assests.

  marjanalbooyeh

  committed
  9cb3b9a

• Fix formatting, remove type hints.

  marjanalbooyeh

  committed
  ce39bb1

• Add system unit tests.

  marjanalbooyeh

  committed
  0df05b0

• fix inheritence in LJChain class

  chrisjonesBSU

  committed
  d4a5dd6

• fix conflict

  chrisjonesBSU

  committed
  570b96e

Commits on Aug 5, 2023

• rename ff stuff for use on fry

  chrisjonesBSU

  committed
  1d01e72

• Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polymers into mol-generator

  chrisjonesBSU

  committed
  381f4de

Commits on Aug 7, 2023

• add if statement before calling apply in gmso

  chrisjonesBSU

  committed
  86354e0

• restructure files and dirs per convo with Marjan

  chrisjonesBSU

  committed
  15f39ba

• Add new ff files.

  marjanalbooyeh

  committed
  71e3771

• update atom type names.

  marjanalbooyeh

  committed
  11bb7c8

• add two new molecule classes.

  marjanalbooyeh

  committed
  e8ef3c3

• update molecule unit tests.

  marjanalbooyeh

  committed
  1641c33

• add more system unit tests.

  marjanalbooyeh

  committed
  55af48d

Commits on Aug 8, 2023

• update polymer fixtures.

  marjanalbooyeh

  committed
  af8635d

• update n_particles and mass in system.

  marjanalbooyeh

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  9d7b742

• update fixtures.

  marjanalbooyeh

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  b13e731

• add more unit tests for system.

  marjanalbooyeh

  committed
  a09492f

• fix lattice bugs.

  marjanalbooyeh

  committed
  36ec9d5

• add lattice unit tests.

  marjanalbooyeh

  committed
  951d40a

Commits on Aug 9, 2023

• fix env files

  chrisjonesBSU

  committed
  e0f3a1b

• clone mbuild comp in _load and fix _generate.

  marjanalbooyeh

  committed
  e6a8fc2

• lattice unite tests.

  marjanalbooyeh

  committed
  f1e029d

• format code and sort imports.

  marjanalbooyeh

  committed
  c26e494

• use get for reduced values.

  marjanalbooyeh

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  60e6be1

• add simulation tests.

  marjanalbooyeh

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  0c363f9

• add system fixtures.

  marjanalbooyeh

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  112c0f1

• use unit tests for ref values.

  marjanalbooyeh

  committed
  46e3004

• fix ref values type.

  marjanalbooyeh

  committed
  a8b2736

• change base_units default type to dict.

  marjanalbooyeh

  committed
  5f8d900

• remove if condition from hoomd ff and snapshot.

  marjanalbooyeh

  committed
  eb30e17

• add missing return for mass.

  marjanalbooyeh

  committed
  21dbffc

• add unit test with updated ref values.

  marjanalbooyeh

  committed
  21a340a

• add simulation unit test.

  marjanalbooyeh

  committed
  9b8fe8e

• compare updated snapshot epsilon and gmso epsilon.

  marjanalbooyeh

  committed
  f027542

Commits on Aug 10, 2023

• set reference values when auto_scale=False.

  marjanalbooyeh

  committed
  50ded54

• fix test names and parameters.

  marjanalbooyeh

  committed
  72c51fa

• remove extra test files.

  marjanalbooyeh

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  4f02a08

• change fixture system.

  marjanalbooyeh

  committed
  0f8df64

• add simulation unit tests.

  marjanalbooyeh

  committed
  de857b0

Commits on Aug 17, 2023

• organize files.

  marjanalbooyeh

  committed
  446bb23

• sort imports.

  marjanalbooyeh

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  2d1e466

• Polymers unit tests.

  marjanalbooyeh

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  034ac2a

• remove extra files.

  marjanalbooyeh

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  4c58454

• sort test imports.

  marjanalbooyeh

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  e8e27d9

• add unit tests for forcefields in library.

  marjanalbooyeh

  committed
  3ad9f8e

Commits on Aug 18, 2023

• arrange test files.

  marjanalbooyeh

  committed
  2ee293f

• fix formatting.

  marjanalbooyeh

  committed
  a78a7be

• unit tests for weld and tensile.

  marjanalbooyeh

  committed
  090504f

• code formatting and style.

  marjanalbooyeh

  committed
  e7c02a6

• run pre-commit.

  marjanalbooyeh

  committed
  b6ece0b

• create first tutorial.

  marjanalbooyeh

  committed
  a14b22f

Commits on Aug 21, 2023

• pin to latest hoomd v3

  chrisjonesBSU

  committed
  2e8a573

• add test to run weld sim

  chrisjonesBSU

  committed
  220475a

Commits on Aug 22, 2023

• move apply forcefield if condition.

  marjanalbooyeh

  committed
  de3358b

• fill test_ff.xml

  marjanalbooyeh

  committed
  63f0ec7

• change title style.

  marjanalbooyeh

  committed
  db47b4a

• Merge pull request #8 from marjanAlbouye/mol-generator

  Show description for ba82d6a
  marjanalbooyeh

  authored
  ba82d6a

• fix reference valu units for mass

  chrisjonesBSU

  committed
  45cb464

• install gmso from source in env files

  chrisjonesBSU

  committed
  0f6cc50

• precommit fix

  chrisjonesBSU

  committed
  5b82ae4

• add more content to base tutorial.

  marjanalbooyeh

  committed
  2d11a04

• add unit tests for BeadSpring class

  chrisjonesBSU

  committed
  4699fb3

• Merge branch 'refactor' of github.com:chrisjonesBSU/hoomd-polymers into refactor

  chrisjonesBSU

  committed
  a2ac9f5

• update codecov yml ignore paths

  chrisjonesBSU

  committed
  fac616c

Commits on Aug 23, 2023

• change gmso param to False for now

  chrisjonesBSU

  committed
  35c41df