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Refactor #10

Merged
merged 182 commits into from
Aug 24, 2023
Merged

Refactor #10

merged 182 commits into from
Aug 24, 2023

Commits on Apr 20, 2023

  1. add bead spring forcefield class

    @chrisjonesBSU
    chrisjonesBSU committed Apr 20, 2023
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Commits on Apr 21, 2023

  1. move forces into method

    @chrisjonesBSU
    chrisjonesBSU committed Apr 21, 2023
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  2. Merge branch 'cg/sims' into add/mol_generator

    @chrisjonesBSU
    chrisjonesBSU committed Apr 21, 2023
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  3. add build and generate methods to molecule class

    @chrisjonesBSU
    chrisjonesBSU committed Apr 21, 2023
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  4. add to_snapshot func

    @chrisjonesBSU
    chrisjonesBSU committed Apr 21, 2023
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Commits on Apr 22, 2023

  1. fix to_hoomd_snapshot

    @chrisjonesBSU
    chrisjonesBSU committed Apr 22, 2023
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Commits on Apr 24, 2023

  1. Convert all classes to new structure

    @chrisjonesBSU
    chrisjonesBSU committed Apr 24, 2023
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  2. trying out new class structure

    @chrisjonesBSU
    chrisjonesBSU committed Apr 24, 2023
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Commits on Apr 25, 2023

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

    …e molecule classes instead of system class
    @chrisjonesBSU
    chrisjonesBSU committed Apr 25, 2023
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  2. moving specific classes over to library

    @chrisjonesBSU
    chrisjonesBSU committed Apr 25, 2023
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Commits on Apr 26, 2023

  1. finish CoPolymer class, move polymers.py to library

    @chrisjonesBSU
    chrisjonesBSU committed Apr 26, 2023
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  2. fix length in CoPolymer class

    @chrisjonesBSU
    chrisjonesBSU committed Apr 26, 2023
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  3. fix pekk_meta class, remove print statements

    @chrisjonesBSU
    chrisjonesBSU committed Apr 26, 2023
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Commits on Apr 28, 2023

  1. move things around a bit

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2023
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  2. fix imports with new structure of repo

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2023
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  3. import system classes

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2023
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  4. add gmso to env files

    @chrisjonesBSU
    chrisjonesBSU committed Apr 28, 2023
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Commits on May 2, 2023

  1. Update base classes.

    Marjan authored and Marjan committed May 2, 2023
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Commits on May 4, 2023

  1. Add a sample run script.

    Marjan authored and Marjan committed May 4, 2023
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  2. Fix cirucular dependency.

    Marjan authored and Marjan committed May 4, 2023
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Commits on May 8, 2023

  1. Identify bonded and non-bonded interactions.

    Marjan authored and Marjan committed May 8, 2023
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  2. Update forcefield validation.

    Marjan authored and Marjan committed May 8, 2023
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Commits on May 9, 2023

  1. Fix Molecule generate method.

    @marjanalbooyeh
    marjanalbooyeh committed May 9, 2023
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  2. add coarse grain method to Molecule class, update env files

    @chrisjonesBSU
    chrisjonesBSU committed May 9, 2023
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Commits on May 17, 2023

  1. Get topology information from first molecule.

    @marjanalbooyeh
    marjanalbooyeh committed May 17, 2023
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Commits on May 31, 2023

  1. install gmso from conda forge now that changes are merged, remove noh… 

    …oomd env file
    @chrisjonesBSU
    chrisjonesBSU committed May 31, 2023
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  2. change atom_type to atom_type.name when populating topology info

    @chrisjonesBSU
    chrisjonesBSU committed May 31, 2023
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  3. import System from base.py; add atom type fix to impropers

    @chrisjonesBSU
    chrisjonesBSU committed May 31, 2023
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  4. remove old forcefield, molecule and system py files

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    chrisjonesBSU committed May 31, 2023
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Commits on Jun 1, 2023

  1. changes to fix CoPolymer class

    @chrisjonesBSU
    chrisjonesBSU committed Jun 1, 2023
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  2. Add comment for getting topology info after applying ff.

    @marjanalbooyeh
    marjanalbooyeh committed Jun 1, 2023
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  3. Update atom_type name in topology information.

    @marjanalbooyeh
    marjanalbooyeh committed Jun 1, 2023
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Commits on Jun 2, 2023

  1. Merge branch 'main' of github.com:chrisjonesBSU/hoomd-polymers into m… 

    …ol-generator
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    chrisjonesBSU committed Jun 2, 2023
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  2. add PEKK to polymer library

    @chrisjonesBSU
    chrisjonesBSU committed Jun 2, 2023
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  3. add force_field param to CoPolymer

    @chrisjonesBSU
    chrisjonesBSU committed Jun 2, 2023
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Commits on Jun 6, 2023

  1. organize project directories.

    Marjan authored and Marjan committed Jun 6, 2023
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  2. Add exceptions classes.

    Marjan authored and Marjan committed Jun 6, 2023
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  3. Add __init__ files.

    Marjan authored and Marjan committed Jun 6, 2023
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  4. Update validate_hoomd_ff.

    Marjan authored and Marjan committed Jun 6, 2023
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  5. Fix bugs in system class.

    Marjan authored and Marjan committed Jun 6, 2023
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  6. Add remove_hydrogens arg to validate_hoomd_ff method.

    Marjan authored and Marjan committed Jun 6, 2023
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  7. Rename forcefield utils file.

    Marjan authored and Marjan committed Jun 6, 2023
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  8. Handle remove_hydrogen=True case.

    Marjan authored and Marjan committed Jun 6, 2023
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  9. Convert particles set to list.

    Marjan authored and Marjan committed Jun 6, 2023
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Commits on Jun 7, 2023

  1. Remove bond direction from topology information.

    Marjan authored and Marjan committed Jun 7, 2023
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  2. Add missing bond potential exception.

    Marjan authored and Marjan committed Jun 7, 2023
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  3. Validate hoomd bond potentials.

    Marjan authored and Marjan committed Jun 7, 2023
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  4. Add a method to identify h in connections.

    Marjan authored and Marjan committed Jun 7, 2023
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  5. Avoid having repetetive angles.

    Marjan authored and Marjan committed Jun 7, 2023
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  6. Add missing angle potential exception.

    Marjan authored and Marjan committed Jun 7, 2023
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  7. Validate hoomd angle potentials.

    Marjan authored and Marjan committed Jun 7, 2023
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  8. Avoid adding repeated dihedral in topology information.

    Marjan authored and Marjan committed Jun 7, 2023
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  9. Refactor exception classes.

    Marjan authored and Marjan committed Jun 7, 2023
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  10. Validate hoomd dihedral potentials.

    Marjan authored and Marjan committed Jun 7, 2023
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  11. Refactor molecule class.

    Marjan authored and Marjan committed Jun 7, 2023
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  12. Add missing coulomb force exception.

    Marjan authored and Marjan committed Jun 7, 2023
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  13. Validate hoomd Coulombic forces.

    Marjan authored and Marjan committed Jun 7, 2023
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Commits on Jun 8, 2023

  1. Sort imports.

    Marjan authored and Marjan committed Jun 8, 2023
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  2. Accept different types for molecules and forcefield.

    Marjan authored and Marjan committed Jun 8, 2023
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  3. Updated abstractmethods for system.

    Marjan authored and Marjan committed Jun 8, 2023
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  4. sort imports.

    Marjan authored and Marjan committed Jun 8, 2023
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Commits on Jun 9, 2023

  1. Remove test particle charge.

    Marjan authored and Marjan committed Jun 9, 2023
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  2. Refactoring base classes.

    Marjan authored and Marjan committed Jun 9, 2023
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Commits on Jun 13, 2023

  1. Organizing system class.

    Marjan authored and Marjan committed Jun 13, 2023
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  2. Add Pack and Lattice to base system.

    Marjan authored and Marjan committed Jun 13, 2023
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  3. Organize imports.

    Marjan authored and Marjan committed Jun 13, 2023
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  4. Delete repeated classes from system in library.

    Marjan authored and Marjan committed Jun 13, 2023
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  5. Temporary run script.

    Marjan authored and Marjan committed Jun 13, 2023
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Commits on Jun 16, 2023

  1. fix imports, _build_system func returns mb Compound, remove descripti… 

    …on attribute from molecules
    @chrisjonesBSU
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  2. move attributes above super func in Pack and Lattice; add condition t… 

    …o handle list of Molecule classes passed to system
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    chrisjonesBSU committed Jun 16, 2023
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Commits on Jun 20, 2023

  1. update apply_forcefield and properties that return snapshot and hoomd… 

    … force list
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    chrisjonesBSU committed Jun 20, 2023
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Commits on Jun 21, 2023

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

    Marjan authored and Marjan committed Jun 21, 2023
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  2. add remove hydrogens method

    @chrisjonesBSU
    chrisjonesBSU committed Jun 21, 2023
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  3. Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polyme… 

    …rs into mol-generator
    @chrisjonesBSU
    chrisjonesBSU committed Jun 21, 2023
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  4. add ref setters, move things around a bit

    @chrisjonesBSU
    chrisjonesBSU committed Jun 21, 2023
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  5. Merge new changes, update molecule and ff_utils.

    Marjan authored and Marjan committed Jun 21, 2023
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  6. Remove type hints.

    Marjan authored and Marjan committed Jun 21, 2023
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  7. Check string type in check_return_iterable.

    Marjan authored and Marjan committed Jun 21, 2023
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  8. Add assign_name func.

    Marjan authored and Marjan committed Jun 21, 2023
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  9. Handle different versions of molecules.

    Marjan authored and Marjan committed Jun 21, 2023
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  10. Fix bug.

    Marjan authored and Marjan committed Jun 21, 2023
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Commits on Jun 22, 2023

  1. Collect ff from input.

    @marjanalbooyeh
    marjanalbooyeh committed Jun 22, 2023
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  2. Apply gmso ff.

    @marjanalbooyeh
    marjanalbooyeh committed Jun 22, 2023
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  3. Convert xml to gmso ff.

    @marjanalbooyeh
    marjanalbooyeh committed Jun 22, 2023
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  4. Complete init method.

    Marjan authored and Marjan committed Jun 22, 2023
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  5. Move Simulation class to base.

    Marjan authored and Marjan committed Jun 22, 2023
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  6. Add units to reference values in system.

    Marjan authored and Marjan committed Jun 22, 2023
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  7. add unit error exceptions.

    Marjan authored and Marjan committed Jun 22, 2023
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  8. organize imports.

    Marjan authored and Marjan committed Jun 22, 2023
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  9. add units to simulations reference values.

    Marjan authored and Marjan committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. fix import, fix param names in polymers.py, move name += 1 line below… 

    … FF dict addition
    @chrisjonesBSU
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Commits on Jun 26, 2023

  1. add oplsaa.xml file

    @chrisjonesBSU
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Commits on Jun 27, 2023

  1. define a couple parameters in gmso.apply

    @chrisjonesBSU
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Commits on Jul 6, 2023

  1. some small formatting fixes

    @chrisjonesBSU
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  2. simplify things; set init params for remove_hydrogens, remove_charges… 

    …, scale_chargers; do all of these in _apply_forcefield
    @chrisjonesBSU
    chrisjonesBSU committed Jul 6, 2023
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Commits on Jul 9, 2023

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

    @chrisjonesBSU
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  2. Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polyme… 

    …rs into mol-generator
    @chrisjonesBSU
    chrisjonesBSU committed Jul 9, 2023
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Commits on Jul 10, 2023

  1. add remove charges logic

    @chrisjonesBSU
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Commits on Jul 11, 2023

  1. Adding predefined FF classes.

    @marjanalb
    marjanalb committed Jul 11, 2023
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  2. Forcefield exception.

    @marjanalb
    marjanalb committed Jul 11, 2023
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  3. Allow system to use gmso ff from provided forcefields.

    @marjanalb
    marjanalb committed Jul 11, 2023
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Commits on Jul 31, 2023

  1. Add forcefield class.

    @marjanalb
    marjanalb committed Jul 31, 2023
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Commits on Aug 1, 2023

  1. Add base molecule tests.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  2. Fix num_mols.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  3. Add new fixtures to base_test.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  4. Update MissingPotentialError msg.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  5. Check required potentials.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  6. Add n_particles and n_bonds properties.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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  7. Add some tests for polymer class.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 1, 2023
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Commits on Aug 3, 2023

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

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  2. Add Polymer and Copolymer unit tests.

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Commits on Aug 4, 2023

  1. Remove unused variables.

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    marjanalbooyeh committed Aug 4, 2023
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  2. Check site.element is not None.

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    marjanalbooyeh committed Aug 4, 2023
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  3. Remove mapping from coarse grain method.

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    marjanalbooyeh committed Aug 4, 2023
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  4. Add coarse grain tests.

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    marjanalbooyeh committed Aug 4, 2023
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  5. Add new smiles.

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    marjanalbooyeh committed Aug 4, 2023
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  6. Move molecule and ff xmls to assests.

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    marjanalbooyeh committed Aug 4, 2023
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  7. Fix formatting, remove type hints.

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    marjanalbooyeh committed Aug 4, 2023
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  8. Add system unit tests.

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    marjanalbooyeh committed Aug 4, 2023
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  9. fix inheritence in LJChain class

    @chrisjonesBSU
    chrisjonesBSU committed Aug 4, 2023
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  10. fix conflict

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    chrisjonesBSU committed Aug 4, 2023
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Commits on Aug 5, 2023

  1. rename ff stuff for use on fry

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  2. Merge branch 'mol-generator' of github.com:marjanAlbouye/hoomd-polyme… 

    …rs into mol-generator
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Commits on Aug 7, 2023

  1. add if statement before calling apply in gmso

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    chrisjonesBSU committed Aug 7, 2023
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  2. restructure files and dirs per convo with Marjan

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    chrisjonesBSU committed Aug 7, 2023
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  3. Add new ff files.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 7, 2023
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  4. update atom type names.

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    marjanalbooyeh committed Aug 7, 2023
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  5. add two new molecule classes.

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    marjanalbooyeh committed Aug 7, 2023
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  6. update molecule unit tests.

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    marjanalbooyeh committed Aug 7, 2023
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  7. add more system unit tests.

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Commits on Aug 8, 2023

  1. update polymer fixtures.

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    marjanalbooyeh committed Aug 8, 2023
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  2. update n_particles and mass in system.

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    marjanalbooyeh committed Aug 8, 2023
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  3. update fixtures.

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    marjanalbooyeh committed Aug 8, 2023
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  4. add more unit tests for system.

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    marjanalbooyeh committed Aug 8, 2023
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  5. fix lattice bugs.

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    marjanalbooyeh committed Aug 8, 2023
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  6. add lattice unit tests.

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    marjanalbooyeh committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. fix env files

    @chrisjonesBSU
    chrisjonesBSU committed Aug 9, 2023
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  2. clone mbuild comp in _load and fix _generate.

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    marjanalbooyeh committed Aug 9, 2023
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  3. lattice unite tests.

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    marjanalbooyeh committed Aug 9, 2023
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  4. format code and sort imports.

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    marjanalbooyeh committed Aug 9, 2023
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  5. use get for reduced values.

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    marjanalbooyeh committed Aug 9, 2023
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  6. add simulation tests.

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    marjanalbooyeh committed Aug 9, 2023
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  7. add system fixtures.

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    marjanalbooyeh committed Aug 9, 2023
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  8. use unit tests for ref values.

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    marjanalbooyeh committed Aug 9, 2023
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  9. fix ref values type.

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    marjanalbooyeh committed Aug 9, 2023
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  10. change base_units default type to dict.

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  11. remove if condition from hoomd ff and snapshot.

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    marjanalbooyeh committed Aug 9, 2023
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  12. add missing return for mass.

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    marjanalbooyeh committed Aug 9, 2023
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  13. add unit test with updated ref values.

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    marjanalbooyeh committed Aug 9, 2023
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  14. add simulation unit test.

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    marjanalbooyeh committed Aug 9, 2023
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  15. compare updated snapshot epsilon and gmso epsilon.

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    marjanalbooyeh committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. set reference values when auto_scale=False.

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    marjanalbooyeh committed Aug 10, 2023
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  2. fix test names and parameters.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 10, 2023
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  3. remove extra test files.

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    marjanalbooyeh committed Aug 10, 2023
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  4. change fixture system.

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    marjanalbooyeh committed Aug 10, 2023
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  5. add simulation unit tests.

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Commits on Aug 17, 2023

  1. organize files.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 17, 2023
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  2. sort imports.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 17, 2023
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  3. Polymers unit tests.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 17, 2023
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  4. remove extra files.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 17, 2023
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  5. sort test imports.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 17, 2023
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  6. add unit tests for forcefields in library.

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    marjanalbooyeh committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. arrange test files.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 18, 2023
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  2. fix formatting.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 18, 2023
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  3. unit tests for weld and tensile.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 18, 2023
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  4. code formatting and style.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 18, 2023
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  5. run pre-commit.

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    marjanalbooyeh committed Aug 18, 2023
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  6. create first tutorial.

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    marjanalbooyeh committed Aug 18, 2023
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Commits on Aug 21, 2023

  1. pin to latest hoomd v3

    @chrisjonesBSU
    chrisjonesBSU committed Aug 21, 2023
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  2. add test to run weld sim

    @chrisjonesBSU
    chrisjonesBSU committed Aug 21, 2023
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Commits on Aug 22, 2023

  1. move apply forcefield if condition.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 22, 2023
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  2. fill test_ff.xml

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    marjanalbooyeh committed Aug 22, 2023
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  3. change title style.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 22, 2023
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  4. Merge pull request #8 from marjanAlbouye/mol-generator 

    Refactoring hoomd polymers
    @marjanalbooyeh
    marjanalbooyeh authored Aug 22, 2023
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  5. fix reference valu units for mass

    @chrisjonesBSU
    chrisjonesBSU committed Aug 22, 2023
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  6. install gmso from source in env files

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    chrisjonesBSU committed Aug 22, 2023
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  7. precommit fix

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    chrisjonesBSU committed Aug 22, 2023
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  8. add more content to base tutorial.

    @marjanalbooyeh
    marjanalbooyeh committed Aug 22, 2023
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  9. add unit tests for BeadSpring class

    @chrisjonesBSU
    chrisjonesBSU committed Aug 22, 2023
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  10. Merge branch 'refactor' of github.com:chrisjonesBSU/hoomd-polymers in… 

    …to refactor
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    chrisjonesBSU committed Aug 22, 2023
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  11. update codecov yml ignore paths

    @chrisjonesBSU
    chrisjonesBSU committed Aug 22, 2023
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Commits on Aug 23, 2023

  1. change gmso param to False for now

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    chrisjonesBSU committed Aug 23, 2023
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