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Add support for writing rigid bodies when converting to HOOMD formats. #850

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Add support for writing rigid bodies when converting to HOOMD formats. #850

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Commits on Sep 17, 2024

  1. add rigid_body field to atom, populate in from_mbuild

    @chrisjonesBSU
    chrisjonesBSU committed Sep 17, 2024
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  2. move rigid_id property to abstract_site from atom, write out rigid_id… 

    … in to_mbuild
    @chrisjonesBSU
    chrisjonesBSU committed Sep 17, 2024
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  3. add rigid types and typeids

    @chrisjonesBSU
    chrisjonesBSU committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. Merge branch 'fix/molecule' into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU committed Sep 18, 2024
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  2. add test for rigid_id assignment

    @chrisjonesBSU
    chrisjonesBSU committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/gmso into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU committed Sep 19, 2024
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Commits on Sep 23, 2024

  1. write out rigid xyz, com, tags

    @chrisjonesBSU
    chrisjonesBSU committed Sep 23, 2024
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  2. add if statement before writing rigid tags

    @chrisjonesBSU
    chrisjonesBSU committed Sep 23, 2024
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  3. add basic rigid body snapshot test

    @chrisjonesBSU
    chrisjonesBSU committed Sep 23, 2024
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  4. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
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    pre-commit-ci[bot] committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. Merge branch 'main' of github.com:mosdef-hub/gmso into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU committed Sep 24, 2024
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Commits on Sep 25, 2024

  1. remove rigid id from convert mbuild, remove rigid id prop from abstra… 

    …ct site
    @chrisjonesBSU
    chrisjonesBSU committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. parse rigid sites from site.molecule, update test

    @chrisjonesBSU
    chrisjonesBSU committed Sep 26, 2024
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Commits on Sep 30, 2024

  1. remove un-needed var

    @chrisjonesBSU
    chrisjonesBSU committed Sep 30, 2024
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Commits on Oct 14, 2024

  1. Merge branch 'main' into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU authored Oct 14, 2024
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Commits on Oct 16, 2024

  1. update tests

    @chrisjonesBSU
    chrisjonesBSU committed Oct 16, 2024
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  2. Merge branch 'main' of github.com:mosdef-hub/gmso into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU committed Oct 16, 2024
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Commits on Oct 17, 2024

  1. fix charge array in np.concatenate call

    @chrisjonesBSU
    chrisjonesBSU committed Oct 17, 2024
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  2. adjust snapshot groups by num rigid bodies

    @chrisjonesBSU
    chrisjonesBSU committed Oct 17, 2024
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  3. update tests

    @chrisjonesBSU
    chrisjonesBSU committed Oct 17, 2024
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  4. fix _parse_pairs

    @chrisjonesBSU
    chrisjonesBSU committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. use unyt_arrays for charges and mass instead of lists

    @chrisjonesBSU
    chrisjonesBSU committed Oct 18, 2024
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Commits on Oct 22, 2024

  1. Merge branch 'main' into rigid-bodies

    @chrisjonesBSU
    chrisjonesBSU authored Oct 22, 2024
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Commits on Oct 30, 2024

  1. handle mix of rigid and non rigid

    @chrisjonesBSU
    chrisjonesBSU committed Oct 30, 2024
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  2. remove if statement to filter -1 ids

    @chrisjonesBSU
    chrisjonesBSU committed Oct 30, 2024
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