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Cassandra gmso #756

Merged
merged 52 commits into from
Sep 22, 2023
Merged

Cassandra gmso #756

merged 52 commits into from
Sep 22, 2023

Commits on Aug 11, 2023

  1. Add fixed length bonds and angles to potential templates library.

    @rsdefever @emarinri
    rsdefever authored and emarinri committed Aug 11, 2023
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  2. Working to make MCF writer feature complete. Tests in progress. 

    * Add fixed angle support
* Fix charge sign error (gmso-wide)
* Update ring identification to handle fused systems (mbuild mosdef-hub#744)
* Increase floating point accuracy
* Increase element type length and atom type length
* Correctly write atom indices for bonds/angles/dihedrals/impropers
    @rsdefever @emarinri
    rsdefever authored and emarinri committed Aug 11, 2023
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci @emarinri
    pre-commit-ci[bot] authored and emarinri committed Aug 11, 2023
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  4. Add dimensions to Fixed Bond and Angle templates

    @emarinri
    emarinri committed Aug 11, 2023
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  5. Update keys in OPLS dihedral parameters dict 

    * Modify dihedral constant indexing from k0 to k3
to k1 to k4 in the OPLSTorsionPotential template.
    @emarinri
    emarinri committed Aug 11, 2023
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  6. Fix typed OPLS ethane test for MCF format 

    * Updated from old Mie Xenon test to OPLS ethane.
* Remove assertions related to n and m parameters of the Mie potential.
* Fix floating point format issues in MCF writer.
    @emarinri
    emarinri committed Aug 11, 2023
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  7. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 11, 2023
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Commits on Aug 13, 2023

  1. Add typed ethane test. 

    This test is not complete yet. The 1/2 factor
in the angles and OPLS dihedral is not
accounted for.
    @emarinri
    emarinri committed Aug 13, 2023
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  2. Fix code style

    @emarinri
    emarinri committed Aug 13, 2023
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  3. Add fixture to parse mcf into sections

    @emarinri
    emarinri committed Aug 13, 2023
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  4. Support Pydantic v1 and v2 (mosdef-hub#752) 

    Co-authored-by: Co Quach <[email protected]>
    @mattwthompson @daico007 @emarinri
    2 people authored and emarinri committed Aug 13, 2023
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Commits on Aug 15, 2023

  1. Update MCF with GMSO builtin top site sorting

    @emarinri
    emarinri committed Aug 15, 2023
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  2. Use PotentialFilters to check for unique atomtypes

    @emarinri
    emarinri committed Aug 15, 2023
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  3. Add test to check charge neutrality

    @emarinri
    emarinri committed Aug 15, 2023
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  4. Add test for incompatible expressions

    @emarinri
    emarinri committed Aug 15, 2023
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Commits on Aug 16, 2023

  1. Test full MCF for Mie-Xe and LJ-Ar

    @emarinri
    emarinri committed Aug 16, 2023
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  2. Check charge neutrality in each molecule test

    @emarinri
    emarinri committed Aug 16, 2023
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  3. Add exception for not neutral system in MCF writer

    @emarinri
    emarinri committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Move parsing and neutrality check as utils

    @emarinri
    emarinri committed Aug 17, 2023
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Commits on Sep 2, 2023

  1. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 2, 2023
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Commits on Sep 6, 2023

  1. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 6, 2023
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Commits on Sep 11, 2023

  1. minor docstring/comment fixes, swap out simplify with symengine expand

    @daico007
    daico007 committed Sep 11, 2023
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  2. Merge branch 'main' of https://github.com/mosdef-hub/gmso into cassan… 

    …dra-gmso
    @daico007
    daico007 committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. [pre-commit.ci] pre-commit autoupdate (mosdef-hub#763) 

    updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](psf/black@23.7.0...23.9.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    @pre-commit-ci @emarinri
    pre-commit-ci[bot] authored and emarinri committed Sep 12, 2023
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  2. Test for 0.5 factor of OPLS dihedral potential

    @emarinri
    emarinri committed Sep 12, 2023
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  3. Test to account for 0.5 factor in harmonic angles

    @emarinri
    emarinri committed Sep 12, 2023
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  4. Test for rigid angles using the TIP3P model

    @emarinri
    emarinri committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. MCF writer test with topology with 10 argon mols

    @emarinri
    emarinri committed Sep 13, 2023
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  2. Tentative output of multiple MCF from one Topology

    @emarinri
    emarinri committed Sep 13, 2023
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  3. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 13, 2023
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Commits on Sep 14, 2023

  1. Change psi to phi and consts for ethylene xml test

    @emarinri
    emarinri committed Sep 14, 2023
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  2. Test for 0.5 factor in OPLS dihedrals

    @emarinri
    emarinri committed Sep 14, 2023
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Commits on Sep 18, 2023

  1. Add cassandra test for gmso

    @CalCraven
    CalCraven committed Sep 18, 2023
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  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. Add test for two atom fragment

    @emarinri
    emarinri committed Sep 19, 2023
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  2. Test for molecule with one ring

    @emarinri
    emarinri committed Sep 19, 2023
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  3. Change nitrogen test to ethane ua

    @emarinri
    emarinri committed Sep 19, 2023
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  4. Add ethane rigid reference xml

    @emarinri
    emarinri committed Sep 19, 2023
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  5. Use Fourier dihedrals as MCF standard dihedrals.

    @emarinri
    emarinri committed Sep 19, 2023
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  6. Fix dihedral type output fourier to opls

    @emarinri
    emarinri committed Sep 19, 2023
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Commits on Sep 20, 2023

  1. Match MCF GMSO Angle header to mb Angle header

    @emarinri
    emarinri committed Sep 20, 2023
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  2. Add a test comparing gmso and mbuild mcf writers

    @emarinri
    emarinri committed Sep 20, 2023
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  3. Use the Fourier converter for ethylene dihedrals

    @emarinri
    emarinri committed Sep 20, 2023
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  4. Write atom type masses instead of atom masses to account for UA beads

    @emarinri
    emarinri committed Sep 20, 2023
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  5. Output correct case for dihedral styles in MCFs

    @emarinri
    emarinri committed Sep 20, 2023
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  6. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 20, 2023
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  7. Merge branch 'cassandra-gmso' of https://github.com/emarinri/gmso int… 

    …o cassandra-gmso
    @emarinri
    emarinri committed Sep 20, 2023
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  8. Run an energy calculation to compare GMSO and mBuild MCF writers

    @emarinri
    emarinri committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 21, 2023
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  2. Update gmso/tests/test_mcf.py

    @daico007
    daico007 authored Sep 21, 2023
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  3. Update gmso/tests/test_mcf.py

    @daico007
    daico007 authored Sep 21, 2023
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Commits on Sep 22, 2023

  1. Merge branch 'main' into cassandra-gmso

    @daico007
    daico007 authored Sep 22, 2023
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