gromacs+gsd/hoomd readers, general dist function, issues fixed#70

Merged

hechtprojects merged 51 commits intodevelopfrom gromacs_reader

Nov 13, 2024

+1,397-33

Commits on Aug 16, 2024

Commits on Aug 19, 2024

WIP: added quaternion orientations and started quaternion angmoms
Kay-Robert Dormann
committed
WIP: added diameter, mass, charge, body, moment of inertia
Kay-Robert Dormann
committed
WIP: some changes
Kay-Robert Dormann
committed
gsd reader first working version
Kay-Robert Dormann
committed

Commits on Aug 20, 2024

WIP: gsd reader angmoms implemented - check angmom from quaternion!!
Kay-Robert Dormann
committed
fixed angmom dataset not created (done in other branch)
Kay-Robert Dormann
committed

Commits on Sep 9, 2024

angmom and omega = 0
Kay-Robert Dormann
committed

Commits on Oct 9, 2024

WIP: gromacs chemfiles - chemfiles very slow!
Kay-Robert Dormann
committed
WIP: GSD reader basic features working (no angmom!)
Kay-Robert Dormann
committed

Commits on Oct 11, 2024

WIP: fixed naming issue
Kay-Robert Dormann
committed
WIP: added quaternion operations
Kay-Robert Dormann
committed
WIP: angular momentum and angular velocity in principal frame
Kay-Robert Dormann
committed

Commits on Oct 17, 2024

WIP: fixed orientation hoomd
Kay-Robert Dormann
committed
WIP: fixed average_func times
Kay-Robert Dormann
committed
WIP: removed thetas from quaternions
Kay-Robert Dormann
committed
WIP: made GROMACS molecule identification orders of magnitude faster
Kay-Robert Dormann
committed
fixes #60
Kay-Robert Dormann
committed
WIP: fixing the ClusterGrowth mode="largest" issue
Kay-Robert Dormann
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fixes #59
Kay-Robert Dormann
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fixes #58
Kay-Robert Dormann
committed

Commits on Oct 18, 2024

reordered folding and shifting coordinates. fixes #65
Kay-Robert Dormann
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this branch fixes #37 and #47
Kay-Robert Dormann
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added example data for gromacs
Kay-Robert Dormann
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added example for hoomd/gsd and gromacs
Kay-Robert Dormann
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added frame.data(list). fixes #35
Kay-Robert Dormann
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fixed #68
Kay-Robert Dormann
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fixed small issue with returned list in frame.data()
Kay-Robert Dormann
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implemented general distribution function. fixes #57
Kay-Robert Dormann
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added example with image to evaluate.Dist
Kay-Robert Dormann
committed
renamed gsdreader to hoomdreader
Kay-Robert Dormann
committed
WIP: added tests
Kay-Robert Dormann
committed
WIP: fixed pbc.kdtree() box boundary.
Kay-Robert Dormann
committed

Commits on Oct 21, 2024

tests updated
Kay-Robert Dormann
committed
fixed rotation for omegas
Kay-Robert Dormann
committed
example to general distribution function added
Kay-Robert Dormann
committed
added chemfiles dependency
Kay-Robert Dormann
committed
restored tests
Kay-Robert Dormann
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fixed tests
Kay-Robert Dormann
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GROMACSDIR added to tests
Kay-Robert Dormann
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reduced plot test duration
Kay-Robert Dormann
committed

Commits on Oct 22, 2024

Merge pull request #75 from amepproject/release-1.0.x
hechtprojects
authored

Commits on Oct 23, 2024

fixed angmom in hoomdreader
Kay-Robert Dormann
committed
specified warning in traj.load
Kay-Robert Dormann
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minor cleanup
Kay-Robert Dormann
committed

Commits on Nov 5, 2024

Added the radius keyword to the frames in the hoomd dataset. Maybe we should only keep either radii or diameters.
kai-luca
committed

Commits on Nov 8, 2024

removed diameter from hoomdreader, using radius instead.
Kay-Robert Dormann
committed

Commits on Nov 13, 2024

Merge branch 'main' into gromacs_reader
kay-ro
authored