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Mesh dynamic bonding #2093

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Mesh dynamic bonding #2093

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SchoeniPhlippsn
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Description

Adds a mesh dynamical bonding updater that allows flipping edges within a mesh.

Motivation and context

This addition allows modelling fluidized membranes.

How has this been tested?

added pytests

Checklist:

  • I have reviewed the Contributor Guidelines.
  • I agree with the terms of the HOOMD-blue Contributor Agreement.
  • My name is on the list of contributors (sphinx-doc/credits.rst) in the pull request source branch.
  • I have summarized these changes in CHANGELOG.rst following the established format.

SchoeniPhlippsn added 30 commits March 10, 2025 16:23
update MeshBonds
246f27e
remove group_size_half
d5304be
creat neighbor lists
306cb3f
first backbone of MeshUpdater
c5be9bd
update parts of the mesh updater
f6968b1
conseptualize edge flip
e2c90bb
first version of MeshUpdater
5da031a
creat MeshForceCompute class
0fbaf1c
reverse MeshForceCmpute
ac7defb
rename precomputeParameters
855b9cb
add precomputeParameter to ForceCompute
8b062cb
add all necesarry functions to Helfrich
80883ac
prepare TriangleArea
fc1fb5b
prepare AreaConservationMeshForceCompute
b086575
update ForceCompute
85d2e83
update BendingRigidity
fbdebfd
compiling version
d8b3488
write python updater object
5a13772
working Updater without forces list
0edc574
working with force though integrator
8028ce4
add reorder group
ac36c12
no write out
51f616f
fix dublicating edges when fliping
55df2db
working mesh dynamic updater with write out
b50b713
fix another bug in mesh updater with write outs
ed7b4c1
remove writers
60901ba
force list in Meshupdater works
5410ab2
random order
79030a5
allow to attach mesh forces to intefrator and meshupdater
b332b14
only one time in list for all syced lists except for mesh updater
a23c727
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This pull request has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

@github-actions github-actions bot added the stale There has been no activity on this for some time. label Aug 10, 2025
@joaander joaander removed the stale There has been no activity on this for some time. label Aug 11, 2025
joaander
joaander reviewed Aug 11, 2025
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@joaander joaander left a comment

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Sorry for the delay. I have some questions about some of the changes and some suggestions for improvement.

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@joaander joaander Awaiting requested review from joaander

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2 participants
@SchoeniPhlippsn @joaander