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Mesh area conservation #1795

Merged
merged 106 commits into from
Oct 23, 2024
Merged

Mesh area conservation #1795

merged 106 commits into from
Oct 23, 2024

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SchoeniPhlippsn
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Description

This adds two area constraint potentials which can be applied to the mesh data structure.

Motivation and context

These area constraints allow applying a global target area per mesh type or a local target area per mesh triangle to membranes represented by a particle mesh.

How has this been tested?

I added pytests and used this potential in my current studies.

Change log

Addition of area constraint mesh potentials

Checklist:

syjlee and others added 30 commits January 19, 2022 11:47
@syjlee
Added area conservation potential of mesh structure. pytest not start…
e743a53 
…ed yet
@syjlee
fix invalid second loop and keep only single loop which calculates bo…
63f24f6 
…th energy and forces by iterating triangles in mesh
@syjlee
add comments on the variable At which is A0 divided by Nt
6f7cec1
@syjlee
fixes missing lines to connect area conservation in python to cpp
6035adf
@syjlee
Merge branch 'mesh-data-structure' into mesh_area_conservation
b6ab04d 
mesh_area_conservation should be updated as its parent branch mesh-data-structure has updated
@syjlee
fixes len_key in area_conservation.py
f88f2c1
@syjlee
fixes mistakes in computeForces and add get method for area
febeca0
@syjlee
add three statepoints for area conservation in test_meshbond file of …
670858f 
…helfrich branch
@syjlee
implement GPU code
0b9a747
@syjlee
Merge branch 'mesh-data-structure' into mesh_area_conservation
0bedd84
@syjlee
fixes pytest values and remove unnecessary loop for getArea
4aea9cc
@syjlee
remove a space
e675003
@syjlee
temporarily removed m_area in GPU
4131ec1
simplify Area conservation
f9914bb
Clean up Area conservation GPU code
5362300
Merge branch 'mesh_area_conservation' of https://github.com/glotzerla…
dce6ebe 
…b/hoomd-blue into mesh_area_conservation
simplify GPU code
57c417a
fix GPU anc CPU code for area conservation
0654f73
set up area getter for GPU
294e63f
fix minor bugs in Area conservation getter
64f5f33
pytest for Area getter
ce6de06
rename AreaConservation to TriangleAreaConservation
813ac7a
add whole Area conservation
9ca84cf
fix minor bugs in GPU calculations
65ff0c0
Merge branch 'mesh-data-structure' into mesh_area_conservation
e14e7b5
Merge branch 'trunk-minor' into mesh_area_conservation
879ce08
remove debug printf line
cb4be87
Merge branch 'mesh_rewrite' into mesh_area_conservation
91159ba
update Area conservation
c8701ed
update headers
9d3ce91
@SchoeniPhlippsn
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pre-commit.ci autofix

@SchoeniPhlippsn
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pre-commit.ci autofix

@SchoeniPhlippsn
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pre-commit.ci autofix

@SchoeniPhlippsn
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@joaander @tcmoore3
Ready for review!

@SchoeniPhlippsn
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pre-commit.ci autofix

joaander
joaander requested changes Oct 21, 2024
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Thanks! Now that volume conservation is merged, you need to merge trunk-minor into this branch and resolve conflicts.

The code looks great. I found a few duplicate or unused lines of code that can be removed.

hoomd/md/TriangleAreaConservationMeshForceCompute.h Outdated Show resolved Hide resolved
hoomd/md/TriangleAreaConservationMeshForceComputeGPU.cu Outdated Show resolved Hide resolved
hoomd/md/TriangleAreaConservationMeshForceComputeGPU.cu Outdated Show resolved Hide resolved
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pre-commit.ci autofix

@joaander joaander added the validate Execute long running validation tests on pull requests label Oct 23, 2024
joaander
joaander approved these changes Oct 23, 2024
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Thanks!

@joaander joaander merged commit ca42b1a into trunk-minor Oct 23, 2024
66 checks passed
@joaander joaander deleted the mesh_area_conservation branch October 23, 2024 19:48
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@joaander joaander joaander approved these changes

@tcmoore3 tcmoore3 Awaiting requested review from tcmoore3

@mariaward10 mariaward10 Awaiting requested review from mariaward10

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3 participants
@SchoeniPhlippsn @joaander @syjlee