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26d43f8
Implement CPU dynamic bond forming algorithm
astatt Jun 10, 2020
c0236f9
Own neighbour tree for dynamic bonds
astatt Jun 24, 2020
0c71990
first draft CPU version working
astatt Jul 2, 2020
df11255
Add Nparticle and box size change reallocation
astatt Jul 3, 2020
313ba54
Add empty files for GPU implementation
astatt Jul 6, 2020
d590e64
Merge remote-tracking branch 'origin/develop' into feature/dynamic-bo…
astatt Jul 6, 2020
e641a2a
Bond sorting/selecting -> GPU
astatt Jul 16, 2020
a7cea56
Copied tree neighbor list, CUDA error
astatt Jul 27, 2020
9557c5f
Working version, need to check for group=all
astatt Aug 4, 2020
e95679b
Add unit tests, fix small mistakes
astatt Aug 6, 2020
33913da
Remove stray printf/cout
astatt Aug 6, 2020
dcb4b32
Switch to sorted possible bond pairs
astatt Aug 7, 2020
d34e419
Downsize nlist from Nparticles to Ngroup1 size
astatt Aug 13, 2020
6f4bad3
Cleanup unused variables/functions
astatt Aug 27, 2020
66fcb50
Merge branch 'main' into feature/dynamic-bonding
Apr 13, 2022
87e0a13
cleanup
May 24, 2022
e794108
Merge branch 'main' into feature/dynamic-bonding
Jul 7, 2022
87aa00a
Fix stray merge leftovers
Jul 7, 2022
983005e
Fix naming scheme for cuda 11
Aug 2, 2022
0a11d4e
Merge branch 'feature/dynamic-bonding' of https://github.com/mphoward…
Sep 13, 2022
c7d6a04
Add missing argument to DynamicBondUpdateGPU
Sep 13, 2022
9683c58
Add seed for random numbers
Sep 13, 2022
6e0cb0d
Add missing seed argument
Sep 13, 2022
65da381
Merge remote-tracking branch 'origin/main' into feature/dynamic-bonding
Dec 19, 2025
3e6accc
Update namespaces,arguments etc to compile with hoomd 5
Dec 19, 2025
e389791
Add python code
Dec 20, 2025
25573d5
add python code, export error
Dec 20, 2025
90d826a
remove unneccessary imports
Dec 22, 2025
c882e50
re-added __HIPCC__ flags
Dec 22, 2025
ddb7822
fix compiler/export issues
Dec 23, 2025
9b6a934
code dublication
Mar 20, 2026
4311d06
started fixing GPU implentation, still lots of issues
astatt Mar 20, 2026
2f06bde
mark issues in code
astatt Mar 23, 2026
ffa911c
Add test, not finished
Apr 29, 2026
46f1927
resolve merge
Apr 29, 2026
0023b66
need wrapper code for neighbor
Apr 29, 2026
9b8707e
remove neighbor, use wrapper from Tree Neigh list
astatt May 1, 2026
643e836
add internal neigh list
May 4, 2026
83b8c95
Merge branch 'main' into feature/dynamic-bonding
May 4, 2026
1c872e4
replace aabb trees with neighbor list, first draft
May 6, 2026
484b860
start GPU implementation
May 6, 2026
0c21a39
remove stray autotuners
May 6, 2026
936af3e
delete stray m_stream leftover
May 6, 2026
92ec2da
add missing thrust header
May 6, 2026
171f64a
fix unit tests for CPU code
May 8, 2026
f2220b9
add group check to GPU code
astatt May 11, 2026
42369c8
fix copy_possible_bonds const issue
astatt May 11, 2026
dbd311e
typo in defintion of copy_possible_bonds
astatt May 12, 2026
3ccbb4c
fix formatting
May 13, 2026
ccb3fdd
remove leftover couts
May 13, 2026
7335d1d
whitespace fix
May 13, 2026
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4 changes: 4 additions & 0 deletions src/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -4,20 +4,23 @@ set(COMPONENT_NAME azplugins)
# TODO: List all host C++ source code files in _${COMPONENT_NAME}_sources.
set(_${COMPONENT_NAME}_sources
ConstantFlow.cc
DynamicBondUpdater.cc
export_ImagePotentialBondHarmonic.cc
module.cc
ParabolicFlow.cc
VelocityCompute.cc
)
if (ENABLE_HIP)
list(APPEND _${COMPONENT_NAME}_sources
DynamicBondUpdaterGPU.cc
export_ImagePotentialBondHarmonicGPU.cc
VelocityComputeGPU.cc
)
endif()

# TODO: List all GPU C++ source code files in _${COMPONENT_NAME}_cu_sources.
set(_${COMPONENT_NAME}_cu_sources
DynamicBondUpdaterGPU.cu
ImagePotentialBondGPUKernel.cu
VelocityComputeGPU.cu
VelocityFieldComputeGPU.cu
Expand All @@ -31,6 +34,7 @@ set(python_files
conftest.py
external.py
flow.py
update.py
pair.py
wall.py
)
Expand Down
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