fix(ml/mm): do ONIOM - #11

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HaoZeke wants to merge 23 commits into

fix/oniom-subtraction

Commits on Mar 20, 2026

fix(mta): implement ONIOM subtractive scheme for ML/MM boundary terms
HaoZeke
committed
7abf851

Commits on Mar 22, 2026

fix(mta): always set PyTorch threads to ntomp (fixes thread-MPI blow-up)
HaoZeke
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8cdda86
feat(mta): add link-atoms and electrostatic-embedding MDP options
HaoZeke
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e45f75e
feat(mta): NNPot-style link atom replacement (correct ONIOM approach)
HaoZeke
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2314cd5

Commits on Mar 24, 2026

fix(mta): correct threading comment, model-driven embedding, link docs
HaoZeke
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16ba984

Commits on May 5, 2026

fix(mta): provide requested charge inputs
HaoZeke
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89616ec

Commits on May 6, 2026

merge: update metatomic base
HaoZeke
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dbb491e
test(mta): align ONIOM topology expectations
HaoZeke
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4c2bc65
test(threadmpi): wait on Windows thread handles
HaoZeke
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0674569
fix(mta): map link atoms by global atom index
HaoZeke
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b21a99b
chore(mta): avoid shadowed model index
HaoZeke
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2799a41
fix(mta): support multiple link caps per boundary atom
HaoZeke
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08b4864
fix(mta): use active link distance value
HaoZeke
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5cafa17
fix(mta): honor PBC shifts for link caps
HaoZeke
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e4f532e
test(topology): cover shifted link force spread
HaoZeke
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42270f2
fix(mta): redistribute link cap output forces
HaoZeke
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eaae9b7
test(topology): use tolerance for link force spread
HaoZeke
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cb7505c
fix(mta): single-own link cap outputs
HaoZeke
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8d92223
test(mta): require opt-in ONIOM preprocessing
HaoZeke
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787a5f9
test(mta): fix ONIOM option test scaffolding
HaoZeke
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ea93e8a
feat(mta): make ONIOM preprocessing opt in
HaoZeke
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fa82917
test(mta): update ONIOM option refdata
HaoZeke
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9ffa3fe
fix(mta): build model pairlist from all plain pairs
HaoZeke
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d905082