[pull] develop from lammps:develop - #173

Merged

pull[bot] merged 99 commits into

comphy-lab:developfrom

Jul 21, 2026

Commits on Jun 17, 2026

Adding example bpm/zero bond style
jtclemm
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8fdb693
Merge branch 'develop' into port-peri-to-bpm
akohlmey
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95937ee

Commits on Jun 18, 2026

BPM/peri Stage 0: scaffold bond_style bpm/peri (PMB, zero force)

akohlmey
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claude
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682f8b3
BPM/peri: hard pair handshake + modernized error messages

akohlmey
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claude
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9c385c7
BPM/peri Stage 1a: PMB force law

akohlmey
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claude
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1a4f21d
BPM/peri Stage 1b: per-type-pair (#984) bond breaking

akohlmey
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1ed77b7
BPM/peri Stage 2: pair_style bpm/peri short-range contact

akohlmey
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70269f8
BPM/peri Stage 3: LPS state-based model + dilatation

akohlmey
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claude
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b5dae46
BPM/peri: error message suggests 'all' for the d_vfrac property/atom fix

akohlmey
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5e36b26
BPM/peri Stage 4: VES viscoelastic model (evolving history)

akohlmey
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4ea34ef
BPM/peri Stage 5: EPS elastic-plastic model + peridynamic stress fix

akohlmey
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fb2cb1d
BPM/peri: dimensionally-consistent EPS plastic return mapping

akohlmey
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9e9cc8d
BPM/peri Stage 6: volume-weighted damage diagnostic

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41cd313
BPM/peri Stage 7: documentation, examples, attribution, and citations

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8264349
BPM/peri Stage 8: generic BPM pair+bond test harness (unittest/bpm)

akohlmey
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70c6af0
BPM/peri Stage 9: review cleanup (factor taper, fix shutdown leak)

akohlmey
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ee327ca
BPM/peri: performance benchmark vs legacy PERI + transition-guide note

akohlmey
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d88ece2
BPM: document bond_style bpm/zero

akohlmey
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f6dc3a2
BPM/peri: refuse rRESPA, add horizon consistency check, optional d_theta

akohlmey
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81338dc
BPM/peri tests: add lps_dilatation analytic model + restart round-trip

akohlmey
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78989d5
BPM/peri: performance optimizations (pair force caching, reciprocal wvolume)

akohlmey
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27eaee1
BPM tests: add lps_force analytic model + bond_style bpm/zero coverage

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ba06026
BPM tests: add bond_style bpm/spring and bpm/spring/plastic coverage

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9d9a624
unittest: fix test_error_stats include after the shared-infra move

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8dbfd6c
BPM/peri: say "excluded" not "censored" for special-bond skipping

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6f92e20
BPM/doc: say "exclude" not "censor" for special-bond/lifetime skipping

akohlmey
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6de0dd1
Revert pair_tracker.rst wording change (moved to the doc-updates PR)

akohlmey
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40c6b63

Commits on Jun 19, 2026

add another peri/eps unittest
akohlmey
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c1db2e6

Commits on Jun 20, 2026

Merge branch 'develop' into port-peri-to-bpm
akohlmey
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3147814

Commits on Jun 21, 2026

removed dead code and reduce compiler warnings
akohlmey
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b1c3b57

Commits on Jun 30, 2026

Merge branch 'develop' into port-peri-to-bpm
akohlmey
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a67a475
BPM: point peri/eps plastic-update comment to the PERI derivation

akohlmey
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claude
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cb5bbc8
BPM/PERI docs: note the faster bpm/peri alternative in the legacy PERI docs

akohlmey
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claude
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04229bd

Commits on Jul 3, 2026

Merge remote-tracking branch 'github/develop' into port-peri-to-bpm
akohlmey
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ca0dd9f

Commits on Jul 4, 2026

Merge branch 'develop' into port-peri-to-bpm
akohlmey
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ac3f5c8

Commits on Jul 6, 2026

silence compiler warning
akohlmey
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e0fadf6
apply clang-format
akohlmey
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d640e74
make certain that r0 is always initialized and thus we don't return garbage results in single()
akohlmey
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f8f8f81

Commits on Jul 10, 2026

Merge branch 'develop' into port-peri-to-bpm
akohlmey
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ac249c1

Commits on Jul 13, 2026

Commits on Jul 15, 2026

Merge branch 'develop' into remove-agni-and-ml-rann
akohlmey
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c8c7e3f

Commits on Jul 16, 2026

Commits on Jul 17, 2026

update dump image settings
akohlmey
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9d13f70
add dump_modify gtrans keyword to set transparency of rendered grids
akohlmey
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0013193
change epsilon so that tests pass on ARM64
akohlmey
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cdd370b
fix variable shadow bug
akohlmey
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35c8935
improve invalid triangle error message
akohlmey
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c806152
avoid crash when estimating memory usage
akohlmey
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143d3ec
skip importing degenerate triangles rather then just erroring out
akohlmey
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03169e2
avoid corrupting the connectivity list from repeated coordinates
akohlmey
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3d3ebc7
check memory pools for overflows
akohlmey
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e29ea5f

Commits on Jul 18, 2026

correctly compute and set the buffer size for border and exchange communication
akohlmey
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66944cb
correct warning about increasing communication cutoff
akohlmey
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2a56dfc
fix copy-n-paste bug
akohlmey
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89c96e0
add missing checks for chunk pool overflows
akohlmey
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976ca27
we don't need to check data for chunck overflows that has already been checked
akohlmey
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34022a8
update visualization, set communication cutoff as needed
akohlmey
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42cc5bc
update log files
akohlmey
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93c4759
add note about remeshing STL files for 3d-printing
akohlmey
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2f20e5a
add cement mixer drum input example
akohlmey
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53b4c09
small updates
akohlmey
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a0bdf1d
improve error and warning messages in fix pour
akohlmey
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de44835
add commented out visualization commands
akohlmey
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b162d1f
turn error of missing connected surface atoms into warning
akohlmey
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359db72
update mixer-drum input to avoid issues
akohlmey
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056359e
improve visuals by rotating drum to the other direction, speed up rotation a tiny bit
akohlmey
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e1e0a37

Commits on Jul 19, 2026

Small clean ups for peri pair style, test pushing commit
jtclemm
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ac062be
forgot to comment out dump_modify
akohlmey
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e0575c5
correct links into the new LAMMPS homepage
akohlmey
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ff6a056

Commits on Jul 20, 2026

improve settings for fewer artifacts
akohlmey
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2d21f58
support extracting colloid pair style settings
akohlmey
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ede49b0
update examples for visualization showcase on home page
akohlmey
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bc10f49
correct indentation
akohlmey
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526f1f6
More small clean ups
jtclemm
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fd4d009
removing damage peri compute
jtclemm
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3fae457

Commits on Jul 21, 2026

apply RAII principle and avoid a lot of pointer chasing
akohlmey
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5f8ec0f
make sure *all* pointers are initialized to null in the initializer list
akohlmey
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be68f6a
removing files
jtclemm
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4d431d4
Updating examples to remove compute damage peri
jtclemm
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0f89abf
improve visualizations
akohlmey
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b9026b4
Merge branch 'develop' into port-peri-to-bpm
akohlmey
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904d513
make shared file inclusion consistent
akohlmey
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2b81677
update dump image visualization
akohlmey
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ddf6133
silence compiler warning
akohlmey
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5b165b4
small doc tweaks, add local TOC to Peridynamics howto page
akohlmey
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9cad4b1
Merge branch 'develop' into remove-agni-and-ml-rann
akohlmey
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fa26886
provide more details about the status of ML-RANN
akohlmey
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0165185
allow string style variables to self-reference by performing the substitution early
akohlmey
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c1959e9
Merge pull request #5045 from akohlmey/port-peri-to-bpm
akohlmey
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3024721
Merge pull request #5096 from akohlmey/collected-small-changes
akohlmey
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d76d25f
Merge pull request #5090 from akohlmey/remove-agni-and-ml-rann
akohlmey
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d3b14f6