[pull] develop from lammps:develop - #169

Merged

pull[bot] merged 137 commits into

comphy-lab:developfrom

Jul 11, 2026

Commits on Jul 3, 2026

Fix wrong column selection in 2d single-value fix ave/grid averaging

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d480bbe
Fix corrupted sorting of 1-3 neighbors in AMOEBA kmpole()

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3638e4f
Fix garbage per-atom energy indexing in TIP4P OpenMP pair styles

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f54c758
Fix garbage Coulomb tables for pair lj/cut/coul/esp with run_style respa

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e5db2d5
Fix garbage heat flux on neighbor atoms in pair edpd beyond the temperature cutoff

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4931d70
Clamp the correct random number for the eDPD random heat flux

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1084e10
Fix stale unwrapped coordinates and wrong energy indexing in fix efield/tip4p

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45441e6
Do not tally stale sub-particle force data in pair line/lj and tri/lj

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0b3c4bf
Fix stale electric field contribution in pair lj/cut/coul/msm/dielectric

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b35e22a
Fix triclinic atom placement using uninitialized fractional coordinates in fix gemc

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5aa9d91
Fix momentum resampling for rigid bodies outside the fix group

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39acc44
Avoid multiplying by uninitialized inverse distance in angle cosine/buck6d

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8c75fd5
Fix three copy-paste errors in the region cone hi-boundary parsing

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c02a80b
Fix garbage contact point for rim contacts with open-side region cylinders

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3306e08
Fix reads past the neighbor count in compute ackland/atom

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3a56ef5
Initialize members read before first use in three fixes/computes

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3f9fb77
Preserve the limit_damping setting of granular pair styles across restarts

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fa154ae
Preserve all pair dsmc global settings across restarts

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307e055
Preserve the seqav/seqdep setting of oxDNA/oxRNA pair styles across restarts

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3ae573a
Preserve pair eff/cut settings and ECP parameters across restarts

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a36bbc7
Guard against invalid variable references crashing instead of erroring

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c93a835
Honor the documented default output file of dynamical_matrix and third_order

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679525d
Harden potential file parsing in pair styles agni and rann

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23ef94c
Fix integer overflow before the intended 64-bit handling in two places

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5285df6
Fix error-path destructor safety and missing size guards

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ac8f845
Fix memory reporting and remaining uninitialized members

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525af5c
Fix six correctness defects in KOKKOS package styles

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4b2f422
Add missing rx mixing-weight sanity checks and release Kokkos views promptly

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5bf8d9b
Initialize class members missed by the earlier pointer-initialization batch

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9893e49
Validate size and index fields read from restart and map files

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5565704
Validate user parameters that are used as divisors or lookups

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1aeb38c
Harden geometrically guaranteed searches and degenerate region cases

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b0c1927
Assorted defensive hardening from the Coverity scan triage

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782d9d9
Add regression tests for invalid variable and corrupt restart handling

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609419b
Add regression tests for restart settings preservation and input validation

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e93a793
Overhaul regression test reporting and add result merging tool

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d64e1d7
Test per-atom energy tallying without virial in the pair style driver

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3f72b39
Add DEM regression test for rim contacts with an open-side region cylinder

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f3ede6d
Merge branch 'develop' into coverity-scan-fixes
akohlmey
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6d09e18
simplify demo modeling file (we are on 64-bit Linux)
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dc33eb5
Merge branch 'develop' into coverity-hardening
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965cacf
Merge branch 'coverity-hardening' into coverity-tests
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a02848e

Commits on Jul 4, 2026

Fix eatom_only subtest failure for pair styles without per-atom virial

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639b073
Merge branch 'develop' of github.com:lammps/lammps into regression-test-reporting
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0da84f8
Merge branch 'develop' into coverity-scan-fixes
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4a83d11
GRANSURF: fix realloc of wrong pointer when growing the model list

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9f9080a
MANYBODY: avoid out-of-bounds read in pair local/density single()

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a1811a8
Return no contact from fully open regions instead of reading garbage

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28afa88
tools: fix logic, uninitialized-data, and error-path defects from Coverity

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92cdf13
PHONON: plug two block leaks and guard ferror in third_order

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44a99cc
coverity: model Kokkos::abort as noreturn

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f5ddca0
Merge branch 'coverity-scan-fixes' into coverity-hardening
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981cf7d
Complete constructor member initialization flagged by the rescan

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6150831
More input validation and robustness guards from the Coverity rescan

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2bcd8ef
Merge branch 'coverity-hardening' into coverity-tests
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c984e09
Correct member names for the qeq/reaxff sparse matrix init

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40f7ec6
Merge branch 'coverity-hardening' into coverity-tests
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e24cea8
Merge remote-tracking branch 'akohlmey/coverity-scan-fixes' into coverity-scan-fixes
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0b92e8b
Final hardening pass for the remaining Coverity rescan findings

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489a19a
coverity: align modeling file with the simplified bigint typedef

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0d8be04
Merge branch 'coverity-hardening' into coverity-tests
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5229cb9
Do not reject zero-size global fix state when reading a restart file

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aad01a4
Merge branch 'coverity-hardening' into coverity-tests
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3a15a59

Commits on Jul 5, 2026

Commits on Jul 6, 2026

do not embed a static LAMMPS library into the in-tree example plugins

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1cd10a2
use qualified auto and apply clang-format
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65eab59
use std::vector<>.data() instead of applying addressof to the first element
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9e9d820
use uppercase float qualifier
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e3fbed2
exclude VMD plugin headers from static code analysis
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ab077bd
correct link
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98cd290
convert a few more qualifier suffixes to upper case for consistency
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5b18e3c
apply RAII and pass reference instead of pointer
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fd74722
cleaner for static code analysis
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623982a
modernize
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7b3a8f1
modernize and skip linting on imported legacy code
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c1fc66f
make one more attribute suffix uppercase
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d1fb14f

Commits on Jul 7, 2026

fix granular/mdr: get the granular neighbor history fix from the pair style

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39f69d8
Coverity followup: consistent MDR wall guard, MDI plugin leak, single() history init

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e2aeede
Initialize the remaining constructor members flagged by the Coverity rescan

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9d7085c
Fix three defects the Coverity rescan re-reported under existing CIDs

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d13a455
Initialize all remaining uninitialized constructor members, own ragged arrays via Memory

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3c6d650
some more programming style and initialization hardening changes
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2613b0a
fix typos
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02906a2
fix slab correction energy accumulation in pppm/tip4p
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80a3bb1
evaluate all TIP4P slab correction terms at the virtual charge site
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2a05ce7

Commits on Jul 8, 2026

Commits on Jul 9, 2026

we don't want to run coverity scan on GitHub anymore
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56da6ef
import updated and revised coding agent config that is shared between claude code copilot
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87bf224
ignore downloaded files and defect triage results
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28e4842
revise and update AI tool usage information and suggestions
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6599aa1
don't leak memory when using the same argument multiple times
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9c487a6
fix cut-n-paste bug
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6c6f7f5
remove dead code
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f1524e8
use correct data type for loops
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f633284
remove dead code
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0aa54e1
use consistent types
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3cf18d4
fix up one more loop variable
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67c98e4
clean up last batch of loop indices
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1932de5
silence compiler warnings
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a9b58e2
add YAML-based test harness for dump image / GRAPHICS rendering
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4b1fa23
add dump image basics tests: color attributes, camera, autobond, box drawing
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4bd4c85
fix inconsistent transparency of the two bond halves in dump image
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d8abad3
add dump_modify feature matrix tests for dump image rendering
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cf68826
fix inconsistent transparency of the two bond halves in dump image
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35b0c43
add region drawing tests for dump image
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42c062b
add YAML-driven tester for minimizer styles to force-styles tests
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5c264a5
add YAML-driven tester for the output data of computes and fixes
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92a7e56
add 63 more tests for the output data of computes and fixes
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5993d69
fix swapped std::clamp arguments in dump image light restoration
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e02e210
fix swapped std::clamp arguments in dump image light restoration
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10bac6e
refactor force-style test yaml parsing to use Tokenizer classes

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cc4950e
adapt output-style reference data parsing to the Tokenizer classes
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6752ef5
restrict minimizer style tests to platform-portable observables
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2782f19
extend force-style test JSON schema for the new testers
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16a9cf1
document the minimizer style and output data test programs
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73f62dd
document the dump image rendering tests
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ddbeaf2

Commits on Jul 10, 2026

fix typos in comments
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9ce13d5
fix typo
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61ddab3
flag as development version
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e21e8a2
Merge pull request #5072 from akohlmey/coverity-scan-fixes
akohlmey
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da82150
Merge pull request #5073 from akohlmey/coverity-hardening
akohlmey
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14b74b9
Merge branch 'develop' into collected-small-changes
akohlmey
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6f33c68
Merge pull request #5074 from akohlmey/coverity-tests
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f42a2dc
Merge pull request #5083 from akohlmey/force-style-testers
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cf5ec94
Merge pull request #5082 from akohlmey/more-testing
akohlmey
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959b087
Merge pull request #5070 from akohlmey/regression-test-reporting
akohlmey
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63411d1
Merge branch 'develop' into collected-small-changes
akohlmey
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789a531
adjust epsilon to pass on ARM64
akohlmey
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05b5e96
Merge pull request #5076 from akohlmey/collected-small-changes
akohlmey
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7b8a425