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d480bbe
Fix wrong column selection in 2d single-value fix ave/grid averaging
akohlmey Jul 3, 2026
3638e4f
Fix corrupted sorting of 1-3 neighbors in AMOEBA kmpole()
akohlmey Jul 3, 2026
f54c758
Fix garbage per-atom energy indexing in TIP4P OpenMP pair styles
akohlmey Jul 3, 2026
e5db2d5
Fix garbage Coulomb tables for pair lj/cut/coul/esp with run_style respa
akohlmey Jul 3, 2026
4931d70
Fix garbage heat flux on neighbor atoms in pair edpd beyond the tempe…
akohlmey Jul 3, 2026
1084e10
Clamp the correct random number for the eDPD random heat flux
akohlmey Jul 3, 2026
45441e6
Fix stale unwrapped coordinates and wrong energy indexing in fix efie…
akohlmey Jul 3, 2026
0b3c4bf
Do not tally stale sub-particle force data in pair line/lj and tri/lj
akohlmey Jul 3, 2026
b35e22a
Fix stale electric field contribution in pair lj/cut/coul/msm/dielectric
akohlmey Jul 3, 2026
5aa9d91
Fix triclinic atom placement using uninitialized fractional coordinat…
akohlmey Jul 3, 2026
39acc44
Fix momentum resampling for rigid bodies outside the fix group
akohlmey Jul 3, 2026
8c75fd5
Avoid multiplying by uninitialized inverse distance in angle cosine/b…
akohlmey Jul 3, 2026
c02a80b
Fix three copy-paste errors in the region cone hi-boundary parsing
akohlmey Jul 3, 2026
3306e08
Fix garbage contact point for rim contacts with open-side region cyli…
akohlmey Jul 3, 2026
3a56ef5
Fix reads past the neighbor count in compute ackland/atom
akohlmey Jul 3, 2026
3f9fb77
Initialize members read before first use in three fixes/computes
akohlmey Jul 3, 2026
fa154ae
Preserve the limit_damping setting of granular pair styles across res…
akohlmey Jul 3, 2026
307e055
Preserve all pair dsmc global settings across restarts
akohlmey Jul 3, 2026
3ae573a
Preserve the seqav/seqdep setting of oxDNA/oxRNA pair styles across r…
akohlmey Jul 3, 2026
a36bbc7
Preserve pair eff/cut settings and ECP parameters across restarts
akohlmey Jul 3, 2026
c93a835
Guard against invalid variable references crashing instead of erroring
akohlmey Jul 3, 2026
679525d
Honor the documented default output file of dynamical_matrix and thir…
akohlmey Jul 3, 2026
23ef94c
Harden potential file parsing in pair styles agni and rann
akohlmey Jul 3, 2026
5285df6
Fix integer overflow before the intended 64-bit handling in two places
akohlmey Jul 3, 2026
ac8f845
Fix error-path destructor safety and missing size guards
akohlmey Jul 3, 2026
525af5c
Fix memory reporting and remaining uninitialized members
akohlmey Jul 3, 2026
4b2f422
Fix six correctness defects in KOKKOS package styles
akohlmey Jul 3, 2026
5bf8d9b
Add missing rx mixing-weight sanity checks and release Kokkos views p…
akohlmey Jul 3, 2026
9893e49
Initialize class members missed by the earlier pointer-initialization…
akohlmey Jul 3, 2026
5565704
Validate size and index fields read from restart and map files
akohlmey Jul 3, 2026
1aeb38c
Validate user parameters that are used as divisors or lookups
akohlmey Jul 3, 2026
b0c1927
Harden geometrically guaranteed searches and degenerate region cases
akohlmey Jul 3, 2026
782d9d9
Assorted defensive hardening from the Coverity scan triage
akohlmey Jul 3, 2026
609419b
Add regression tests for invalid variable and corrupt restart handling
akohlmey Jul 3, 2026
e93a793
Add regression tests for restart settings preservation and input vali…
akohlmey Jul 3, 2026
d64e1d7
Overhaul regression test reporting and add result merging tool
akohlmey Jul 3, 2026
3f72b39
Test per-atom energy tallying without virial in the pair style driver
akohlmey Jul 3, 2026
f3ede6d
Add DEM regression test for rim contacts with an open-side region cyl…
akohlmey Jul 3, 2026
6d09e18
Merge branch 'develop' into coverity-scan-fixes
akohlmey Jul 3, 2026
dc33eb5
simplify demo modeling file (we are on 64-bit Linux)
akohlmey Jul 3, 2026
965cacf
Merge branch 'develop' into coverity-hardening
akohlmey Jul 3, 2026
a02848e
Merge branch 'coverity-hardening' into coverity-tests
akohlmey Jul 3, 2026
639b073
Fix eatom_only subtest failure for pair styles without per-atom virial
akohlmey Jul 4, 2026
0da84f8
Merge branch 'develop' of github.com:lammps/lammps into regression-te…
akohlmey Jul 4, 2026
4a83d11
Merge branch 'develop' into coverity-scan-fixes
akohlmey Jul 4, 2026
9f9080a
GRANSURF: fix realloc of wrong pointer when growing the model list
akohlmey Jul 4, 2026
a1811a8
MANYBODY: avoid out-of-bounds read in pair local/density single()
akohlmey Jul 4, 2026
28afa88
Return no contact from fully open regions instead of reading garbage
akohlmey Jul 4, 2026
92cdf13
tools: fix logic, uninitialized-data, and error-path defects from Cov…
akohlmey Jul 4, 2026
44a99cc
PHONON: plug two block leaks and guard ferror in third_order
akohlmey Jul 4, 2026
f5ddca0
coverity: model Kokkos::abort as noreturn
akohlmey Jul 4, 2026
981cf7d
Merge branch 'coverity-scan-fixes' into coverity-hardening
akohlmey Jul 4, 2026
6150831
Complete constructor member initialization flagged by the rescan
akohlmey Jul 4, 2026
2bcd8ef
More input validation and robustness guards from the Coverity rescan
akohlmey Jul 4, 2026
c984e09
Merge branch 'coverity-hardening' into coverity-tests
akohlmey Jul 4, 2026
40f7ec6
Correct member names for the qeq/reaxff sparse matrix init
akohlmey Jul 4, 2026
e24cea8
Merge branch 'coverity-hardening' into coverity-tests
akohlmey Jul 4, 2026
0b92e8b
Merge remote-tracking branch 'akohlmey/coverity-scan-fixes' into cove…
akohlmey Jul 4, 2026
489a19a
Final hardening pass for the remaining Coverity rescan findings
akohlmey Jul 4, 2026
0d8be04
coverity: align modeling file with the simplified bigint typedef
akohlmey Jul 4, 2026
5229cb9
Merge branch 'coverity-hardening' into coverity-tests
akohlmey Jul 4, 2026
aad01a4
Do not reject zero-size global fix state when reading a restart file
akohlmey Jul 4, 2026
3a15a59
Merge branch 'coverity-hardening' into coverity-tests
akohlmey Jul 4, 2026
aab82b8
fall back to Plumed-2.9.5 as 2.10.x has trouble building for Windows
akohlmey Jul 5, 2026
58e401c
add utility to rebalance reStructuredText tables
akohlmey Jul 5, 2026
c32b937
ignore Claude related paths
akohlmey Jul 5, 2026
aee472d
add much improve diagram for hydrogen bond setup
akohlmey Jul 5, 2026
0280d41
spelling
akohlmey Jul 5, 2026
a53bca4
revise figures for transparent background
akohlmey Jul 5, 2026
1cd10a2
do not embed a static LAMMPS library into the in-tree example plugins
akohlmey Jul 6, 2026
65eab59
use qualified auto and apply clang-format
akohlmey Jul 6, 2026
9e9d820
use std::vector<>.data() instead of applying addressof to the first e…
akohlmey Jul 6, 2026
e3fbed2
use uppercase float qualifier
akohlmey Jul 6, 2026
ab077bd
exclude VMD plugin headers from static code analysis
akohlmey Jul 6, 2026
98cd290
correct link
akohlmey Jul 6, 2026
5b18e3c
convert a few more qualifier suffixes to upper case for consistency
akohlmey Jul 6, 2026
fd74722
apply RAII and pass reference instead of pointer
akohlmey Jul 6, 2026
623982a
cleaner for static code analysis
akohlmey Jul 6, 2026
7b3a8f1
modernize
akohlmey Jul 6, 2026
c1fc66f
modernize and skip linting on imported legacy code
akohlmey Jul 6, 2026
d1fb14f
make one more attribute suffix uppercase
akohlmey Jul 6, 2026
39f69d8
fix granular/mdr: get the granular neighbor history fix from the pair…
akohlmey Jul 7, 2026
e2aeede
Coverity followup: consistent MDR wall guard, MDI plugin leak, single…
akohlmey Jul 7, 2026
9d7085c
Initialize the remaining constructor members flagged by the Coverity …
akohlmey Jul 7, 2026
d13a455
Fix three defects the Coverity rescan re-reported under existing CIDs
akohlmey Jul 7, 2026
3c6d650
Initialize all remaining uninitialized constructor members, own ragge…
akohlmey Jul 7, 2026
2613b0a
some more programming style and initialization hardening changes
akohlmey Jul 7, 2026
02906a2
fix typos
akohlmey Jul 7, 2026
80a3bb1
fix slab correction energy accumulation in pppm/tip4p
akohlmey Jul 7, 2026
2a05ce7
evaluate all TIP4P slab correction terms at the virtual charge site
akohlmey Jul 7, 2026
ce12b24
Merge remote-tracking branch 'github/develop' into collected-small-ch…
akohlmey Jul 8, 2026
1beca8e
small edits to hbond/local figure
akohlmey Jul 8, 2026
31777c8
add some bar charts to visualize the numbers on the Speed_measure doc…
akohlmey Jul 8, 2026
9db9aa3
upgrade MathJax to bugfix release 4.1.3
akohlmey Jul 8, 2026
56da6ef
we don't want to run coverity scan on GitHub anymore
akohlmey Jul 9, 2026
87bf224
import updated and revised coding agent config that is shared between…
akohlmey Jul 9, 2026
28e4842
ignore downloaded files and defect triage results
akohlmey Jul 9, 2026
6599aa1
revise and update AI tool usage information and suggestions
akohlmey Jul 9, 2026
9c487a6
don't leak memory when using the same argument multiple times
akohlmey Jul 9, 2026
6c6f7f5
fix cut-n-paste bug
akohlmey Jul 9, 2026
f1524e8
remove dead code
akohlmey Jul 9, 2026
f633284
use correct data type for loops
akohlmey Jul 9, 2026
0aa54e1
remove dead code
akohlmey Jul 9, 2026
3cf18d4
use consistent types
akohlmey Jul 9, 2026
67c98e4
fix up one more loop variable
akohlmey Jul 9, 2026
1932de5
clean up last batch of loop indices
akohlmey Jul 9, 2026
a9b58e2
silence compiler warnings
akohlmey Jul 9, 2026
4b1fa23
add YAML-based test harness for dump image / GRAPHICS rendering
akohlmey Jul 9, 2026
4bd4c85
add dump image basics tests: color attributes, camera, autobond, box …
akohlmey Jul 9, 2026
d8abad3
fix inconsistent transparency of the two bond halves in dump image
akohlmey Jul 9, 2026
cf68826
add dump_modify feature matrix tests for dump image rendering
akohlmey Jul 9, 2026
35b0c43
fix inconsistent transparency of the two bond halves in dump image
akohlmey Jul 9, 2026
42c062b
add region drawing tests for dump image
akohlmey Jul 9, 2026
5c264a5
add YAML-driven tester for minimizer styles to force-styles tests
akohlmey Jul 9, 2026
92a7e56
add YAML-driven tester for the output data of computes and fixes
akohlmey Jul 9, 2026
5993d69
add 63 more tests for the output data of computes and fixes
akohlmey Jul 9, 2026
e02e210
fix swapped std::clamp arguments in dump image light restoration
akohlmey Jul 9, 2026
10bac6e
fix swapped std::clamp arguments in dump image light restoration
akohlmey Jul 9, 2026
cc4950e
refactor force-style test yaml parsing to use Tokenizer classes
akohlmey Jul 2, 2026
6752ef5
adapt output-style reference data parsing to the Tokenizer classes
akohlmey Jul 9, 2026
2782f19
restrict minimizer style tests to platform-portable observables
akohlmey Jul 9, 2026
16a9cf1
extend force-style test JSON schema for the new testers
akohlmey Jul 9, 2026
73f62dd
document the minimizer style and output data test programs
akohlmey Jul 9, 2026
ddbeaf2
document the dump image rendering tests
akohlmey Jul 9, 2026
9ce13d5
fix typos in comments
akohlmey Jul 10, 2026
61ddab3
fix typo
akohlmey Jul 10, 2026
e21e8a2
flag as development version
akohlmey Jul 10, 2026
da82150
Merge pull request #5072 from akohlmey/coverity-scan-fixes
akohlmey Jul 10, 2026
14b74b9
Merge pull request #5073 from akohlmey/coverity-hardening
akohlmey Jul 10, 2026
6f33c68
Merge branch 'develop' into collected-small-changes
akohlmey Jul 10, 2026
f42a2dc
Merge pull request #5074 from akohlmey/coverity-tests
akohlmey Jul 10, 2026
cf5ec94
Merge pull request #5083 from akohlmey/force-style-testers
akohlmey Jul 10, 2026
959b087
Merge pull request #5082 from akohlmey/more-testing
akohlmey Jul 10, 2026
63411d1
Merge pull request #5070 from akohlmey/regression-test-reporting
akohlmey Jul 10, 2026
789a531
Merge branch 'develop' into collected-small-changes
akohlmey Jul 10, 2026
05b5e96
adjust epsilon to pass on ARM64
akohlmey Jul 10, 2026
7b8a425
Merge pull request #5076 from akohlmey/collected-small-changes
akohlmey Jul 10, 2026
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13 changes: 13 additions & 0 deletions .claude/CLAUDE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
# LAMMPS Project Instructions (Claude Code entry point)

@../.github/copilot-instructions.md

The imported file above is the always-loaded core shared with GitHub Copilot. Its
"Task-Specific Guides" index lists the detailed guides in `.github/instructions/` and
`.github/dev-docs/`; read the matching guide BEFORE starting that kind of work. The
files in `.claude/rules/` load the path-scoped guides automatically when matching
source files are read.

Machine- and user-specific facts (local build directory, git remotes, worktrees) live
in the untracked, gitignored `CLAUDE.local.md` at the repository root, which Claude
Code loads automatically when present.
8 changes: 8 additions & 0 deletions .claude/rules/documentation.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
---
paths:
- "doc/**"
---

Working on documentation: read `.github/instructions/documentation.instructions.md`
now (versionadded/versionchanged policy, build/spelling mechanics, wording rules,
figure workflow).
8 changes: 8 additions & 0 deletions .claude/rules/force-style-tests.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
---
paths:
- "unittest/**"
---

Working on unit tests: read `.github/instructions/force-style-tests.instructions.md`
now (YAML force-style test mechanics, accelerator-suffix auto-testing, respa
tolerances, reference regeneration).
9 changes: 9 additions & 0 deletions .claude/rules/granular-tests.md
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@@ -0,0 +1,9 @@
---
paths:
- "unittest/granular/**"
- "src/GRANULAR/**"
---

Working on granular/DEM code or tests: read
`.github/instructions/granular-tests.instructions.md` now (test-suite architecture,
YAML regeneration, atom-map and physics-setup gotchas).
10 changes: 10 additions & 0 deletions .claude/rules/kokkos.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
---
paths:
- "src/KOKKOS/**"
---

Working on KOKKOS package files: read `.github/instructions/kokkos.instructions.md`
now (rules and policies). When porting a style to KOKKOS, also read
`.github/dev-docs/kokkos-porting-guide.md` (templates, lessons) and
`.github/dev-docs/kokkos-porting-backlog.md` (what remains; trust `ls src/KOKKOS/`
and `git log` over its tables).
1 change: 1 addition & 0 deletions .gitattributes
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
.claude export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore
CITATION.cff export-ignore
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