add compatibility to fix bond/react with a REACTER JSON - #153

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salamaaya wants to merge 775 commits into

jrgissing:rate_limit_multifrom

salamaaya:fix-bond-react-json

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Commits on Nov 28, 2025

Fixing a few leftover force references, integrating into commands lists
jtclemm
committed
d4c3ee3
fore error message improvements in input processing
akohlmey
committed
025d3b3
Add KOKKOS version of dihedral_fourier and improper_cvff
stanmoore1
committed
147ebc7

Commits on Nov 29, 2025

Add virial support to fix_addforce_kokkos
stanmoore1
committed
19e04da
Fix compile issue
stanmoore1
committed
3d963b2
whitespace
stanmoore1
committed
8437a51
update death tests for echo command
akohlmey
committed
2f1572a
improve error messages
akohlmey
committed
d29df2f
some more error message improvements
akohlmey
committed
5891939
Renaming addtorque example
jtclemm
committed
33cd65a
Updating purge list, force->torque in comments, warning for old addtorque name
jtclemm
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0302274
Merge branch 'develop' into granular-updates
jtclemm
authored
697b4b6
Removing minimization notes for setting torques
jtclemm
committed
4cd7407
make more compact and consistent
akohlmey
committed
6b281c0
Adding reference to fix freeze
jtclemm
committed
5acf5cd
rename CMAKE_CUSTOM_LINKER CMake variable to LAMMPS_CUSTOM_LINKER
akohlmey
committed
be46b96
update discussions of testing / code analysis link to software engineering paper
akohlmey
committed
b4ea708

Commits on Nov 30, 2025

move doxygen related changes out of this branch to PR #4793
akohlmey
committed
eddad5e

Commits on Dec 1, 2025

Commits on Dec 2, 2025

correct metadata for mW potential file
akohlmey
committed
6d47678
Merge pull request #4791 from akohlmey/collected-small-changes
akohlmey
authored
792d014
Merge branch 'develop' into kk_new_styles
stanmoore1
authored
9e7095b

Commits on Dec 3, 2025

Commits on Dec 4, 2025

Merge pull request #4707 from chogene/fix_elastic_born_silicon
akohlmey
authored
f084c98
Notes on use with rigid
jtclemm
committed
dc59fb7
Merge branch 'develop' of github.com:lammps/lammps into kk_new_styles
stanmoore1
committed
e7cbdce
bugfix from @ndtrung81 for fix rigid/small when using langevin thermostat
akohlmey
committed
cebaa8c
Merge pull request #4689 from bbbaer/develop
akohlmey
authored
4105717
Fix missing data transfer for pair_hybrid_scaled_kokkos
stanmoore1
committed
1bbfc06
Warnings for changing torques w/ rigid
jtclemm
committed
f9c3bce
Fix compile
stanmoore1
committed
5b7a27a
Merge branch 'develop' into kk_new_styles
stanmoore1
authored
f57a600
Use device virial_fdotr
stanmoore1
committed
5ed70a7
Merge remote-tracking branch 'github/develop' into collected-small-fixes
akohlmey
committed
fa89b95
Fix issue in dihedral_fourier_kokkos
stanmoore1
committed
6505391
improve error messages in fix rigid/small
akohlmey
committed
a22ac21

Commits on Dec 5, 2025

remove unused class members
akohlmey
committed
05681a8
remove dead code
akohlmey
committed
13ea2b2
Fix memory allocation issue
stanmoore1
committed
b6ff6dc
Fix compile
stanmoore1
committed
a660132
use branch names to select manual version, add source snapshot download
akohlmey
committed
1a38e8a
Merge branch 'develop' into srd-fix-pbcs
akohlmey
committed
c3e919d
remove debug/development code
akohlmey
committed
4ffc4e6
rename putflag member to unbiasflag for better consistency with the corresponding keyword
akohlmey
committed
a5425fb
Fix more issues in dihedral_fourier_kokkos
stanmoore1
committed
367c705
Fix compile
stanmoore1
committed
2414144
Remove host copy
stanmoore1
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a6b81d5
Small tweaks
stanmoore1
committed
c81cdc9
Tweak data transfer
stanmoore1
committed
ee1164f
improve error messages.
akohlmey
committed
952e7a5
disallow use of INTEL package pair styles with MC fixes that call Pair::compute()
akohlmey
committed
cb6881e
improve some error messages
akohlmey
committed
47c211a
Merge pull request #4590 from taenzel/srd-fix-pbcs
akohlmey
authored
84e757f
Merge remote-tracking branch 'github/develop' into collected-small-fixes
akohlmey
committed
ff884e2
add missing versionadded tag
akohlmey
committed
1633b88

Commits on Dec 6, 2025

Fix segfault
stanmoore1
committed
a14ddc8
Merge branch 'lammps:develop' into harmWallsReturned
Eddy-Barraud
authored
f2dac6c
Update fix_wall documentation, add citations in constructor, and add examples for harmonic/returned wall style
Eddy-Barraud
committed
ae54b67
Refactor fix "propel/selfalign" to "align/self"
jeremyaqp
committed
2321c8c
Alphabetical order for align/self in fix.rst
jeremyaqp
committed
8ac8e76
small changes for consistency and clarity
akohlmey
committed
d8a8380
add a thresh keyword to fix store/state to store data only when the threshold condition is met
akohlmey
committed
44f5e01
add false positive
akohlmey
committed
ca8f7e9
improve error messages
akohlmey
committed
b7db5b1
apply GitHub Copilot suggested minor corrections
akohlmey
committed
a2a07e2

Commits on Dec 7, 2025

Merge branch 'develop' into informative_thermo_column_titles
jrgissing
authored
405642e
Update thermo_modify.rst
jrgissing
committed
f5e8e6f
adjust minimum required GCC compiler version
akohlmey
committed
424e7e5
Merge remote-tracking branch 'github/develop' into BROWNIAN-selfalign
akohlmey
committed
0922a8b
small doc improvements
akohlmey
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61f08b3
small error message improvements, apply clang-format
akohlmey
committed
fb48033
small example updates, use consistent naming (for regression testing)
akohlmey
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ca2da24
reaxff/speces: delete subgroup
jrgissing
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85fa29f
docs
jrgissing
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15245b1
glitch in the matrix
jrgissing
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b97801e
bad logic
jrgissing
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c5a734d

Commits on Dec 9, 2025

Commits on Dec 10, 2025

Merge pull request #4795 from jtclemm/granular-updates
akohlmey
authored
3fe3ea4
fully integrate fix wall/harmonic/outside address rst syntax issues
akohlmey
committed
8c9ce03
add versionadded tags
akohlmey
committed
a5a8499
add missing escapes and make formatting consistent with other doc files
akohlmey
committed
55ac8f3
Merge branch 'develop' into last-minute-fixes
akohlmey
committed
05b796c
correct reference
akohlmey
committed
572790a
add versionadded tag
akohlmey
committed
2f1873f
Merge pull request #4792 from jasnacios/BROWNIAN-selfalign
akohlmey
authored
fc7e70f
Merge branch 'develop' into last-minute-fixes
akohlmey
committed
88500a1
correct reference for recently changed command name
akohlmey
committed
56806c0
spelling
akohlmey
committed
4e80714
Merge pull request #4802 from jrgissing/reaxff-species-delete-subgroup
akohlmey
authored
07dc5c3
apply fixes from static code analysis
akohlmey
committed
213edd7
address minor issues flagged by coverity scan
akohlmey
committed
1aa5c6c
Merge branch 'develop' into nick-pppm-performance-improvements
akohlmey
authored
cec67c8
Rename flag
stanmoore1
committed
f89472b
Update version strings for a 10 December 2025 release date
akohlmey
committed
396b36b
Merge remote-tracking branch 'github/develop' into next_release
akohlmey
committed
cbb089f
update tag
akohlmey
committed
3127d2a
update release step docs for lack of Jenkins processing and immutable releases
akohlmey
committed
0aa0811
Merge remote-tracking branch 'github/develop' into last-minute-fixes
akohlmey
committed
9e8296d
simplify handling of collective and nonblocking exclusivity
akohlmey
committed
b0e6197
add version tag
akohlmey
committed
033af47
avoid memory leaks and correct call to free plan
akohlmey
committed
f98de9e
Merge pull request #4789 from hagertnl/nick-pppm-performance-improvements
akohlmey
authored
eb1f7aa
Merge remote-tracking branch 'github/develop' into last-minute-fixes
akohlmey
committed
9f9e7e2
add missing false positive
akohlmey
committed
96a15e2
plug tiny memory leak
akohlmey
committed
5362692
simplify logic to free allocated plan buffers
akohlmey
committed
cda77b8
translate remap memory leak fix to KOKKOS
akohlmey
committed
df27384
need explicit destructor to free bond/angle/dihedral/improper lists in KOKKOS
akohlmey
committed
78da5f9
Merge remote-tracking branch 'github/doc-page-mc-only-hint' into last-minute-fixes
akohlmey
committed
5ca3545
Merge pull request #4805 from akohlmey/last-minute-fixes
akohlmey
authored
33499fd
Merge branch 'develop' into next_release
akohlmey
committed
d065633
add a few more version tags
akohlmey
committed
47ea8be
correct indentation
akohlmey
committed
341ea48
avoid malloc(0)
akohlmey
committed
62b9d8a

Commits on Dec 11, 2025

Merge pull request #4806 from akohlmey/next_release
akohlmey
authored
cd8851c
add scripts for building and updates source tarballs and release manual
akohlmey
committed
8e78b4c
avoid malloc(0)
akohlmey
committed
e323cd2
remove AWPMD package doc files that somehow must have crept back in
akohlmey
committed
f324826
Merge branch 'develop' into kk_update_5.0
akohlmey
authored
45ea468
improve kspace_modify error messages. Print setting summary for some settings
akohlmey
committed
2625f10
improve some more kspace base class error messages
akohlmey
committed
4bb98e2
whitespace
akohlmey
committed
b5ecffa
fix bugs in forward_comm_kokkos
wcwitt
committed
51a567c
fix bugs in reverse_comm_kokkos
wcwitt
committed
3eb6798
fix additional bug in unpack_reverse_comm_kokkos
wcwitt
committed
1afc42c
remove KOKKOS package from legacy build system
akohlmey
committed
abcadad
update manual for removal of traditional build support with KOKKOS
akohlmey
committed
70cf3af
remove obsolete machine makefile
akohlmey
committed
a572d8d

Commits on Dec 12, 2025

free all allocated memory blocks in remap plan when one of them fails
akohlmey
committed
7772b50
Fix loop condition bug in BondHybrid::copy_svector
poyais001
committed
1102141
Fix loop condition bug in PairHybrid::copy_svector
poyais001
committed
7b8dbdf
add copilot instructions for some code maintenance tasks needed to be checked in review
akohlmey
committed
cb4f2ec
Fix loop condition bug in PairHybrid::copy_svector

poyais001
authored and
akohlmey
committed
d86cb48
Fix loop condition bug in BondHybrid::copy_svector

poyais001
authored and
akohlmey
committed
9cf22c4
Merge pull request #4807 from akohlmey/collected-small-changes
akohlmey
authored
372c8cd
flag branch as development branch again
akohlmey
committed
bee36ac
Merge pull request #4809 from poyais001/develop
akohlmey
authored
c6a51b6
add support for brotli and 7-zip compression formats and use more checks
akohlmey
committed
733c0a4
add support for writing compressed data files
akohlmey
committed
c26ec14
update docs with additional compression format info
akohlmey
committed
1332ec0
Merge branch 'develop' into add-brotli-support
akohlmey
committed
2290d26
implement the suggestions from GitHub Copilot what were correct
akohlmey
committed
4302838

Commits on Dec 13, 2025

Commits on Dec 14, 2025

move enum for object types passed from external code to header for consistency
akohlmey
committed
425fe42
improve dump image support for rendering objects from fixes
akohlmey
committed
d9e0c5e
add support for rendering indenter objects with dump image
akohlmey
committed
242803a
add color name "none" which will return a null pointer
akohlmey
committed
4b44086
document Fix::image() in fix modification/addition docs
akohlmey
committed
7e5f869
small improvements and corrections suggested by GitHub Copilot
akohlmey
committed
bbea941
invert logic for fflag2 dump image settings to avoid double negative adjustments
akohlmey
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0c3e513
add support for planar indenter
akohlmey
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e7ea831
apply clang-format
akohlmey
committed
6df3e01
add dump image support to walls derived from FixWall
akohlmey
committed
62c37e3

Commits on Dec 15, 2025

render planar indenters or walls as cylinders in 2d.
akohlmey
committed
84d8f0d
add check if valid image data is available from fix for dump image
akohlmey
committed
0a4db01
fix typos
akohlmey
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f7567cc
support rendering of objects from multiple fixes
akohlmey
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bf8a2cc
enable and apply clang-format
akohlmey
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e840a14
add dump image support to fix smd/wall_surface
akohlmey
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0f3d67e
add note for @sjplimp
akohlmey
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1df94f4
update docs
akohlmey
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08b5086
improve comment
akohlmey
committed
ffe3210
fix copy-n-modify bug
akohlmey
committed
6207eb6
Merge pull request #4811 from akohlmey/remap-refactor
akohlmey
authored
425b793

Commits on Dec 16, 2025

add support for rendering bonds from fixes
akohlmey
committed
4a25792
Merge pull request #4808 from wcwitt/mliap-bugfix
akohlmey
authored
e9c20b8
remove dead code
akohlmey
committed
15a84ce
add support for dump image to fix reaxff/bonds
akohlmey
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f00a3f2
add dump image fix support to reflective walls
akohlmey
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e73b101
avoid segfault for unknown color with dump modify fcolor
akohlmey
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35fd125
draft implementation of fix graphics
akohlmey
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5cd1d31
Merge remote-tracking branch 'github/develop' into fix-indent-dump-image
akohlmey
committed
fe614a1
The kspace_modify keyword "eigtol" was renamed to "splittol" in the manual but not in the code
akohlmey
committed
dc2f32d
small update to regression script from Trung
akohlmey
committed
629e75f
input radius instead of diameter for consistency with other LAMMPS commands describing spheres
akohlmey
committed
e546ac4
wrap around type index for fix object coloring if the type exceeds the number of available types
akohlmey
committed
f772850
add documentation for fix graphics command
akohlmey
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6ede156
avoid redundant code
akohlmey
committed
85868ba

Commits on Dec 17, 2025

add cylinder object to fix graphics
akohlmey
committed
2f61af6
add draft/partial versions of arrow and progress bar
akohlmey
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4f0a5da
complete progress bar implementation
akohlmey
committed
dd010d9
make sure that theta for regions is always initialized
akohlmey
committed
4f81b9b
small correction to dump command docs reported on MatSci.org
akohlmey
committed
f25186f
add missing .. versionadded:: tag
akohlmey
committed
4e0d42b
implement fixes suggested by GitHub Copilot
akohlmey
committed
c004374
grammar
akohlmey
committed
0942389
Merge pull request #4778 from stanmoore1/kk_update_5.0
akohlmey
authored
97341a8
update fix graphics docs and add example
akohlmey
committed
3f956fc
consolidate the code to render planar walls and constants into FixWall
akohlmey
committed
c15eefb
add dump image support to fix wall/gran mostly reusing and adapting to FixWall code
akohlmey
committed
3fcc428
cosmetic changes
akohlmey
committed
4a3f648
Merge remote-tracking branch 'github/develop' into fix-indent-dump-image
akohlmey
committed
8dad551
bracket progress value to [0,1] rather than throwing an error
akohlmey
committed
71ea35f
apply clang-format
akohlmey
committed
a604c03
add some more docs to fix graphics
akohlmey
committed
9c19362
Merge remote-tracking branch 'github/develop' into collected-small-fixes
akohlmey
committed
4c64f5f
fix typo
akohlmey
committed
c73a8c8
correct section reference numbers
akohlmey
committed
5f93028
remove needless indentation and make "none" sections consistent
akohlmey
committed
2042104

Commits on Dec 18, 2025

add support for screen-door transparency to Image class
akohlmey
committed
6561ebb
add support for opacity to regions and graphics from fixes using triangulated surfaces
akohlmey
committed
5ac14d1
update docs for transparency support of regions and fixes
akohlmey
committed
0151d29
fix typos
akohlmey
committed
69ac919
add forgotten opacity argument
akohlmey
committed
4518d7f
remove redundant code
akohlmey
committed
6898322
add support for transparency to atoms, bonds, box, subbox, and axes
akohlmey
committed
f3137c5
document transparency settings
akohlmey
committed
6b1d4d3
add alternate threshold matrix and use symbolic constants instead of magic numbers
akohlmey
committed
bd0effb
it's -> its
akohlmey
committed
4ea6385
remove zcylinder option from fix wall/gran
akohlmey
committed
9d36d64

Commits on Dec 19, 2025

stick to Bayer matrix only and recommend 0.25, 0.5, or 0.75 with FSAA
akohlmey
committed
59d391e
silence warning
akohlmey
committed
304994a
Clarify fix align-self doc
jeremyaqp
committed
4a36b4e
small corrections and updates
akohlmey
committed
44954f7
Merge pull request #80 from jasnacios/fix-align-self-doc-correction
akohlmey
authored
5e14b2d
Merge branch 'collected-small-fixes' of github.com:akohlmey/lammps into collected-small-fixes
akohlmey
committed
12df8d5
Merge pull request #4812 from akohlmey/fix-indent-dump-image
akohlmey
authored
c4e55dc
Merge branch 'develop' into collected-small-fixes
akohlmey
committed
43a051e
rewrap text
akohlmey
committed
81c2423
Merge pull request #4816 from akohlmey/collected-small-fixes
akohlmey
authored
a51f9ba

Commits on Dec 25, 2025

reacter json and constraint keyword
salamaaya
committed
5a5c859
update constraints json
salamaaya
committed
34ccb92
functional parsing of constraints json
salamaaya
committed
7dd208d