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Develop#25

Merged
ohenrich merged 878 commits intooxdna3from
develop
Jul 24, 2025
Merged

Develop#25
ohenrich merged 878 commits intooxdna3from
develop

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@ohenrich ohenrich commented Jul 24, 2025 •
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Merging latest changes from upstream develop into oxdna3

akohlmey and others added 30 commits July 6, 2025 05:25
@akohlmey
improve error message
cdded2d
@akohlmey
remove unused class member and dead code
72d73c4
@akohlmey
modernize
8e75c38
@akohlmey
Mention LAMMPS-GUI as an example application for liblammpsplugin.h/.c
fbf8856
@akohlmey
reorder initializer
eaa3159
@akohlmey
use bool literals instead of integer constants
8ba1b9b
@akohlmey
use using
916655e
@akohlmey
make sure these variables are always initialized
a239e2b
@akohlmey
display new LAMMPS-GUI banner image in docs and empty editor windows
9f05511
@akohlmey
fix typo
ddfc3f2
@akohlmey
avoid crash from out-of-range access to string for partially quoted text
806000c
@akohlmey
must clear variables before starting a new run since "clear" does not…
477c352 
… delete them
@akohlmey
update changelog
ea939f6
@akohlmey
avoid crash when splitting line with incomplete quoting into words
40b510c
@akohlmey
align with common conventions for pages documenting multiple similar …
adead22 
…styles
@akohlmey
simplify
e4f9874
@akohlmey
simplify
adc202b
@akohlmey
add unit tests for additional conditions for splitting strings
25556a1
@akohlmey
small tweaks to error message boxes
5a158d5
@akohlmey
add a timeout option to the geturl command and set a default of 5 mins
1dc8c2d 
the library default is to wait forever. Also the limit for connecting
was reduced to 30 seconds from 300.
@akohlmey
must use error->one() since only rank 0 is active at this point
0502d42
@stanmoore1
Fix issue with Kokkos SNAP on GPUs
a243903
@stanmoore1
Merge branch 'develop' into backport_bugfixes
fd86fea
@akohlmey
save and restore PATH and LD_LIBRARY_PATH, so that xdg-open can launc…
892c969 
…h a native executable
@akohlmey
fix typo
fd98ef2
@akohlmey
document Relaunch LAMMPS Instance
4b2a04a
@akohlmey
prevent using Restart LAMMPS while running and rename to Relaunch LAMMPS
5ec4a6b
@akohlmey
delete app bundle folder. It will be recreated by macdeplotqt.
7a2c051
@akohlmey
fix grammar and reformat
2b8b847
@akohlmey
must use a platform specific copy command
ace1b80
akohlmey added 29 commits July 19, 2025 10:05
@akohlmey
update theme to version 3.0.2, make search box local by default.
8e361c0
@akohlmey
some more small updates to suppress or avoid clang-tidy and clangsa w…
a4dd1a0 
…arnings
@akohlmey
replace MyMult everywhere with AkMult. Results are unchanged. Runs fa…
5abcd77 
…ster.
@akohlmey
avoid needless conversion to double and back.
6b6e04d
@akohlmey
suppress more clang-tidy warnings. add missing override qualifiers
8a5b32e
@akohlmey
reduce excessive warnings in Lepton package with clang
045d8c0
@akohlmey
cosmetic
4962bcf
@akohlmey
test a few more features of the plugin command
6baea75
@akohlmey
add test for occasional command list
82ea12f
@akohlmey
add test for pair style set to none
e82d0f7
@akohlmey
fix syntax error
bc72e12
@akohlmey
use alternate approach for matching output
164208a
@akohlmey
add tests for thermo keywords
5564920
@akohlmey
cosmetic
45e4725
@akohlmey
change bond coeffs to have better test coverage
1f892eb
@akohlmey
make names of neighbor list pair builds consistent
22e1be3
@akohlmey
copy and adapt neighbor list tests of OPENMP package
40645d9
@akohlmey
add missing property
8745a1e
@akohlmey
check for Pair::extract() also when using OPENMP
be9103d
@akohlmey
skip unsupported tests
6523f6c
@akohlmey
output nested coverage pages
2acea45
@akohlmey
add tests for atom style template
19b9366
@akohlmey
set version date for next release
b9db65b
@akohlmey
add missing checks for installed MEAM package
b3f4fa6
@akohlmey
correctly detect if OPENMP packages is installed
0189e0a
@akohlmey
Merge pull request lammps#4661 from akohlmey/collected-small-changes
684ca17 
Collected small fixes and updates
@akohlmey
Merge branch 'develop' into next_release
b3590a9
@akohlmey
flag bond quartic test as unstable for passing arm64 test
3c517b7
@akohlmey
Merge pull request lammps#4662 from akohlmey/next_release
51d6927 
Set version date for stable release candidate
@ohenrich ohenrich merged commit c65cb12 into oxdna3 Jul 24, 2025
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9 participants

@ohenrich @akohlmey @stanmoore1 @jmgoff @jtavenner-dev @Bibobu @yotamfe @evoyiatzis @weinbe2