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766c20f
add test to detect if a potential file was incorrectly used with lgvd…
akohlmey Feb 26, 2025
a540efb
bugfix from Trung to avoid problems with read_dump when not all MPI r…
akohlmey Feb 26, 2025
4d68e17
only trim if neighbor list request has a custom cutoff
akohlmey Mar 5, 2025
f184540
use pairwise cutoff for trimming unless a custom cutoff if given
akohlmey Mar 5, 2025
3e7aea5
use different method to enforce the C locale in LAMMPS GUI
akohlmey Mar 5, 2025
cb92b11
reverse normalization between type pairs if the types were swapped on…
akohlmey Mar 6, 2025
3c681fb
rewrite incorrect statement
akohlmey Mar 6, 2025
158d94c
error out when trying unsupported pimd method with multiple processor…
akohlmey Mar 7, 2025
717eb39
set stores_ids flag for some fixes as suggested by @sjplimp
akohlmey Mar 7, 2025
4ddfcf9
properly tally the SYNC time contributions to the ALL time entry
akohlmey Mar 10, 2025
ac03e71
fix bug missing a read_int() when reading general triclinic rotation …
akohlmey Mar 14, 2025
ae324cc
update to WHAM version 2.1.0
akohlmey Mar 16, 2025
384f2ef
temporarily comment out incomplete run WHAM and plot results dialog f…
akohlmey Mar 16, 2025
5f2e86e
flag as maintenance version again
akohlmey Mar 17, 2025
3a8b083
fix indexing bug for optional arguments of compute reduce and reduce/…
akohlmey Mar 19, 2025
35b071a
wrong qi*qj cuda code
Eddy-Barraud Mar 24, 2025
f33a908
fix logic bug when writing coeffs to data file
akohlmey Mar 25, 2025
2226314
added boolean
Eddy-Barraud Mar 24, 2025
913b9a9
correct data in data file and pair_coeff changes are no longer needed
akohlmey Mar 25, 2025
83c3c61
fix bug with addstep_compute skipping on first step
akohlmey Mar 27, 2025
c699394
must use addstep_compute() on next time based or variable step dump o…
akohlmey Mar 28, 2025
c23f821
forgot handling addstep_compute in setup()
akohlmey Mar 28, 2025
b6189b2
switch CWD to home if default is "/" or contains "AppData"
akohlmey Apr 1, 2025
7de3ef4
fix syntax error
akohlmey Apr 1, 2025
4f27878
looking for libcurl components fails for some installations
akohlmey Apr 3, 2025
8caa997
set LAMMPS-GUI version
akohlmey Apr 4, 2025
680d39f
allow to set https_proxy via preferences if not set via environment v…
akohlmey Apr 4, 2025
d97fd0a
synchronize LAMMPS-GUI with upstream
akohlmey Apr 4, 2025
54a3508
don't mix malloc() and delete
akohlmey Apr 4, 2025
be88d7a
make consistent, remove ghost member map
akohlmey Apr 4, 2025
87e4566
add support for compiling fully static LAMMPS executable with libcurl
akohlmey Apr 4, 2025
c753d52
cutghost is not used anyware; remove to plug memory leaks
akohlmey Apr 4, 2025
465d074
must not allocate eatom and vatom in base class to avoid big memory leak
akohlmey Apr 4, 2025
2701592
no need to call allocate() of the base class
akohlmey Apr 4, 2025
0df511f
fix memory leak in test
akohlmey Apr 5, 2025
5009d63
must not call plain ev_init() from KOKKOS without setting alloc to 0 …
akohlmey Apr 5, 2025
4001c5f
plug memory leak
akohlmey Apr 5, 2025
d5f22c0
fix acks2/reaxff/kk should use post_constructor() like base class for…
akohlmey Apr 5, 2025
70f14c0
synchronize valgrind suppressions with develop tree
akohlmey Apr 6, 2025
a9c2346
avoid accessing uninitialized data. was missing from bugfix backport
akohlmey Apr 6, 2025
9ceb0a3
replace WHERE construct with simple DO loop over number of atoms to a…
akohlmey Apr 6, 2025
998aedf
must force OMP_NUM_THREADS=1 for all tests to pass
akohlmey Apr 6, 2025
98cc1b1
must not allocate eatom and vatom when called from KOKKOS version (wh…
akohlmey Apr 6, 2025
ce079bb
plug memory leak in SO3 descriptor for pair style mliap/kk
akohlmey Apr 6, 2025
a8169c7
simplify suppression fingerprint to match more cases
akohlmey Apr 6, 2025
2a44d09
backport mliappy bugfix from upstream
akohlmey Apr 7, 2025
fb13484
add missing entry to OpenMP reduction clause.
akohlmey Apr 8, 2025
5cfc80a
backport ML-IAP / KOKKOS fixes from upstream
akohlmey Apr 8, 2025
fb99dda
only compute special neighbors of a template if it has bonds
akohlmey Apr 9, 2025
c933c27
sync LAMMPS-GUI with upstream
akohlmey Apr 10, 2025
ef25be2
synchronize LAMMPS-GUI and docs with upstream
akohlmey Apr 14, 2025
6aa2280
Rephrasing suggested by @simongravelle
akohlmey Apr 14, 2025
5bae363
make minimize work with KOKKOS package without -suffix or suffix command
akohlmey Apr 14, 2025
a8d32e2
error out or ignore on displacements in z-direction with 2d system
akohlmey Apr 16, 2025
b6e2570
don't increment iarg twice for the same keywords, backported from PR …
akohlmey Apr 21, 2025
3921db5
implement workaround for compilers that require -DFMT_STATIC_THOUSAND…
akohlmey Apr 23, 2025
abc22c1
two more workarounds for compilation with -DFMT_STATIC_THOUSANDS_SEPA…
akohlmey Apr 25, 2025
55b27f7
Fix typo in src/timer.cpp
akohlmey Apr 24, 2025
d72cab9
sync LAMMPS-GUI with state from develop branch
akohlmey Apr 29, 2025
7d7cfd5
update reference data in test which was updated in KIM database
akohlmey Apr 29, 2025
47fcf25
add citation reminder
akohlmey Apr 30, 2025
793af90
indexing bug fix for ghost comm of remapped velocities across PBC whe…
sjplimp Apr 24, 2025
d3dc2ae
port ghost atom velocity bugfix to KOKKOS
akohlmey Apr 30, 2025
4938fb3
improve warning and explanation about too short communication cutoff
akohlmey Apr 30, 2025
3b382d8
update magic file and point to origin
akohlmey May 29, 2025
cf9c2bd
eliminate warning (doesn't change results since we don't compute pair…
akohlmey May 28, 2025
de3ce13
avoid problems with consteval
akohlmey May 30, 2025
c2d8807
cstdbool header is deprecated and no longer needed with recent compilers
akohlmey Feb 1, 2025
dbd7b94
silence compiler warnings
akohlmey May 30, 2025
f080a8a
Marking scalar intensive in elec/stop/fit fix
jtclemm Jan 29, 2025
e7b3fbe
Bugfix from Trung for running EAM on GPUs with OpenCL.
akohlmey May 30, 2025
d003f78
fix minimum image bug detected by GitHub Copilot
akohlmey Jun 1, 2025
6178fdc
apply `-DLAMMPS_${LAMMPS_SIZES}` consistently across all platforms
akohlmey Jun 3, 2025
16f5c1e
sync application of LAMMPS integer size settings with upstream
akohlmey Jun 3, 2025
c90060b
remove undesired tag from test yaml file
akohlmey Jun 3, 2025
fb675e8
accept denormal floating point numbers in tokenizer class and utils::…
akohlmey Jun 5, 2025
a143af6
add special case for setting locale on macOS based on suggestion from…
akohlmey Jun 8, 2025
2b44c30
record changes to LAMMPS-GUI for flatpak build
akohlmey Jun 8, 2025
7295b5e
sync with upstream
akohlmey Jun 8, 2025
1a83d54
flag version as stable update
akohlmey Jun 9, 2025
2ce0507
Insert pre-titlepage text asking about removal of PDF version.
akohlmey Jun 10, 2025
5817f4c
backport bugfix for segfaulting (kspace) styles from plugins from ups…
akohlmey Jun 11, 2025
c93a8f1
unscale for error message. use correct array for masses
akohlmey Jun 11, 2025
51cf696
dipole moment z-component must be zero for 2d sims
akohlmey Jun 12, 2025
c034139
Revert "Insert pre-titlepage text asking about removal of PDF version."
akohlmey Jun 12, 2025
2a79afe
Fix GPU architecture in CUDA preset for Kokkos
DaKerboul Jun 12, 2025
1213ff8
Merge pull request #4531 from lammps/maintenance
akohlmey Jun 13, 2025
7479dd7
flag branch as maintenance branch again
akohlmey Jun 13, 2025
bdb9ac0
add error to CreateAtoms for per-atom systems
FelixWodaczek Jun 11, 2025
5673d89
Merge branch 'stable' into maintenance
akohlmey Jun 14, 2025
0d17c8d
move redundant code to find pointer to main widget to helper function
akohlmey Jun 14, 2025
f92ef21
update label only when needed
akohlmey Jun 14, 2025
e377177
update changelog
akohlmey Jun 14, 2025
cf91942
error out of compute msd if the number of atoms in the compute group …
akohlmey Jun 17, 2025
07f54af
backport fixes from upstream to make molecule command behave like doc…
akohlmey Jun 17, 2025
0acb5ce
fix out-of-bounds access bug reported in issue #4632
akohlmey Jun 17, 2025
6a185ee
fix out-of-bounds initialization for cvatom array
akohlmey Jun 17, 2025
37b79f5
fix indexing bugs in Shake Atoms and Shake Bond Types sections
akohlmey Jun 18, 2025
0aa16b1
correct error message
akohlmey Jun 20, 2025
3cbcd80
correctly count created bodies
akohlmey Jun 20, 2025
501bbce
must require Masses section with Body sections
akohlmey Jun 20, 2025
9931862
stricter matching of header keywords
akohlmey Jun 20, 2025
cfd57fc
correctly honor atom-id in Special Bond Counts section
akohlmey Jun 21, 2025
6f180f0
Merge branch 'maintenance' of github.com:lammps/lammps into maintenance
akohlmey Jun 21, 2025
c491222
fix up special_read() function to honor atom-IDs
akohlmey Jun 21, 2025
5e3a518
there is no need to using tagints in molecule templates
akohlmey Jun 21, 2025
c5b8ab0
make python lammps_open() unit test compatible with mpi4py version 4
akohlmey Jun 21, 2025
c35ccff
Revert "there is no need to using tagints in molecule templates"
akohlmey Jun 21, 2025
e71597b
add missing check for atom-ids
akohlmey Jun 21, 2025
5e2d66a
avoid out-of-bounds memory access when registering fix external callb…
akohlmey Jun 21, 2025
8befb8d
make fix deposit and fix pour compatible with body particles from mol…
akohlmey Jun 21, 2025
f13a31b
backport KOKKOS fixes from upstream
akohlmey Jun 27, 2025
b55945f
Merge branch 'maintenance' of github.com:lammps/lammps into maintenance
akohlmey Jun 27, 2025
008925d
backport significant fixes from PR #4634
akohlmey Jun 28, 2025
f16adc8
recognize a couple more Windows build numbers
akohlmey Jun 28, 2025
0d6622a
bugfix for improper style class2/kk taken from PR 4593
akohlmey Jun 29, 2025
4bd215a
fix bug detected by static code analysis
akohlmey Jun 30, 2025
5495855
fix up emitterutils source file in bundled yaml-cpp in ML-PACE for GC…
akohlmey Jun 30, 2025
640eef4
remove accidentally included file
akohlmey Jun 30, 2025
2d36fd7
Sync LAMMPS-GUI code with upstream
akohlmey Jul 3, 2025
4b7d38b
More fixes and optimizations for LAMMPS-GUI from upstream
akohlmey Jul 3, 2025
33d5546
cache spcpu and tpcpu values so these thermo keywords can be used mul…
akohlmey Jul 5, 2025
20e61ca
update handling of threads. make nthreads and LammpsGui class member
akohlmey Jul 4, 2025
4fefa71
only reset cached thermo data if first run or thermo style changed
akohlmey Jul 5, 2025
24ab7e4
make handling of threads and accelerator selection more consistent, a…
akohlmey Jul 5, 2025
9686bdb
update nthreads text field when accelerator is selected
akohlmey Jul 5, 2025
9355fd7
resolve hotkey conflict for selecting GPU accelerator package
akohlmey Jul 5, 2025
46b23a0
set LAMMPS-GUI version to 1.6.15
akohlmey Jul 5, 2025
55a652e
support setting intel precision and gpu neigh and pair/only from pref…
akohlmey Jul 5, 2025
766ae5a
add cpuuse thermo keyword needed for LAMMPS-GUI
akohlmey Jul 5, 2025
1a78d3c
add a CPU usage percentage indicator to the status bar
akohlmey Jul 5, 2025
bd3a9d6
small improvements suggested by GitHub Copilot
akohlmey Jul 6, 2025
46ba6a2
update LAMMPS-GUI documentation for most recent changes
akohlmey Jul 6, 2025
0378aac
reduce overhead and avoid stalling by increasing the pipe buffer from…
akohlmey Jul 6, 2025
2592f2f
track buffer usage and add API to query the maximum buffer use ratio
akohlmey Jul 6, 2025
8d13b87
show warning dialog at end of run, if I/O buffer usage was very high
akohlmey Jul 6, 2025
093a68c
support extracting thermo settings for use with LAMMPS-GUI
akohlmey Jul 6, 2025
cf60e5b
add missing screenshot
akohlmey Jul 6, 2025
b6a671e
implement suggestion from GitHub CoPilot to make code consistent and …
akohlmey Jul 6, 2025
36ccd88
remove dead code and apply changes for clean compilation w/o OpenMP
akohlmey Jul 6, 2025
5406f12
display new LAMMPS-GUI banner image in docs and empty editor windows
akohlmey Jul 7, 2025
183eec3
fix typo
akohlmey Jul 7, 2025
abedb90
avoid crash from out-of-range access to string for partially quoted text
akohlmey Jul 7, 2025
3ab3441
must clear variables before starting a new run since "clear" does not…
akohlmey Jul 7, 2025
30b5d49
update changelog
akohlmey Jul 7, 2025
0871a4d
avoid crash when splitting line with incomplete quoting into words
akohlmey Jul 7, 2025
544325e
simplify
akohlmey Jul 7, 2025
2e4e637
small tweaks to error message boxes
akohlmey Jul 7, 2025
940b975
save and restore PATH and LD_LIBRARY_PATH, so that xdg-open can launc…
akohlmey Jul 8, 2025
295b3fd
fix typo
akohlmey Jul 8, 2025
c186e03
document Relaunch LAMMPS Instance
akohlmey Jul 8, 2025
bc7087a
prevent using Restart LAMMPS while running and rename to Relaunch LAMMPS
akohlmey Jul 8, 2025
2f2ea0a
delete app bundle folder. It will be recreated by macdeplotqt.
akohlmey Jul 8, 2025
1ef3180
must use a platform specific copy command
akohlmey Jul 8, 2025
cf3c994
there is not much meaning in completing capture in the destructor.
akohlmey Jul 8, 2025
08f7b86
automatically quit the entire application when closing the editor window
akohlmey Jul 8, 2025
274b57c
redesign the General settings preference tab and add defaults for tut…
akohlmey Jul 8, 2025
187fb06
must use recursive delete on app bundle folder
akohlmey Jul 8, 2025
6ee3f23
to update the time stamp on the app bundle purge it during configure
akohlmey Jul 8, 2025
fbbb693
make precence explicit
akohlmey Jul 8, 2025
7e0b5f1
fix crash on trying to free a NULL communicator
akohlmey Jul 8, 2025
361d0f8
set LAMMPS-GUI version number to 1.7
akohlmey Jul 8, 2025
ebc2ca3
apply and edit some changes suggested by @simongravelle
akohlmey Jul 9, 2025
680580d
remove rubberband feature since undoing the zoom doesn't work properly
akohlmey Jul 9, 2025
80b1964
refactor chart viewer title line. Now has two rows. display units and…
akohlmey Jul 9, 2025
0d4a372
add rangeslider custom widget
akohlmey Jul 10, 2025
9369877
add rangeslider to chart window to plot subsets of data
akohlmey Jul 10, 2025
53dcc52
intergrate the rest of simon's suggestions
akohlmey Jul 10, 2025
1e5763c
add tooltips
akohlmey Jul 10, 2025
b28b3e3
avoid crashes when switching to a new file or a new empty document an…
akohlmey Jul 10, 2025
acaa627
avoid uninitialized access to normflag
akohlmey Jul 10, 2025
93b8242
add a couple horizontal separator lines
akohlmey Jul 10, 2025
bd2d8fc
update docs and screen shot
akohlmey Jul 10, 2025
ec026ad
minor doc tweaks for readability
akohlmey Jul 10, 2025
ba21aef
enable option to open the tutorial webpage for tutorial 8
akohlmey Jul 10, 2025
3cde83c
fix halt may only reset the timer timeout, if it trigged the timeout …
akohlmey Jul 10, 2025
18acaba
add ticks to range sliders
akohlmey Jul 10, 2025
3f192de
cosmetic suggestions from GitHub Copilot
akohlmey Jul 10, 2025
29ff248
fully restore original script code
akohlmey Jul 11, 2025
0cb9732
only restore old paths, if they exist, i.e. we are called from within…
akohlmey Jul 11, 2025
f4a67a3
add small tweaks to the LAMMPS-GUI banner and how it is shown
akohlmey Jul 11, 2025
74b2286
silence compiler warnings and apply small corrections
akohlmey Jul 11, 2025
d5a42bd
correct implementation of restart for fix sprint/chunk
akohlmey Jul 11, 2025
98694d4
Fix issues in GNU Makefile build system with KOKKOS package
stanmoore1 Jul 11, 2025
58bf339
Merge branch 'maintenance' of github.com:lammps/lammps into maintenance
akohlmey Jul 11, 2025
b5fc77d
make Atom::set_mass() as called from pair styles compatible with per-…
akohlmey Jul 11, 2025
2007160
make sure that qtype is set consistently across all processors
akohlmey Jul 11, 2025
4da4e14
fix_modify colname has no effect, remove
akohlmey Jul 13, 2025
dbfdf7c
make "weight" variable double and thus avoid multiple int<->double co…
akohlmey Jul 15, 2025
789e6bb
neighbor list selection tuning bugfix from Stan
akohlmey Jul 16, 2025
733671f
Revert "neighbor list selection tuning bugfix from Stan"
akohlmey Jul 21, 2025
0c0be33
flag version as stable release update 4
akohlmey Jul 21, 2025
1f40194
Merge pull request #4629 from lammps/maintenance
akohlmey Jul 22, 2025
21c9dba
Merge branch 'release' into stable
akohlmey Jul 22, 2025
adb90ef
sync with release branch
akohlmey Jul 22, 2025
b9523c0
flag as maintenance version
akohlmey Jul 22, 2025
1908574
fix incorrect conversion of argument to integer into conversion to do…
akohlmey Aug 2, 2025
2283a9f
correct misformed or broken external URLs
akohlmey Aug 3, 2025
031949e
remove or fix up external URLs and internal references
akohlmey Aug 3, 2025
b04b952
step LAMMPS-GUI version number to 1.7.1
akohlmey Aug 4, 2025
4ee4ffa
update requirements for current sphinx theme
akohlmey Aug 4, 2025
eded277
update help info for doc folder makefile
akohlmey Aug 4, 2025
a9ff376
ignore copied file
akohlmey Aug 4, 2025
580f868
backport fix bond/react bugfixes from upstream
jrgissing Aug 4, 2025
55a29ae
update or fix some more URLs
akohlmey Aug 5, 2025
811fcdc
stop with error instead of segfault if we have inconsistent topology …
akohlmey Aug 7, 2025
80b36bd
update fix python/move example to match current code, add group example
akohlmey Aug 7, 2025
4cc98d0
change behavior of lmp.available_ids() for groups to account for "hol…
akohlmey Aug 7, 2025
036ea4f
update unit tests for change in lmp.available_ids()
akohlmey Aug 7, 2025
8df1fd9
correct overlooked deprecation note
akohlmey Aug 8, 2025
d1ffcfd
avoid segfault
akohlmey Aug 10, 2025
05cb622
refactor how fix shake applies restraints during minimization
akohlmey Aug 11, 2025
c5ed21b
correct error message
akohlmey Aug 11, 2025
7b0da6d
backport bugfixes to BPM/RHEO/GRANULAR from PR #4685
akohlmey Aug 12, 2025
64fea0e
protect shell command against path names with whitespace
akohlmey Aug 12, 2025
5de31e6
move split_line function to helpers so it can be reused
akohlmey Aug 12, 2025
9fb5343
must use split_line() to properly handle command lines with quotes
akohlmey Aug 12, 2025
89432fd
fix bug ignoring user cutoff in compute rdf
akohlmey Aug 15, 2025
396a26c
revert back to version 1.7.0 for LAMMPS-GUI to tell it apart from 1.7.1
akohlmey Aug 16, 2025
8f4e4a2
document required versions and refuse to run with an too old LAMMPS v…
akohlmey Aug 17, 2025
1faca5d
update tutorial authors
akohlmey Aug 17, 2025
b93cce4
fix typo
akohlmey Aug 17, 2025
79430ee
update changelog
akohlmey Aug 17, 2025
dcdb65d
static global properties/functions can be accessed without a LAMMPS i…
akohlmey Aug 21, 2025
29d4826
update backported bug fixes to BPM/RHEO from PR #4685
akohlmey Aug 22, 2025
f786dca
avoid accessing already freed memory while deleting all computes
akohlmey Aug 23, 2025
260663f
correct error in CMake based html doc generation
akohlmey Aug 25, 2025
ddafeb4
correct embedded doxygen documentation comments
akohlmey Aug 25, 2025
f6b803c
update Pygments lexer for LAMMPS input file commands
akohlmey Aug 24, 2025
2e0367d
must not use .rst suffix when referring to doc files.
akohlmey Aug 25, 2025
64108d2
fix typo
akohlmey Aug 25, 2025
de81a3a
GPU package bugfix from Trung for run style respa
akohlmey Aug 25, 2025
cfa144b
upgrade plumed default support to version 2.9.4
akohlmey Aug 25, 2025
0a73ac2
also include changes to be able to use plumed version 2.10.x
akohlmey Aug 25, 2025
ec58567
fix typo
akohlmey Aug 26, 2025
2be4155
sync code for plugin loading at start and corresponding preferences w…
akohlmey Aug 27, 2025
6342dbd
generalize script to build linux .tgz file to support Qt5 *and* Qt6
akohlmey Aug 28, 2025
18d9933
step "stable" compatible LAMMPS-GUI version to 1.7.1 (use 1.8.x for d…
akohlmey Aug 28, 2025
9568ab5
backport compatible changes from LAMMPS-GUI version 1.8.x
akohlmey Aug 28, 2025
32bece3
restore colvars package define
akohlmey Aug 28, 2025
5516a0d
update pattern to also find versioned shared libs
akohlmey Aug 28, 2025
fd5847f
preserve current buffer and directory, if no file selected to open
akohlmey Aug 28, 2025
aa08b55
Adding exception to special flags
jtclemm Aug 28, 2025
a56e22e
silence compiler warnings and apply fixes suggested by clang-tidy
akohlmey Aug 28, 2025
d6f4ddc
Colvars bugfixes
giacomofiorin Aug 29, 2025
6d32e65
Merge pull request #4705 from Colvars/colvars-bugfix-update
akohlmey Aug 29, 2025
801cb6d
work around frozen cursor bug
akohlmey Aug 30, 2025
3e7d3a5
add support for drag-n-drop of text blocks
akohlmey Aug 31, 2025
63382e0
Rebase rigid-shear onto develop branch - [FestoMuhire97]
akohlmey Sep 1, 2025
d0c67d1
add missing override
akohlmey Sep 1, 2025
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4 changes: 2 additions & 2 deletions .github/CODEOWNERS
Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,8 @@ src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-DUMP/dump_extxyz.* @fxcoudert
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl
src/EXTRA-PAIR/pair_dispersion_d3.* @soniasalomoni @arthurfl
src/EXTRA-PAIR/d3_parameters.h @soniasalomoni @arthurfl
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps
Expand Down
2 changes: 1 addition & 1 deletion cmake/Modules/Documentation.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ if(BUILD_DOC)
# download mathjax distribution and unpack to folder "mathjax"
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)
Expand Down
1 change: 1 addition & 0 deletions cmake/Modules/Packages/COLVARS.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ if(BUILD_OMP)
endif()

if(BUILD_MPI)
target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
endif()

Expand Down
4 changes: 2 additions & 2 deletions cmake/Modules/Packages/PLUMED.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,9 @@ endif()

# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-src-2.9.3.tgz"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.4/plumed-src-2.9.4.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "e540bf5132e3270e843398a6080d00c7" CACHE STRING "MD5 checksum of PLUMED tarball")

mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
Expand Down
20 changes: 10 additions & 10 deletions cmake/packaging/build_linux_tgz.sh
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ DESTDIR=${PWD}/../LAMMPS_GUI
VERSION="$1"

echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
rm -rf ${DESTDIR} ../LAMMPS-GUI-Linux-amd64*.tar.gz

echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
Expand All @@ -25,18 +25,18 @@ rm -f ${DESTDIR}/lib/libgcc_s*
rm -f ${DESTDIR}/lib/libstdc++*

# get qt dir
QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt.Core | sed -e 's/^.*=> *//' -e 's/libQt\(.\)Core.so.*$/qt\1/')
cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
Plugins = ../qtplugins
EOF

# platform plugin
mkdir -p ${DESTDIR}/qt5plugins/platforms
cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
mkdir -p ${DESTDIR}/qtplugins/platforms
cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qtplugins/platforms

# get platform plugin dependencies
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt[56] | sed -e 's/^.*=> *//' -e 's/\(libQt[56].*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
Expand All @@ -45,13 +45,13 @@ done
echo "Add additional plugins for Qt"
for dir in styles imageformats
do \
cp -r ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
cp -r ${QTDIR}/plugins/${dir} ${DESTDIR}/qtplugins/
done

# get imageplugin dependencies
for s in ${DESTDIR}/qt5plugins/imageformats/*.so
for s in ${DESTDIR}/qtplugins/imageformats/*.so
do \
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt.|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
for dep in ${QTDEPS}
do \
cp ${dep} ${DESTDIR}/lib
Expand All @@ -72,7 +72,7 @@ do \
done

pushd ..
tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
tar -czvvf LAMMPS-GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
popd

echo "Cleanup dir"
Expand Down
2 changes: 2 additions & 0 deletions doc/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -66,11 +66,13 @@ help:
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@echo " fasthtml approximate HTML page creation in fasthtml dir (for development)"
@echo " upgrade upgrade sphinx, extensions, and dependencies to latest supported versions"
@echo " clean remove all intermediate files"
@echo " clean-all reset the entire build environment"
@echo " anchor_check scan for duplicate anchor labels"
@echo " style_check check for complete and consistent style lists"
@echo " package_check check for complete and consistent package lists"
@echo " char_check check for non-ASCII characters"
@echo " role_check check for misformatted role keywords"
@echo " spelling spell-check the manual"

Expand Down
7 changes: 2 additions & 5 deletions doc/src/Bibliography.rst
Original file line number Diff line number Diff line change
Expand Up @@ -380,7 +380,7 @@ Bibliography
Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).

**(Elliott)**
Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api/ <https://openkim.org/kim-api/>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_

**(Ellis)**
Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
Expand Down Expand Up @@ -1098,9 +1098,6 @@ Bibliography
**(Parrinello)**
Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).

**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS

**(Paula Leite2016)**
Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).

Expand Down Expand Up @@ -1213,7 +1210,7 @@ Bibliography
S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141

**(Roberts)**
R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<https://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_

**(Rohart)**
Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
Expand Down
5 changes: 2 additions & 3 deletions doc/src/Build_cmake.rst
Original file line number Diff line number Diff line change
Expand Up @@ -217,6 +217,5 @@ Most Linux distributions offer pre-compiled cmake packages through their
package management system. If you do not have CMake or a recent enough
version (Note: for CentOS 7.x you need to enable the EPEL repository),
you can download the latest version from `https://cmake.org/download/
<https://cmake.org/download/>`_. Instructions on how to install it on
various platforms can be found `on this page
<https://cmake.org/install/>`_.
<https://cmake.org/download/>`_. Links to more details on CMake can
be found `on this page <https://cmake.org/resources/>`_.
4 changes: 2 additions & 2 deletions doc/src/Build_extras.rst
Original file line number Diff line number Diff line change
Expand Up @@ -1752,7 +1752,7 @@ within CMake will download the non-commercial use version.
PLUMED package
-------------------------------------

.. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
.. _plumedinstall: https://www.plumed.org/doc-v2.9/user-doc/html/_installation.html

Before building LAMMPS with this package, you must first build PLUMED.
PLUMED can be built as part of the LAMMPS build or installed separately
Expand Down Expand Up @@ -2379,7 +2379,7 @@ SCAFACOS package
-----------------------------------------

To build with this package, you must download and build the
`ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_
`ScaFaCoS Coulomb solver library <http://www.scafacos.de/>`_

.. tabs::

Expand Down
8 changes: 6 additions & 2 deletions doc/src/Build_manual.rst
Original file line number Diff line number Diff line change
Expand Up @@ -82,14 +82,18 @@ folder. The following ``make`` commands are available:

make fasthtml # generate approximate HTML in fasthtml dir using pandoc

make upgrade # upgrade sphinx, extensions, and dependencies to latest supported versions
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
make upgrade # upgrade the python packages in the virtual environment

make anchor_check # check for duplicate anchor labels
make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
make link_check # check for broken or outdated URLs
make char_check # check for non-ASCII characters
make role_check # check for misformatted role keywords

make link_check # check for broken external URLs
make spelling # spell-check the manual

----------
Expand Down Expand Up @@ -303,7 +307,7 @@ be multiple tests run automatically:

In addition, there is the option to run a spellcheck on the entire
manual with ``make spelling``. This requires `a library called enchant
<https://github.com/AbiWord/enchant>`_. To avoid printing out *false
<https://github.com/rrthomas/enchant>`_. To avoid printing out *false
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.

Expand Down
2 changes: 1 addition & 1 deletion doc/src/Build_settings.rst
Original file line number Diff line number Diff line change
Expand Up @@ -286,7 +286,7 @@ find a heFFTe installation with the correct back end (e.g., FFTW or
MKL), it will attempt to download and build the library automatically.
In this case, LAMMPS CMake will also accept all heFFTe specific
variables listed in the `heFFTe documentation
<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
<https://icl-utk-edu.github.io/heffte/md_doxygen_installation.html>`_
and those variables will be passed into the heFFTe build.

----------
Expand Down
7 changes: 5 additions & 2 deletions doc/src/Developer_code_design.rst
Original file line number Diff line number Diff line change
Expand Up @@ -397,8 +397,11 @@ value, for example "{:{}d}" will consume two integer arguments, the
first will be the value shown and the second the minimum width.

For more details and examples, please consult the `{fmt} syntax
documentation <https://fmt.dev/latest/syntax.html>`_ website.

documentation <https://fmt.dev/latest/syntax/>`_ website. Since we
plan to eventually transition from {fmt} to using ``std::format()``
of the C++ standard library, it is advisable to avoid using any
extensions beyond what the `C++20 standard offers
<https://en.cppreference.com/w/cpp/utility/format/format.html>`_.

Memory management
^^^^^^^^^^^^^^^^^
Expand Down
19 changes: 12 additions & 7 deletions doc/src/Developer_notes.rst
Original file line number Diff line number Diff line change
Expand Up @@ -292,16 +292,21 @@ processing similar to the "format()" functionality in Python.

.. note::

For commands like :doc:`fix ave/time <fix_ave_time>` that accept
wildcard arguments, the :cpp:func:`utils::expand_args` function
may be passed as an optional argument where the function will provide
a map to the original arguments from the expanded argument indices.
Commands that accept wildcard arguments, for example
:doc:`fix ave/time <fix_ave_time>`, use
:cpp:func:`utils::expand_args() <LAMMPS_NS::utils::expand_args>`
to convert the wildcards into a list of explicit arguments.
This function accepts a pointer address as an optional argument,
which will be set to a map to the original arguments from the
expanded argument indices. Please see the corresponding source
code for details on how to apply this map in error messages.

For complex errors, that can have multiple causes and which cannot be
explained in a single line, you can append to the error message, the
string created by :cpp:func:`utils::errorurl`, which then provides a
URL pointing to a paragraph of the :doc:`Errors_details` that
corresponds to the number provided. Example:
string created by :cpp:func:`utils::errorurl()
<LAMMPS_NS::utils::errorurl>`, which then provides a URL pointing to a
paragraph of the :doc:`Errors_details` that corresponds to the number
provided. Example:

.. code-block:: c++

Expand Down
5 changes: 3 additions & 2 deletions doc/src/Developer_updating.rst
Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ New:
.. seealso::

:cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
:cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
:cpp:func:`utils::trim_comment() <LAMMPS_NS::utils::trim_comment>`


Use utils::numeric() functions instead of force->numeric()
Expand Down Expand Up @@ -663,7 +663,8 @@ Use utils::logmesg() instead of error->warning()
.. versionchanged:: 22Jul2025

The ``Error::message()`` method has been removed since its functionality
has been superseded by the :cpp:func:`utils::logmesg` function.
has been superseded by the :cpp:func:`utils::logmesg()
<LAMMPS_NS::utils::logmesg>` function.

Old:

Expand Down
2 changes: 1 addition & 1 deletion doc/src/Developer_write_command.rst
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ Interfacing the *libcurl* library
"""""""""""""""""""""""""""""""""

Rather than implementing the various protocols for downloading files, we
rely on an external library: `libcurl library <https:://curl.se/libcurl/>`_.
rely on an external library: `libcurl library <https://curl.se/libcurl/>`_.
This requires that the library and its headers are installed. For the
traditional GNU make build system, this simply requires edits to the machine
makefile to add compilation flags like for other libraries. For the CMake
Expand Down
3 changes: 2 additions & 1 deletion doc/src/Howto_amoeba.rst
Original file line number Diff line number Diff line change
Expand Up @@ -281,7 +281,8 @@ Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format:

* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://dasher.wustl.edu/tinker/distribution/doc/sphinx/tinker/_build/html/text/file-types.html <https://dasher.wustl.edu/tinker/distribution/doc/sphinx/tinker/_build/html/text/file-types.html>`_
* `https://openbabel.org/docs/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_

Expand Down
68 changes: 37 additions & 31 deletions doc/src/Howto_bpm.rst
Original file line number Diff line number Diff line change
Expand Up @@ -85,50 +85,56 @@ files to render bond data.

----------

As bonds can be broken between neighbor list builds, the
:doc:`special_bonds <special_bonds>` command works differently for BPM
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can overlay
pair forces with bond forces such that all bonded particles also
feel pair interactions. This can be accomplished by setting the *overlay/pair*
keyword present in all bpm bond styles to *yes* and requires using the
following special bond settings
As bonds can potentially be broken between neighbor list builds, BPM bond
styles may place restrictions on the :doc:`special_bonds <special_bonds>` command. There are three possible scenarios which determine how pair
interactions between bonded particles and special bond weights work.

The first option is the simplest. If bonds cannot break, then one can use any
special bond settings to control pair forces. Namely, this is accomplished by
setting the *break* keyword to *no*. Note that a zero coul weight for 1-2 bonds
can be used to exclude bonded atoms from the neighbor list builds

.. code-block:: LAMMPS

special_bonds lj 0 1 1 coul 0 1 1

This can be useful for post-processing, or to determine pair interaction
properties between distinct bonded particles.

If bonds can break, the second scenario is if pair forces are overlaid
on top of bond forces such that atoms can simultaneously exchange both types
of forces. This is accomplished by setting the *overlay/pair* keyword present
in all bpm bond styles to *yes*. This case requires the following special
bond settings

.. code-block:: LAMMPS

special_bonds lj/coul 1 1 1

Alternatively, one can turn off all pair interactions between bonded
particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
by subtracting pair forces during the bond computation, but rather by
dynamically updating the special bond list. This is the default behavior
of BPM bond styles and is done by updating the 1-2 special bond list as
bonds break. To do this, LAMMPS requires :doc:`newton <newton>` bond off
such that all processors containing an atom know when a bond breaks.
Note that this scenario does not update special bond lists when bonds break,
hence why fractional weights are not allowed. Whether or not two particles
are bonded has no bearing on pair forces.

In the third scenario, bonds can break but pair forces are disabled between
bonded particles. This is the default behavior of BPM bond styles. Unlike
:doc:`bond quartic <bond_quartic>`, pair forces are not removed by subtracting
pair forces during the bond computation, but rather by dynamically updating the
1-2 special bond list. To do this, LAMMPS requires :doc:`newton <newton>` bond
off such that all processors containing an atom know when a bond breaks.
Additionally, one must use the following special bond settings

.. code-block:: LAMMPS

special_bonds lj 0 1 1 coul 1 1 1

These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
special bond lists, which are not currently supported for breakable BPMs.
As BPMs often have dense bond networks, generating/updating 1-3 and 1-4
special bond lists can be expensive. By setting the lj weight for 1-2
bonds to zero, this turns off pairwise interactions. Even though there
are no charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds. If bond breakage is
disabled during a simulation run by setting the *break* keyword to *no*,
a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
from the neighbor list builds

.. code-block:: LAMMPS

special_bonds lj 0 1 1 coul 0 1 1

This can be useful for post-processing, or to determine pair interaction
properties between distinct bonded particles.
in case bonds break between neighbor list builds.

To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using
Expand Down
2 changes: 1 addition & 1 deletion doc/src/Howto_couple.rst
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ the context of your application.
make library calls to the other code, which has been linked to LAMMPS
as a library. This is the way the :ref:`VORONOI <PKG-VORONOI>`
package, which computes Voronoi tesselations using the `Voro++
library <http://math.lbl.gov/voro++>`_, is interfaced to LAMMPS. See
library <https://math.lbl.gov/voro++/>`_, is interfaced to LAMMPS. See
the :doc:`compute voronoi <compute_voronoi_atom>` command for more
details. Also see the :doc:`Modify <Modify>` pages for information
on how to add a new fix or compute to LAMMPS.
Expand Down
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