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Author SHA1 Message Date
Axel Kohlmeyer
ad63eb8bf7 Merge branch 'develop' into cmake-adjustments 2025-05-19 21:03:07 -04:00
Axel Kohlmeyer
b3402eaae8 Merge pull request #4424 from jtavenner-dev/kmc 
add fix neighbor/swap
 2025-05-19 20:57:00 -04:00
Axel Kohlmeyer
fd8fb74a88 cannot use Kokkos-OpenMP with recent hipcc 2025-05-15 07:47:19 -04:00
Axel Kohlmeyer
35f08232ba update for Fedora 41/42 2025-05-15 07:46:48 -04:00
Axel Kohlmeyer
2b7c05c057 properly select linker for modern clang compilers 2025-05-15 04:02:44 -04:00
Axel Kohlmeyer
9abb171d05 more CMake scripting updates to use C style MPI libraries not C++ 2025-05-15 02:49:02 -04:00
Axel Kohlmeyer
b3e7121535 modernize project() command and create project version string with dots 2025-05-15 02:14:35 -04:00
Axel Kohlmeyer
85f0853910 Merge branch 'develop' into cmake-adjustments 2025-05-14 20:11:01 -04:00
Jacob Tavenner
ef89edc4c6 Additional edits 2025-05-09 14:53:27 -06:00
Jacob Tavenner
bb62f46404 Merge branch 'kmc' of https://github.com/jtavenner-dev/lammps into kmc 2025-05-09 14:27:05 -06:00
Jacob Tavenner
17da04f07b Cleaned up language errors 2025-05-09 14:25:08 -06:00
Jacob Tavenner
6436cc87b7 Corrected inconsistent voro-ID compute references and examples 2025-05-09 14:23:03 -06:00
Axel Kohlmeyer
3215141d9e Merge pull request #4584 from navlalli/update-docs 
Update fix qtpie/reaxff and fix qeq/rel/reaxff docs
 2025-05-08 01:59:10 -04:00
Axel Kohlmeyer
3be9a40bf8 Merge branch 'develop' into update-docs 2025-05-08 01:09:17 -04:00
Axel Kohlmeyer
b69e8fff1f Merge pull request #4587 from akohlmey/collected-small-changes 
Collected small changes and fixes
 2025-05-08 01:07:29 -04:00
Axel Kohlmeyer
458c0844a8 fix typo 2025-05-07 17:44:38 -04:00
Axel Kohlmeyer
acd53ebd7c update flag to accommodate changes in clang 2025-05-07 17:13:36 -04:00
Axel Kohlmeyer
ac556104c1 link to MPI C interface instead of C++ 2025-05-07 17:12:57 -04:00
Axel Kohlmeyer
22cddeee78 fix spelling in comments 2025-05-07 16:49:43 -04:00
Axel Kohlmeyer
60fe08c328 clarify and rewrap 2025-05-07 15:47:35 -04:00
jtclemm
38dffe2283 Properly processing >1 fix set force 2025-05-07 15:42:57 -04:00
jtclemm
45944c4dc9 Fixing passed arg from type to index 2025-05-07 15:42:40 -04:00
Stan Moore
6c2f11ce75 Merge branch 'develop' into update-docs 2025-05-07 13:21:39 -06:00
Axel Kohlmeyer
7c2c9ea286 add missing versionadded tag 2025-05-07 02:00:40 -04:00
Axel Kohlmeyer
615dd589dd replace slow pow() function with faster and more accurate alternatives 2025-05-06 15:21:06 -04:00
Axel Kohlmeyer
c0a41bd638 Merge remote-tracking branch 'github/develop' into collected-small-changes 2025-05-06 15:06:43 -04:00
Axel Kohlmeyer
c1e9adbd80 Merge pull request #4574 from talinke/develop 
New Fix for GJF Langevin Dynamics
 2025-05-06 13:24:06 -04:00
Axel Kohlmeyer
48df0448df spelling 2025-05-06 12:05:12 -04:00
Axel Kohlmeyer
2d22092078 additional info for pair style lj/smooth from Aidan 2025-05-06 12:00:55 -04:00
Axel Kohlmeyer
afcb97aaf2 address spelling issues 2025-05-05 20:22:00 -04:00
Axel Kohlmeyer
fbfe1e6a7c Merge remote-tracking branch 'github/develop' into collected-small-changes 2025-05-05 20:13:42 -04:00
Axel Kohlmeyer
a528b88d8a Merge branch 'update-docs' of github.com:navlalli/lammps-qtpie into collected-small-changes 2025-05-05 20:13:23 -04:00
Axel Kohlmeyer
750cfbedd3 Merge pull request #4579 from gsalkuin/bpm-fix-rigid 
Update atom->quat in rigid fixes for bpm/rotational compatibility
 2025-05-05 20:09:53 -04:00
Axel Kohlmeyer
a1cd18e4cf Merge pull request #4522 from willzunker/mdr-dev 
MDR contact model updates: radius update and damping
 2025-05-05 20:07:36 -04:00
Axel Kohlmeyer
3b17ea5363 Merge pull request #4556 from Colvars/colvars-update 
Update Colvars library to version 2025-04-18
 2025-05-05 20:03:27 -04:00
Axel Kohlmeyer
0d7e07b9be export bond topology related per-atom data via library interface 2025-05-05 06:25:22 -04:00
Axel Kohlmeyer
7ec7745640 make neighbor list settings, status, and bond/angle/dihedral/improper lists available to library interface 2025-05-05 05:21:18 -04:00
Axel Kohlmeyer
8d38ec4f18 Merge branch 'mliap-torch-load-fix' of https://github.com/fglines-nv/lammps into collected-small-changes 2025-05-03 21:22:53 -04:00
Axel Kohlmeyer
3fafec9cba do not try to suppress nvcc warning with LLVM based compilers. those fail when configuring MPI. 2025-05-02 16:02:42 -04:00
Navraj Lalli
37221c080b Add self-citation 2025-05-02 13:52:17 +01:00
Axel Kohlmeyer
55a13efad0 small update 2025-05-02 00:30:22 -04:00
Axel Kohlmeyer
a388bd38ee add LAMMPS-GUI screenshot image 2025-05-02 00:21:41 -04:00
Forrest Glines
1f5b64bca4 torch.load fix for torch>=2.6 in ML-IAP 2025-05-01 15:22:05 -07:00
Axel Kohlmeyer
165f34bc12 Merge pull request #4571 from akohlmey/collected-small-fixes 
Collected small fixes
 2025-05-01 11:43:50 -04:00
Axel Kohlmeyer
2ab7eda64a improve warning and explanation about too short communication cutoff 2025-04-30 16:46:22 -04:00
Giacomo Fiorin
cba479bf6e Update Colvars library to version 2025-04-18 
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06:

- 752 New tool poisson_integrator_conv
  https://github.com/Colvars/colvars/pull/752 (@jhenin)

- 733 Custom grids for all biases
  https://github.com/Colvars/colvars/pull/733 (@giacomofiorin, @jhenin)

- 776 Avoid error in acos and asin with fast-math
  https://github.com/Colvars/colvars/pull/776 (@jhenin)

- 773 fix: fix the clang build test failure of OPES
  https://github.com/Colvars/colvars/pull/773 (@HanatoK)

- 768 fix: clamp the input values of asin and acos in case of fast math on aarch64
  https://github.com/Colvars/colvars/pull/768 (@HanatoK)

- 761 Add debug code for the Jacobi failure
  https://github.com/Colvars/colvars/pull/761 (@HanatoK)

- 759 min_image fix; Saves long runs from crashes;
  https://github.com/Colvars/colvars/pull/759 (@PolyachenkoYA)

- 757 Fix MSVC OpenMP issue
  https://github.com/Colvars/colvars/pull/757 (@HanatoK)

- 755 Fix indentation of 'Init CVC' message in standard output
  https://github.com/Colvars/colvars/pull/755 (@jhenin)

- 750 Optimize and simplify the calculation of dihedral gradients
  https://github.com/Colvars/colvars/pull/750 (@HanatoK)

- 749 Add references to new Colvars paper
  https://github.com/Colvars/colvars/pull/749 (@jhenin, @giacomofiorin)

- 740 Report the specific C++ standard at init time, stop warning about C++97/03
  https://github.com/Colvars/colvars/pull/740 (@giacomofiorin)

- 731 Improve detection of hard/mathematical boundaries
  https://github.com/Colvars/colvars/pull/731 (@giacomofiorin)

- 729 Optimize the fit gradients
  https://github.com/Colvars/colvars/pull/729 (@HanatoK, @jhenin)

- 728 Fix undefined behavior when getting the current working directory from std::filesystem
  https://github.com/Colvars/colvars/pull/728 (@giacomofiorin)

- 727 Add patchversion scripting command
  https://github.com/Colvars/colvars/pull/727 (@giacomofiorin)

- 724 Fix gradients and metric functions of distanceDir
  https://github.com/Colvars/colvars/pull/724 (@giacomofiorin)

- 715 Add missing rotation in orientation component
  https://github.com/Colvars/colvars/pull/715 (@giacomofiorin)

- 713 fix: try to solve #87 for non-scala components
  https://github.com/Colvars/colvars/pull/713 (@HanatoK)

- 709 Implementation of OPES in Colvars
  https://github.com/Colvars/colvars/pull/709 (@HanatoK, @giacomofiorin, @jhenin)

- 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off
  https://github.com/Colvars/colvars/pull/706 (@alphataubio)

- 570 enable use of CVs defined by PyTorch neural network models
  https://github.com/Colvars/colvars/pull/570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin)

Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
 2025-04-30 15:32:30 -04:00
Axel Kohlmeyer
f9ba063c4a add citation reminder 2025-04-30 12:17:31 -04:00
talinke
def38bf0f3 Updated fix langevin algorithm citation 2025-04-29 15:03:49 -07:00
Axel Kohlmeyer
2fa9cc7ae1 correct 2025-04-29 17:52:48 -04:00
Axel Kohlmeyer
0ce5d68455 Merge branch 'develop' into talinke/develop 2025-04-29 17:20:15 -04:00