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Author SHA1 Message Date
Germain Clavier
10077b057c Update fix_ave_moments.rst 
Emphasized the difference in behavior between this fix and other fix ave/* commands with regards to Nevery, Nrepeat and Nfreq.
 2025-05-02 21:42:33 +02:00
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
Sebastian Hütter
edb060ccf5 Add examples and expected output for ave/moments 2025-05-02 01:20:37 +02:00
Sebastian Hütter
565e7b2c2b Add documentation for ave/moments 2025-05-02 01:20:36 +02:00
Sebastian Hütter
b2001e999c Implement moments calculation fix ave/moments 2025-05-02 01:20:36 +02:00
Sebastian Hütter
f8a0ff011b Skeleton implementation of fix ave/moments 2025-05-02 01:20:36 +02:00
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
Axel Kohlmeyer
1062a8fb3a add deprecation warning to fix langevin and document it 2025-04-29 17:20:04 -04:00
talinke
332006923d Name change: langevin/gjf to gjf 2025-04-29 12:00:06 -07:00
Gabriel Alkuino
169f8ffd73 Merge branch 'lammps:develop' into bpm-fix-rigid 2025-04-29 13:23:36 -04:00
Axel Kohlmeyer
f9a55c0f49 update reference data in test which was updated in KIM database 2025-04-29 08:40:47 -04:00
Axel Kohlmeyer
053792ed47 fix typo detected by copilot 2025-04-28 23:14:54 -04:00
Axel Kohlmeyer
2fc7d287d4 Merge branch 'develop' into collected-small-fixes 2025-04-28 22:27:32 -04:00
Axel Kohlmeyer
440e24c60e Merge pull request #4559 from lammps/gcmc-eatom 
Added atomic energy option for energy change calculation in fix sgcmc
 2025-04-28 22:26:15 -04:00
Axel Kohlmeyer
d4867ab55e add false positives 2025-04-28 22:22:47 -04:00
Axel Kohlmeyer
2927b08792 correct reference 2025-04-28 22:20:57 -04:00
Axel Kohlmeyer
4a3c08576f small formal updates 2025-04-28 22:19:14 -04:00
Aidan Thompson
c886fff624 Merge branch 'develop' into gcmc-eatom 2025-04-28 17:55:48 -06:00
Axel Kohlmeyer
e5854ced41 backward compatibility not needed here 2025-04-28 18:56:32 -04:00
Axel Kohlmeyer
0768aac1fd update Qt platform version for flatpak build to latest 5.15 branch 2025-04-28 18:45:57 -04:00
Axel Kohlmeyer
75d3d79fca open available error URLs with double click or from context menu 2025-04-28 18:25:40 -04:00
talinke
fc0788f61c Styling 2025-04-28 13:18:33 -07:00
talinke
b5f3660101 Merge branch 'lammps:develop' into develop 2025-04-28 13:16:24 -07:00
talinke
11f6b3483b Updated documentation, updated log files 2025-04-28 13:02:47 -07:00
Axel Kohlmeyer
db3d93210d highlight error URLs in logwindow 2025-04-28 10:56:37 -04:00
Axel Kohlmeyer
7151f261a0 address sphinx formatting issue due to added paragraph 2025-04-27 10:04:41 -04:00
Axel Kohlmeyer
31b18ad24e update help index table 2025-04-27 10:03:35 -04:00
Axel Kohlmeyer
bef695f70b fix copy-n-paste error 2025-04-27 07:39:58 -04:00
Axel Kohlmeyer
5169a633e5 make sure cut_respa is initialized 2025-04-26 17:04:14 -04:00
Axel Kohlmeyer
2c27ea3706 Fix spelling in comment 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
 2025-04-26 13:32:21 -04:00
Axel Kohlmeyer
1a1f4b1a82 correct reference 2025-04-26 02:17:54 -04:00
Axel Kohlmeyer
092df8ed8f add copyright header 2025-04-26 00:56:47 -04:00
Axel Kohlmeyer
4897fbb210 Merge branch 'develop' into collected-small-fixes 2025-04-26 00:50:58 -04:00
Axel Kohlmeyer
40d8e1b95f Merge pull request #4535 from Bibobu/plot_forces_tool 
Adding python tool to plot tabulated forces
 2025-04-26 00:50:32 -04:00
Axel Kohlmeyer
4b2163666c Merge pull request #4545 from jtclemm/rheo 
Small patches to various packages
 2025-04-26 00:46:49 -04:00
Axel Kohlmeyer
7102cc2588 use bold font for column titles 2025-04-25 20:31:16 -04:00
Axel Kohlmeyer
f1edc7f222 whitespace 2025-04-25 20:15:36 -04:00
Axel Kohlmeyer
706aa19710 Use type/ratio instead of type/fraction to select charged types 2025-04-25 20:05:09 -04:00
Axel Kohlmeyer
67c6dc492b update to ScaFaCoS version 1.0.4 2025-04-25 20:03:06 -04:00
Axel Kohlmeyer
d406289a7a propagate changes from library.cpp/library.h to swig and plugin interface 2025-04-25 17:04:32 -04:00
Axel Kohlmeyer
1969c28e0c delete unused variables 2025-04-25 16:35:54 -04:00