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1010 Commits

Author SHA1 Message Date
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
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
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
67c6dc492b update to ScaFaCoS version 1.0.4 2025-04-25 20:03:06 -04:00
Richard Berger
4e69046e54 cmake: fix omp.h detection 
CMAKE_REQUIRED_LINK_OPTIONS needs to be a ;-separated list.
See https://cmake.org/cmake/help/latest/module/CheckIncludeFileCXX.html.
Fixes OpenMP detection with AppleClang when libomp is manually provided.
 2025-04-20 00:40:24 -06:00
Jacob Tavenner
ca246a50f1 Merge branch 'develop' of https://www.github.com/lammps/lammps into kmc 2025-04-14 15:37:47 -06:00
Axel Kohlmeyer
cdea2737c7 remove CMAKE_TUNE_FLAGS 2025-04-06 07:06:20 -04:00
Axel Kohlmeyer
9d61ff4bba add support for compiling fully static LAMMPS executable with libcurl 2025-04-04 00:45:19 -04:00
Axel Kohlmeyer
1892189eaa looking for libcurl components fails for some installations 2025-04-03 18:46:16 -04:00
Stan Moore
a4f7c7e4c5 Update CMake for KOKKOS package 2025-03-31 12:29:08 -06:00
Axel Kohlmeyer
cea31e463d remove references to -DLAMMPS_SMALLSMALL and trigger error when used 2025-03-14 10:20:31 -04:00
Axel Kohlmeyer
1c65907d72 Merge branch 'develop' into bye-bye-python-zwei 2025-02-13 17:01:39 -05:00
Axel Kohlmeyer
b188cdc044 add check for Python version. Require minimum of Python 3.6 (Sphinx requires 3.8) 2025-02-07 20:51:50 -05:00
Axel Kohlmeyer
6eddb3a33f various minor tweaks and reformatting for CMake scripts 2025-02-07 20:50:14 -05:00
Axel Kohlmeyer
2ae07ec1cb sync C++ standard selection with main CMakeLists.txt file 2025-02-04 17:00:12 -05:00
Jacob Tavenner
ea6e702184 Merge branch 'develop' of https://www.github.com/lammps/lammps into kmc 2025-01-28 19:00:08 -07:00
Axel Kohlmeyer
651c1b2bc2 Merge branch 'develop' into collected-small-changes 2025-01-21 20:06:50 -05:00
Stan Moore
fbfdcbbac1 Merge branch 'develop' into kk_bug_fixes 2025-01-21 14:50:34 -07:00
Axel Kohlmeyer
f4b8200bcc download plumed-2.9.3 by default now 2025-01-21 10:39:08 -05:00
Stan Moore
9cb67de38f Merge branch 'develop' of github.com:lammps/lammps into kk_bug_fixes 2025-01-20 15:50:48 -07:00
Axel Kohlmeyer
781b40643c add deprecation warning for using accelerator offload with INTEL package 2025-01-14 20:49:00 -05:00
Axel Kohlmeyer
38c3477d2f Merge pull request #4394 from rbberger/find-package-pace 
ml-pace: allow linking to existing pace library
 2025-01-09 19:41:19 -05:00
Richard Berger
668435380b Make sure that yaml-cpp::yaml-cpp exists 2025-01-08 15:41:37 -07:00
Richard Berger
ec7be395ea ml-pace: update tag 2025-01-08 11:48:34 -07:00
Stan Moore
8595d8f05c Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.5.0 2025-01-07 10:04:43 -07:00
Stan Moore
9e373e7cc1 Merge branch 'develop' of github.com:lammps/lammps into kk_bug_fixes 2025-01-07 10:02:34 -07:00
Stan Moore
e31ca3c9c5 Update CMake 2024-12-24 10:35:05 -07:00
Axel Kohlmeyer
49b2b978e6 build system updates to skip fix neighbor/swap if VORONOI package is not installed 2024-12-20 19:20:51 -05:00
Axel Kohlmeyer
74cf599778 work around bug in FindVTK.cmake shipped with VTK 9.1 (and possibly other versions) 2024-12-19 08:32:34 -05:00
Stan Moore
9e3f7e55ee Update build systems for Kokkos v4.5.0 2024-12-13 09:32:45 -07:00
Axel Kohlmeyer
c2b6ce5786 remove src/KOKKOS/group_kokkos.cpp 2024-12-04 18:02:44 -05:00
Richard Berger
88807c6ae6 ml-pace: allow linking to existing pace library 2024-11-25 16:18:50 -07:00
Stan Moore
46c365f75c Merge branch 'develop' of github.com:lammps/lammps into alphataubio-kokkos-fixes 2024-10-23 09:32:27 -06:00
Christoph Junghans
73eb7de7aa cmake: voro target to upstream name 2024-10-18 09:26:23 -06:00
Axel Kohlmeyer
f8a8783044 Merge branch 'develop' into alphataubio-kokkos-fixes 2024-10-12 20:09:59 -04:00
Axel Kohlmeyer
49a850c8aa add cmake support for make-globbed-toc 2024-10-10 17:25:05 -04:00
alphataubio
1f61c42745 add GroupKokkos 2024-10-05 16:40:10 -04:00
Axel Kohlmeyer
b2e8648e6c enable deprecated APIs for HDF5 2024-10-04 12:32:09 -04:00
Stan Moore
80832ce763 Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.4.0 2024-09-23 16:14:12 -06:00
Stan Moore
e95de835c0 Tweak build defaults 2024-09-23 15:38:29 -06:00
Axel Kohlmeyer
1ac9f0801c update build support for using LAPACK with RHEO instead of GSL 2024-09-18 19:55:59 -04:00
Stan Moore
5075c7cfa1 Update CMake 2024-09-13 12:16:58 -06:00
Axel Kohlmeyer
5699e3c8cf add overridable settings 2024-09-12 17:34:12 -04:00
Stan Moore
dc15e4ae81 Enforce options in CMake 2024-09-12 10:50:19 -06:00
Richard Berger
0ebd4f5ddb Make CMake Doc build docenv optional 2024-09-11 21:33:07 -06:00
Stan Moore
64db592a84 Update Kokkos version in CMake 2024-09-11 09:45:21 -06:00
Axel Kohlmeyer
b09e88a179 Merge pull request #4314 from akohlmey/collected-small-changes 
Collected small changes and fixes
 2024-09-06 16:24:31 -04:00
Axel Kohlmeyer
842896040d Merge branch 'develop' into aurora_updates, resolve merge conflicts 2024-09-06 11:20:29 -04:00
Richard Berger
37e6f3ef21 kspace: add NVPL FFT support 2024-09-04 12:00:31 -06:00
Axel Kohlmeyer
ec98481d01 move check for libcurl to EXTRA-COMMAND.cmake package CMake module 2024-09-04 04:22:49 -04:00