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1747 Commits

Author SHA1 Message Date
Vsevak
e9051620a5 Cleanup 2022-05-28 00:39:07 +03:00
Vsevak
d8f8a3a36a Handle inconsistent J molecules in tip4p/gpu 2022-05-28 00:24:24 +03:00
Yury Lysogorskiy
2085c10002 update version of lib-pace to v.2021.10.25.fix2 2022-05-25 17:56:24 +02:00
Axel Kohlmeyer
7e75b7bff5 whitespace 2022-05-19 12:16:31 -04:00
Axel Kohlmeyer
e94275391c Merge branch 'develop' into collected-small-changes 2022-05-17 22:10:15 -04:00
Axel Kohlmeyer
55e0af930b Merge pull request #3269 from yury-lysogorskiy/master 
Update ML-PACE installation to v.2021.10.25.fix version
 2022-05-17 19:50:49 -04:00
Yury Lysogorskiy
8ffe2a206c Update ML-PACE installation to v.2021.10.25.fix version 2022-05-17 22:41:43 +02:00
Axel Kohlmeyer
9a9bb749fa Merge remote-tracking branch 'github/develop' into collected-small-changes 2022-05-14 10:39:18 -04:00
Axel Kohlmeyer
d4ea5ca49e more clang-tidy fixes after re-running it with added settings 2022-05-14 07:18:05 -04:00
Stan Moore
979f84f96f Merge branch 'develop' of https://github.com/lammps/lammps into kk_update_3.6.0 2022-05-13 14:03:09 -04:00
Giacomo Fiorin
1220bea011 Update Colvars to version 2022-05-09 
This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.

Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).

Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers.  Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.

The following pull requests in the Colvars repository are relevant to LAMMPS:

- 475 Remove fatal error condition
  https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)

- 474 Allow normalizing eigenvector vector components to deal with unit change
  https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)

- 470 Better error handling in the initialization of NeuralNetwork CV
  https://github.com/Colvars/colvars/pull/470 (@HanatoK)

- 468 Add examples of histogram configuration, with and without explicit grid parameters
  https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)

- 464 Fix #463 using more fine-grained features
  https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)

- 447 [RFC] New option "scaledBiasingForce" for colvarbias
  https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)

- 444 [RFC] Implementation of dense neural network as CV
  https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)

- 443 Fix explicit gradient dependency of sub-CVs
  https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)

- 442 Persistent bias count
  https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)

- 437 Return type of bias from scripting interface
  https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)

- 434 More flexible use of boundaries from colvars by grids
  https://github.com/Colvars/colvars/pull/434 (@jhenin)

- 433 Prevent double-free in linearCombination
  https://github.com/Colvars/colvars/pull/433 (@HanatoK)

- 428 More complete documentation for index file format (NDX)
  https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)

- 426 Integrate functional version of backup_file() into base proxy class
  https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)

- 424 Track CVC inheritance when documenting feature usage
  https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)

- 419 Generate citation report while running computations
  https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)

- 415 Rebin metadynamics bias from explicit hills when available
  https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)

- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
  https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)

Authors: @giacomofiorin, @HanatoK, @jhenin
 2022-05-10 11:24:54 -04:00
Stan Gerald Moore
b79c0bc7b4 Update Kokkos library in LAMMPS to v3.6.0 2022-05-05 11:44:47 -06:00
Axel Kohlmeyer
4a3bcd9230 Merge branch 'develop' into collected-small-changes 2022-04-29 20:15:36 -04:00
Axel Kohlmeyer
9c48a75c8e fix issues reported by coverity scan 2022-04-29 06:49:47 -04:00
Axel Kohlmeyer
f09556018b fix bugs reported by @jibril-b-coulibaly 2022-04-28 14:47:53 -04:00
Ludwig Ahrens
7aaa71d22e Merge remote-tracking branch 'lammps/develop' into electrode 2022-04-26 10:29:39 +02:00
Trung Nguyen
531e553162 Merge branch 'amoeba' into amoeba-gpu 2022-04-22 16:10:24 -05:00
Axel Kohlmeyer
aa4787f604 complete region handling refactor 2022-04-16 00:17:39 -04:00
Axel Kohlmeyer
64b1c45a49 update MDI library and checksum 2022-04-14 17:27:20 -04:00
Steve Plimpton
20827b4105 sync with new version of MDI library 2022-04-14 15:00:09 -06:00
Steve Plimpton
bc2b600f09 changes to use new MDI library functions 2022-04-13 16:26:48 -06:00
Axel Kohlmeyer
bd6d7b9136 clarify CUDA versus OpenCL build and runtime restrictions 2022-04-13 14:24:43 -04:00
Axel Kohlmeyer
f3363070e7 remove support for CUDA toolkits before version 8 and GPUs older than Kepler 2022-04-12 15:48:16 -04:00
Axel Kohlmeyer
b36262cd11 cosmetic 2022-04-10 20:47:42 -04:00
Axel Kohlmeyer
d6f7570d57 avoid redundant use of boolean literals 2022-04-10 20:47:31 -04:00
Axel Kohlmeyer
39b316729b use auto type when assigning from cast or using new 2022-04-10 18:16:36 -04:00
Axel Kohlmeyer
6071376d42 derive ATC_Error exception class from std::exception 2022-04-10 15:25:37 -04:00
Axel Kohlmeyer
413a01ade5 apply clang-tidy updates 2022-04-10 12:07:54 -04:00
Axel Kohlmeyer
19b42bc726 Merge branch 'develop' into electrode 2022-04-09 06:31:22 -04:00
Axel Kohlmeyer
674d2a6788 Merge branch 'develop' into remove-message-package 2022-04-09 00:25:11 -04:00
Axel Kohlmeyer
093667799d Merge branch 'develop' into mdi-expand 2022-04-08 20:58:53 -04:00
Axel Kohlmeyer
2c509d96a6 we are not compatible with those old versions for the MDI library 2022-04-08 16:43:41 -04:00
Nick Curtis
77565add6e Add C++14 to Makefile build system 
Change-Id: I24f72b4aaca93a49877775c3d181507c83cd7f82
 2022-04-07 17:54:20 -04:00
Steve Plimpton
792ae5dae5 remove src/MESSAGE package and supporting dirs and doc pages 2022-04-07 15:44:48 -06:00
Steve Plimpton
f40180f7fb lib README edit 2022-04-07 15:15:50 -06:00
Ludwig Ahrens-Iwers
65be564cd6 Review akohlmey 2022-04-05 15:35:04 +00:00
Axel Kohlmeyer
a4018dbb4b update MDI library to version 1.3.0 2022-03-23 17:18:19 -04:00
Steve Plimpton
c4425a1b0e debugging plugin mode 2022-03-23 11:17:51 -06:00
Axel Kohlmeyer
11ba2adbe7 add support for plumed 2.6.6, 2.7.4, and 2.8.0 (default 2.7.4) 2022-02-25 16:34:37 -05:00
Axel Kohlmeyer
9a1c994a8e Merge branch 'develop' into rename_comm_forw_rev 
# Conflicts:
#	src/KOKKOS/comm_kokkos.cpp
#	src/KOKKOS/fix_qeq_reaxff_kokkos.cpp
 2022-02-22 16:45:06 -05:00
Axel Kohlmeyer
a3524fc7a1 update atc lib 2022-02-21 21:33:27 -05:00
Axel Kohlmeyer
537e3f2539 silence compiler warnings 2022-02-17 23:13:13 -05:00
Axel Kohlmeyer
5f47ff770c Merge pull request #3127 from akohlmey/gpu-opencl-updates 
Update compiling OpenCL loader lib
 2022-02-14 16:10:53 -05:00
Axel Kohlmeyer
83beffbb9f whitespace 2022-02-13 17:08:18 -05:00
Trung Nguyen
193dea6327 Updated the comment to be precise on the case 2022-02-13 14:51:00 -06:00
Trung Nguyen
159f107abd Corrected the added comment 2022-02-13 11:16:01 -06:00
Trung Nguyen
bae4e45978 Added a comment to the added check while looping over the neighbors of ghost atoms 2022-02-13 09:17:05 -06:00
Trung Nguyen
55a500cf8a Fixed bugs with in the kernel sw_three_end kernel 2022-02-13 00:42:26 -06:00
Axel Kohlmeyer
a17bdf5652 silence compiler warnings and avoid infinite recursion in aspherical pair styles 2022-02-11 21:06:16 -05:00
Axel Kohlmeyer
093c54d8ed update to use settings from upstream 2022-02-07 14:42:07 -05:00