2028c68bec
remove unused imports
2022-06-14 10:45:05 -04:00
c53e53d701
must set suffix variable only when suffixflag is true
2022-06-13 17:47:20 -04:00
31f7798720
Merge pull request #3278 from yury-lysogorskiy/feature/ml-pace-multispecies
...
ML_PACE package hybrid support and small updates
2022-06-02 19:27:53 -04:00
2a054c17be
- set species type for NULL atom type to -1. species_type=-1 value will not reach ACE Evaluator::compute_atom, but if it will ,then error will be thrown there
...
- updating lib pace MD5SUM (for both make and cmake installation scenario), but use same tag name v.2021.10.25.fix2 (add override keyword to ACERadialFunctions, add check for species_type==-1, fix yaml_cpp CMakeLists.txt)
2022-06-02 23:01:54 +02:00
04586e634e
Remove trailing whitespace from Lepton per suggestion from @akohlmey
2022-06-02 11:52:39 -04:00
3a1423dc48
Update Colvars to 2022-05-24 and copy of Lepton library
...
One bugfix for the Colvars library in the ABF method, and update of the copy
of the Lepton library as per the OpenMM repository.
List of relevant PR.
- 483 Update Lepton via patching procedure
https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)
- 482 Fix integer overflow in log_gradient_finite_diff and gradient_finite_diff
https://github.com/Colvars/colvars/pull/482 (@HanatoK)
2022-06-02 11:24:04 -04:00
c0bd4185f8
Merge branch 'develop' into feature/ml-pace-multispecies
2022-06-01 21:10:59 -04:00
2085c10002
update version of lib-pace to v.2021.10.25.fix2
2022-05-25 17:56:24 +02:00
7e75b7bff5
whitespace
2022-05-19 12:16:31 -04:00
e94275391c
Merge branch 'develop' into collected-small-changes
2022-05-17 22:10:15 -04:00
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
8ffe2a206c
Update ML-PACE installation to v.2021.10.25.fix version
2022-05-17 22:41:43 +02:00
9a9bb749fa
Merge remote-tracking branch 'github/develop' into collected-small-changes
2022-05-14 10:39:18 -04:00
d4ea5ca49e
more clang-tidy fixes after re-running it with added settings
2022-05-14 07:18:05 -04:00
979f84f96f
Merge branch 'develop' of https://github.com/lammps/lammps into kk_update_3.6.0
2022-05-13 14:03:09 -04:00
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
b79c0bc7b4
Update Kokkos library in LAMMPS to v3.6.0
2022-05-05 11:44:47 -06:00
4a3bcd9230
Merge branch 'develop' into collected-small-changes
2022-04-29 20:15:36 -04:00
9c48a75c8e
fix issues reported by coverity scan
2022-04-29 06:49:47 -04:00
f09556018b
fix bugs reported by @jibril-b-coulibaly
2022-04-28 14:47:53 -04:00
7aaa71d22e
Merge remote-tracking branch 'lammps/develop' into electrode
2022-04-26 10:29:39 +02:00
aa4787f604
complete region handling refactor
2022-04-16 00:17:39 -04:00
64b1c45a49
update MDI library and checksum
2022-04-14 17:27:20 -04:00
20827b4105
sync with new version of MDI library
2022-04-14 15:00:09 -06:00
bc2b600f09
changes to use new MDI library functions
2022-04-13 16:26:48 -06:00
bd6d7b9136
clarify CUDA versus OpenCL build and runtime restrictions
2022-04-13 14:24:43 -04:00
f3363070e7
remove support for CUDA toolkits before version 8 and GPUs older than Kepler
2022-04-12 15:48:16 -04:00
b36262cd11
cosmetic
2022-04-10 20:47:42 -04:00
d6f7570d57
avoid redundant use of boolean literals
2022-04-10 20:47:31 -04:00
39b316729b
use auto type when assigning from cast or using new
2022-04-10 18:16:36 -04:00
6071376d42
derive ATC_Error exception class from std::exception
2022-04-10 15:25:37 -04:00
413a01ade5
apply clang-tidy updates
2022-04-10 12:07:54 -04:00
19b42bc726
Merge branch 'develop' into electrode
2022-04-09 06:31:22 -04:00
674d2a6788
Merge branch 'develop' into remove-message-package
2022-04-09 00:25:11 -04:00
093667799d
Merge branch 'develop' into mdi-expand
2022-04-08 20:58:53 -04:00
2c509d96a6
we are not compatible with those old versions for the MDI library
2022-04-08 16:43:41 -04:00
77565add6e
Add C++14 to Makefile build system
...
Change-Id: I24f72b4aaca93a49877775c3d181507c83cd7f82
2022-04-07 17:54:20 -04:00
792ae5dae5
remove src/MESSAGE package and supporting dirs and doc pages
2022-04-07 15:44:48 -06:00
f40180f7fb
lib README edit
2022-04-07 15:15:50 -06:00
65be564cd6
Review akohlmey
2022-04-05 15:35:04 +00:00
a4018dbb4b
update MDI library to version 1.3.0
2022-03-23 17:18:19 -04:00
c4425a1b0e
debugging plugin mode
2022-03-23 11:17:51 -06:00
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
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
a3524fc7a1
update atc lib
2022-02-21 21:33:27 -05:00
537e3f2539
silence compiler warnings
2022-02-17 23:13:13 -05:00
5f47ff770c
Merge pull request #3127 from akohlmey/gpu-opencl-updates
...
Update compiling OpenCL loader lib
2022-02-14 16:10:53 -05:00
83beffbb9f
whitespace
2022-02-13 17:08:18 -05:00
193dea6327
Updated the comment to be precise on the case
2022-02-13 14:51:00 -06:00
159f107abd
Corrected the added comment
2022-02-13 11:16:01 -06:00
