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1355 Commits

Author SHA1 Message Date
yskmiyazaki
fc741e0df6 changed names of files, and added a lj12-5 function type. 2022-07-08 17:28:50 +09:00
Yury Lysogorskiy
dcf9082591 Makefile.lammps: add empty line 
Install.py: remove older versions
 2022-07-07 23:35:58 +02:00
Axel Kohlmeyer
b8acd2e31d Merge pull request #3329 from stanmoore1/kk_update_3.6.1 
Update Kokkos library in LAMMPS to v3.6.1
 2022-07-04 10:43:55 -04:00
Stan Gerald Moore
2bfbd6fba1 Update Kokkos library in LAMMPS to v3.6.1 2022-07-01 13:17:50 -06:00
Axel Kohlmeyer
e34e9aca48 improve consistency between CMake and GNU make build. Must explicitly link python when building a static mdi lib 2022-06-30 15:45:52 -04:00
Axel Kohlmeyer
373c719f4f make compilation settings consistent with CMake 2022-06-28 15:22:54 -04:00
Axel Kohlmeyer
56cb2f3077 update external library version and md5sum 2022-06-28 13:44:41 -04:00
Axel Kohlmeyer
141d09ab9b Merge branch 'develop' into fix-mdi-aimd-enhance 
# Conflicts:
#	doc/src/fix_mdi_aimd.rst
 2022-06-28 13:38:43 -04:00
Yury Lysogorskiy
80e1020648 update ML-PACE.cmake and lib/pace for v.2022.06.27 2022-06-27 18:47:09 +02:00
Yury Lysogorskiy
bd10d17be9 (WIP) 
lib/pace/Install.py: add --local flag to be able to use local PACE codebase
lib/pace/Makefile and Makefile.lammps: update, include wigner-cpp and cnpy
 2022-06-23 16:55:56 +02:00
Steve Plimpton
f4342ea7e4 use new version of MDI lib and include Python support 2022-06-21 15:03:22 -06:00
Axel Kohlmeyer
2028c68bec remove unused imports 2022-06-14 10:45:05 -04:00
Axel Kohlmeyer
c53e53d701 must set suffix variable only when suffixflag is true 2022-06-13 17:47:20 -04:00
Axel Kohlmeyer
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
Yury Lysogorskiy
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
Giacomo Fiorin
04586e634e Remove trailing whitespace from Lepton per suggestion from @akohlmey 2022-06-02 11:52:39 -04:00
Giacomo Fiorin
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
Axel Kohlmeyer
c0bd4185f8 Merge branch 'develop' into feature/ml-pace-multispecies 2022-06-01 21:10:59 -04:00
Vsevak
59dc63d003 Add typecasting for consts in tip4p GPU kernels 2022-06-01 01:29:18 +03:00
Vsevak
4b2509beed Merge branch 'develop' into tip4p_bug 2022-05-30 18:54:28 +03:00
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
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