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20336 Commits

Author SHA1 Message Date
W. Michael Brown
bbfd909be6 Adding redundant call to sync Intel package arrays with native arrays for methods such as MC that do not need pre_reverse. 2023-06-06 23:56:16 -07:00
rohskopf
a42bfb0e26 Make cutoff factor 1 instead of 0 to prevent zero valued descriptors 2023-06-02 17:26:40 -06:00
Axel Kohlmeyer
77340921ff Merge pull request #3800 from jrgissing/fix/deposit-per_atom_property_bug 
fix deposit: per atom property bug
 2023-06-01 14:19:53 -04:00
Axel Kohlmeyer
869780828b Merge pull request #3802 from stanmoore1/acks2_warnings 
Fix (harmless) compiler warnings in Kokkos ACKS2
 2023-06-01 12:57:55 -04:00
Axel Kohlmeyer
bda933e0db Merge pull request #3793 from srtee/reaxff-varstyle-efield 
Enable `fix qeq/reaxff` with variable `fix efield`
 2023-06-01 10:01:56 -04:00
Jacob Gissinger
a0461d29dd Update atom.cpp 2023-05-31 17:04:49 -04:00
Stan Gerald Moore
cae2414126 Fix compiler warnings in Kokkos ACKS2 2023-05-31 13:09:07 -06:00
Axel Kohlmeyer
cb02563d3d the potential keyword is not (yet) supported by fix efield/tip4p 2023-05-31 13:29:41 -04:00
Axel Kohlmeyer
c0602b6500 make using energy and potential keyword at the same time an error 2023-05-31 13:20:35 -04:00
Axel Kohlmeyer
70709f2f08 simplify error messages 2023-05-31 08:25:45 -04:00
Axel Kohlmeyer
9ec55dcb1f silence compiler warning 2023-05-30 19:10:11 -04:00
jrgissing
088d870e20 check remaining per-atom initializations 2023-05-30 17:17:54 -04:00
jrgissing
c934208a4a only update ivector if it still exists 2023-05-28 14:07:25 -04:00
Stan Moore
01b481ec4f Small tweaks 2023-05-26 15:27:15 -07:00
srtee
d190249e98 add documentation and checks 2023-05-22 00:10:01 +10:00
srtee
fe7a6fce29 make QEQ work with atom-style potential 2023-05-20 14:33:24 +10:00
srtee
8d0eb9b1f7 hook up efield variables to qeq/reaxff 2023-05-20 14:10:07 +10:00
Jacob Gissinger
5fac8f483e last typo 2023-05-19 23:51:01 -04:00
Jacob Gissinger
d7b7d1d323 make sure error messages not wrong 2023-05-19 23:48:41 -04:00
Jacob Gissinger
aaabe41b22 typo 2023-05-19 22:54:23 -04:00
Jacob Gissinger
ad7b27a67a correct logic 2023-05-19 22:27:28 -04:00
jrgissing
b9f01f106e is_typelabel function 2023-05-19 21:20:34 -04:00
Axel Kohlmeyer
ed03d04a70 Merge pull request #3779 from lammps/fix-ttm-mod-arrays 
Reorder fix ttm/mod 3d arrays to be consistent with fix ttm and fix ttm/grid
 2023-05-18 18:33:25 -04:00
Steve Plimpton
c73b7483b2 swtich loop order back to be consistent with rest of file 2023-05-18 11:47:20 -06:00
Axel Kohlmeyer
6585151ce1 reorder loops to compute properties vector 2023-05-17 22:04:32 -04:00
Axel Kohlmeyer
d206f583c4 whitespace 2023-05-17 21:57:14 -04:00
Steve Plimpton
f1aca8b71a formatting tweaks 2023-05-17 16:39:14 -06:00
Axel Kohlmeyer
10880332ed Merge pull request #3783 from Colvars/colvars-update 
Update Colvars library to version 2023-05-01
 2023-05-17 18:26:41 -04:00
Axel Kohlmeyer
5be9eda905 Merge pull request #3780 from srtee/patch-3 
Bugfix fix_efield.cpp for atom-style energy
 2023-05-17 16:33:37 -04:00
Giacomo Fiorin
377c652a83 Update Colvars library to version 2023-05-01 
This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
 2023-05-17 13:29:00 -04:00
Steve Plimpton
88d9d39bab Merge branch 'fix-ttm-mod-arrays' of github.com:lammps/lammps into fix-ttm-mod-arrays 2023-05-17 08:17:11 -06:00
Steve Plimpton
d98b1e9f04 fix left/right indices 2023-05-17 08:15:42 -06:00
Axel Kohlmeyer
166301180b Merge pull request #3769 from stanmoore1/kk_optimize 
Kokkos package optimizations
 2023-05-17 07:13:04 -04:00
Shern Tee
e044ccbbb3 Bugfix fix_efield.cpp for atom-style energy 2023-05-17 16:41:21 +10:00
Axel Kohlmeyer
4f57026dc0 whitespace 2023-05-16 21:15:01 -04:00
Axel Kohlmeyer
2e58a9ecf8 whitespace 2023-05-16 21:13:48 -04:00
Steve Plimpton
05b8082e3c code cleanup 2023-05-16 17:03:34 -06:00
Steve Plimpton
0d31ab9c88 one more change 2023-05-16 16:51:00 -06:00
Steve Plimpton
2b9c65855a swap 3d array indices in fix ttm/mod 2023-05-16 16:38:12 -06:00
Stan Moore
858fd4cc2c Small optimization 2023-05-16 15:23:31 -06:00
Stan Moore
b1ee177c0a Must use local variable for lambda capture 2023-05-16 12:43:19 -06:00
Stan Moore
b9256fa492 Reduce memory allocations 2023-05-16 11:09:37 -06:00
Stan Moore
2328cae55f Merge branch 'develop' of https://github.com/lammps/lammps into kk_optimize 2023-05-15 10:48:51 -06:00
Axel Kohlmeyer
91e0d0411b one more programming style tweak 2023-05-15 02:04:17 -04:00
Axel Kohlmeyer
ed958d8aed Merge branch 'develop' into kim_adapt 2023-05-15 02:01:01 -04:00
Axel Kohlmeyer
d584f2fe50 follow LAMMMPS' programming style more closely 2023-05-15 01:58:45 -04:00
ilia Nikiforov
17747a3c58 moved scaling to immediately after compute and removed virial scaling 2023-05-14 15:07:31 -05:00
Axel Kohlmeyer
c76e85c445 Merge pull request #3770 from akohlmey/collected-small-fixes 
Collected small fixes and updates
 2023-05-13 15:19:13 -04:00
Axel Kohlmeyer
d6d825258e Merge pull request #3771 from lammps/variable-current 
Change how variables check if computes are current
 2023-05-12 19:26:36 -04:00
Axel Kohlmeyer
8414d23c2b use symbolic constants 2023-05-12 18:04:37 -04:00