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Author SHA1 Message Date
jrgissing
b9f01f106e is_typelabel function 2023-05-19 21:20:34 -04:00
jtclemm
0dd26189d4 Adding missing factor in bpm/rotational single method 2023-05-19 13:52:35 -06:00
jtclemm
cb5934cbcd Adding option to doc files, clarifying normal forces in compute pair/bond local 2023-05-19 13:51:53 -06:00
jtclemm
7ec842d9cb Adding requested feature to normalize forces 2023-05-19 13:50:11 -06:00
Wengen Ouyang
0334ddb7c6 Update pair_ilp_water_2dm.rst 2023-05-19 22:57:45 +08:00
oywg11
22d9c047f4 update doc file 2023-05-19 22:52:18 +08:00
Axel Kohlmeyer
7c14b750ef improve error message 2023-05-19 00:40:54 -04:00
Axel Kohlmeyer
9da310a33e spelling 2023-05-19 00:40:45 -04:00
Axel Kohlmeyer
842016e997 Merge branch 'develop' into collected-small-fixes 2023-05-19 00:13:15 -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
Steve Plimpton
af71279df1 Merge branch 'fix-ttm-mod-arrays' of github.com:lammps/lammps into fix-ttm-mod-arrays 2023-05-18 11:44:31 -06:00
Steve Plimpton
50858205f6 refresh log files for fix ttm/mod example 2023-05-18 11:43:54 -06:00
oywg11
bbff6c25b3 add examples 2023-05-18 22:01:19 +08:00
oywg11
3d35d68a4b add doc file 2023-05-18 22:00:03 +08:00
oywg11
af04ecc532 add potential file 2023-05-18 21:59:07 +08:00
oywg11
cc30c4478d add optmized verion of ilp_water_2dm 2023-05-18 21:58:40 +08:00
oywg11
81a497adcd add standard version of ilp_water_2dm 2023-05-18 21:51:53 +08:00
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
d8ca6274e7 Merge branch 'develop' into pimd_langevin 2023-05-17 18:26:59 -04:00
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
5d66dc6659 apply clang-format 2023-05-17 17:50:15 -04:00
Axel Kohlmeyer
79f3eb6a4d remove debug code 2023-05-17 17:35:22 -04:00
Axel Kohlmeyer
8736f97792 remove dead code 2023-05-17 17:35:14 -04:00
Axel Kohlmeyer
39f61b6af3 Merge branch 'develop' into pimd_langevin 2023-05-17 17:30:49 -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
Axel Kohlmeyer
7c98d4dba3 avoid null pointer dereferences by allocating a buffer for at least 1 item 2023-05-17 10:26:33 -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
Axel Kohlmeyer
a84470383b Merge pull request #3777 from ilia-nikiforov-umn/kim_adapt 
Add "scale" attribute to pair_kim to be used with fix adapt
 2023-05-16 07:08:40 -04:00
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
cf51c94be0 update unit test for presence of Pair::extract() function in pair style kim 2023-05-15 02:02:36 -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
2d18883e8b Merge pull request #3755 from jtclemm/doc-edits 
Reorganization of the programming guide
 2023-05-13 17:22:41 -04:00