ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
36,076 Commits 12 Branches 209 Tags
5d4f9abf5b6604414e8f82537e49b21fbbfb65bc
Commit Graph

10208 Commits

Author SHA1 Message Date
Axel Kohlmeyer
d6ad52ea66 allow wildcards with "cutoff" keyword to fix reaxff/species 
this also switched to using fmtlib for column aligned output formatting
and re-applies clang-format.
 2023-06-08 09:46:33 -04:00
Axel Kohlmeyer
2272d8dd20 add new library interface function to documentation 2023-06-08 09:45:12 -04:00
Axel Kohlmeyer
9235377b44 Merge branch 'develop' into collected-small-fixes 2023-06-07 20:05:06 -04:00
Axel Kohlmeyer
de561737a3 update docs 2023-06-07 15:28:35 -04:00
Axel Kohlmeyer
af25bd87fb Merge branch 'develop' into collected-small-fixes 2023-06-07 15:23:54 -04:00
Axel Kohlmeyer
5fdba37492 Merge pull request #3807 from jtclemm/BPM 
Misc minor patches/features in BPM/Granular packages
 2023-06-07 13:55:00 -04:00
Axel Kohlmeyer
73693ca25b Merge pull request #3787 from oywg11/ilp-water-graphene 
Registry-Dependent Potential for Interfaces of Water with Graphene
 2023-06-07 11:48:43 -04:00
Axel Kohlmeyer
57f166670f fix versionadded macro so it is detected when actual version is added 2023-06-07 06:38:52 -04:00
Axel Kohlmeyer
37d894db51 update/clarify docs 2023-06-07 06:30:07 -04:00
Axel Kohlmeyer
f406aa1492 Merge pull request #3792 from evoyiatzis/master 
Inclusion of bond & angle contributions to "compute stress/mop"
 2023-06-07 06:09:58 -04:00
Axel Kohlmeyer
0f925f7a39 reformat, add versionadded marker 2023-06-07 04:33:37 -04:00
Axel Kohlmeyer
b81b1f5ecc switch dump yaml/netcdf thermo output to use new caching API. remove old API. 2023-06-06 22:40:13 -04:00
Axel Kohlmeyer
74a9cfc110 Merge pull request #3660 from Yi-FanLi/pimd_langevin 
Add fix style pimd/langevin
 2023-06-06 21:31:28 -04:00
Yifan Li李一帆
ee6b12ee30 Correct reference info 2023-06-06 18:04:26 -04:00
jtclemm
0ec5274873 Merge branch 'develop' into BPM 2023-06-06 14:40:51 -06:00
Axel Kohlmeyer
e954d8f050 correctly indicate OPT package version of pair style 2023-06-06 16:11:03 -04:00
Axel Kohlmeyer
c4d49324b5 various documentation updates 
- spelling fixes
- formatting conventions
- grammar fixes and clarifications
- full integration into manual build procedure
 2023-06-06 16:08:50 -04:00
Axel Kohlmeyer
9cc6839a8b Merge branch 'develop' into collected-small-fixes 2023-06-06 08:36:25 -04:00
Evangelos Voyiatzis
3782eeee2b remove whitespace from compute_stress_mop.rst 2023-06-04 13:47:54 +03:00
oywg11
196641927f correct a typo in the doc file 2023-06-03 23:07:55 +08:00
oywg11
b5ab173763 update the doc file 2023-06-03 23:03:12 +08:00
oywg11
a25100120b update the doc file 2023-06-03 20:36:12 +08:00
jtclemm
241f3b751e Unifying syntax for BPM bond options 2023-06-02 15:45:53 -06:00
Evangelos Voyiatzis
c30762ca8b Update documentation for compute stress/mop/profile 2023-06-02 19:44:37 +03:00
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
Evangelos Voyiatzis
c310616bb7 Update compute_stress_mop.rst to reflect the added keywords 2023-06-01 15:34:41 +03:00
Axel Kohlmeyer
90000ca166 update docs 2023-05-31 13:29:48 -04:00
Axel Kohlmeyer
4073241413 correct docs about label2type() function 2023-05-31 09:57:19 -04:00
Axel Kohlmeyer
8602ecd57f update/correct docs 2023-05-31 08:59:36 -04:00
Evangelos Voyiatzis
b28ee36f00 update documentation for compute stress/mop 2023-05-27 14:50:31 +03:00
Stan Moore
01b481ec4f Small tweaks 2023-05-26 15:27:15 -07:00
Axel Kohlmeyer
3d8df660c3 make rigid water examples more realistic and consistent. avoid warnings. 2023-05-25 18:08:42 -04:00
jtclemm
ceed30e7c6 Fixing mistakes in doc pages 2023-05-25 12:58:57 -06:00
srtee
d190249e98 add documentation and checks 2023-05-22 00:10:01 +10:00
oywg11
685255083e clean the duplicate info 2023-05-21 11:43:39 +08:00
oywg11
91ac9ef3fc update doc file 2023-05-21 11:29:28 +08:00
oywg11
276bc39a51 delete rst 2023-05-21 11:02:17 +08:00
jrgissing
0a45d1f9ac Update variable.rst 2023-05-19 21:31:51 -04:00
jtclemm
cb5934cbcd Adding option to doc files, clarifying normal forces in compute pair/bond local 2023-05-19 13:51:53 -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
9da310a33e spelling 2023-05-19 00:40:45 -04:00
oywg11
3d35d68a4b add doc file 2023-05-18 22:00:03 +08:00
Axel Kohlmeyer
d8ca6274e7 Merge branch 'develop' into pimd_langevin 2023-05-17 18:26:59 -04:00
Axel Kohlmeyer
39f61b6af3 Merge branch 'develop' into pimd_langevin 2023-05-17 17:30:49 -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
ed958d8aed Merge branch 'develop' into kim_adapt 2023-05-15 02:01:01 -04:00
Axel Kohlmeyer
2d18883e8b Merge pull request #3755 from jtclemm/doc-edits 
Reorganization of the programming guide
 2023-05-13 17:22:41 -04:00
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