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7403 Commits

Author SHA1 Message Date
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
Germain Clavier
68ec36b006 Added the flip keyword to the documentation of fix_press_langevin. 2023-05-20 09:16:30 +02:00
Germain Clavier
9440f26355 Merge branch 'develop' of github.com:lammps/lammps into NPTLangevin 2023-05-20 08:59:29 +02:00
Germain Clavier
93402f61d8 Updated the documentation to include triclinic commands and other info. 2023-05-20 08:58:52 +02:00
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
Germain Clavier
1c33aec5dc Wrote the documentation for fix_press_langevin 2023-05-17 18:28:49 +02:00
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
Axel Kohlmeyer
96af466f4a as a few details to the discussion of programming languages and their standards 2023-05-12 15:45:55 -04:00
Axel Kohlmeyer
cd79276309 small formatting tweaks 2023-05-12 15:45:24 -04:00
Axel Kohlmeyer
aa069b2cfb fix typos 2023-05-12 15:44:54 -04:00
Axel Kohlmeyer
9a8640ca1a Merge pull request #3767 from lammps/vector-variable 
Vector-style variable enhancements
 2023-05-12 15:18:08 -04:00
Axel Kohlmeyer
0abb217d59 whitespace 2023-05-12 15:13:29 -04:00
Steve Plimpton
b54d39adf9 minor editing changes 2023-05-12 11:18:07 -06:00
jtclemm
35418afd6b Rename CRK -> RK 2023-05-11 14:19:32 -06:00
Axel Kohlmeyer
dd3d4e2b50 bump minimum requirement for building docs to python 3.8 2023-05-10 19:09:13 -04:00
Axel Kohlmeyer
a92e0030e8 whitespace 2023-05-10 17:24:29 -04:00
Axel Kohlmeyer
9890987eec Merge remote-tracking branch 'github/develop' into variable-current 2023-05-10 16:53:49 -04:00
ilia Nikiforov
ee5a300643 updated doc for kim adapt 2023-05-09 09:24:53 -05:00
Axel Kohlmeyer
4c51264b15 explain how to keep pairs in the neighbor list even if the scaling factor should be 0.0 2023-05-09 08:24:02 -04:00
Axel Kohlmeyer
820899cd5e use more obvious pair style dpd thermostat examples 2023-05-08 11:51:30 -04:00
Steve Plimpton
200f740c06 update variable doc page to explain new behavior 2023-05-08 09:48:27 -06:00
Axel Kohlmeyer
abe238ce61 use correct spelling for semicolon 2023-05-08 05:54:33 -04:00
Axel Kohlmeyer
a6f60405b6 resolve formatting issues and add a few style tweaks from languagetool.org 2023-05-08 05:52:18 -04:00
Axel Kohlmeyer
7342f27fb1 clarify download info 2023-05-06 22:40:58 -04:00
Axel Kohlmeyer
7b46f15068 use macOS consistently (missed a few places in the last round) 2023-05-06 22:40:58 -04:00
Axel Kohlmeyer
0cd95d64e2 Merge pull request #3768 from jrgissing/fix_reaxff/species-variable_Nlimit 
reax/species: variable input for Nlimit keyword
 2023-05-06 11:15:48 -04:00
Axel Kohlmeyer
aa62a2a9cf Merge branch 'doc-edits' of https://github.com/jtclemm/lammps into doc-edits 2023-05-05 11:44:32 -04:00
Joel Thomas Clemmer
56f06bc9e0 Reordering styles by priority, misc clean ups 2023-05-05 09:41:54 -06:00
Axel Kohlmeyer
c328761c78 Merge branch 'develop' into doc-edits 2023-05-05 11:30:48 -04:00
Axel Kohlmeyer
0de35dee29 spelling 2023-05-04 20:34:41 -04:00
Axel Kohlmeyer
6ffa720f87 Merge branch 'develop' into vector-variable 2023-05-04 20:14:51 -04:00
jrgissing
0b71371597 reax/species: variable input for Nlimit keyword 2023-05-04 20:10:13 -04:00
Axel Kohlmeyer
5da1df5004 add versionadded tag 2023-05-04 20:08:36 -04:00
Steve Plimpton
93100adbe0 debugging and doc pages 2023-05-04 16:24:15 -06:00
Axel Kohlmeyer
269f07a137 fix a few more sphinx issues and inconsistencies 2023-05-04 16:45:30 -04:00
Axel Kohlmeyer
d4554fc89e Merge branch 'develop' into doc-edits 2023-05-04 16:35:55 -04:00