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20273 Commits

Author SHA1 Message Date
Axel Kohlmeyer 19d334908b
replace raw html with embedded math expressions and fix related issues 2020-02-28 17:39:57 +01:00
Giacomo Fiorin 7be004512f Update Colvars to version 2020-02-27 
This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
 2020-02-27 19:55:31 -05:00
Axel Kohlmeyer 03985454ed
some more formatting and math conversion improvements 2020-02-27 18:18:49 -05:00
Sievers fbee5966f6 added cstring back to includes 2020-02-27 14:42:31 -07:00
Sievers 7a720ee9cf removed cstring from includes and fixed style warnings 2020-02-27 13:54:29 -07:00
Axel Kohlmeyer d242051c8e
Merge pull request #1898 from akohlmey/next_lammps_version 
Update version info for next release candidate
 2020-02-27 14:38:08 -05:00
Sievers 10fa9aa074 added cstring to includes 2020-02-27 11:37:02 -07:00
Sievers 35f4a62566 Change final displace atom to reset atom to save on memory and computation 2020-02-27 11:31:33 -07:00
Axel Kohlmeyer 6e7e365981
Merge pull request #1888 from lammps/release-preparation 
Documentation and Build script and Info updates for stable release
 2020-02-27 13:23:08 -05:00
Sievers 236535f61b fixed include, fixed numdiff forces getting called before initialization 2020-02-27 10:48:46 -07:00
Axel Kohlmeyer 3c277409c2
switch parsed-literal to code-block in Howto files where applicable 2020-02-27 12:45:14 -05:00
Axel Kohlmeyer 669a49e994
Merge pull request #1908 from stanmoore1/kk_finalize 
Finalize Kokkos on error exit
 2020-02-27 12:05:17 -05:00
Steve Plimpton 67bfda532f mods to fix numdiff 2020-02-27 09:52:23 -07:00
Axel Kohlmeyer 06ede499c1
use only the LAMMPS logo in the navigation bar 2020-02-27 11:36:00 -05:00
Axel Kohlmeyer eb8531062c
Merge branch 'doc-updates' of github.com:rbberger/lammps into release-preparation 2020-02-27 11:26:15 -05:00
Richard Berger 25ec8d36a8 Final batch of index cleanup and code-blocks 2020-02-27 11:08:04 -05:00
Stan Moore 704207f3c8 Finalize Kokkos on error exit 2020-02-27 08:51:02 -07:00
Evangelos Voyiatzis d89db2ac2a
files generated by the in.slater example script 2020-02-27 16:03:07 +01:00
Evangelos Voyiatzis 7849de15b0
Create in.slater 2020-02-27 16:01:38 +01:00
Axel Kohlmeyer 2d2cb46dc0
move release date 2020-02-27 08:58:09 +01:00
Axel Kohlmeyer 1bb38ed09b
Merge commit 'refs/pull/1903/head' of github.com:lammps/lammps into release-preparation 2020-02-27 01:15:17 -05:00
jrgissing fe1ac99ae7 bond/react: docs tweak 2020-02-26 20:08:58 -07:00
Richard Berger 9ef5949798 Second batch of index cleanup and code-blocks 2020-02-26 16:31:05 -05:00
Axel Kohlmeyer 3563d2f10d
remove references to html-offline and only produce the offline viewable html manual 2020-02-26 16:01:03 -05:00
Axel Kohlmeyer 7bd3215226
Merge pull request #1894 from stanmoore1/kk_snap_chunk 
Make Kokkos pair SNAP chunksize variable user-settable
 2020-02-26 15:27:37 -05:00
Axel Kohlmeyer ba560bc99e
Merge pull request #1905 from akohlmey/compute-pair-neigh-request 
Correct compute entropy/atom to work with "avg" flag enabled
 2020-02-26 14:23:57 -05:00
Axel Kohlmeyer 275626a1de
re-enable perpertual neighborlist for compute entropy/atom if avg flag is used only 2020-02-26 13:57:11 -05:00
Stan Moore 49b07a2360 Keep original chunksize value set by user in case atom count changes 2020-02-26 09:42:59 -07:00
Axel Kohlmeyer a828facbd8
Merge pull request #1900 from akohlmey/couple-lammps-plugin 
Example for loading LAMMPS as a plugin from a shared library
 2020-02-26 10:40:24 -05:00
Axel Kohlmeyer 37e6fd1bae
Merge pull request #1901 from stanmoore1/compea_neigh 
Change compute entropy/atom to use occasional neigh list
 2020-02-26 10:39:37 -05:00
Evangelos Voyiatzis de9691a751
Update README 2020-02-26 14:06:38 +01:00
Evangelos Voyiatzis 04e48999b2
Delete pair_coul_slater_cut.h 
move this file to USER-MISC
 2020-02-26 14:04:12 +01:00
Evangelos Voyiatzis 895f7aa46d
Delete pair_coul_slater_cut.cpp 
move this file to USER-MISC
 2020-02-26 14:03:43 +01:00
Evangelos Voyiatzis 5be0f1525a
source files for pair coul/slater 
Source files for long- and short-range coulombic interactions which are smeared with an exponential function (slater-type of smearing)
 2020-02-26 14:02:53 +01:00
Axel Kohlmeyer dcb83d41af
Merge pull request #1899 from agiliopadua/thole 
Added safeguard to thole pair styles
 2020-02-26 07:44:04 -05:00
Axel Kohlmeyer e766518062
Merge pull request #1896 from pmla/user-ptm-group-fix 
Apply compute group correctly for compute ptm/atom
 2020-02-26 07:28:01 -05:00
Axel Kohlmeyer f81b963a8a
more strict argument checking and initializing output data to zero 2020-02-26 13:12:39 +01:00
Axel Kohlmeyer c92378eaca
add explanation of use of group2 and document effect of compute group 2020-02-26 13:12:14 +01:00
Axel Kohlmeyer 526c9a548f
need to set single_enable to 0 after single() was removed 2020-02-26 12:58:10 +01:00
Axel Kohlmeyer 91c31da576
remove trailing whitespace 2020-02-26 12:52:21 +01:00
Sievers 49873f765c Added comment to credit myself 2020-02-25 16:53:04 -07:00
Sievers f18f2537e6 Updated error/warnings section 2020-02-25 16:35:54 -07:00
Sievers b0eb940b05 Added numdiff to false positives 2020-02-25 16:30:13 -07:00
Sievers 72891aacb2 Fixed groups not working 2020-02-25 16:23:35 -07:00
Sievers 809d481fd1 Merge branch 'master' of https://github.com/charlessievers/lammps into fix_numerical_differentiation 2020-02-25 15:35:53 -07:00
Sievers 13bff07606 Added documentation, added an example, avoided position round off, added in compute_pe's compute_scalar, now fix produces per-atom array instead of global array 2020-02-25 15:32:37 -07:00
Richard Berger 8e1928aa65 First batch of index cleanup and code-blocks 2020-02-25 14:46:22 -05:00
Axel Kohlmeyer e87b3a21c2
complete documentation for LAMMPS plugin coupling example 2020-02-25 14:10:55 -05:00
Axel Kohlmeyer e083f38c59
Merge pull request #1892 from sef43/master 
temper timeout synchronization fix
 2020-02-25 13:26:30 -05:00
Axel Kohlmeyer 958d5ca05b
Merge pull request #1897 from akohlmey/user-sdpd-atom-style-check 
Add check for required atom properties in USER-SDPD
 2020-02-25 13:26:00 -05:00