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19886 Commits

Author SHA1 Message Date
Axel Kohlmeyer 8662733dcd
convert the remainder of raw html typesetting in pair style smtbq 2020-02-29 14:45:39 -05:00
Axel Kohlmeyer 228a0bfa2e
replace hi- with high- 2020-02-29 11:37:47 -05:00
Axel Kohlmeyer 6f47f110f1
use k_B consistently, fix some more math. convert some transcriptions to math 2020-02-29 11:37:31 -05:00
Axel Kohlmeyer 07fc624509
typeset reduced units 2020-02-29 06:41:28 -05:00
Axel Kohlmeyer 66a0e27edf
some more cases where we can use embedded math 2020-02-29 04:57:44 -05:00
Axel Kohlmeyer e6c9efe6bf
convert lists to tables for more compact presentation 2020-02-28 18:52:13 +01:00
Axel Kohlmeyer f02b2485fa
tweak command overview table width so it is readable in PDF 2020-02-28 18:51:52 +01:00
Axel Kohlmeyer 71c11c32e3
replace more raw html code and add syntax highlighting 2020-02-28 18:00:43 +01:00
Axel Kohlmeyer 19d334908b
replace raw html with embedded math expressions and fix related issues 2020-02-28 17:39:57 +01:00
Axel Kohlmeyer 03985454ed
some more formatting and math conversion improvements 2020-02-27 18:18:49 -05:00
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
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
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
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
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
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
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
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
Axel Kohlmeyer 4180b4a7d6
add example to COUPLE folder demonstrating loading LAMMPS as a plugin. 2020-02-25 19:07:49 +01:00
Stan Moore eb51511ddf Change compute entropy/atom to use occasional neigh list 2020-02-25 10:48:00 -07:00
pmla 1fc4dc151f typo 2020-02-25 18:11:31 +01:00
pmla 7acba4584d added group2ID 2020-02-25 18:05:36 +01:00
Axel Kohlmeyer 1a2a9f2209
small correction/simplification of the linking to LAMMPS library examples 2020-02-25 17:36:37 +01:00
Richard Berger 96d04b8a6c Update LAMMPS lexer for docs 2020-02-25 11:30:20 -05:00
Agilio Padua 00137765a8
Delete fix_propel_self.h 2020-02-25 17:17:13 +01:00
Agilio Padua cdfb1d5026
Delete fix_propel_self.cpp 2020-02-25 17:16:59 +01:00
Agilio Padua 6956dc1a33 Added safeguard to thole pair styles 2020-02-25 16:50:49 +01:00
Axel Kohlmeyer 26f11f19a7
update LAMMPS version string 2020-02-25 15:04:56 +01:00
pmla 3168c1116f fixed group selection 2020-02-25 14:16:21 +01:00
Axel Kohlmeyer bf62646977
add check for required atom properties to USER-SDPD 2020-02-25 14:08:55 +01:00