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5010 Commits

Author SHA1 Message Date
jrgissing 5608f87c15 bond/react:unfix_deletes_internal_groups 2019-03-13 21:55:17 -06:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Axel Kohlmeyer 5486896876
Merge pull request #1350 from akohlmey/next-patch-release 
Step version string for next patch release
 2019-02-28 17:56:51 -05:00
Axel Kohlmeyer 14e6c126a8
Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix 
add command to compute the Dynamical Matrix
 2019-02-28 17:08:36 -05:00
Axel Kohlmeyer 50fef541c2
add x-ref 2019-02-28 15:50:59 -05:00
Axel Kohlmeyer 5fd033c0a2
add one more false positive required by recent changes 2019-02-28 15:49:48 -05:00
Axel Kohlmeyer 1d2eab5e1b
update attribution information in Package details documentation 2019-02-28 15:26:36 -05:00
Axel Kohlmeyer 16946d8c6d
integrate dynamical_matrix command into LAMMPS manual 2019-02-28 14:45:07 -05:00
Axel Kohlmeyer 326a97624e
Merge pull request #1317 from ornladios/adios2-master 
USER-ADIOS package with ADIOS 2.x
 2019-02-27 17:24:12 -05:00
Axel Kohlmeyer b60f0f754c
small tweaks to USER-ADIOS docs 2019-02-27 17:18:08 -05:00
Axel Kohlmeyer 6bf9c06a5a
Step version string for next patch release 2019-02-27 16:19:20 -05:00
Axel Kohlmeyer 9185f28a12
correct compute group/group documentation for use with EAM styles 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer 9bec93faa9
update spell-checking false positives for USER-ADIOS package 2019-02-26 19:51:18 -05:00
Axel Kohlmeyer 9178b9446a
remove trailing whitespace 2019-02-26 19:50:50 -05:00
Axel Kohlmeyer d76569c033
Merge pull request #1320 from eofetis/manual-pdf-support 
Add support for Sphinx+PDF+MathJax
 2019-02-22 15:10:13 -05:00
Axel Kohlmeyer e6df92e65a
Merge pull request #1011 from ellio167/kim-v2-update 
KIM v2 update
 2019-02-21 20:06:59 -05:00
Axel Kohlmeyer e6a7c8b03b
Merge pull request #1335 from donatas-surblys/langevin-tally-zero 
correct fix langevin with tally yes zero yes
 2019-02-21 20:06:44 -05:00
Norbert Podhorszki 3ad268739b Add dump adios to PDF build. Update example config with better documentation 2019-02-20 17:02:48 -05:00
Norbert Podhorszki 2de01cef45 Dump atom/adios and dump custom/adios command notifications 2019-02-20 16:21:07 -05:00
Norbert Podhorszki 1179beb543 Makefile build support for USER-ADIOS and build documentation 2019-02-20 14:42:28 -05:00
pmla bae2e61fa0 documentation bugfix 2019-02-15 19:40:37 -05:00
pmla 8a28046b4c typo in PTM docs 2019-02-15 18:52:40 -05:00
pmla 35d2de298f added license information to all files 
updated documentation
added example file
added graphene structure
 2019-02-15 18:49:23 -05:00
Ryan S. Elliott c193a9aee9 Updated Errors_messages.txt & false_positives.txt 2019-02-14 19:28:18 -06:00
Ryan S. Elliott e95cf4e917 Some various doc updates for kim-api support 2019-02-14 13:38:28 -06:00
Ryan S. Elliott 333154633b Merge branch 'master' into kim-v2-update 2019-02-14 13:29:50 -06:00
Axel Kohlmeyer d0ed6f2bf5
reflect changes to fix langevin also in the manual 2019-02-14 05:45:52 -05:00
Axel Kohlmeyer 0108855930
update .gitignore for the doc folder 2019-02-14 02:54:02 -05:00
jrgissing d08979737c bond/react:partially_revert_bonding_atom_choice 
choose closest eligible bonding partner, unless directly bonded (in which case we assume a bond-breaking reaction)
 2019-02-13 22:56:56 -07:00
Axel Kohlmeyer 88b62fa6bd
add old style PDF build to "make old" target. 
this will create the old style Manual.pdf in the old folder and put Developer.pdf there, too.
 2019-02-13 12:43:35 -05:00
Axel Kohlmeyer 581b7d3543
update list of false positives after docs changes 2019-02-13 09:23:54 -05:00
Axel Kohlmeyer eb8a6512e2 rename and document script to automatically convert 'default(none)' to 'default(shared)' OpenMP pragmas 2019-02-12 09:44:19 -05:00
Axel Kohlmeyer a0b7bf0f5c reformat fix wall/gran/region docs 
this should make it easier to recognize that these walls can be
moving/rotating/growing/shrinking due to using time dependent
equal style variables in the region definition
 2019-02-12 08:07:28 -05:00
Axel Kohlmeyer b29d526632
Merge pull request #1323 from akohlmey/next-patch-release 
Patch release 8 February 2019
 2019-02-08 21:43:39 +01:00
Axel Kohlmeyer 77c24f1b79 Merge branch 'master' into next-patch-release 
# Conflicts:
#	.github/PULL_REQUEST_TEMPLATE.md
 2019-02-08 15:34:40 -05:00
Axel Kohlmeyer f286155dd3
Merge pull request #1306 from stanmoore1/kk_angle_cosine 
Add Kokkos version of angle/cosine
 2019-02-08 21:07:36 +01:00
Axel Kohlmeyer b871b4e13d
Merge pull request #1321 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch release
 2019-02-08 17:19:01 +01:00
Axel Kohlmeyer a35f407dfc Patch release 8 February 2019 2019-02-08 17:15:22 +01:00
Axel Kohlmeyer a71159578e fix typo 2019-02-08 02:29:03 -05:00
Axel Kohlmeyer 622eb47902
some small tweaks, fixes for typos, and url corrections for the manual 2019-02-07 01:19:29 -05:00
Axel Kohlmeyer 019e534f80
some small tweaks, fixes for typos, and url corrections for the manual 2019-02-07 01:16:48 -05:00
efetis 7c1fb847f4 Slight tweak to sed in doc/Makefile 2019-02-06 18:00:23 -08:00
efetis 4fe6528ed4 Add support for Sphinx+PDF+MathJax 2019-02-06 17:14:50 -08:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
Axel Kohlmeyer d6eaf73db1
Merge pull request #1307 from akohlmey/next-patch-release 
Patch release 1 February 2019
 2019-02-01 20:22:18 +01:00
Axel Kohlmeyer f2a977884c
Merge pull request #1290 from akohlmey/python-script-portability 
Use argparse module in for Install.py scripts in lib and further portability and consistency enhancements. Some lint removal as well.
 2019-02-01 01:18:40 +01:00
Axel Kohlmeyer a9f8b17cbd
Merge pull request #1282 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2019-02-01 00:24:15 +01:00
Axel Kohlmeyer d6a918f4fd
Merge pull request #1270 from akohlmey/get-moltemplate-from-web 
Replace bundled moltemplate distribution with installation instructions only
 2019-01-31 22:58:31 +01:00
Axel Kohlmeyer 7606529f03
Merge pull request #1302 from akohlmey/combined-user-fep-soft-updates 
Combined USER-FEP related updates
 2019-01-31 22:57:51 +01:00
Axel Kohlmeyer c5256624e8 document coul/streitz and reax/c keywords to extract qeq parameters from pair styles 2019-01-31 13:48:06 +01:00