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21366 Commits

Author SHA1 Message Date
Axel Kohlmeyer 2e844971a8
extend PotentialFileReader class to check for a UNITS: tag and error out if it doesn't match the current units 2020-06-14 06:23:49 -04:00
Axel Kohlmeyer 0481184862
add utility function to get the units tag value from a potential file 2020-06-14 06:22:47 -04:00
Axel Kohlmeyer d84b4a3fff
Merge pull request #2152 from stanmoore1/kk_snap_mem 
Remove unnecessary memory allocation in Kokkos PairSNAP
 2020-06-12 15:28:28 -04:00
Stan Moore 49556edd50 Remove unnecessary allocation 2020-06-12 12:39:03 -06:00
Axel Kohlmeyer 0c23fcae91
Merge pull request #2149 from jtclemm/sort-atom-callbacks 
Sort atom callbacks
 2020-06-12 08:22:02 -04:00
Axel Kohlmeyer cf359dede2
Merge pull request #2139 from akohlmey/fetch-potentials 
Add feature to transparently download external potential files when packages are enabled
 2020-06-12 06:28:42 -04:00
Axel Kohlmeyer 22ed175632
Merge pull request #2151 from akohlmey/move-ubuf-to-lmptype 
Move definition(s) of union ubuf to lmptype.h
 2020-06-12 05:51:41 -04:00
Axel Kohlmeyer 5f86bac419
Merge pull request #2144 from rbberger/tokenizer-performance-fixes 
Performance optimization of Tokenizer
 2020-06-12 04:20:05 -04:00
Axel Kohlmeyer 3c99471df8
add a few more unit tests for functions in utils 2020-06-12 01:29:42 -04:00
Axel Kohlmeyer 8c470b9e8b
Merge branch 'master' into tokenizer-performance-fixes 2020-06-12 00:43:43 -04:00
Axel Kohlmeyer 6b783d31ad
fix spelling 2020-06-11 21:28:32 -04:00
Axel Kohlmeyer 219a3e4ce2
fix format (again) 2020-06-11 21:27:27 -04:00
Axel Kohlmeyer bb144f0d1b
Merge branch 'reset-ids-sort' into move-ubuf-to-lmptype 
# Conflicts:
#	src/reset_ids.h
 2020-06-11 20:12:37 -04:00
Axel Kohlmeyer 965ec37e80
whitespace/format fixes 2020-06-11 20:11:38 -04:00
Axel Kohlmeyer 1e8ef99fa7
use compile time tests instead of runtime checks for skipping 64bit tests on 32bit integers 2020-06-11 19:17:17 -04:00
Axel Kohlmeyer 9ca0d01a5b
silence compiler warnings 2020-06-11 19:05:06 -04:00
Axel Kohlmeyer a8c1ce98cf
remove trailing whitespace 2020-06-11 19:04:15 -04:00
Axel Kohlmeyer 6274234376
have a single union ubuf definition in lmptype.h and remove others 2020-06-11 18:37:31 -04:00
jtclemm 883a6c5aa1 Addressing include conflict 2020-06-11 16:24:29 -06:00
Axel Kohlmeyer 006f7956c1
Merge remote-tracking branch 'github/reset-ids-sort' into move-ubuf-to-lmptype 2020-06-11 18:11:51 -04:00
Axel Kohlmeyer fc9bbd4d06
Merge pull request #2121 from rbberger/gran-wall-store-contacts-fix 
Document and fix store_contacts in fix gran/wall and gran/wall/region
 2020-06-11 18:04:23 -04:00
Axel Kohlmeyer bdce720337
Merge pull request #2143 from lammps/hyper-eligible 
fix a bug with checking too early for ineligibilty for biasing
 2020-06-11 18:02:19 -04:00
jtclemm e70f23cdcc
Switching to std::sort 2020-06-11 15:42:37 -06:00
Axel Kohlmeyer b9303378ac
move pair style mesocnt from USER-MISC to (upcoming) USER-MESONT package 
the remaining documentation and README files will be updated once USER-MESONT is integrated
 2020-06-11 17:41:19 -04:00
Axel Kohlmeyer 9ca7091385
Merge pull request #2141 from akohlmey/kokkos-make-arch-case-insensitive 
Make kokkos configuration keywords with gmake case insensitive
 2020-06-11 17:20:43 -04:00
Axel Kohlmeyer 77a38c2a0a
remove (unsupported) reference to AMD Ryzen 2020-06-11 17:03:20 -04:00
Axel Kohlmeyer 9896d10d0c
whitespace cleanup 2020-06-11 16:52:38 -04:00
Axel Kohlmeyer d95859c73b
update hyperdynamics example log files 2020-06-11 16:52:30 -04:00
Axel Kohlmeyer 96a6afd42a
Merge pull request #2148 from akohlmey/kim-echo-log-refactor 
KIM package echo/log refactor and bugfix
 2020-06-11 16:46:41 -04:00
Axel Kohlmeyer 765b547a40
Merge pull request #2147 from stanmoore1/kk_sw 
Fix compile error with pair_sw_kokkos
 2020-06-11 16:20:03 -04:00
jtclemm ca424772df
Improving clarity of loops 2020-06-11 14:10:26 -06:00
jtclemm 006ada3a52
Sorting atom callback lists 2020-06-11 14:03:59 -06:00
Richard Berger 3a5cdd384f
vector -> array 2020-06-11 14:51:36 -04:00
Richard Berger 43d3133583
Whitespace 2020-06-11 14:00:13 -04:00
Richard Berger f25f7fee8d
Only count new words 2020-06-11 13:56:47 -04:00
Richard Berger 6a9073a0cb
Add count_words for C-Strings 2020-06-11 13:50:26 -04:00
Richard Berger 645d3b61ba
Only count new words 2020-06-11 13:49:58 -04:00
Richard Berger 6cb5345cd0
Add optimized version of count_words for default whitespace chars 2020-06-11 13:37:22 -04:00
Axel Kohlmeyer 505cc1036f
refactor KIM package code for using {fmt} and std::string 2020-06-11 13:25:41 -04:00
Stan Moore 61d0592e6a Fix compile error with pair_sw_kokkos 2020-06-11 11:13:36 -06:00
Richard Berger 558b9201ac
Fix typo 2020-06-11 12:37:44 -04:00
Richard Berger e9a52a2b1b
More doc updates 2020-06-11 12:30:02 -04:00
Richard Berger b299601a41
Update fix_wall_gran docs 2020-06-11 12:22:55 -04:00
Richard Berger ff35f421ac
Don't store atom tag, just if there is a contact 2020-06-11 11:35:27 -04:00
Axel Kohlmeyer 7ace10238d
change interface to Input::write_echo() to accept const std::string 2020-06-11 10:23:44 -04:00
Axel Kohlmeyer 9945f73743
fix spelling in a few more files 2020-06-11 01:05:58 -04:00
Richard Berger 81d937ee97
Performance optimization of Tokenizer 
Reduces string allocations and removes std::vector from Tokenizer
Most processing now happens on-demand.
 2020-06-11 00:22:04 -04:00
Steve Plimpton b287651ed6 fix a bug with checking too early for ineligibilty for biasing 2020-06-10 16:56:52 -06:00
Steve Plimpton e4d1068c70 flag a couple fixes and their derived clases as incompatible with resetting atom IDs 2020-06-10 16:47:55 -06:00
Steve Plimpton d02363b8fb adding a reset_ids sort option 2020-06-10 16:33:05 -06:00