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25490 Commits

Author SHA1 Message Date
Axel Kohlmeyer 71dbf43e09
error our when Fix:set_molecule() is called with unsupported fixes 
also add example input for using fix rigid/small with fix deposit
 2021-03-30 11:10:59 -04:00
Axel Kohlmeyer 57ad6d50f4
silence compiler warnings 2021-03-30 10:36:00 -04:00
Axel Kohlmeyer bfca619957
fix typos 2021-03-30 07:49:15 -04:00
Axel Kohlmeyer 40f1a74a7f
use more precise detection of verlet and respa run styles 2021-03-30 07:37:39 -04:00
Axel Kohlmeyer 3041561383
add proper r-RESPA support for fix cmap 2021-03-30 07:36:53 -04:00
Axel Kohlmeyer ea105a3c9a
fix typo 2021-03-30 07:36:22 -04:00
Axel Kohlmeyer 41de02ee9d
update granular howto 2021-03-29 23:44:38 -04:00
Axel Kohlmeyer 2b11848fcc
bugfix from dan bolintineanu for issue reported on lammps-users by Deng Pan 2021-03-29 15:26:57 -04:00
Axel Kohlmeyer 9058216a54
silence compiler warnings 2021-03-29 14:11:56 -04:00
Axel Kohlmeyer 180d2895c4
Merge pull request #2678 from akohlmey/collected-small-changes 
Collected small changes and fixes
 2021-03-29 14:05:08 -04:00
Axel Kohlmeyer dbc30f9c19
Merge pull request #2683 from akohlmey/pair-map-refactor 
Refactor element to type mapping code  in pair styles
 2021-03-29 12:15:02 -04:00
Axel Kohlmeyer 1e3f1c584c
simplify by using utils::strdup() fmt::format() and reorder includes 2021-03-29 08:12:37 -04:00
Axel Kohlmeyer 806f4e73ed
make dihedral style table/cut a derived class from table and remove redundant code 2021-03-29 07:32:43 -04:00
Axel Kohlmeyer e481eb1154
simplify by using utils::strdup() fmt::format() and reorder includes 2021-03-29 07:29:14 -04:00
Axel Kohlmeyer b32570c15e
simplify by using utils::strdup() and reorder includes 2021-03-28 22:22:13 -04:00
Axel Kohlmeyer 31726f56e6
refactor group2ndx and ndx2group commands to use fmtlib, tokenizer and utils 2021-03-28 14:48:39 -04:00
Axel Kohlmeyer dfb18caf5a
simplify using utils::strdup(), update order of include files 2021-03-27 16:25:55 -04:00
Axel Kohlmeyer 436be824e1
use std:: namespace for STL containers 2021-03-27 12:10:40 -04:00
Axel Kohlmeyer 0b73ab96d2
avoid replicated code, consolidate variables and element mapping 2021-03-27 12:09:36 -04:00
Axel Kohlmeyer 35abca1b40
we should include <strings.h> when using strcasecmp() 2021-03-27 11:18:59 -04:00
Axel Kohlmeyer e85f945d8e
fix typos 2021-03-26 23:12:29 -04:00
Axel Kohlmeyer 756d935d06
use std:: namespace for STL containers 2021-03-25 21:13:24 -04:00
Axel Kohlmeyer 53f32cea7e
simplify using utils::strdup() 2021-03-25 19:42:41 -04:00
Axel Kohlmeyer 2baafda517
simplify 2021-03-25 17:19:11 -04:00
Axel Kohlmeyer 2b34d88b71
fix bug 2021-03-25 17:19:03 -04:00
Axel Kohlmeyer 27e31c4b15
simplify 2021-03-25 14:49:49 -04:00
Axel Kohlmeyer 47b7653d4d
Merge pull request #2653 from rbberger/code_coverage 
Add tests to increase code coverage
 2021-03-24 20:57:46 -04:00
Axel Kohlmeyer 73b9f22681
Merge pull request #2675 from jrgissing/bond/react-tweak-recent-updates 
Bond/react: tweak recent updates
 2021-03-23 13:51:48 -04:00
Axel Kohlmeyer b7296b6d0b
consolidate documentation for dihedral styles table and table/cut into one file 2021-03-23 13:49:37 -04:00
Axel Kohlmeyer 403a7a6f84
Merge pull request #2677 from stanmoore1/kk_snap_opt 
Optimizations to Kokkos SNAP
 2021-03-23 13:32:02 -04:00
Axel Kohlmeyer 4b076e01be
silence compiler warning 2021-03-22 21:36:33 -04:00
Axel Kohlmeyer ca1496e028
simplify 2021-03-22 21:36:25 -04:00
Axel Kohlmeyer 56121a524c
correct equilibrium angle computation for angle style cosine/periodic if b < 0 2021-03-22 16:26:50 -04:00
Axel Kohlmeyer 58744f0a49
correct expression for K 2021-03-22 15:32:24 -04:00
Axel Kohlmeyer aabfe40ad3
add missing 1/n**2 term to pair style cosine/periodic energy function 2021-03-22 15:10:45 -04:00
Axel Kohlmeyer e8c8ceaf81
correct attribution of angle style cosine/squared with DREIDING 2021-03-22 11:28:22 -04:00
Stan Moore e2591a90cf Merge branch 'master' of https://github.com/lammps/lammps into kk_snap_opt 2021-03-22 11:24:46 -04:00
Axel Kohlmeyer b8f6063578
correct documentation of angle style cosine/periodic 2021-03-22 10:47:49 -04:00
Stan Moore 2bab4808b6 Improve memory coalescing in Kokkos snap force computation, pointed out by @weinbe2 2021-03-22 08:28:43 -06:00
jrgissing b3f465babe decrease foward_comm nsize 
due to new placement of probability evaluation
 2021-03-20 16:34:55 -04:00
jrgissing 012cdf3763 performance improvement bugfix 2021-03-20 16:20:57 -04:00
Axel Kohlmeyer c4e1255f3e
Merge pull request #2674 from rbberger/small_changes 
Small code changes
 2021-03-19 20:05:41 -04:00
Richard Berger dbe41778fa
Merge branch 'small_changes' of github.com:rbberger/lammps into small_changes 2021-03-19 18:51:44 -04:00
Richard Berger 06ee5be2ce
Fix unhandled cases in docs LAMMPS syntax highlighting 2021-03-19 18:51:21 -04:00
Stan Moore 4269eeeef7 Optimize quadratic Kokkos SNAP, pointed out by @weinbe2 2021-03-19 17:22:40 -04:00
Axel Kohlmeyer 125ddb0c82
Merge pull request #2670 from stanmoore1/kk_debye 
Fix issues in pair_coul_debye_kokkos
 2021-03-19 16:13:28 -04:00
Axel Kohlmeyer 9707771f1c
apply UTF-8 character replacement before creating tokens 2021-03-19 16:10:37 -04:00
Axel Kohlmeyer 6503a7c3ba
skip explicit temporaries 2021-03-19 15:52:27 -04:00
Richard Berger 1f50557b38
Adopt utils::strdup in dump styles 2021-03-19 15:34:43 -04:00
Richard Berger a33a04a392
Remove redundant has_next() check in Tokenizer 2021-03-19 14:12:09 -04:00