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16323 Commits

Author SHA1 Message Date
Axel Kohlmeyer a93d8dda3c add example input and logfiles for using fix qeq/shielded with pair style reax/c 2019-01-31 14:14:29 +01:00
Axel Kohlmeyer 327ca344ff make fix qeq/shielded fully compatible with pair style reax/c as a replacement for fix qeq/reax 2019-01-31 13:49:05 +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
Axel Kohlmeyer 06d5c1d62f
Merge pull request #1279 from akohlmey/create-atoms-bounding-box 
Optimize performance of create_atoms for large boxes and small regions
 2019-01-31 09:39:55 +01:00
Axel Kohlmeyer 0e1c6082b0
Merge pull request #1309 from PabloPiaggi/pair_entropy 
compute entropy/atom - enhancement/optimization
 2019-01-31 09:36:44 +01:00
PabloPiaggi ccdfde4978 Update example log file 2019-01-30 15:16:35 +01:00
PabloPiaggi 136e247cd8 compute entropy/atom - Use NL with ghost atoms only with avg yes 2019-01-30 14:59:23 +01:00
Axel Kohlmeyer 8cc593fe6b
Merge pull request #1308 from agiliopadua/master 
Fix in extract() method of pair_thole
 2019-01-30 08:12:30 +01:00
Agilio Padua f7bb48102f Fix in extract() method of pair_thole 2019-01-29 18:03:12 +01:00
Axel Kohlmeyer fb30d2d078
Merge pull request #1303 from pastewka/19_dump_nc1 
ENH: Output computes/fixes of with arbitrary number of columns to NetCDF
 2019-01-25 10:42:46 +01:00
Axel Kohlmeyer 57b804eecf
Merge pull request #1301 from stevenvdb/add-user-yaff 
Fix mistake in mixing rules for mm3/switch3
 2019-01-24 14:16:36 +01:00
Steven Vandenbrande a432b668f6 Fix mistake in mixing rules for mm3/switch3 2019-01-24 13:52:46 +01:00
Axel Kohlmeyer 985913bce2
Merge pull request #1297 from stevenvdb/add-user-yaff 
Add USER-YAFF package for MOF simulations with QuickFF
 2019-01-24 11:05:55 +01:00
Axel Kohlmeyer f88c5e147a
Merge pull request #1298 from jrgissing/bond/react-distance_constraints 
Bond/react: add reaction constraints support
 2019-01-24 10:55:22 +01:00
Axel Kohlmeyer 098f2906e0
Merge pull request #1299 from ohenrich/user-cgdna 
USER-CGDNA PDF docs update
 2019-01-24 10:50:44 +01:00
Axel Kohlmeyer f2544fa738 remove (evil) tabs 2019-01-24 04:44:54 -05:00
Lars Pastewka 5f3a7cbc33 MAINT: Replaced special character with a space. 2019-01-23 11:29:49 +01:00
jrgissing fbee21f495 distance constraint: clarify use case in docs 2019-01-22 23:22:51 -07:00
jrgissing 7a10ac2019 bond/react:reaction_constraints 
introduce a distance constraint between any two reaction-site atoms, in order for reaction to occur
 2019-01-22 23:14:58 -07:00
Axel Kohlmeyer 54a481ef1f use correct pair style name in comment about error messages 2019-01-22 12:33:17 -05:00
Axel Kohlmeyer dd3dbfaee2 restore aphabetical order of improper styles 2019-01-22 12:26:51 -05:00
Axel Kohlmeyer 9caf0ce3e1 add USER-YAFF package to build system 2019-01-22 12:17:04 -05:00
Steven Vandenbrande ca31147d00 Fix USER-YAFF documentation issues 2019-01-22 14:58:38 +01:00
Oliver Henrich 7ec6e4b262 Merge branch 'master' into user-cgdna 2019-01-22 13:06:42 +00:00
Oliver Henrich 874e4fdafc Corrected required input angular velocity -> momentum 2019-01-22 13:05:15 +00:00
Steven Vandenbrande 60b137f241 Add examples for the USER-YAFF package 2019-01-22 10:09:10 +01:00
Steven Vandenbrande 794bf5084c Implementation and documentation for USER-YAFF package 2019-01-22 10:09:10 +01:00
Jacob Gissinger fb6942a325
Merge pull request #41 from lammps/master 
rebase
 2019-01-21 20:22:23 -07:00
Lars Pastewka 0fde0f99bc ENH: Support for outputting computes and fixes with arbitrary number of columns. 2019-01-21 23:04:22 +01:00
Axel Kohlmeyer bd3b712902
Merge pull request #1263 from stanmoore1/kk_snap 
Optimize Kokkos SNAP energy calculation
 2019-01-18 21:12:56 +01:00
Stan Moore e5b86910e9 Merge branch 'master' of https://github.com/lammps/lammps into kk_snap 2019-01-18 12:03:09 -07:00
Stan Moore b3747ce99b Fix some issues in new version of pair_snap_kokkos_impl.h 2019-01-18 11:58:10 -07:00
Axel Kohlmeyer 037cdfe046
Merge pull request #1291 from stevenvdb/bugfix_improper_virial 
Fix bug in virial calculation for impropers fourier and umbrella
 2019-01-18 13:51:04 +01:00
Axel Kohlmeyer 3609a33eb8
Merge pull request #1292 from jrgissing/bond/react-limit-total-number-of-reactions 
bond/react: strict reaction limit and serial compilation bugfix
 2019-01-18 13:16:56 +01:00
jrgissing 94dc5e1133 bond/react: strict reaction limit 
also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases
 2019-01-17 23:13:21 -07:00
Steven Vandenbrande 6702f65fbb Fix mistake in virial calculation for improper_fourier and improper_umbrella 2019-01-15 10:06:42 +01:00
Axel Kohlmeyer a5ce656c32
Merge pull request #1288 from jrgissing/bond/react-limit-total-number-of-reactions 
Bond/react: limit number of reactions, bugfixes
 2019-01-13 10:26:06 -05:00
jrgissing b0af54ac37 bond/react:limit reaction occurrences 2019-01-13 00:07:03 -07:00
Jacob Gissinger 4ec21e1b31
Merge pull request #40 from lammps/master 
rebase
 2019-01-12 23:28:09 -07:00
Axel Kohlmeyer 3cbf009ce6
Merge pull request #1286 from jrgissing/bond_react-memory_correction 
Bond/react: memory correction
 2019-01-10 07:09:45 -05:00
jrgissing 8387b2953b bond_react:correctly delete internally-created fixes 2019-01-09 23:14:24 -07:00
Jacob Gissinger e82999ecb4
Merge pull request #39 from lammps/master 
rebase
 2019-01-09 22:17:33 -07:00
Axel Kohlmeyer e572235ecf optimize create_atoms performance for large boxes and small regions. warn if taking a long time 2019-01-08 14:33:07 -05:00
Stan Moore 60693a5f8a Change Kokkos SNAP energy shared arrays from thread to team 2019-01-07 16:26:16 -07:00
Axel Kohlmeyer 61c36dd768
Merge pull request #1277 from stanmoore1/kk_reax_bugfix 
Fix memory issue in Kokkos Reax
 2019-01-07 14:36:22 -05:00
Stan Moore 7fe7dd95d0 Fix memory issue in pair_reaxc_kokkos 2019-01-07 12:09:36 -07:00
Axel Kohlmeyer 06f9933c55
Merge pull request #1276 from akohlmey/rename-lebedva-sources 
Rename pair style lebedeva/z sources
 2019-01-07 11:32:54 -05:00
Stan Moore 3d374aa8b3 Merge branch 'master' into kk_snap 2019-01-07 08:44:36 -07:00
Axel Kohlmeyer 98e0d6eab2 rename sources for pair style lebedeva to be consistent with style name 2019-01-06 21:42:08 -05:00
Axel Kohlmeyer 5ec9623294
Merge pull request #1274 from lammps/rerun-doc 
add parallel dump file info to rerun doc page
 2019-01-06 21:36:56 -05:00