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13506 Commits

Author SHA1 Message Date
Christoph Junghans 66f59f9ec0 FindLATTE.cmake: fixed a typo 2017-09-13 15:51:03 -06:00
Christoph Junghans d84825fd7f remove useless files 2017-09-13 14:37:24 -06:00
Christoph Junghans b861ea342e cmake: fix LATTE linkage 2017-09-08 11:54:32 -06:00
Christoph Junghans fce633aa5f cmake: tweaks for EXAALT superbuild, add latte_fix 2017-09-08 11:33:49 -06:00
Christoph Junghans 2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
Richard Zamora 7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
Steve Plimpton c80203cb01 Merge pull request #641 from lammps/doc-tweak 
small update to docs for new commands
 2017-09-06 08:52:51 -06:00
Steve Plimpton 4161868bcf Merge pull request #640 from ohenrich/user-cgdna 
USER-CGDNA - sequence-dependent stacking and h-bonding strength
 2017-09-06 08:52:05 -06:00
Steve Plimpton 9ca39c89a6 Merge pull request #639 from rbberger/python_interface_improvements 
Python interface improvements
 2017-09-06 08:51:27 -06:00
Steve Plimpton 99791ce01c Merge pull request #632 from timattox/USER-DPD_kokkos_merge 
Add Kokkos version of the USER-DPD package
 2017-09-06 08:50:43 -06:00
Tim Mattox 0248a7b98e remove duplicate listing of deleted USER-DPD files from Purge.list 2017-09-06 09:24:05 -05:00
Axel Kohlmeyer d886cc91f3 fix syntax error in fix saed/vtk docs example 
This addresses the issue reported on github
by @subhammridha closes thus clodes #642
 2017-09-05 17:45:56 -04:00
Axel Kohlmeyer 4c5d901e2b fix stupid typo (too much compiling of fortran codes...) 2017-09-05 16:45:03 -04:00
Axel Kohlmeyer c8f92c1a61 add a couple deleted files from USER-DPD to Purge.list 2017-09-05 16:42:58 -04:00
Axel Kohlmeyer dec1d7b2dc re-indent so that gcc no longer complains about inconsistent indentation 2017-09-05 16:41:19 -04:00
Axel Kohlmeyer 45602e58f9 fix another couple of typos 2017-09-05 12:48:28 -04:00
Axel Kohlmeyer cd72532fb9 fix typo 2017-09-05 12:47:34 -04:00
Steve Plimpton b170606052 Merge pull request #620 from amilumas/master 
Temper_NPT
 2017-09-05 10:08:55 -06:00
Steve Plimpton 65b295e826 Merge pull request #638 from jdevemy/master 
Mods for extra/special/per/atom and add toluene
 2017-09-05 10:05:49 -06:00
Steve Plimpton 89a0bc947f small update to docs for new commands 2017-09-05 10:04:20 -06:00
Oliver Henrich c8967a335f Included hyperlink to package 2017-09-05 11:45:32 +01:00
Oliver Henrich 2105145f55 More minor changes 2017-09-05 11:40:36 +01:00
Oliver Henrich f7715ab6ce Added comment about optimised damping coefficient for BD 2017-09-05 11:35:26 +01:00
Oliver Henrich 12fe614ddf Added sequence-dependent stacking and base-pairing strength 2017-09-05 10:48:38 +01:00
Richard Berger 0b5a2e199d Add way of getting correct ctypes integer type for bigint, tagint, and imageint 2017-09-04 20:01:31 -04:00
Richard Berger 09bb687918 Correct indentation 2017-09-04 20:01:04 -04:00
Richard Berger bb3ee752e5 Added optional numpy access to atom data 
The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
 2017-09-04 19:59:50 -04:00
Richard Berger 6b2d321d18 Add missing globals in library interface 2017-09-04 19:57:02 -04:00
Steve Plimpton 2b9646097c Merge branch 'master' of github.com:lammps/lammps 2017-09-01 09:16:11 -06:00
Steve Plimpton f58088ae61 patch 1Sep17 2017-09-01 09:15:37 -06:00
Axel Kohlmeyer 397bc225b2 add temper/npt to src/USER-MISC/README 2017-08-31 14:56:43 -04:00
Axel Kohlmeyer d9d9ba8244 update .gitignore 2017-08-31 14:52:56 -04:00
Axel Kohlmeyer eba4be18c2 adapt formatting and naming conventions to fully match LAMMPS style. allow rigid and accelerated integrators. 2017-08-31 14:48:30 -04:00
Axel Kohlmeyer 4d2ed30b35 add reference outputs to temper/npt example 2017-08-31 14:13:02 -04:00
Axel Kohlmeyer f3dda30f8e fully integrate temper/npt command into manual 2017-08-31 13:53:40 -04:00
Stan Moore d95a5f219e Remove all thread fences except one in verlet_kokkos 2017-08-31 10:38:36 -06:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Tim Mattox 3e6cdd1400 USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT 2017-08-30 14:58:38 -05:00
Tim Mattox dc7f1281b8 USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet 
The Constant Energy DPD (DPDE) was our primary usage case, so only stubs
for the Constant Temperature case were included in Kokkos code so far.
The non-Kokkos version works fine for Constant Temperature DPD.
 2017-08-30 11:01:17 -05:00
Tim Mattox 2dd202cc76 USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp 2017-08-30 10:34:09 -05:00
Tim Mattox f2d8c37f27 Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT 2017-08-30 10:24:29 -05:00
Stan Moore a4a45f1d9c Remove unnecessary check in npair_kokkos 2017-08-29 17:25:13 -06:00
Amulya f57d194920 Add files via upload 
documentation for temper/npt
 2017-08-29 10:40:37 -04:00
Tim Mattox 736e063971 Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge 
Resolved conflicts in src/KOKKOS/npair_kokkos.cpp
 2017-08-28 14:46:50 -05:00
Amulya 6a4bbddb3b Add files via upload 
data file for example
 2017-08-28 14:56:37 -04:00
Amulya 2add18e013 Create in.temper_npt 
example for temper/npt
 2017-08-28 14:55:43 -04:00
Amulya d0efd3a422 Add files via upload 
Updated command to temper/npt instead of temper_npt
 2017-08-28 14:48:00 -04:00
Steve Plimpton 21893539cb Merge pull request #633 from lammps/doc-user-meso 
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
 2017-08-25 17:41:00 -06:00
Steve Plimpton dd101db79c Merge pull request #582 from stanmoore1/kk_changes 
Fixing execution space issues in KOKKOS package
 2017-08-25 17:06:26 -06:00
Steve Plimpton 81ba181349 tweak an eq in USER-MESO, also allow neigh to be built w/out styles 2017-08-25 17:04:36 -06:00