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4105 Commits

Author SHA1 Message Date
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 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
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 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
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 f3dda30f8e fully integrate temper/npt command into manual 2017-08-31 13:53:40 -04:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
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
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
Stan Moore e52a28f8af Update docs for Kokkos version of USER-DPD package 2017-08-25 16:20:42 -06:00
Axel Kohlmeyer 6db3bd87ee correct typo in header formatting 2017-08-23 17:52:09 -04:00
Steve Plimpton 7b7a5076d0 Merge pull request #624 from akohlmey/compute-fragment 
Add computes fragment/atom and aggregate/atom
 2017-08-23 14:14:33 -06:00
Steve Plimpton f7a0a6eb70 Merge pull request #622 from akohlmey/collected-small-fixes 
Collected small fixes
 2017-08-23 14:12:45 -06:00
Axel Kohlmeyer 97edf90a73 update fix qeq docs for the new, more flexible parameter file format 2017-08-23 11:22:09 -04:00
Axel Kohlmeyer cdfb1aa043 make links unique, fix doc format warnings and add entries to administrative files 2017-08-23 00:39:52 -04:00
Axel Kohlmeyer b80752a40c restore changes to read_data docs, that would have been lost due to merging an outdated version 2017-08-23 00:01:19 -04:00
Axel Kohlmeyer 5a0c3aea8a add a compute aggregate/atom, that combines the rules for compute cluster/atom and fragment/atom 2017-08-21 13:12:43 -04:00
Axel Kohlmeyer f5b8f722ee remove non-portable non-ascii blanks from fix wall/ees docs 2017-08-20 10:09:21 -04:00
Axel Kohlmeyer 39e51df2c0 add missing entry in pdf manual 2017-08-20 10:02:11 -04:00
Axel Kohlmeyer 4dc1195cd8 add docs for compute fragment/atom 2017-08-20 09:41:49 -04:00
Steve Plimpton f945d4567d new USER-MESO package 2017-08-18 17:33:42 -06:00
Steve Plimpton 7ddcb6812b patch 17Aug17 2017-08-17 16:02:20 -06:00
Steve Plimpton 76cd61350d Merge pull request #613 from akohlmey/collected-small-changes 
Collected small changes and bug fixes
 2017-08-17 11:34:52 -06:00
Steve Plimpton fa3c0c61d6 Merge pull request #618 from lammps/intel 
USER-INTEL add-ons from Mike
 2017-08-17 11:32:53 -06:00
Steve Plimpton c46d5ff422 Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10 
Minor fixes to Colvars module
 2017-08-17 11:32:38 -06:00
Axel Kohlmeyer 7175abcc71 flag more pair styles as supporting USER-INTEL to match newly added code 2017-08-16 13:58:46 -04:00
Axel Kohlmeyer e34b20405c Fix a couple of typos in the docs 2017-08-15 21:10:05 -04:00
Steve Plimpton 1d4d2155a2 USER-INTEL add-ons from Mike 2017-08-15 17:12:07 -06:00
Axel Kohlmeyer cee87d7a54 update manual to point to packages.lammps.org instead of rpm.lammps.org 2017-08-15 16:19:09 -04:00
Steve Plimpton 0b3f1b8a15 patch 11Aug17 2017-08-11 12:19:02 -06:00
Steve Plimpton 52bec0f380 patch 10Aug17 2017-08-10 16:44:09 -06:00
Axel Kohlmeyer c8741f3a01 remove special_bonds extra keyword and refer to read_data and create_box instead 2017-08-10 15:12:56 -04:00
Giacomo Fiorin da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Axel Kohlmeyer f9a515efd3 add some remarks about makefile settings on windows 2017-08-10 07:24:24 -04:00
Axel Kohlmeyer 5b55744209 fix a header line formatting issue 2017-08-10 07:21:39 -04:00
Axel Kohlmeyer f01103dd08 correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda) 2017-08-09 19:08:23 -04:00
Axel Kohlmeyer 81f4d7ecb5 rework section 4 (Packages) in the manual to match Install.py scripts 2017-08-09 19:07:20 -04:00
Steve Plimpton 0a54c34e34 Merge pull request #600 from akohlmey/install-and-docs-reviewed 
Installation scripts and docs reviewed for release
 2017-08-07 08:02:04 -06:00
Richard Berger e0f9a7c34c Adds BOW tutorial link in main menu 2017-08-07 00:06:53 -04:00