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14358 Commits

Author SHA1 Message Date
Axel Kohlmeyer 3528f9ca27 fix bugs in documentation and implementation of atom style mdpd 2018-02-09 15:19:01 +01:00
Axel Kohlmeyer 2e99e54e23 Merge branch 'patch-2' of https://github.com/amilumas/lammps into collected-small-changes 2018-02-09 14:44:11 +01:00
Axel Kohlmeyer a0de2f27a5 avoid segfaults in USER-MESO by checking for required atom style flags 2018-02-08 19:15:09 +01:00
Axel Kohlmeyer 21fe88ffa8 remove dead code in various neighbor list related source files 2018-02-08 13:07:56 -05:00
Jacob Gissinger 3d63c29abd
Merge pull request #2 from lammps/master 
rebase
 2018-02-07 21:35:26 -07:00
Amulya b49806d36a
correct the logic for checking if fix is right 
previously had incorrect logic for checking if fix is acceptable
 2018-02-07 16:35:49 -05:00
Axel Kohlmeyer 49745968f2 make link unambiguous so sphinx is not confused 2018-02-06 16:57:27 +01:00
Axel Kohlmeyer f914da62e0 fix typo 2018-02-06 16:57:27 +01:00
Axel Kohlmeyer 669ae02a85 apply pattern to ignore OPT package sources 2018-02-06 16:57:27 +01:00
Aidan Thompson 1d403b2aa3 Added warning to discourage use of group all and fixed some segfault cases 2018-02-05 13:29:14 -07:00
Steve Plimpton fa4c7fc664
Merge pull request #781 from wmbrownIntel/user-intel-2018u1p2 
USER-INTEL: Adding missing backslash for two Makefiles using Intel co…
 2018-02-02 14:51:23 -07:00
Steve Plimpton 401bfc52e1
Merge pull request #798 from akohlmey/always-use-internal-xdr 
Replace OS provided XDR support with bundled code
 2018-02-02 14:47:40 -07:00
Steve Plimpton 984fda5e78
Merge pull request #797 from akohlmey/multifile-restart-bugfix 
Address bug in multifile restart writing with step number included
 2018-02-02 14:47:09 -07:00
Steve Plimpton 196b3c81ef
Merge pull request #796 from akohlmey/create-bonds-sanity-check 
Sanity check on created/read-in bonds/angles/dihedrals/impropers
 2018-02-02 14:46:46 -07:00
Steve Plimpton f4a79b4d8e
Merge pull request #794 from akohlmey/tersoff-fixes 
Consistent checking of Tersoff potential parameters
 2018-02-02 14:46:11 -07:00
Steve Plimpton 7441b062e9
Merge pull request #792 from pastewka/18_dump_nc1 
Dumping to multiple files failed with an error message complaining about a missing 'append yes' option.
 2018-02-02 14:45:52 -07:00
Steve Plimpton 10d80ba9c3
Merge pull request #791 from akohlmey/charmm-cmap-docs-reference 
Update CMAP related docs and rebuild example input decks
 2018-02-02 14:44:58 -07:00
Steve Plimpton 5383035828
Merge pull request #787 from akohlmey/user-atc-dep 
Make the USER-ATC package depend on MANYBODY
 2018-02-02 14:44:36 -07:00
Steve Plimpton dc4dd1591f
Merge pull request #785 from jrgissing/imp_dihed_print 
modifications to correctly print modified dihedrals, impropers
 2018-02-02 14:44:15 -07:00
Steve Plimpton e4a1826dee
Merge pull request #783 from numericalfreedom/lammps-doxygen 
Added double quotes to a word in Section_tools.txt file
 2018-02-02 14:41:56 -07:00
Steve Plimpton 160edc9532
Merge pull request #782 from hheenen/user-mofff-contribution 
User mofff contribution
 2018-02-02 14:41:28 -07:00
Steve Plimpton 553b3ff69a
Merge pull request #778 from athomps/fix_gcmc_segfault_fix 
Fixed recent segfault in fix gcmc and added mcmoves keyword
 2018-02-02 14:40:14 -07:00
Steve Plimpton 2913d3da60
Merge pull request #777 from lammps/fix_prop_atom 
Fix bug in FixPropertyAtom
 2018-02-02 14:39:42 -07:00
Steve Plimpton 4af14becb5
Merge pull request #710 from rpleite/add-pair-ufm 
Add the UFM pair potential - (GPU/OPT/OMP)
 2018-02-02 14:38:28 -07:00
Axel Kohlmeyer 85fdf9eaba make links to papers unique across files 2018-02-02 10:10:27 +01:00
Axel Kohlmeyer 2ff278defa fully integrate ufm into documentation 2018-02-02 10:02:44 +01:00
Axel Kohlmeyer bfcb71a8be add package file to .gitignore 2018-02-02 09:27:09 +01:00
Axel Kohlmeyer c3d1cee5f9 try to use OS-provided (and obsoleted) RPC headers for XDR. always use bundled code 2018-02-02 09:23:02 +01:00
Axel Kohlmeyer 3e0cb9b463 rename examples to match usual naming conventions and add reference output. 2018-02-01 18:56:10 +01:00
Axel Kohlmeyer b70149e86a include added docpages in toctrees for sphinx 2018-02-01 18:50:25 +01:00
Axel Kohlmeyer 080ce422ae correct incorrect reference 2018-02-01 18:40:28 +01:00
Axel Kohlmeyer cc54848f7b adapt to current manual conventions 2018-02-01 18:40:17 +01:00
Axel Kohlmeyer 090ce7cecb remove tab char 2018-02-01 18:19:37 +01:00
Axel Kohlmeyer 3bc1c6b59e Address bug in multifile restart writing with step number included 2018-02-01 14:25:55 +01:00
Axel Kohlmeyer 38715d7f85 do not allow illegal combination of atom IDs in data files for bonds/angles/dihedrals/impropers 2018-01-31 06:08:04 -05:00
Axel Kohlmeyer 54a3096278 do not allow single bond/angle/dihedral definitions with illegal atom ID combinations 2018-01-31 05:59:19 -05:00
Axel Kohlmeyer 17d98d0915 make checking for tersoff parameters consistent across all implementations 2018-01-30 04:53:57 -05:00
Lars Pastewka 9cf4ac8b7c DOC: Added netcdf and netcdf/mpiio to dump style supporting atom attributes. 2018-01-28 14:24:28 +01:00
Lars Pastewka 4e4fd5f07c BUG: Dumping to multiple files failed with an error message complaining about a missing 'append yes' option. 2018-01-28 14:23:05 +01:00
Axel Kohlmeyer 9fd1e47968 ignore generated/copied files 2018-01-28 06:24:03 -05:00
Axel Kohlmeyer 6753977837 recreate 1ac7 input deck with up to date tools and LAMMPS binary. 2018-01-28 06:23:09 -05:00
Axel Kohlmeyer 031812b2bf recreate 1gb1 input deck with CMAP included. 2018-01-28 06:22:03 -05:00
Axel Kohlmeyer cf8dae5ef3 explain position of fix cmap command in input for data and restart files 2018-01-28 06:20:03 -05:00
Axel Kohlmeyer ba68548e38 clarify ch2lmp commands purpose in tools section 2018-01-28 06:19:33 -05:00
Axel Kohlmeyer 448c9c8d8a add a dependency on PairEAM/MANYBODY for installing USER-ATC 2018-01-23 16:27:06 +01:00
jrgissing 13c08225ed per-atom property dynamic group 2018-01-23 00:16:51 -07:00
jrgissing d2da49cdf9 modifications to correctly print modified dihedrals, impropers 2018-01-22 23:56:11 -07:00
Dr. Nandor Tamaskovics e72faf3d7f Added double quotes to a word in Section_tools.txt file in order to activate 
Sphinx hyperlink.
 2018-01-21 20:55:04 +01:00
Christoph Junghans 3f967e3d84
cmake: add USER-MOFFF 2018-01-21 08:10:38 -07:00
Hendrik Heenen 5212e95787 added src/USER-MOFFF/README 2018-01-21 13:34:02 +01:00