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12711 Commits

Author SHA1 Message Date
Axel Kohlmeyer 05fbf93455 skip deleting internal data before setup has been run 2017-06-23 10:37:00 -04:00
Axel Kohlmeyer 73b948dcfc pppm must be fully reinitialized after switching to triclinic box to avoid memory corruption 2017-06-23 10:01:45 -04:00
Axel Kohlmeyer 374eef2b17 add first draft of issue template 2017-06-23 01:13:10 -04:00
Axel Kohlmeyer dc7243838b first draft of a contributor's guide file 2017-06-23 00:54:20 -04:00
Axel Kohlmeyer 57d5cfede3 add first draft of a pull request template 2017-06-22 23:07:09 -04:00
Axel Kohlmeyer feb500b526 reword the kspace_modify fftbench keyword docs to reflect the current state (i.e. off by default) of code 2017-06-22 19:17:41 -04:00
Axel Kohlmeyer a714b57741 make neighbor list reset message for minimization more explicit 2017-06-22 19:07:57 -04:00
Axel Kohlmeyer c5430b0a26 print info messages when changing qqr2e constant in fully CHARMM compatible pair styles 2017-06-22 18:41:44 -04:00
Stefan Paquay c081d383d1 Merge branch 'master' of https://www.github.com/lammps/lammps 2017-06-22 18:37:37 -04:00
Axel Kohlmeyer f8364342c2 port corrected triclinic handling from pppm/tip4p to pppm/tip4p/omp 2017-06-22 18:12:28 -04:00
Axel Kohlmeyer 488d1b7a79 correct find_M() function in pppm/tip4p to properly account for ghost atoms not being in lamda space with triclinic cells 2017-06-22 17:36:18 -04:00
Sebastian Hütter dadd1c8b4d Remove neigh_f2c/c2f, related cleanup 
- neighbour lists now use C indexing
- removed many arr*v() macros
- removed some unneccessary pointers
- minor reformatting
 2017-06-22 19:02:14 +02:00
Steve Plimpton 60c3f3d64c use CHARMM energy conversion factor with new CHARMM pair styles 2017-06-22 09:15:15 -06:00
sjplimp 7a4a569859 Merge pull request #540 from lammps/neighrespa 
fix issue with rRESPA inner/middle neighbor lists
 2017-06-22 07:54:12 -06:00
sjplimp 4fc3f4f7e5 Merge pull request #538 from akohlmey/collected-small-changes 
Collected small changes and bugfixes
 2017-06-22 07:52:21 -06:00
Sebastian Hütter f092da80a9 Fix some shadowing warnings 2017-06-22 13:28:12 +02:00
Axel Kohlmeyer b0ddabbcde update examples for fix filter/corotate to comply with new CHARMM restrictions 2017-06-22 00:19:21 -04:00
Axel Kohlmeyer b9029ada77 fix bug in incorrect use of O coordinate instead of M coordinate in pppm/tip4p 2017-06-22 00:07:59 -04:00
Axel Kohlmeyer de3157f720 document new restrictions to CHARMM compatible dihedral styles 2017-06-21 19:31:40 -04:00
Axel Kohlmeyer 0c6a751751 may check for 1-4 scaling factors in CHARMM dihedral styles only when "weightflag" is set, since they may be used with amber 2017-06-21 19:29:31 -04:00
Axel Kohlmeyer 612b44a895 enforce using 'special_bonds charmm' for dihedral styles charmm and charmmfsw 2017-06-21 19:15:52 -04:00
Axel Kohlmeyer 684b7334a5 enforce that CHARMM dihedral styles are run at the same r-RESPA level as pair 2017-06-21 19:08:02 -04:00
Steve Plimpton 1fc2eb1e3e fix issue with rRESPA inner/middle neighbor lists 2017-06-21 15:12:51 -06:00
sjplimp e69ef56f10 Merge pull request #539 from lammps/neighsize 
insure compute pair/property local will use a copy of granular neighbor list
 2017-06-21 15:03:12 -06:00
Steve Plimpton 7dc380b113 insure compute pair/property local will use a copy of granular neigh list 2017-06-21 12:44:35 -06:00
Stefan Paquay f47aaa5f3c Merge branch 'master' of https://www.github.com/lammps/lammps 2017-06-21 14:11:12 -04:00
Axel Kohlmeyer 5e165e6782 fix array bounds issue due to typo. spotted by GCC. 2017-06-21 13:33:26 -04:00
Sebastian Hütter 02625b2855 fix typos introduced in original translation: results are correct again 2017-06-21 18:54:21 +02:00
Axel Kohlmeyer 1a77135ed6 whitespace cleanup in docs 2017-06-21 09:38:10 -04:00
Axel Kohlmeyer f45c7e1fb0 update fix ti/spring docs to reflect it is part of USER-MISC 2017-06-21 09:36:30 -04:00
Axel Kohlmeyer 0cfe8980d4 dead code removal 2017-06-20 22:07:40 -04:00
Axel Kohlmeyer 2988508cee correct indexing bug in pair style lj/long/tip4p/long 2017-06-20 17:53:45 -04:00
Axel Kohlmeyer 15c596153a remove dead code 2017-06-20 17:38:28 -04:00
Axel Kohlmeyer e13c94ed4f fix uninitialized variable bug spotted by coverity scan 2017-06-20 17:25:01 -04:00
Axel Kohlmeyer 812f1a8fab remove local variables shadowing global ones in BondsOMP() 2017-06-20 17:20:57 -04:00
Axel Kohlmeyer 218bc92c82 make pre-processor defines for using libc's qsort() consistent 2017-06-20 17:13:42 -04:00
Axel Kohlmeyer ffa906de6f add C++ format identifiers to .h files 2017-06-20 16:18:34 -04:00
Axel Kohlmeyer cccf72a21d make certain class member list is initialized to NULL before assigned to a neighbor list 2017-06-20 16:09:11 -04:00
Steve Plimpton 87c028ed02 patch 20Jun17 2017-06-20 12:06:02 -06:00
Sebastian Hütter bb47fa8783 Change indexing of all MEAM element arrays 
- arrays in MEAM class
- eltind setting
- remove fmap translation
 2017-06-20 19:56:14 +02:00
Sebastian Hütter c79dc53c6a code improvement, less pointer params 2017-06-20 19:36:07 +02:00
Axel Kohlmeyer 72a1364d85 Merge branch 'master' into package-meamc 2017-06-20 13:21:46 -04:00
Sebastian Hütter 198fe7ecd7 fix storing of invalid memory pointer 2017-06-20 19:00:57 +02:00
sjplimp 84b530cca1 Merge pull request #537 from lammps/neb 
minor changes to NEB doc pages and examples
 2017-06-20 09:38:32 -06:00
Axel Kohlmeyer 50c9167913 small formatting correction in fix neb docs 2017-06-20 10:36:30 -04:00
Steve Plimpton d2610d9e7c minor changes to NEB doc pages and examples 2017-06-20 08:19:23 -06:00
sjplimp 326a8a1289 Merge pull request #536 from akohlmey/fix-nvcc-openmp-conflicts 
Implement workaround for NVCC incompatibilities with OpenMP directives
 2017-06-20 07:44:40 -06:00
sjplimp b5300724bb Merge pull request #533 from lammps/user-intel 
Updates for USER-INTEL package and NEB command flags/docs updates and issues
 2017-06-20 07:44:17 -06:00
sjplimp e129f18e6f Merge pull request #530 from akohlmey/no_static_sort_in_dump 
Refactor Dump and Irregular classes to remove static class members
 2017-06-20 07:43:49 -06:00
Axel Kohlmeyer 8c54fcd1b6 cleanup from aidan for fix reax/c/species and its KOKKOS version 
this version eliminates the need for the PBCconnected list and avoids having to access the spec_atom array for ghost atoms
 2017-06-19 17:31:54 -04:00