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12684 Commits

Author SHA1 Message Date
Axel Kohlmeyer 066123007c avoid undesired negative forces for high particle velocities in granular models 2017-05-30 21:54:16 -04:00
Axel Kohlmeyer 167a51538e support atom style variables for assigning image flags with the set command 2017-05-30 21:52:32 -04:00
Axel Kohlmeyer 5c6f63d8b4 Merge branch 'fix_adapt_doc_fix' of https://github.com/Pakketeretet2/lammps into collected-small-changes 2017-05-30 17:06:25 -04:00
Axel Kohlmeyer 03ab8d0f48 major neighbor list style whitespace cleanup 2017-05-30 17:04:48 -04:00
Axel Kohlmeyer 75b567a457 add "atomonly" optimized neighbor list build styles to USER-OMP 2017-05-30 16:50:38 -04:00
Stefan Paquay cace3e3530 Added missing :pre to doc/src/fix_adapt.txt 2017-05-30 16:08:32 -04:00
sjplimp 286d4f2743 Merge pull request #506 from lammps/snap 
SNAP changes by Aidan
 2017-05-30 13:32:00 -06:00
sjplimp 952b18fc02 Merge pull request #494 from rbberger/small_updates 
Collection of minor updates
 2017-05-30 10:51:24 -06:00
sjplimp 816fa93429 Merge pull request #499 from akohlmey/add-fix-compute-style-bugfix 
Fix bug where fix/compute style names were not correctly set with suffixes
 2017-05-30 10:49:27 -06:00
sjplimp f4f975edd6 Merge pull request #495 from akohlmey/doc-fixes 
Collected small updates and bugfixes
 2017-05-30 10:48:57 -06:00
sjplimp cff4e4a837 Merge pull request #468 from andeplane/gcmc_fix_nlocal 
Using correct value for atom->nlocal in translate/rotate in fix_gcmc.cpp
 2017-05-30 10:45:39 -06:00
sjplimp 32db4660bd Merge pull request #460 from andeplane/gcmc_fix 
Setting molecule COM to 0 after moving atoms
 2017-05-30 10:45:23 -06:00
Steve Plimpton 22fdb1fc14 SNAP changes by Aidan 2017-05-30 10:21:07 -06:00
Axel Kohlmeyer 412cb8f089 avoid hang in fix reax/c/species when multiple atoms have the exact same x-coordinate 2017-05-30 08:15:55 -04:00
Axel Kohlmeyer 092806ad4f no need for special whitespace handling in library interface 2017-05-30 07:55:48 -04:00
Axel Kohlmeyer 4ae314731d must not use strtok() in library function as it is not re-entrant and may be used inside LAMMPS commands 2017-05-30 07:42:10 -04:00
Axel Kohlmeyer 4b8d2e829c triclinic member variable is referenced in destructor and thus must be initialized in constructor 2017-05-30 07:41:01 -04:00
Axel Kohlmeyer d93938f7e1 displace_atom rotate needs to operate on unwrapped coordinates with image flags set to zero 2017-05-29 16:57:35 -04:00
Emile Maras c904cfb8bc removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 15:49:04 +02:00
Emile Maras 32c87f3131 removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 14:00:13 +02:00
Anders Hafreager ba0ddea5e1 Using correct ndegree instead of nnn 2017-05-28 15:44:12 -07:00
Axel Kohlmeyer c0339120d2 add missing neighbor list class definitions to USER-OMP 2017-05-26 21:28:41 -04:00
Axel Kohlmeyer 5a23d2d1da fix bug in computing mixed EAM potentials introduced by TI modifications 2017-05-26 20:28:45 -04:00
Axel Kohlmeyer de446ace2f Merge branch 'user-manifold-doc-fix' of https://github.com/Pakketeretet2/lammps into doc-fixes 2017-05-26 18:44:29 -04:00
Stefan Paquay 2055110e05 Fixed typo in dox. 2017-05-26 17:38:21 -04:00
Axel Kohlmeyer 5b1e582f03 prevent segfault when defining pair_style comb3 without arguments 2017-05-26 10:52:20 -04:00
Axel Kohlmeyer f1ec6dc41a dead code removal and reformatting 2017-05-25 18:55:07 -04:00
Axel Kohlmeyer c3f6e27bfe augment documentation for newly added multi-threaded reax/c styles 2017-05-25 17:00:19 -04:00
Axel Kohlmeyer 0a2fe70511 remove redundant code from fix qeq/reax and qeq/reax/omp 2017-05-25 16:31:31 -04:00
Axel Kohlmeyer 53e7fee5b7 Merge branch 'doc-fixes' of github.com:akohlmey/lammps into doc-fixes 2017-05-25 10:11:31 -04:00
Axel Kohlmeyer 5291f2ed6e fix bug in fix shear/history reported by kevin hanley. see #500 2017-05-25 10:11:24 -04:00
Axel Kohlmeyer 99a68e487f fix suffix style handling bug for adding fixes and computes 2017-05-25 02:01:04 -04:00
Axel Kohlmeyer 271431ab18 clean up code so it can be compiled with and without OpenMP enabled regardless of whether the USER-OMP package is installed 2017-05-24 17:25:57 -04:00
Axel Kohlmeyer 88d4150d2b remove trailing whitespace 2017-05-24 16:29:56 -04:00
Axel Kohlmeyer 0e3cfbc007 remove trailing whitespace 2017-05-24 16:29:26 -04:00
Axel Kohlmeyer 5345ad2da7 merge in the remainder of the USER-REAXC-OMP code. still a lot of work to do. compiles only with -fopenmp active 2017-05-24 16:24:43 -04:00
Axel Kohlmeyer ead05f81c0 Merge branch 'pair_morse_soft-doc-fix' of https://github.com/Pakketeretet2/lammps into doc-fixes 2017-05-24 13:56:54 -04:00
Stefan Paquay 4f9e7cbd16 Cleaned up docs for pair_mores, a missing :pre ruined formatting. 2017-05-24 13:36:14 -04:00
Axel Kohlmeyer bb890941ca first chunk of code from USER-REAXC-OMP imported and adapted into USER-REAXC 2017-05-24 00:19:36 -04:00
Axel Kohlmeyer 4002dce639 restore explicit NAN constants in output 2017-05-22 22:39:52 -04:00
Axel Kohlmeyer c801cdd81f some more formatting cleanup in fix neb 2017-05-22 22:33:14 -04:00
Axel Kohlmeyer 9008a31190 more formatting cleanup 
This cleans up and simplifies the neb command code some more
 2017-05-22 21:55:55 -04:00
Richard Berger bdfb7c69ea Remove unused code detected by coverity CID 177700 2017-05-22 17:51:40 -04:00
Richard Berger 084626e60b Fixes coverity issue CID 179426 2017-05-22 17:36:16 -04:00
Richard Berger a7d790a827 Fixes coverity issue CID 179439 2017-05-22 17:33:47 -04:00
Richard Berger 8a630ff4ec Fixes coverity issue CID 179440 2017-05-22 17:32:07 -04:00
Richard Berger 617ca4e0c8 Fixes coverity issue CID 179436 2017-05-22 17:30:46 -04:00
Axel Kohlmeyer 62601678cd when growing arrays with reallocate, always check against atom->nmax and not atom->nlocal or else these arrays may be of inconsistent size and communication can lead to data corruption 2017-05-22 17:16:19 -04:00
Axel Kohlmeyer 081910adbc do not try to free null communicators 2017-05-22 17:15:14 -04:00
Axel Kohlmeyer f73fd0625d rename nall class member to numall to avoid confusion with the common convention nall = atom->nlocal+atom->nghost 2017-05-22 17:14:38 -04:00