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12556 Commits

Author SHA1 Message Date
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
Richard Berger 06a4f47a4c Merge remote-tracking branch 'upstream/master' into small_updates 2017-05-22 17:14:29 -04:00
Axel Kohlmeyer 7185db98b4 NEBLongRange was incorrectly set to false by default. revert to true. 2017-05-22 17:13:38 -04:00
Axel Kohlmeyer 4780d72809 use '&&' and '||' instead of 'and' and 'or' operators for consistency 2017-05-22 14:42:42 -04:00
Axel Kohlmeyer 3fd91a239f avoid use '&&' and '||' instead of 'and' and 'or' for consistency 2017-05-22 14:41:01 -04:00
Axel Kohlmeyer 8bc829c7f1 change example inputs to be backward compatible 2017-05-22 14:40:01 -04:00
Axel Kohlmeyer 97d3c843c4 small documentation fixes to fix typos and formatting issues 2017-05-21 11:13:47 -04:00
Axel Kohlmeyer 546aed7ccd plug some memory leaks 2017-05-19 16:14:59 -04:00
Axel Kohlmeyer 6ef79d3715 silence several compiler warnings 2017-05-19 15:13:19 -04:00
Axel Kohlmeyer c2bf3269ac formatting cleanup. combine 8 MPI_Allreduce() calls into 1 2017-05-19 15:02:29 -04:00
Axel Kohlmeyer aca16745e4 restore spelling fix and semantic fix from upstream 2017-05-19 12:17:19 -04:00
Axel Kohlmeyer a5110d81ea correct a bunch of documentation formatting issues for updated neb and fix neb commands 2017-05-19 12:13:23 -04:00
Steve Plimpton 2225fce94e patch 19May17 2017-05-19 07:35:36 -06:00
Richard Berger 9593e05c9e Force PDF documentation build to fail on first error 2017-05-18 19:37:08 -04:00
sjplimp 941b737319 Merge pull request #493 from akohlmey/doc-and-example-fixes 
Doc and example fixes
 2017-05-18 16:40:46 -06:00
Axel Kohlmeyer 654e09e999 correct input examples affected by the Pair::settings() bugfix 2017-05-18 18:34:27 -04:00
Axel Kohlmeyer 8751850eca a few formatting fixes for pair style python 2017-05-18 18:34:03 -04:00
sjplimp 0f88348917 Merge pull request #492 from lammps/pre-patch 
update docs before patch release
 2017-05-18 13:44:34 -06:00
Emile Maras d4ee03c778 changed doc links 2017-05-18 21:31:39 +02:00
Emile Maras 069f3e746b small formating changes 2017-05-18 21:23:29 +02:00
Steve Plimpton b28ecd44c2 update docs before patch release 2017-05-18 13:14:47 -06:00
sjplimp 9db9fc9de3 Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug 
convert bigint values for bonds/angles/dihedrals/impropers to doubles
 2017-05-18 13:08:42 -06:00
sjplimp 6ac9b7a1b0 Merge pull request #482 from akohlmey/add-pair-python 
Add python pair style for implementing simple pairwise additive potentials in python
 2017-05-18 11:15:58 -06:00
Axel Kohlmeyer 34dbf6b225 do not compute properties twice 2017-05-18 12:45:43 -04:00
Axel Kohlmeyer 26d71b66e4 convert bigint values for bonds/angles/dihedrals/impropers to doubles when evaluating those keywords in variable expressions 2017-05-18 12:41:48 -04:00
Richard Berger 65eacb6b90 Fix compilation warnings in fix_python 2017-05-18 12:20:39 -04:00
sjplimp cb3344a337 Merge pull request #489 from akohlmey/thread-safe-biasing 
port thread-safe temperature biasing from LAMMPS-ICMS
 2017-05-18 09:15:07 -06:00
sjplimp 5d38cbbce9 Merge pull request #487 from akohlmey/pair_edip_multi_element 
Import multi-element compatible pair style edip as edip/multi
 2017-05-18 09:13:30 -06:00
sjplimp 30babd8157 Merge pull request #485 from akohlmey/pair_settings_cut_bugfix 
Bugfix for correct resetting of previously set cutoffs to various Pair::settings() functions
 2017-05-18 09:12:47 -06:00