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10741 Commits

Author SHA1 Message Date
Steve Plimpton 6c65af710c bad file? 2016-08-31 16:10:20 -06:00
Steve Plimpton 7c01ef57ee sync with SVN 2016-08-31 15:17:00 -06:00
sjplimp 0316bb579b Merge pull request #3 from akohlmey/fix-flow-gauss 
Fix flow/gauss for USER-MISC package
 2016-08-31 15:03:27 -06:00
sjplimp f89448d73c Merge pull request #6 from akohlmey/manifold-doc-update 
Small update for USER-MANIFOLD docs.
 2016-08-31 14:53:16 -06:00
Steve Plimpton ad879d97db sync w/ SVN 2016-08-31 14:29:44 -06:00
Steve Plimpton 4051aedf2c Merge branch 'small' into integration 
Conflicts:
	src/compute_omega_chunk.cpp
 2016-08-31 13:58:12 -06:00
Steve Plimpton ec8b9e21db sync with SVN 2016-08-31 13:28:26 -06:00
Axel Kohlmeyer a2ea263652 remove vector/array class members shadowing the base class 2016-08-30 07:04:54 -04:00
Axel Kohlmeyer 493613b495 avoid NaNs in MEAM 2016-08-30 06:54:36 -04:00
Axel Kohlmeyer 021ade199a null-ing of pointers and a couple select integers for fix ave/chunk 2016-08-30 06:41:50 -04:00
Axel Kohlmeyer b7749ab212 individual computes do not need to set vector/array to NULL. reordering fixes to silence compiler warnings 2016-08-30 06:41:02 -04:00
Efrem Braun 554ac7dd12 Use MPI_Allreduce values instead of each processor's values 
(cherry picked from commit f30232b41e)
 2016-08-30 06:38:15 -04:00
Axel Kohlmeyer ef86d11729 Merge branch 'integration' into small-bugfixes 2016-08-30 06:29:41 -04:00
Steve Plimpton 62b7b69a87 Merge branch 'init' into integration 2016-08-29 17:45:56 -06:00
Axel Kohlmeyer 1c1c9c3101 use correct order when initializing arrays 2016-08-28 22:23:22 -04:00
Anders Hafreager 48ba812f0a Fixed initialization of arrays in computes/fixes in MC package 2016-08-28 22:23:22 -04:00
Anders Hafreager f9a21ae654 Fixed initialization of arrays in computes/fixes in MANYBODY package 2016-08-28 22:23:22 -04:00
Anders Hafreager d6b9d0b9b6 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager 36e085e393 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager 425142ba2e Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager 07eb1d443b Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager 265cc14125 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager fd05a1325e Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager b5a562788b Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager 2c7241bfe2 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager ee2f6ded29 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Anders Hafreager db077ef186 Fixed initialization of arrays in fixes 2016-08-28 22:23:22 -04:00
Axel Kohlmeyer fc5db8a737 fix off-by one bug when looking for bonds. 2016-08-28 14:20:43 -04:00
Axel Kohlmeyer 56d0ab9474 updated doc build readme for current Fedora and RHEL/CentOS 2016-08-28 14:20:23 -04:00
Axel Kohlmeyer f8d6b979ec Merge branch 'integration' into small-bugfixes 2016-08-28 14:16:14 -04:00
Axel Kohlmeyer 4e03df2d19 Merge branch 'integration' into fix-flow-gauss 2016-08-28 06:55:12 -04:00
Axel Kohlmeyer e1045851c0 incorporate bugfix and cleanup from lammps-icms and upstream 2016-08-28 06:52:03 -04:00
sjplimp 0192d2e359 Merge pull request #5 from akohlmey/initialize-pointers 
enforce initializing pointers in constructors to NULL
 2016-08-27 17:14:27 -06:00
Steve Plimpton 3a1397dc7c sync with SVN 2016-08-27 17:11:16 -06:00
Axel Kohlmeyer bb721db8de Merge branch 'integration' into fix-flow-gauss 2016-08-27 19:02:33 -04:00
sjplimp 0c2e643062 Merge pull request #9 from rbberger/remove_sha1sum_dependency 
Remove sha1sum dependency for doc generation
 2016-08-27 17:02:17 -06:00
sjplimp ef69bf8695 Merge pull request #11 from akohlmey/python3-for-make-py 
Python 3 support for Make.py with Python 2.7 compatibility
 2016-08-27 17:01:29 -06:00
sjplimp 6a4633af0a Merge pull request #12 from akohlmey/shell-script-paranoia 
Disable custom locale and grep options in shell scripts
 2016-08-27 16:59:43 -06:00
Steve Plimpton c80dad0028 new fix flow/gauss command 2016-08-27 16:25:01 -06:00
Axel Kohlmeyer 1c13b30a70 small cleanup and generalization of fix flow/gauss 
- remove unused or unneeded class members
- make the code compatible with per-atom masses
- test for and abend in case of an invalid group mass

(cherry picked from commit e017b33898)
 2016-08-27 17:33:46 -04:00
Axel Kohlmeyer c570bf26e0 enforce C or POSIX locale in all shell scripts and turn of enforced global grep options 2016-08-27 01:57:45 -04:00
Axel Kohlmeyer 742c853775 need to ignore src/Make.py.last as well 2016-08-26 17:48:59 -04:00
Axel Kohlmeyer 9932b73227 Merge branch 'integration' into python3-for-make-py 2016-08-26 17:48:06 -04:00
Axel Kohlmeyer 90272f6c71 some more tweaks needed to improve python2/3 compatibility 2016-08-26 17:46:57 -04:00
Axel Kohlmeyer 8dd42789f8 correct for futurize not being able to fully convert functionality of the commands module 2016-08-26 17:15:39 -04:00
Steve Plimpton a0592d1b64 Merge branch 'gitignore-improvements' into integration 2016-08-26 13:54:29 -06:00
Axel Kohlmeyer 9be235d872 improved .gitignore files to show only changes in relevant folders and files 2016-08-26 14:34:42 -04:00
Steve Plimpton 2beecd1e73 removal of doc/html/_sources and minor sync with SVN 2016-08-26 11:34:37 -06:00
Richard Berger 95aabdf51a Add MacOS X instructions to doc generation README 2016-08-26 10:08:22 -04:00
Richard Berger ea368919f3 Remove sha1sum dependency for doc generation 
On MacOS X there is no sha1sum. So to simplify doc generation on those systems
use a Python script instead to generate a unique string from the repository
path.
 2016-08-26 00:01:34 -04:00