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10764 Commits

Author SHA1 Message Date
Steve Plimpton 3bb3c1a45c add pppm/kk and fix reax/c issues 2016-09-06 10:46:51 -06:00
sjplimp c543cba95c Merge pull request from akohlmey/clean-up-docs-for-sphinx 
Clean up incorrect link targets in documentation
 2016-09-06 10:31:33 -06:00
Axel Kohlmeyer 7de57ffd94 generate updated html files for corrected .txt files 2016-09-01 00:02:40 -04:00
Axel Kohlmeyer ff75cf51bb correct link targets 2016-09-01 00:01:26 -04:00
sjplimp fb2c18ee88 Merge pull request from akohlmey/small-doc-fixes 
corrections for various compute something/chunk examples
 2016-08-31 19:57:36 -06:00
Steve Plimpton b5c758f22c Merge branch 'goo' into integration 2016-08-31 19:53:50 -06:00
Steve Plimpton de0036fafd removing searchindex.js 2016-08-31 19:52:28 -06:00
Axel Kohlmeyer c3c9788dc7 include autogenerated html code 2016-08-31 21:49:06 -04:00
Axel Kohlmeyer 2abd5ad28a Merge branch 'integration' into small-doc-fixes 2016-08-31 21:42:22 -04:00
sjplimp 1c3302d1db Merge pull request from rbberger/pylammps-improvements 
PyLammps improvements
 2016-08-31 16:34:59 -06:00
Steve Plimpton 24409b6178 Merge branch 'error' into integration 2016-08-31 16:16:47 -06:00
Steve Plimpton de21cb2cd5 small changes to doc page 2016-08-31 16:16:43 -06:00
Steve Plimpton 639ab0fd3e Merge branch 'core/cpp_exceptions' of https://github.com/rbberger/lammps into error 2016-08-31 16:11:08 -06:00
Steve Plimpton 6c65af710c bad file? 2016-08-31 16:10:20 -06:00
Axel Kohlmeyer 29e480ad66 corrections for various compute something/chunk examples 2016-08-31 17:31:14 -04:00
Steve Plimpton 7c01ef57ee sync with SVN 2016-08-31 15:17:00 -06:00
sjplimp 0316bb579b Merge pull request 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 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
Richard Berger 1986eda4d5 Remove no longer needed generated files in doc 
If we use the Google Custom Search API, we do not need to keep the
generated searchindex.js file anymore. We also can safely remove
the _sources directory for good.

Since these get generated during each Sphinx build, additional
steps have been added to the Makefile to get rid of them. They
are also added to .gitignore to avoid commiting them by accident.
 2016-08-31 00:36:56 -04:00
Richard Berger e71fafdd25 Use Google Custom Search API for searching in docs 2016-08-31 00:28:27 -04:00
Richard Berger 6cbdad7a97 Add utility function to IPyLammps for embedding videos 2016-08-30 11:34:16 -04:00
Richard Berger a08cf7a4b6 Add verbose option in PyLammps methods 
This option allows forcing LAMMPS output to be printed to the console.
 2016-08-30 11:34:16 -04:00
Richard Berger 691de01b33 Allow setting the position of atoms 2016-08-30 11:34:16 -04:00
Richard Berger 33a87a470a Return 2D vectors in 2D cases 2016-08-30 11:34:15 -04:00
Richard Berger 59dc83eadb Fix resource leak 2016-08-30 11:34:15 -04:00
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