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10789 Commits

Author SHA1 Message Date
Axel Kohlmeyer 44ce6fac4b replace backquote with regular quote and `` + '' with double quote. 2016-09-07 08:29:16 -04:00
Axel Kohlmeyer 70d6718aa3 Update discussion on parallel python packages. There seem to be only two left. 2016-09-07 07:42:06 -04:00
Axel Kohlmeyer 348b677148 Make formatting and links more consistent and unique 2016-09-07 07:41:17 -04:00
Richard Berger 4c783ea3b7 Enforce l,ule or l,ole command order for RST 
(cherry picked from commit 79e867c213)
 2016-09-07 02:16:55 -04:00
Richard Berger 9e8256aeb0 Refactored code and escape RST special character '_' 
(cherry picked from commit 4629a464f7)
 2016-09-07 02:16:55 -04:00
Richard Berger 925f1bfb6f Escape RST special character '^' and take care of special math cases 
(cherry picked from commit 453521c8e6)
 2016-09-07 02:16:55 -04:00
Richard Berger 3f312244a0 Escape RST special character '*' in final output 
(cherry picked from commit 7cb39811d4)
 2016-09-07 02:16:54 -04:00
Axel Kohlmeyer 55022d1263 replace :l,ule and :l,ole with :l :ule or :l :ole 2016-09-07 02:11:59 -04:00
Axel Kohlmeyer 0d491d483c avoid Inline substitution_reference start-string without end-string 2016-09-07 02:10:49 -04:00
Axel Kohlmeyer a31c507370 correct error message text, sync with source 2016-09-06 22:15:49 -04:00
Axel Kohlmeyer fc2d878305 update manual introduction to represent current status. correct some markup to better pass through sphinx 2016-09-06 21:20:47 -04:00
Axel Kohlmeyer 1c17b98500 Merge branch 'integration' into doc-corrections-and-updates 2016-09-06 20:19:02 -04:00
Axel Kohlmeyer ace5dc3c7c Merge remote-tracking branch 'lammps-rw/clean-up-docs-for-sphinx' into clean-up-docs-for-sphinx 2016-09-06 19:54:35 -04:00
Steve Plimpton 0252347d43 sync with 7Sep16 patch 2016-09-06 17:00:32 -06:00
sjplimp c9455c90de Merge pull request #20 from akohlmey/lammps-contribute 
Update description of submitting contributions to LAMMPS
 2016-09-06 16:55:16 -06:00
sjplimp 1e4d6fee93 Merge pull request #19 from akohlmey/clean-up-docs-for-sphinx 
Clean up docs for sphinx (redo)
 2016-09-06 16:54:39 -06:00
Axel Kohlmeyer 42db93e198 one more small correction to document recent fix ave/time changes 2016-09-06 16:10:16 -04:00
Axel Kohlmeyer 906bd24543 fix typos 2016-09-06 16:03:16 -04:00
Axel Kohlmeyer 4f88c75401 update the discussion on how to submit modifications 2016-09-06 16:02:59 -04:00
Axel Kohlmeyer 1a7b04e8a6 generate updated html files for corrected .txt files 
(cherry picked from commit 7de57ffd94)
 2016-09-06 13:40:11 -04:00
Axel Kohlmeyer fbc955e549 correct link targets 
(cherry picked from commit ff75cf51bb)
 2016-09-06 13:40:11 -04:00
Steve Plimpton 3bb3c1a45c add pppm/kk and fix reax/c issues 2016-09-06 10:46:51 -06:00
sjplimp c543cba95c Merge pull request #18 from akohlmey/clean-up-docs-for-sphinx 
Clean up incorrect link targets in documentation
 2016-09-06 10:31:33 -06:00
Axel Kohlmeyer 431d1a6dae mention stable releases 2016-09-01 02:37:55 -04:00
Axel Kohlmeyer ab84acc2cd synchronize LAMMPS developer list with webpage and move ray to "past" 2016-09-01 02:26:49 -04:00
Axel Kohlmeyer fc093a0aab replace :ule,l and :ole,l with :l<br>:ule and :l<br>:ole 2016-09-01 02:07:16 -04:00
Axel Kohlmeyer 5e6dff36e4 add new commands to lammps.book 2016-09-01 02:01:47 -04:00
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 #17 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 #15 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 #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
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