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10847 Commits

Author SHA1 Message Date
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 3a74ccffa2 update colvars library to version 2016-09-03 
(cherry picked from commit 4181f5ac9d)
 2016-09-06 21:28:59 -04:00
Axel Kohlmeyer c8cfd53c1b adjust makefiles in lib tree, so they don't return an error exit code on "make clean" targets. 
(cherry picked from commit 4117218ca3)
 2016-09-06 21:28:55 -04:00
Axel Kohlmeyer 16607a0132 update colvars library to version 2016-08-19 
(cherry picked from commit c67326be6d)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 3b476d914f update colvars to version 2016-08-10 
(cherry picked from commit eba3ad9abb)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 977b9e542f update colvars to another set of changes from the upstream repo 
(cherry picked from commit cb816f8cba)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 1b33d00785 update colvars makefile dependencies 
(cherry picked from commit df99a85930)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 3d2e5d0a50 suppress compiler warning 
(cherry picked from commit 6f227e194e)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer ec2a6b9f0d update colvars to version 2016-08-10 
(cherry picked from commit f2ddf828e4)
 2016-09-06 21:27:41 -04:00
Axel Kohlmeyer 77620106a4 update colvars library to version 2016-08-05 
(cherry picked from commit 459db2eb6b)

# Conflicts:
#	doc/src/PDF/colvars-refman-lammps.pdf
 2016-09-06 21:26:50 -04:00
Axel Kohlmeyer f56c41eec0 update with correct error description. sync with manual. 2016-09-06 21:21:28 -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 9138152563 Merge branch 'integration' into small-bugfixes 2016-09-06 20:17:07 -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 4314299be9 harden fix shear/history against use-after-delete and from incorrect use of reverse communication 2016-09-06 14:50:04 -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