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3719 Commits

Author SHA1 Message Date
Steve Plimpton 493873fb93 clean up doc src 2016-10-06 13:00:46 -06:00
Steve Plimpton c46be7db62 changes to imbalance weight factors 2016-10-05 10:33:39 -06:00
Steve Plimpton 11c2892e54 Merge branch 'restrict-weights-and-weight-factors' of https://github.com/akohlmey/lammps 2016-10-04 09:49:09 -06:00
sjplimp e079362776 Merge pull request #190 from akohlmey/small-bufixes-and-enhancements 
Small bufixes and enhancements
 2016-10-03 17:58:36 -06:00
Steve Plimpton c3ff8812b3 added XOR operator to variable command 2016-10-03 17:57:33 -06:00
Axel Kohlmeyer 1985db4fb1 correct designation of meam supporting USER-OMP and meam/spline not 2016-10-01 23:05:05 -04:00
Axel Kohlmeyer d45e333f7c restrict choice of weight factors and guarantee that weights are >= 0.001 2016-09-30 11:11:32 -04:00
Axel Kohlmeyer 6d200061ca update colvars library to version 2016-09-30 2016-09-30 08:15:44 -04:00
Steve Plimpton 446e7e7369 patch for allowing prd command to work with sorted atoms 2016-09-28 16:33:30 -06:00
sjplimp 829d11e88b Merge pull request #44 from rbberger/doc-fixes 
Some documentation fixes and IPython updates
 2016-09-27 15:36:10 -06:00
sjplimp 96f31d6dad Merge pull request #43 from akohlmey/doc-fixes 
Documentation fixes
 2016-09-27 15:35:41 -06:00
Steve Plimpton 35705217f4 enable multi-processor NEB replicas 2016-09-27 15:34:08 -06:00
Steve Plimpton 9a2f738673 sync with SVN 2016-09-27 15:32:57 -06:00
Steve Plimpton f9677e6d7b released version of weighted balancing 2016-09-27 10:52:27 -06:00
Richard Berger a3277117e2 Add filter which merges preformatted sections 2016-09-26 18:52:43 -04:00
Richard Berger 67d4c07689 Do not escape underscore inside preformat blocks 2016-09-26 18:52:31 -04:00
Richard Berger 877a504933 Fix typo in Section_howto.txt 2016-09-26 18:44:25 -04:00
Axel Kohlmeyer 8a951f9d79 fix typo 2016-09-26 18:43:03 -04:00
Axel Kohlmeyer 69a8842ecb update load balance weights documentation for fix balance and balance 2016-09-26 18:33:50 -04:00
Axel Kohlmeyer 7732548b3c correct issues related to the addition of fix cmap 2016-09-26 18:14:32 -04:00
Axel Kohlmeyer 2c5f6e1a99 fix a broken link that slipped through the cracks in the previous cleanup 2016-09-26 18:13:18 -04:00
Richard Berger d0aa13b543 Fix broken link in Section_packages.txt 2016-09-26 16:53:18 -04:00
Axel Kohlmeyer 47b52ed2dd Merge branch 'integration' into balance2 2016-09-26 15:19:48 -04:00
Steve Plimpton b97b9dd661 new fix cmap command 2016-09-26 08:40:53 -06:00
sjplimp c00cd6192d Merge pull request #41 from akohlmey/doc-fixes 
Documentation updates and corrections
 2016-09-23 14:57:23 -06:00
Steve Plimpton 6f4b7268de sync with SVN 2016-09-23 14:52:45 -06:00
Steve Plimpton 08f0bf9025 new verion of balance weighting 2016-09-23 14:37:53 -06:00
Axel Kohlmeyer 3d5f5bf40e a few more consolidations of link anchors 2016-09-23 10:25:10 -04:00
Axel Kohlmeyer 065d35eefa update kokkos compilation instructions to use provided preset makefiles 2016-09-22 23:53:19 -04:00
Axel Kohlmeyer 3785249033 use "make mpi" instead of "make g++" in examples 2016-09-22 23:52:52 -04:00
Axel Kohlmeyer e18941e865 delete bogus line (how did this get into the docs?) 2016-09-22 23:41:53 -04:00
Axel Kohlmeyer c6cebe66c7 making more links and anchors consistent and correct errors 2016-09-22 22:26:17 -04:00
Axel Kohlmeyer 08d9792ec8 add an additional explanation to compute XXX/tally docs and fix a typo 2016-09-22 21:46:45 -04:00
Axel Kohlmeyer c10aa55fc1 Merge branch 'integration' into doc-fixes 2016-09-22 09:19:45 -04:00
Steve Plimpton b3217218d6 doc page sync with SVN 2016-09-21 20:54:20 -06:00
Axel Kohlmeyer 2943dd5c12 correct another broken link in fix ti/spring 2016-09-20 19:02:13 -04:00
Axel Kohlmeyer 33d9a55d35 remove references to docs for fix ti/rs 2016-09-20 19:01:58 -04:00
Axel Kohlmeyer 5345efb5b8 correct broken link in updated fix ti/spring docs 2016-09-20 18:57:01 -04:00
Axel Kohlmeyer 9bedb8a1c9 ignore generated files in html folder 2016-09-20 18:54:51 -04:00
Axel Kohlmeyer 0d7e4f1e88 update docs for pair style gauss/cut to document optional per pair cutoff 2016-09-20 18:51:50 -04:00
Steve Plimpton 9ef748bbaa remvoing doc/html 2016-09-20 16:46:59 -06:00
Steve Plimpton 5c37fccf49 fix ti/spring for eam/allow and eam/fs 2016-09-20 12:10:58 -06:00
Steve Plimpton b9b044e180 new fix ti/spring command, remove fix ti/rs 2016-09-20 10:44:12 -06:00
Axel Kohlmeyer aa9fe38c5c consolidate ignoring python bytecompiled cache files 2016-09-17 09:50:49 -04:00
Steve Plimpton abf05eed61 comm tiled bug fix 2016-09-16 10:31:52 -06:00
Steve Plimpton 2f298951cf resolved conflicts 2016-09-14 10:22:46 -06:00
Steve Plimpton 717e719b83 HTML update 2016-09-14 09:35:03 -06:00
Steve Plimpton 10b4411d5b Merge branch 'integration' of github.com:akohlmey/lammps into integration 2016-09-13 17:22:14 -06:00
Steve Plimpton c744b23c4c doc updates 2016-09-13 17:15:15 -06:00
sjplimp a69e059be3 Merge pull request #27 from akohlmey/small-bugfixes 
Collected small changes and bugfixes
 2016-09-13 17:11:23 -06:00
sjplimp dbc548dd88 Merge pull request #26 from rbberger/is_available_feature 
Extend is_available() function to query optional features
 2016-09-13 17:10:10 -06:00
Steve Plimpton 25e518a4f4 added options to compute bond/local 2016-09-13 17:03:37 -06:00
Steve Plimpton ed52f9ea5e pair vashishta/table 2016-09-13 14:54:12 -06:00
Steve Plimpton 944289b018 final version of pair vashishta/table 2016-09-13 14:45:53 -06:00
Axel Kohlmeyer 51e4a568c9 Merge branch 'small-bugfixes' of github.com:akohlmey/lammps into small-bugfixes 2016-09-13 14:32:27 -04:00
Steve Plimpton a8081d4507 fix qeq Kokkos bug fix by Stan 2016-09-13 10:54:04 -06:00
Axel Kohlmeyer e53862ca4a update html file updated boundary.txt file 2016-09-11 14:55:13 -04:00
Axel Kohlmeyer a64eb330e3 document how using shrink-wrap boundaries can cause lost atoms in parallel 2016-09-11 14:48:37 -04:00
Axel Kohlmeyer d70e051ecd update docs for lj/sf/dipole/sf 2016-09-09 10:00:15 -04:00
Richard Berger e27869daf6 Add updated HTML documentation about new is_available feature category 2016-09-09 05:56:24 -04:00
Richard Berger dc0c0ab214 Add documentation about new is_available feature category 2016-09-09 05:55:28 -04:00
Axel Kohlmeyer 956af8cebb update html file 2016-09-08 17:41:46 -04:00
Axel Kohlmeyer 71eed1d612 update documentation for vashishta pair style 2016-09-08 17:20:52 -04:00
Axel Kohlmeyer fe581e8ced Merge remote-tracking branch 'lammps-rw/integration' into vashishta-tabulation 2016-09-08 16:21:05 -04:00
sjplimp b866e0663b Merge pull request #24 from rbberger/info_command_styles 
Info command extensions
 2016-09-08 14:16:41 -06:00
sjplimp 5d0da95a0b Merge pull request #23 from akohlmey/doc-corrections-and-updates 
Doc corrections and updates
 2016-09-08 14:15:56 -06:00
Richard Berger 1f901c9b2d Update generated HTML docs of info command 2016-09-08 09:53:57 -04:00
Richard Berger 79b8f6320d Update docs of info command 2016-09-08 09:53:14 -04:00
Steve Plimpton 43b05a60c7 created vashishta/table variant 2016-09-07 11:56:38 -06:00
Axel Kohlmeyer 0fe7d1d361 correct internal links for Modify LAMMPS section 2016-09-07 10:13:34 -04:00
Axel Kohlmeyer 346ff42498 correct reference in modify section 2016-09-07 10:10:12 -04:00
Axel Kohlmeyer 5feedbd829 regenerate html pages with new txt2rst tool 2016-09-07 10:09:53 -04:00
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 16607a0132 update colvars library to version 2016-08-19 
(cherry picked from commit c67326be6d)
 2016-09-06 21:27:46 -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 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
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
Axel Kohlmeyer b12ad2cecf Merge branch 'integration' into vashishta-tabulation 2016-09-01 08:25:31 -04:00
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 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
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 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
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 cdf06646ef Update documentation for tabulation in vashista pair style 2016-08-27 23:05:17 -04:00
Richard Berger f5a50c3cd1 Added documentation about -DLAMMPS_EXCEPTIONS flag 2016-08-27 22:13:36 -04:00
Steve Plimpton 3a1397dc7c sync with SVN 2016-08-27 17:11:16 -06:00
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
Steve Plimpton c80dad0028 new fix flow/gauss command 2016-08-27 16:25:01 -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
Stefan Paquay b8e7f53017 Small update for USER-MANIFOLD docs. 
(cherry picked from commit d188bdbd86)
 2016-08-24 23:36:04 -04:00
Axel Kohlmeyer ff541e9a84 fix typo in compute omega/chunk usage example 2016-08-24 23:04:27 -04:00
Steve Plimpton e27196e91c doc files 2016-08-23 16:28:36 -06:00
Steve Plimpton 270b07b035 Merge branch 'integration' into small-bugfixes 2016-08-23 15:35:31 -06:00
athomps 55fe1f6b29 fixed integer division problem in python code snippet 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15486 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-22 22:35:23 +00:00
Axel Kohlmeyer c88e9b46cf thread timing summare needs to be marked as preformatted 
(cherry picked from commit b745636a67)
 2016-08-22 14:35:11 -04:00
sjplimp 2fff78a78e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15484 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:43:04 +00:00
sjplimp ccf8cf20b3 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15482 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-20 22:42:17 +00:00
sjplimp b1829c107c git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15479 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 15:03:16 +00:00
sjplimp 832f6a9f11 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15475 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-13 14:52:15 +00:00
sjplimp c03252f08d git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15471 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-12 14:34:16 +00:00
sjplimp 112c98159b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15469 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-12 13:49:50 +00:00
sjplimp b3364ae943 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15467 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-10 14:46:16 +00:00
sjplimp 563e069971 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15461 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-08 13:50:31 +00:00
sjplimp 17e8e9a9c9 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15460 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-08 13:48:22 +00:00
sjplimp 0029040f11 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15456 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 22:12:27 +00:00
sjplimp 30d6007565 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15454 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 20:45:14 +00:00
sjplimp 390b492d08 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15453 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 18:28:23 +00:00
sjplimp 9a3b988b2b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15452 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 18:28:02 +00:00
athomps 36a0c644a9 Attempted to straighten out italics 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15451 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-05 18:21:12 +00:00
sjplimp 96a73d51cd git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15450 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-08-05 18:16:10 +00:00
athomps 32c8c9d63e clarified energy contribution to minimization energy 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15448 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-05 16:27:48 +00:00