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251 Commits

Author SHA1 Message Date
Richard Berger eaef8089a1 Add LAMMPSLexer for LAMMPS code-blocks in docs 2019-11-06 17:40:39 -05:00
Richard Berger 9ac9ba6401 Merge branch 'master' into doc_updates 2019-11-06 11:35:35 -05:00
Axel Kohlmeyer efcf919ede
Merge branch 'master' into feature_parameterupdate 2019-11-06 08:21:33 -05:00
Anne Gunn 5e6694f3bc Re-enabled conversion of equations arrays. Disabled works even worse 2019-11-05 15:27:21 -05:00
Richard Berger 423a3bb99f Add initial version of updated tools from #1533 2019-11-05 15:27:21 -05:00
Richard Berger 12cb19090a Remove txt2html and htmldoc from doc build 2019-11-02 23:07:49 -04:00
Richard Berger aeaa289d1d Merge branch 'master' into docs_to_rst_migration 2019-11-02 22:57:43 -04:00
Yaser Afshar 63cce391ca Adding the documentation for the new 'kim_param' command 
New documnetation is added and the whole document is checked
and partly rewritten for clarity and errors are corrected

Adding the word "Zm" to prevent the spelling error in document
building check.
 2019-10-29 11:51:05 -05:00
Axel Kohlmeyer 22288e06b7
Merge branch 'master' into fix-compiler-warnings 2019-10-25 14:07:50 -04:00
jguenole 549c8ee734 Renamed: adaptglok -> fire2 2019-10-24 14:11:16 +02:00
jrgissing a69bd0405a add lowercase 'arrhenius' keyword to spellcheck 2019-10-19 23:09:10 -06:00
Axel Kohlmeyer bb21847f8a
have sphinx configuration switch math formula renderer for epub 
this still needs work, that has to be done after we switched to RST
 2019-10-18 04:47:18 -04:00
Axel Kohlmeyer 68adc56e93
Merge branch 'master' into fix-compiler-warnings 2019-10-17 06:03:59 -04:00
Evangelos Voyiatzis 10031e91bd
Update false_positives.txt 
Added the name of Mattice in the list
 2019-10-16 20:25:53 +02:00
Axel Kohlmeyer f3b2ec80af
add false positives and correct spelling to have a clean spellcheck run on centos 7 2019-10-15 16:56:23 +02:00
Axel Kohlmeyer 0e10fbb133
Merge pull request #1690 from charlessievers/third_order 
Added third order, added documentation, took out extraneous lines, ad…
 2019-10-08 21:57:15 +02:00
julient31 ed467d8867 Merge branch 'master' of github.com:alxvov/lammps into OSO 
- solved conflict in doc/src/fix_nve_spin.txt
 2019-10-04 08:56:49 -06:00
Axel Kohlmeyer ed5678d646
Merge pull request #1673 from charlessievers/lammps_gjf 
Lammps fix langevin updates for gjf option
 2019-10-04 10:02:46 +02:00
Axel Kohlmeyer ed5407e998
add spellchecker false positives 2019-09-24 14:19:43 -04:00
julient31 a31aa5debc Merge branch 'master' of github.com:alxvov/lammps into OSO 2019-09-23 14:22:26 -06:00
Axel Kohlmeyer fddc164d5b
register a couple more false positives to clear doc test 2019-09-23 11:54:46 -04:00
Axel Kohlmeyer ed6dd1a632
Merge pull request #1666 from tanmoy7989/local_density 
added LD potential and wrote html-style doc
 2019-09-19 11:45:46 -04:00
jguenole de78e309cf Resolved merge conflict by accepting incomming changes 2019-09-19 15:59:38 +02:00
Axel Kohlmeyer 572235e66a
Merge pull request #1660 from tanmoy7989/reorder_remd_traj 
python tool to reorder replica traj
 2019-09-17 17:29:50 -04:00
Axel Kohlmeyer 7386956dc5
remove misspelled word from false positives list 2019-09-13 08:52:09 -04:00
charlie sievers a948a34f8a added false positive, removed graphs from examples, updated langevin kokkos, improved diff readability in langevin 2019-09-12 16:34:15 -07:00
tanmoy.7989 22fde86fd0 possible spelling mistake report from Sphinx for unidentified word ccache; added this to the false_positives.txt file 2019-09-09 02:27:54 -07:00
tanmoy.7989 e7d8165a46 fixed spelling mistakes reported by sphix 2019-09-09 02:16:30 -07:00
tanmoy.7989 96c21bec98 added new valid words to doc/utils/sphinx-config/false_positives.txt 2019-09-04 23:16:19 -07:00
Richard Berger ddab4eeb1a Remove SHA1 utility used in doc Makefile 2019-08-22 14:11:32 -06:00
alxvov 12c73e7a61 Merge branch 'upstream-master' into OSO 2019-08-21 14:03:42 +00:00
Axel Kohlmeyer cfa9179b28
Merge pull request #1503 from etomica/master 
Implement HMA compute in LAMMPS
 2019-08-21 00:12:16 -04:00
Stan Moore 9a849a4d4f
Merge branch 'master' into master 2019-08-19 15:55:39 -06:00
Axel Kohlmeyer 18725ce060
reformat documentation to match typical LAMMPS conventions, change links 2019-08-09 15:42:32 -04:00
Axel Kohlmeyer 5f442d7b64
add a couple of false positives 2019-08-09 15:31:22 -04:00
Richard Berger bd87b67232
Update false_positives.txt 2019-08-02 17:35:26 -04:00
julient31 f4e3186abf Commit JT 073019 
- modified the false_positive file to correct errors
- improved the doc page of fix nve/spin
 2019-07-30 13:10:27 -06:00
Axel Kohlmeyer 8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models 
Develop native support for KIM simulator models
 2019-07-30 10:53:58 -04:00
Axel Kohlmeyer d2c4989dbf
Merge pull request #1583 from evoyiatzis/gyration_shape 
computing the eigenvalues of gyration tensor & shape parameters
 2019-07-29 22:16:13 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 0beb39c1af
fully integrate compute gyration/shape into doc build system 2019-07-29 16:14:29 -04:00
Axel Kohlmeyer e0b20c4fd4
add false positive 2019-07-29 15:23:23 -04:00
Axel Kohlmeyer 52e1755464
fix spelling errors and false positives 2019-07-25 21:20:42 -04:00
Ryan S. Elliott 03d26f6f6f Merge branch 'master' into kim-simulator-models 2019-07-21 13:59:48 -05:00
julient31 22b73a316f Commit2 JT 071719 
- added 'magnetons' to false-positive for doc
 2019-07-17 22:15:23 -06:00
Andrew Schultz b675edcf5c More false positives 2019-07-03 16:28:37 -04:00
Axel Kohlmeyer 41e8cf3d69
Merge branch 'master' into kim-simulator-models 
# Conflicts:
#	src/input.cpp
 2019-07-02 01:15:29 -04:00
Richard Berger a720aedabc Workaround to make formatting of code blocks consistent 2019-06-28 20:54:10 -04:00
Ellad Tadmor 483353a017 Merge remote-tracking branch 'lammps/master' into kim-simulator-models 2019-06-24 15:35:06 -05:00
Vishnu V. Krishnan 2159a8c44a
Arch specific words 2019-06-24 16:14:29 +05:30
Axel Kohlmeyer 493269431c
add a few more false positives 2019-06-23 14:17:30 -04:00
Axel Kohlmeyer a6f6c9bed0
fix up links, spelling issues, and inconsistent names in kim commands docs 2019-06-23 12:41:29 -04:00
Andrew Schultz fe5e952319 Fix docs issues 2019-06-19 19:17:20 -04:00
Andrew Schultz 87e6fda820 Merge remote-tracking branch 'upstream/master' 2019-06-19 18:52:47 -04:00
Axel Kohlmeyer daa53e3008
Merge pull request #1469 from julient31/pppm_spin 
Adding PPPM and Ewald solvers for electric dipoles and magnetic spins
 2019-06-12 14:50:18 -04:00
Andrew Schultz d9206127fb Add hyphen to roundoff, fix false positives 2019-06-12 11:40:21 -04:00
Axel Kohlmeyer 972a7a5c4d
add false positive for spell checking 2019-05-31 05:58:47 -04:00
Axel Kohlmeyer edecd2b760
fix typo and update list of false positives for updated docs 2019-05-30 22:19:47 -04:00
jguenole 58d99f5e1f add keywords in false_positive.txt to correct doc comppilation warnings 2019-05-27 18:38:13 +02:00
Stan Moore 0ee1daa46d Add Lenz to false-positive list 2019-05-21 10:24:24 -06:00
Axel Kohlmeyer d0c6484fb0
add false positive 2019-05-20 15:15:51 -04:00
Axel Kohlmeyer 091dbfa265
Merge pull request #1457 from julient31/fix_cubic_aniso 
Adding a cubic anisotropy in the SPIN package, documentation corrections
 2019-05-14 15:08:21 -04:00
julient31 8e18f2bf7e Commit2 JT 051319 
- corrected doc issues
 2019-05-13 17:32:44 -06:00
Steven Strong 805cc18b2d
Merge branch 'master' into e3b 2019-05-12 22:22:31 -05:00
Axel Kohlmeyer 47cf17e5c8
Merge branch 'master' into pair_drip 2019-05-09 12:19:41 -04:00
Axel Kohlmeyer d86a7b95de
fix spelling issues 2019-05-05 08:48:27 -04:00
Axel Kohlmeyer a9388e86e3
add one more false positive 2019-04-25 18:00:27 -04:00
Steven Strong 47d4aa6803 add new false positives 2019-04-24 17:35:17 -05:00
Steven Strong f548e2717e add new false positives 2019-04-24 17:31:44 -05:00
julient31 b8ae466999 Commit4 JT 040819 
- added unknown names/acronyms in doc/utils/sphinx-config/false_positives.txt
 2019-04-08 14:00:49 -06:00
Axel Kohlmeyer e57c4c60bd
fix spelling issue 2019-04-07 05:59:28 -04:00
Axel Kohlmeyer 494e76da7d
add false positive 2019-04-06 17:29:04 -04:00
Axel Kohlmeyer ac7312caf1
Merge pull request #1409 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2019-04-05 15:39:16 -04:00
Axel Kohlmeyer 2757e4e6e6
two more false positives 2019-04-05 10:53:41 -04:00
Risto Toijala 619c2322e5 Merge remote-tracking branch 'upstream/master' into fix-elstop 2019-04-04 10:03:36 +03:00
Risto Toijala 0d78c7b43d fix elstop: Rename to fix electron/stopping 2019-04-04 09:57:15 +03:00
Risto Toijala 61d4b7a47f Add Kai as spelling false positive 2019-04-01 09:14:47 +03:00
Axel Kohlmeyer 17cd650622
Merge branch 'master' into collected-small-changes 2019-03-29 11:35:15 -04:00
Axel Kohlmeyer 75382cf265
update documentation tweaks to run cleanly 2019-03-29 10:34:34 -04:00
Axel Kohlmeyer 2fa6e913ef
Merge branch 'master' into gran_mods 2019-03-28 11:46:44 -04:00
Axel Kohlmeyer e63d2cee87
Merge pull request #1375 from akohlmey/install-python-for-cmake 
Refactor python module installer and add install-python target to CMake
 2019-03-27 16:47:25 -04:00
Risto Toijala 8c99752cec Add fix elstop to USER-MISC 
Implements inelastic energy loss for fast particles in solids.
 2019-03-26 10:08:20 +02:00
Axel Kohlmeyer 22be3bd37e
fix spelling error and add false positives for spellchecking 2019-03-22 17:33:16 -04:00
Axel Kohlmeyer 2dbc2c5916
fix spelling issues in documentation and some minor clarification 2019-03-19 16:04:53 -04:00
Axel Kohlmeyer b6459b3f74
Merge branch 'master' into gran_mods 2019-03-15 14:30:36 -04:00
Axel Kohlmeyer 3f0f2383b4
fix spelling and record false positives 2019-03-15 14:18:04 -04:00
Axel Kohlmeyer 14e6c126a8
Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix 
add command to compute the Dynamical Matrix
 2019-02-28 17:08:36 -05:00
Axel Kohlmeyer 5fd033c0a2
add one more false positive required by recent changes 2019-02-28 15:49:48 -05:00
Axel Kohlmeyer 16946d8c6d
integrate dynamical_matrix command into LAMMPS manual 2019-02-28 14:45:07 -05:00
Axel Kohlmeyer 326a97624e
Merge pull request #1317 from ornladios/adios2-master 
USER-ADIOS package with ADIOS 2.x
 2019-02-27 17:24:12 -05:00
Axel Kohlmeyer 9bec93faa9
update spell-checking false positives for USER-ADIOS package 2019-02-26 19:51:18 -05:00
Axel Kohlmeyer d76569c033
Merge pull request #1320 from eofetis/manual-pdf-support 
Add support for Sphinx+PDF+MathJax
 2019-02-22 15:10:13 -05:00
Ryan S. Elliott c193a9aee9 Updated Errors_messages.txt & false_positives.txt 2019-02-14 19:28:18 -06:00
Axel Kohlmeyer 581b7d3543
update list of false positives after docs changes 2019-02-13 09:23:54 -05:00
Axel Kohlmeyer 622eb47902
some small tweaks, fixes for typos, and url corrections for the manual 2019-02-07 01:19:29 -05:00
Axel Kohlmeyer 019e534f80
some small tweaks, fixes for typos, and url corrections for the manual 2019-02-07 01:16:48 -05:00
efetis 4fe6528ed4 Add support for Sphinx+PDF+MathJax 2019-02-06 17:14:50 -08:00
Axel Kohlmeyer 1e3cc7784b update false positives list for spell checking 2019-01-24 11:06:22 -05:00
Steven Vandenbrande ca31147d00 Fix USER-YAFF documentation issues 2019-01-22 14:58:38 +01:00
Axel Kohlmeyer 89ca07c76e Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-29 12:05:30 -05:00
Axel Kohlmeyer 5fb8f23cb4 update false positives list for recent manual changes 2018-12-19 02:24:16 -05:00
Axel Kohlmeyer 0ed4da0bf9 Merge branch 'bond/react-delete_atoms' of https://github.com/jrgissing/lammps into collected-post-stable-patches 2018-12-12 00:20:17 -05:00
Axel Kohlmeyer 02bdda0d05 Merge branch 'remove-reax-meam' into collected-post-stable-patches 2018-12-12 00:14:58 -05:00
Axel Kohlmeyer be3c80829a Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-12 00:14:41 -05:00
Axel Kohlmeyer 0a610cb482 Merge branch 'sllod' into collected-post-stable-patches 2018-12-12 00:14:33 -05:00
Axel Kohlmeyer f2f7bcfa5a add new false positive 2018-12-11 23:45:27 -05:00
Axel Kohlmeyer d15e4b1546
Merge branch 'master' into remove-reax-meam 2018-12-11 23:31:48 -05:00
Axel Kohlmeyer 1933c2eb5f next chunk of documentation changes for the removal of REAX and MEAM 2018-12-10 14:51:21 -05:00
Axel Kohlmeyer 52a1f257c5 fix typo 2018-12-10 14:19:03 -05:00
jrgissing afaaf442d3 bond/react doc tweaks 2 2018-12-06 21:32:10 -07:00
Axel Kohlmeyer ee82143a29 more false positives to handle 2018-12-03 16:21:18 -05:00
Axel Kohlmeyer aeb7854aca update false positives list for newly added documentation 2018-12-03 16:11:39 -05:00
Axel Kohlmeyer 6be4ce7137 found a new false positive word in docs with spellchecker 2018-11-28 23:14:45 -05:00
Axel Kohlmeyer d1255ab572 we are LAMMPS, not LIGGGHTS 2018-11-22 09:22:09 -05:00
Axel Kohlmeyer 4251c70e93 update list of false positives for spellchecking 2018-11-20 00:08:07 -05:00
Axel Kohlmeyer 440338d769 last round of spelling fixes 2018-08-22 22:35:35 -04:00
Axel Kohlmeyer 0cd71ee582 more false positives 2018-08-22 22:18:35 -04:00
Axel Kohlmeyer 5da714bcc8 fix another source of broken links inserted into processed files 2018-08-22 21:33:40 -04:00
Axel Kohlmeyer 2d6d635ce0 update list of false positives 2018-08-22 21:30:40 -04:00
Axel Kohlmeyer ffb1a9c46a update link in lammps theme for sphinx 2018-08-22 20:36:01 -04:00
Axel Kohlmeyer c8ac88dd87 update link in LAMMPS theme for Sphinx 2018-08-22 19:46:49 -04:00
Richard Berger 9ffd262039 Add CMake target for html documentation 2018-07-27 02:46:36 -04:00
Richard Berger 819e47b69e Add output dir and verbose option to txt2rst 2018-07-27 02:30:28 -04:00
Axel Kohlmeyer 7c7a80b31a restore deleted file 2018-06-18 17:59:22 -04:00
julient31 f409f4ff53 Commit JT 021318 2018-04-26 15:02:15 -06:00
julient31 72d9795d7f Commit Julien 10/19/2017 
- New files for the pair interactions
- New files for the documentation
- Spin orbit coupling via Neel approach
 2018-04-26 14:58:41 -06:00
Axel Kohlmeyer 5863f115dd correctly escape 'a_ ' text, which is not a reference unlike 'a_b ' 2018-01-12 12:26:50 -05:00
Axel Kohlmeyer ed8680d695 suspend support for sphinxcontrib.images 
the sphinxcontrib.image extension was broken with sphinx 16.x.
however, sphinx 15.x breaks with newer version of the multiprocessor module.
so we suspend the thumbnail processing and lift the lock to sphinx 15.x

also, the number of parallel sphinx tasks is can be overridden with SPHINXEXTRA="-j #'.
default is to try use all local CPU cores.
 2017-12-07 15:38:15 -05:00
Axel Kohlmeyer 0c9cd11b4e have the relevant LAMMPS version embedded into top part of the html manual 2017-03-20 18:25:11 -04:00
Richard Berger 621d7d5ce0 Correct off-by-one error in line number reported 2017-03-16 23:05:03 -04:00
Richard Berger efb2a942e0 Add utility to detect duplicate anchors in documentation files 2017-03-16 22:21:12 -04:00
Richard Berger 21be86c423 Fix typos in txt2html 2017-03-07 00:58:03 -05:00
Richard Berger 007f3c66a0 Third batch of spelling fixes in manual 2017-03-07 00:51:31 -05:00
Richard Berger 32708860a9 Add remaining false positives 2017-03-07 00:27:35 -05:00
Richard Berger fc9eebb936 Added spellcheck utility to documentation build 
Uses the sphinxcontrib-spelling extension and requires PyEnchant and
aspell-en to be installed.

Adds the optional make target 'spelling' which produces the file
spelling/output.txt. It contains all words it detects.

Due to the large number of false positives, words in
utils/sphinx-config/false_positives.txt are ignored.
 2017-03-05 21:23:41 -05:00
Axel Kohlmeyer 2cf77ff778 Add support for ebook generation in ePUB and mobi format 2016-10-20 16:16:17 -04:00
Richard Berger e78b4267b7 Fix issue with external links containing anchors 2016-10-06 20:29:07 -04:00
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
Axel Kohlmeyer aa9fe38c5c consolidate ignoring python bytecompiled cache files 2016-09-17 09:50:49 -04:00
Steve Plimpton 2f298951cf resolved conflicts 2016-09-14 10:22:46 -06:00
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
Richard Berger e71fafdd25 Use Google Custom Search API for searching in docs 2016-08-31 00:28:27 -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
sjplimp 8a7fb8e7e0 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15137 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-07 16:21:00 +00:00
sjplimp 10be4c06bd git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15103 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-02 14:12:27 +00:00
sjplimp c2f479c5fc git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14981 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-10 14:05:06 +00:00