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20025 Commits

Author SHA1 Message Date
Axel Kohlmeyer f1679cd58c
update false positives 2020-03-18 06:37:51 -04:00
Axel Kohlmeyer 5992bd24e7
some more converted atc fix_modify docs 2020-03-18 06:29:17 -04:00
Axel Kohlmeyer 4cdb904e54
next chunk of converted html files 2020-03-16 07:34:56 -04:00
Axel Kohlmeyer b3040db1e7
Merge branch 'master' into atc-doc-to-rst 
# Conflicts:
#	doc/src/fix_atc.rst
 2020-03-13 21:12:12 -04:00
Axel Kohlmeyer 7c6353731e
Merge pull request #1938 from akohlmey/doc-remove-backslash-underscore 
Remove unneeded escapes in documentation source files
 2020-03-13 21:01:04 -04:00
Axel Kohlmeyer f1cc6c6e57
Merge pull request #1928 from akohlmey/collected-small-fixes 
Collected small fixes and updates for the next patch release
 2020-03-13 19:44:04 -04:00
Axel Kohlmeyer 6805113780
some more typesetting improvements 2020-03-13 19:41:33 -04:00
Axel Kohlmeyer 6d9064f98f
Revert "fix bug in pair styles lubricate and lubricate/poly" 
This reverts commit e368ae9f22.
As it contradicts the comments in the code above the segment.
 2020-03-13 18:41:37 -04:00
Axel Kohlmeyer 097a4fb52e
Merge branch 'doc-lammps-highlights' of github.com:rbberger/lammps into doc-remove-backslash-underscore 2020-03-13 18:39:40 -04:00
Axel Kohlmeyer cdec46ba6a
Some more code-blocks instead of parsed-literal 2020-03-13 18:38:47 -04:00
Axel Kohlmeyer e4d6214d3b
reformat source 2020-03-13 18:08:47 -04:00
Axel Kohlmeyer f11e431300
some updates to building with cmake 2020-03-13 18:07:49 -04:00
Axel Kohlmeyer 8063088149
fix a couple of settings 2020-03-13 18:07:32 -04:00
Richard Berger cf21affd38 Add special highlights for commands which use IDs 2020-03-13 17:31:08 -04:00
Axel Kohlmeyer a946a3b1b2
Merge pull request #1936 from rbberger/doc-fixes 
Documentation updates
 2020-03-13 17:07:05 -04:00
Axel Kohlmeyer 0c0308db3e
some more fixups 2020-03-13 17:02:59 -04:00
Axel Kohlmeyer a990f1dc89
some minor fixups 2020-03-13 16:42:08 -04:00
Axel Kohlmeyer 0b88950e03
replace '\_' with '_' in plain text where possible 2020-03-13 16:34:57 -04:00
Axel Kohlmeyer 924629538f
restore support for triclinic cells with pppm/intel by calling the corresponding functions in PPPM in that case 2020-03-13 16:01:00 -04:00
Axel Kohlmeyer 4e525f1d56
PPPM in USER-INTEL does not support triclinic cells 2020-03-13 15:30:52 -04:00
Richard Berger 1554aef454 Avoid syntax highlighting in blocks that don't specify language 2020-03-13 15:25:11 -04:00
Axel Kohlmeyer e368ae9f22
fix bug in pair styles lubricate and lubricate/poly 
Closes #1933
 2020-03-13 11:11:27 -04:00
Axel Kohlmeyer 80d413b86c
add reference to the fix_modify command overview in fix atc docs into all atc subcommand docs 2020-03-13 11:06:11 -04:00
Axel Kohlmeyer 5a81f69495
next set of converted AtC documentation 2020-03-13 10:19:12 -04:00
Axel Kohlmeyer 3574673901
four more atc subcommand doc files converted 2020-03-13 05:15:35 -04:00
Axel Kohlmeyer 0548dbc729
a couple more inputs and some formatting tuning/tweaking 2020-03-12 22:41:23 -04:00
Axel Kohlmeyer 3708c9f3f1
fix spelling issues 2020-03-12 21:32:06 -04:00
Axel Kohlmeyer 4df25d9c0b
four more subcommands converted 2020-03-12 21:27:44 -04:00
Axel Kohlmeyer cbd8d07daf
convert elementset AtC commands 2020-03-12 16:34:42 -04:00
Axel Kohlmeyer 0a21cdadb5
converted 4 more fix_modify atc commands 2020-03-12 15:49:05 -04:00
Axel Kohlmeyer c139898f9f
Convert a first set of AtC documentation html files to rst and add infrastructure files and links 2020-03-12 14:26:04 -04:00
Axel Kohlmeyer fa7085be07
Merge pull request #1930 from giacomofiorin/remove-lepton-cxx11-check 
Remove now unneeded check for C++11 in Lepton CMake build
 2020-03-12 13:09:44 -04:00
Axel Kohlmeyer 3b73b88b57
Merge pull request #1926 from akohlmey/doc-cleanup 
Documentation cleanup
 2020-03-12 11:49:54 -04:00
Giacomo Fiorin de6d1efe7a Remove now unneeded check for C++ standard in Lepton CMake build 2020-03-12 10:33:48 -04:00
Axel Kohlmeyer 010b1f7434
more conversion of parsed-literal to code-block and a bunch of other issues 2020-03-12 08:11:10 -04:00
Axel Kohlmeyer e2b7054f74
include required header 2020-03-12 06:59:04 -04:00
Axel Kohlmeyer 4f0e9e2d26
some cleanup and consistency improvements in MESSAGE package code and docs 2020-03-12 06:51:06 -04:00
Axel Kohlmeyer 524b37598f
correct various misspelled words and remove corresponding false positives 2020-03-12 06:25:42 -04:00
Axel Kohlmeyer 1372c20d94
Merge branch 'DOI' of github.com:e-kwsm/lammps into doc-cleanup 2020-03-12 05:43:44 -04:00
Eisuke Kawashima 8af9d40392
Update DOI resolver 
https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
 2020-03-12 16:53:24 +09:00
Axel Kohlmeyer 23a402ddd3
convert all remaining compute styles to use code-block instead of parsed literal 2020-03-12 01:56:13 -04:00
Axel Kohlmeyer c6f846b925
converter tool for inlining external math is no longer needed 2020-03-12 01:20:30 -04:00
Axel Kohlmeyer 7e656b6cea
convert more LAMMPS script examples to use code-block instead of parsed-literal 2020-03-12 01:11:38 -04:00
Axel Kohlmeyer 2775ebeb9d
update trilinos URL 2020-03-12 00:47:00 -04:00
Axel Kohlmeyer 8a799c4b5f
update cslib URLs to use https:// 2020-03-12 00:46:50 -04:00
Axel Kohlmeyer 30817162b9
update moltemplate URL to https:// 2020-03-12 00:42:23 -04:00
Axel Kohlmeyer 2c3d196ce8
remove broken link 2020-03-12 00:41:57 -04:00
Axel Kohlmeyer 3317f90940
update plumed URLs to use https:// 2020-03-12 00:32:44 -04:00
Axel Kohlmeyer b961aa0542
update lammps.sandia.gov URLs to use https:// 2020-03-12 00:28:28 -04:00
Axel Kohlmeyer 6dd9a507ef
update PyMol URLs 2020-03-12 00:21:20 -04:00