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6344 Commits

Author SHA1 Message Date
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 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 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
Axel Kohlmeyer 23569e67a0
update Ensight URL 2020-03-12 00:20:59 -04:00
Axel Kohlmeyer e58aeebcce
update URLs for pizza.py homepage 2020-03-12 00:13:58 -04:00
Axel Kohlmeyer 667c9f2a9f
update AtomEye related URLs 2020-03-12 00:08:57 -04:00
Axel Kohlmeyer cf48a0f01d
use the name MacOS consistently 2020-03-11 19:32:43 -04:00
Axel Kohlmeyer d0f57289fc
finish updating docs for fixes using code-block plus a few other improvements 2020-03-11 12:58:57 -04:00
Axel Kohlmeyer 5029bc9e1e
more conversions from parsed-literal to code-block 2020-03-11 10:19:19 -04:00
Axel Kohlmeyer 8546bb51bf
Layout images so they show up side-by-side in html and pdf and adapt to screen/paper size 2020-03-11 10:18:48 -04:00
jrgissing 43a6c13f01 change 'groups' to 'fragments' 2020-03-10 21:11:34 -06:00
Sievers b4919756d4 Fixed up delta note 2020-03-10 16:58:47 -06:00
Sievers a1188c035b Merge branch 'master' of https://github.com/charlessievers/lammps into fix_numerical_differentiation 2020-03-10 16:14:20 -06:00
Sievers 7dafec1700 Removed misleading doc information and included errors 2020-03-10 16:12:02 -06:00
Axel Kohlmeyer 1f4725d652
replace parsed-literal with code-block where appropriate. typeset keywords in cursive 2020-03-10 16:54:04 -04:00
Axel Kohlmeyer 2d329a8b76
typeset symbols in water model howtos 2020-03-10 16:20:52 -04:00
Axel Kohlmeyer ae9255e057
collapse multiple empty lines into a single empty line 2020-03-10 15:56:11 -04:00
Axel Kohlmeyer e643e88913
remove trailing whitespace from documentation sources 2020-03-10 15:51:06 -04:00
Axel Kohlmeyer 5ffc12ffc0
Merge remote-tracking branch 'github/master' into collected_small_fixes 2020-03-10 15:16:07 -04:00
Axel Kohlmeyer b9ff623c16
Merge pull request #1920 from jguenole/fire-debug 
fire bug fix to avoid crashes due to lost atoms
 2020-03-10 15:08:58 -04:00
Evangelos Voyiatzis be037e222c
Update pair_coul_slater.rst 2020-03-10 16:21:15 +01:00
Evangelos Voyiatzis 30e997df69
Update false_positives.txt 2020-03-10 16:20:42 +01:00
Evangelos Voyiatzis f73e21f2ca
Update false_positives.txt 2020-03-10 16:05:25 +01:00
Evangelos Voyiatzis b477d8920b
Update pair_coul_slater.rst 2020-03-10 15:42:32 +01:00
Evangelos Voyiatzis 8332afd2b2
one more spelling error 2020-03-10 15:27:51 +01:00
Evangelos Voyiatzis 866899da21
correct spelling error in equation 2020-03-10 15:18:04 +01:00
Evangelos Voyiatzis 35a63e21a0
Update pair_coul_slater.rst 2020-03-10 14:34:40 +01:00
Evangelos Voyiatzis 4f917fff43
increase the Title underline 2020-03-10 11:51:17 +01:00
Axel Kohlmeyer 66c019e78b
more explicitly describe how force/virial depend on random numbers 2020-03-10 06:43:13 -04:00
Evangelos Voyiatzis 7959e3ff81
Move rst file to the correct location 2020-03-10 11:26:52 +01:00
Evangelos Voyiatzis 6fb84eba32
Update false_positives.txt 2020-03-10 10:47:54 +01:00
Evangelos Voyiatzis 3092ee89d3
Update Commands_pair.rst 2020-03-10 09:55:04 +01:00
Axel Kohlmeyer cf64ba4059
whitespace cleanup 2020-03-09 16:31:53 -04:00
Axel Kohlmeyer 69a206f720
add diskfree check to fix halt 2020-03-09 16:23:20 -04:00
Axel Kohlmeyer 072ce8947b
list errors and warnings from fix halt 2020-03-09 16:23:02 -04:00
Axel Kohlmeyer a0fb7c812c
Merge branch 'master' into collected_small_fixes 2020-03-09 10:53:42 -04:00
Axel Kohlmeyer 740717d114
add false positives 2020-03-09 10:00:14 -04:00
Axel Kohlmeyer a6086c279b
rename USER-MESO package to USER-MESODPD and update related files and folders 2020-03-09 09:48:49 -04:00
Axel Kohlmeyer 45902772b7
Merge branch 'minimizer' of github.com:yafshar/lammps into collected_small_fixes 2020-03-09 09:15:40 -04:00
jrgissing d717eeba66 Update molecule.rst 2020-03-07 22:57:44 -07:00
jrgissing 21ae5ac533 groups in molecule templates: docs 2020-03-07 20:03:33 -07:00
jrgissing e71d298f65 molecule template molecule IDs: error docs 2020-03-06 20:40:34 -07:00
Julien Guénolé ddc36973f0 final reference info 2020-03-06 14:55:52 +01:00
Jacob Gissinger a70aac2f24
Merge pull request #74 from lammps/master 
rebase
 2020-03-05 22:49:41 -07:00
Jacob Gissinger 21f2ec3a25
Merge branch 'master' into bond/react-new-examples-and-package 2020-03-05 20:08:19 -07:00
Axel Kohlmeyer 8c48a27c1d
fix another display issue in pair style srp docs 2020-03-05 15:39:13 -05:00
Axel Kohlmeyer c38380afc2
bugfix and small tweak for pair style srp docs 2020-03-05 15:36:15 -05:00
Axel Kohlmeyer 1fb54c307c
Merge pull request #1918 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch
 2020-03-05 15:16:50 -05:00
Axel Kohlmeyer 54a37aa4ef
fix spelling issue 2020-03-05 14:43:22 -05:00
Sievers 606eaf61f7 Merge branch 'master' into fix_numerical_differentiation 2020-03-05 09:58:50 -07:00
Axel Kohlmeyer fb3a8f5bb1
Merge pull request #1909 from giacomofiorin/colvars-update 
Update Colvars to version 2020-02-27
 2020-03-05 10:18:01 -05:00
Sievers ae045e4445 indented note block in fix_num_diff.rst 2020-03-04 19:48:12 -07:00
Sievers 02bdccbae1 added yyy to false positives 2020-03-04 19:45:13 -07:00
Sievers be138d368e Merge branch 'master' into fix_numerical_differentiation 2020-03-04 19:11:39 -07:00
Sievers 968f44601c Updated doc page with delta info and simplified example 2020-03-04 19:08:57 -07:00
Axel Kohlmeyer 6786efa224
Merge commit 'refs/pull/1916/head' of github.com:lammps/lammps into collected-small-fixes 2020-03-04 17:04:45 -05:00
Jinzhe Zeng 14d17b3513
clean the superfluous newline 
I believe this newline in the document is superfluous.
 2020-03-04 16:41:27 -05:00
Axel Kohlmeyer 7bbf070757
document new C++ and CMake requirements in manual 2020-03-04 14:37:51 -05:00
Axel Kohlmeyer e9544218e6
some corrections to the building the manual documentation 2020-03-04 14:14:12 -05:00
Axel Kohlmeyer 3eeb7547b5
step version string for next patch and stable version 2020-03-03 07:25:18 -05:00
Axel Kohlmeyer 7d598ba8d7
synchronize list of hardware architectures supported by KOKKOS with list in cmake file 2020-03-03 03:33:23 -05:00
Axel Kohlmeyer a4a5d24a69
add link to github support for subversion clients 2020-03-03 03:19:25 -05:00
jrgissing 9339bb085f Update molecule.rst 2020-03-02 01:06:42 -07:00
Axel Kohlmeyer 8f608f6a35
lo-level -> low-level 2020-03-01 10:30:06 -05:00
Axel Kohlmeyer ff614957c6
encode some more mathematical expressions and symbols 2020-03-01 09:25:20 -05:00
Axel Kohlmeyer 2455e35fd8
typeset mixing rules with embedded math 2020-03-01 08:51:29 -05:00
Axel Kohlmeyer 8662733dcd
convert the remainder of raw html typesetting in pair style smtbq 2020-02-29 14:45:39 -05:00
Axel Kohlmeyer 228a0bfa2e
replace hi- with high- 2020-02-29 11:37:47 -05:00
Axel Kohlmeyer 6f47f110f1
use k_B consistently, fix some more math. convert some transcriptions to math 2020-02-29 11:37:31 -05:00
Axel Kohlmeyer 07fc624509
typeset reduced units 2020-02-29 06:41:28 -05:00
Axel Kohlmeyer 66a0e27edf
some more cases where we can use embedded math 2020-02-29 04:57:44 -05:00
Axel Kohlmeyer e6c9efe6bf
convert lists to tables for more compact presentation 2020-02-28 18:52:13 +01:00
Axel Kohlmeyer f02b2485fa
tweak command overview table width so it is readable in PDF 2020-02-28 18:51:52 +01:00
Axel Kohlmeyer 71c11c32e3
replace more raw html code and add syntax highlighting 2020-02-28 18:00:43 +01:00
Axel Kohlmeyer 19d334908b
replace raw html with embedded math expressions and fix related issues 2020-02-28 17:39:57 +01:00
Giacomo Fiorin 7be004512f Update Colvars to version 2020-02-27 
This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
 2020-02-27 19:55:31 -05:00
Axel Kohlmeyer 03985454ed
some more formatting and math conversion improvements 2020-02-27 18:18:49 -05:00
Axel Kohlmeyer d242051c8e
Merge pull request #1898 from akohlmey/next_lammps_version 
Update version info for next release candidate
 2020-02-27 14:38:08 -05:00
Axel Kohlmeyer 6e7e365981
Merge pull request #1888 from lammps/release-preparation 
Documentation and Build script and Info updates for stable release
 2020-02-27 13:23:08 -05:00
Axel Kohlmeyer 3c277409c2
switch parsed-literal to code-block in Howto files where applicable 2020-02-27 12:45:14 -05:00
Steve Plimpton 67bfda532f mods to fix numdiff 2020-02-27 09:52:23 -07:00
Axel Kohlmeyer 06ede499c1
use only the LAMMPS logo in the navigation bar 2020-02-27 11:36:00 -05:00
Axel Kohlmeyer eb8531062c
Merge branch 'doc-updates' of github.com:rbberger/lammps into release-preparation 2020-02-27 11:26:15 -05:00
Richard Berger 25ec8d36a8 Final batch of index cleanup and code-blocks 2020-02-27 11:08:04 -05:00
Axel Kohlmeyer 2d2cb46dc0
move release date 2020-02-27 08:58:09 +01:00
Axel Kohlmeyer 1bb38ed09b
Merge commit 'refs/pull/1903/head' of github.com:lammps/lammps into release-preparation 2020-02-27 01:15:17 -05:00
jrgissing fe1ac99ae7 bond/react: docs tweak 2020-02-26 20:08:58 -07:00
Richard Berger 9ef5949798 Second batch of index cleanup and code-blocks 2020-02-26 16:31:05 -05:00
Axel Kohlmeyer 3563d2f10d
remove references to html-offline and only produce the offline viewable html manual 2020-02-26 16:01:03 -05:00
Axel Kohlmeyer 7bd3215226
Merge pull request #1894 from stanmoore1/kk_snap_chunk 
Make Kokkos pair SNAP chunksize variable user-settable
 2020-02-26 15:27:37 -05:00
Axel Kohlmeyer a828facbd8
Merge pull request #1900 from akohlmey/couple-lammps-plugin 
Example for loading LAMMPS as a plugin from a shared library
 2020-02-26 10:40:24 -05:00
Axel Kohlmeyer c92378eaca
add explanation of use of group2 and document effect of compute group 2020-02-26 13:12:14 +01:00
Sievers b0eb940b05 Added numdiff to false positives 2020-02-25 16:30:13 -07:00
Sievers 13bff07606 Added documentation, added an example, avoided position round off, added in compute_pe's compute_scalar, now fix produces per-atom array instead of global array 2020-02-25 15:32:37 -07:00
Richard Berger 8e1928aa65 First batch of index cleanup and code-blocks 2020-02-25 14:46:22 -05:00
Axel Kohlmeyer e87b3a21c2
complete documentation for LAMMPS plugin coupling example 2020-02-25 14:10:55 -05:00
pmla 1fc4dc151f typo 2020-02-25 18:11:31 +01:00
pmla 7acba4584d added group2ID 2020-02-25 18:05:36 +01:00
Axel Kohlmeyer 1a2a9f2209
small correction/simplification of the linking to LAMMPS library examples 2020-02-25 17:36:37 +01:00
Richard Berger 96d04b8a6c Update LAMMPS lexer for docs 2020-02-25 11:30:20 -05:00
Axel Kohlmeyer 26f11f19a7
update LAMMPS version string 2020-02-25 15:04:56 +01:00
Axel Kohlmeyer 8d427b54ec
small tweaks 2020-02-25 00:42:57 -05:00
Axel Kohlmeyer 11cda92ebb
add some false positives 2020-02-24 17:19:29 -05:00
Aidan Thompson 4ed1b4c3c7 Moved the chunking keyword to pair_snap.rst 2020-02-24 15:09:51 -07:00
Axel Kohlmeyer 003ef9d98a
add missing table 2020-02-24 17:03:06 -05:00
Axel Kohlmeyer bf4ad9ddd7
remove unused equation file 2020-02-24 16:45:42 -05:00
Axel Kohlmeyer 351bca4ccb
convert pair style bop to class2 2020-02-24 16:43:40 -05:00
Axel Kohlmeyer 3aa6f39425
convert pair styles colloid to dipole 2020-02-24 16:19:24 -05:00
Axel Kohlmeyer 02e287bf51
convert pair styles dpd to exp6 2020-02-24 15:41:16 -05:00
Stan Moore 7ee39416b4 Small doc tweak 2020-02-24 13:08:31 -07:00
Stan Moore 406ead64b5 Update docs 2020-02-24 13:04:34 -07:00
Axel Kohlmeyer 9955c8f94b
convert pair styles gauss to gromacs 2020-02-24 13:30:58 -05:00
Axel Kohlmeyer 8774ec04a9
convert pair styles hbond to lebedeva 2020-02-24 12:01:22 -05:00
Axel Kohlmeyer 6139617458
convert remaining lj pair styles 2020-02-24 10:50:31 -05:00
Axel Kohlmeyer d00f8fcd0a
convert pair styles local/density to meam/c 2020-02-24 09:21:08 -05:00
Axel Kohlmeyer 0b10c0ac60
convert math in more pair styles 2020-02-24 07:46:51 -05:00
Axel Kohlmeyer 54b7480478
convert pair styles sdk to soft 2020-02-23 16:33:37 -05:00
Axel Kohlmeyer eaeb9cad33
trim the lammps logo a little bit 2020-02-23 15:01:10 -05:00
Axel Kohlmeyer 0cc3f234dc
convert math in spin and sph pair styles 2020-02-23 15:00:43 -05:00
Axel Kohlmeyer d9a7edcf1a
Merge commit 'refs/pull/1893/head' of github.com:lammps/lammps into release-preparation 2020-02-23 13:38:26 -05:00
Oliver Henrich 607604d38c Added oxrna2 information 2020-02-23 17:36:57 +00:00
Axel Kohlmeyer 31165082c1
change pseudo external link to internal link. provide links to the command subpages 2020-02-22 18:41:36 -05:00
Axel Kohlmeyer ac639fe629
replace parsed-literal with code-block where applicable. improve typesetting 2020-02-22 13:50:35 -05:00
Axel Kohlmeyer cdf795652a
fix typesetting issues 2020-02-22 13:50:15 -05:00
Axel Kohlmeyer ca650ba43f
add some missing dependencies 2020-02-22 13:49:57 -05:00
Axel Kohlmeyer 6b79b1f978
use table_from_list in Packages_details and check for completenes there, too 2020-02-22 13:25:21 -05:00
Axel Kohlmeyer b1757bb26c
make names/lables more consistent and avoid reference errors in sphinx 2020-02-22 13:24:23 -05:00
Axel Kohlmeyer e8d1288527
added script to check for missing packages in package tables in manual 2020-02-22 11:46:31 -05:00
Axel Kohlmeyer ffabee6ae5
move logo symlink 2020-02-22 10:43:58 -05:00
Axel Kohlmeyer 57711f0dcb
improve layout and logical structure. add references 2020-02-22 10:39:15 -05:00
Axel Kohlmeyer 44a54324c1
more typesetting updates 2020-02-22 07:40:31 -05:00
Axel Kohlmeyer a915397668
more code-blocks 2020-02-22 06:14:52 -05:00