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5253 Commits

Author SHA1 Message Date
Axel Kohlmeyer e83600eee3 make naming of extract-able parameters consistent across similar pair styles (a/b/cparm -> a/b/c) 2019-01-24 10:54:17 -05:00
Axel Kohlmeyer 5c09732dc3 file spelling 2019-01-24 10:49:47 -05:00
Axel Kohlmeyer 82905dc62d correctly spell "through" 2019-01-24 10:29:51 -05:00
Axel Kohlmeyer 89a3f60289 replace references to pair_lj_soft with pair_fep_soft in docs 2019-01-24 15:49:46 +01:00
Axel Kohlmeyer a6ecd3d08c Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates 
Resolved Conflicts:
	doc/src/compute_fep.txt
	doc/src/fix_adapt_fep.txt
 2019-01-24 15:41:41 +01:00
Axel Kohlmeyer 1be589fb33 Merge branch 'patch-2' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates 2019-01-24 15:35:52 +01:00
Axel Kohlmeyer 4464f62c8f another permission fix 2019-01-24 08:20:24 -05:00
Axel Kohlmeyer 985913bce2
Merge pull request #1297 from stevenvdb/add-user-yaff 
Add USER-YAFF package for MOF simulations with QuickFF
 2019-01-24 11:05:55 +01:00
Axel Kohlmeyer f88c5e147a
Merge pull request #1298 from jrgissing/bond/react-distance_constraints 
Bond/react: add reaction constraints support
 2019-01-24 10:55:22 +01:00
Axel Kohlmeyer 48542f1832 permission update for some bundled PDF files 2019-01-24 04:51:55 -05:00
Agilio Padua 0bfb34389b Consolidated doc of soft-core pair styles 2019-01-23 20:56:54 +01:00
Agilio Padua 012d5a55bf Consolidated doc for soft pair styles 2019-01-23 12:02:23 +00:00
jrgissing fbee21f495 distance constraint: clarify use case in docs 2019-01-22 23:22:51 -07:00
jrgissing 7a10ac2019 bond/react:reaction_constraints 
introduce a distance constraint between any two reaction-site atoms, in order for reaction to occur
 2019-01-22 23:14:58 -07:00
Evangelos Voyiatzis a5248090fa
Update fix_adapt.txt 2019-01-22 19:46:35 +01:00
Evangelos Voyiatzis ade023861d
Update compute_fep.txt 2019-01-22 19:42:52 +01:00
Evangelos Voyiatzis 24bede9fff
Update fix_adapt_fep.txt 2019-01-22 19:37:58 +01:00
Axel Kohlmeyer dd3dbfaee2 restore aphabetical order of improper styles 2019-01-22 12:26:51 -05:00
Steven Vandenbrande ca31147d00 Fix USER-YAFF documentation issues 2019-01-22 14:58:38 +01:00
Oliver Henrich 7ec6e4b262 Merge branch 'master' into user-cgdna 2019-01-22 13:06:42 +00:00
Oliver Henrich 874e4fdafc Corrected required input angular velocity -> momentum 2019-01-22 13:05:15 +00:00
Steven Vandenbrande 794bf5084c Implementation and documentation for USER-YAFF package 2019-01-22 10:09:10 +01:00
Evangelos Voyiatzis e789715d92
Update fix_adapt_fep.txt 2019-01-21 23:12:34 +01:00
Evangelos Voyiatzis cab3380b55
Updating the list of potentials in fix_adapt_fep.txt 
There are several potentials that contain the method extract() but they are not included in the "fix adapt" and "fix adapt/fep"
A small update of the list is attempted here. The same potentials might be added to the documentation of fix_adapt if it is useful.
 2019-01-20 13:35:40 +01:00
Ryan S. Elliott 23ce00f366 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-01-16 21:49:14 -06:00
dsbolin 6e4e244e65 More doc page additions 2019-01-15 13:31:16 -07:00
dsbolin ef803be08e Moved all model option syntax for pair granular to pair coeff command; 
added global cutoff option for pair style granular command; initial
write-up of documentation.
 2019-01-15 10:18:46 -07:00
Axel Kohlmeyer 1e1f754d0c make gpu library Install.py use argparse module 2019-01-14 12:52:21 -05:00
jrgissing b0af54ac37 bond/react:limit reaction occurrences 2019-01-13 00:07:03 -07:00
Steve Plimpton 0cc9a445e8 add parallel dump file info to rerun doc page 2019-01-04 17:09:11 -07:00
Axel Kohlmeyer c26b2078ee
Merge pull request #1271 from akohlmey/next-patch-release 
Patch release 4 January 2019
 2019-01-03 22:28:55 -05:00
Axel Kohlmeyer 7323179de3 rename pair style lebedeva to lebedeva/z to be consistent with kolmolgorov/crespi/z 2019-01-03 17:30:16 -05:00
Axel Kohlmeyer 19e12aada5 Patch release 4 January 2019 2019-01-03 13:44:18 -05:00
Axel Kohlmeyer f96f98241c replace outdated moltemplate distribution with README explaining how to install the latest version 2019-01-03 00:39:58 -05:00
Axel Kohlmeyer 6d5ab3dac1 Merge branch 'github-rebo-bugfix' of https://github.com/CF17/lammps into test-rebo 
# Conflicts:
#	examples/airebo/log.23Jun17.airebo-m.g++.1
#	examples/airebo/log.23Jun17.airebo-m.g++.4
#	examples/airebo/log.23Jun17.airebo.g++.1
#	examples/airebo/log.23Jun17.airebo.g++.4
#	examples/airebo/log.27Nov18.airebo-m.g++.1
#	examples/airebo/log.27Nov18.airebo-m.g++.4
#	examples/airebo/log.27Nov18.airebo.g++.1
#	examples/airebo/log.27Nov18.airebo.g++.4
#	examples/airebo/log.29Jun18.airebo-m.g++.1
#	examples/airebo/log.29Jun18.airebo-m.g++.4
#	examples/airebo/log.29Jun18.airebo.g++.1
#	examples/airebo/log.29Jun18.airebo.g++.4
 2018-12-30 03:44:38 -05:00
Axel Kohlmeyer 37a597cc0f Merge branch 'master' into collected-post-stable-patches 2018-12-29 14:51:21 -05:00
Axel Kohlmeyer 444dcca433
Merge pull request #1254 from akohlmey/remove-reax-meam 
Remove REAX and MEAM packages
 2018-12-29 13:06:07 -05:00
Axel Kohlmeyer 9355e7e5cc
Merge pull request #1243 from athomps/snap-foundtest 
Removed redundant element list from pair_coeff snap syntax
 2018-12-29 13:04:47 -05:00
Axel Kohlmeyer cf3aee06f3
Merge pull request #1239 from jrgissing/bond/react-delete_atoms 
fix bond/react: allow deleting atoms
 2018-12-29 13:04:23 -05:00
Axel Kohlmeyer 89ca07c76e Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-29 12:05:30 -05:00
Axel Kohlmeyer cc1c93a3d9 correct broken formatting and add explicit links to ParmEd and InterMol, a few tweaks 2018-12-28 00:29:40 -05:00
Christoph Junghans e2d871ac23 update Fedora rpm docu 2018-12-20 09:01:44 -07:00
Christoph Junghans 6ebef96c23 Gentoo is not pre-built 2018-12-20 08:58:32 -07:00
Axel Kohlmeyer 685ed827d7 small formatting changes 2018-12-19 06:46:19 -05:00
Axel Kohlmeyer 5fb8f23cb4 update false positives list for recent manual changes 2018-12-19 02:24:16 -05:00
Axel Kohlmeyer ba3ee71edf update the github workflow checklist with a missing requirement 2018-12-19 02:09:31 -05:00
Axel Kohlmeyer caba050f29 update list of items to check for contributing code to current status 2018-12-19 02:03:27 -05:00
Axel Kohlmeyer 6dcd0ccfc3 Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-17 14:15:28 -05:00
Axel Kohlmeyer 90e125a73a make error message for input parameter type mismatch more specific to show what is incorrect 2018-12-17 14:03:26 -05:00
Axel Kohlmeyer 980f7e3b36 Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-16 20:41:02 -05:00
Ryan S. Elliott 6c0b100a53 Merge branch 'master' into kim-v2-update 2018-12-16 15:56:33 -06:00
Axel Kohlmeyer f7a2cd689b document default setting for flip flag 2018-12-15 19:14:59 -05:00
Axel Kohlmeyer deb21ad4e2 support variables for more region properties 
add code to allow the center of a spherical or cylindrical
region to be determined as variables and thus change over time.
 2018-12-13 14:06:12 -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 96c7f256f9 Merge branch 'snap-foundtest' of https://github.com/athomps/lammps into collected-post-stable-patches 2018-12-12 00:16:36 -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 ba98cff5a8 avoid merge conflict 2018-12-11 23:03:01 -05:00
Axel Kohlmeyer 35cfedab39 document PDF manual generation 2018-12-11 21:13:03 -05:00
Axel Kohlmeyer 3ad4c0db35 expose "make spelling" in the doc folder to the documentation 2018-12-11 21:02:52 -05:00
Axel Kohlmeyer 70868ca070 remove extra line from PDF manual config 2018-12-10 15:31:38 -05:00
Axel Kohlmeyer 052828284d fix typo 2018-12-10 14:53:31 -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 e2c39a1acd rename page for fix reax/c/bonds 2018-12-10 14:38:58 -05:00
Axel Kohlmeyer e86b933862 remove meam and reax from documentation 2018-12-10 14:38:25 -05:00
Axel Kohlmeyer 52a1f257c5 fix typo 2018-12-10 14:19:03 -05:00
Axel Kohlmeyer dedc6cf20c remove obsolete reax tools and rename pair_meam.txt to pair_meamc.txt 2018-12-10 14:16:08 -05:00
Axel Kohlmeyer 93efe3e40e update docs for meam and meam/c pair style 2018-12-10 12:21:15 -05:00
Axel Kohlmeyer 7d3caaa1a4 step version date for stable release on wednesday 2018-12-10 11:24:35 -05:00
Axel Kohlmeyer 8f95cdcb27 small update to the fix rigid/meso command docs 2018-12-09 16:24:06 -05:00
Axel Kohlmeyer e6321e1020
Merge pull request #1246 from akohlmey/next-patch-release 
Patch release 7 December 2018
 2018-12-07 14:15:12 -05:00
Axel Kohlmeyer 0165f18d59
Merge pull request #1241 from akohlmey/collected-small-fixes 
Collected small changes and updates for stable release
 2018-12-07 11:28:26 -05:00
Axel Kohlmeyer c36f8390d2
Merge pull request #1240 from akohlmey/fix-tune-kspace-limits 
Detect fix tune/kspace incompatible configurations
 2018-12-07 11:28:02 -05:00
Axel Kohlmeyer 57204a0f66 reformat recently changed paragraphs in the manual 2018-12-07 10:38:01 -05:00
Axel Kohlmeyer 4f00984bbc Merge branch 'master' into collected-small-fixes 2018-12-07 10:32:33 -05:00
Gareth Tribello 29dcf8348b No longer require LAPACK and BLAS to compile PLUMED+LAMMPS so removed this statement from docs 2018-12-07 15:16:40 +00:00
Gareth Tribello 1bd81db9b3 Fixed spelling mistakes 2018-12-07 15:15:35 +00:00
Gareth Tribello 4a4dbc7da5 Added further instructions on building of PLUMED+LAMMPS 2018-12-07 12:49:00 +00:00
Axel Kohlmeyer ee98dc0b96 step version number to 7 December 2018 2018-12-07 06:11:30 -05:00
Gareth Tribello d802817cca Small changes to the documentation for building and using PLUMED 2018-12-07 10:39:10 +00:00
jrgissing afaaf442d3 bond/react doc tweaks 2 2018-12-06 21:32:10 -07:00
Axel Kohlmeyer e37436d646 plug memory leak and avoid accessing uninitialized memory in virial computation and properly handle PPPM/Ewald cases that don't compute a virial 2018-12-06 18:54:25 -05:00
Aidan Thompson 00d719459f Fixed one error 2018-12-04 17:46:31 -07:00
Axel Kohlmeyer 9ee076e4c7 correct formatting of preformatted text 2018-12-04 10:40:31 -05:00
Aidan Thompson fa7e02ea71 Removed redundant element list from pair_coeff snap syntax 2018-12-03 20:28:01 -07:00
jrgissing cf3aee9083 bond/react doc tweaks 2018-12-03 20:12:38 -07:00
Axel Kohlmeyer ee82143a29 more false positives to handle 2018-12-03 16:21:18 -05:00
Axel Kohlmeyer a0bd1bd755 fix typo 2018-12-03 16:12:32 -05:00
Axel Kohlmeyer aeb7854aca update false positives list for newly added documentation 2018-12-03 16:11:39 -05:00
Axel Kohlmeyer 22f99be57e Merge remote-tracking branch 'github/read-dump-parallel' into collected-post-stable-patches 
# Conflicts:
#	src/read_dump.cpp
 2018-12-03 15:28:34 -05:00
Axel Kohlmeyer 55077cea4d Merge branch 'lebedeva2' of https://github.com/zbych127/lammps into collected-post-stable-patches 2018-12-03 15:24:31 -05:00
Axel Kohlmeyer 4af7e706d7 correctly compute hash for temporary directory used by manual building 2018-12-03 14:59:43 -05:00
Axel Kohlmeyer c69fc90588 detect more incompatible setups for fix tune/kspace, and document 2018-12-01 02:48:22 -05:00
jrgissing 53e66dcd15 bond/react: delete atoms 
allows deleting of a user-specified set of atoms, based on topology
 2018-11-30 22:35:10 -07:00
Axel Kohlmeyer e3ddefb38b update docs and header for removed error message 2018-11-29 02:03:56 -05:00
Axel Kohlmeyer 6be4ce7137 found a new false positive word in docs with spellchecker 2018-11-28 23:14:45 -05:00
Zbigniew Koziol 2d0d08093b Another attempt to add Lebedeva potential 2018-11-28 09:33:44 +01:00
Axel Kohlmeyer c0ab126e77
Merge pull request #1223 from akohlmey/next-patch-release 
Patch release 27 November 2018
 2018-11-27 16:37:10 -05:00
Axel Kohlmeyer f254b8e3a3
Merge pull request #1226 from akohlmey/cmake-gpu-enhancements 
Enhancements for using CMake with the GPU package, improved compatibility with cmake 3.x versions, improved handling of shared library building.
 2018-11-27 16:05:47 -05:00
Axel Kohlmeyer 1fdfc89d25 make $HOME/.local the default LAMMPS installation destination 2018-11-26 22:27:21 -05:00
Axel Kohlmeyer 05fb2d7587 more generated files/symlinks to ignore 2018-11-26 18:23:06 -05:00
Axel Kohlmeyer 55359789fb improve docs for building the GPU library with CUDA and CMake/make with fat binaries 2018-11-26 18:13:50 -05:00
Axel Kohlmeyer 4434481c91 remove trailing whitespace in manual source files 2018-11-26 14:48:53 -05:00
Axel Kohlmeyer c42d07d907 Merge branch 'master' into doc-adjust3 2018-11-26 14:47:29 -05:00
Axel Kohlmeyer 79b3e9e27d some clarifications and corrections on the wildcard command line docs 2018-11-26 14:46:39 -05:00
Axel Kohlmeyer cce874dfb4 step version number to 27 November 2018 2018-11-26 14:28:57 -05:00
Steve Plimpton bfaa2e9ee1 more adjustments to style pages 2018-11-26 11:24:48 -07:00
Steve Plimpton a010780808 merged in current master 2018-11-26 11:00:22 -07:00
Axel Kohlmeyer 5af7f52370 formatting tweak for labels, add checking item for added pair styles 2018-11-24 16:47:18 -05:00
Axel Kohlmeyer d1255ab572 we are LAMMPS, not LIGGGHTS 2018-11-22 09:22:09 -05:00
Axel Kohlmeyer 5efd8c06b1 correct formatting for examples when discussing the non-incremental nature of special_bonds 2018-11-22 06:25:39 -05:00
Axel Kohlmeyer 900ecc170a document that rcb balancing depends on comm_style tiled which in turn is not compatible with triclinic cells 2018-11-21 16:08:24 -05:00
Axel Kohlmeyer 090fc7bc8a remove unused sphinx-images extension from virtualenv setup 2018-11-20 22:14:24 -05:00
Axel Kohlmeyer e51720a2de add code to detect inconistent use of AIREBO/REBO potential files 2018-11-20 13:59:14 -05:00
Axel Kohlmeyer d359beb170
Merge pull request #1215 from jrgissing/bond/react-doc-corrections,mostly-formatting 
Bond/react doc corrections,mostly formatting
 2018-11-20 10:50:55 -05:00
Axel Kohlmeyer 421f97e444
Merge pull request #1214 from akohlmey/collected-small-changes 
Collected small changes and many spelling fixes for next release candidate
 2018-11-20 10:34:58 -05:00
Axel Kohlmeyer 981f56840e update workflow tips for checking new LAMMPS contributions 2018-11-20 00:30:45 -05:00
Axel Kohlmeyer 4251c70e93 update list of false positives for spellchecking 2018-11-20 00:08:07 -05:00
Axel Kohlmeyer 0bcb1bd301 more spelling fixes and occational re-edits 2018-11-20 00:06:40 -05:00
Axel Kohlmeyer c6c00ee7ee more spelling fixes 2018-11-19 20:46:32 -05:00
Axel Kohlmeyer 13ae678f39 more manual spelling fixes 2018-11-19 16:13:57 -05:00
Axel Kohlmeyer 8a94a32551 avoid duplicate label 2018-11-19 15:19:23 -05:00
Axel Kohlmeyer b6f0fe4c2d more changes for correct and consistent spelling in the manual 2018-11-19 11:47:33 -05:00
Axel Kohlmeyer 809bd855b6 adjust wording of non-features discussion to be more in-sync with recent developments 2018-11-19 11:24:55 -05:00
Axel Kohlmeyer 4dc2f9c6c4 fix some spelling errors in the manual 2018-11-19 11:24:17 -05:00
jrgissing 1d4e1f1425 bond/react:doc corrections 2018-11-16 20:47:51 -07:00
jrgissing d7abb8cf4d Revert "bond/react: doc corrections, mostly formatting" 
This reverts commit da88305f4d.
 2018-11-16 20:42:52 -07:00
jrgissing da88305f4d bond/react: doc corrections, mostly formatting 2018-11-16 20:41:49 -07:00
Axel Kohlmeyer bbcb659158 render fix commands in 6 columns instead of 8 so only narrow screens need to scroll horizontally 2018-11-16 22:09:07 -05:00
Axel Kohlmeyer dc6054fc2d rename "All commands" headers to "General commands" 2018-11-16 22:04:35 -05:00
Axel Kohlmeyer 0264edfcec provide example for how to set Tdamp correctly to 100 timesteps for all choices of unit 2018-11-16 16:27:47 -05:00
Axel Kohlmeyer a66384cfea update github tutorial/howto for recent changes in the development workflow 2018-11-16 16:27:05 -05:00
Axel Kohlmeyer 0d72c3769d
Merge pull request #1212 from stanmoore1/git_doc 
Tweak to github-development-workflow.md
 2018-11-16 12:44:58 -05:00
Axel Kohlmeyer 177733ecdd
Merge pull request #1211 from lammps/doc-hyper 
change warning to just a note
 2018-11-16 12:11:54 -05:00
Steve Plimpton c5c26abdd3 change warning to just a note 2018-11-16 09:26:37 -07:00
Stan Moore 5974741eea Tweak to github-development-workflow.md 2018-11-16 09:26:12 -07:00
Giacomo Fiorin 11de8dafe3 Update Colvars library to version 2018-11-16 
Fixes several issues with running averages and time correlation function
computations.  Details are in:

https://github.com/Colvars/colvars/issues/143
https://github.com/Colvars/colvars/issues/193
https://github.com/Colvars/colvars/pull/194
 2018-11-16 09:57:07 -05:00
Axel Kohlmeyer cf79751f4f
Merge pull request #1207 from akohlmey/next-patch-release 
Patch release 15 November 2018
 2018-11-15 19:33:52 -05:00
Axel Kohlmeyer e4dee3de17
Merge pull request #1206 from akohlmey/collected-small-changes 
Collected small changes for next release
 2018-11-15 17:29:26 -05:00
Axel Kohlmeyer db29ec7eee complete workflow document 2018-11-15 14:58:02 -05:00
Axel Kohlmeyer 090778c42b
Merge pull request #1204 from lammps/doc-plumed 
Linkage mode improvements and documentation updates for USER-PLUMED package
 2018-11-15 13:48:58 -05:00
Axel Kohlmeyer e160376365 incomplete first draft. committed for checking the markup in github. 2018-11-15 12:45:15 -05:00
Axel Kohlmeyer 4d9e2a014b add detailed build instructions and discussion of linkage modes for PLUMED library and USER-PLUMED package 2018-11-15 11:35:04 -05:00
Axel Kohlmeyer 8a4983e4bc reformatting and simplification of fix plumed docs 2018-11-15 10:53:38 -05:00
Axel Kohlmeyer 82d6aa9add interlink fixes colvars, plumed, and smd 2018-11-15 10:52:41 -05:00
Axel Kohlmeyer 4231ab3d57 correct some links 2018-11-15 10:52:03 -05:00
Axel Kohlmeyer 25914ea3f3 patch 15Nov2018 2018-11-15 10:17:25 -05:00
Axel Kohlmeyer 2c644c5f2e
Merge pull request #1197 from akohlmey/collected-small-fixes 
Collection of small changes and bugfixes for the next release
 2018-11-13 15:18:09 -05:00
Steve Plimpton 4805e1df22 doc page additions for USER-PLUMED package 2018-11-13 08:29:07 -07:00
Axel Kohlmeyer a026ce9669 correct broken links detected by make mobi 2018-11-12 21:38:26 -05:00
Axel Kohlmeyer 7e779d16de correct broken links in manual reported by 'make html' 2018-11-12 21:33:37 -05:00
Steve Plimpton 0ca02b6f41 added new commands to doc pages, fixed a few missing entries as well 2018-11-12 17:23:15 -07:00
Steve Plimpton 90caf0019c fix doc page errors 2018-11-12 12:32:53 -07:00
Steve Plimpton 3b7ebbb8df new hyper examples 2018-11-12 12:32:53 -07:00
Steve Plimpton 0c8ce199af more updates to hyper docs 2018-11-12 12:32:52 -07:00
Steve Plimpton 4a6f088c0b updates to hyper doc pages 2018-11-12 12:32:52 -07:00
Steve Plimpton 56598fcd0b changes to prd command doc page 2018-11-12 12:32:52 -07:00
Steve Plimpton 265c11dca9 more edits to hyper docs 2018-11-12 12:32:52 -07:00
Steve Plimpton d6631266ce doc files in wrong dir 2018-11-12 12:32:52 -07:00
Steve Plimpton fbd610b8a9 global/local hyperdynamics src and doc files 2018-11-12 12:32:52 -07:00
Axel Kohlmeyer f68d77c7af correct formatting 2018-11-09 08:03:58 -05:00
Axel Kohlmeyer 7a4f534676 replace non-ASCII character 2018-11-09 08:03:41 -05:00
Axel Kohlmeyer 729201ab93 fix typo reported in #1199 2018-11-09 08:03:19 -05:00
Axel Kohlmeyer 1651a21f92
Merge pull request #1198 from akohlmey/next-patch-release 
Patch release 9 November 2018
 2018-11-08 20:49:49 -05:00
Axel Kohlmeyer f2a29880e2 patch 9Nov2018 2018-11-08 16:48:43 -05:00
Axel Kohlmeyer e0955f6434 Merge branch 'master' into sdpd to resolve merge conflicts 
# Conflicts:
#	cmake/CMakeLists.txt
#	src/Makefile
 2018-11-08 16:32:02 -05:00
Axel Kohlmeyer 3681bc853d
Merge pull request #1195 from jrgissing/bond/react-custom_edges 
Bond/react: charge update for custom edges
 2018-11-08 16:19:23 -05:00
Axel Kohlmeyer a6e9b99295
Merge pull request #1180 from gtribello/master 
Add natively supported PLUMED interface to LAMMPS
 2018-11-08 16:16:50 -05:00
Axel Kohlmeyer a1e8992eac replace non-ASCII characters 2018-11-06 22:21:19 -05:00
jrgissing 84fcf01bed bond/react: allow custom update of charges near template edges 
also, fixes a bug introduced in PR #1189, when not using stabilization
 2018-11-06 19:59:22 -07:00
Oliver Henrich 4e6253254c Merge branch 'master' into user-cgdna 2018-11-06 19:48:06 +00:00
Oliver Henrich 562296bdb7 Updated link to preprint article 2018-11-06 19:44:35 +00:00
Axel Kohlmeyer 91c4ef6f64
Merge pull request #1189 from jrgissing/bond/react-custom_group 
Bond/react custom group support
 2018-11-06 10:32:06 -05:00
Ryan S. Elliott 29ae88e309 Update docs for KIM 2018-11-05 09:37:35 -06:00
jrgissing ab7aa9dfda correction to fix group property doc 2018-11-05 00:49:33 -07:00
jrgissing f7aa01d74a bond/react: convert group-ID to group-ID-prefix 
enables consistent syntax when using custom groups
 2018-11-03 11:57:46 -06:00
Axel Kohlmeyer b7e507a258 fix typo and reformat 2018-11-02 21:08:45 -04:00
Axel Kohlmeyer ea9746f26d insert fix plumed docs into manual generation 2018-11-02 21:08:32 -04:00
Giacomo Fiorin 85a5cab663 Update Colvars library to version 2018-10-16 2018-11-02 17:45:20 -04:00
Gareth Tribello b1c50e3bbe Added plumed documentation in a txt file 2018-11-02 19:50:49 +00:00
Ryan S. Elliott b0938b70d5 Merge branch 'master' into kim-v2-update 2018-11-01 19:41:13 -05:00
jrgissing b67e54dd7d reciprocal 'related commands' 2018-11-01 01:09:52 -06:00
jrgissing 5821a5ecc8 bond/react: custom group with stabilization option 2018-11-01 01:04:45 -06:00
jrgissing 3faecc4d28 add option to update all atoms' atomic charges 
option to update all atomic charges, even when edge atoms are defined
 2018-10-30 22:11:52 -06:00
Ryan S. Elliott 1b98c0e40d Merge remote-tracking branch 'lammps/master' into kim-v2-update 2018-10-30 18:40:55 -05:00
Morteza Jalalvand ba6f6f73f1 first commit: added SDPD 2018-10-30 17:40:00 +03:30
Steve Plimpton a2671f8943 doc files for new parallel dump file read capability 2018-10-26 18:06:34 -06:00
Gareth Tribello 4fa78a78de Added instructions on PLUMED to build extras and Package details pages of manual 2018-10-26 22:12:17 +01:00
Gareth Tribello ff9f836be4 Merge remote-tracking branch 'upstream/master' 2018-10-26 22:01:05 +01:00
Steve Plimpton 2c1f420a48 more tweaks 2018-10-24 13:43:26 -06:00
Steve Plimpton 07f92d225e formatting tweak 2018-10-24 12:03:51 -06:00
Steve Plimpton 7e5ec96bcd more tweaks from style check script 2018-10-24 12:02:36 -06:00
Steve Plimpton c8870f1b78 change intro to each list of commands 2018-10-24 11:57:34 -06:00
Axel Kohlmeyer 7069b52a44
Merge pull request #1172 from akohlmey/next-patch-release 
Patch release 24 October 2018
 2018-10-23 18:08:38 -04:00
Axel Kohlmeyer fccc26758b
Merge pull request #1152 from lammps/doc-adjust2 
More Documentation consistency improvements
 2018-10-23 13:05:04 -04:00
Axel Kohlmeyer 0293dee9b2 patch 24Oct2018 2018-10-23 11:03:51 -04:00
Axel Kohlmeyer 6107f00e9d
Merge pull request #1164 from akohlmey/fix-halt-for-minimize 
Enable use of fix halt for minimizations
 2018-10-23 10:35:26 -04:00
Axel Kohlmeyer aa27c8f733 convert double quotes to latex style 2018-10-23 09:17:00 -04:00
Axel Kohlmeyer 8649081904 fix broken links in manual 2018-10-21 18:39:25 -04:00
Axel Kohlmeyer c0dd187802 make sure all pictures are includes in epub/mobi files 2018-10-21 18:38:46 -04:00
Aidan Thompson 8223f5e0a3 Eliminated another initialization error and tweaked rdf-adf example 2018-10-20 16:46:45 -06:00
Axel Kohlmeyer 07a499fcc1 improve check for missing styles in lammps.book 2018-10-20 10:01:55 -04:00
Axel Kohlmeyer fb6f019a11 correct link to output options 2018-10-20 06:45:57 -04:00
Axel Kohlmeyer 79da210dc4 integrate compute adf into manual build infrastructure 2018-10-20 06:45:28 -04:00
Aidan Thompson 0783f8ad2f Added compute_rdf.txt 2018-10-19 18:43:58 -06:00
Aidan Thompson 04a4a29fcf Creatd new compute ADF for angular distribution function 2018-10-19 18:36:11 -06:00
Steve Plimpton 1c994bda46 corrections to fix neb doc page 2018-10-19 09:53:19 -06:00
Steve Plimpton f5206d2f7b more one-liner in pair_style doc page 2018-10-19 09:53:19 -06:00
Steve Plimpton 9bca5ae607 added one-line pair descriptions 2018-10-19 09:53:19 -06:00
Steve Plimpton d1f260a765 undo changes to PRD doc from another branch 2018-10-19 09:53:19 -06:00
Steve Plimpton 36a1ca7e72 updates some one-line style defs 2018-10-19 09:53:19 -06:00
Steve Plimpton 5f1c77ced2 tweaks to USER-PTM package doc 2018-10-19 09:53:18 -06:00
Steve Plimpton dc89bdd924 more changes augmenting lists with USER styles and to core/shell doc pages 2018-10-19 09:53:18 -06:00
Steve Plimpton a979c6eeec updating files that have lists of command styles 2018-10-19 09:53:18 -06:00
Axel Kohlmeyer cc6f1be82d first attempt to port fix halt to minimizations 2018-10-19 07:26:49 -04:00
Steve Plimpton d9dd80b368 added -restart2dump command-line option 2018-10-18 14:24:48 -06:00
Axel Kohlmeyer 382e91cf5b
Merge pull request #1156 from wmbrownIntel/user-intel-hybrid 
Adding hybrid support to USER-INTEL package + EAM/intel bug fix
 2018-10-12 12:35:36 -04:00
Michael Brown c37deebffa Adding full hybrid support to USER-INTEL package and fixing bug with EAM parameter initialization. 2018-10-11 05:12:00 -07:00
Stan Moore 3d0722b974 Merge branch 'master' of github.com:lammps/lammps into granular-kokkos 2018-10-10 10:43:54 -06:00
Axel Kohlmeyer 1b76e14224
Merge pull request #1151 from akohlmey/next-patch-release 
update version number for next patch release
 2018-10-10 02:20:50 +02:00
Axel Kohlmeyer 9a0c02a845
Merge pull request #1150 from mkanski/compute_pair_multiple_pstyles 
Extend compute pair to handle multiple instances of a sub-style in pair style hybrid
 2018-10-10 00:48:52 +02:00
Axel Kohlmeyer 70bee26641 update version number 2018-10-09 12:59:12 -04:00
Axel Kohlmeyer 791024586e
Merge pull request #1131 from ckadding/master 
Add compute_pressure_cylinder to USER-MISC package
 2018-10-09 18:40:02 +02:00
Axel Kohlmeyer 962fd1df90
Merge pull request #1146 from jrgissing/maxspecial_restarts 
put atom->maxspecial in restarts
 2018-10-09 17:55:24 +02:00
Axel Kohlmeyer 3c41295e70 change implementation to be consistent with pair_coeff and remain backward compatible 2018-10-08 17:23:22 +02:00
mkanski 8b944e06f0 Small changes in doc file 2018-10-05 21:08:18 +02:00
mkanski 1e9778b81e Extend compute pair to handle multiple instances of a given pair style 2018-10-05 20:34:12 +02:00
Axel Kohlmeyer d805796cd7
Merge pull request #1133 from lammps/doc-adjust 
Multiple documentation adjustments and corrections from Steve and Axel
 2018-10-05 20:20:18 +02:00
jrgissing fd20eb93b2 remove listing of extinct special_bonds 'extra' keyword 2018-10-04 21:30:34 -06:00
Axel Kohlmeyer f81836d605 reformat compute pressure/cylinder docs and integrate it into the manual 2018-10-02 11:51:23 -04:00
Axel Kohlmeyer b5a5270f4a fix typos in compute msd/chunk 
as reported by @evoyiatzis the example is incorrect,
but also a mention of the compute a few lines above.
 2018-10-02 16:29:18 +02:00
ckadding 69c3ff560e
Clarify restrictions and output 2018-10-02 10:11:57 -04:00
Axel Kohlmeyer dba8f9c62b
Merge pull request #1137 from dilkins/fast-forward-langevin 
Fast-forward Langevin functionality included in USER-MISC package
 2018-10-02 14:19:37 +02:00
Axel Kohlmeyer 4b4f7d6ee0 implement conventions for unique links in docs 2018-10-02 11:25:12 +02:00
Axel Kohlmeyer 66bfdd20d4 fully integrate fix ffl docs into the manual system 2018-10-02 11:24:45 +02:00
Axel Kohlmeyer 990a93f9d9 fix typo in example input 2018-10-02 10:58:28 +02:00
Ryan S. Elliott f61f43a56b Merge branch 'master' into kim-v2-update 2018-10-01 21:17:26 -05:00
dilkins 799ffc58d9 C++ system headers included and enumeration of flip_int used;documentation corrected 2018-10-01 17:13:56 +02:00
Axel Kohlmeyer a333fdac30 correct some documentation issues with the recently added USER-PTM package 2018-09-28 18:02:13 +02:00
Axel Kohlmeyer ffbc33bea5 Merge branch 'master' into doc-adjust 2018-09-28 17:07:51 +02:00
Axel Kohlmeyer 12d2dd201a update description of RPM based LAMMPS packages with info from @junghans 
this fixes #1135
 2018-09-28 15:47:56 +02:00
Axel Kohlmeyer 497af2ebb9 document eam/cd/old 2018-09-28 13:44:42 +02:00
dilkins 21c59d4cf0 Fast-forward Langevin functionality included 2018-09-28 12:46:11 +02:00
Axel Kohlmeyer 4fe23c3854
Merge pull request #1120 from pmla/polyhedral-template-matching 
Added compute for Polyhedral Template Matching
 2018-09-28 12:26:06 +02:00
Axel Kohlmeyer f58aa05e02 remove references to USER-OMP version of pair style nb3b/harmonic 2018-09-27 07:44:54 -04:00
Axel Kohlmeyer e1627caf04 integrate compute ptm/atom and USER-PTM into the docs 2018-09-27 07:20:03 -04:00
Axel Kohlmeyer 91286ddb0e remove references to fix ave/spatial and ave/spatial/sphere 2018-09-27 06:51:30 -04:00
Axel Kohlmeyer cf0f3b6b61 Update manual for renamed or removed files 2018-09-27 06:23:59 -04:00
Axel Kohlmeyer 8e7ddff6dc reverse order in which pdf files are created. 
Creating Developer.pdf first and Manual.pdf later makes
any warnings from the latter step, e.g. about missing
files in doc/src/lammps.book more visible.
 2018-09-27 06:15:03 -04:00
Axel Kohlmeyer 7987f3319e remove outdated references to linux rpms on rpm.lammps.org 2018-09-27 06:05:26 -04:00
Axel Kohlmeyer b07adbf98c Update installing/running LAMMPS on ubuntu for daily binary 2018-09-27 05:49:43 -04:00
Steve Plimpton a9b8a6521d more mis-matches between doc pages and src files 2018-09-25 13:18:54 -06:00
Steve Plimpton 5a6226caa5 jive src headers with doc page entries and example scripts 2018-09-25 10:50:43 -06:00
Axel Kohlmeyer 36c5fb2ec6 update formatting 2018-09-24 10:37:52 -04:00
Axel Kohlmeyer 918030bf1c Merge branch 'master' of https://github.com/oywg11/lammps into ilp-update 2018-09-24 10:29:08 -04:00
ckadding dd39bc44ee
Add compute_pressure_cylinder documentation 2018-09-20 09:16:58 -04:00
Axel Kohlmeyer 8dff5fd5d7 patch 18Sep18 2018-09-18 17:24:10 -04:00
Axel Kohlmeyer e2293cc7df
Merge pull request #1119 from lammps/doc-clarify 
doc page clarifications
 2018-09-17 06:10:25 -04:00
Axel Kohlmeyer 0c287a55cd
Merge pull request #1092 from RomainVermorel/master 
New stress/mop and stress/mop/profile computes for USER-MISC
 2018-09-17 05:16:42 -04:00
Axel Kohlmeyer 5f6b5c5400
fix typo 2018-09-17 05:11:59 -04:00
Axel Kohlmeyer 494b149272
fix typo 2018-09-17 05:10:56 -04:00
Axel Kohlmeyer 39ee7876c4
fix typo 2018-09-17 05:09:23 -04:00
Axel Kohlmeyer 8fa80081df
fix typo 2018-09-17 05:08:22 -04:00
Steve Plimpton e14db00d52 doc link adjustments 2018-09-14 17:31:33 -06:00
oywg11 7054800932
Merge branch 'master' into master 2018-09-12 22:13:43 +03:00
oywg11 01beaf38a1 small modifications for potential #839 2018-09-12 21:51:57 +03:00
oywg11 83b6d6ae96 small modifications of potential #839 2018-09-12 17:47:16 +03:00
Richard Berger 6ae4bdead5
Merge pull request #1089 from lammps/spread 
2 new computes: chunk/spread/atom and reduce/chunk
 2018-09-11 21:21:02 -04:00
Richard Berger 92b508f14c
Merge pull request #1097 from lammps/localvars 
add variable option to compute bond/angle/dihedral local
 2018-09-11 21:18:15 -04:00
pmla b7c75b6c4e Added compute for Polyhedral Template Matching 2018-09-11 16:41:44 -04:00
Steve Plimpton c3ece2f086 typo in fix relax/box doc page 2018-09-11 12:44:35 -06:00
Steve Plimpton 7f328d3f79 cite a good book on SLLOD thermostatting for molecular systems 2018-09-11 11:49:46 -06:00
Steve Plimpton 983e8bb110 doc page clarifications 2018-09-11 11:36:37 -06:00
Axel Kohlmeyer 02b653c0ce correct end of itemized list to be compatible with txt2rst conversion 2018-09-10 22:22:42 -04:00
Axel Kohlmeyer 075d366051
Merge pull request #1116 from akohlmey/correct-doc-build 
Correct multiple issues in manual build
 2018-09-09 01:28:29 -04:00
Steve Plimpton b488f1072e recent package links 2018-09-07 14:22:38 -06:00
Steve Plimpton 0384ef8967 more tweaks to client/server doc pages 2018-09-07 14:00:39 -06:00
Steve Plimpton 25907c856e small doc page changes, format and content on doc page tarballs 2018-09-07 09:56:03 -06:00
Axel Kohlmeyer dd64c063cf various fixes for the manual to address breakage from merging MESSAGE and USER-SCAFACOS packages 2018-09-06 22:28:20 -04:00
Axel Kohlmeyer 947f574503 Merge branch 'master' into compute_mop 
# Conflicts:
#	cmake/CMakeLists.txt
 2018-09-06 21:13:42 -04:00
Stan Moore 95c3d2fc8e
Merge pull request #1051 from stanmoore1/data_dup 
Add data duplication option to the KOKKOS package
 2018-09-05 17:09:09 -06:00
Richard Berger 510e09f4ef patch 5Sep18 2018-09-05 13:39:18 -04:00
Axel Kohlmeyer 0c92c22755 moved contents of USER-MOP package to USER-MISC as suggested by @sjplimp 2018-09-05 10:56:12 -04:00
Richard Berger ff2e13e063 Merge branch 'master' into ScaFaCoS 2018-09-04 21:35:46 -04:00
Steve Plimpton bcecc0389e add variable option to compute bond/angle/dihedral local 2018-09-04 14:48:44 -06:00
Axel Kohlmeyer cb4ffaf95c update docs and references for name changes in USER-MOP package, remove obsoleted files 2018-09-04 08:42:32 -04:00
RomainVermorel a797a0d193 changed computes names to stress/mop and stress/mop/profile 2018-09-04 14:02:19 +02:00
Axel Kohlmeyer 7b423c6d4b integrate USER-MOP package into build and documentat system. apply latest LAMMPS programming style conventions 2018-09-03 23:37:25 -04:00
Steve Plimpton 5f0423b97d change -mpi to -mpicolor 2018-08-31 17:04:27 -06:00
Steve Plimpton 78301e5e93 Merge branch 'master' into cslib 2018-08-31 16:30:28 -06:00
Steve Plimpton bc62002b1c units and doc changes 2018-08-31 16:05:24 -06:00
Steve Plimpton e3ce702eec doc adjust 2018-08-31 13:53:02 -06:00
Steven J. Plimpton c4c5f9a32e 2 new computes: chunk/spread/atom and reduce/chunk 2018-08-31 13:44:49 -06:00
Steven J. Plimpton 8f5512eafe patch 31Aug18 2018-08-31 09:49:35 -06:00
Steve Plimpton a8f1fe8f96
Merge pull request #1078 from junghans/manpage 
added manpage from debian package
 2018-08-29 07:48:48 -06:00
Steve Plimpton c61f9248f4
Merge pull request #987 from sergeylishchuk/master 
Added Axilrod-Teller manybody potential
 2018-08-29 07:48:22 -06:00
Christoph Junghans 0661a800a7 lammps.1: add options block 2018-08-24 14:57:49 -06:00
Ryan S. Elliott 796b6b2d9c Merge branch 'master' into kim-v2-update 2018-08-24 14:28:33 -05:00
Steven J. Plimpton d8b087aeb4 docs for MD protocol enhancements 2018-08-24 11:11:34 -06:00
Steven J. Plimpton 33d5fe457c re-merge with current master 2018-08-24 09:57:08 -06:00
Steven J. Plimpton 44bda245a6 resolution of cutoff issues 2018-08-24 09:36:39 -06:00
Christoph Junghans bd1e89ac4c lammps.1: use -in syntax 2018-08-24 06:55:59 -06:00
Christoph Junghans 3622cb9b28 lammps.1: some update 2018-08-23 19:16:41 -06:00
Christoph Junghans 9eacabd821 added manpage from debian package 2018-08-23 14:43:31 -06:00
Axel Kohlmeyer a04008cdfd fully integrate atm pair style into manual 2018-08-23 10:27:40 -04:00
Axel Kohlmeyer 648d8c3d2a adapt docs to refactored manual 2018-08-23 10:15:17 -04:00
Axel Kohlmeyer c5d3274222 restore files 2018-08-23 10:13:06 -04:00
Axel Kohlmeyer 4f36f077ff whitespace cleanup 2018-08-23 10:08:36 -04:00
Axel Kohlmeyer 929185da07 Merge branch 'master' into axilrod-teller 
# Conflicts:
#	cmake/CMakeLists.txt
#	doc/src/Commands.txt
#	doc/src/Commands_bond.txt
#	doc/src/Howto.txt
#	doc/src/Howto_bioFF.txt
#	doc/src/Howto_coreshell.txt
#	doc/src/Howto_couple.txt
#	doc/src/Howto_diffusion.txt
#	doc/src/Howto_dispersion.txt
#	doc/src/Howto_granular.txt
#	doc/src/Howto_library.txt
#	doc/src/Howto_multiple.txt
#	doc/src/Howto_replica.txt
#	doc/src/Howto_restart.txt
#	doc/src/Howto_temperature.txt
#	doc/src/Howto_tip4p.txt
#	doc/src/Intro.txt
#	doc/src/Intro_authors.txt
#	doc/src/Intro_features.txt
#	doc/src/Intro_nonfeatures.txt
#	doc/src/Manual.txt
#	doc/src/Manual_version.txt
#	doc/src/Packages.txt
#	doc/src/Packages_details.txt
#	doc/src/Packages_standard.txt
#	doc/src/Packages_user.txt
#	doc/src/Section_start.txt
#	doc/src/Speed.txt
#	doc/src/Speed_compare.txt
#	doc/src/Speed_gpu.txt
#	doc/src/Speed_intel.txt
#	doc/src/Speed_kokkos.txt
#	doc/src/Speed_measure.txt
#	doc/src/Speed_omp.txt
#	doc/src/Speed_opt.txt
#	doc/src/Speed_packages.txt
#	doc/src/Speed_tips.txt
#	doc/src/fix_deform.txt
#	doc/src/fix_external.txt
#	doc/src/fix_property_atom.txt
#	doc/src/lammps.book
#	doc/src/neb.txt
#	doc/src/pair_eam.txt
#	doc/src/prd.txt
#	doc/src/run_style.txt
#	doc/src/temper.txt
#	src/version.h
 2018-08-23 10:06:47 -04:00
Axel Kohlmeyer 440338d769 last round of spelling fixes 2018-08-22 22:35:35 -04:00
Axel Kohlmeyer af35c3bcca atomID -> atom-ID 2018-08-22 22:28:53 -04:00
Axel Kohlmeyer c0d9d96e09 better help message in make file 2018-08-22 22:24:51 -04:00
Axel Kohlmeyer 0cd71ee582 more false positives 2018-08-22 22:18:35 -04:00
Axel Kohlmeyer b00046fd34 fix typo 2018-08-22 22:18:27 -04:00
Axel Kohlmeyer 4b2629d8ba recompile/recompute/reinit -> re-compile/re-compute/re-init 2018-08-22 22:18:16 -04:00
Axel Kohlmeyer 193f46dd9f spelling fix 2018-08-22 22:04:03 -04:00
Axel Kohlmeyer 96bde51ae4 autodetect -> auto-detect 2018-08-22 22:03:53 -04:00
Axel Kohlmeyer 683c87347c neighborlist -> neighbor list 2018-08-22 22:02:24 -04:00
Axel Kohlmeyer fe6debfe9a precompiled -> pre-compiled 2018-08-22 22:02:01 -04:00
Axel Kohlmeyer 9a8c09288f use Hyper-Threading consistently 2018-08-22 21:54:41 -04:00
Axel Kohlmeyer eca0487daf subdomain -> sub-domain 2018-08-22 21:50:56 -04:00
Axel Kohlmeyer 4278a284e4 fix one more broken link 2018-08-22 21:48:42 -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 e632acec29 fix a bunch more spelling errors 2018-08-22 21:30:21 -04:00
Axel Kohlmeyer 1bd5626140 fix some more spelling issues 2018-08-22 20:43:35 -04:00
Axel Kohlmeyer ffb1a9c46a update link in lammps theme for sphinx 2018-08-22 20:36:01 -04:00
Axel Kohlmeyer 9e37ea16ac fix some speelink ehrrors 2018-08-22 20:35:35 -04:00
Axel Kohlmeyer c8ac88dd87 update link in LAMMPS theme for Sphinx 2018-08-22 19:46:49 -04:00
Axel Kohlmeyer 0e292b397f even more broken links detected by ePUB to MOBI conversion 2018-08-22 19:41:44 -04:00
Axel Kohlmeyer d5089858bd add support for the conversion of ePUB to MOBI (compatible with Kindle) 2018-08-22 19:17:21 -04:00
Axel Kohlmeyer 357ffef09c fix some more broken links detected by ebook conversion 2018-08-22 19:16:36 -04:00
Axel Kohlmeyer 2aa4770e0d correct link in AtC html docs 2018-08-22 19:16:11 -04:00
Axel Kohlmeyer 4074c4c67f correct some more broken or outdated links 2018-08-22 19:08:07 -04:00
Axel Kohlmeyer a1098d5796 fix broken and inconsistent links in the manual 2018-08-22 18:45:32 -04:00
Steven J. Plimpton 03b880a31c more doc page updates 2018-08-22 11:42:41 -06:00
Steven J. Plimpton 89a3670fb5 merge master into cslib branch, update docs 2018-08-22 11:19:55 -06:00
Steven J. Plimpton c4b55385e2 doc updates 2018-08-22 10:40:39 -06:00
Steven J. Plimpton cb8482b0e6 another doc change 2018-08-22 10:22:51 -06:00
Steven J. Plimpton a9fb8636ad doc page updates and changed domain->remap() call 2018-08-22 09:52:44 -06:00
Steven J. Plimpton 9a15d0bd83 Merge branch 'master' into scafacos 2018-08-22 09:25:29 -06:00
Steven J. Plimpton f466c64071 enable merge to current GH master 2018-08-22 09:21:54 -06:00
Steven J. Plimpton b47e492233 patch 22Aug18 2018-08-22 08:45:41 -06:00
Steve Plimpton bb72604eec
Merge pull request #1071 from akohlmey/doc-updates-for-release 
Doc updates for release
 2018-08-22 08:37:44 -06:00
Steve Plimpton 316f265e3d
Merge pull request #1067 from jrgissing/bond/react-better-template-checks 
Bond/react: better template validity checks
 2018-08-22 08:36:44 -06:00
Richard Berger 9d4994b383 Add missing bullet points 2018-08-22 10:08:56 -04:00
Axel Kohlmeyer fc47b8c6dd some more tweaks and epxlanations for windows support 2018-08-22 09:51:29 -04:00