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5010 Commits

Author SHA1 Message Date
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 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