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5253 Commits

Author SHA1 Message Date
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 4e74ccbbbe
restore building developer pdf before manual pdf 2019-03-25 21:18:17 -04:00
Axel Kohlmeyer 19d25203ad
add min_style spin to commands overview 2019-03-25 21:05:13 -04:00
Axel Kohlmeyer 36b645d238
add min_spin page to toclist 2019-03-25 20:46:42 -04:00
julient31 81a4d293db Commit4 JT 032519 
- corrected documentation (errors in min_spin.txt and
min_modify.txt)
- changed the code accordingly
 2019-03-25 15:43:58 -06:00
julient31 7a00997a14 Commit2 JT 032519 
- added equations for documentation
- updated examples (not calling fix nve/spin)
- replaced error message by warning in all pair/spin
 2019-03-25 14:03:28 -06:00
julient31 a726362888 Commit JT 032519 
- adding all min files into new branch
- preparing branch for pull request of spin minimizer
 2019-03-25 12:57:42 -06:00
Axel Kohlmeyer 2f20581b29
Merge pull request #1374 from akohlmey/collected-small-fixes 
Collected small changes for the next patch release
 2019-03-25 13:15:45 -04:00
Steve Plimpton 5554deda39 fixed 2 spelling errors 2019-03-25 10:07:07 -06:00
Steve Plimpton 881cc71a44 Merge branch 'master' into hyper 2019-03-25 09:21:09 -06:00
Ryan S. Elliott 3464464ea9 Update kim example query and log files 2019-03-22 20:20:47 -05:00
Axel Kohlmeyer 22be3bd37e
fix spelling error and add false positives for spellchecking 2019-03-22 17:33:16 -04:00
Axel Kohlmeyer f69173f410
partial documentation update 2019-03-22 17:25:03 -04:00
Axel Kohlmeyer 52f9e4a960
allow overriding the location of the molfile plugin headers with CMake 2019-03-22 14:11:02 -04:00
julient31 c23ace9c97 Commit JT 032219 
- fixed bug 1: precession_spin had no min_setup
- fixed bug 2: incorrect init of spins in neb/spin
- improved doc min_spin.txt (added eqs, and connected to related
files).
 2019-03-22 11:52:09 -06:00
julient31 2cbf56846a Commit JT 032019 
- moved gneb files from src/REPLICA to src/SPIN
- changed name of min/spin
- implemented read_param in min.cpp and min_spin.cpp
- set sp_flag tests in min_spin.cpp and neb_spin.cpp
 2019-03-20 10:41:36 -06:00
Axel Kohlmeyer 2dbc2c5916
fix spelling issues in documentation and some minor clarification 2019-03-19 16:04:53 -04:00
Axel Kohlmeyer 1c3e3ce548
add kim_query command to commands list 2019-03-19 15:57:19 -04:00
Axel Kohlmeyer 38c373a0e4
integrate new kim_query command into the documentation environment 2019-03-19 15:42:35 -04:00
julient31 0d4dbb8d73 Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 2019-03-19 09:01:27 -06:00
Axel Kohlmeyer 2bac365081
support old style PDF build for new pair style granular 2019-03-15 15:51:08 -04:00
Axel Kohlmeyer a7a1fd4ee5
remove reference to USER-OMP version of fix wall/gran 2019-03-15 15:50:44 -04:00
Axel Kohlmeyer b6459b3f74
Merge branch 'master' into gran_mods 2019-03-15 14:30:36 -04:00
Axel Kohlmeyer 8845a1a0ae
whitespace cleanup (remove ctrl-m, trailing whitespace) 2019-03-15 14:20:10 -04:00
Axel Kohlmeyer 3f0f2383b4
fix spelling and record false positives 2019-03-15 14:18:04 -04:00
jrgissing 5608f87c15 bond/react:unfix_deletes_internal_groups 2019-03-13 21:55:17 -06:00
julient31 8c50c3d7c8 Commit JT 031319 
- improved gneb functions
- correct name in fix_neb (Weinan)
 2019-03-13 17:02:40 -06:00
Steve Plimpton aca8ce1f53 Merge branch 'master' into hyper 
sync with GH master
 2019-03-13 12:19:06 -06:00
Dan S. Bolintineanu 2cc35ee777 A few additional enhancements to pair granular and fix wall granular option: 
- NULL option for tangential stiffness, to set it based on shear modulus
- calculation of effective shear moduli from elastic moduli and Poisson's ratio
- updates to doc page example syntax
 2019-03-13 00:42:08 -06:00
julient31 f6fb8b220d Commit 2 JT 031219 
- modified examples (gneb and spinmin now distinct)
- started documention for spinmin
 2019-03-12 16:59:13 -06:00
Stan Moore 0d73fe99fd Update Kokkos docs 2019-03-12 15:34:12 -06:00
Dan S. Bolintineanu e0c935b52d Additional changes to pair_granular: 
-added mindlin and mindlin/rescale tangential model options
-torque from tangential force is now applied at the same point on both contacting particles
-updated doc page to reflect changes above
 2019-03-11 14:28:44 -06:00
Dan S. Bolintineanu 4ee98d18da Fixed missing reference in pair_granular doc page 2019-03-06 14:15:19 -07:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Steve Plimpton f0ec2e3279 refactoring of global and local hyper, including amended doc pages 2019-03-01 18:47:34 -07:00
Axel Kohlmeyer 5486896876
Merge pull request #1350 from akohlmey/next-patch-release 
Step version string for next patch release
 2019-02-28 17:56:51 -05:00
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 50fef541c2
add x-ref 2019-02-28 15:50:59 -05:00
Axel Kohlmeyer 5fd033c0a2
add one more false positive required by recent changes 2019-02-28 15:49:48 -05:00
Axel Kohlmeyer 1d2eab5e1b
update attribution information in Package details documentation 2019-02-28 15:26:36 -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 b60f0f754c
small tweaks to USER-ADIOS docs 2019-02-27 17:18:08 -05:00
Axel Kohlmeyer 6bf9c06a5a
Step version string for next patch release 2019-02-27 16:19:20 -05:00
Axel Kohlmeyer 9185f28a12
correct compute group/group documentation for use with EAM styles 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer 9bec93faa9
update spell-checking false positives for USER-ADIOS package 2019-02-26 19:51:18 -05:00
Axel Kohlmeyer 9178b9446a
remove trailing whitespace 2019-02-26 19:50:50 -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
Axel Kohlmeyer e6df92e65a
Merge pull request #1011 from ellio167/kim-v2-update 
KIM v2 update
 2019-02-21 20:06:59 -05:00
Axel Kohlmeyer e6a7c8b03b
Merge pull request #1335 from donatas-surblys/langevin-tally-zero 
correct fix langevin with tally yes zero yes
 2019-02-21 20:06:44 -05:00
Norbert Podhorszki 3ad268739b Add dump adios to PDF build. Update example config with better documentation 2019-02-20 17:02:48 -05:00
Norbert Podhorszki 2de01cef45 Dump atom/adios and dump custom/adios command notifications 2019-02-20 16:21:07 -05:00
Norbert Podhorszki 1179beb543 Makefile build support for USER-ADIOS and build documentation 2019-02-20 14:42:28 -05:00
Dan S. Bolintineanu 4e26ca29f7 Changes to new generalized granular pair styles and fix wall/gran 
-Clean-up of unused variables in code
-Bug fix for single method of pair granular
-Changes to fix wall/gran to fix issues with JKR
-Doc page updates for fix wall/gran and fix wall/gran/region
 2019-02-19 16:47:13 -07:00
Dan S. Bolintineanu ff795e761a Added generalized granular option to fix wall/gran and fix wall/gran/region; some minor bug fixes for pair granular 2019-02-19 14:31:27 -07:00
Dan S. Bolintineanu d8e8a0d2d2 More changes to pair granular: 
- tangential damping now set by scaling the normal damping
- some fixes to the twisting coefficients for the Marshall twist model
- progress (completion?) of doc page
 2019-02-18 09:58:34 -07:00
pmla bae2e61fa0 documentation bugfix 2019-02-15 19:40:37 -05:00
pmla 8a28046b4c typo in PTM docs 2019-02-15 18:52:40 -05:00
pmla 35d2de298f added license information to all files 
updated documentation
added example file
added graphene structure
 2019-02-15 18:49:23 -05:00
Ryan S. Elliott c193a9aee9 Updated Errors_messages.txt & false_positives.txt 2019-02-14 19:28:18 -06:00
Ryan S. Elliott e95cf4e917 Some various doc updates for kim-api support 2019-02-14 13:38:28 -06:00
Ryan S. Elliott 333154633b Merge branch 'master' into kim-v2-update 2019-02-14 13:29:50 -06:00
Axel Kohlmeyer d0ed6f2bf5
reflect changes to fix langevin also in the manual 2019-02-14 05:45:52 -05:00
Axel Kohlmeyer 0108855930
update .gitignore for the doc folder 2019-02-14 02:54:02 -05:00
jrgissing d08979737c bond/react:partially_revert_bonding_atom_choice 
choose closest eligible bonding partner, unless directly bonded (in which case we assume a bond-breaking reaction)
 2019-02-13 22:56:56 -07:00
Axel Kohlmeyer 88b62fa6bd
add old style PDF build to "make old" target. 
this will create the old style Manual.pdf in the old folder and put Developer.pdf there, too.
 2019-02-13 12:43:35 -05:00
Axel Kohlmeyer 581b7d3543
update list of false positives after docs changes 2019-02-13 09:23:54 -05:00
Axel Kohlmeyer eb8a6512e2 rename and document script to automatically convert 'default(none)' to 'default(shared)' OpenMP pragmas 2019-02-12 09:44:19 -05:00
dsbolin 6ff1557af8 More progress on doc page 2019-02-12 07:42:26 -07:00
Axel Kohlmeyer a0b7bf0f5c reformat fix wall/gran/region docs 
this should make it easier to recognize that these walls can be
moving/rotating/growing/shrinking due to using time dependent
equal style variables in the region definition
 2019-02-12 08:07:28 -05:00
Dan S. Bolintineanu b7413226e0 Several changes to new consolidated granular code: 
- Normal contact models take Young's modulus and Poisson's ratio (instead of Young's and shear modulus)
- Mixing of Young's moduli corrected
- Changes to cutoffs corrected for JKR pulloff distance
- Renamed 'mindlin' to 'linear_history'
- Progress on doc page
 2019-02-11 21:37:06 -07:00
Axel Kohlmeyer b29d526632
Merge pull request #1323 from akohlmey/next-patch-release 
Patch release 8 February 2019
 2019-02-08 21:43:39 +01:00
Axel Kohlmeyer 77c24f1b79 Merge branch 'master' into next-patch-release 
# Conflicts:
#	.github/PULL_REQUEST_TEMPLATE.md
 2019-02-08 15:34:40 -05:00
Axel Kohlmeyer f286155dd3
Merge pull request #1306 from stanmoore1/kk_angle_cosine 
Add Kokkos version of angle/cosine
 2019-02-08 21:07:36 +01:00
Axel Kohlmeyer b871b4e13d
Merge pull request #1321 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch release
 2019-02-08 17:19:01 +01:00
Axel Kohlmeyer a35f407dfc Patch release 8 February 2019 2019-02-08 17:15:22 +01:00
Axel Kohlmeyer a71159578e fix typo 2019-02-08 02:29:03 -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 7c1fb847f4 Slight tweak to sed in doc/Makefile 2019-02-06 18:00:23 -08:00
efetis 4fe6528ed4 Add support for Sphinx+PDF+MathJax 2019-02-06 17:14:50 -08:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
Axel Kohlmeyer d6eaf73db1
Merge pull request #1307 from akohlmey/next-patch-release 
Patch release 1 February 2019
 2019-02-01 20:22:18 +01:00
Axel Kohlmeyer f2a977884c
Merge pull request #1290 from akohlmey/python-script-portability 
Use argparse module in for Install.py scripts in lib and further portability and consistency enhancements. Some lint removal as well.
 2019-02-01 01:18:40 +01:00
Axel Kohlmeyer a9f8b17cbd
Merge pull request #1282 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2019-02-01 00:24:15 +01:00
Axel Kohlmeyer d6a918f4fd
Merge pull request #1270 from akohlmey/get-moltemplate-from-web 
Replace bundled moltemplate distribution with installation instructions only
 2019-01-31 22:58:31 +01:00
Axel Kohlmeyer 7606529f03
Merge pull request #1302 from akohlmey/combined-user-fep-soft-updates 
Combined USER-FEP related updates
 2019-01-31 22:57:51 +01:00
Axel Kohlmeyer c5256624e8 document coul/streitz and reax/c keywords to extract qeq parameters from pair styles 2019-01-31 13:48:06 +01:00
Axel Kohlmeyer 14ab0ec459 remove references to pre-installed packages as this was changed with the 22 August 2018 version 2019-01-31 12:02:22 +01:00
Axel Kohlmeyer ef5c327f74 Merge branch 'master' into collected-small-changes 2019-01-31 11:45:15 +01:00
Axel Kohlmeyer d2846404bd update development workflow description to state of latest discussions 2019-01-31 02:55:11 -05:00
Axel Kohlmeyer ee5f39d895 Patch release 1 February 2019 2019-01-30 16:16:32 -05:00
Axel Kohlmeyer bad6c8aa35 Patch release 30 January 2019 2019-01-29 13:37:50 +01:00
Stan Moore 54b9a1335c Add Kokkos version of angle_cosine 2019-01-28 11:29:28 -07:00
Axel Kohlmeyer 21dac57c7c fix typo 2019-01-26 05:16:38 -05:00
Axel Kohlmeyer 6c72d15c31 Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates 
Resolved Conflicts:
	doc/src/Commands_pair.txt
	doc/src/pair_fep_soft.txt
	doc/src/pair_style.txt
	doc/src/pairs.txt
 2019-01-25 16:25:19 +01:00
Agilio Padua f2aab01e96 Approximation in tail correction better explained 2019-01-25 15:04:52 +01:00
Axel Kohlmeyer 272ff1dbdf link class2 soft-core pair styles from pair style overviews 2019-01-24 11:20:12 -05:00
Agilio Padua 06c8a67247 Updated broken links to pair_fep_soft 2019-01-24 17:10:39 +01:00
Axel Kohlmeyer 1e3cc7784b update false positives list for spell checking 2019-01-24 11:06:22 -05:00
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