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5253 Commits

Author SHA1 Message Date
jrgissing e133c60ff5 bond/react docs: better English 2019-05-26 20:28:28 -06:00
jrgissing 97be57be7b additional topology overflow check for reactions 2019-05-26 15:53:49 -06:00
Vishnu V. Krishnan c2a200fe85
A function logfreq3(), for logarithmical spacing 
Unlike logfreq(), this also allows for fractional ratios
Resolves #1471
 2019-05-26 14:00:21 +05:30
Axel Kohlmeyer e82e1c695a
correct links in package documentation 2019-05-24 19:45:48 -04:00
Axel Kohlmeyer cfad0634ac
Merge pull request #1465 from akohlmey/collected-minor-changes 
Collected small changes and bugfixes
 2019-05-21 16:55:19 -04:00
Stan Moore 0ee1daa46d Add Lenz to false-positive list 2019-05-21 10:24:24 -06:00
Stan Moore 95ab056576 Add PPPM dipole reference 2019-05-21 10:07:41 -06:00
julient31 82b50706bd Commit2 JT 052019 
- some corrections in the examples
- deleted an old doc files (now redundant)
 2019-05-20 22:09:59 -06:00
julient31 5f2f7d1575 Merge branch 'pppm_spin' of github.com:julient31/lammps into pppm_spin 2019-05-20 21:35:52 -06:00
julient31 3e60ec9be1 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 2019-05-20 21:35:16 -06:00
Axel Kohlmeyer d0c6484fb0
add false positive 2019-05-20 15:15:51 -04:00
Axel Kohlmeyer 0349e9fee9
update/correct list of example folders 2019-05-20 15:08:33 -04:00
Axel Kohlmeyer 55116db8fb
avoid segfault and print more meaningful error message with empty lines in coeff sections 2019-05-20 14:15:04 -04:00
Axel Kohlmeyer 50082c287d
sphinxcontrib-spelling has been updated for Sphinx 2.x. remove enforcing to use old version 2019-05-18 15:41:38 -04:00
Axel Kohlmeyer e3823a521c
remove leftover references to removed MEAM package 2019-05-18 15:36:13 -04:00
Axel Kohlmeyer dc8b43a95f
update docs and sources and for changes in this branch 2019-05-18 15:16:10 -04:00
Axel Kohlmeyer 35bb2ac2a3
fix typo 2019-05-18 09:25:20 -04:00
julient31 fbb78e7b78 Commit JT 051719 
- removed qsymp pair style
- cleaned doc (pair/spin/diole and kspace_style)
- cleaned kspace .cpp/h files
 2019-05-17 15:04:14 -06:00
Stan Moore e2ed9330b7 Merge branch 'master' into team_opt 2019-05-16 12:31:26 -06:00
Axel Kohlmeyer fb8d31422d
fix typo 2019-05-16 09:06:17 -04:00
Axel Kohlmeyer 27a2d0cbd4
add option to restrict coordination number by group 2019-05-16 08:55:03 -04:00
julient31 0c0b106924 Commit2 JT 051519 
- started doc pair_spin_dipole.txt
- renamed all pair/spin/dipole
- created and tested example pair/spin/dipole/cut
 2019-05-15 20:49:05 -06:00
Axel Kohlmeyer 267782d689
Merge pull request #1459 from akohlmey/next-patch-release 
Step version string for next patch release
 2019-05-14 21:30:28 -04:00
julient31 fd168068a1 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 
Conflicts:
	src/SPIN/fix_nve_spin.h
 2019-05-14 17:41:58 -06:00
Axel Kohlmeyer f2b293d93b
Merge pull request #1460 from akohlmey/collected-small-changes 
Some more small changes
 2019-05-14 17:55:36 -04:00
Axel Kohlmeyer 6e842ba84a
fix typo 2019-05-14 17:36:26 -04:00
Axel Kohlmeyer 30dc7f70b5
correct repeated words in docs 2019-05-14 17:13:46 -04:00
Steve Plimpton 67532684f9 add missing formatting info 2019-05-14 14:02:54 -06:00
Axel Kohlmeyer 091dbfa265
Merge pull request #1457 from julient31/fix_cubic_aniso 
Adding a cubic anisotropy in the SPIN package, documentation corrections
 2019-05-14 15:08:21 -04:00
Axel Kohlmeyer d8fb17e2cb
Step version string for next patch release 2019-05-14 10:01:43 -04:00
Axel Kohlmeyer 322c244bec
Merge pull request #1456 from akohlmey/fix-mapping-for-KC-etc 
Fix element mapping and a few other issues for interlayer potentials
 2019-05-13 21:12:58 -04:00
Axel Kohlmeyer 52e3aeab33
revert incorrect changes in commands_list.txt 2019-05-13 21:05:26 -04:00
julient31 8e18f2bf7e Commit2 JT 051319 
- corrected doc issues
 2019-05-13 17:32:44 -06:00
julient31 11f223416c Commit JT 051319 
- added a cubic anisotropy in fix_precession_spin
- added associated doc and examples
- corrected neb/spin commands in doc/src/
- added tools/spin/ description
 2019-05-13 16:59:39 -06:00
Steven Strong 805cc18b2d
Merge branch 'master' into e3b 2019-05-12 22:22:31 -05:00
Axel Kohlmeyer c581e9349a
update interlayer potential examples for now requiring CH.rebo potential file with rebo pair style 2019-05-11 16:46:21 -04:00
Axel Kohlmeyer a7c9560dc1
Merge pull request #1453 from mjwen/pair_drip 
add pair style drip
 2019-05-10 20:44:28 -04:00
Steve Plimpton 2bc089db27 mis-labeling of some rigid fixes 2019-05-10 07:42:11 -06:00
Axel Kohlmeyer 47cf17e5c8
Merge branch 'master' into pair_drip 2019-05-09 12:19:41 -04:00
Axel Kohlmeyer 928600a878
Merge pull request #1452 from akohlmey/github-rebo-bugfix 
Resubmission of REBO bugfix for easier review
 2019-05-09 12:18:05 -04:00
Axel Kohlmeyer 7b2d526f86
Merge pull request #1448 from akohlmey/collected-small-changes 
Collected small changes and bugfixes
 2019-05-09 12:17:19 -04:00
Axel Kohlmeyer 0034473e66
update legacy pdf manual input config 2019-05-08 10:19:21 -04:00
Steven Strong da75fc3eaa incorporate compute_pe_e3b into compute_pair 2019-05-08 09:05:09 -05:00
Axel Kohlmeyer 711cd4122f
corrections to documentation and implementation of pair styles lj/mdf, buck/mdf, and lennard/mdf 2019-05-07 19:52:00 -04:00
Axel Kohlmeyer 45e6ed018e
correct formula for lennard/mdf potential 2019-05-07 19:45:13 -04:00
Axel Kohlmeyer 12f8834b80
correction of the incomplete implementation warning in write_coeff 2019-05-07 19:26:57 -04:00
Axel Kohlmeyer a87d8e124f
Merge pull request #1449 from akohlmey/fix-print-w-variable-step 
Support using a variable instead of a constant interval for fix print
 2019-05-06 12:10:42 -04:00
Axel Kohlmeyer cc30688137
Merge pull request #1364 from stanmoore1/kk_binsize 
Change defaults for KOKKOS package
 2019-05-06 12:10:08 -04:00
Axel Kohlmeyer b3f4e2055e
Merge pull request #1438 from giacomofiorin/colvars-update 
Update Colvars library to version 2019-04-26
 2019-05-06 12:08:50 -04:00
Mingjian Wen f163d7dc9b typo fix 2019-05-05 08:56:15 -05:00
Axel Kohlmeyer 4d4219ca3e
integrate drip pair style more closely into manual 2019-05-05 08:59:03 -04:00
Axel Kohlmeyer d86a7b95de
fix spelling issues 2019-05-05 08:48:27 -04:00
Mingjian Wen 24e41bc085 Update doc and examples due to the change of parameters 2019-05-04 22:24:05 -05:00
Axel Kohlmeyer fd3eade6d2
update reference date and examples for changes in REBO 2019-05-04 20:42:36 -04:00
Axel Kohlmeyer c2b2be5d6f
Merge branch 'master' into github-rebo-bugfix 2019-05-04 19:09:52 -04:00
Axel Kohlmeyer a70f9c4f95
support using a variable instead of a constant interval for fix print 2019-05-04 13:47:57 -04:00
Axel Kohlmeyer 4f3c87f8c4
Merge pull request #1423 from akohlmey/next-patch-release 
Step version string for next patch release
 2019-04-30 19:52:35 -04:00
Giacomo Fiorin 7e00acce53 Update Colvars library to version 2019-04-26 
The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
 2019-04-30 13:46:37 -04:00
Axel Kohlmeyer 8d9697dbf6
Merge pull request #1420 from dsbolin/gran_mods 
Updates and bugfixes to GRANULAR package
 2019-04-29 14:16:25 -04:00
Axel Kohlmeyer f052509015
Merge pull request #1421 from julient31/gneb_spin 
Adding a GNEB implementation in the SPIN package
 2019-04-29 14:14:58 -04:00
Axel Kohlmeyer af8a71b1ad
while space and source formatting cleanup 2019-04-29 09:17:29 -04:00
Axel Kohlmeyer 21d0a16b6f
minor tweak 2019-04-25 18:06:09 -04:00
Axel Kohlmeyer a9388e86e3
add one more false positive 2019-04-25 18:00:27 -04:00
Axel Kohlmeyer 80af0281d1
replace non-ASCII characters 2019-04-25 17:54:27 -04:00
Axel Kohlmeyer 8882436078
add e3b styles to legacy documentation build 2019-04-25 17:49:35 -04:00
Axel Kohlmeyer 8d9a44a837
set april 30th for next patch release 2019-04-25 16:55:46 -04:00
julient31 16fd5904ed Commit2 JT 042519 
- slight correction in doc/src/command_list.txt
 2019-04-25 09:31:57 -06:00
julient31 7c3f619e13 Commit JT 042519 
- moved examples/SPIN/gneb/interpolate/ toward
tools/spin/interpolate/gneb
- added gneb in the command files in doc/src
- modified the error messages in neb_spin.h/cpp
 2019-04-25 09:18:33 -06:00
Steven Strong 47d4aa6803 add new false positives 2019-04-24 17:35:17 -05:00
Steven Strong f548e2717e add new false positives 2019-04-24 17:31:44 -05:00
julient31 a696b26301 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 
Conflicts:
	src/SPIN/pair_spin_exchange.cpp
	src/atom.cpp
	src/pair.cpp
 2019-04-19 15:02:25 -06:00
Mingjian Wen c6d0f7ca87 Update equations 2019-04-19 14:27:03 -05:00
Mingjian Wen d3c5d7e423 Add documentation 2019-04-19 13:56:26 -05:00
Steven Strong dec1ad19b5 added e3b.jpg 2019-04-19 10:33:51 -05:00
Steven Strong 0eebb31903 update contact info 2019-04-16 11:48:45 -05:00
Steven Strong 69e7a2a237 add e3b water model 2019-04-16 11:32:47 -05:00
Dan S. Bolintineanu 0b24a3d830 Added a 'mass_velocity' damping option to the new granular pair styles and granular wall interaction. 
This is to more closely match the old style pair gran/hooke/* damping behavior.
Updated doc page accordingly, as well as adding some examples on how to match old pair gran/* styles.
 2019-04-15 16:14:02 -06:00
Dan S. Bolintineanu 14d3d09de3 Fixed several errors in granular doc pages, particularly coefficients in examples 2019-04-13 23:36:40 -06:00
julient31 5e3929de56 Commit2 JT 041019 
- correct spelling in Howto_spin.txt
 2019-04-10 13:35:58 -06:00
julient31 70c816aa02 Commit JT 041019 
- corrected setforce/spin
- added an example
- added the documentation (in setforce)
- updated the Howto_spin documentation
 2019-04-10 13:18:33 -06:00
Stan Moore 073f003470 Doc tweak 2019-04-09 15:17:40 -06:00
Stan Moore 82be3ee32c Only use team with full neigh list 2019-04-09 09:17:07 -06:00
Stan Moore 16b17f812c Update docs 2019-04-09 08:51:24 -06:00
Axel Kohlmeyer 915c3a6001
step version number for next patch release 2019-04-09 03:06:04 -04:00
Stan Moore c11b1edc1f Avoid spell checker error 2019-04-08 16:35:36 -06:00
Axel Kohlmeyer db74f14f33
Merge branch 'master' into report-uninstalled-pkg-style 
# Conflicts:
#	cmake/CMakeLists.txt
 2019-04-08 17:16:30 -04:00
julient31 b8ae466999 Commit4 JT 040819 
- added unknown names/acronyms in doc/utils/sphinx-config/false_positives.txt
 2019-04-08 14:00:49 -06:00
Stan Moore fbda72891c Fix spelling error 2019-04-08 13:41:33 -06:00
Stan Moore ece46dbfa5 Small tweak to Kokkos docs 2019-04-08 13:12:21 -06:00
Stan Moore 2bb69773d3 Update Kokkos docs 2019-04-08 13:07:29 -06:00
Stan Moore aa336c2bb4 Merge branch 'master' into kk_binsize 2019-04-08 12:07:58 -06:00
julient31 814b9b9378 Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 2019-04-08 11:26:48 -06:00
julient31 57247142d2 Commit2 JT 040819 
- finished doc (compiled and spell check)
- compiled with -Wall -Wextra, unused var. removed
 2019-04-08 11:08:06 -06:00
julient31 fcb4b75589 Commit JT 040819 
- improved documentation neb/spin
 2019-04-08 07:24:18 -06:00
Axel Kohlmeyer f2113ab04a
update manual and headers for updated error message 2019-04-08 07:16:22 -04:00
Axel Kohlmeyer cb559659f8
write a full-fledged LAMMPS manpage. 2019-04-07 10:35:00 -04:00
Axel Kohlmeyer 5c5b57be5a
minor tweaks 2019-04-07 10:34:25 -04:00
Axel Kohlmeyer e57c4c60bd
fix spelling issue 2019-04-07 05:59:28 -04:00
Axel Kohlmeyer 6f7b3643ef
document clang/clang++ preset with settings for MPI and OpenMP 2019-04-07 00:46:43 -04:00
Axel Kohlmeyer b40c4d1641
update version number and some reformatting of the LAMMPS manpage 2019-04-06 23:45:01 -04:00