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4364 Commits

Author SHA1 Message Date
Giacomo Fiorin 0c005f5cb0 Small fixes to Colvars library 
Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
 2018-05-02 15:03:56 -04:00
Michael DeLyser efbee4a292
Delete man_fix_bocs.html 2018-05-02 11:27:31 -04:00
Axel Kohlmeyer 25ac1fd16c mention that fix reax/bonds and reax/c/bonds do not honor the group id 2018-05-01 18:55:00 -04:00
MICHAEL ROBERT DELYSER c5e884fb41 USER-BOCS 2018-04-26 09:34:47 -04:00
Steven J. Plimpton d5ec76290b patch 20Apr18 2018-04-20 17:22:38 -06:00
jrgissing 91b407570a docfix 
remove mention of as yet unreleased feature
 2018-04-19 20:23:58 -06:00
Steve Plimpton 48e42a4e1e
Merge pull request #824 from jrgissing/write_data-noextra 
Write_data nofix option
 2018-04-13 10:27:21 -06:00
Axel Kohlmeyer 398f3173aa remove trailing whitespace 2018-04-13 11:38:02 -04:00
Axel Kohlmeyer 798fcacd77 update example for API change in Fix::copy_arrays() 2018-04-13 11:37:51 -04:00
Steven J. Plimpton bc0fd5496a add info to compute heat/flux doc page 2018-04-13 08:57:24 -06:00
jrgissing 6e31b7da63 doc typos 2018-04-11 22:06:22 -06:00
Axel Kohlmeyer 12bc84163d remove or reformulate references to USER-CUDA package, which no longer exists 2018-04-04 11:06:20 -04:00
Steven J. Plimpton 7786cb5a4b patch 30Mar18 2018-03-30 15:21:55 -06:00
Steve Plimpton a19e8fb269
Merge branch 'master' into resetids 2018-03-30 09:15:24 -06:00
Steve Plimpton 81caeffb38
Merge pull request #855 from lammps/dumpinc 
new dump_modify refresh and compute displace/atom refresh commands fo…
 2018-03-30 09:07:19 -06:00
Axel Kohlmeyer a4795df5f9 complete integration of reset_ids into the documentation build system 2018-03-30 10:49:38 -04:00
Axel Kohlmeyer ef8423918a
fix typo 2018-03-29 17:04:53 -04:00
Steven J. Plimpton 09313cf3b5 shift files into doc/src 2018-03-28 13:35:13 -06:00
Steven J. Plimpton 5fd17670b1 new reset_ids command and dump_modify delay option 2018-03-28 11:31:35 -06:00
Steve Plimpton a524d8c193
Merge pull request #854 from lammps/readdump 
new option *add keep* added to read_dump
 2018-03-27 14:39:35 -06:00
Steve Plimpton b571f5423a
Merge pull request #850 from lammps/addlib 
a few new lib interface methods
 2018-03-27 14:39:16 -06:00
Steven J. Plimpton 2aef3a0e96 new dump_modify refresh and compute displace/atom refresh commands for incremental dump files 2018-03-27 14:37:04 -06:00
Steven J. Plimpton e8b8428f6b new option *add keep* added to read_dump 2018-03-27 10:08:58 -06:00
Steven J. Plimpton 1956d93af9 doc tweak on added lib functions 2018-03-27 09:58:53 -06:00
Axel Kohlmeyer f38169f19c do not capitalize library.cpp, even if it is at the beginning of a sentence 2018-03-23 16:08:40 -04:00
Steve Plimpton 5770a59ead
Merge pull request #846 from akohlmey/pdf-manual-reorg 
Refactor PDF Manual Structure
 2018-03-23 13:40:35 -06:00
Steve Plimpton 318877ada3
Merge pull request #839 from oywg11/master 
New registry dependent interlayer potential in LAMMPS
 2018-03-23 13:38:48 -06:00
Steven J. Plimpton d14c16a47c a few new lib interface methods 2018-03-23 13:34:22 -06:00
Axel Kohlmeyer 5a341bee09 minor cleanup in docs and updated log files for kolmogorov/crespi/full 2018-03-23 06:42:04 -04:00
oywg11 78e09e1854 refine the code and documentation 2018-03-23 13:26:40 +03:00
Axel Kohlmeyer 04c968362f fix up and integrate documentation for contributed pair styles 2018-03-22 18:20:19 -04:00
Axel Kohlmeyer 1a402d4002 refactor headline levels to result in a more structured PDF manual 2018-03-20 15:42:13 -04:00
Steven J. Plimpton f6c76e04b8 patch 16Mar18 2018-03-19 08:26:58 -06:00
oywg11 6415befb5b Add more examples 2018-03-14 16:30:54 +02:00
oywg11 375cf6124f Finally updated the github tutorial 2018-03-13 17:27:23 +02:00
Steven J. Plimpton 0c4c002f34 patch 8Mar18 2018-03-08 08:19:46 -07:00
Steven J. Plimpton 070e85b44b add restartinfo=0 to manbody file it was missing from 2018-03-06 12:45:40 -07:00
Axel Kohlmeyer 64779eb576 documentation update for MEAM to clarify the I,J,K indices in the MEAM parameter file 2018-03-06 13:21:34 -05:00
Axel Kohlmeyer 959883ad03
rename noextra option to nofix 
since this corresponds to the `fix` option of `read_data`, calling this flag `nofix` seems more consistent and descriptive.
 2018-03-04 09:49:50 -05:00
jrgissing a323147819 noextra option for write_data 2018-03-03 14:28:35 -07:00
Steve Plimpton 22b6764304
Merge pull request #819 from stanmoore1/package_installed 
Add make package-installed command
 2018-03-02 14:40:36 -07:00
Steve Plimpton 812a45451a
Merge pull request #816 from giacomofiorin/colvars-update-2018-02-23 
Collected fixes and updates to Colvars library
 2018-03-02 13:15:56 -07:00
Stan Moore 8d0fdb17a6 Add make package-installed command 2018-03-01 10:39:06 -07:00
Jacob Gissinger 3b90f60064
Merge pull request #3 from lammps/master 
rebase
 2018-02-24 23:49:27 -07:00
jrgissing 7d1de34533 gatherv fix, doc updates 2018-02-24 22:49:28 -07:00
Axel Kohlmeyer bba4bd1489 support offsets for molecule IDs (if available) in read_data similar to atomIDs 
suggested by felipe perez in https://sourceforge.net/p/lammps/mailman/message/36236631/
 2018-02-23 18:02:05 -05:00
Giacomo Fiorin f3cf407a21 Collected fixes and updates to Colvars library 
This commit includes several fixes to moving restraints; also added is support
for runtime integration of 2D and 3D PMFs from ABF.

Mostly changes to existing member functions, with few additions in classes not
directly accessible by LAMMPS.  Also removed are calls to std::pow(), replaced
by a copy of MathSpecial::powint().

Relevant commits in Colvars repository:

7307b5c 2017-12-14 Doc improvements [Giacomo Fiorin]
7f86f37 2017-12-14 Allow K-changing restraints computing accumulated work; fix staged-k TI estimator [Giacomo Fiorin]
7c1c175 2017-12-14 Fix 1D ABF trying to do pABF [Jérôme Hénin]
b94aa7e 2017-11-16 Unify PMF output for 1D, 2D and 3D in ABF [Jérôme Hénin]
771a88f 2017-11-15 Poisson integration for all BC in 2d and 3d [Jérôme Hénin]
6af4d60 2017-12-01 Print message when issuing cv delete in VMD [Giacomo Fiorin]
4413972 2017-11-30 Check for homogeneous colvar to set it periodic [Jérôme Hénin]
95fe4b2 2017-11-06 Allow abf_integrate to start in bin with 1 sample [Jérôme Hénin]
06eea27 2017-10-23 Shorten a few constructs by using the power function [Giacomo Fiorin]
3165dfb 2017-10-20 Move includes of colvarproxy.h from headers to files [Giacomo Fiorin]
32a867b 2017-10-20 Add optimized powint function from LAMMPS headers [Giacomo Fiorin]
3ad070a 2017-10-20 Remove some unused includes, isolate calls to std::pow() [Giacomo Fiorin]
0aaf540 2017-10-20 Replace all calls to std::pow() where the exponent is not an integer [Giacomo Fiorin]
 2018-02-23 08:34:53 -05:00
Steven J. Plimpton bfdf464ee3 patch 22Feb18 2018-02-22 08:46:03 -07:00
Steve Plimpton aa1503b7e0
Merge pull request #800 from athomps/fix_gcmc_segfault_fix 
Added warning to discourage use of group all and fixed some segfault …
 2018-02-21 09:50:22 -07:00
Steve Plimpton a3cd600052
Merge pull request #786 from jrgissing/per_atom_prop_group 
per-atom property dynamic group
 2018-02-21 09:48:49 -07:00
Axel Kohlmeyer 38ce56f252 fix documentation issues: non-ASCII characters, broken/missing links, formatting 2018-02-21 11:53:18 +01:00
Steven J. Plimpton c399b75dec 2nd try on LATTE error returns, plus a couple minor doc edits 2018-02-20 12:52:12 -07:00
Steve Plimpton 9cf99ef479
Merge pull request #806 from vishalkenchan/new_pair_lj_cut_coul_wolf 
Lennard-Jones with Coulomb interactions accounted through Wolf sum
 2018-02-20 11:55:37 -07:00
Axel Kohlmeyer 7ec4a5818d add USER-OMP versions of lj/cut/coul/wolf 2018-02-18 16:38:50 +01:00
Axel Kohlmeyer 65870843a5 fix typo in stride2() description in variable command docs reported by Jerome Guterl 2018-02-18 15:37:35 +01:00
vishalkenchan c864e55adb Lennard-Jones potential with Coulomb interactions accounted through Wolf summations 2018-02-18 14:20:59 +01:00
Axel Kohlmeyer 3d12cff8a5 Merge branch 'patch-1' of https://github.com/evoyiatzis/lammps into collected-small-changes 2018-02-16 10:55:25 +01:00
Axel Kohlmeyer a30ede80a6 avoid triggering misformatting of manual overview table with txt2html 2018-02-15 12:12:19 +01:00
Axel Kohlmeyer 2aa693c46c update authors list and packages from http://lammps.sandia.gov/authors.html 2018-02-15 05:06:54 -05:00
Axel Kohlmeyer 69f813b22e fix up formatting of tutorials for PDF manual 2018-02-13 16:41:23 +01:00
Axel Kohlmeyer b3693f891b different style of AtC page headers that works well with html and pdf 2018-02-13 16:40:50 +01:00
Axel Kohlmeyer 1a213363f1 add group style to create an empty group directly 2018-02-13 14:54:30 +01:00
Axel Kohlmeyer 63714c7079 remove PDF-only .txt file from Sphinx documentation processing 2018-02-13 13:10:20 +01:00
Axel Kohlmeyer 60f411d655 update manual content list for recent updates 2018-02-13 12:47:36 +01:00
Axel Kohlmeyer 7b551bb594 add a short command overview page for the PDF manual only 2018-02-13 12:47:05 +01:00
Axel Kohlmeyer b0d8fb2170 promote header levels for better formatting in pdf manual 2018-02-13 12:43:56 +01:00
Axel Kohlmeyer 44faa8e9f5 insert new toplevel text into USER-ATC docs, change header levels. 2018-02-13 12:43:32 +01:00
Axel Kohlmeyer 3ceec36b84 improve format 2018-02-13 12:38:48 +01:00
Axel Kohlmeyer f890cdfb9e correct formatting in fix atc docs 2018-02-13 11:44:07 +01:00
Axel Kohlmeyer 3a909e15ae remove non-functional doxygen generated navigation header from AtC doc files 2018-02-13 11:43:52 +01:00
jrgissing a04a975d3a add large nylon example for parallel validation, reformat doc page 2018-02-11 17:35:47 -07:00
Steven J. Plimpton 7e78738c73 patch 5Feb18 2018-02-09 14:26:21 -07:00
Axel Kohlmeyer 3528f9ca27 fix bugs in documentation and implementation of atom style mdpd 2018-02-09 15:19:01 +01:00
jrgissing 996c62f4e0 fix bond/react: generalized classical chemical reactions 2018-02-07 21:58:05 -07:00
Axel Kohlmeyer 49745968f2 make link unambiguous so sphinx is not confused 2018-02-06 16:57:27 +01:00
Aidan Thompson 1d403b2aa3 Added warning to discourage use of group all and fixed some segfault cases 2018-02-05 13:29:14 -07:00
Steve Plimpton 401bfc52e1
Merge pull request #798 from akohlmey/always-use-internal-xdr 
Replace OS provided XDR support with bundled code
 2018-02-02 14:47:40 -07:00
Steve Plimpton 7441b062e9
Merge pull request #792 from pastewka/18_dump_nc1 
Dumping to multiple files failed with an error message complaining about a missing 'append yes' option.
 2018-02-02 14:45:52 -07:00
Steve Plimpton 10d80ba9c3
Merge pull request #791 from akohlmey/charmm-cmap-docs-reference 
Update CMAP related docs and rebuild example input decks
 2018-02-02 14:44:58 -07:00
Steve Plimpton e4a1826dee
Merge pull request #783 from numericalfreedom/lammps-doxygen 
Added double quotes to a word in Section_tools.txt file
 2018-02-02 14:41:56 -07:00
Steve Plimpton 160edc9532
Merge pull request #782 from hheenen/user-mofff-contribution 
User mofff contribution
 2018-02-02 14:41:28 -07:00
Steve Plimpton 553b3ff69a
Merge pull request #778 from athomps/fix_gcmc_segfault_fix 
Fixed recent segfault in fix gcmc and added mcmoves keyword
 2018-02-02 14:40:14 -07:00
Steve Plimpton 4af14becb5
Merge pull request #710 from rpleite/add-pair-ufm 
Add the UFM pair potential - (GPU/OPT/OMP)
 2018-02-02 14:38:28 -07:00
Axel Kohlmeyer 85fdf9eaba make links to papers unique across files 2018-02-02 10:10:27 +01:00
Axel Kohlmeyer 2ff278defa fully integrate ufm into documentation 2018-02-02 10:02:44 +01:00
Axel Kohlmeyer c3d1cee5f9 try to use OS-provided (and obsoleted) RPC headers for XDR. always use bundled code 2018-02-02 09:23:02 +01:00
Axel Kohlmeyer b70149e86a include added docpages in toctrees for sphinx 2018-02-01 18:50:25 +01:00
Axel Kohlmeyer 080ce422ae correct incorrect reference 2018-02-01 18:40:28 +01:00
Axel Kohlmeyer cc54848f7b adapt to current manual conventions 2018-02-01 18:40:17 +01:00
Lars Pastewka 9cf4ac8b7c DOC: Added netcdf and netcdf/mpiio to dump style supporting atom attributes. 2018-01-28 14:24:28 +01:00
Axel Kohlmeyer cf8dae5ef3 explain position of fix cmap command in input for data and restart files 2018-01-28 06:20:03 -05:00
Axel Kohlmeyer ba68548e38 clarify ch2lmp commands purpose in tools section 2018-01-28 06:19:33 -05:00
jrgissing 13c08225ed per-atom property dynamic group 2018-01-23 00:16:51 -07:00
Dr. Nandor Tamaskovics e72faf3d7f Added double quotes to a word in Section_tools.txt file in order to activate 
Sphinx hyperlink.
 2018-01-21 20:55:04 +01:00
Hendrik Heenen f7e2bf239f Added MOF-FF src, doc and example files 2018-01-21 11:40:48 +01:00
Aidan Thompson 9bb7f1ddf6 Fixed recent segfault in fix gcmc and added mcmoves keyword 2018-01-17 13:45:15 -07:00
Steven J Plimpton 5e9d257ec2 patch 17Jan18 2018-01-17 13:00:48 -07:00
Axel Kohlmeyer 1b91c0eab0 fix typo in docs resulting in broken link 2018-01-16 21:01:25 -05:00
Dr. Nandor Tamaskovics f2c0c4a7d1 Merge branch 'lammps-tools-doxygen' of https://github.com/numericalfreedom/lammps into lammps-tools-doxygen 2018-01-16 18:39:08 +01:00
Steve Plimpton e07a6d1e34
Merge pull request #768 from akohlmey/collected-doc-fixes 
collected documentation fixes
 2018-01-16 09:03:45 -07:00