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11399 Commits

Author SHA1 Message Date
sjplimp efaa8feab5 Merge pull request #239 from akohlmey/static-analysis-fixes 
Static analysis fixes
 2016-10-25 10:32:55 -06:00
sjplimp ad5f7c4581 Merge pull request #238 from giacomofiorin/colvars-2016-10-24 
Colvars fixes and small changes
 2016-10-25 10:32:41 -06:00
sjplimp 6b33499135 Merge pull request #231 from akohlmey/collected-doc-fixes 
Collected doc fixes
 2016-10-25 10:30:34 -06:00
Axel Kohlmeyer 63eada2425 fix issue with docs for orientorder/atom compute reported by @andeplane 
this closes #243
 2016-10-25 12:12:48 -04:00
Axel Kohlmeyer 1a436bd7a9 Merge branch 'collected-doc-fixes' of github.com:akohlmey/lammps into collected-doc-fixes 2016-10-25 11:58:42 -04:00
Axel Kohlmeyer 52dd9aee5f Merge branch 'master' into collected-doc-fixes 2016-10-25 11:55:09 -04:00
Steve Plimpton eca96e21ef Merge branch 'doc' 2016-10-25 09:46:07 -06:00
Steve Plimpton 9c81ad1ab6 doc page changes 2016-10-25 09:45:55 -06:00
Axel Kohlmeyer f8367e3d0f update documentation pdf for updated colvars lib 2016-10-24 17:49:53 -04:00
Axel Kohlmeyer ba6d1528bb Merge branch 'colvars-2016-10-24' of https://github.com/giacomofiorin/lammps into colvars-update 2016-10-24 17:34:28 -04:00
Giacomo Fiorin 182141b850 Make SMP parallelism for Colvars optional 2016-10-24 17:13:34 -04:00
Axel Kohlmeyer 512c413b7e whitespace cleanup 2016-10-24 17:13:21 -04:00
Axel Kohlmeyer 7b89e47a38 apply corrections to issues reported by static code analysis 2016-10-24 17:12:28 -04:00
Giacomo Fiorin e02505c8cc Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH) 2016-10-24 17:11:09 -04:00
Giacomo Fiorin be2d155cef Minor changes and fixes not relevant to LAMMPS 2016-10-24 17:10:52 -04:00
Giacomo Fiorin c243093980 Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF 2016-10-24 17:05:47 -04:00
Giacomo Fiorin ad57a17f48 Add C-linkage wrapper for colvarscript (useful with ctypes) 2016-10-24 16:48:20 -04:00
sjplimp 477ddaf112 Merge pull request #232 from akohlmey/small-bugfixes 
Small bugfixes
 2016-10-24 08:15:08 -06:00
sjplimp 4f69d91a99 Merge pull request #230 from akohlmey/manual-in-ebook-format 
generate LAMMPS manual in ebook format
 2016-10-24 08:12:08 -06:00
Axel Kohlmeyer bc44988003 correct typo in write_dump docs 
this closes #233
 2016-10-23 15:18:25 -04:00
Axel Kohlmeyer db36c8bcc3 stop with error, if molecule command requires special bond auto-generation before box is defined 2016-10-21 14:51:09 -04:00
Axel Kohlmeyer 991034b632 have bond style table exit when bond length is outside table range 2016-10-21 14:01:06 -04:00
Axel Kohlmeyer 607246f923 ignore mobi file as well 2016-10-21 13:25:53 -04:00
Axel Kohlmeyer 6742fb634a remove mobi file format creation from makefile and explain it in README instead 2016-10-21 12:05:21 -04:00
Axel Kohlmeyer ed3f02f249 ignore generated PDF and ePUB files 2016-10-21 12:04:48 -04:00
Axel Kohlmeyer a2e34aab0a make certain, that atom->maxspecial is incremented with extra special space 2016-10-21 11:55:36 -04:00
Axel Kohlmeyer 6cd6c106ef Merge branch 'collected-small-changes' into collected-doc-fixes 2016-10-20 19:27:18 -04:00
Axel Kohlmeyer a9572275ee Revert "support generation of manual in ePUB format" 
This reverts commit 8c3f5cb307.
 2016-10-20 16:27:00 -04:00
Axel Kohlmeyer 2cf77ff778 Add support for ebook generation in ePUB and mobi format 2016-10-20 16:16:17 -04:00
Axel Kohlmeyer f022f6d88a fix various formatting and broken link issues identified by ebook-convert 2016-10-20 14:40:18 -04:00
Axel Kohlmeyer 8c3f5cb307 support generation of manual in ePUB format 2016-10-20 09:27:26 -04:00
Axel Kohlmeyer e8359923f1 update packages section in manual with information about USER-NC-DUMP 2016-10-19 15:58:50 -04:00
Steve Plimpton 9954d5d346 forgot pair table change 2016-10-19 10:47:07 -06:00
Steve Plimpton 3d254780de Merge branch 'master' of github.com:lammps/lammps 2016-10-19 08:58:22 -06:00
sjplimp b0cf1ded38 Merge pull request #229 from akohlmey/small-corrections 
collected various small corrections and updates
 2016-10-19 08:57:54 -06:00
sjplimp 0891ed83a5 Merge pull request #228 from akohlmey/correct-prd-for-bigbig 
make PRD code compatible with -DLAMMPS_BIGBIG
 2016-10-19 08:56:19 -06:00
Axel Kohlmeyer ffb8eb36da Revert "recognize any word starting with FP as FPRIME style table" 
This reverts commit 86f5b51133.
 2016-10-19 10:44:38 -04:00
Axel Kohlmeyer 1a10857244 make PRD code compatible with -DLAMMPS_BIGBIG 2016-10-19 10:43:25 -04:00
Axel Kohlmeyer 2634468676 dead code removal 2016-10-19 10:42:02 -04:00
Steve Plimpton 58141e0559 text edit 2016-10-19 08:41:44 -06:00
sjplimp 393337e7cf Merge pull request #226 from akohlmey/pair-gauss-mixing 
add mixing support for pair styles gauss and gauss/cut
 2016-10-19 08:37:32 -06:00
sjplimp e0ed218cc4 Merge pull request #224 from akohlmey/get-vars 
provide an accessor for names of LAMMPS variables
 2016-10-19 08:36:52 -06:00
sjplimp efc7b23bd8 Merge pull request #216 from akohlmey/user-nc-dump 
USER-NC-DUMP package
 2016-10-19 08:33:59 -06:00
Axel Kohlmeyer 566effc9c9 account for new fix halt properly in PDF and online docs 2016-10-19 09:08:20 -04:00
Axel Kohlmeyer 86f5b51133 recognize any word starting with FP as FPRIME style table 2016-10-19 09:05:25 -04:00
Axel Kohlmeyer ccca642b3a fix typo 2016-10-19 08:08:52 -04:00
Axel Kohlmeyer 019bc0ba0b fix typos in Makefile.lammps for NetCDF support 2016-10-19 07:39:03 -04:00
Axel Kohlmeyer 7b7cb297e6 add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data. 2016-10-18 22:26:47 -04:00
Axel Kohlmeyer 5a6dea7a22 Merge branch 'master' into user-nc-dump 2016-10-18 15:36:18 -04:00
Axel Kohlmeyer 27796b431e avoid distracting error output 2016-10-18 15:32:20 -04:00