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13694 Commits

Author SHA1 Message Date
Axel Kohlmeyer cee87d7a54 update manual to point to packages.lammps.org instead of rpm.lammps.org 2017-08-15 16:19:09 -04:00
Axel Kohlmeyer 60e14f1490 add comment to msi2lmp README about symmetry limitations 2017-08-14 08:54:26 -04:00
Axel Kohlmeyer 81e7d4a942 fix incorrect preprocessor define for windows 2017-08-12 00:35:50 -04:00
Tim Mattox 13b804eeeb Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks as of patch 10Aug17 2017-08-11 14:53:44 -04:00
Steve Plimpton 0b3f1b8a15 patch 11Aug17 2017-08-11 12:19:02 -06:00
Tim Mattox 4041db8d1a Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17 2017-08-11 13:25:28 -04:00
Steve Plimpton b209a4e246 Merge pull request #614 from akohlmey/fixes-for-stable 
Fixes for stable
 2017-08-11 08:35:20 -06:00
Axel Kohlmeyer 27553283c3 fix bug with pair_modify <style> compute not triggering the correct global change 2017-08-11 08:28:37 -04:00
Axel Kohlmeyer df56b2d6a4 trigger relink after package library build through updating the time stamp on main.cpp 2017-08-11 08:16:20 -04:00
Axel Kohlmeyer c6d923b6c8 make download function more resilient by also catching failed execution 2017-08-10 21:15:35 -04:00
Axel Kohlmeyer 6d24be8bb7 whitespace cleanup 2017-08-10 21:14:40 -04:00
Steve Plimpton 52bec0f380 patch 10Aug17 2017-08-10 16:44:09 -06:00
Axel Kohlmeyer 8c16ea1bfc add automatic triggering of review requests with a code owners file 2017-08-10 15:58:51 -04:00
Axel Kohlmeyer c8741f3a01 remove special_bonds extra keyword and refer to read_data and create_box instead 2017-08-10 15:12:56 -04:00
Axel Kohlmeyer 2a7d2dee36 add more strict checking of data when parsing molecule files to detect format errors 2017-08-10 14:49:51 -04:00
Tim Mattox 378989e065 Merge pull request #27 from timattox/USER-DPD_kokkos_update 
Merge changes thru July 27, 2017 from master 6d0a2286 into USER-DPD_kokkos

Includes 67a0183b which partially reverted 7f9a331c (from May 16, 2017) in USER-DPD,
since SSA neighbor lists use ghost info, so they can't currently be used as "occasional" lists.
 2017-08-10 13:21:53 -04:00
Steve Plimpton f68c6254d4 Merge pull request #611 from akohlmey/final-tweaks 
More tweaks for stable release
 2017-08-10 08:02:55 -06:00
Giacomo Fiorin da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Axel Kohlmeyer 146aa4cdbd fall back to wget when curl is not available 2017-08-10 09:05:23 -04:00
Axel Kohlmeyer 2f3747eb6e we need to override compiler flags in lib/voronoi/Install.py 
The default compiler flags in voro++'s config.mk file do not include
-fPIC, which makes it incompatible with building the shared object for
the python wrapper.
 2017-08-10 08:34:46 -04:00
Axel Kohlmeyer 2bc6ad80d4 avoid writable string and deprecated implicit conversion warning 2017-08-10 07:45:21 -04:00
Axel Kohlmeyer f9a515efd3 add some remarks about makefile settings on windows 2017-08-10 07:24:24 -04:00
Axel Kohlmeyer 5b55744209 fix a header line formatting issue 2017-08-10 07:21:39 -04:00
Axel Kohlmeyer 0dc3cbaa8a Revert "remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability" 
This reverts commit 4e97b57508.
 2017-08-10 06:51:57 -04:00
Axel Kohlmeyer ce62c41252 when recomputing special bonds, make certain we do not shrink atom->maxspecial and add force->special_extra only once 2017-08-10 06:47:26 -04:00
Axel Kohlmeyer 4e97b57508 remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability 2017-08-10 05:46:42 -04:00
Steve Plimpton 7f437d7690 Merge pull request #609 from akohlmey/doc-changes-for-stable 
Final tweaks and doc changes for stable release
 2017-08-09 17:37:35 -06:00
Axel Kohlmeyer 77a628e4ef make the deprecation warning nicer looking 2017-08-09 19:13:40 -04:00
Axel Kohlmeyer f01103dd08 correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda) 2017-08-09 19:08:23 -04:00
Axel Kohlmeyer 81f4d7ecb5 rework section 4 (Packages) in the manual to match Install.py scripts 2017-08-09 19:07:20 -04:00
Axel Kohlmeyer 210a77c5a0 add a deprecation warning to pair style meam and make the reax one consistent with it 2017-08-09 16:36:51 -04:00
Tim Mattox e86b139817 Merge pull request #25 from timattox/USER-DPD_GBhacks_cudafix 
Fix CUDA runtime issues for USER-DPD Kokkos code.
 2017-08-09 15:32:03 -04:00
Trung Nguyen 3e9b41c6b7 Added references to GPU package citations 2017-08-09 10:09:40 -05:00
Axel Kohlmeyer 6780c73907 restore mpic++ makefile to resolve regression test failure 2017-08-09 07:10:08 -04:00
Axel Kohlmeyer be25a7d9a4 updated comment for fix neb by steve 2017-08-08 20:37:20 -04:00
Steve Plimpton 691d1b730d Merge pull request #607 from akohlmey/final-changes-for-stable 
Final build system changes for stable release
 2017-08-08 17:26:22 -06:00
Axel Kohlmeyer 95ece8a6c0 consistently use $(PYTHON) in the master makefile (which defaults to "python") 2017-08-08 17:03:52 -04:00
Axel Kohlmeyer b7b1257b01 remove attempts to use urllib and use curl for all downloading. restore printing help with no flags. 2017-08-08 17:00:09 -04:00
Axel Kohlmeyer 30431d4edb rework Install.py for gpu library. make it consistent with other lib folders and support python3 2017-08-08 16:57:27 -04:00
Stan Moore 8a7a831bd6 Remove redundant check in Makefile.kokkos 2017-08-08 12:57:22 -06:00
Axel Kohlmeyer c53a84a967 update README file for lib/mscg 2017-08-08 13:55:12 -04:00
Axel Kohlmeyer b7b62f6893 do not pollute global namespace by including mscg header in fix header 2017-08-08 13:20:25 -04:00
Axel Kohlmeyer d2b0c287d2 add local makefile overrides to be compatible with standard suffixes 2017-08-08 13:19:44 -04:00
Axel Kohlmeyer b3244f9c98 more lib compilation updates 2017-08-08 07:20:33 -04:00
Axel Kohlmeyer 8bba29d91e more lib installation cleanup 2017-08-07 17:21:45 -04:00
Axel Kohlmeyer 135b1650f1 revamp of library builds 
- remove cross compiler stuff
- make use of Install.py consistent
- provide options for Makefile.serial and Makefile.mpi that match those in src
 2017-08-07 17:13:01 -04:00
Steve Plimpton 0a54c34e34 Merge pull request #600 from akohlmey/install-and-docs-reviewed 
Installation scripts and docs reviewed for release
 2017-08-07 08:02:04 -06:00
Steve Plimpton a8f6a95cba Merge pull request #605 from rbberger/bash_on_windows 
Adds tutorial for using LAMMPS in Bash on Windows
 2017-08-07 08:00:56 -06:00
Richard Berger e0f9a7c34c Adds BOW tutorial link in main menu 2017-08-07 00:06:53 -04:00
Richard Berger aaf17bde3f Added tutorial for using LAMMPS in Bash on Windows 2017-08-07 00:06:12 -04:00