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Merge pull request #27 from timattox/USER-DPD_kokkos_update
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Authored by Tim Mattox <timattox@users.noreply.github.com> on Aug 10 2017, 19:21.

Description

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.

Details

Committed
GitHub <noreply@github.com>Aug 10 2017, 19:21
Pushed
jungeOct 19 2017, 09:53
Parents
rLAMMPS9695aa60925d: Merge branch 'master' into USER-DPD_kokkos_testing
rLAMMPSbceaa5761426: Merge branch 'master' into USER-DPD_kokkos as of patch 31Mar17
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Reverts
rLAMMPS7f9a331c7355: bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.
CommitAuthorDetailsCommitted
9695aa60925dStan Moore
Merge branch 'master' into USER-DPD_kokkos_testing 
Jul 27 2017
6d0a2286240asjplimp/GitHub
Merge pull request #599 from lammps/kim-doc 
Jul 27 2017
934cbbbecaffSteve Plimpton
restore lost KIM doc section in Section packages 
Jul 27 2017
2806f070a40fsjplimp/GitHub
Merge pull request #598 from akohlmey/last-minute-changes 
Jul 26 2017
f7a243a4d9eeAxel Kohlmeyer
convert explicit copies back into symbolic links 
Jul 26 2017
f0d286358ea0Axel Kohlmeyer
must not include system headers within 'extern "C"' blocks. breaks with MPICH 
Jul 26 2017
51a06334ad84Axel Kohlmeyer
avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL 
Jul 26 2017
aa5ea95a0f34Axel Kohlmeyer
avoid integer overflow and remove unused function argument causing it 
Jul 26 2017
60c67b07dc37Axel Kohlmeyer
import updated fix msst file with some additional cleanup and simplification 
Jul 26 2017
bc446bb8b01bStan Moore
Merge branch 'master' into USER-DPD_kokkos_testing 
Jul 25 2017
a59b7e4d5647Steve Plimpton
patch 24Jul17 
Jul 24 2017
2eaea2d274e5sjplimp/GitHub
Merge pull request #594 from junghans/license 
Jul 24 2017
1ddace4dba51sjplimp/GitHub
Merge pull request #595 from libAtoms/idces2quip 
Jul 24 2017
af3d0ca381ddsjplimp/GitHub
Merge pull request #593 from akohlmey/collected-bug-fixes-and-small-updates 
Jul 24 2017
c24e316baaa6Axel Kohlmeyer
avoid floating point overflows in iterative solvers of fix shake 
Jul 23 2017
2c6e177d5c55Axel Kohlmeyer
avoid reporting negative memory allocation when memory_usage() is called before… 
Jul 23 2017
7b2182833feaAxel Kohlmeyer
disallow binary output with dump style local. fixes #596 
Jul 22 2017
1afab981b022Max Veit
Clarified some points in in.molecular example 
Jul 22 2017
1af937e99d71Axel Kohlmeyer/GitHub
Update in.molecular 
Jul 22 2017
4e0a249e2779Max Veit
Add a (contrived) molecular example for USER-QUIP 
Jul 22 2017
edc756a65f76Christoph Junghans
LICENSE: update address of Free Software Foundation 
Jul 22 2017
a477f26477faAxel Kohlmeyer
add support for trapping floating point exception as an optional compile time… 
Jul 21 2017
b1b399d5c3ddAxel Kohlmeyer
update readme for examples 
Jul 21 2017
00474ab09dcdAxel Kohlmeyer
handle one more case where allowing shifted potential with cutoff 0.0 would… 
Jul 21 2017
733ea61bf107Axel Kohlmeyer
correct typo in USER-REAXC code 
Jul 21 2017
5c13b087e4a1sjplimp/GitHub
Merge pull request #592 from akohlmey/reaxc-bugfix 
Jul 21 2017
ec23aef20b22Axel Kohlmeyer
fix reaxc division by zero bug also for USER-OMP variant 
Jul 21 2017
61b1487cbd93Axel Kohlmeyer
avoid division by zero in reaxff bond interaction computations in very rare… 
Jul 21 2017
e53583d9c652sjplimp/GitHub
Merge pull request #590 from lammps/fortran-dftb 
Jul 20 2017
551001f172a3Axel Kohlmeyer
revert change, that is part of the kim-install branch and changeset 
Jul 20 2017
5dbe2df85455Axel Kohlmeyer
revert change that accidentally undoes part of PRs #583 and #588 
Jul 20 2017
3f83396837easjplimp/GitHub
Merge pull request #588 from akohlmey/colvars-quickfix 
Jul 20 2017
59db5f6a1782Steve Plimpton
update of Fortran-DFTB interface to be compatible with fix msst 
Jul 20 2017
1b704bab18baAxel Kohlmeyer
Merge branch 'colvars-safer-makefiles' of https://github. 
Jul 20 2017
c98f6140e755Giacomo Fiorin
Change order of targets in Makefiles for Colvars 
Jul 20 2017
5031f5b8079cGiacomo Fiorin
Comment out use by Colvars of Makefile.lammps from other packages 
Jul 20 2017
9d0d90c03860Axel Kohlmeyer
README clarification from giacomo 
Jul 20 2017
66154e8a8b31Axel Kohlmeyer
avoid makefile failure, if LAMMPS has not been configured yet 
Jul 20 2017
3cd597e948fasjplimp/GitHub
Merge pull request #585 from akohlmey/make-py-manual-cleanup 
Jul 20 2017
eca61226c267sjplimp/GitHub
Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19 
Jul 20 2017
fac3e3daa237sjplimp/GitHub
Merge pull request #581 from libAtoms/idces2quip 
Jul 20 2017
72e5f537c8d0sjplimp/GitHub
Merge pull request #576 from akohlmey/sanitizer-changes 
Jul 20 2017
bdd2f3a6b2c7Axel Kohlmeyer
remove references to Make.py and USER-CUDA 
Jul 20 2017
a351977c5904Axel Kohlmeyer
update manual links that got broken when removing and renumbering a section 
Jul 20 2017
8499e72cdc91Axel Kohlmeyer
updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with… 
Jul 20 2017
ef9fb944c727Giacomo Fiorin
Detect number of processors for make 
Jul 20 2017
187a80be7738Giacomo Fiorin
Add forgotten decode() in Install.py 
Jul 20 2017
ee6cac826e65Giacomo Fiorin
Update Colvars to version 2017-07-15 and support automated builds for it 
Jul 19 2017
52a1c54d500eAxel Kohlmeyer
support QUIP wrapper API version query, relax hybrid restriction to allow… 
Jul 19 2017
fcf9607a6666Max Veit
Update USER_QUIP docs to clarify use of "special_bonds" 
Jul 19 2017

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