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14378 Commits

Author SHA1 Message Date
Steve Plimpton e798cdf31f
Merge pull request #771 from stanmoore1/reax_example 
Add ReaxFF Example
 2018-01-16 09:05:36 -07:00
Steve Plimpton 97dd812647
Merge pull request #769 from rbberger/cmake_compilation_fixes 
CMake compilation fixes
 2018-01-16 09:04:04 -07:00
Steve Plimpton e07a6d1e34
Merge pull request #768 from akohlmey/collected-doc-fixes 
collected documentation fixes
 2018-01-16 09:03:45 -07:00
Steve Plimpton 6e37272c9d
Merge pull request #764 from akohlmey/improved-variable-error-reporting 
Improved error messages when defining or evaluating variables
 2018-01-16 09:02:20 -07:00
Steve Plimpton 6bd6e62767
Merge pull request #763 from stanmoore1/kk_neighlist 
Enhance Kokkos Neighbor lists
 2018-01-16 09:01:15 -07:00
Steve Plimpton 57dd6c78c1
Merge pull request #761 from stanmoore1/kk_snap 
Kokkos version of Pair SNAP and ZBL
 2018-01-16 09:00:52 -07:00
Steve Plimpton 9e413bf57a
Merge pull request #760 from akohlmey/info-coeffs 
New "coeffs" keyword added to "info" command
 2018-01-16 09:00:34 -07:00
Stan Moore b374813104 Add reax example 2018-01-16 08:50:30 -07:00
Michael Brown 07ddb5e62c USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2018u1 compilers. 2018-01-15 23:54:48 -08:00
Stan Moore 72b479d42e Add missing return value in pair_snap_kokkos 2018-01-15 11:01:07 -07:00
Axel Kohlmeyer c8b5d83cc7 mention tool/doxygen folder in tools section and refer to README file 2018-01-15 10:43:30 -05:00
smoore a5998179bf Fix issues with Kokkos skip lists 2018-01-15 08:23:39 -07:00
Dr. Nandor Tamaskovics 26d6f6d1f1 Tools for LAMMPS documentation with the "doxygen" documentation platform 
are provided.

        New directory: tools/doxygen

        New file:      tools/doxygen/Developer.dox.lammps
        New file:      tools/doxygen/Doxyfile.lammps
        New file:      tools/doxygen/doxygen.sh
        New file:      tools/doxygen/README

The Developer.dox.lammps file contains a slightly revised version of the
Developer.pdf file adopted to the LAMMPS "doxygen" documentation.

The Doxyfile.lammps file is a first proposal for a LAMMPS "doxygen"
documentation flavor and can be adjusted to specific requirements.

The "doxygen.sh" shell script generates the LAMMPS "doxygen"
documentation.

Detailed instructions can be found in the README file.
 2018-01-15 15:42:31 +01:00
Axel Kohlmeyer f37f4f0041 support more cases where the variable name is reported on errors 2018-01-14 17:56:03 -05:00
Richard Berger d2983caad4 CMake: limit visibility of COLVARS lepton library headers 2018-01-14 18:01:19 +01:00
Richard Berger 2b7c233791 Simplify change to CMake build for USER-COLVARS 2018-01-14 08:44:50 +01:00
smoore 9e35e76b8c Fix issues in Kokkos npair_halffull and npair_skip 2018-01-13 21:32:59 -07:00
smoore 7a78875911 Fix issues in Kokkos pair snap and zbl 2018-01-13 21:31:11 -07:00
Richard Berger 1cfc3118cc CMake: remove BUILD_SHARED_LIBS requirement from PYTHON package 2018-01-13 22:17:23 +01:00
Richard Berger 23e8fb0542 Update CMake build for USER-COLVARS 2018-01-13 21:57:24 +01:00
Richard Berger 72eb2dab52 Add missing math.h header 2018-01-13 20:41:05 +01:00
Stan Moore f6075c9d2c One last tweak to npair_halffull_newtoff.cpp 2018-01-12 16:12:57 -07:00
Stan Moore 24f1889b02 Only include ghosts for newton off, since this style exists as a standalone build, but the newton on method doesn't 2018-01-12 16:10:42 -07:00
Stan Moore dea8d592da Optimize npair_halffull styles; the number of i atoms, whether owned or ghost, must match between the child half list and parent full list 2018-01-12 15:51:54 -07:00
Stan Moore 52d3e98f3b Fix issue in npair_skip_kokkos 2018-01-12 15:45:24 -07:00
Stan Moore 6e3acce3be Relax restriction in neighbor.cpp 2018-01-12 15:44:11 -07:00
Stan Moore 1ec54827d6 Add Kokkos halffull neighbor list capability 2018-01-12 15:41:59 -07:00
Axel Kohlmeyer 61ebf6265a address some formatting/markup issues reported by Nandor Tamaskovics 2018-01-12 12:50:02 -05:00
Axel Kohlmeyer 190cc78034 add dummy doc files for not-yet-implemented features 2018-01-12 12:29:03 -05:00
Axel Kohlmeyer 5863f115dd correctly escape 'a_ ' text, which is not a reference unlike 'a_b ' 2018-01-12 12:26:50 -05:00
Axel Kohlmeyer 75d259f5ee improve PDF reader compatibility for the created PDF file. 2018-01-12 12:00:53 -05:00
Axel Kohlmeyer 3b1b9a2cbf replace non-ASCII quotation marks with ASCII equivalent 2018-01-12 11:30:27 -05:00
mkanski 17b6a4c3cd Added more permanent citation 2018-01-12 11:47:35 +01:00
Stan Moore 1c10c78684 Add ghost option to npair_halffull 2018-01-11 15:15:04 -07:00
Axel Kohlmeyer 26917280be state name of the affected variable in error messages where possible 2018-01-11 15:01:08 -05:00
Stan Moore 45674e6cd3 Add Kokkos skip list capability 2018-01-11 10:07:44 -07:00
Stan Moore 22d2d1cdf3 Fix issue in pair_snap_kokkos memory_usage 2018-01-11 10:01:34 -07:00
Stan Moore 0d7bee40ae Add newline at end of pair_snap_kokkos_impl.h 2018-01-11 09:41:37 -07:00
Stan Moore db1ed32a51 Fix minor issues in pair_snap_kokkos 2018-01-11 09:39:53 -07:00
Stan Moore d7d087ae67 Fix issue with peratom energy/virial in pair_snap_kokkos 2018-01-10 10:20:40 -07:00
Stan Moore 92e2df74c1 Fix bug in Kokkos peratom energy/virial with newton on 2018-01-10 10:20:12 -07:00
mkanski 92742c5373 Introduced the change in reax/c/omp 2018-01-10 18:00:22 +01:00
Stan Moore 2047ae76e3 Move compute_bi outside of j-loop 2018-01-09 17:05:57 -07:00
Stan Moore 4adbb882b3 Temper SNAP output 2018-01-09 17:05:34 -07:00
Stan Moore 275c08453f Add Kokkos versions of pair_style snap and zbl 2018-01-09 17:03:49 -07:00
Axel Kohlmeyer 91107cc1f3 add a "coeffs" keyword to the info command for debugging "All XXX coeffs are not set" errors. 2018-01-09 12:47:33 -05:00
mkanski e26c170679 Added example and tabulated close-range correction 2018-01-09 15:08:08 +01:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Steve Plimpton 9e9cfe5869
Merge pull request #754 from rbberger/cmake_kokkos_bugfix 
CMake bugfixes for KOKKOS builds
 2018-01-08 09:16:43 -07:00
Steve Plimpton 85ff0c1e46
Merge pull request #750 from stanmoore1/kk_fences 
Add Kokkos thread fences to comm pack/unpack routines
 2018-01-08 09:16:16 -07:00