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15743 Commits

Author SHA1 Message Date
Steve Plimpton 25907c856e small doc page changes, format and content on doc page tarballs 2018-09-07 09:56:03 -06:00
Christoph Junghans 861a7acdf0 cmake: fix globbing in some more places 2018-09-07 06:40:06 -06:00
Jacob Gissinger f7cdf2a7b8
Merge pull request #26 from lammps/master 
rebase
 2018-09-06 21:37:52 -06:00
Richard Berger aea148a86a
Merge pull request #1100 from rbberger/info-command-refactoring 
Avoid unnecessary sorting in print_columns
 2018-09-06 22:55:56 -04:00
Axel Kohlmeyer dd64c063cf various fixes for the manual to address breakage from merging MESSAGE and USER-SCAFACOS packages 2018-09-06 22:28:20 -04:00
Axel Kohlmeyer 44fcdc4024 update reference examples with versions that do not vary by MPI rank count 2018-09-06 21:20:47 -04:00
Axel Kohlmeyer 947f574503 Merge branch 'master' into compute_mop 
# Conflicts:
#	cmake/CMakeLists.txt
 2018-09-06 21:13:42 -04:00
Axel Kohlmeyer 5c4434b283
Merge pull request #1113 from akohlmey/more-codeowners 
Expand the list of code owners for more automated review requests
 2018-09-06 20:59:07 -04:00
Christoph Junghans 8f8aee65d2 cmake: fix globbing of emacs files 
Done by: sed -i '/GLOB/s@/\*\.@/[^.]*.@g' CMakeLists.txt
 2018-09-06 14:52:49 -06:00
Christoph Junghans d7b00f86f8 cmake: fix Eigen3 detection 
For some reason FindEigen3.cmake defines all cap. variables, i.e.
Eigen3_FOUND -> EIGEN3_FOUND
 2018-09-06 14:18:31 -06:00
Axel Kohlmeyer efd582fb21 update list of code owners for automatic review requests. started assigning core files 2018-09-06 13:13:20 -04:00
Axel Kohlmeyer b915716b60 fix inconsistency resulting from error in auto-replace macro 2018-09-06 12:27:10 -04:00
Axel Kohlmeyer b3079f3aec rename files and classes for pair style eam/cd/omp to follow the rename of the non-threaded classes 2018-09-06 12:07:25 -04:00
Axel Kohlmeyer 84657f1531 final pass at sprintf() buffer overflow prevention. also fix typo in previous commit 2018-09-06 12:00:04 -04:00
Axel Kohlmeyer db510af582 more fixes for potential buffer overflows by using snprintf() instead of sprintf() 2018-09-06 11:32:44 -04:00
Axel Kohlmeyer 9c27548a5c more replacing of sprintf() with snprintf() 2018-09-06 10:45:48 -04:00
Axel Kohlmeyer 4d52cb9245 more buffer overflow avoiding through using snprintf() 2018-09-06 09:57:43 -04:00
Axel Kohlmeyer fbc1c1cfdd replace fixed buffer sprintf() with straight fprintf() 2018-09-06 09:57:10 -04:00
Axel Kohlmeyer ca04e8f31c use snprintf() in a bunch of cases to avoid overflowing fixed size buffers with unchecked strings 2018-09-06 02:57:53 -04:00
Richard Berger ba1c5d3191 Avoid buffer overflow during errors with long filenames 2018-09-05 21:39:09 -04:00
Richard Berger 0b951840f2
Merge pull request #1103 from rbberger/cmake-fix-user-omp 
cmake: add missing fix_omp.h and fix_omp.cpp to compilation
 2018-09-05 21:27:24 -04:00
Stan Moore 95c3d2fc8e
Merge pull request #1051 from stanmoore1/data_dup 
Add data duplication option to the KOKKOS package
 2018-09-05 17:09:09 -06:00
Richard Berger ad498811b1 cmake: add missing fix_omp.h and fix_omp.cpp to compilation 2018-09-05 16:04:35 -04:00
Richard Berger 510e09f4ef patch 5Sep18 2018-09-05 13:39:18 -04:00
Stefan Paquay 5003354fba Replaced a tab with whitespace. 2018-09-05 11:42:48 -04:00
Stefan Paquay 9b38a5b359 Replaced gpu Makefile with the one from upstream so as not to delete it. 2018-09-05 11:39:41 -04:00
Stefan Paquay 1c8feed69f Removed gpu makefile from wrong branch. 2018-09-05 11:38:04 -04:00
Stefan Paquay 84de0d38ea Replaced files with those from upstream. 2018-09-05 11:34:07 -04:00
Stefan Paquay c192236a7e Commit before switching to old master. 2018-09-05 11:28:06 -04:00
Stefan Paquay 779f1bd0b1 Fixes a bug in pair_morse_smooth_linear where the cutoff was not properly initialized. 2018-09-05 11:27:10 -04:00
Richard Berger a28990ed8d
Merge pull request #989 from rhalver/ScaFaCoS 
[Feature Contribution] Scafacos
 2018-09-05 11:24:13 -04:00
Axel Kohlmeyer 0c92c22755 moved contents of USER-MOP package to USER-MISC as suggested by @sjplimp 2018-09-05 10:56:12 -04:00
Richard Berger 4a5e28af81 Avoid unnecessary sorting in print_columns 
std::map is a sorted associative container. We don't need to
first copy it into a vector and sort that one.
print_columns has been refactored as a template function and
makes use of this property.
 2018-09-05 10:35:47 -04:00
Steve Plimpton d3d16882ca remove note for Rene 2018-09-05 08:12:19 -06:00
jrgissing ae7b18fb77 only one call to extract needed 2018-09-05 00:11:50 -06:00
Jacob Gissinger efd81a2854
Merge branch 'master' into bond/react-efficient-competing_reactions 2018-09-04 22:34:04 -06:00
jrgissing a5f7b418de bond/react: efficient competing reactions 2018-09-04 22:06:49 -06:00
Richard Berger 09ef2bc829
Merge pull request #1093 from rbberger/cmake-fixes 
Collection of CMake fixes
 2018-09-04 21:51:47 -04:00
Richard Berger f8b8ebed5b
Merge pull request #1098 from junghans/cmake_testing 
cmake: only add tests if exe is build
 2018-09-04 21:50:23 -04:00
Richard Berger ff2e13e063 Merge branch 'master' into ScaFaCoS 2018-09-04 21:35:46 -04:00
Richard Berger 8608b4f93c Remove extra libm in LAMMPS_LINK_LIBS 2018-09-04 21:31:08 -04:00
Christoph Junghans db7c2549d0
cmake: inject with-pic into Scafacos 2018-09-04 17:05:59 -06:00
Christoph Junghans 037420b611 cmake: only add tests if exe is build 2018-09-04 14:59:30 -06:00
Steve Plimpton bcecc0389e add variable option to compute bond/angle/dihedral local 2018-09-04 14:48:44 -06:00
Richard Berger 5edff5d970
Merge pull request #1095 from rbberger/cmake-add-core-tests 
Add core tests to CMake
 2018-09-04 16:28:26 -04:00
Richard Berger af4b2b9354 Add LAMMPS_TESTING_SOURCE_DIR and LAMMPS_TESTING_GIT_TAG options 2018-09-04 15:37:32 -04:00
Richard Berger 842136afc8 Add core tests to CMake 2018-09-04 12:12:49 -04:00
Axel Kohlmeyer 990f733d22
Merge pull request #1091 from akohlmey/less-compiler-warnings 
Collected diverse small changes
 2018-09-04 10:30:04 -04:00
Richard Berger f18f12d1a6 Fix NETCDF include and libs in CMake 2018-09-04 09:15:00 -04:00
Axel Kohlmeyer a6dfab6f27 recover some const'ness in Domain class, that was lost when merging MESSAGE package. fixes lib/atc compilation issue 2018-09-04 09:13:22 -04:00