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16712 Commits

Author SHA1 Message Date
Axel Kohlmeyer b6459b3f74
Merge branch 'master' into gran_mods 2019-03-15 14:30:36 -04:00
Axel Kohlmeyer 28607f156e
use C++ style include headers for accessing C library functions 2019-03-15 14:25:14 -04:00
Axel Kohlmeyer c26068a57a
use LAMMPS style indentation for class definitions 2019-03-15 14:24:45 -04:00
Axel Kohlmeyer 8845a1a0ae
whitespace cleanup (remove ctrl-m, trailing whitespace) 2019-03-15 14:20:10 -04:00
Axel Kohlmeyer 3f0f2383b4
fix spelling and record false positives 2019-03-15 14:18:04 -04:00
Axel Kohlmeyer 3abfce01ca
remove diverged fix wall/gran/omp 2019-03-15 14:06:03 -04:00
Axel Kohlmeyer 2558509b70
Merge pull request #1366 from jrgissing/bond/react-delete_internal_groups 
Bond/react: unfixing deletes internal groups
 2019-03-14 19:29:39 -04:00
jrgissing 5608f87c15 bond/react:unfix_deletes_internal_groups 2019-03-13 21:55:17 -06:00
Jacob Gissinger 5556567e91
Merge pull request #46 from lammps/master 
rebase
 2019-03-13 21:41:08 -06:00
Dan S. Bolintineanu 2cc35ee777 A few additional enhancements to pair granular and fix wall granular option: 
- NULL option for tangential stiffness, to set it based on shear modulus
- calculation of effective shear moduli from elastic moduli and Poisson's ratio
- updates to doc page example syntax
 2019-03-13 00:42:08 -06:00
Dan S. Bolintineanu e0c935b52d Additional changes to pair_granular: 
-added mindlin and mindlin/rescale tangential model options
-torque from tangential force is now applied at the same point on both contacting particles
-updated doc page to reflect changes above
 2019-03-11 14:28:44 -06:00
Axel Kohlmeyer c3acb3e4ef
Merge pull request #1361 from akohlmey/collected-small-changes 
Collected small changes for the next patch release
 2019-03-08 12:11:59 -05:00
Axel Kohlmeyer 4e2ebf7feb
Merge pull request #1352 from mkanski/reax_var_atoms 
A partial fix for ReaxFF failure when the number of atoms increases during a simulation
 2019-03-07 15:44:15 -05:00
Axel Kohlmeyer 2077df5465
Merge pull request #1363 from stanmoore1/kk_deprecated 
Remove deprecated code in KOKKOS package
 2019-03-07 15:42:58 -05:00
Axel Kohlmeyer e62746ef27
protect group command against options that require unavailble properties resulting in segfaults 2019-03-07 15:38:23 -05:00
Axel Kohlmeyer a5c93e75a5
ignore src/lmpgitversion.h 2019-03-07 15:12:22 -05:00
Axel Kohlmeyer 3bc815efe8
fix a memory leak in fix bocs 2019-03-07 15:11:33 -05:00
Stan Moore 9cb2a56194 Remove deprecated Kokkos code 2019-03-07 10:47:40 -07:00
Stan Moore 0edc588458 Replace deprecated Kokkos capacity() with span() 2019-03-07 10:23:17 -07:00
Stan Moore f0e48931e4 Remove deprecated KOKKO_HAVE macros 2019-03-07 10:17:32 -07:00
Axel Kohlmeyer 9408dd6e92
use simpler way whether we are inside a git checkout in conventional build 2019-03-06 18:41:43 -05:00
Axel Kohlmeyer 4e632d1b79
implement another suggestion from @junghans 2019-03-06 17:32:08 -05:00
Axel Kohlmeyer 2918dae87e
correct variable name and path to find the local .git folder 2019-03-06 17:12:41 -05:00
Axel Kohlmeyer fe56cf04bc
simplify the detection of whether the source folder is checked out from a local git repo 2019-03-06 17:04:14 -05:00
Axel Kohlmeyer 436e02aa6e
small corrections/clarifications to the pull request template 2019-03-06 16:59:17 -05:00
Dan S. Bolintineanu 4ee98d18da Fixed missing reference in pair_granular doc page 2019-03-06 14:15:19 -07:00
Dan S. Bolintineanu 9a6dc2ff11 Removed several files that should not have been included 2019-03-06 13:54:32 -07:00
Axel Kohlmeyer c0ce8591e7
Merge pull request #1358 from ellio167/kim-link-update 
Update openkim.org urls in various places
 2019-03-06 12:22:12 -05:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Axel Kohlmeyer 4a17cb3467
Merge pull request #1357 from akohlmey/embed-git-revision 
Embed git branch and revision info into LAMMPS class
 2019-03-05 23:31:16 -05:00
Axel Kohlmeyer c5a3b034ce
implement various suggestions to improve the use of git information gathered 2019-03-05 17:29:34 -05:00
mkanski bfa950a7e9 Added initialization for grown arrays 2019-03-05 22:40:10 +01:00
Axel Kohlmeyer 390fc873bc
Merge pull request #1355 from julient31/bfo_spin 
bugfix update for SPIN package
 2019-03-05 14:27:28 -05:00
Axel Kohlmeyer 6b8a768f6c
Merge pull request #1356 from akohlmey/address-user-smtbq-vla-issue 
Address Variable-Length-Array issues, memory leaks, uninitialized data access issues in USER-SMTBQ
 2019-03-05 14:26:30 -05:00
Axel Kohlmeyer 1c7d191988
also print git version (if available) in multi-partition runs and in help message 2019-03-05 09:03:12 -05:00
Axel Kohlmeyer 1e573bd557
when compiling LAMMPS in a git checkout, embed and print git branch and revision info into the executable 2019-03-05 08:35:53 -05:00
Axel Kohlmeyer bc4a80d9e8
Merge pull request #1354 from akohlmey/collected-small-fixes 
Collected small fixes and updates for the next patch release
 2019-03-05 00:55:36 -05:00
Axel Kohlmeyer fa7b5ecfa3
disable chimet array in pair style smtbq, which was never set anywhere 2019-03-05 00:45:40 -05:00
Axel Kohlmeyer 6ed8fbbd51
handle uninitialized data access issues and out-of-bounds access for single element calculations 2019-03-04 18:01:55 -05:00
Axel Kohlmeyer 0d1524526a
work around the remaining variable length array cases. fix an off-by-one error, too. 2019-03-04 17:26:55 -05:00
julient31 ab0c35be93 Commit JT 030419 
- correction of pair_spin calculations
- corrects an error between i and ii lists in single/pair calc.
 2019-03-04 08:04:11 -07:00
julient31 849e52040a Merge branch 'clean-master2' of github.com:julient31/lammps into bfo_spin 2019-03-04 07:51:12 -07:00
Axel Kohlmeyer 5ecbb8bd01
fix int vs. bigint issue and add NULL file pointer check to dynamical_matrix 2019-03-01 09:46:13 -05:00
Axel Kohlmeyer 30ee2f3d78
avoid windows portability issues with int32_t 2019-03-01 09:37:38 -05:00
Axel Kohlmeyer 0f0a65bb48
plug small memory leak in USER-ADIOS 2019-03-01 09:37:33 -05:00
mkanski d8845b6817 Added initialization of the entire num_bonds and num_hbonds arrays 2019-03-01 13:13:11 +01:00
Dan S. Bolintineanu 87a243203b Removed pair_granular.cpp/h from src directory 2019-02-28 16:46:21 -07:00
Axel Kohlmeyer 5486896876
Merge pull request #1350 from akohlmey/next-patch-release 
Step version string for next patch release
 2019-02-28 17:56:51 -05:00
Axel Kohlmeyer 47b0c77dd9
replace variable length arrays with std::vector 2019-02-28 17:53:50 -05:00
Axel Kohlmeyer fbc9cf8354
fix huge memory leak 2019-02-28 17:53:17 -05:00