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16905 Commits

Author SHA1 Message Date
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
Steve Plimpton f0ec2e3279 refactoring of global and local hyper, including amended doc pages 2019-03-01 18:47:34 -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
Axel Kohlmeyer c555f7e2ed
update permissions 2019-02-28 17:52:53 -05:00
Axel Kohlmeyer 14e6c126a8
Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix 
add command to compute the Dynamical Matrix
 2019-02-28 17:08:36 -05:00
Axel Kohlmeyer 50fef541c2
add x-ref 2019-02-28 15:50:59 -05:00
Axel Kohlmeyer 5fd033c0a2
add one more false positive required by recent changes 2019-02-28 15:49:48 -05:00
Axel Kohlmeyer 1d2eab5e1b
update attribution information in Package details documentation 2019-02-28 15:26:36 -05:00
Axel Kohlmeyer 7062bc862e
remove third_order command and ASE based examples to be added in a new pull request 2019-02-28 15:21:48 -05:00
Axel Kohlmeyer 9298fe7868
fix segfault and copy-n-modify issues with third order command 2019-02-28 14:45:42 -05:00
Axel Kohlmeyer 16946d8c6d
integrate dynamical_matrix command into LAMMPS manual 2019-02-28 14:45:07 -05:00
Axel Kohlmeyer 286112ffbc
count each force computation as one simulation step. this avoids accessing uninitialized data, too. 2019-02-28 11:00:55 -05:00
Axel Kohlmeyer 326a97624e
Merge pull request #1317 from ornladios/adios2-master 
USER-ADIOS package with ADIOS 2.x
 2019-02-27 17:24:12 -05:00
Axel Kohlmeyer 80392224cd
Merge pull request #1351 from ellio167/kim-2.0.1 
Bump KIM API version to 2.0.1
 2019-02-27 17:21:30 -05:00
Axel Kohlmeyer b60f0f754c
small tweaks to USER-ADIOS docs 2019-02-27 17:18:08 -05:00
Axel Kohlmeyer 6bd56c2a85
update author attribution 2019-02-27 17:08:13 -05:00
Axel Kohlmeyer a4e580879c
Merge pull request #1347 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch release
 2019-02-27 17:02:21 -05:00
Ryan S. Elliott 54e5c76333 Bump KIM API version to 2.0.1 2019-02-27 15:50:08 -06:00
Axel Kohlmeyer 6bf9c06a5a
Step version string for next patch release 2019-02-27 16:19:20 -05:00
Axel Kohlmeyer 9cc7bea05d
bugfix for changes in #1340 2019-02-27 16:09:46 -05:00