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16323 Commits

Author SHA1 Message Date
Axel Kohlmeyer aeb7854aca update false positives list for newly added documentation 2018-12-03 16:11:39 -05:00
Axel Kohlmeyer ac51d0fb89 remove old versions of read_dump and rerun w/o parallel reading support 2018-12-03 15:32:43 -05:00
Axel Kohlmeyer 22f99be57e Merge remote-tracking branch 'github/read-dump-parallel' into collected-post-stable-patches 
# Conflicts:
#	src/read_dump.cpp
 2018-12-03 15:28:34 -05:00
Axel Kohlmeyer 55077cea4d Merge branch 'lebedeva2' of https://github.com/zbych127/lammps into collected-post-stable-patches 2018-12-03 15:24:31 -05:00
Axel Kohlmeyer 98728cddbe Merge remote-tracking branch 'devel/python-script-portability' into collected-post-stable-patches 2018-12-03 15:18:03 -05:00
Axel Kohlmeyer e1aff27cd4 Merge remote-tracking branch 'devel/whitespace-cleanup' into collected-small-fixes 2018-12-03 15:06:23 -05:00
Axel Kohlmeyer 4af7e706d7 correctly compute hash for temporary directory used by manual building 2018-12-03 14:59:43 -05:00
Axel Kohlmeyer 1c795a6be3 remove trailing blanks 2018-12-01 21:38:22 -05:00
jrgissing d14404254e check for illegally deleted atoms 2018-12-01 15:18:11 -07:00
Axel Kohlmeyer 4ec05a3389 remove some more trailing whitespace 2018-12-01 08:14:02 -05:00
Axel Kohlmeyer c69fc90588 detect more incompatible setups for fix tune/kspace, and document 2018-12-01 02:48:22 -05:00
jrgissing 53e66dcd15 bond/react: delete atoms 
allows deleting of a user-specified set of atoms, based on topology
 2018-11-30 22:35:10 -07:00
Jacob Gissinger 482e120af4
Merge pull request #35 from lammps/master 
rebase
 2018-11-30 21:36:01 -07:00
Axel Kohlmeyer 67041a5446
Merge pull request #1231 from lammps/update-log-files 
Update log files for example inputs, part 1
 2018-11-30 11:07:44 -05:00
Axel Kohlmeyer f380a03a07
Merge pull request #1237 from akohlmey/compute-mop-bugfix 
Make compute stress/mop and stress/mop/profile compatible with per-atom masses
 2018-11-30 11:07:17 -05:00
Axel Kohlmeyer 7b68655c4d remove trailing whitespace 2018-11-30 08:00:08 -05:00
Axel Kohlmeyer dd84b5c975 make compute stress/mop and stress/mop/profile compatible with per-atom masses 2018-11-30 07:50:57 -05:00
Axel Kohlmeyer 1f210a246e
Merge pull request #1234 from lammps/read-dump-keep 
bug-fix for miscounting atoms for read_dump add keep
 2018-11-29 18:33:45 -05:00
Axel Kohlmeyer 5d2730f055 update log files for rigid, shear, snap, srd, streitz, threebody, vashsista, and voronoi examples 2018-11-29 18:22:18 -05:00
Axel Kohlmeyer e4ca5b1889
Merge pull request #1232 from akohlmey/collected-small-fixes 
First chunk of collected small fixes for the stable release
 2018-11-29 18:19:12 -05:00
Steve Plimpton 4e9b987fec bug fix in original read_dump for add keep atom count 2018-11-29 15:54:14 -07:00
Steve Plimpton f92e61c58d bug-fix for miscounting atoms for read_dump add keep 2018-11-29 15:37:58 -07:00
Axel Kohlmeyer cda3227b05 plug memory leak in poems library 2018-11-29 16:41:11 -05:00
Axel Kohlmeyer 6705777f7b fix memory issue in POEMS library, where auxiliary data was cast to a data structure of different (smaller) size when deleting. 
this commit adds support to a callback function that allows to delete aux data in the Tree with its native size.
 2018-11-29 16:34:41 -05:00
Axel Kohlmeyer 4b8c6d40e2 update log files for qeq and rdf-adf examples 2018-11-29 15:15:14 -05:00
Axel Kohlmeyer 46bf4b7efb update log files for peptide, peri, pour and python examples 2018-11-29 14:51:25 -05:00
Axel Kohlmeyer cef4164460 update log files for min, msst, nb3b, nemd, and obstacle examples 2018-11-29 14:13:11 -05:00
Axel Kohlmeyer 074a9663cb update log files for melt and micelle example 2018-11-29 14:05:28 -05:00
Axel Kohlmeyer d67dad9d67 update log files for meam examples 2018-11-29 12:47:15 -05:00
Axel Kohlmeyer 41e24f6e8b update log files for gcmc example 2018-11-29 12:35:07 -05:00
Axel Kohlmeyer e3ddefb38b update docs and header for removed error message 2018-11-29 02:03:56 -05:00
Axel Kohlmeyer ea6d8a5dca replace hard crash with disabling atom sorting, when no suitable binsize is found 2018-11-29 01:38:04 -05:00
Richard Berger 09abc0c75a Fix memory leak in Variable::compute_atom 2018-11-29 00:41:40 -05:00
Axel Kohlmeyer 6be4ce7137 found a new false positive word in docs with spellchecker 2018-11-28 23:14:45 -05:00
Axel Kohlmeyer 78f86d5f16 silence compiler warning about singed vs. unsigned 2018-11-28 22:23:09 -05:00
Axel Kohlmeyer cb2964af4c silence compiler warning about unused parameter 2018-11-28 22:20:42 -05:00
Axel Kohlmeyer c42776e4e1 ignore valgrind core dumps 2018-11-28 21:22:46 -05:00
Axel Kohlmeyer c763916f9e update log files for granregion hugoniostat and indent examples 2018-11-28 21:21:54 -05:00
Axel Kohlmeyer eda79bd1c2 use shutil.rmtree() instead of calling 'rm -rf' for increased portability 2018-11-28 20:46:50 -05:00
Axel Kohlmeyer 798f098e4a remove USER-OMP version of fix nphug, which had intermittant and difficult to track down memory corruption issues with multiple threads. 2018-11-28 18:57:26 -05:00
Axel Kohlmeyer 3508eca337 make sure all local Tree pointers are initialized, either to a newly allocated Tree() or NULL 2018-11-28 18:49:37 -05:00
Axel Kohlmeyer 9646d4614f plug small memory leak in fix gcmc 2018-11-28 18:45:32 -05:00
Axel Kohlmeyer 48a408bb19 update log files for friction example 2018-11-28 18:42:48 -05:00
Axel Kohlmeyer a4d21370bf
Merge pull request #1229 from invemichele/fix_plumed_memory_leak 
fix plumed memory leak
 2018-11-28 16:42:16 -05:00
Axel Kohlmeyer 9702899d1c
Merge pull request #1228 from invemichele/fix_plumed_install 
Fix bug in lib/plumed/Install.py, some small cleanup and support parallel compile of plumed sources
 2018-11-28 16:32:04 -05:00
Axel Kohlmeyer 8e07aaf005 update log files for ellipse and flow examples 2018-11-28 16:16:19 -05:00
Axel Kohlmeyer 4a8f1a7a08 update log files for eim example 2018-11-28 16:11:15 -05:00
Axel Kohlmeyer 37289f7476 update log files for dipole and dreiding example inputs. add running some MD steps for dreiding 2018-11-28 16:07:12 -05:00
Axel Kohlmeyer 3ce61c42d6 update log files for crack and deposit examples 2018-11-28 16:01:42 -05:00
Axel Kohlmeyer 98c8f22046 update log files for coreshell examples 2018-11-28 15:56:58 -05:00