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22864 Commits

Author SHA1 Message Date
Axel Kohlmeyer 80e07c69f0
add part of developer guide as to showcase the integration of the programmer guide 2020-08-25 15:07:09 -04:00
Richard Berger df8fb26272
Refactor changes to documentation build 
- Added CMake variables for readability
- Moved Mathjax files to _static to avoid special copy logic
- Moved JPG/lammps-logo.png to _static to avoid special copy logic
- Removed dead CMake code
 2020-08-25 13:41:31 -04:00
Axel Kohlmeyer 14b66d1f84
tweak test tolerance of reax/c tests for running on ubuntu 18.04 2020-08-25 12:15:19 -04:00
Axel Kohlmeyer f965786e74
refactor C library interface and add doxygen decorations 2020-08-25 11:45:07 -04:00
Axel Kohlmeyer 69cffb2d04
import test infrastructure for c, c++ and python library usage 2020-08-25 11:03:31 -04:00
Axel Kohlmeyer 024e4c5f21
make formatting and doxygen decorations for utils functions consistent 2020-08-24 20:55:13 -04:00
Axel Kohlmeyer 3f685c346f
add doxygen integration with conventional and cmake doc build 2020-08-24 17:58:37 -04:00
Axel Kohlmeyer dc241abb85
Merge pull request #2305 from akohlmey/next_patch_version 
Update version strings for updated patch release
 2020-08-24 13:46:50 -04:00
Axel Kohlmeyer 93e4ed9770
Merge pull request #2304 from akohlmey/collected-small-changes 
Collected small changes for the next patch release
 2020-08-24 11:43:42 -04:00
Axel Kohlmeyer 7e1a3bd4d5
Merge pull request #2302 from akohlmey/consistent-doc-headers 
Consistent subsection headers for commands
 2020-08-24 10:52:09 -04:00
Axel Kohlmeyer 47a44732e7
add test for fix restrain 2020-08-23 15:29:58 -04:00
Axel Kohlmeyer 8f5e8300ea
fix typos in fix restrain docs 2020-08-23 15:29:49 -04:00
Vsevak 0842911cd8 Rename local buffers 'red_acc' in lal_tersoff* 
Rename __local red_acc in lal_tersoff
 2020-08-23 22:22:28 +03:00
Jacob Gissinger 10080079e3 ISO compliance 2020-08-23 11:44:48 -04:00
Jacob Gissinger 63abb2dff9 fix broken reset_mol_ids command 2020-08-23 11:32:54 -04:00
Jacob Gissinger 01dd80f35e bond/react: actually make reset_mol_ids the default 2020-08-23 11:21:43 -04:00
Axel Kohlmeyer fb634658de
add tests for a few more force manipulation fixes 2020-08-23 07:01:38 -04:00
Axel Kohlmeyer c503bba008
add custom pair style tests for reax/c and edip/multi 2020-08-23 06:44:33 -04:00
Axel Kohlmeyer 0fb8f6e779
add test for pair style momb 2020-08-22 23:15:20 -04:00
Axel Kohlmeyer 66b17fd2ce
dispersion only tests for buckingham 2020-08-22 23:03:20 -04:00
Axel Kohlmeyer 3def826dbe
add more tests for variants using long-range dispersion pair styles 2020-08-22 22:55:15 -04:00
Axel Kohlmeyer f18d0507b3
fix issues with lj/long pair styles when not using long-range for dispersion 2020-08-22 22:54:38 -04:00
Axel Kohlmeyer c8f2634b44
add tests for tabulated msm coulomb 2020-08-22 22:08:08 -04:00
Axel Kohlmeyer e78100bdba
add (partial) tests for pair styles dpd and dpd/tstat 2020-08-22 22:00:13 -04:00
Axel Kohlmeyer 2907a10937
update version strings for new attempt for a patch release 2020-08-22 16:42:39 -04:00
Axel Kohlmeyer 1879106cc3
Merge pull request #2299 from rbberger/doc_file_size 
Avoids HTML doc pages from becoming too large
 2020-08-22 15:45:06 -04:00
Axel Kohlmeyer 9152a8e98f
avoid division by zero in imaging code 2020-08-22 15:32:04 -04:00
Axel Kohlmeyer 2fd654f4fd
silence compiler warnings about unused variables 2020-08-22 15:06:00 -04:00
Axel Kohlmeyer 86153a0f77
avoid division by zero in MathExtra normalize functions 2020-08-22 15:03:27 -04:00
Axel Kohlmeyer 9136f9b9c9
Merge pull request #2303 from rbberger/binary2txt_bug 
Fixes a bug in binary2txt
 2020-08-22 14:46:29 -04:00
Richard Berger f82b19e21f
Fix off-by-one mistake, Fixes #2300 2020-08-22 12:03:24 -04:00
Axel Kohlmeyer b776e1ee3c
convert remaining style doc sections to be a logical header 2020-08-21 23:33:41 -04:00
Richard Berger 66438539f2
Avoids HTML doc pages from becoming too large 2020-08-21 19:47:46 -04:00
Stan Moore 450fd12d31 Changes needed for Kokkos v3.2 2020-08-21 14:45:12 -05:00
Jacob Gissinger 6fc2ab07ef reset_mol_ids: unique created computes 2020-08-21 14:52:39 -04:00
Axel Kohlmeyer 2a6546d6f0
Merge pull request #2296 from akohlmey/next_patch_version 
Update version strings for next patch release
 2020-08-21 14:43:56 -04:00
Jibril B. Coulibaly 921b6d8135 relative threshold for contact frame update based on tangential critical force 2020-08-21 13:20:53 -05:00
Axel Kohlmeyer cffc667259
Merge pull request #2298 from stanmoore1/mv2_var 
Fix MVAPICH2 env variable for CUDA/aware
 2020-08-21 14:04:57 -04:00
Stan Moore e0c74a30bc Fix MV2 env variable 2020-08-21 11:08:49 -06:00
Axel Kohlmeyer 7f87ccccc8
Merge branch 'collected-small-changes' into next_patch_version 2020-08-21 11:18:10 -04:00
Axel Kohlmeyer 3c7d59401c
Merge pull request #2107 from junghans/offline_gtest 
cmake: allow to overwrite GTest URL for offline machines
 2020-08-21 10:57:08 -04:00
Axel Kohlmeyer 19c1fa8c94
need to re-initialize lattice variable after new lattice command 2020-08-21 01:01:12 -04:00
Axel Kohlmeyer ee6ef98b9b
remove trailing whitespace 2020-08-21 00:43:40 -04:00
Axel Kohlmeyer e742ae7475
fix RST syntax and spelling issues in granular pair style docs 2020-08-21 00:31:55 -04:00
Axel Kohlmeyer 900830a4a1
Merge branch 'master' into mindlin_rescale 2020-08-21 00:24:07 -04:00
Axel Kohlmeyer c9773fc288
Merge branch 'master' into bond/react-reset_mol_ids 2020-08-21 00:19:52 -04:00
Axel Kohlmeyer 4c46119a48
Merge pull request #2280 from lammps/gridcomm-tiled 
Support for tiled decompositions in PPPM
 2020-08-21 00:16:20 -04:00
Axel Kohlmeyer 42018d3b35
add dispersion only kspace style tests 2020-08-20 23:42:23 -04:00
Axel Kohlmeyer 3183af9b85
fix a few more initialization issues in pppm/disp and pppm/disp/intel 2020-08-20 23:42:00 -04:00
Axel Kohlmeyer 2855f04363
tweak output format 2020-08-20 23:41:32 -04:00