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25654 Commits

Author SHA1 Message Date
Yury Lysogorskiy 3de3302767 remove source files from lib/pace; 
add lib/pace/Install.py to automatically download the source files from github/ICAMS/lammps-user-pace;
add lib/pace/CMakeLists.txt to build libpace.a
add lib/pace/README
update src/USER-PACE/Install.sh
 2021-04-07 12:20:24 +02:00
Yury Lysogorskiy 6a99f5b5c5 WIP: 
-  no auto-download of user-pace src yet
-  lib/pace/*.cpp,*.h are provided explicitly yet.
- implement CMake integration in USER-PACE.cmake and in CMakeLists.txt
 2021-04-06 17:24:54 +02:00
Axel Kohlmeyer 9da49d9c6f
Merge pull request #2685 from akohlmey/collected-small-changes 
Collected small changes and fixes
 2021-04-02 19:42:04 -04:00
Axel Kohlmeyer 66e885b6e5
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
#	src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
 2021-04-02 17:57:54 -04:00
Axel Kohlmeyer b976c2d13c
Merge pull request #2679 from akohlmey/more-unittests 
Expand unit tests
 2021-04-02 17:51:29 -04:00
Axel Kohlmeyer 1c43b4a4c3
Merge branch 'fix_ave_chunk_cdof_bug' into collected-small-changes 2021-04-02 17:50:33 -04:00
Axel Kohlmeyer 90ab63f9ad
Merge branch 'master' into collected-small-changes 2021-04-02 17:49:27 -04:00
Axel Kohlmeyer 2c00136f22
used correct suffix when installing plugin binaries for testing 2021-04-02 17:49:15 -04:00
Axel Kohlmeyer abfe8bab59
fix uninitialized memory access issues. consolidate enumerators. 2021-04-02 17:32:29 -04:00
Axel Kohlmeyer 2a10b5ba69
fix bug causing segfaults 2021-04-02 17:21:34 -04:00
Axel Kohlmeyer af6452065f
correct URL to XTC file format docs on the gromacs homepage 2021-04-02 16:48:13 -04:00
Richard Berger 7d85461e97
Prevent compilation from breaking with Python 2 2021-04-02 16:32:25 -04:00
Axel Kohlmeyer 79a413aeea
replace calls to sqrt() in constant initializers with precomputed numbers. 
this also moves those arrays into a separate file and out of the header
 2021-04-02 16:15:28 -04:00
Axel Kohlmeyer 7995fd8923
Merge pull request #2689 from bhanudaysharma/patch-1 
Update units.rst (documentation for units commands)
 2021-04-02 16:09:56 -04:00
Axel Kohlmeyer c62b1b1050
Merge remote-tracking branch 'github/master' into collected-small-changes 2021-04-02 16:08:51 -04:00
Axel Kohlmeyer c4f59764d4
reformat pair_coeff section that got misformatted as string 2021-04-02 15:28:09 -04:00
Axel Kohlmeyer e613da98d6
Merge pull request #2650 from akohlmey/plugin-loader 
New PLUGIN package with a LAMMPS plugin loader command
 2021-04-02 15:08:44 -04:00
Axel Kohlmeyer d24f74b582
add stop on file example to fix halt docs 2021-04-02 12:31:46 -04:00
Axel Kohlmeyer 887eb40ad4
fix crash when requesting verbose output. 2021-04-02 12:07:59 -04:00
Axel Kohlmeyer 2dfafe4adb
add is_file() special variable function and unit tests for it 2021-04-02 12:07:43 -04:00
Axel Kohlmeyer c3eb52f46a
add force tests for USER-YAFF pair styles 2021-04-01 12:43:24 -04:00
Axel Kohlmeyer 994ee59fd5
correct single() functions for USER-YAFF pair styles to be consistent with compute() 2021-04-01 12:42:48 -04:00
Axel Kohlmeyer b5ef98cc22
consolidate the documentation for lj/switch3/coulgauss/long and mm3/switch3/coulgauss/long into a single file 2021-04-01 12:42:07 -04:00
Axel Kohlmeyer 9ac246011e
remove flags and setup for multi-cutoff r-RESPA support which is missing 2021-04-01 12:14:40 -04:00
Axel Kohlmeyer e7422a6bf7
silence compiler warnings 2021-04-01 11:28:18 -04:00
Axel Kohlmeyer 3668ce1374
Merge branch 'master' into more-unittests 
# Conflicts:
#	unittest/testing/core.h
 2021-04-01 11:11:18 -04:00
Axel Kohlmeyer 0b60650c1b
Merge branch 'master' into collected-small-changes 2021-04-01 10:11:59 -04:00
Axel Kohlmeyer 21c934d2cd
Merge pull request #2682 from rbberger/python_unittests 
Python package unit tests
 2021-04-01 10:11:26 -04:00
Axel Kohlmeyer f2a28dea4e
Merge pull request #2686 from ProfessorMiller/master 
Better handling of incorrect boundary conditions for KIM models with Coulomb interactions
 2021-04-01 10:11:08 -04:00
Axel Kohlmeyer 52e5f1e962
Merge pull request #2690 from ohenrich/user-cgdna 
USER-CGDNA: Corrected error message
 2021-04-01 09:54:45 -04:00
Axel Kohlmeyer b5d2f5f2b2
address whitespace issues 2021-04-01 09:45:01 -04:00
Axel Kohlmeyer e0aec1b5d9
remove obsoleted comment 2021-04-01 09:39:17 -04:00
Axel Kohlmeyer f867e69290
include new split_lines() function in Developer docs 2021-04-01 09:35:52 -04:00
Axel Kohlmeyer c9652f3aa6
update documentation for the extract_global() method of the lammps.lammps class 2021-04-01 09:31:54 -04:00
Axel Kohlmeyer eeaa221ee7
Merge pull request #2691 from wmbrownIntel/gpu_cudpp_fix 
Fixing bug with GPU neighboring when using builds supporting CUDPP.
 2021-04-01 09:21:18 -04:00
Axel Kohlmeyer d72b390c41
correct check for box changing fixes 2021-04-01 08:48:39 -04:00
Axel Kohlmeyer f48af95d49
update gcmc example to use fix rigid/small 2021-04-01 08:23:10 -04:00
Ronald E. Miller bed57e02f7 avoiding static variable 2021-03-31 16:18:05 -04:00
Axel Kohlmeyer 7699fb3708
generalize some checks in fix rigid and rigid/small 2021-03-31 15:55:31 -04:00
Axel Kohlmeyer c53f2d4629
correct USER-OMP respa/omp check 2021-03-31 14:55:07 -04:00
Michael Brown 9e412bb7a6 Fixing bug with GPU neighboring when using builds supporting CUDPP. 
...introduced in Feb 2021 GPU package update. Manifests when GPU library is built with -DUSE_CUDPP and -DLAL_USE_OLD_NEIGHBOR (latter forced with CUDA 11.2).
 2021-03-31 11:42:39 -07:00
Axel Kohlmeyer 0bde6c82a3
remove newton bond off check again 2021-03-31 14:40:54 -04:00
Oliver Henrich e1cf6a312f Corrected error message 2021-03-31 18:56:50 +01:00
Bhanuday Sharma 7092a7769c
Update units.rst 
In LJ units, the conversion formula between rho and rho* should be corrected to   
\rho^* = \rho \frac{\sigma^{dim}}{m}
 2021-03-31 06:44:52 +05:30
Axel Kohlmeyer 183b30abd7
use strmatch() consistently to detect respa and verlet runstyles with optional suffix 2021-03-30 18:30:22 -04:00
Axel Kohlmeyer eea2f45a95
force newton bond to be on since we don't support it to be off (yet) 2021-03-30 17:19:28 -04:00
Axel Kohlmeyer e22f9c4768
newton bond off does not work with atom style template currently 2021-03-30 16:48:51 -04:00
Axel Kohlmeyer 2e86cb4176
for atom style template number of bonds does not depend on newton_bond 2021-03-30 15:33:11 -04:00
Axel Kohlmeyer 8f5d11c0c5
add missing return 2021-03-30 13:34:31 -04:00
Axel Kohlmeyer 4ee24b85b0
fix a few minor issues with the docs 2021-03-30 11:45:47 -04:00