6833d6def6
Merge branch 'master' into kim-simulator-models
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# Resolved Conflicts:
# src/KIM/kim_query.cpp
# src/KIM/pair_kim.cpp
2019-07-29 20:43:10 -04:00
5cb02781c2
simplify checking for per chunk compute
2019-07-29 20:35:24 -04:00
180c90acfb
use utils::strmatch() to more safely detect gravity fix
2019-07-29 20:21:31 -04:00
2e6850835f
Merge pull request #1542 from akohlmey/improve-include-consistency
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Improve Consistency of Include Statements (mostly complete)
2019-07-29 20:12:41 -04:00
7043b9f620
Merge pull request #1548 from jrgissing/bond/react-clarify-how-stabilization-works
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Bond/react clarify how stabilization works
2019-07-29 19:55:24 -04:00
91e0bebdfa
Merge pull request #1576 from Adrian-Diaz/patch-rcb
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patch niche rcb issue
2019-07-29 19:54:45 -04:00
d688624335
Merge pull request #1581 from akohlmey/comm-cutoff-with-bond
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Include bonds in communication cutoff estimate when no pair style is present or print warning, if cutoff may be too small.
2019-07-29 19:54:24 -04:00
191044ab94
Merge pull request #1588 from akohlmey/cmake-installation-folder-bugfix
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Fix bugs with CMake potentials and frc folder installation. Include base C++ headers for library install, too, so one can use the C++ interface as well.
2019-07-29 19:53:36 -04:00
c03e9c9711
Adjust write_echo() within kim_query
2019-07-29 16:11:29 -05:00
2ffc35297b
make kim_query log of variable setting look more like other KIM log messages
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this adds BEGIN/END marker comments and echoes the actual command line
that the kim_query command implicitly executes
2019-07-29 16:57:34 -04:00
514608b82f
Merge branch 'kim-simulator-models' of github.com:ellio167/lammps into kim-simulator-models
2019-07-29 16:40:29 -04:00
ea4107c4b4
add write_echo() method to Input class for logging implicit commands where the echo command would send explicit ones
2019-07-29 16:36:57 -04:00
0f059c56f9
Add details about installing models to KIM example input
2019-07-29 15:30:46 -05:00
0820ebc143
cleanup of compute gyration/shape code.
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- use MathSpecial::square(x) instead of pow(x,2) for improved precision
and handling of small and negative numbers
- remove unused include statements
- no need to refetch the compute in every step. during init() is sufficient
2019-07-29 16:16:24 -04:00
0beb39c1af
fully integrate compute gyration/shape into doc build system
2019-07-29 16:14:29 -04:00
2afc498a2b
Add logging to kim_query (compile error at moment)
2019-07-29 15:04:15 -05:00
e0b20c4fd4
add false positive
2019-07-29 15:23:23 -04:00
6a1b61637b
provide some more details about 'make install' with CMake
2019-07-29 13:43:06 -04:00
96e0b03ede
.frc files only need to be installed if msi2lmp is built
2019-07-29 13:38:38 -04:00
5307558727
need to install some base C++ headers for C++ library use
2019-07-29 13:34:04 -04:00
a0abd270b5
kim_query check for empty query result
2019-07-29 11:41:01 -05:00
838ea2eca1
Merge branch 'improve-include-consistency' of github.com:akohlmey/lammps into improve-include-consistency
2019-07-29 10:55:24 -04:00
2fba3d027a
fix small formatting issue
2019-07-28 14:44:47 -04:00
0f10c55c1c
avoid recursive header inclusion
2019-07-26 17:26:59 -04:00
9477df4244
Merge branch 'master' into improve-include-consistency
2019-07-26 17:24:32 -04:00
863ae35658
Merge branch 'fix-plumed-issues' into collected-small-changes
2019-07-26 15:45:41 -04:00
94126e5424
use MPI_Get_library_version() API to provide a more detailed version info, not just the MPI standard level
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very chatty output (e.g. from MPICH) is truncated to the next line after 80 characters.
2019-07-26 15:44:10 -04:00
a0e005f93c
include LAMMPS version in STUBS library version string.
2019-07-26 15:43:01 -04:00
a5a1e27fb1
refactor commands in the STUBS folder for 'make serial' and 'make clean-serial'
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make so that for the "serial" make target we not only automatically build
the STUBS library, if it is missing, but also update its compilation when
there are changes and remove it on the "clean-serial" target.
2019-07-26 15:42:34 -04:00
35cee904d7
Merge pull request #1580 from stanmoore1/kk_cuda_aware
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Fix CUDA-aware MPI issues with KOKKOS package
2019-07-26 15:17:49 -04:00
f2dbe186ca
Fix typo
2019-07-26 11:45:50 -06:00
e816f0e7a6
Cleanup of CUDA-aware MPI code
2019-07-26 11:24:15 -06:00
0ba854b4ab
Add MPI_Get_library_version to STUBS library
2019-07-26 11:23:46 -06:00
f4a984175c
Merge pull request #1587 from valleymouth/bug_nve
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Fixing bugs in nve/kk when using rmass.
2019-07-26 13:15:30 -04:00
17d6b317a7
Better workaround for Spectrum MPI
2019-07-26 10:37:22 -06:00
6a5902ec48
Update kim_init to use KIM::Collections::GetItemType()
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A bit of a cleaner solution. Should be no visible change for users.
2019-07-26 11:14:46 -05:00
010cb0edf3
Add warning to cmake if PKG_KIM=ON but DOWNLOAD_KIM not set & KIM is not found
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This can be a scenario where the user has KIM installed but does not have the
environment setup correctly to be found. The config. step should provide some
warning of this. Otherwise, it is easy to miss the fact that KIM is being
downloaded and built.
2019-07-26 11:10:54 -05:00
0bb9df76c2
correct shell profile variables to point to the installation directory
2019-07-26 09:58:18 -04:00
8d4f189699
Revert "new versions of jacobi() method"
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This reverts commit 39315268e8
2019-07-26 09:38:32 -04:00
ca1fece850
Fixing remaining wrong indexing of rmass in nve/kk.
2019-07-26 12:46:04 +01:00
e8d891c0dd
simplify installation of data folders and make it consistent
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fixes #1586
2019-07-26 06:06:03 -04:00
47689b4ad3
make include files independent of previously included headers. include them first in implementation files.
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this is to be compliant with upcoming definition of include file policy
2019-07-26 06:03:21 -04:00
179b507107
Fixing bug in nve/kk when using rmass.
2019-07-26 10:55:27 +01:00
9bedd0d0d0
Merge pull request #1584 from akohlmey/bonded-hybrid-restart
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Correct restarting of bonded hybrid styles for table styles
2019-07-25 21:26:17 -04:00
52e1755464
fix spelling errors and false positives
2019-07-25 21:20:42 -04:00
60dfa7daf8
doc spelling update
2019-07-25 18:31:40 -05:00
fe83e4de2e
revise logic and documentation of communication cutoff selection one more time
2019-07-25 16:00:01 -04:00
fadb40051b
Update kim_query & clear and update examples/kim
2019-07-25 14:03:35 -05:00
ab74bfef20
Small logic tweak
2019-07-25 12:52:16 -06:00
7c1fedff18
Fix var name
2019-07-25 12:30:45 -06:00
