d4503a05a4
mention that cstdlib is included in lmptype.h now, too.
2019-07-30 14:22:33 -04:00
47fc31d005
move inline functions to the only place they are used. no need to use size_t for indices that are small
2019-07-30 14:21:53 -04:00
2d93a713e2
Merge branch 'master' into collected-small-changes
2019-07-30 14:14:11 -04:00
6d94fc1b3d
include cstdlib in lmptype.h since we define ATOX() macros.
2019-07-30 14:07:30 -04:00
8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models
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Develop native support for KIM simulator models
2019-07-30 10:53:58 -04:00
3eadfa15ef
Merge pull request #1512 from mkanski/rotate_molecules
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Extend support of "rotate" keyword to all styles of "create_atoms"
2019-07-30 10:53:37 -04:00
b0bccfd8a1
fix typo
2019-07-30 06:55:47 -04:00
3559c25bd9
add missing parenthesis
2019-07-30 06:35:35 -04:00
3fdadb5875
add configuration for linking VTK 7.1 on Ubuntu 18.04
2019-07-30 06:02:47 -04:00
7ab7691c51
update PLUMED support to version 2.5.2
2019-07-30 05:57:57 -04:00
3ee86470bb
correct documentation URL for PLUMED
2019-07-30 05:53:28 -04:00
d201d6c2d1
fix grammar error
2019-07-30 10:18:53 +02:00
88523fdd6e
Merge pull request #1529 from rupertnash/compute_momentum
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add compute momentum command
2019-07-29 22:51:29 -04:00
c9f3f99ee8
Update to kim-api-2.1.2
2019-07-29 21:48:12 -05:00
4289dbb78d
clean up includes and whitespace
2019-07-29 22:28:29 -04:00
d2c4989dbf
Merge pull request #1583 from evoyiatzis/gyration_shape
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computing the eigenvalues of gyration tensor & shape parameters
2019-07-29 22:16:13 -04:00
edf64ed16c
Merge pull request #1511 from jdevemy/master
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Add keyword hybrid/pair for compute_pressure
2019-07-29 22:15:20 -04:00
9004ebc3fe
one more fixup for compatibility for old PDF build scheme
2019-07-29 21:11:13 -04:00
90c678849a
replace non-ascii characters with ASCII equivalents
2019-07-29 21:10:49 -04:00
9f276be0e5
fix up legacy doc building for final kim doc files
2019-07-29 20:48:47 -04:00
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
