8803183b8b
Merge pull request #1593 from akohlmey/next_version
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Step version string for next patch release
2019-07-30 22:25:26 -04:00
11a3fd6ce4
Merge pull request #1556 from lammps/bug-maxexchange
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more robust version of atom exchange size
2019-07-30 17:09:18 -04:00
e3b1673c8c
Merge pull request #1597 from stanmoore1/eff_be_test
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Fix failing regression test /examples/USER/eff/Be-solid/in.Be-solid.spe
2019-07-30 17:07:55 -04:00
69a5ff2240
Merge pull request #1592 from akohlmey/collected-small-changes
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Collected small changes for next patch release
2019-07-30 17:06:48 -04:00
2b288bc9e0
add missing mode keyword for substitution
2019-07-30 16:53:27 -04:00
882b2301bb
handle shared library extension on macosx for plumed runtime build
2019-07-30 16:48:50 -04:00
528ec75f88
special case for MacOSX not needed
2019-07-30 16:38:40 -04:00
f5bf86b32d
more improvements to CMake build for USER-PLUMED on MacOSX
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default to shared linkage on MacOSX to avoid linker issues from
configure/cmake library detection differences
link/depend on GSL and LAPACK explicitly only for static linkage
2019-07-30 16:27:00 -04:00
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
602b4a47c0
Fix failing regression test
2019-07-30 10:37:27 -06:00
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
3548551479
Fix Kokkos package compile error
2019-07-30 08:49:58 -06:00
d1e8d7cbf8
Step version string for next patch release
2019-07-30 08:26:11 -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
