69a8dfe4d9
whitespace
2021-10-02 18:12:32 -04:00
dcaed72b6d
update embedded docs
2021-10-02 17:29:21 -04:00
c6bdab8b4c
disable optimization of cputime function for MSVC++ to avoid bogus 0s reports
2021-10-02 17:29:05 -04:00
2dcaa47b0e
unfreeze versions of python packages used to build the documentation
2021-10-02 16:55:19 -04:00
37bfe3d0ce
integrate platform sub-namespace into source code and documentation
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this updates function calls to functions that have been moved from
the utils namepsace or the Info class to platform::
2021-10-02 16:55:11 -04:00
195fe81c60
correct test for loading shared objects and libraries
2021-10-01 23:52:02 -04:00
a8193f42b8
Merge branch 'master' into platform-namespace
2021-10-01 21:58:52 -04:00
05b368e1c6
Merge pull request #2971 from lammps/doc-thermostats
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Clarify thermostat doc pages to mention applying the thermostat only to regions of atoms
2021-10-01 12:18:38 -04:00
912d55c46a
Merge pull request #2975 from rbberger/external_kokkos_fix
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Avoid assertions in PythonCapabilities check when using external KOKKOS
2021-10-01 11:56:43 -04:00
dcf4b75ca2
Merge pull request #2973 from akohlmey/32bit-pointer-bugfix
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32-bit pointer bugfix in bond/angle style gaussian
2021-10-01 11:36:26 -04:00
211df8b7b0
Avoid assertions in PythonCapabilities check when using external KOKKOS
2021-10-01 11:08:02 -04:00
434c170097
apply clang-format
2021-10-01 00:58:38 -04:00
01fb33cb5d
fix memory allocation bug causing memory corruption on 32-bit arches
2021-10-01 00:57:02 -04:00
b5b2f5c03c
additional tweak
2021-09-30 17:11:49 -06:00
f20bd63edf
clarify doc pages for thermostatting fixes to mention regions
2021-09-30 16:55:22 -06:00
4d84ceb822
Merge pull request #2951 from akohlmey/parse-logical-keyword
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Add utility function to parse boolean parameters
2021-09-30 00:09:37 -04:00
56cd66a6c3
Merge branch 'master' into parse-logical-keyword
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# Conflicts:
# src/H5MD/dump_h5md.cpp
2021-09-29 23:05:59 -04:00
c30ba70fab
Merge pull request #2957 from akohlmey/next_release_version
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Step version strings for stable release
2021-09-29 20:40:00 -04:00
8d6adfa0d1
Merge pull request #2966 from akohlmey/cmake-tweaks
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Tweaks to CMake build for portability and early detection of build problems
2021-09-29 19:46:33 -04:00
111e9d9060
Merge pull request #2969 from jrgissing/bond/react-make-Nevery-per-reaction
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bond/react: fix nevery keyword bug
2021-09-29 18:42:00 -04:00
15b3e875d5
import files for platform namespace from standalone project w/o updating LAMMPS
2021-09-29 16:29:25 -04:00
7fbd2138bd
recover cross-compilation with mingw64
2021-09-29 15:13:55 -04:00
a5ed701908
make Nevery keyword per-reaction
2021-09-29 14:40:22 -04:00
dd4b195552
silence compiler warnings
2021-09-29 14:04:01 -04:00
2651e6ec2f
make C library example work with strict C compilers
2021-09-29 10:37:15 -04:00
81d3eb0b2e
add missing keyword
2021-09-29 10:29:09 -04:00
3381f72b80
correctly handle Tcl stub library if available
2021-09-29 09:19:47 -04:00
b4307e2354
only need Tcl not Tk to compile Tcl swig wrapper
2021-09-29 09:01:01 -04:00
aa59f7bd91
must have patch command available to compile ScaFaCoS
2021-09-29 07:50:53 -04:00
af7c613200
portability improvement
2021-09-29 07:50:13 -04:00
f7238de5d5
detect and error out if BLAS/LAPACK libraries variables are a list
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This will cause external project compilation to fail since the semi-colons
are converted to blanks, but one cannot properly escape the variables.
So far the only viable solution seems to be to convert the scripts from
using ExternalProject_add() to FetchContent and add_subdirectory()
2021-09-29 07:45:07 -04:00
23e173d44f
compiling ML-HDNNP with downloaded n2p2 lib requires the sed command
2021-09-29 07:27:49 -04:00
9e49a934c2
Merge pull request #2965 from stanmoore1/neigh_cutoff
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Bugfix: prevent neigh list from copying "unique" stencil/bin
2021-09-28 19:28:32 -04:00
8a35ea05bc
Prevent neigh list from copying "unique" stencil/bin
2021-09-28 15:33:44 -06:00
ee0d439bbd
Merge pull request #2963 from akohlmey/hybrid-one-coeff-bugfix
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Make sure the one_coeff flag is applied to hybrid sub-styles
2021-09-28 09:44:10 -04:00
b3c8f85ff9
make sure the one_coeff flag is applied to sub-styles
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since the check for Pair::one_coeff was moved to the Input class (to
reduce redundant code), hybrid substyles could "escape" that requirement.
Thus checks have to be added to the hybrid coeff() methods.
2021-09-28 04:39:46 -04:00
c4616d4a11
Merge pull request #2962 from akohlmey/doc-updates
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A few final updates to the LAMMPS manual
2021-09-27 20:39:06 -04:00
9d5aa757c3
Merge pull request #2961 from akohlmey/makefile-updates
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Add -std=c++11 to a number of machine makefiles for the traditional make build system
2021-09-27 19:42:49 -04:00
34fe792fad
freeze versions of pip packages for processing the manual of the stable version
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this way we avoid surprises in case one of the packages get updated
to an incompatible new version. these are know-to-work versions.
2021-09-27 18:31:46 -04:00
d171b92a57
Merge pull request #2959 from Colvars/fix-colvars-run0
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Fix Colvars output files not written with "run 0"
2021-09-27 18:08:45 -04:00
53e227766a
make "make package-update" and "make package-overwrite" less verbose
2021-09-27 18:01:37 -04:00
09e0214f7d
remove references to USER packages, have package lists alphabetically sorted
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"make package-update" or "make pu" must be processed in the special order
because of inter-package dependencies
2021-09-27 18:01:01 -04:00
913ce25a01
small tweak
2021-09-27 17:13:32 -04:00
9c4a82f286
be more specific about what the name of the LAMMPS executable can be
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also provide a few more examples without a machine suffix
2021-09-27 16:50:25 -04:00
9dbd5bb27d
copy request to mention lammps.org form home page instructions for citing
2021-09-27 16:49:29 -04:00
395e22457c
add -std=c++11 to a number of machine makefiles for traditional make build
2021-09-27 16:28:55 -04:00
7601001632
Fix Colvars output files not written with "run 0"
...
See:
https://github.com/Colvars/colvars/commit/ff2f0d39ee5
which fixes a bug introduced in:
https://github.com/Colvars/colvars/commit/1e964a542b
The message applies to NAMD, but the logic used in LAMMPS when handling "run 0" is very similar.
The Colvars version string is also updated, however this commit does not
include other changes, such as the following:
https://github.com/Colvars/colvars/pull/419
which were not fully completed before the LAMMPS Summer 2021 finalization.
2021-09-27 13:38:30 -04:00
7b11f916b7
Merge pull request #2952 from akohlmey/collected-small-changes
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Final changes and bugfixes for the stable release
2021-09-26 20:18:34 -04:00
ea030c6dd8
Merge branch 'master' into collected-small-changes
2021-09-26 18:12:40 -04:00
f3b1da83f7
Merge pull request #2956 from stanmoore1/kk_eam_alloy
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Fix bug in Kokkos pair_eam_alloy on GPUs
2021-09-26 17:57:03 -04:00
