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
373dbcd9ae
fix typo
2021-10-02 16:40:05 -04:00
35bef7b1d3
unfreeze versions of python packages used to build the documentation
2021-10-02 16:32:58 -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
0cbf70a385
make compatible with C
2021-10-01 15:24:59 -04:00
60c6669d68
Remove lammpsplugin.h from .gitignore
2021-10-01 13:21:42 -06:00
cf06620538
raise the C++ standard to be at least C++14 when Kokkos is enabled.
...
This still allows to request a later standard for as long as it is C++14 or later
2021-10-01 15:16:40 -04:00
139dfd89e2
for improved C++20 compatibility
2021-10-01 15:14:53 -04:00
cc2d08506e
accelerator_*.h files should not be ignored
2021-10-01 12:55:39 -06:00
bed1ff9a95
Remove more files from .gitignore
2021-10-01 12:46:06 -06:00
61c465c6f3
simplify creation of computes in fix ipi and fix plumed
2021-10-01 14:32:19 -04:00
7e7b8acf4b
Update .gitignore
2021-10-01 12:12:53 -06:00
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
