7d5fc356fe
Merge pull request #3311 from akohlmey/next-stable-release
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Update stable branch to next stable release
2022-06-22 17:33:34 -04:00
8103e5a18f
Merge branch 'release' into next-stable-release
2022-06-22 16:29:19 -04:00
e5b56b67fe
Merge branch 'next_patch_release' into next-stable-release
2022-06-21 09:00:40 -04:00
8ffb7e5f89
Merge branch 'collected-small-fixes' into next-stable-release
2022-06-21 09:00:31 -04:00
cb9ab48ce7
Merge branch 'develop' into next-stable-release
2022-06-21 09:00:12 -04:00
1ebb1cee40
Merge branch 'release' into next-stable-release
2022-06-02 21:49:47 -04:00
f0e7101bd2
Merge branch 'develop' into next-stable-release
2022-05-18 06:35:57 -04:00
6fd8b2b177
Merge pull request #3122 from akohlmey/maintenance-2021-09-29
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Third round of maintenance fixes for the stable release
2022-03-24 14:20:52 -04:00
6edaf42b3d
fix temperature initialization bug in KOKKOS nose-hoover code
2022-03-24 11:44:24 -04:00
79c047487d
fix parallel execution bug for shell command
2022-03-24 07:38:44 -04:00
ac5acb9abf
update threebody example
2022-03-24 07:31:02 -04:00
87fbbd3b13
small kokkos fixes from upstream
2022-03-24 07:18:24 -04:00
8ac0ec6473
Changes needed to compile LAMMPS with latest Kokkos develop
2022-03-24 06:09:03 -04:00
8acba74c4d
correct input to load potential file from local folder
2022-03-22 22:32:39 -04:00
34bcbdf41d
update extep potential file
2022-03-22 22:31:48 -04:00
d519ca0213
add missing reaxff files to purge list
2022-03-21 14:34:14 -04:00
a392e8dc09
accept infile with 0 lines, so we can create a template from the restart
2022-03-21 00:33:40 -04:00
a4d4f77bc2
run setup_bodies_dynamic() before processing infile in case that is not resetting all data
2022-03-21 00:32:49 -04:00
83a8f72d83
fix off-by-one bug when writing restart files for rigid bodies
2022-03-20 19:14:13 -04:00
3c54b56cfe
update overlooked date stamp
2022-03-19 21:00:14 -04:00
ff1a08f148
fixes to CMake build for ML-QUIP package from upstream
2022-03-17 18:07:12 -04:00
5a53b0fc03
import python3 compatibility changes to tools/python from upstream
2022-03-16 13:24:53 -04:00
e550600ebe
Error fixed. Epsilon and sigma must also be symmetric
2022-03-16 09:09:52 -04:00
7cb13be52a
fix bug where it was not possible to use an absolute path for write_coeff
2022-03-16 09:08:47 -04:00
ab56d7ecd7
augment cmake library search path to include the CUDA stubs library folder
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this will help configuring and compiling LAMMPS with CUDA support on
machines where there is no CUDA driver installed
2022-03-10 23:02:57 -05:00
bd6ac3ee6d
for 2d systems, rigid bodies always have a moment of inertia and no DOFs need to be subtracted
2022-03-02 16:41:35 -05:00
27ca0a8f41
trigger building an "intel" style neighbor list so that buffers are allocated
2022-02-27 14:50:48 -05:00
f688b9b6b5
use consistent names, avoid memory leaks, fix off-by-1 error in fourier dihedral
2022-02-27 12:25:32 -05:00
16c61b3cc0
add support for plumed 2.6.5, 2.6.6, 2.7.3, 2.7.4, and 2.8.0 (default 2.7.4)
2022-02-25 16:37:00 -05:00
fb480f22fc
make cythonize detection compatible with /bin/dash on ubunutu
2022-02-24 21:24:04 -05:00
d0507559a4
when updating ML-IAP due to adding/removing PYTHON we need to delete and re-add cythonize support
2022-02-24 20:40:55 -05:00
58eb331b08
Python 3 compatibility for log commands in tools/python
2022-02-23 10:22:29 -05:00
c68015ca87
Bug fix for Intel package skip lists with multiple runs.
2022-02-18 05:11:34 -05:00
583c22d6e0
update tools/eam_database from upstream
2022-02-16 11:46:11 -05:00
58a4694d92
Remove incorrect error check in ReaxFF
2022-02-11 16:19:00 -05:00
97cf345528
don't allow exceptions to "escape" a destructor
2022-02-10 21:13:26 -05:00
0658abbdd4
silence possible warnings about missing files on "make clean-all"
2022-02-10 21:10:34 -05:00
72026a58bf
make certain that "offset" is always initialized
2022-02-10 21:05:12 -05:00
7152231a10
plug memory leak
2022-02-10 20:56:51 -05:00
8fe8a667b6
update create.f with changes from NIST database
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also add parameters for Cr and document in README file and change
the code to create output files with .eam.alloy extension
2022-02-10 20:45:16 -05:00
560c543e69
add extra communication of special neighbors when using angle constraints
2022-02-10 20:44:39 -05:00
c5e6650924
import bugfixes for crashes and memory leaks in MSM kspace style from develop
2022-02-10 20:36:35 -05:00
10373ea5c9
avoid failures with "most" presets
2022-02-10 20:11:00 -05:00
992b1cf582
label as update #3
2022-01-25 07:42:00 -05:00
1505f3de06
fix tag caching issue in INTEL package
2022-01-25 07:41:37 -05:00
566efe04f2
always fall back to using the .so extension if available in the LAMMPS module folder
2022-01-19 10:12:50 -05:00
7586adbb6a
Merge pull request #3029 from akohlmey/maintenance-2021-09-29
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Second round of maintenance fixes for the stable release
2022-01-06 19:58:51 -05:00
69d6ddccc5
create missing de,df table elements from linear extrapolation
2022-01-05 15:34:30 -05:00
5ae496dcef
backport array dimension bugfix for NETCDF package in simplified form
2022-01-03 19:55:23 -05:00
bc5d742623
explain that the computed force in python pair is force/r same as in Pair:single()
2022-01-03 10:12:38 -05:00
882e699163
Incorporate bugfixes from issue #3074 , a few additional cleanups
2022-01-03 10:11:18 -05:00
9c725d79d6
correct code example for current code
2022-01-01 16:42:28 -05:00
79fbf437a3
correct format string for Error::one()
2021-12-29 16:19:10 -05:00
d130aa4289
address segfault issue with fix nve/gpu when group is not "all"
2021-12-29 14:06:52 -05:00
5d8b83a251
backport GPU package build system updates from upstream
2021-12-27 20:30:43 -05:00
5a2548a83d
have internal fix/compute ids include the fix id for fix reaxff/species
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this allows using the fix multiple times
also remove code and warning that checks for multiple fix instances
# Conflicts:
# src/REAXFF/fix_reaxff_species.cpp
2021-12-23 11:36:28 -05:00
a85b310e1f
add missing fclose()
2021-12-23 11:28:24 -05:00
e51fd40547
correct names of the pack/unpack routines for forward communication
2021-12-09 18:33:13 -05:00
62f271658b
correct setting forward/reverse buffer size info
2021-12-08 13:58:12 -05:00
0aa742934f
correct docs for pair style local/density
2021-12-08 00:51:52 -05:00
a26a709a7b
correct handling of data packing for forward and reverse communication
2021-12-08 00:51:52 -05:00
027293d285
whitespace
2021-11-24 15:47:05 -05:00
f7d049ac2d
generate atom tags for newly created atoms, if tags are enabled. triclinic support.
2021-11-24 15:36:16 -05:00
ea0ff1c8f7
Update CMake utility function get_lammps_version()
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With the introduction of LAMMPS_UPDATE, version.h is no longer a single line
file. With this change the CMake utility will only process the LAMMPS_VERSION
line. Fixes issue #3038
2021-11-23 10:44:40 -05:00
5c1bb5f13a
Write dump header after sort to fix incorrect atom count for multiproc
2021-11-22 15:52:27 -05:00
24d9b4b611
Update lebedeva potential file and docs based on email on mailing list
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https://matsci.org/t/lammps-users-webpage-and-parameter-file-for-the-lebedeva-potential/39059
2021-11-17 08:45:55 -05:00
a0e75c9006
correct unit description of eta_n0 parameters. fixes #3016
2021-11-17 08:38:09 -05:00
2435b953e1
increment update counter
2021-11-17 07:04:44 -05:00
c042e12323
clarifications and corrections for the discussion of the main git branches
2021-11-17 07:04:13 -05:00
e9efe46db9
update branch names
2021-11-17 07:03:56 -05:00
ecc14b7308
update documentation to refer to the new branch names (develop, release)
2021-11-17 07:03:27 -05:00
0152fe5cdf
fix segfault when using atom style smd as part of a hybrid style
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also remove redundant for clearing
2021-11-16 21:49:56 -05:00
892d17af22
plug memory leaks
2021-11-16 21:49:41 -05:00
2cca00203e
Avoid file name collisions in dump unit tests
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# Conflicts:
# unittest/formats/test_dump_atom.cpp
2021-11-16 15:08:27 -05:00
9f4626a62a
correct uninitialized data access bug due to shadowing of a base class member
2021-11-16 10:51:46 -05:00
e890a0b45e
Merge pull request #2999 from akohlmey/maintenance-2021-09-29
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Maintenance fixes for the stable release
2021-11-09 15:11:19 -05:00
68223f0385
mention that dump sorting is limited to less than 2 billion atoms
2021-11-07 08:31:15 -05:00
1291a88bff
skip MPI tests if they would be oversubscribing the available processors
2021-11-07 08:30:19 -05:00
d9b687450a
account for increased floating point errors when summing numbers to zero
2021-11-07 08:30:04 -05:00
bd950b37d7
change git:// protocol for accessing github to https:// protocol
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https://github.blog/2021-09-01-improving-git-protocol-security-github/
2021-11-02 15:30:27 -04:00
21fcdf8c56
Fix bug in Kokkos neighborlist where stencil wasn't updated for occasional list
2021-11-02 13:17:28 -04:00
6b400fb4bf
fix indexing bug
2021-10-31 16:19:17 -04:00
d982298ab2
update new LAMMPS paper citation info
2021-10-28 10:09:01 -04:00
765fd7f763
Use correct sizeof in memset
2021-10-27 17:46:37 -04:00
0325047c01
update a few GPU kernels so they can be compiled on GPUs without double precisions support
2021-10-21 07:34:05 -04:00
2dce8923ee
more direct version of clearing out loaded plugins
2021-10-19 08:28:19 -04:00
8d1ba074be
wipe out all loaded plugins before destroying the LAMMPS instance
2021-10-18 18:06:09 -04:00
4675a3b560
Only check for GPU double precision support if a GPU is present
2021-10-18 13:44:37 -04:00
8999b1f69f
add a LAMMPS_UPDATE string define to signal updates to stable releases
2021-10-17 18:06:04 -04:00
6c2b19c11b
Add support for an "Update #" appendix to the version string
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This is for informative output only, so that any code depending
on the LAMMPS_VERSION define will not have to be changed and no
warnings will be printed etc.
2021-10-17 18:05:29 -04:00
a425334928
port dump vtk to correctly support custom per-atom arrays and fix some bugs
2021-10-17 11:00:33 -04:00
db2faf2789
fix bugs related to custom per-atom properties in dump style custom
2021-10-17 11:00:21 -04:00
fdbb7d0da4
Report only compatible GPU, i.e. no GPU if mixed/double precision is requested by the hardware does not support it
2021-10-15 20:26:47 -04:00
52cd99918f
pppm kspace styles also require -DFFT_SINGLE when using GPUs in single precision
2021-10-15 20:24:47 -04:00
a3e6a95ffb
allow single precision FFT introspection
2021-10-15 20:24:47 -04:00
5b65169997
correct expansion of fix/compute/variable arguments to avoid bogus thermo outpu
2021-10-15 20:23:57 -04:00
5f3bf69e30
plug memory leaks
2021-10-15 17:00:46 -04:00
507c02b9af
must set define to "see" the lammps_open() library function
2021-10-09 10:21:31 -04:00
b7fe47ba48
Fix bugs and compilation issues in KOKKOS
2021-10-08 09:39:53 -04:00
7dfd11da4b
re-freeze Sphinx and other pip installed packages for doc build
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The change relative to the stable release fixes a bug with python 3.10 support
2021-10-05 10:52:34 -04:00
97ba95f30e
fix a couple more bugs like in 5246cedda6
2021-10-05 10:39:03 -04:00
c1945b4ec9
Fix misplaced MPI calls bug in pair style drip
2021-10-04 07:12:50 -04:00
c4291a4b8e
unfreeze versions of python packages used to build the documentation
2021-10-02 23:57:23 -04:00
5b5dfa86c5
also update eigen download for traditional build
2021-10-02 23:56:28 -04:00
3ca3f6959f
update eigen3 to the latest release and move download to our own server
2021-10-02 22:55:06 -04:00
f7b7bfa406
Avoid assertions in PythonCapabilities check when using external KOKKOS
2021-10-01 12:05:59 -04:00
3d2f29c92d
fix memory allocation bug causing memory corruption on 32-bit arches
2021-10-01 01:16:45 -04:00
