27d065a682
sync with develop
2023-08-03 11:33:14 -04:00
f1dd7f1415
Merge tag 'patch_2Aug2023' into maintenance
...
LAMMPS feature release 2 August 2023
2023-08-03 11:14:29 -04:00
59e8b9370f
plug memory leak in FixNHIntel class
2023-04-24 20:58:33 -04:00
39fa2021e2
avoid 32-bit integer overflow when allocating memory for neighbor list copy
2023-04-24 20:45:49 -04:00
83f492a195
must initialize vest_temp to null to avoid segfaults
2023-04-24 20:44:44 -04:00
933457acbe
Templated functions calling math libraries should use type-aware calls
2023-04-24 19:55:39 -04:00
06f4099566
Vector masking is part of AVX512, not limited to Intel compiler
2023-04-24 19:54:19 -04:00
5624a78b17
Fix uninitialized memebr
2023-04-24 19:53:57 -04:00
47e875142f
update version string
2023-04-22 18:37:52 -04:00
62c844d5ac
update version string for stable release update
2023-04-22 14:56:44 -04:00
263b6d4d6f
compilation fix for Fedora 38 from upstream
2023-04-22 14:32:11 -04:00
4acca38a65
remove text that only applies to newer LAMMPS versions
2023-04-22 12:19:37 -04:00
4cf642b526
correct docs for fix edpd/source and fix tdpd/source
2023-04-22 12:12:38 -04:00
52fc8f05ee
update CMake script for PLUMED package to support cross-compilation to Windows
2023-04-10 09:23:19 -04:00
047df9aa9e
mark as maintenance branch version
2023-03-31 09:52:58 -04:00
fb3bd20dff
update fmtlib to version 9.1.0 to avoid compilation issues with PGI/NVHPC compilers
2023-03-23 18:34:42 -04:00
c7d62c4709
fix ids once bug in compute chunk/atom
2023-03-22 22:21:13 -04:00
b18008c58d
add useful comments
2023-03-22 22:18:29 -04:00
9469321e3d
Fixed bug in fep tools
2023-03-22 22:18:04 -04:00
a4a9efeefc
Fixed bug in fep tools
2023-03-22 22:17:55 -04:00
70744f10e0
backport fix property/atom bugfix for KOKKOS
2023-03-22 22:17:10 -04:00
9bea55bd77
update fix mscg example
2023-03-16 14:55:20 -04:00
73525b3bbc
Download the latest MSCG snapshot to address bug in library.
2023-03-16 14:55:05 -04:00
9cf67699cc
include fixes and updates from upstream
2023-03-16 12:44:18 -04:00
666fe4cfbe
fix two bugs in the ndx2group command
2023-03-16 12:35:53 -04:00
ed7bd50500
must recompile main.o when MDI package is installed/uninstalled
2023-03-12 22:31:06 -04:00
d241e26d03
allow dynamic groups with fix oneway
2023-02-25 12:03:40 -05:00
73e7163ed6
don't store topology information with ghost atoms. they will be ignored.
2023-02-24 22:56:17 -05:00
5a5a86684a
Fix the adios2::ADIOS constructor calls that were deprecated in adios 2.8 and removed in 2.9. The fix is backward compatible with older adios2 versions as well.
2023-02-23 15:39:01 -05:00
ae3f57e89a
fix bug in fix wall/morse that was computing forces incorrectly
2023-02-23 15:38:20 -05:00
fff7b2a859
update unit test for correct fix wall/morse
2023-02-23 15:37:58 -05:00
83ba1c9d20
Merge pull request #3645 from akohlmey/more-backports-to-stable
...
More backports of fixes to stable release
2023-02-17 16:27:13 -05:00
ce10614cab
backport region check move to init() function for fix gcmc and fix widom
2023-02-17 12:44:58 -05:00
facbeac052
move definition of MAXBIGINT_DOUBLE to variable.cpp
2023-02-17 12:29:17 -05:00
188ee5af15
use MAXBIGINT_DOUBLE which does not overflow when casting back to bigint
2023-02-12 04:08:11 -05:00
f176b8b14c
consistently support special_bonds settings in pair style gauss
2023-02-10 05:09:58 -05:00
2396b2feea
Fixed bugs with gauss/gpu in bonded systems, including factor_lj in forces and energies
2023-02-10 05:02:43 -05:00
4399c1b6c1
Merge pull request #3593 from akohlmey/maintenance-2022-06-23
...
Third round of maintenance fixes and backports for the stable release
2023-02-09 22:53:11 -05:00
fd046c8fd8
Merge branch 'maintenance' into maintenance-2022-06-23
2023-02-09 20:17:06 -05:00
09b7694601
Merge pull request #3595 from akohlmey/maintenance-many-files
...
Additional non-functional maintenance changes for the stable version
2023-02-09 20:09:28 -05:00
df20503434
make fallback url function available to plugin compilations
2023-02-09 08:14:23 -05:00
f4aa24a36a
roll back changes for vec3_scale() and vec3_scaleadd() and use temporary vector
2023-02-08 20:33:38 -05:00
007c04bc97
correct preprocessor logic for non-Linux machines
2023-02-08 16:45:48 -05:00
418d1e16e1
recover compilation of tersoff kernels with CUDA
2023-02-08 11:17:09 -05:00
6471d781d0
recover kernel failure for tersoff with mixed and single precision
2023-02-08 09:14:37 -05:00
97ddc5917c
another OpenCL bugfix attempt from Trung
2023-02-08 08:26:22 -05:00
a95ff20647
swap nvcc default arch from Maxwell to Pascal
...
This is to avoid deprecation warnings with CUDA 11.6 and later
2023-02-07 08:34:01 -05:00
9e0a9e2601
correct logic
2023-02-07 00:00:17 -05:00
8b34d65970
add download fallback handling
2023-02-07 00:00:07 -05:00
0a1c2bcccc
fix failing unit tests with OpenCL
2023-02-06 18:40:07 -05:00
c9442c591c
re-enable new neighbor lists for CUDA 12.0 and later
2023-02-05 03:01:46 -05:00
b7d316031d
nullify freed pointers in list of dump data
2023-02-03 20:39:47 -05:00
361e9f3ea5
avoid illegal memory access in destructor after variables have been deleted
2023-02-03 20:26:42 -05:00
28120793b8
backport PR #3631
2023-02-02 22:21:15 -05:00
f32ce8377e
change default arch in nvcc_wrapper, so it can still run with cuda 12
2023-02-01 11:35:59 -05:00
9021b8bc6a
implement download fallback for traditional make build
2023-02-01 06:53:53 -05:00
838fe3020d
add support for building a static lammps-shell executable with Linux/MUSL
2023-01-31 22:23:41 -05:00
b4d4dcbcbc
simplify
2023-01-31 20:35:18 -05:00
52a892ec46
simplify
2023-01-31 20:32:41 -05:00
0ee3d9da5d
port triclinic region vs box check from fix gcmc to fix widom
2023-01-31 20:29:18 -05:00
50afb292b0
compare region extent with box bounds for triclinic
2023-01-31 20:28:25 -05:00
275ef9da17
update n2p2 lib version for traditional make, too.
2023-01-31 20:28:15 -05:00
b6a87390a3
revert MD5 hash to current value after GitHub reversed its change
2023-01-31 20:28:04 -05:00
72178631c5
update N2P2 library to version 2.2.0
2023-01-31 20:27:57 -05:00
f8859c5fca
implement download fallback URLs pointing to download.lammps.org for CMake
2023-01-31 20:22:06 -05:00
979119a29b
backport fixes to KOKKOS and REAXFF from PR #3621
2023-01-31 20:18:38 -05:00
bc66572275
Fix out of bounds access in pair_vashishta_kokkos with skip list
2023-01-31 20:00:45 -05:00
609231675f
Allow neighbor class to set newton flag in Kokkos neigh list
2023-01-31 19:55:07 -05:00
d9675b5da4
Fix QUIP compilation with Intel compilers.
2023-01-30 08:11:52 -05:00
7d32b4f42a
make Kokkos lib compatible with musl-libc
...
Note: this was adapted from https://github.com/kokkos/kokkos/pull/5678
to be usable without requiring C++17
2023-01-27 12:21:39 -05:00
697e5b15ec
forcibly disable COMPRESS package is zlib is not found
2023-01-27 07:29:25 -05:00
ade0718c11
make compatible to non-glibc Linux
2023-01-27 07:26:23 -05:00
31033ff6e0
must initialize "np" in constructor
2023-01-26 18:34:21 -05:00
9a598ba5a8
backport fix pimd bugfix from develop
2023-01-26 15:59:26 -05:00
ff20448b1d
add image to the cover page of the PDF version of the manual
2023-01-26 11:23:46 -05:00
af5229ba58
swap constexpr back to const
2023-01-26 09:58:26 -05:00
b180200c48
check if variable value is a valid number before converting it
2023-01-26 07:10:50 -05:00
27441cf2ea
update developer contact info in a few more files
2023-01-25 22:24:22 -05:00
db61bf609b
plug memory leaks in couple examples
2023-01-25 21:48:29 -05:00
015fa4cb0a
update embedded docs
2023-01-25 21:44:04 -05:00
62f6f91146
minor typo and rewording
2023-01-25 21:42:37 -05:00
e163b0b1d7
portability improvements for Solaris/OpenIndiana
2023-01-25 21:40:23 -05:00
169a886898
cannot test PYTHON package if it is not installed
2023-01-25 21:37:22 -05:00
cbd276c49d
correct prototype for documentation
2023-01-25 21:32:03 -05:00
183c6c06ff
small tweaks to the "breadcrumbs" part of the theme to avoid double inserting a separation character
2023-01-25 21:28:18 -05:00
93a46da58e
add image to the cover page of the PDF version of the manual
2023-01-25 21:24:27 -05:00
6b6a47bd3c
Small tweaks
2023-01-25 21:21:08 -05:00
4a0a98a0fd
Small bugfixes for Kokkos
2023-01-25 21:20:59 -05:00
369ea4fd26
Add this
2023-01-25 21:17:30 -05:00
d63c002bf5
Use group for Kokkos nvt temp compute
2023-01-25 21:17:22 -05:00
e931d3153b
small improvements from upstream
2023-01-13 17:52:28 -05:00
2913c063d4
whitespace
2023-01-13 14:51:21 -05:00
5606b57646
Update SECURITY.md
...
I found the overlapping meanings of release/update/patch a bit confusing, especially when sometimes referring to a branch name and sometimes used as a general description. So I reworked it, trying to preserve meaning. I deleted the last sentence, because I did not understand it, it may need to be added again.
2023-01-13 11:30:07 -07:00
0fafe34008
import updates to library plugin loader from upstream
2023-01-13 05:21:33 -05:00
a9a1640d67
reorder
2023-01-12 18:28:17 -05:00
812363fb99
lammpsplugin bugfix from Stan
2023-01-12 18:24:04 -05:00
b40e0be1c9
reset to current state of the library interface and remove parts from upstream that have crept in
2023-01-12 12:08:00 -05:00
1be973da07
update from upstream
2023-01-11 22:31:06 -05:00
aca2c52795
update LAMMPS developer contact info
2023-01-11 22:25:25 -05:00
536b2ab7e5
restore accidentally deleted file
2023-01-11 22:16:31 -05:00
ccef293161
remove obsolete comment
2023-01-11 22:11:53 -05:00
4b0de87813
silence compiler warning
2023-01-11 21:59:35 -05:00
fa22aef31b
Fix obscure bug in Kokkos neigh list build
2023-01-11 21:53:16 -05:00
cb7544a615
import modernization from upstream
2023-01-11 21:41:58 -05:00
a9be4906b7
import safer ghost cutoff determination for manybody GPU styles from upstream
2023-01-11 21:41:43 -05:00
6f36d21a04
GPU library updates
2023-01-11 21:34:42 -05:00
c55a15c4dc
make AWPMD compatible with MSVC and c++-linalg on Windows
2023-01-11 21:23:03 -05:00
8f01dad1a9
add tools/tabulate
2023-01-11 21:21:51 -05:00
db6e1aa20d
some more documentation updates
2023-01-11 21:21:03 -05:00
3cee69a077
correct Kokkos device/arch info ouput in CMake summary
2023-01-11 18:15:56 -05:00
69ffe71595
update unit tests for code corrections
2023-01-11 07:45:50 -05:00
16fa033111
fix issues with bundled meam/spline potentials
2023-01-11 06:40:54 -05:00
8e494aa771
updates and bugfixes for liblammpsplugin plugin loader for LAMMPS shared lib
2023-01-11 06:11:46 -05:00
d203cce8b5
documentation updates from upstream
2023-01-11 06:07:19 -05:00
f8de1b1a75
use official API for utils::logmesg(), stricter/consistent checking for integer and floats
2023-01-11 05:54:35 -05:00
de89a25a25
final CMake sync with upstream
2023-01-11 05:03:00 -05:00
f982e95267
update developer info in unittest tree
2023-01-11 01:28:52 -05:00
293d0cdb58
fix typo
2023-01-11 01:26:54 -05:00
011f2651ee
update
2023-01-11 01:26:48 -05:00
a8d3c43a77
update version
2023-01-11 01:26:35 -05:00
c19641f8b3
synchronize CMake scripting with upstream
2023-01-11 01:04:32 -05:00
6596b343ff
sync docs with fire minimizer code features
2023-01-10 21:55:56 -05:00
b6dbb0330c
update list of commands in pygments LAMMPS lexer
2023-01-10 21:55:56 -05:00
0dd138666a
update for accelerated versions
2023-01-10 21:55:56 -05:00
33b9fec150
synchronize sphinx configuration with upstream
2023-01-10 21:55:56 -05:00
32b020a165
Increase communication cutoff for TIP4P pair styles, if needed
...
This avoids error of H atom not found when the O atom is a ghost.
2023-01-10 21:55:56 -05:00
c1db230331
Fix bug in Kokkos ReaxFF on GPUs
2023-01-10 21:55:56 -05:00
254c052ecc
Fix GPU tag issues in other Kokkos styles
2023-01-10 21:55:56 -05:00
8e889dfa7c
offset is not used (by construction of the potential)
2023-01-10 21:55:55 -05:00
5b6a52a646
correct suffix handling with compute fep
2023-01-10 21:55:55 -05:00
55f56deb63
bugfix for minimization with KOKKOS when using fix box/relax
2023-01-10 21:55:55 -05:00
bfe127a720
cosmetic
2023-01-10 21:55:55 -05:00
d95c8911a3
tweak intel compiler settings
2023-01-10 21:55:55 -05:00
0380f9d854
consistently prefix deep_copy() with Kokkos::
2023-01-10 21:55:55 -05:00
71b1d60363
bugfix for gaussian bond/angle styles to avoid premature truncation of potential
2023-01-10 21:55:55 -05:00
8b1f92fabd
better error handling when reading table files
2023-01-10 21:55:55 -05:00
419af0cf28
dead code removal
2023-01-10 21:55:45 -05:00
9030c59932
bugfix for nm/cut argument parsing
2023-01-10 21:55:21 -05:00
ee88078150
bugfix for DPD with exclusions other than 0.0 or 1.0
2023-01-10 21:55:21 -05:00
04451f6072
recover compilation
2023-01-10 21:55:21 -05:00
2364f7f08b
bugfix for incorrect stress tally in dihedral style table
2023-01-10 21:55:21 -05:00
7f82a58f51
auto loop optimizations
2023-01-10 21:55:21 -05:00
1caf074ba1
avoid excess string copy in auto loops
2023-01-10 21:55:20 -05:00
34677f78c2
initialize ADIOS dumps only the first time when used in multiple runs
2023-01-10 21:55:20 -05:00
e095609ac6
update lammps theme base theme from read-the-docs version 1.0.0 to 1.1.1
2023-01-10 21:54:35 -05:00
1122408957
dynamic cast whitespace
2023-01-10 21:53:53 -05:00
5f9b78ca01
update developer reference text
2023-01-10 21:53:09 -05:00
fe138fc75c
add support for building/using the ADIOS package without MPI
...
This needs the ADIOS2 installation being configured accordingly.
2023-01-10 12:38:20 -05:00
31c324ff61
remove references to long obsolete .d dependency files
2023-01-10 12:32:22 -05:00
30564ed8b7
import traditional build system updates and fixes from develop branch
2023-01-10 12:16:59 -05:00
f05bfe45a8
Synchronize GitHub related files and settings with develop branch
2023-01-10 11:50:49 -05:00
88c8b6ec6f
Merge pull request #3460 from akohlmey/maintenance-2022-06-23
...
Second round of maintenance fixes and backports for the stable release
2022-11-03 12:21:59 -04:00
f01e28f574
add missing parts to ELECTRODE package docs for traditional make. sync with upstream.
2022-10-27 16:29:28 -04:00
96627d27b1
add support to detect the BuildID of Windows 10 22H2
2022-10-27 12:56:30 -04:00
b3fc574a6a
use googletest aliased targets consistently
2022-10-26 22:46:31 -04:00
8a3f7560c9
drop special OpenMP flags from presets. Will be detected by FindOpenMP.
2022-10-26 22:46:21 -04:00
8406e92a9a
downgrade KOKKOS OpenMP check to version 3.1
...
need to apply special exception for NVHPC/PGI compilers
2022-10-26 22:46:13 -04:00
3b376b4448
modernize OpenMP detection and check for omp.h in CMake
2022-10-26 22:46:03 -04:00
ca3b7be623
add compatibility to VTK version 9.0 and above
2022-10-24 16:25:25 -04:00
c825c52d2f
update required version
2022-10-23 03:45:57 -04:00
0ea0e4ce59
modernize calls to access the list of fixes in the Modify class
2022-10-23 03:16:26 -04:00
d53d4b4d99
use inline insertion sort for short array
2022-10-23 03:16:13 -04:00
b37cd14dd1
avoid superfluous calls to utils::strdup and improve error messages
2022-10-23 03:15:58 -04:00
a921a6bdc1
silence compiler warning about not copying the final null byte
2022-10-23 03:15:47 -04:00
51a0345941
Update fix_bond_react.rst
2022-10-23 03:15:35 -04:00
8d70960e2d
bond/react: create atoms error check
...
check that post-reaction template has 'Coords' section if it has 'CreateIDs' section
2022-10-23 03:15:12 -04:00
5661703b30
Update pair_threebody_table.cpp
...
Correcting for hard coded ntheta = 79 in the extreme case that theta is exactly equal to 180.0 degrees.
2022-10-23 03:13:50 -04:00
bc30304f72
update plumed package version to 2.8.1
2022-10-22 23:01:47 -04:00
c76da483fb
must bootstrap centos 7 from dockerhub now
2022-10-22 22:59:52 -04:00
036a1e47d2
replace one more suffix
2022-10-22 22:28:35 -04:00
5430c3b592
add workaround for missing links to fortran functions in sphinx output
2022-10-21 19:01:31 -04:00
9b7cb8200c
small sphinx tweaks. require sphinx 5.2 or later.
2022-10-21 19:01:24 -04:00
550eedbb1f
make Linux behavior default for loading Python shared lib
...
This adds portability to platforms like FreeBSD
2022-10-21 15:52:26 -04:00
3a058f278d
Python support in ML-IAP requires NumPy. Check for it if CMake supports it.
2022-10-21 15:50:08 -04:00
0f7f0b5f86
find cythonize executable on recent FreeBSD versions
2022-10-21 11:39:02 -04:00
3de7534b84
try to make more portable (in case this ever gets ported to windows)
2022-10-21 11:38:50 -04:00
7065462faf
add md5sums for plumed 2.7.5 and 2.8.1, update default version to 2.8.1
2022-10-21 11:38:40 -04:00
2e9d8e1ccb
preserve pair/only package setting during clear command
2022-10-19 14:50:27 -04:00
19b84f7cbd
delete atomfile variables when using the clear command
2022-10-19 14:44:10 -04:00
9b7c445a15
include non-buffered flag
2022-10-19 14:44:04 -04:00
91e56444ce
add CMake check that will refuse compilation of unit tests or skip tests
...
This is mainly because the default compilers on RHEL/CentOS 7.x are
not sufficient to compile googletest. Also some Fortran module test
requires a working F90 module and others are more recent Fortran compiler.
2022-10-17 18:12:21 -04:00
9b3c8c36bd
update version
2022-10-14 21:35:16 -04:00
3403520967
Fix issue with KSpace slab correction energy with non-neutral systems
2022-10-11 16:37:45 -04:00
d8f969f1df
update python package requirements for building the manual
2022-09-30 20:18:05 -04:00
3487deccb6
update broken URLs
2022-09-27 08:03:11 -04:00
0926fc627d
step update counter
2022-09-25 09:04:45 -04:00
7999778d94
initialize sllod fixes consistently
2022-09-25 07:02:35 -04:00
b4ef4c1ff2
correct indentation
2022-09-25 07:02:35 -04:00
72b08e4b87
backport dump fixes from develop
2022-09-25 07:02:28 -04:00
faa64a84e8
bugfixes and updates to the DIELECTRIC package from upstream
2022-09-09 19:42:01 -04:00
32b67fff2b
print an error if the filename before '*' is too long for the regex matcher
2022-09-07 21:06:19 -04:00
f3dbf4122d
extend the length to which the regex matcher checks strings to 256 chars.
2022-09-07 20:47:16 -04:00
e25ac786da
must apply bond/angle offsets when determining shake bond/angle types
2022-09-05 10:52:06 -04:00
f30fba0061
support paths with blanks and avoid race condition when updating potentials
2022-09-02 21:33:30 -04:00
03f319604f
recover dump_modify every behavior
2022-08-31 17:26:09 -04:00
0782dab1ec
properly initialize result storage for per-chunk arrays
2022-08-29 13:04:40 -04:00
c43cce54ab
re-initialize neighbor lists at end to clear out the occasional list entry
2022-08-28 11:47:27 -04:00
281a368702
correct pair coeff mixing diagnostic for CLASS2 pair styles
2022-08-28 05:51:38 -04:00
f28d69b429
bugfix for writing data files with atom style dielectric
2022-08-19 16:18:38 -04:00
e674e0c927
correctly handle the case where there are no atoms in the fix group
2022-08-14 03:53:02 -04:00
eebabf99b8
adjust location of local ref targets for recent sphinx versions
2022-08-05 22:09:01 -04:00
23a19f4431
need new CSS hack to hide duplicate headers derived from the navigation bar
2022-08-05 21:46:38 -04:00
d618b0ffc0
Merge pull request #3324 from akohlmey/maintenance-2022-06-23
...
First round of maintenance fixes for the stable release
2022-08-05 16:57:43 -04:00
ffc71b8733
energy is not an array
2022-08-05 08:23:23 -04:00
564df78698
fix typo
2022-08-05 08:22:59 -04:00
8db0b5ca39
fix index copy-n-paste error
2022-08-05 08:22:09 -04:00
79e26fe829
correct bond style bpm/rotational example
2022-08-05 03:24:29 -04:00
523d4b0242
correct issues in fix adapt and fix adapt/fep related to using fix STORE
2022-08-04 10:19:26 -04:00
fe39a3e581
Documentation updates for simulations including dipoles
2022-08-03 16:47:29 -04:00
081cc1f992
clarification on what constituets single, double, and triple quotes.
2022-08-03 01:51:43 -04:00
53c80c2c00
match pow(0,0) = 1.0 behavior in powint()
2022-07-31 18:52:08 -04:00
554b64a147
avoid deprecation warning and update PyPy package requirements
2022-07-30 17:37:35 -04:00
dc08dba592
update embedded search box
2022-07-28 18:58:58 -04:00
0eaa2775cd
document missing call
2022-07-27 22:13:33 -04:00
852673ce41
fix off-by-one bug
2022-07-27 21:44:22 -04:00
8c711e405a
correct make command line example
2022-07-27 08:38:37 -04:00
25b9f95061
add check on extracting elements twice from the library to avoid opaque error later
2022-07-26 15:01:03 -04:00
ee66a6f8c1
correct formatting
2022-07-26 12:34:05 -04:00
b694a5f582
add reference
2022-07-26 12:33:57 -04:00
7ab3fce93f
correct typos
2022-07-26 12:33:48 -04:00
1f9509cb6f
strip off -pendantic-errors flag when compiling with nvcc_wrapper to fix error compiling ML-PACE
2022-07-18 14:00:53 -04:00
cad1d8ece4
correct unit tests for dump local
2022-07-17 12:16:01 -04:00
b709d75f80
add support for dump_modify colname to dump local
2022-07-17 11:52:15 -04:00
5839909061
fix cut-n-paste error and improve error message
2022-07-17 11:46:51 -04:00
30f374de58
clarify
2022-07-16 06:42:19 -04:00
0f9fec05fb
disallow use of variable functions vdisplace(), swiggle(), and cwiggle() with fix dt/reset
2022-07-16 06:42:11 -04:00
972a86f0ec
fix cut-n-paste typo
2022-07-15 19:06:14 -04:00
7338ebfc94
Update Errors_warnings.rst
2022-07-15 12:28:07 -04:00
7132152693
Update Errors_messages.rst
2022-07-15 12:27:57 -04:00
c9925f64f7
cosmetic changes, silence warnings, avoid temporary char buffers
2022-07-15 12:27:48 -04:00
6da523c8b8
very-small-templates bugfix
2022-07-15 12:27:36 -04:00
0522284589
bugfix: specials update corner case
2022-07-15 12:27:26 -04:00
e10a66dabc
allow ramp(x,y) to be used in between runs (returning x) and avoid division by zero on run 0
2022-07-15 05:41:12 -04:00
51dd631a76
Fix bug in vtk dump
2022-07-15 04:29:54 -04:00
d37249787e
work around issues with Intel compilers compiling the GPU package
2022-07-12 00:38:51 -04:00
f44841de69
update unit test
2022-07-07 10:32:47 -04:00
54c5337d2d
apply clang-format
2022-07-07 10:32:32 -04:00
efb0e63bf6
correct force and energy for excluded pairs
2022-07-07 10:32:20 -04:00
13d78c3afa
Update Kokkos version in CMake
2022-07-04 10:49:03 -04:00
f2910b1d9c
Update Kokkos library in LAMMPS to v3.6.1
2022-07-04 10:48:51 -04:00
78b22a64aa
formatting corrections and minor tweaks to the Argon viscosity howto
2022-07-01 09:27:43 -04:00
8bb1880c9d
Fixed temperature in argon GK example
2022-07-01 09:27:36 -04:00
e7b36c7b90
make certain to switch to the expected source folder when building n2p2 lib
2022-07-01 05:49:07 -04:00
d7804e3770
MPI may need to include multiple folders (e.g. on Ubuntu with OpenMPI)
2022-06-30 23:53:57 -04:00
8d0f9695d2
update googletest to version 1.12.1
2022-06-30 14:57:22 -04:00
52b2e4f364
add Update 1 string to version info
2022-06-29 17:44:29 -04:00
41140149ea
whitespace
2022-06-29 17:06:11 -04:00
85e556ac8f
add more unit tests for boolean expressions
2022-06-29 17:05:37 -04:00
cd5437a7e2
fix bug in recent bugfix
2022-06-29 17:05:27 -04:00
00cc82ac94
update and expand unit tests for if() command boolean evaluation
2022-06-29 17:04:49 -04:00
20f87e3f1d
change boolean = single string to an error
2022-06-29 17:04:34 -04:00
97e34f0667
better error strings
2022-06-29 17:04:23 -04:00
3e5da9b09a
more consistency checks
2022-06-29 17:04:12 -04:00
a62fcca7a4
Boolean expression corner case
2022-06-29 17:04:01 -04:00
778d59fa6b
whitespace
2022-06-29 05:19:10 -04:00
3833a85d7a
Add missing grow to Kokkos unpack_exchange
2022-06-29 05:17:55 -04:00
6d961ab29f
Fix small memory leak in SNAP
2022-06-29 05:17:46 -04:00
001824e0f6
Small tweaks
2022-06-29 05:17:36 -04:00
953d32f9b3
Prevent view bounds error when a proc has no atoms
2022-06-29 05:17:26 -04:00
edba922665
Add missing GPU <--> CPU data transfer in minimize Kokkos
2022-06-29 05:17:17 -04:00
53806d4601
Add more missing Kokkos data movement
2022-06-29 05:17:06 -04:00
67597722d5
intergrate references to dump cfg/uef into the dump command docs
2022-06-25 06:19:04 -04:00
337794a9e9
add crosscompiling with MPI support to plugins package
2022-06-24 06:52:08 -04:00
5f5fb895ff
add "package" target to support building a windows installer with NSIS
2022-06-24 01:25:54 -04:00
0302d03bc6
must set thirdparty download URL variable for downloading MPICH4Win
2022-06-23 23:20:49 -04:00
0a4fef369f
may check for MPI library Fortran support only if MPI is enabled
2022-06-23 15:57:54 -04:00
7d5fc356fe
Merge pull request #3311 from akohlmey/next-stable-release
...
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
...
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
...
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
...
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
...
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
...
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()
...
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
...
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
...
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
...
# 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
...
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
...
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
...
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
...
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
