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
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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
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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
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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
ae18e1e01c
Merge pull request #3310 from akohlmey/next_patch_release
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Update version strings for the next patch release
2022-06-22 16:26:46 -04:00
ad35bbcb65
Merge pull request #3309 from akohlmey/collected-small-fixes
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More fixes and small changes for the stable release
2022-06-22 15:16:01 -04:00
1099199e93
remove any remap related documentation. add paragraph about file compatibility
2022-06-22 14:22:23 -04:00
c5999df303
remove dead code and silence compiler warning about it
2022-06-22 10:32:03 -04:00
9b8c19c1a5
correct docs about how to get synchronized timings
2022-06-22 10:24:56 -04:00
2fb3608462
update/correct contact info
2022-06-22 07:06:16 -04:00
37f056c455
get array and vector sizes from the avaiable APIs
2022-06-22 07:06:00 -04:00
49331be33e
simplify
2022-06-22 07:05:30 -04:00
3f6add4c40
Merge branch 'fortran2_updates' of github.com:hammondkd/lammps into collected-small-fixes
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# Conflicts:
# examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
# examples/COUPLE/fortran2/LAMMPS-wrapper.h
2022-06-22 06:41:37 -04:00
c0b109f715
Fixed some typos and updated e-mail addresses in examples/COUPLE/fortran2
2022-06-21 20:53:45 -05:00
b0c673d856
updates from Karl Hammond to adjust his email and correct an error message
2022-06-21 20:37:20 -04:00
b0f4ef8a39
update docs for noremap option to read_restart
2022-06-21 20:19:13 -04:00
7d49ad5924
enable remap for restarting by default, add noremap option
2022-06-21 19:42:17 -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
6815b27cd5
step version strings for the next patch release
2022-06-21 08:52:11 -04:00
ad20e54638
fix typos
2022-06-20 23:19:00 -04:00
ec46510d2e
add local extract_compute() tests
2022-06-20 23:07:01 -04:00
033af0c507
add unit test for extracting local vector and array via numpy
2022-06-20 18:48:50 -04:00
78129f9078
update embedded docs for LMP_SIZE_VECTOR update for extract_compute()
2022-06-20 18:23:20 -04:00
ac615059a7
update some linewraps for 100 col limit
2022-06-20 18:15:02 -04:00
ffc5b12c5f
correct handling data of local computes which always needs to check rows and cols
2022-06-20 18:10:57 -04:00
3828c857f7
accept LMP_SIZE_VECTOR as alias for LMP_SIZE_ROWS with local computes
2022-06-20 18:10:19 -04:00
063fc47f64
tweak to avoid test failure on FreeBSD
2022-06-19 06:38:14 -04:00
f831a776be
correct python example
2022-06-18 22:25:32 -04:00
b46773e398
add support for writing a dump file footer
2022-06-17 15:53:04 -04:00
fe1feb58d8
Merge pull request #3306 from akohlmey/makewheel-fix
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Fix issues with building a wheel file during 'make install-python'
2022-06-17 11:58:18 -04:00
deac9f05b1
move the created wheel to the build folder at the end
2022-06-17 08:05:28 -04:00
18f9e5836b
support installing the built wheel into virtual environment, if active
2022-06-17 06:52:25 -04:00
21b3020a97
make the "makewheel.py" script independent from the activate_this.py script
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The "activate_this.py" script only seems to be included in virtualenv,
but not venv. Now we implement its effect directly.
2022-06-17 00:10:06 -04:00
dd3aab0c66
Merge pull request #3300 from lammps/doc-package-update
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Update package affiliation for Zhen Li
2022-06-16 18:04:45 -04:00
58152cdc68
Merge pull request #3304 from lammps/dependabot/github_actions/actions/cache-3
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Bump actions/cache from 2 to 3
2022-06-16 17:48:30 -04:00
04bb611bf2
Merge pull request #3303 from lammps/dependabot/github_actions/actions/setup-python-4
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Bump actions/setup-python from 2 to 4
2022-06-16 17:21:53 -04:00
2fc0a44ab2
Bump actions/cache from 2 to 3
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Bumps [actions/cache](https://github.com/actions/cache ) from 2 to 3.
- [Release notes](https://github.com/actions/cache/releases )
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md )
- [Commits](https://github.com/actions/cache/compare/v2...v3 )
---
updated-dependencies:
- dependency-name: actions/cache
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com >
2022-06-16 19:41:23 +00:00
ba4cbf7055
Bump actions/setup-python from 2 to 4
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Bumps [actions/setup-python](https://github.com/actions/setup-python ) from 2 to 4.
- [Release notes](https://github.com/actions/setup-python/releases )
- [Commits](https://github.com/actions/setup-python/compare/v2...v4 )
---
updated-dependencies:
- dependency-name: actions/setup-python
dependency-type: direct:production
update-type: version-update:semver-major
...
Signed-off-by: dependabot[bot] <support@github.com >
2022-06-16 19:41:20 +00:00
f75115d801
Merge pull request #3301 from turrisxyz/Dependabot-GitHub-Actions
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Included githubactions in the dependabot config
2022-06-16 15:40:59 -04:00
0a5d921f3f
update affiliation in source code as well
2022-06-16 15:37:55 -04:00
cdc0b48a0b
chore: Included githubactions in the dependabot config
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This should help with keeping the GitHub actions updated on new releases. This will also help with keeping it secure.
Dependabot helps in keeping the supply chain secure https://docs.github.com/en/code-security/dependabot
GitHub actions up to date https://docs.github.com/en/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
https://github.com/ossf/scorecard/blob/main/docs/checks.md#dependency-update-tool
Signed-off-by: naveen <172697+naveensrinivasan@users.noreply.github.com >
2022-06-16 01:33:01 +00:00
9840aad703
Merge pull request #3299 from akohlmey/fix-codeql-workflow
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Update GitHub workflow files
2022-06-15 10:49:58 -04:00
1403a0dd94
update affilication for Zhen Li
2022-06-15 08:22:59 -06:00
9842879db1
fix typos
2022-06-15 08:14:53 -04:00
03c0b4ae27
upgrade action versions
2022-06-14 19:08:28 -04:00
728e4a5910
add permissions for codeql action
2022-06-14 19:08:01 -04:00
cfe5025495
Merge pull request #3296 from akohlmey/collected-small-changes
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Collected small changes for the next release
2022-06-14 18:18:28 -04:00
927287e3e5
fixes from clang-tidy
2022-06-14 14:06:11 -04:00
35a48f273b
rename local variable shadowing a global one
2022-06-14 10:45:31 -04:00
2028c68bec
remove unused imports
2022-06-14 10:45:05 -04:00
6abb316dba
avoid resource leak
2022-06-14 10:36:21 -04:00
7a64d1358e
remove unused module
2022-06-14 10:36:11 -04:00
26dcb649bb
remove redundant check
2022-06-13 22:10:51 -04:00
423c511d7a
use explicit scoping in destructor
2022-06-13 22:10:43 -04:00
b44d769024
Merge branch 'collected-small-changes' of https://github.com/akohlmey/lammps into collected-small-changes
2022-06-13 22:01:54 -04:00
ea48dd3019
avoid file pointer leakage in dump reader base class.
2022-06-13 22:01:30 -04:00
0f5ae6d48c
remove references to "plugin" options from fix mdi/aimd
2022-06-13 22:00:36 -04:00
c53e53d701
must set suffix variable only when suffixflag is true
2022-06-13 17:47:20 -04:00
33f4bb525b
remove redundant condition
2022-06-13 17:43:40 -04:00
ef48fd2d9c
remove unused imports
2022-06-12 23:36:43 -04:00
ed702aab05
update for renamed style names
2022-06-10 13:00:36 -04:00
82185046ae
Merge pull request #3293 from stanmoore1/compute_ave_sphere_atom
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Fix issues in compute ave/sphere/atom
2022-06-10 12:57:35 -04:00
ac48852b2d
edits to 1st paragraph of description
2022-06-10 08:30:23 -06:00
495418158a
Clarify doc page
2022-06-09 15:51:31 -06:00
5d7b1f3ebb
fix small issues
2022-06-09 15:36:17 -06:00
80727e47f4
Add attribution
2022-06-09 15:31:48 -06:00
9be6e2a064
Use COM velocity
2022-06-09 15:29:40 -06:00
7f1e76b7a5
Don't compute count twice
2022-06-09 14:53:44 -06:00
174219383a
Merge pull request #3290 from akohlmey/collected-small-changes
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Collected small bugfixes and changes and plugin building improvements
2022-06-08 20:13:22 -04:00
1acfb78b3a
Merge pull request #3295 from stanmoore1/kk_reax_tagint
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Fix int32 overflow in Kokkos ReaxFF
2022-06-08 18:29:59 -04:00
483396c757
Merge branch 'collected-small-changes' of https://github.com/akohlmey/lammps into collected-small-changes
2022-06-08 18:06:59 -04:00
68a9db0950
fix typos
2022-06-08 17:07:08 -04:00
5fca9f4d1f
update mathjax version with bugfix release
2022-06-08 17:04:26 -04:00
b6e0d76123
fix some docs formatting issues
2022-06-08 12:47:30 -04:00
7769a8e0de
update ROCm to version 5.1.3 consistently
2022-06-08 12:18:17 -04:00
55fdb7f12a
update GPU container definitions for CUDA 11.7 and singularity -> apptainer
2022-06-08 08:19:54 -04:00
42694ba640
reduce warnings when compiling with KOKKOS
2022-06-07 19:39:36 -04:00
d7680dd785
Fix int32 overflow in Kokkos ReaxFF
2022-06-07 10:11:39 -06:00
96b5a706da
apply clang-format
2022-06-06 21:39:10 -04:00
67d367e714
Fix copy/paste bug
2022-06-06 15:28:40 -07:00
7e77b61042
simplify
2022-06-06 15:23:03 -07:00
5c68fe6e81
Fix issues in compute ave/sphere/atom
2022-06-06 15:15:47 -07:00
8f773be2d6
must open files for xtc dump in binary mode
2022-06-06 15:01:25 -04:00
dcbc5256fa
additional OpenMP suppressions for newer GCC
2022-06-05 12:37:03 -04:00
b338781f88
cosmetic
2022-06-05 06:52:15 -04:00
b0d2cc3052
we can build a plugin instead
2022-06-04 19:23:32 -04:00
3af9546b94
provide README files with pointers to the developer info for plugins
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also add a paragraph with information about the ML-PACE plugin to the
plugin developer info docs.
2022-06-04 11:49:33 -04:00
a232bd3302
refactor LAMMPS plugin building to share more code and to add a demo for ML-PACE
2022-06-04 10:59:25 -04:00
3beb071d38
make plugin compilation settings with MSVC consistent and more compile specific
2022-06-04 05:15:14 -04:00
0dc486c90b
fix bug introduced during stringification
2022-06-04 05:00:28 -04:00
fa9ad10bc1
add missing line to read_data docs about atom style dielectric
2022-06-04 05:00:12 -04:00
25c74652e3
remove bogus tags
2022-06-04 04:25:13 -04:00
587438eb30
fix typo in read_data add merge example
2022-06-03 09:14:34 -04:00
7c4d77f776
tweak epsilon for portability
2022-06-03 07:36:25 -04:00
f9b5679c00
remove unused function arguments
2022-06-03 07:16:19 -04:00
f68247ad6a
add ML-PACE and PLUGIN packages to be compiled with MinGW cross-compilers
2022-06-03 05:10:00 -04:00
1ebb1cee40
Merge branch 'release' into next-stable-release
2022-06-02 21:49:47 -04:00
ceb9466172
Merge pull request #3283 from akohlmey/next_patch_release
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Step version strings for next patch release
2022-06-02 21:22:16 -04:00
2da61d69a1
Merge pull request #3289 from akohlmey/collected-small-changes
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A few last minutes updates and fixes for the next patch release
2022-06-02 20:16:39 -04:00
31f7798720
Merge pull request #3278 from yury-lysogorskiy/feature/ml-pace-multispecies
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ML_PACE package hybrid support and small updates
2022-06-02 19:27:53 -04:00
aad4d093b8
correctly handle the situation that the build folder may have multiple libs downloaded
2022-06-02 18:18:32 -04:00
ad97d18ac7
Merge pull request #3286 from Colvars/update-colvars-lepton
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Update Colvars to 2022-05-24 and copy of Lepton library
2022-06-02 18:09:05 -04:00
4913c72795
Merge pull request #3288 from olavgal/clean_stress_cartesian
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Clean stress cartesian
2022-06-02 17:19:19 -04:00
2a054c17be
- set species type for NULL atom type to -1. species_type=-1 value will not reach ACE Evaluator::compute_atom, but if it will ,then error will be thrown there
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- updating lib pace MD5SUM (for both make and cmake installation scenario), but use same tag name v.2021.10.25.fix2 (add override keyword to ACERadialFunctions, add check for species_type==-1, fix yaml_cpp CMakeLists.txt)
2022-06-02 23:01:54 +02:00
260a5f4d52
update false positives
2022-06-02 14:39:08 -04:00
90add188cb
Merge pull request #3279 from schererc/develop
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Addition of two new MANYBODY pair styles (sw/angle/table and threebody/table)
2022-06-02 14:24:44 -04:00
9d252fe0d2
remove error docs and apply clang-format
2022-06-02 12:57:45 -04:00
a74f64a737
do not allow per-atom arrays to shrink
2022-06-02 12:55:47 -04:00
fc468accf5
clang-format and removed more unused variables
2022-06-02 18:34:48 +02:00
954700dea5
Updated memory calculation and removed unused variables
2022-06-02 18:28:04 +02:00
2742517a4f
Clean up of stress/cartesian
2022-06-02 18:26:09 +02:00
7a02043f18
update docs to list examples and include links to the tutorials
2022-06-02 12:11:10 -04:00
04586e634e
Remove trailing whitespace from Lepton per suggestion from @akohlmey
2022-06-02 11:52:39 -04:00
6c375ffade
Update PDF Colvars manual
2022-06-02 11:48:19 -04:00
3a1423dc48
Update Colvars to 2022-05-24 and copy of Lepton library
...
One bugfix for the Colvars library in the ABF method, and update of the copy
of the Lepton library as per the OpenMM repository.
List of relevant PR.
- 483 Update Lepton via patching procedure
https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)
- 482 Fix integer overflow in log_gradient_finite_diff and gradient_finite_diff
https://github.com/Colvars/colvars/pull/482 (@HanatoK)
2022-06-02 11:24:04 -04:00
5a4688ed44
Update pair_pace.cpp
2022-06-02 09:05:15 -06:00
fdc8bcfbfc
I removed the comment attributed to me, it is now outdated.
2022-06-02 09:03:16 -06:00
e214013a91
tweak epsilon to avoid failure on FreeBSD
2022-06-02 07:53:41 -04:00
8e415f0c00
try to enforce QUIP submodule update strategy
2022-06-01 22:26:35 -04:00
c028dcbdf7
small tweak
2022-06-01 22:14:04 -04:00
e36620059d
simplify, apply clang-format
2022-06-01 22:08:35 -04:00
866391e830
modify so pair style pace will work as pair style hybrid substyle
2022-06-01 21:56:13 -04:00
9f021ba490
whitespace
2022-06-01 21:54:33 -04:00
c0bd4185f8
Merge branch 'develop' into feature/ml-pace-multispecies
2022-06-01 21:10:59 -04:00
30ae7fe66b
Merge pull request #3285 from akohlmey/clang-format-clang-tidy
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Apply clang-tidy and clang-format to update/modernize/simplify recently modified code
2022-06-01 19:04:43 -04:00
bf9b79b734
Merge pull request #3284 from stanmoore1/kk_3280
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Port changes in #3280 to Kokkos
2022-06-01 18:54:58 -04:00
4bf90988e2
Fix bug when comparing equal tags
2022-06-01 14:52:07 -06:00
b45117655e
move patch release date
2022-06-01 16:13:45 -04:00
217b070204
add unit tests
2022-06-01 15:31:49 -04:00
7d31544cc2
simplify and avoid memory access and leak issues in parallel
2022-06-01 15:04:28 -04:00
8a055fdcfa
merge with third manybody table example and provide updated log files
2022-06-01 15:04:07 -04:00
b9b0d7207c
apply clang-format
2022-06-01 14:24:23 -04:00
edea4fa9a2
fix memory allocation/communication issues. avoid memory leaks.
2022-06-01 14:23:30 -04:00
8e9071b01f
move and update threebody/table examples
2022-06-01 14:22:53 -04:00
ee6e18f08e
Merge branch 'develop' into schererc/develop
2022-06-01 12:07:06 -04:00
b85b3e1f4c
fix doc file names and links
2022-06-01 12:06:56 -04:00
95a979c657
examples/PACKAGES: rename pair_sw_3b_table to pair_sw_angle_table
...
including all input and documentation files
2022-06-01 16:34:10 +02:00
e8d9bf0507
examples/PACKAGES: renamed pair_3b_table to pair_threebody_table
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including all input and documentation files
2022-06-01 16:30:37 +02:00
3a19b1eb4b
Update pair_style.rst
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pair_style.rst: update due to name changes from 3b/table to threebody/table and sw/3b/table to sw/angle/table
2022-06-01 16:16:13 +02:00
f6fab8365a
Update Commands_pair.rst
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Commands_pair.rst: update due to name change from 3b/table to threebody/table and sw/3b/table to sw/angle/table
2022-06-01 16:14:37 +02:00
64d67f7604
Update pair_sw_angle_table.rst
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pair_sw_angle_table.rst: minor correction
2022-06-01 16:12:13 +02:00
c1e301ac1a
Update pair_3b_table.rst
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changed documentation and file name from pair style 3b/table to threebody/table
2022-06-01 16:11:47 +02:00
a833baac80
Update pair_sw_angle_table.cpp
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Minor correction in pair_sw_angle_table.cpp
2022-06-01 16:04:09 +02:00
187ccdd222
Update and rename pair_3b_table.cpp to pair_threebody_table.cpp
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changed pair 3b/table to pair threebody/table including name of .cpp file
2022-06-01 16:03:06 +02:00
5756dedfed
Update and rename pair_3b_table.h to pair_threebody_table.h
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changed pair style and file name of header file from 3b/table to threebody/table
2022-06-01 15:52:46 +02:00
ebce66389e
Update and rename pair_sw_3b_table.rst to pair_sw_angle_table.rst
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changed documentation and file name from sw/3b/table to sw/angle/table
2022-06-01 14:24:40 +02:00
8dfa4a8682
Update and rename pair_sw_3b_table.cpp to pair_sw_angle_table.cpp
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Changed .cpp file for pair style sw/3b/table to sw/angle/table
2022-06-01 14:20:30 +02:00
25f24fbab1
Update and rename pair_sw_3b_table.h to pair_sw_angle_table.h
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Renamed header file from sw/3b/table to sw/angle/table
2022-06-01 14:11:32 +02:00
9da3dd796a
delete undesired default members instead of making them inaccessible
2022-06-01 02:30:25 -04:00
5abb6c76af
small tweak
2022-06-01 02:13:02 -04:00
ef6c48dad7
Whack tabs
2022-05-31 14:53:17 -06:00
b675372d99
Use MIN_SINE and add comment
2022-05-31 14:44:18 -06:00
234b9f180a
use clang-tidy and clang-format to update/modernize/simplify code
2022-05-31 14:46:57 -04:00
3b4e698421
Merge branch 'develop' of github.com:lammps/lammps into kk_3280
2022-05-31 12:38:03 -06:00
77835a4258
Port changes in #3280 to Kokkos
2022-05-31 12:36:04 -06:00
7c0c7ce93c
Merge pull request #3281 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2022-05-31 13:10:35 -04:00
b8599ccb42
fix small local vs. ghost atom access inconsistency in pair style bop
2022-05-31 11:52:16 -04:00
de5c2629ac
small tweak
2022-05-31 06:53:19 -04:00
3f332ab0c1
step version strings for next patch release
2022-05-31 06:51:13 -04:00
cc86e9e8a8
remove windows+gcc test (for now)
2022-05-29 19:56:39 -04:00
fa79a66734
feof() returns non-zero not necessarily 1
2022-05-29 19:53:11 -04:00
562cd12d82
revert github action build to LAMMPS repo and develop branch
2022-05-29 15:04:41 -04:00
90730f0d3c
update windows version history
2022-05-29 02:01:21 -04:00
4c36c79652
remove feature for automatic jpeg/png/zlib library download and build
...
this is a post-stable feature and would require a general rewrite of offline processing
2022-05-28 15:20:22 -04:00
81c327edd8
add missing override. remove redundant functionality and disable warnings differently
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this removes an inconsistent overload due to mismatch of arguments
2022-05-28 11:56:26 -04:00
d0edd7129c
update workflows
2022-05-28 04:55:27 -04:00
3615639bdd
Check for a working internet connection.
...
With this check we only do automatic downloads if the check passes
2022-05-28 04:55:10 -04:00
e2dd08a93e
Better handle file- or path-names with spaces
2022-05-28 04:55:10 -04:00
5f811f852f
stop with detailed parser error message with incorrect potential tables
2022-05-28 04:45:52 -04:00
886ad8359e
use venv instead of virtualenv
2022-05-28 04:45:52 -04:00
0b3efa4dd6
set masses from BOP potential files, update unit tests accordingly
2022-05-28 04:45:52 -04:00
e91d1dba98
Merge pull request #3280 from athomps/reaxff-torsion-zero-sine
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Eliminated bad torsion forces for sin(theta) = 0
2022-05-27 12:11:46 -04:00
cfb3d6bdf8
simplify, remove inactive code, plug memory leaks
2022-05-27 07:48:00 -04:00
3ecb6bb54a
Update pair_3b_table.cpp
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Added (forgotten) line "u=pm->mltable->efile[itable];" to compute energy due to read in table values
2022-05-27 12:34:53 +02:00
49a75d576e
Eliminated bad torsion forces when when sin(theta) is zero
2022-05-26 17:28:05 -06:00
ab2b7a2c01
Merge pull request #3275 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-05-26 18:07:43 -04:00
f09e4c7583
remove check on box size from pair style bop
2022-05-26 16:56:43 -04:00
587999fabb
mention that MSM does not support shrink-wrap
2022-05-26 15:33:23 -04:00
f0f6660050
join lines
2022-05-26 12:15:27 -04:00
d9b560e70b
properly integrate into manual
2022-05-26 12:08:21 -04:00
2a7407aa38
programming style updates
2022-05-26 11:41:51 -04:00
48f477e4b4
Update pair_sw_3b_table.rst
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Small correction
2022-05-26 15:19:41 +02:00
e890e5718e
examples/PACKAGES/pair_3b_table: added example for new pair style 3b/table
2022-05-26 14:45:22 +02:00
b8dfb23ede
examples/PACKAGES/pair_sw_3b_table/README: corrections in the text
2022-05-26 14:32:12 +02:00
18c9960db0
examples/pair_sw_3b_table/README: minor correction
2022-05-26 14:25:24 +02:00
f9fbc7f94b
doc/src/pair_3b_table.rst: documentation for added pair style 3b/table
2022-05-26 14:17:36 +02:00
27524742e5
src/MANYBODY/pair_3b_table.h, src/MANYBODY/pair_3b_table.cpp: added pair style for generic fully tabulated three-body forces which has been developed for simulations with Kernel-based machine learning potentials.
2022-05-26 14:16:26 +02:00
770454cb8b
examples/PACKAGES/pair_sw_3b_table: added example for new pair style sw/3b/table
2022-05-26 14:00:06 +02:00
0e114b1041
doc/src/pair_sw_3b_table.rst: documentation for added pair style sw/3b/table
2022-05-26 13:35:40 +02:00
1cfba3d8bb
src/MANYBODY/pair_sw_3b_table.h, src/MANYBODY/pair_sw_3b_table.cpp: added pair style sw/3b/table which is a modification of the SW pair style with tabulated angular potentials
2022-05-26 13:21:47 +02:00
1ae62793eb
src/MANYBODY/pair_sw.h: made read_file(char *) virtual to allow overriding
2022-05-26 13:17:45 +02:00
dba9fdb1ef
Merge branch 'develop' into collected-small-changes
2022-05-26 06:37:24 -04:00
2085c10002
update version of lib-pace to v.2021.10.25.fix2
2022-05-25 17:56:24 +02:00
f6680861a0
BUGFIX: bad array length: initialize maximum number of neighbours with max_jnum=0
2022-05-25 17:27:12 +02:00
7c2a548015
Merge pull request #3277 from erozic/feature-pylammps-verbose
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Verbose object-level option for PyLammps
2022-05-25 10:57:58 -04:00
3ee209d031
update singularity definition for ubuntu22.04LTS
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This now has the changes required to include the openkim-api package
2022-05-25 06:35:08 -04:00
c6c0b269ec
Merge pull request #3276 from shankar1729/develop
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Fixed TIP4P handling in PPPM slab correction.
2022-05-24 17:20:42 -04:00
1aaa9ca4ae
Added documentation for verbose option
2022-05-24 12:02:34 +02:00
b66702c285
Added verbose class option + removed empty output lines
2022-05-24 11:37:44 +02:00
43b57b8aa5
update unit test reference data
2022-05-23 20:14:10 -04:00
ef80bb194a
Fixed TIP4P handling in PPPM slab correction.
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Overridded the slabcorr() function to handle the charge being on the TIP4P "M" site in the dipole calculation (and corresponding force correction). This is important for any long-range electrostatics in aqueous interfaces with the TIP4P model.
2022-05-23 17:28:32 -04:00
3662d998ee
fix typo + cut-n-paste error
2022-05-23 11:53:58 -04:00
bead819070
changes missing from the previous commit
2022-05-23 11:37:00 -04:00
b461a49eee
use _EXECUTABLE consistently instead of _BINARY
2022-05-23 11:14:17 -04:00
9f7833668a
whitespace
2022-05-22 18:15:10 -04:00
0069c4b562
update docs for automatic jpeg/png/zlib library download and build with CMake
2022-05-22 18:10:26 -04:00
46df8abe75
rename jpeg cmake file for consistency
2022-05-22 17:49:54 -04:00
3c3c1377c8
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-22 17:47:58 -04:00
d905d3fbf5
reorganize build settings and presets
2022-05-22 17:46:12 -04:00
1959cd7037
download, build, and link missing png and zlib libraries with CMake
2022-05-22 17:45:42 -04:00
7d3d986d18
download, build, and link a missing jpeg library with CMake
2022-05-22 14:03:20 -04:00
cd8bef3b0b
enable and apply clang-format
2022-05-22 07:04:35 -04:00
9a973e67fa
enable and apply clang-format
2022-05-22 06:46:24 -04:00
b407b2f239
apply clang-format
2022-05-21 23:35:47 -04:00
93692ce308
Improved Windows and Visual Studio version detection
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This now uses the CurrentBuild key to detect the Windows version and only falls back to product name, if that fails.
This is needed because Windows 11 reports itself as Windows 10 in the product name key.
2022-05-21 23:33:13 -04:00
007588f9cb
use GZIP executable variable name consistently
2022-05-21 18:56:58 -04:00
e3e849b266
skip compressed file format tests if gzip executable is not found
2022-05-21 07:37:25 -04:00
18df50356e
Merge pull request #3273 from stanmoore1/kk_mem
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Initial refactor of view allocation in Kokkos package
2022-05-20 16:34:28 -04:00
c3ce77bc8c
improve energy scaling sanity checks
2022-05-20 16:33:46 -04:00
2c5ce83d59
must set Output::next_dump_any to current step with rerun
2022-05-20 09:27:16 -04:00
7eb926c853
clarify the description of pair style none
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explain that pair style none is effectively deleting any existing
pair style and that communication and neighbor list cutoff are affected.
update those explanations for changes to LAMMPS that allow adjusting
those not just with the neighbor list skin.
Also add that pair_coeff must not be used.
2022-05-20 07:14:05 -04:00
08b1034d54
enable and apply clang-format
2022-05-20 07:12:25 -04:00
a16974ca48
enable and apply clang-format
2022-05-20 06:51:36 -04:00
21c2f8a74b
fix miscalculated example
2022-05-20 01:06:21 -04:00
814daf7f4f
fix cut-n-paste error
2022-05-20 01:06:09 -04:00
bfb126ec7c
make neighbor list searches optionally check for the request ID
2022-05-19 23:37:55 -04:00
07e93a643a
spelling
2022-05-19 23:36:54 -04:00
13fc4f3588
must install wheel package before all other packages
2022-05-19 23:07:12 -04:00
36d091baeb
fix underline
2022-05-19 23:06:54 -04:00
4801fa00f8
update MathJax to latest bugfix release
2022-05-19 22:53:48 -04:00
75df9d4f2c
Merge pull request #3271 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-05-19 13:27:28 -04:00
a9431208a2
Use c++11 variadic magic, suggested by @weinbe2
2022-05-19 10:35:10 -06:00
7b0c7c04ed
address sphinx issues and make command list consistently list all min styles
2022-05-19 12:21:06 -04:00
2138aea01f
Merge branch 'two-command-tables' into collected-small-changes
2022-05-19 12:16:37 -04:00
7e75b7bff5
whitespace
2022-05-19 12:16:31 -04:00
5990241fbe
refactor min_style spin doc page
2022-05-19 09:13:47 -06:00
d8d6884def
Remove use_count check, reduce memory use in ReaxFF
2022-05-19 09:10:20 -06:00
eb4c1cd14f
update attempt to hide hwloc pci bus warnings
2022-05-19 07:28:57 -04:00
361e303177
fix cut-n-paste error
2022-05-19 04:14:31 -04:00
898eda794c
minor updates
2022-05-19 00:06:11 -04:00
5ac8e5639a
more information about compiling LAMMPS on windows
2022-05-19 00:06:00 -04:00
cb2126f313
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-18 23:21:52 -04:00
0c73c9307f
Add configurations for Intel Compilers on Windows
2022-05-18 23:20:57 -04:00
c0a8458d89
remove unused class members
2022-05-18 22:06:31 -04:00
b5830aae83
suppress excessive warnings and undesired aborts with Intel LLVM compiler
2022-05-18 21:43:09 -04:00
06ad119844
Initial refactor of view allocation in Kokkos package
2022-05-18 17:15:36 -06:00
fa6c81849b
split Command table into two tables
2022-05-18 16:26:58 -06:00
d323b7817d
put back some whitespace
2022-05-18 14:59:15 -04:00
eb3ee96b9c
also apply 2 atom minimum to balance() and packing atom IDs
2022-05-18 14:22:43 -04:00
bfd6efcedb
no need to sort dump if there are less than 2 atoms
2022-05-18 13:48:06 -04:00
c16f40eb7c
don't enable OpenMP together with CUDA for KOKKOS by default
2022-05-18 12:23:38 -04:00
acbeae075a
no need to suppress nvcc warnings about pragmas with Clang as host compiler
2022-05-18 12:17:06 -04:00
4f45ae2ef6
improve support for intel compilers on windows
2022-05-18 09:14:18 -04:00
5559491d7b
add missing overrides
2022-05-18 09:13:52 -04:00
ba0efbef31
include presets for intel compiler names on windows
2022-05-18 09:13:37 -04:00
7646592f05
recognize the new LLVM based intel compiler as intel compiler
2022-05-18 08:54:26 -04:00
02908f0468
modernize MKL FFT interface
2022-05-18 08:42:40 -04:00
6475d4b956
Skip Fortran unittests if no Fortran MPI support is found
2022-05-18 07:16:16 -04:00
f0e7101bd2
Merge branch 'develop' into next-stable-release
2022-05-18 06:35:57 -04:00
d54f97736e
whitespace
2022-05-18 06:32:52 -04:00
1466620750
update googletest to the latest github commit
2022-05-18 06:09:42 -04:00
baa48946e5
add comment to please CodeQL
2022-05-18 00:56:10 -04:00
e7b9d03573
crank up epsilon for tip4p/cut styles some more
2022-05-18 00:28:42 -04:00
d8b37601a8
Merge pull request #3262 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-05-18 00:11:05 -04:00
d94bcd043b
enforce using a single thread with Kokkos and SNAP or PACE
2022-05-17 23:42:24 -04:00
15a727a7ff
avoid segfaults with Kokkos threads
2022-05-17 23:41:46 -04:00
e94275391c
Merge branch 'develop' into collected-small-changes
2022-05-17 22:10:15 -04:00
935c9a02d7
Merge pull request #3267 from athomps/born-rotated
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Added Python wrapper that handles rotations to and from LAMMPS frame
2022-05-17 19:52:52 -04:00
55e0af930b
Merge pull request #3269 from yury-lysogorskiy/master
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Update ML-PACE installation to v.2021.10.25.fix version
2022-05-17 19:50:49 -04:00
a5171beacd
make lammps-shell test compatible with MULTI-CONFIG CMake builders
2022-05-17 18:26:27 -04:00
72209b0617
Merge pull request #3258 from akohlmey/create-atoms-mesh
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Create atoms from STL mesh
2022-05-17 18:11:41 -04:00
899764c00c
Merge pull request #3268 from akohlmey/update-kappa-example
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Update KAPPA example
2022-05-17 17:18:45 -04:00
cebbd471cf
tweak unit test epsilon for portability to MacOS /w ARM
2022-05-17 17:15:42 -04:00
8ffe2a206c
Update ML-PACE installation to v.2021.10.25.fix version
2022-05-17 22:41:43 +02:00
f9efa426a7
Merge pull request #3256 from lammps/delete-atoms-exact
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Delete atoms exactly by fraction or count
2022-05-17 16:25:21 -04:00
ae979aca4e
consistently use prefactor instead of pre-factor (the former was more common)
2022-05-17 16:20:10 -04:00
38d7fcee92
correct and update create_atoms mesh documentation
2022-05-17 16:16:32 -04:00
e7d072c593
add sanity check on radscale value, set radius also for quasi-random mode
2022-05-17 16:15:46 -04:00
d487ab10e2
doc page and unittest tweaks
2022-05-17 12:00:40 -06:00
853e3ae99b
fix typo and clarify error message
2022-05-17 13:52:29 -04:00
dbb3e75f24
change partial to random
2022-05-17 11:02:42 -06:00
fe4782696e
silence compiler warnings
2022-05-17 06:03:01 -04:00
326b833d7f
(temporarily) disable Kokkos deprecation warnings in CMake presets in preparation for stable release
2022-05-17 06:02:50 -04:00
bf98df3264
silence compiler warnings
2022-05-16 23:20:04 -04:00
df40732343
Make cast to double explicit
2022-05-16 15:00:13 -04:00
d32885fbe3
Fix compiler warnings
2022-05-16 14:48:02 -04:00
659fd82a9e
Fix compiler warnings
2022-05-16 14:35:24 -04:00
db2d5b863d
Improved MPI portability and added reference log files
2022-05-16 08:22:45 -06:00
ee8a8b6cd0
Added Python wrapper that handles rotations to and from LAMMPS frame
2022-05-15 17:43:18 -06:00
b1ba616470
update KAPPA example for current code, to use thermo_modify colname, and compute kappa in input
2022-05-15 18:58:50 -04:00
44f3ad5620
update singularity image descriptions for newer versions of cuda and rocm
2022-05-15 08:11:50 -04:00
c0e5a03989
update tests for delete_atoms
2022-05-15 01:56:59 -04:00
f62363516c
streamline the refactored interface for delete_atoms partial some more
2022-05-15 01:56:45 -04:00
8e6b0425f7
apply clang-format
2022-05-14 18:01:34 -04:00
a79814793e
improve handling of hybrid styles and their arguments and errors
2022-05-14 17:56:44 -04:00
1f30d3f140
programming style
2022-05-14 17:56:12 -04:00
1b552de1cd
make default settings() functions for bonded interactions error out with arguments
2022-05-14 17:55:56 -04:00
42a4fba390
implement better checking for atom_style arguments and remove redundant code
2022-05-14 15:43:11 -04:00
173e80a970
Merge pull request #71 from jtclemm/create-atoms-mesh
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Fixing typos and cleaning up quasirandom comments
2022-05-14 15:13:27 -04:00
55fef9a482
Fixing typos and cleaning up quasirandom comments
2022-05-14 11:39:20 -06:00
9a9bb749fa
Merge remote-tracking branch 'github/develop' into collected-small-changes
2022-05-14 10:39:18 -04:00
223aebe3fb
Merge pull request #3251 from stanmoore1/kk_update_3.6.0
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Update Kokkos library in LAMMPS to v3.6.0
2022-05-14 10:38:41 -04:00
168d3bdd3c
Correctly handle the case that the YAML python module is not installed
2022-05-14 10:15:40 -04:00
9661711a1e
avoid out-of-bounds access in dump style cfg, update docs with simpler semantic
2022-05-14 09:39:50 -04:00
d4ea5ca49e
more clang-tidy fixes after re-running it with added settings
2022-05-14 07:18:05 -04:00
2f0baa86d6
configure desired clang-tidy settings explicitly, must unset variable to turn off
2022-05-14 07:13:25 -04:00
b8a4ddc42a
Merge pull request #3264 from stanmoore1/kk_pace_release
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Add Kokkos version of ML-PACE
2022-05-13 23:36:05 -04:00
90797d53d9
one more batch of clang-tidy fixes
2022-05-13 23:21:14 -04:00
940e88d2ca
more clang-tidy fixes
2022-05-13 21:12:48 -04:00
9c16819305
update code with clang-tidy fixes
2022-05-13 18:26:38 -04:00
3782eea7c4
must always compile MDI library with position independent code
2022-05-13 18:25:59 -04:00
056fd8be8f
always build yaml-cpp included in PACE as static library
2022-05-13 17:00:37 -04:00
59560c47a7
Small tweak
2022-05-13 14:23:27 -04:00
979f84f96f
Merge branch 'develop' of https://github.com/lammps/lammps into kk_update_3.6.0
2022-05-13 14:03:09 -04:00
66abc00e3c
Add comment about MPI on Crusher
2022-05-13 13:33:27 -04:00
c41ad91a9d
add support for reading binary STL files
2022-05-13 12:18:22 -04:00
545cec1785
Fix copy/paste issue
2022-05-13 10:15:25 -06:00
658a89e401
document .lammpsbin suffix for trajectory files
2022-05-13 11:15:06 -04:00
35dd5bc978
fix typo
2022-05-13 03:00:31 -04:00
90e2d9e966
tweak code comments
2022-05-12 16:51:24 -06:00
042564decd
add deprecation info for old porosity option
2022-05-12 16:48:03 -06:00
3eea2463a1
Tweak error message
2022-05-12 16:00:22 -06:00
d207d53fd1
whitespace
2022-05-12 15:34:08 -06:00
d7bad09d35
Add Kokkos version of ML-PACE
2022-05-12 15:25:07 -06:00
58093fec99
accept .lammpsbin in addition to .bin for binary format output
2022-05-12 15:26:39 -04:00
4077c5c8ba
add get_dump_by_id() API that mirrors other recent additions
2022-05-12 14:48:03 -04:00
0577bb6269
use Output::add_dump() and the dump_creator map and templates etc.
2022-05-12 14:47:16 -04:00
aff72c56a5
make Output::add_dump() return pointer to the created dump
2022-05-12 14:46:02 -04:00
c3a454370e
work around "fix not computed at compatible times" errors with write_dump
2022-05-12 14:12:13 -04:00
301bd95900
small tweak
2022-05-12 13:17:51 -04:00
04537c9f22
Merge pull request #3263 from OrbitalC/compute_mliap_so3
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adding so3 descriptor support for compute_mliap
2022-05-12 11:01:01 -04:00
5ad821ca5e
apply clang-format
2022-05-12 09:24:37 -04:00
78d976bd36
Merge pull request #3260 from Colvars/colvars-update
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Update Colvars to version 2022-05-09
2022-05-12 08:40:29 -04:00
371141f915
adding support for compute_mliap so3
2022-05-12 14:12:57 +02:00
3ea249a576
fix minor documentation issues
2022-05-11 13:23:59 -04:00
4cc3bdd35f
adjust keyword/function names and command line to be simpler to use
2022-05-11 09:25:27 -04:00
227c4853f1
programming style
2022-05-11 08:13:13 -04:00
442116b305
update
2022-05-11 08:12:59 -04:00
ef3b90e838
Merge pull request #70 from jtclemm/create-atoms-mesh
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Adding quasirandom mesh option
2022-05-11 08:12:18 -04:00
c9d350edc2
Adding quasirandom mesh option
2022-05-10 18:35:36 -06:00
bdbab77286
add note about re-generating optimized meshes for STL files
2022-05-10 15:23:54 -04:00
1220bea011
Update Colvars to version 2022-05-09
...
This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.
Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).
Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers. Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.
The following pull requests in the Colvars repository are relevant to LAMMPS:
- 475 Remove fatal error condition
https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)
- 474 Allow normalizing eigenvector vector components to deal with unit change
https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)
- 470 Better error handling in the initialization of NeuralNetwork CV
https://github.com/Colvars/colvars/pull/470 (@HanatoK)
- 468 Add examples of histogram configuration, with and without explicit grid parameters
https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)
- 464 Fix #463 using more fine-grained features
https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)
- 447 [RFC] New option "scaledBiasingForce" for colvarbias
https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)
- 444 [RFC] Implementation of dense neural network as CV
https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)
- 443 Fix explicit gradient dependency of sub-CVs
https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)
- 442 Persistent bias count
https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)
- 437 Return type of bias from scripting interface
https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)
- 434 More flexible use of boundaries from colvars by grids
https://github.com/Colvars/colvars/pull/434 (@jhenin)
- 433 Prevent double-free in linearCombination
https://github.com/Colvars/colvars/pull/433 (@HanatoK)
- 428 More complete documentation for index file format (NDX)
https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)
- 426 Integrate functional version of backup_file() into base proxy class
https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)
- 424 Track CVC inheritance when documenting feature usage
https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)
- 419 Generate citation report while running computations
https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)
- 415 Rebin metadynamics bias from explicit hills when available
https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)
- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)
Authors: @giacomofiorin, @HanatoK, @jhenin
2022-05-10 11:24:54 -04:00
5760c59d83
add a creator: tag to the YAML dump that allows to tell it apart
2022-05-10 08:31:02 -04:00
b6ee64dc12
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-09 21:58:48 -04:00
eb44cbf848
small updates
2022-05-09 15:22:48 -04:00
23e17363f9
Merge remote-tracking branch 'github/doc-variable-extract-settings' into collected-small-changes
2022-05-09 15:03:13 -04:00
6344c667a0
more doc info for variable extrat_setting() func
2022-05-09 09:33:59 -06:00
24ef021fe0
fix typo
2022-05-09 10:05:12 -04:00
1660bae22a
add examples import one image to manual
2022-05-08 21:15:32 -04:00
9ec35f0235
update docs to match the latest code
2022-05-08 19:14:06 -04:00
e0bb27dbb2
make radscale and radthresh class members
2022-05-07 23:04:34 -04:00
e9b1ca16a3
correctly initialize radius and molecule id
2022-05-07 21:24:08 -04:00
60b9fd2db8
minor tweaks simplify algorithm
2022-05-07 17:08:22 -04:00
bcfb6734f3
use average vertex distance from center as particle radius
2022-05-07 16:27:03 -04:00
6722d3fb00
add simple STL binary to ASCII converter (based on Wikipedia specs)
2022-05-07 16:26:25 -04:00
559dc68197
implement revised algorithm with recursion
2022-05-07 15:40:25 -04:00
102b61ae1b
Merge branch 'develop' into create-atoms-mesh
2022-05-07 09:33:40 -04:00
5d08b62622
remove unused class member
2022-05-07 03:48:54 -04:00
4737b9efb7
Merge pull request #3250 from akohlmey/collected-small-changes
...
Collected small changes and bugfixes
2022-05-07 00:14:32 -04:00
d21d9d95fa
Merge pull request #3255 from lammps/timer-variable
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Add a timer-style variable
2022-05-06 17:46:22 -04:00
00bb566893
enforce that the number of neighbors cannot be negative (e.g. w/o neighbor list)
2022-05-06 17:45:01 -04:00
56e36a5df5
Merge pull request #2988 from stanmoore1/coo_opt
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Add optimized version of compute orientorder/atom from Tomas Oppelstr…
2022-05-06 17:11:24 -04:00
21d3de65e6
fix typos
2022-05-06 17:05:18 -04:00
767f512dcf
add "make ni" alias to "make no-installed"
2022-05-06 17:05:03 -04:00
907bc7eaa5
switch to using wall time
2022-05-06 16:58:28 -04:00
051c243cfc
small programming style upgrade, apply clang-format, silence compiler warnings
2022-05-06 16:44:13 -04:00
905034893c
finished testing of new delete_atoms options
2022-05-06 14:15:41 -06:00
6432660bc9
Merge branch 'develop' of https://github.com/lammps/lammps into coo_opt
2022-05-06 13:24:14 -06:00
6e78269612
whitespace
2022-05-06 15:11:15 -04:00
81a8b0cf85
Add Kokkos HIP preset
2022-05-06 12:40:12 -06:00
613ef04357
Merge branch 'develop' into timer-variable
2022-05-06 14:27:52 -04:00
5986e11d43
Merge branch 'develop' of github.com:lammps/lammps into kk_update_3.6.0
2022-05-06 12:04:00 -06:00
97012f2aaa
correct classification of electrode package, as it requires BLAS/LAPACK
2022-05-06 13:57:26 -04:00
62a819d7b6
Tweak launch bounds to improve GPU performance
2022-05-06 13:37:05 -04:00
3bb9c64f9e
update .gitignore and move electrode package for dependency on KSPACE
2022-05-06 13:35:51 -04:00
78f2907cbb
implement a "make no-installed" command
2022-05-06 13:35:21 -04:00
f3fcd16628
adding of timer-style variables and associated doc pages
2022-05-06 11:21:36 -06:00
580e01535a
Update Kokkos AMD Makefiles
2022-05-06 13:04:58 -04:00
8e423f07c5
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-06 12:37:34 -04:00
2549b86d76
update/correct docs for support of compiling LAMMPS with visual studio on windows
2022-05-06 12:37:28 -04:00
ae73a9b7f7
Revert back to original code in npair_ssa_kokkos.h
2022-05-06 10:05:57 -06:00
73670dafc7
Merge branch 'develop' into collected-small-changes
2022-05-06 11:45:51 -04:00
aae44892c0
consolidate all FFT related redundant defines and typedefs in a single header
2022-05-06 11:27:17 -04:00
6ec169fa9d
Fix warnings in Kokkos package
2022-05-06 08:23:45 -06:00
a35a2441ce
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-06 04:48:19 -04:00
abefff828d
plug memory leak
2022-05-06 04:39:38 -04:00
71185b9f98
fix error message
2022-05-06 01:02:40 -04:00
8079f014bc
final tweaks
2022-05-06 00:47:35 -04:00
773e3a87d9
add docs for create_atoms mesh
2022-05-06 00:47:05 -04:00
ff21142042
Merge remote-tracking branch 'github/develop' into create-atoms-mesh
2022-05-05 23:02:53 -04:00
bd373d6038
Merge pull request #3119 from erozic/feature-create-atoms-exclude
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Feature create atoms overlap
2022-05-05 22:42:40 -04:00
7601a5c0fb
correct/improve formatting
2022-05-05 22:20:43 -04:00
8ed401ce12
spelling
2022-05-05 21:34:31 -04:00
664943589e
Merge remote-tracking branch 'github/develop' into feature-create-atoms-exclude
2022-05-05 21:09:39 -04:00
8dbfc0799c
whitespace
2022-05-05 20:15:36 -04:00
46d638af0c
Merge branch 'feature-create-atoms-exclude' of https://github.com/erozic/lammps into feature-create-atoms-exclude
2022-05-06 01:48:37 +02:00
ae230a33f5
Bug fix (user_quat initial value not set)
2022-05-06 01:47:45 +02:00
d4f212183e
initial exact logic for delete_atoms partial
2022-05-05 17:45:42 -06:00
568e9c5878
Merge pull request #3237 from emilyviolet/hipfft
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Add support for hipFFT with PPPMKokkos
2022-05-05 19:39:52 -04:00
5784fab588
starting to add timer-style variable
2022-05-05 17:04:50 -06:00
484a7c5db0
tweaked comments
2022-05-05 16:22:19 -06:00
7071f819d0
Header fix (add_molecule)
2022-05-05 23:53:14 +02:00
93c0f09c31
Logic fix in random-overlap and comment implemented
2022-05-05 23:35:11 +02:00
e5e3478afd
Update CMake
2022-05-05 12:30:37 -06:00
bee7b09377
fix cut-n-paste bug
2022-05-05 14:05:22 -04:00
3b68c0ea24
Update Makefile comment
2022-05-05 14:02:29 -04:00
b79c0bc7b4
Update Kokkos library in LAMMPS to v3.6.0
2022-05-05 11:44:47 -06:00
3b9389e86c
Update .gitignore
2022-05-05 12:23:52 -04:00
2c95f84acc
Tweak error messages
2022-05-05 12:17:00 -04:00
c05af749df
Merge branch 'develop' of https://github.com/lammps/lammps into hipfft
2022-05-05 12:15:28 -04:00
24b94551a2
Update Kokkos AMD Makefiles
2022-05-05 11:59:32 -04:00
99d4f83fa8
preliminary implementation
2022-05-05 09:56:22 -04:00
6c28b55c13
return nullptr instead of out-of-range data
2022-05-05 07:50:45 -04:00
2b1716cb3a
fix more bugs with dump_modify every/time
2022-05-05 00:06:08 -04:00
bd4bbbddbe
Merge pull request #3245 from akohlmey/next_patch_release
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Step version strings for the next patch release
2022-05-04 19:57:23 -04:00
2aa1c6975f
fix typo
2022-05-04 19:09:19 -04:00
e285ba43eb
Merge branch 'develop' into next_patch_release
2022-05-04 19:08:10 -04:00
582de4f951
Merge pull request #3248 from akohlmey/add_set_time
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Add time option to the "reset_timestep" command and make the "time" property restartable
2022-05-04 18:43:07 -04:00
dcd6c18e45
update indent
2022-05-04 17:50:34 -04:00
4c6cb8648b
replace image with embedded latex text
2022-05-04 17:50:25 -04:00
6b47d6246b
more changes and some debugging on a test script
2022-05-04 15:28:50 -06:00
cc437c78a0
some logic and syntax changes to code and doc page
2022-05-04 14:34:05 -06:00
edda6b6f70
Merge remote-tracking branch 'github/develop' into add_set_time
2022-05-04 16:29:54 -04:00
803376b1b4
Merge pull request #3241 from akohlmey/collected-small-changes
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Collected small changes and fixes for the next patch release
2022-05-04 16:26:02 -04:00
e897ab7611
improve error messages
2022-05-04 16:25:12 -04:00
ba3aa8fab5
remove NULL option for reset_timestep
2022-05-04 16:21:06 -04:00
81bb4bfc23
Merge branch 'collected-small-changes' into add_set_time
2022-05-04 15:49:14 -04:00
059c84bf41
Merge branch 'develop' into add_set_time
2022-05-04 15:47:28 -04:00
eec86c8038
Merge branch 'develop' into collected-small-changes
2022-05-04 15:45:38 -04:00
ad6cebb049
Merge pull request #3246 from GenieTim/compute-abs-sum
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Implement a aveabs and sumabs reduce command
2022-05-04 14:46:54 -04:00
61214b9a52
Merge pull request #3243 from akohlmey/delete-by-variable
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Implement variable option for delete_atoms
2022-05-04 13:50:00 -04:00
f8742d599b
merge set_time command into reset_timestep
2022-05-04 13:24:52 -04:00
d4a93ff9c7
Merge pull request #3247 from vladgl/adp-kk
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Kokkos accelerated variant for adp pair style
2022-05-04 13:05:29 -04:00
517d934f7c
more edits
2022-05-04 10:51:00 -06:00
87b99306ba
make force_clear() a public pure function in min.h and integrate.h
...
these are required changes for adding NWChem couping support as a fix
2022-05-04 12:30:17 -04:00
af32267db3
Merge branch 'develop' into compute-abs-sum
2022-05-04 12:23:50 -04:00
7fa2fe134c
Fix typo
2022-05-04 10:18:11 -06:00
515e2928a9
Sync with pair eam
2022-05-04 10:15:36 -06:00
8a5e7fa609
update docs
2022-05-04 12:07:59 -04:00
ed0ee913e1
Small tweaks
2022-05-04 11:18:10 -04:00
a26fa50736
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-05-04 05:47:34 -04:00
5d510ac7b3
Merge remote-tracking branch 'akohlmey/region-tests' into collected-small-changes
2022-05-04 05:46:34 -04:00
c37d5be524
Merge branch 'develop' into collected-small-changes
2022-05-04 05:45:33 -04:00
0bedff1ce0
implement set_time command
2022-05-03 13:15:52 -04:00
e7153d30c8
re-enable dynamic group support for tally computes
2022-05-03 11:22:38 -04:00
257a070666
add test for ellipsoid, check for special case of ellipsoid/prism
2022-05-03 11:02:01 -04:00
bd5858019e
add minimal unit test for Region class
2022-05-02 17:06:28 -04:00
4ef8ca091d
Fix virial computation in adp/kk
2022-05-02 22:16:28 +03:00
8473bc19f5
Merge branch 'develop' into adp-kk
2022-05-02 13:41:03 -04:00
df77641071
fix permissions and whitespace
2022-05-02 13:40:39 -04:00
cb345870a9
Add adp/kk to install script (fix commit #d3843db)
2022-05-02 19:24:01 +03:00
d3843dbf09
Add adp/kk to install script
2022-05-02 19:16:59 +03:00
fef6c37ea7
Merge pull request #3240 from akohlmey/ave-yaml-file-colname
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Add support for custom column names and YAML format output to fix ave/time
2022-05-02 11:45:50 -04:00
0e5a66b1cd
Implement a aveabs and sumabs reduce command
2022-05-02 17:34:08 +02:00
e51c51e7f9
Kokkos accelerator variant for adp pair style
2022-05-02 18:17:49 +03:00
39ee6b6a7f
step version strings for the next patch release
2022-05-02 10:34:43 -04:00
89deab6a3e
silence compiler warnings
2022-04-30 19:51:04 -04:00
1191d08b47
Merge branch 'develop' into collected-small-changes
2022-04-30 19:39:16 -04:00
deef9fae23
fix bug with wrong mapping of pair style classes
2022-04-30 19:15:00 -04:00
1b8641685a
Merge pull request #3242 from dxhisboy/develop
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Adding saip/metal/opt and ilp/tmd/opt
2022-04-30 12:59:41 -04:00
672c063fd8
add unit test for delete_atoms
2022-04-29 22:33:15 -04:00
2f599bace1
enable and apply clang-format
2022-04-29 22:01:34 -04:00
f5113aa84a
better error messages
2022-04-29 21:59:37 -04:00
31d6af6114
add delete_atoms "variable" option
2022-04-29 21:59:22 -04:00
9c45af7730
avoid potential 32-bit integer overflow
2022-04-29 20:53:57 -04:00
cac9fcaf86
cannot build ELECTRODE package by default on native windows because it requires BLAS
2022-04-29 20:18:50 -04:00
4a3bcd9230
Merge branch 'develop' into collected-small-changes
2022-04-29 20:15:36 -04:00
87b0939fe7
Merge pull request #2871 from evoyiatzis/master
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implementation of an "ellipsoidal" region option
2022-04-29 19:46:15 -04:00
44c4d0a4d6
Merge pull request #3194 from robeme/electrode
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ELECTRODE package for constant potential method
2022-04-29 18:30:29 -04:00
ee8d8042e6
add example for YAML processing with Perl
2022-04-29 17:42:23 -04:00
514bfe77df
apply changes suggested by @sjplimp
2022-04-29 17:33:37 -04:00
5e18f15435
remove unused variables
2022-04-29 15:29:04 -04:00
d0938ce398
apply clang-format
2022-04-29 15:13:47 -04:00
80c716b81f
update false positives
2022-04-29 15:11:11 -04:00
f09e886fd2
remove unused function
2022-04-29 15:10:57 -04:00
47f62838db
Merge branch 'develop' into electrode
2022-04-29 14:37:48 -04:00
3c71c07048
Merge pull request #3230 from athomps/snap-inner-mod
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Snap inner cutoff improvements and porting to KOKKOS
2022-04-29 14:36:48 -04:00
37d2d9e013
Remove trailing spaces
2022-04-29 10:56:34 -06:00
3f44f8f50d
Merge pull request #3236 from lammps/fix-adapt-angle2
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bug fix for new fix adapt angle support
2022-04-29 12:50:10 -04:00
df76673bee
bdim --> adim in fix adapt
2022-04-29 10:10:36 -06:00
2f8e708184
more whitespace
2022-04-29 09:37:27 -06:00
894b7810b2
whitespace
2022-04-29 09:32:24 -06:00
57098f3df7
Remove extra files
2022-04-29 09:22:14 -06:00
69a79ba082
whitespace
2022-04-29 09:17:24 -06:00
641e769bde
Revert a3c6baad4c
2022-04-29 09:03:44 -06:00
435f652263
removed trailing whitespace in pair_ilp_tmd_opt and pair_saip_metal_opt
2022-04-29 22:54:41 +08:00
6ced400207
change saip and tmd to virtual public inherit, so that corresponding opt package can compile
2022-04-29 22:28:48 +08:00
f93ac86c53
updated Install.sh for OPT package to adopt new interlayer potential optimizations
2022-04-29 22:05:52 +08:00
943cb531bf
Modified chunk code of pair_ilp_graphene_hbn_opt for adopting pair_saip_metal_opt and pair_ilp_tmd_opt
2022-04-29 21:56:52 +08:00
c34efcc718
fixed multielement assignment error
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tested in CPU and GPU mode, gets same output for eneriges and forces as build without KOKKOS for various settings of sinner, dinner
2022-04-29 07:53:39 -06:00
2292caef38
updated sinner/dinner log output
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now logmsg displays all element params for sinner, dinner on same line (replaces only first param + ...)
2022-04-29 07:48:02 -06:00
9c48a75c8e
fix issues reported by coverity scan
2022-04-29 06:49:47 -04:00
b2300ba9cb
Merge branch 'develop' into collected-small-changes
2022-04-29 05:51:05 -04:00
6fb3cef39f
Merge pull request #3031 from Iximiel/develop
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Second Moment Aproximation to the Tight Binding addes as pair style
2022-04-28 22:32:38 -04:00
cb41e354b8
Merge pull request #3238 from akohlmey/doc-math-funcs
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Document special math functions
2022-04-28 22:11:09 -04:00
7d9cdc7ec4
update documentation. more examples. document fix_modify options
2022-04-28 18:34:49 -04:00
bf8f5e2f87
more compact output
2022-04-28 18:08:59 -04:00
a3e0e1a6eb
fixed multielement assignment error
2022-04-28 15:57:53 -06:00
2ae9ca5073
swap rows and columns back for easier import into pandas
2022-04-28 16:03:04 -04:00
f25b60fded
simplify pandas processing. add missing image with plot
2022-04-28 16:02:45 -04:00
f09556018b
fix bugs reported by @jibril-b-coulibaly
2022-04-28 14:47:53 -04:00
04b46a9ce8
implement yaml output for mode vector
2022-04-28 14:33:15 -04:00
eb5d867adf
Improve erfc
2022-04-28 13:45:57 +00:00
2f71c96bde
add yaml format output for mode scalar
2022-04-28 07:46:47 -04:00
09ed718c14
add example to plot thermo data with pandas+matplotlib
2022-04-28 07:45:51 -04:00
cfc4dcea3d
must quote keyword data to avoid issues parsing the YAML data
2022-04-28 07:34:23 -04:00
33a63e5cd3
remove dead code to silence compiler warnings
2022-04-28 03:03:29 -04:00
a05bdfa76c
add override to polymorph functions
2022-04-27 18:36:00 -04:00
cd3ce8459b
enable and apply clang-format
2022-04-27 18:35:44 -04:00
74afc04580
remove error comments from header
2022-04-27 18:29:41 -04:00
233d4ad349
whitespace fixes
2022-04-27 18:29:27 -04:00
8481abda05
Merge branch 'develop' into ellipsoid-region
2022-04-27 18:28:38 -04:00
55fddf3aac
update (tentative) release date
2022-04-27 18:26:07 -04:00
b76594e551
enforce only newton pair on with smatb pair styles. add unit tests
2022-04-27 18:08:05 -04:00
2d45e3340f
move sources and examples for smatb styles to SMTBQ package folders
2022-04-27 15:14:02 -04:00
585b14f08f
fix memory leak
2022-04-27 15:10:55 -04:00
3cfae26b84
update docs and make part of SMTBQ package
2022-04-27 15:10:46 -04:00
3b1165ccdc
update files to be more compatible with LAMMPS' conventions and for code changes
2022-04-27 15:02:32 -04:00
75d42a87e5
Merge branch 'develop' into Iximiel/develop
2022-04-27 14:15:10 -04:00
cdba0da780
Merge branch 'snap-inner-mod' of github.com:athomps/lammps into snap-inner-mod
2022-04-27 10:58:43 -06:00
a3c6baad4c
Removed CPU specific options
2022-04-27 10:58:22 -06:00
0e1f9968c1
Merge branch 'develop' of github.com:lammps/lammps into snap-inner-mod
2022-04-27 10:48:24 -06:00
6439777406
complete documentation of the MathSpecial namespace
2022-04-27 11:59:25 -04:00
c43bc000d9
Removed unnecessary commented out code section.
2022-04-27 19:46:18 +10:00
d857600d9c
start documenting functions in the MathSpecial namespace
2022-04-27 04:46:18 -04:00
385f0c6c95
Update Kokkos build documentation to include hipFFT options.
2022-04-27 10:13:03 +10:00
8cdbf380cf
Add support for hipFFT backend in PPPMKokkos.
2022-04-27 09:22:59 +10:00
691ba89b6f
Merge pull request #3234 from lammps/variable-vector-wildcard
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add support for wildcards in variable vectors
2022-04-26 18:21:46 -04:00
1fcf82aeef
Merge remote-tracking branch 'github/develop' into variable-vector-wildcard
2022-04-26 17:54:32 -04:00
56b4671cd8
Merge pull request #3233 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2022-04-26 17:54:11 -04:00
d8e98cb99d
make tests more complex and add vector variable expansion
2022-04-26 17:53:47 -04:00
831caaa150
Merge branch 'collected-small-changes' into variable-vector-wildcard
2022-04-26 17:26:17 -04:00
64fff417c3
test more bound variants
2022-04-26 17:25:27 -04:00
7eb6c2652f
update advanced utils tests. include test for expand args
2022-04-26 16:16:44 -04:00
d04cb4ba42
edits to doc page
2022-04-26 13:58:18 -06:00
782add6943
Merge branch 'feature-create-atoms-exclude' of github.com:erozic/lammps into create-overlap
2022-04-26 13:22:10 -06:00
800e0a7357
bug fix for new fix adapt angle support
2022-04-26 09:34:27 -06:00
7663fc6256
correctly use "type" to detect executables/scripts
2022-04-26 11:08:31 -04:00
26278643d4
Port changes to Kokkos
2022-04-26 08:22:00 -06:00
407f6af1ed
Merge branch 'develop' of github.com:lammps/lammps into snap-inner-mod
2022-04-26 08:13:30 -06:00
192b22a6ce
Set rng init for electrode/thermo
2022-04-26 16:03:45 +02:00
837f9040d8
add tests for advanced utility functions that require a LAMMPS instance
2022-04-26 09:30:34 -04:00
4691ff06b5
format
2022-04-26 09:30:10 -04:00
ba02d90bf1
add test for new errorurl() utility function
2022-04-26 09:29:57 -04:00
a649fa3a79
detect yaml file output by file name
2022-04-26 06:20:00 -04:00
72011bf325
Updated doc (use of overlap clarified)
2022-04-26 11:55:24 +02:00
7aaa71d22e
Merge remote-tracking branch 'lammps/develop' into electrode
2022-04-26 10:29:39 +02:00
66b8ab9c6e
Revamped examples
2022-04-26 09:42:45 +02:00
fdb7dfdea7
also remove mode from fix ave/correlate
2022-04-25 17:04:04 -06:00
e7a9073ccd
remove discussion of mode
2022-04-25 17:01:15 -06:00
65978c33b6
2 more doc pages
2022-04-25 16:06:52 -06:00
bb8e953fb5
add support for wildcards in variable vectors
2022-04-25 15:43:08 -06:00
950b175fcd
remove invalid [[noreturn]] attribute
2022-04-25 16:23:48 -04:00
dc605d35ee
Updated ML-IAP package
2022-04-25 13:58:41 -06:00
811e5786fe
Merge branch 'develop' into feature-create-atoms-exclude
2022-04-25 19:30:52 +02:00
c1146ebdcd
Resolved conflicts with develop
2022-04-25 19:11:54 +02:00
8679266db8
add container definitions for Fedora 36 and Ubuntu 22.04LTS
2022-04-25 13:05:43 -04:00
2624043ab6
Synchronisation fix
2022-04-25 17:03:07 +02:00
960d3faa5e
Merge branch 'master' of github.com:z-gong/lammps into collected-small-changes
2022-04-25 02:58:17 -04:00
a5cd95d6c6
Add comment for the units in compute/viscosity
2022-04-25 06:23:54 +02:00
28900925f4
Fix the unit for fix/accelerate/cos
2022-04-25 05:59:41 +02:00
9c46acfd62
fix parallel processing bug with shell mkdir command
2022-04-24 23:23:01 -04:00
45de998aa9
Merge pull request #3231 from akohlmey/remove-error-docs-in-header
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Remove error docs from header files
2022-04-24 18:30:17 -04:00
6cfbd73bcd
add documentation for new error and warning policy
2022-04-23 16:40:28 -04:00
f7e7abc908
fix uninitialized pointer bug
2022-04-23 15:17:26 -04:00
b4c3c479b7
remove error docs from one more file
2022-04-23 13:52:29 -04:00
4d1bdb4741
add python tool to detect and remove (if desired) error docs from headers
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also document the tools in the manual.
2022-04-23 13:52:12 -04:00
78c10bac4a
clang-format update
2022-04-23 13:08:11 -04:00
115962db88
Merge branch 'develop' into remove-error-docs-in-header
2022-04-23 12:46:54 -04:00
ce5d8a578e
Merge pull request #3228 from run-towards-the-future/develop
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A pull request for an optimized ILP(ilp/graphene/hbn) potential
2022-04-23 12:42:27 -04:00
f970a9de6a
Merge pull request #3219 from akohlmey/region-lookup-refactor
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Region lookup refactor
2022-04-23 11:33:01 -04:00
67bcfe3b62
remove unused code and variables, more programming style consistency
2022-04-23 09:26:35 -04:00
b55b9f5a6a
removed request for ghost neighbor list
2022-04-23 20:35:48 +08:00
ef51fb7dea
Fix bugs, Derives from PairILPGrapheneHBN instead of Pair
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Improve the performance of pair style, ilp/graphene/hbn/opt
Updates to the OPT package
2022-04-23 19:45:50 +08:00
8fe0231b75
Fix bugs, Derives from PairILPGrapheneHBN instead of Pair
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Add a new pair style, ilp/graphene/hbn/opt
Updates to the OPT package
2022-04-23 19:43:34 +08:00
e1856dc708
cosmetic
2022-04-23 07:42:31 -04:00
5da6fae9f6
silence compiler warnings
2022-04-23 07:35:18 -04:00
69249e84e1
adjust epsilon
2022-04-23 07:35:00 -04:00
8f019f4800
doc fixes: spelling and links
2022-04-23 07:34:44 -04:00
d55e7f9e51
Merge branch 'develop' into region-lookup-refactor
2022-04-23 07:14:28 -04:00
b1546a725c
Merge pull request #3093 from Bibobu/Elastic_stress
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Add compute born/matrix command to compute elastic stress
2022-04-23 07:07:29 -04:00
113fc0a77a
Merge pull request #3227 from akohlmey/safer-data-file-parsing
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Improve data file parsing and reported error messages
2022-04-23 06:41:17 -04:00
419b0f9494
add missing curly brace
2022-04-23 06:02:14 -04:00
31470819c0
Merge branch 'develop' into Elastic_stress
2022-04-23 04:36:45 -04:00
7bfa368d8d
Merge pull request #2667 from ssande7/compute_temp_profile_dof
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[BUGFIX] Collection of DoF-related fixes for compute temp/profile
2022-04-23 04:31:38 -04:00
c17845276a
Derives from PairILPGrapheneHBN instead of Pair
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Improve the performance of pair style, ilp/graphene/hbn/opt
Updates to the OPT packages
2022-04-23 14:29:03 +08:00
b631411985
Derives from PairILPGrapheneHBN instead of Pair
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Add a new pair style, ilp/graphene/hbn/opt
Updates to the OPT package
2022-04-23 14:26:13 +08:00
26ca371d93
Merge branch 'develop' into region-lookup-refactor
2022-04-22 23:47:49 -04:00
79a7d2abf6
remove error docs from header files
2022-04-22 23:31:15 -04:00
e49930df21
Merge branch 'develop' into safer-data-file-parsing
2022-04-22 23:13:39 -04:00
471c728ac4
Merge pull request #3224 from lammps/dynamic-groups
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change update of dynamic groups to post_force location in timestep
2022-04-22 23:11:17 -04:00
cbefeeb677
Merge pull request #3220 from athomps/specify-verlet
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Explcitly state that fix nve uses velocity-Verlet integrator
2022-04-22 23:10:48 -04:00
8115e8a5a4
Merge pull request #3226 from lammps/error-url
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Add utility to print url with link to error message in online manual
2022-04-22 23:10:21 -04:00
9f9a5ca76f
Merge branch 'develop' into region-lookup-refactor
2022-04-22 22:53:02 -04:00
9be8ef09a2
Merge pull request #3229 from lammps/fix-adapt-angle
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Fix adapt angle
2022-04-22 22:44:18 -04:00
97bfc0bb77
avoid (unlikely) overflow
2022-04-22 22:38:46 -04:00
cf647347c9
Merge branch 'develop' into safer-data-file-parsing
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# Conflicts:
# src/atom.cpp
2022-04-22 22:25:41 -04:00
8e9cc0eb51
Merge branch 'develop' into compute_temp_profile_dof
2022-04-22 22:16:42 -04:00
47564ab6bc
Merge branch 'develop' into region-lookup-refactor
2022-04-22 22:11:41 -04:00
1319cb2cf5
fix typo
2022-04-22 22:08:13 -04:00
aed7bafac0
Merge pull request #3217 from akohlmey/atomvec-strings
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Refactor Atom and AtomVec classes to use std::string and std::vector for setting up per-atom data
2022-04-22 22:03:26 -04:00
3a5ab301b2
propagate changes from previous commit to other packages that were missing them
2022-04-22 21:46:24 -04:00
5aebd151b6
Update compute_temp_profile.rst
2022-04-22 18:47:13 -06:00
16dd89c641
Added qualifier to assertions + note about inhomogeneous rigid systems
2022-04-23 10:30:44 +10:00
a90c632ae2
fix bug when no other post_force fixes are defined
2022-04-22 17:10:56 -06:00
48d8094d95
Merge branch 'develop' into snap-inner-mod
2022-04-22 16:54:21 -06:00
2c71d0eea2
Ported to KOKKOS, untested
2022-04-22 16:43:19 -06:00
01e7530902
shorten URL message text
2022-04-22 17:00:55 -04:00
907bcd16a8
Update compute_temp_profile.rst
2022-04-22 14:21:57 -06:00
b40e662b10
Merge pull request #3223 from akohlmey/less-fmtlib-warnings
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Reduce excessive warnings from fmtlib and assorted small changes
2022-04-22 15:03:49 -04:00
fec5538d3c
fix initialization bugs
2022-04-22 13:52:15 -04:00
1568974e8e
whitespace
2022-04-22 13:39:05 -04:00
c054edda6b
allow larger error margin for pressure computes
2022-04-22 13:22:01 -04:00
23d39c7d02
Merge branch 'develop' into create-overlap
2022-04-22 10:37:39 -06:00
c0d0c84f7d
update unit test files to implementation changes
2022-04-22 12:16:28 -04:00
da520bf8b7
integrate better into manual and traditional build system
2022-04-22 11:38:55 -04:00
68d1c856b3
fix typo
2022-04-22 11:27:08 -04:00
77b563a024
disable unknown pragma warnings for the summit machine when using CUDA
2022-04-22 11:23:54 -04:00
b4e2e2ec34
add support for angle cosine
2022-04-22 09:12:12 -06:00
a6f2f04664
Removed forgotten neighbor->ago condition in compute_born_matrix. Rewritten compute_pair loop so that newton condition does not affect results.
2022-04-22 16:59:52 +02:00
644b3f6933
clarify and remove redundant text
2022-04-22 09:32:10 -04:00
23186da560
Merge branch 'snap-inner-bug-printf' of github.com:megmcca/lammps into less-fmtlib-warnings
2022-04-22 09:26:29 -04:00
3b1021abd1
cosmetic changes. improve programming style conformance
2022-04-22 08:36:20 -04:00
55a7c341af
improve data file section parsing
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- avoid segfaults when dereferencing a null pointer on short files
- allow skipping over empty and comment-only lines.
2022-04-22 08:35:09 -04:00
6d56629660
improve error messages
2022-04-22 08:31:53 -04:00
dc4752ef63
add convenience function for printing a missing arguments error message
2022-04-22 08:28:14 -04:00
079d3ea067
remove extraneous printf line
2022-04-22 06:16:45 -06:00
3e9f207062
Improve the performance of pair style, ilp/graphene/hbn/opt
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Updates to the OPT package
2022-04-22 20:00:28 +08:00
e0049a07f3
Add a new pair style, ilp/graphene/hbn/opt
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Updates to the OPT package
2022-04-22 17:55:05 +08:00
13664a0185
add utility to print url with pointer to error message
2022-04-22 05:25:50 -04:00
4de9ab85ce
Completed inner cutoff, KOKKOS still in progress
2022-04-21 17:30:12 -06:00
3f3c481554
add support to fix adapt for angle coeffs
2022-04-21 17:00:11 -06:00
0b6a689f3c
Removed the domain->minimum_image() calls from dihedral_nharmonic and angle_cosine.
2022-04-22 00:37:49 +02:00
6b3c868c6e
Removed commented previous nb list request.
2022-04-22 00:26:00 +02:00
5fd2311951
Pulled develop. Solved false_positives.txt bond.cpp and bond.h files conflict.
2022-04-22 00:24:50 +02:00
0b0947c167
Solved the dihedral index problem. It was actually the indices used.
2022-04-22 00:20:25 +02:00
ea66d4e73f
mostly doc page edits
2022-04-21 16:00:53 -06:00
0ece11c491
add a code comment
2022-04-21 15:19:04 -06:00
8cb47c8504
change update of dynamic groups to post_force location in timestep
2022-04-21 15:02:47 -06:00
c6abc9e682
need wheel module for modern install procedure
2022-04-21 16:15:42 -04:00
09187801c1
suppress nvcc unknown pragma warnings
2022-04-21 15:01:46 -04:00
247c61c93f
make portable to ubuntu
2022-04-21 13:01:13 -04:00
04afec7771
fix minor doc issues
2022-04-21 13:00:26 -04:00
05a845fafd
compute_dihedral finally agrees with numdiff!
2022-04-21 18:37:26 +02:00
6dcafd693f
Update fix_nve.rst
2022-04-21 10:13:05 -06:00
1df430aef4
align with doc folder makefile
2022-04-21 12:02:05 -04:00
b7a3af7bd1
update plumed version in containers and install python3-venv
2022-04-21 12:01:49 -04:00
556ad777d1
update code to use safe fread() and thus silence compiler warnings on ubuntu
2022-04-21 11:53:59 -04:00
b7d329f9b3
remove unused field in class
2022-04-21 07:58:54 -04:00
1a8ba25444
silence some excessive warning by the new Intel compilers
2022-04-21 07:58:43 -04:00
e9eb74e13a
add missing override
2022-04-21 07:50:48 -04:00
c07551072d
must check if externally set C++ standard is at least c++11
2022-04-21 07:50:30 -04:00
e8cacc4380
Updated example syntax
2022-04-20 18:17:23 -06:00
b4b6ba91e0
Slight adjustment to definition of Sinner and Dinner
2022-04-20 18:01:24 -06:00
9cac62401d
only set the C++ standard value if it is not set externally
2022-04-20 19:32:42 -04:00
96e22b1104
disable CUDA support with Eigen3
2022-04-20 18:50:55 -04:00
5242b5557f
Merge branch 'develop' into less-fmtlib-warnings
2022-04-20 18:24:06 -04:00
4544664edc
comment out assertion causing many warnings
2022-04-20 18:14:10 -04:00
38093ffe47
KOKKOS doesn't require nvcc_wrapper anymore when compiling with CMake
2022-04-20 18:13:42 -04:00
c62e2ad4d1
disable warnings with PGI/NVHPC compilers and import CMAKE_TUNE_FLAGS
2022-04-20 17:39:33 -04:00
aebbd04297
Merge pull request #3222 from akohlmey/fasthtml
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Add fasthtml target for faster testing of .rst to .html translation
2022-04-20 17:16:23 -04:00
da0e0359b6
Merge pull request #3221 from akohlmey/ttm_mod_fix
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Fix file reader bug in fix ttm/mod
2022-04-20 16:55:10 -04:00
a8e5e0e515
use python -m venv instead of virtualenv
2022-04-20 15:49:22 -04:00
42d875a411
add fasthtml target for faster testing of .rst to html translation
2022-04-20 15:02:00 -04:00
bc0236d869
Bugfix tagint type for tags
2022-04-20 18:49:55 +02:00
a3a3354d1b
fix file reader bug and add ttm/mod example
2022-04-20 11:52:36 -04:00
f6523851b5
Explcitly state that fix nve uses velocity-Verlet integrator
2022-04-20 08:58:53 -06:00
c086664c2a
Per-atom vector usage
2022-04-20 16:23:44 +02:00
9d1d552fde
bugfix init_list for etypes
2022-04-20 16:23:44 +02:00
df5b1a228d
tweak epsilon for macos/arm64
2022-04-19 21:57:43 -04:00
71e96e8b7c
Merge pull request #3212 from ndtrung81/dielectric-updates
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Updates to the DIELECTRIC package
2022-04-18 09:33:28 -04:00
f40b8f5694
Merge branch 'develop' into dielectric-updates
2022-04-17 17:47:55 -04:00
9228855257
cosmetic
2022-04-17 17:47:38 -04:00
c820eeb118
re-apply clang-format
2022-04-17 17:47:31 -04:00
7c64ff6634
Improved the precision of the conversion factor epsilon0e2q, added more options for units, ensured that qqrd2e be included in efield in several pair styles, and updated the fix polarize doc page
2022-04-17 12:01:41 -05:00
44e4510251
replace vector for storing regions with unordered_set for simpler processing
2022-04-16 11:17:55 -04:00
aa4787f604
complete region handling refactor
2022-04-16 00:17:39 -04:00
cbb4abc55c
improve formatting
2022-04-15 17:12:31 -04:00
69d9c5187e
refactor group access, enable and apply clang-format
2022-04-15 15:29:43 -04:00
4b400fb4a6
overload count() function to pass in Region pointer directly
2022-04-14 22:00:50 -04:00
21f24ef572
Merge pull request #3218 from lammps/mdi-new-functions
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MDI new functions
2022-04-14 20:48:51 -04:00
a0a82cad0b
Merge pull request #3214 from stanmoore1/kk_tersoff_bugfix
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Fix issues in Kokkos Tersoff and Stillinger-Weber pair styles
2022-04-14 17:28:59 -04:00
e66fb6a1c1
apply clang-format
2022-04-14 17:28:05 -04:00
64b1c45a49
update MDI library and checksum
2022-04-14 17:27:20 -04:00
56bfa90a69
adapt bpm/sphere atom style
2022-04-14 17:23:11 -04:00
20827b4105
sync with new version of MDI library
2022-04-14 15:00:09 -06:00
111111b38b
Merge branch 'develop' into atomvec-strings
2022-04-14 16:52:04 -04:00
26f6976568
move errorfunction complement approximation factor into shared namespace
2022-04-14 16:47:38 -04:00
8b31edb102
programming style updates and clang-format applied
2022-04-14 16:47:10 -04:00
81e203b5fa
only allow "lj" and "real" units for now
2022-04-14 16:43:59 -04:00
4380ed23d1
documentation and LAMMPS homepage URL updates
2022-04-14 15:55:22 -04:00
0cfb26799c
Fix copy/paste error
2022-04-14 13:47:57 -06:00
5bd86a05b2
Merge pull request #2906 from jtclemm/BPM
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Adding package for bonded particle models
2022-04-14 15:43:14 -04:00
c5565a4e02
Small tweaks
2022-04-14 13:16:44 -06:00
5c70f45feb
updates to use new funcs from Python as well
2022-04-14 10:49:12 -06:00
29582f09a1
add missing update to property_atom function API
2022-04-14 12:34:58 -04:00
ac8d97d358
capture by reference
2022-04-14 12:27:45 -04:00
31178661c9
switch to C++11 compatible lambda function capture
2022-04-14 12:27:03 -04:00
095c610a3f
no more need to explicitly initialize empty fields
2022-04-14 12:00:56 -04:00
b5eb5ac686
update docs for adding atom styles to refactored process
2022-04-14 11:48:18 -04:00
500a3426ed
"stringify" and "vectorize" per-atom data handling in Atom class
2022-04-14 11:31:20 -04:00
198d07e905
print warning when fix property/atom is issues before reading a restart
2022-04-14 11:06:35 -04:00
b16d48aa41
"stringify" and "vectorize" processing of per-atom attributs in AtomVec classes
2022-04-14 11:06:10 -04:00
9424c2558e
enable and apply clang-format. minor cosmetic changes
2022-04-13 21:05:19 -04:00
1755d06870
Merge pull request #3216 from lammps/update-citation
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update a citation
2022-04-13 19:16:57 -04:00
bc2b600f09
changes to use new MDI library functions
2022-04-13 16:26:48 -06:00
0946d41c3f
Merge pull request #3215 from megmcca/snap-inner-bug
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fix crash with multielement inner cutoff
2022-04-13 16:17:10 -04:00
30914a73fb
Update error messages
2022-04-13 14:10:52 -06:00
44f67330e2
Port changes to other flavors of Tersoff
2022-04-13 13:50:49 -06:00
21c61a5c77
Merge pull request #3213 from akohlmey/gpu-remove-legacy
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Remove support for CUDA toolkits before version 8 and GPUs older than Kepler
2022-04-13 15:10:17 -04:00
bd6d7b9136
clarify CUDA versus OpenCL build and runtime restrictions
2022-04-13 14:24:43 -04:00
c9ab5ebbf5
cosmetic
2022-04-13 12:59:54 -04:00
2804de8c26
fix refactoring bug
2022-04-13 12:59:41 -04:00
fb37c86632
remove duplicate
2022-04-13 12:59:30 -04:00
0f1097d7e6
recover read_restart and read_data capability for fix property/atom
2022-04-13 12:41:40 -04:00
2d5fadd88f
Switch to const ref to help compiler
2022-04-13 10:27:41 -06:00
230bed0bc4
fix crash with multielement inner cutoff
2022-04-13 09:49:13 -06:00
9e94722987
Remove full neigh option in Kokkos Tersoff and SW pair styles
2022-04-13 08:14:02 -06:00
ef4e41d2a2
programming style and format updates
2022-04-12 22:52:07 -04:00
467cae9436
permissions
2022-04-12 18:43:47 -04:00
09b08ecd85
whitespace
2022-04-12 18:36:51 -04:00
8c153adceb
spelling
2022-04-12 18:36:16 -04:00
e89303c202
Fix compile error with Kokkos CUDA
2022-04-12 16:31:21 -06:00
622a4a6d51
Overallocate slightly to reduce memory reallocs
2022-04-12 16:20:21 -06:00
2998462743
Add const
2022-04-12 16:07:37 -06:00
f64d405ad8
Fixing remaining errors/warnings in doc build
2022-04-12 15:59:38 -06:00
90a6a3c125
Fix typo
2022-04-12 15:57:49 -06:00
2fa99703bf
Fix issues in Kokkos Tersoff and SW pair styles
2022-04-12 15:49:28 -06:00
616349c27b
Merge branch 'develop' into dielectric-updates
2022-04-12 16:33:02 -05:00
f3363070e7
remove support for CUDA toolkits before version 8 and GPUs older than Kepler
2022-04-12 15:48:16 -04:00
ca37c01476
Fixing broken links/references in documentation
2022-04-12 13:36:39 -06:00
e1a7ea38a9
update a citation
2022-04-12 12:59:25 -06:00
929e46b5c7
remove dead code
2022-04-12 11:06:28 -04:00
e1a2423f2e
modernize, initialize pointers, apply clang-format
2022-04-12 11:06:18 -04:00
2ff8ac0cb2
Merge pull request #3210 from arghdos/fix_volatile
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Add non-volatile version of join function to DomainKokkos
2022-04-11 19:48:43 -04:00
12d7ef541b
Need both versions of join
2022-04-11 15:13:44 -06:00
804c43b33c
Merge branch 'develop' of github.com:lammps/lammps into fix_volatile
2022-04-11 15:11:37 -06:00
ef53298f7c
Added the omp version of pair lj/cut/coul/debye/dielectric
2022-04-11 15:45:12 -05:00
2a595713f3
Updated doc page of the set command for the local dielectric constant,
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which could be used as a measure of polarizability in the future
2022-04-11 15:01:19 -05:00
b666f7324c
Updated the example input script with the set command for per-atom dielectric constant
2022-04-11 14:44:02 -05:00
b05aadf877
Allowed to set the atom local dielectric values (epsilon)
2022-04-11 14:18:43 -05:00
49aebf64b9
include BPM package in multiple presets
2022-04-11 12:41:28 -04:00
9d907e31b3
recover compilation
2022-04-11 12:40:59 -04:00
36723853c9
Merge branch 'develop' into BPM
2022-04-11 12:18:34 -04:00
8161dff58a
Added pair style lj/cut/coul/debye/dielectric, added conversion factor epsilon02eq for real units
2022-04-11 10:54:41 -05:00
ebc74d7428
Indice correction in EXTRA-COMPUTE/compute_born_matrix.cpp, some PBC check in EXTRA-MOLECULE/dihedral_nharmonic.cpp and MOLECULA/angle_cosine.cpp. Also added born_matrix to angle_cosine.cpp
2022-04-11 17:53:48 +02:00
236d275b2f
Merge pull request #3211 from akohlmey/collected-small-changes
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Collected clang-tidy updates
2022-04-11 11:07:00 -04:00
b36262cd11
cosmetic
2022-04-10 20:47:42 -04:00
d6f7570d57
avoid redundant use of boolean literals
2022-04-10 20:47:31 -04:00
74f2b67b1a
no if statement required before delete[]
2022-04-10 19:55:24 -04:00
3eec2eec9a
make buffer size a compile time constant and use strncpy() instead of strcpy()
2022-04-10 18:33:17 -04:00
200b4f13c7
use dynamic cast instead of c-style cast when casting from base type to derived class
2022-04-10 18:18:06 -04:00
39b316729b
use auto type when assigning from cast or using new
2022-04-10 18:16:36 -04:00
6071376d42
derive ATC_Error exception class from std::exception
2022-04-10 15:25:37 -04:00
413a01ade5
apply clang-tidy updates
2022-04-10 12:07:54 -04:00
1a2d83ab01
HDF5 library may be parallel which is an error with serial LAMMPS
2022-04-10 12:07:54 -04:00
591498ab31
Updated and fixed typos in doc pages
2022-04-10 10:24:31 -05:00
a9f5a1af51
initialize class member pointers in initializer to null
2022-04-10 11:13:33 -04:00
c54fe7d97d
small update
2022-04-10 08:00:47 -04:00
85b69000cd
revert to use NULL instead of nullptr, so that it compiles without having to enable c++11 compatibility
2022-04-09 20:54:59 -04:00
ddf67ec42d
properly use nullptr on pointers (with a little help from clang-tidy)
2022-04-09 20:27:40 -04:00
2d346638fb
correctly declare and override virtual functions for desired polymorphism
2022-04-09 20:17:36 -04:00
a620f5bd7d
fix pointer type bug
2022-04-09 19:59:43 -04:00
07bc76871c
avoid unsafe strcpy()
2022-04-09 19:01:42 -04:00
4adeb29491
clang-tidy fixes
2022-04-09 19:00:59 -04:00
177f9cabc1
add ELECTRODE package to suitable presets
2022-04-09 18:19:55 -04:00
4e81adaf8c
make buffer size for text file reader adjustable
2022-04-09 17:46:47 -04:00
fcd3e76767
skip unsupported unit tests
2022-04-09 17:45:38 -04:00
c07b06c8d1
skip unsupported unit tests
2022-04-09 17:44:40 -04:00
420dc969d3
need to set buffer size based on generated output format
2022-04-09 17:26:41 -04:00
eb9af11d64
make buffer size for text file reader adjustable
2022-04-09 17:26:03 -04:00
b20c98753f
style changes
2022-04-09 10:10:33 -04:00
44ccbd2184
use internal reader/parser classes for file reading and writing
2022-04-09 10:10:19 -04:00
06fc53ac69
make timer output configurable and off by default
2022-04-09 10:08:58 -04:00
75d87383e2
one more OpenMP fix
2022-04-09 09:10:45 -04:00
a04c0077b9
silence some more compiler warnings and try to resolve issues with old compilers
2022-04-09 09:04:17 -04:00
8625a6d946
apply clang-format
2022-04-09 08:00:11 -04:00
ce62da1cca
compatibility with legacy OpenMP implementations
2022-04-09 07:53:17 -04:00
71f8e11d70
join multi-line strings
2022-04-09 07:45:01 -04:00
a94fa0a840
formatting
2022-04-09 07:44:33 -04:00
23598fa658
spelling
2022-04-09 07:44:15 -04:00
7673eda947
apply clang-format
2022-04-09 07:16:22 -04:00
6dea9fa10c
add missing dependency handling in GNU make build for ELECTRODE package
2022-04-09 07:10:31 -04:00
c04db4b545
modernize
2022-04-09 07:01:42 -04:00
e0c4f6164e
silence compiler warnings
2022-04-09 07:01:35 -04:00
cab6fca22e
update to latest upstream and modernize neighbor list request handling
2022-04-09 07:00:39 -04:00
19b42bc726
Merge branch 'develop' into electrode
2022-04-09 06:31:22 -04:00
8ce2ce8fd4
remove unused import
2022-04-09 04:02:01 -04:00
a71bf4cae5
Merge pull request #3207 from lammps/remove-message-package
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remove MESSAGE package
2022-04-09 03:20:26 -04:00
8dce9f7a60
install pyyaml
2022-04-09 00:39:50 -04:00
6c87962551
fix remaining doc build issues
2022-04-09 00:39:27 -04:00
674d2a6788
Merge branch 'develop' into remove-message-package
2022-04-09 00:25:11 -04:00
8b53ff9383
Merge pull request #2921 from lammps/mdi-expand
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Enhance MDI support in LAMMPS in its MDI package
2022-04-09 00:18:50 -04:00
22122092e4
Merge pull request #3206 from akohlmey/add-kimplugin
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Add kimplugin source and CMake based build support
2022-04-08 23:09:13 -04:00
d0d4bbf5ae
Merge pull request #3196 from akohlmey/avoid-bigint-format-scanf
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Refactor code to avoid XXXINT_FORMAT defines and xxscanf() function calls
2022-04-08 21:24:57 -04:00
5ff42d8993
simplify
2022-04-08 21:21:36 -04:00
81933b7972
silence compiler warnings
2022-04-08 21:19:32 -04:00
f3685fa8de
fix bugs
2022-04-08 21:18:55 -04:00
375062d02c
restore modern API usage
2022-04-08 21:18:28 -04:00
093667799d
Merge branch 'develop' into mdi-expand
2022-04-08 20:58:53 -04:00
1cc913d006
Merge pull request #3205 from akohlmey/dump-style-yaml
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Add dump style yaml
2022-04-08 20:55:01 -04:00
8cdce34b27
Merge branch 'develop' into dump-style-yaml
2022-04-08 18:42:28 -04:00
6849356d63
fix spelling, formatting, and cross-link/indexing issues
2022-04-08 18:35:51 -04:00
530d8c007d
minor tweak
2022-04-08 18:09:10 -04:00
521d45dcc6
remove MESSAGE package from CMake
2022-04-08 18:00:36 -04:00
fbc55937fe
Merge pull request #3198 from bathmatt/pair-dpd
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DPD-BASIC kokkosification
2022-04-08 17:48:28 -04:00
dff3bc5656
Merge branch 'develop' into avoid-bigint-format-scanf
2022-04-08 17:39:25 -04:00
fc24cf15ce
Merge pull request #3197 from akohlmey/custom-thermo-headers
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add support for custom header keywords with thermo output and dump styles
2022-04-08 17:29:35 -04:00
b24d01fae6
remove broken links in the manual from removing packages
2022-04-08 17:27:01 -04:00
d0edc48a65
update purge list with removed source files from MESSAGE package
2022-04-08 17:26:16 -04:00
f405c7acc9
add deprecation handling removed commands and styles
2022-04-08 17:25:56 -04:00
ef7c6a580e
simplify
2022-04-08 16:51:52 -04:00
2c509d96a6
we are not compatible with those old versions for the MDI library
2022-04-08 16:43:41 -04:00
07aecb3678
whitespace fixes and apply clang-format
2022-04-08 16:36:21 -04:00
bfaa1e9ed0
whitespace
2022-04-08 16:28:57 -04:00
a7ccb16aa8
Merge pull request #3192 from davidfir3/fep_ta
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New feature compute fep/ta
2022-04-08 16:27:12 -04:00
33798b99a4
remove debug print statement
2022-04-08 14:08:51 -06:00
caa977e869
Remove redundant calls
2022-04-08 13:28:14 -06:00
f8ec0365c6
Fix a few more issues
2022-04-08 12:52:26 -06:00
d99b1258e3
remove volatile to fix build error from Kokkos commit (5574130fb333ac1745a52d4a6383ac95c64bdc0f)
2022-04-08 11:13:31 -05:00
b73437aa63
Merge pull request #3208 from arghdos/develop
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Fix for building GPU backend on ROCm 5.1+
2022-04-08 07:19:27 -04:00
4efdfaa8f3
simplify and make consistent, fix time based dump bug
2022-04-08 07:05:30 -04:00
bd4d92c76d
entry for mdi sub-dir in Examples.rst
2022-04-07 16:02:45 -06:00
77565add6e
Add C++14 to Makefile build system
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Change-Id: I24f72b4aaca93a49877775c3d181507c83cd7f82
2022-04-07 17:54:20 -04:00
ab0e5d5568
Fix for building GPU backend on ROCm 5.0+
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Change-Id: I32ad9be86d6a0467ccae555a1d0272813c905e97
2022-04-07 17:48:03 -04:00
792ae5dae5
remove src/MESSAGE package and supporting dirs and doc pages
2022-04-07 15:44:48 -06:00
f40180f7fb
lib README edit
2022-04-07 15:15:50 -06:00
adef9b7747
add log files to examples/mdi
2022-04-07 15:13:29 -06:00
40aa146624
Prune unused code and fix virial issue
2022-04-07 15:05:07 -06:00
0b6aa59621
updated doc pages
2022-04-07 14:42:58 -06:00
e2f25a96e1
spelling
2022-04-07 14:50:33 -04:00
ddb6350fe8
Remove unused var
2022-04-07 10:53:38 -06:00
9b969648d5
add kimplugin source and CMake based build support
2022-04-07 12:51:06 -04:00
2956aee8dc
Small tweaks
2022-04-07 10:45:50 -06:00
4f67f586d0
Fix memory issue and leftover debugging
2022-04-07 10:02:58 -06:00
fdf59e6a03
more debugging for plugin library mode
2022-04-07 09:26:43 -06:00
f5add95083
fix syntax error
2022-04-07 06:08:54 -04:00
8a6e6fe523
make dump style yaml test dependent on it being available
2022-04-07 05:59:31 -04:00
3970942028
add test for yaml dump style
2022-04-07 02:44:17 -04:00
0e8e1171c6
add unit test for yaml style thermo output and updated logfile class
2022-04-07 02:07:05 -04:00
59fa0be35f
update for recent changes in thermo output
2022-04-07 02:06:55 -04:00
98b908387f
add unit test for yaml style thermo output and updated logfile class
2022-04-07 02:05:47 -04:00
601bdadf44
update for recent changes in thermo output
2022-04-07 02:05:05 -04:00
082254455b
improve confusing error messages
2022-04-07 00:37:30 -04:00
58ecf03e5d
correct yaml import
2022-04-07 00:37:18 -04:00
348ee5299e
implement a dump style yaml
2022-04-06 19:11:55 -04:00
e944ecd1c2
correct docs
2022-04-06 19:10:16 -04:00
207b34ae12
allow for pre-timestepping comm with engine, e.g. for force eval
2022-04-06 16:38:58 -06:00
b1e92c9ec6
update YAML reading python example to read faster using libyaml.
2022-04-06 17:38:25 -04:00
4bd28cf920
altering how plugin mode works
2022-04-06 15:24:02 -06:00
2b8b916cba
delete unused enums
2022-04-06 10:08:53 -04:00
cd7f08a8e7
support dump_modify for column headers in ADIOS dump styles
2022-04-06 09:31:01 -04:00
387b0df554
Remove gitlab pipeline
2022-04-06 08:21:12 +02:00
b4cc158981
Merge pull request #3182 from charlessievers/mliap
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ML-IAP updates
2022-04-05 22:07:27 -04:00
e4f62cae9a
integrated added styles into manual
2022-04-05 22:01:21 -04:00
4ad8af629d
whitespace
2022-04-05 21:53:29 -04:00
f89a08985e
update DPD-BASIC package examples
2022-04-05 21:50:36 -04:00
607ecf595b
Add ScatterView
2022-04-05 17:04:23 -06:00
8744627059
Tiny tweaks
2022-04-05 16:04:43 -06:00
efa7116b58
Merge branch 'develop' of https://github.com/lammps/lammps into pair-dpd
2022-04-05 15:48:36 -06:00
cd0b921ed2
Merge pull request #3203 from stanmoore1/acks2_bug
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Fix issues in ReaxFF QEq and ACKS2
2022-04-05 16:29:30 -04:00
65be564cd6
Review akohlmey
2022-04-05 15:35:04 +00:00
22392d226a
silence compiler warnings
2022-04-04 21:11:09 -04:00
a5139d7100
make sure "NN" is initialized before it is used
2022-04-04 21:03:15 -04:00
288c154290
Merge pull request #3186 from Ruyk/kokkos-sycl-cmake
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Add kokkos-sycl.cmake preset
2022-04-04 16:12:24 -04:00
c274146358
whitespace
2022-04-04 15:40:19 -04:00
3eb7194619
Merge branch 'develop' into acks2_bug
2022-04-04 15:39:44 -04:00
3e01bc48d4
Need s ghosts
2022-04-04 13:05:10 -06:00
134c77a5c6
reference kokkos-sycl.cmake in the docs
2022-04-04 14:47:53 -04:00
fd80b1bd9b
Merge pull request #3201 from samueljmcameron/bugfix_dumpvtk
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Bug fix in vtk dump.
2022-04-04 14:40:56 -04:00
776dc34411
Add missing vars
2022-04-04 12:28:03 -06:00
f42635a40d
Should be nall not nghost
2022-04-04 12:08:38 -06:00
4fadf4c830
more debugging on plugin mode
2022-04-04 10:30:12 -06:00
b4fc86e467
Fix issues in ReaxFF QEq and ACKS2
2022-04-04 10:24:54 -06:00
02f972292c
spelling
2022-04-04 12:16:28 -04:00
5d4ec45534
Merge branch 'develop' into custom-thermo-headers
2022-04-04 12:08:23 -04:00
d89ff310c1
Merge pull request #3202 from lammps/fix-deform-doc-page-edit
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Fix deform doc page edit
2022-04-04 12:07:10 -04:00
a0b15c2d04
Merge pull request #3199 from lammps/misc
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Misc changes
2022-04-04 11:51:59 -04:00
63a841e300
doc page edit
2022-04-04 08:59:40 -06:00
3ed011dcfb
whitespace
2022-04-03 10:55:56 -04:00
028beb8da4
Merge branch 'develop' into misc
2022-04-03 10:55:24 -04:00
db00b49a50
Merge pull request #3195 from weinbe2/feature/kk-reax-ang-tors-optim
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kk/reax: Preprocessing optimizations to ComputeAngular,Torsion; Modularity/Memory improvements in BuildLists
2022-04-03 09:52:08 -04:00
e5a01026a7
add unit tests for fix move
2022-04-03 03:19:47 -04:00
c9d0889f25
add "transrot" style to fix move that allows to do translation and rotation at the same time
2022-04-02 18:34:17 -04:00
584b166823
enable and apply clang-format
2022-04-02 17:20:34 -04:00
93c67a3c07
make compute msd (and msd/nongauss) error out immediately when used with a dynamic group
2022-04-02 17:13:30 -04:00
8e838c1424
Bug fix in vtk dump.
2022-04-02 12:55:51 +01:00
49abd0d269
update docs
2022-04-01 15:17:10 -04:00
fb9316701b
port colname changes to MPIIO package
2022-04-01 14:57:41 -04:00
dab640220c
Fix name to match code
2022-04-01 12:48:58 -06:00
ea9e3c0860
Update fix ACKS2 docs
2022-04-01 12:45:38 -06:00
2f895d63a6
Add missing variable assignment
2022-04-01 12:32:24 -06:00
fb76cb9a5c
updated virtual
2022-04-01 17:54:12 +02:00
294dcc5f93
more debugging for plugin mode
2022-04-01 09:27:48 -06:00
68f27bb4cd
addressing comments from Evan's review
2022-04-01 17:02:57 +02:00
ce67cb0ca1
first stab at implementing dump_modify colname
2022-04-01 07:41:13 -04:00
9c0934e82c
Have ext-tstat working
2022-04-01 10:37:53 +02:00
c470c204d4
remved unused var
2022-04-01 10:35:05 +02:00
4042a52db1
rename header keyword to colname
2022-03-31 21:58:35 -04:00
4437f16e08
remove references to non-existing folders
2022-03-31 17:49:24 -04:00
335b78b4f2
Add contributing author to list
2022-03-31 15:27:05 -06:00
e3611c5d73
add support for custom keywords with thermo output
2022-03-31 17:26:46 -04:00
19a6eecfbb
more debugging for plugin engine mode
2022-03-31 14:41:38 -06:00
4dc4d74056
Add back in accidentally deleted call
2022-03-31 13:10:22 -06:00
ad4701f4f7
Small tweaks
2022-03-31 12:52:36 -06:00
72874376f0
Remove #ifdef
2022-03-31 12:27:43 -06:00
79fcf18013
Remove #ifdef
2022-03-31 12:25:58 -06:00
229f0af537
enable LAMMPS as driver to use plugin engine
2022-03-31 12:09:05 -06:00
df05bbb72b
moved dpd_tstat to kokkos
2022-03-31 17:20:56 +02:00
28976b8c92
recover compilation on windows with old MPICH version
2022-03-31 08:44:43 -04:00
12ddc4ad12
final set of XXXINT_FORMAT changes
2022-03-31 07:51:14 -04:00
52b563a83e
modernize parsing in fix tmd, add support for comments and empty lines
2022-03-31 07:36:50 -04:00
33b6466611
add minimal fix tmd example
2022-03-31 07:31:43 -04:00
b97c30e6e7
more refactoring, modernizing, removing of debug code
2022-03-31 06:24:44 -04:00
acd9c7950e
update doc and example
2022-03-31 12:25:10 +08:00
b64e90dfe0
simplify. avoid XXXINT_FORMAT macros
2022-03-30 23:43:28 -04:00
1c9dc9c0d9
correct formatting
2022-03-30 22:11:46 -04:00
65a083c83d
add support for </>VELOCITIES command at nodes
2022-03-30 15:52:55 -06:00
993441b25a
avoid XXXINT_FORMAT macros in fix reaxff/bonds
2022-03-30 17:52:21 -04:00
c7a9a3e2f6
simplify and replace use of XXXINT_FORMAT macros
2022-03-30 16:13:38 -04:00
f3fa04ae0a
bugfix
2022-03-30 15:01:03 -04:00
c4729b39b4
replace more uses of XXXINT_FORMAT with fmtlib
2022-03-30 13:53:25 -04:00
14f54aae40
Reax: Preprocessing optimizations to ComputeAngular,Torsion. Modularity boosts + memory reductions for BuildLists
2022-03-30 08:23:41 -07:00
5003c35963
have first cut of just pair-dpd
2022-03-30 16:22:26 +02:00
ddf93eb7ba
removed unused var
2022-03-30 15:42:09 +02:00
69d32f286b
Stan's patch
2022-03-30 15:10:54 +02:00
2517d1fb55
Converted DPD-BASIC-EXT to use Kokkos
2022-03-30 15:10:54 +02:00
9aad583c7d
more parsing updates
2022-03-30 07:38:33 -04:00
999c880dfd
simplify parsing numbers and reduce usage of BIGINT_FORMAT
2022-03-30 07:12:25 -04:00
ff3ac64b7e
spelling
2022-03-30 03:32:26 -04:00
faacf575b5
add support for >+FORCES command
2022-03-29 14:20:44 -06:00
b92d117524
Merge pull request #3191 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-03-29 14:45:18 -04:00
385b7a77e6
Merge pull request #3193 from samueljmcameron/stable_fix_brownian_update
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BROWNIAN package update
2022-03-29 13:03:11 -04:00
2a35ec2d85
Merge pull request #3187 from stanmoore1/kk_opt_neighlist
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Optimize Kokkos neigh list for GPUs
2022-03-29 12:05:34 -04:00
d9880273e3
fix typo
2022-03-29 11:54:34 -04:00
b8c7a6153d
whitespace
2022-03-29 09:49:48 -04:00
bfe361c576
fix doc building issues
2022-03-29 09:47:44 -04:00
5ea526728e
Merge branch 'develop' into stable_fix_brownian_update
2022-03-29 08:26:11 -04:00
88ff2db715
cosmetic updates, print warnings only on MPI rank 0
2022-03-29 08:23:18 -04:00
6f1fac1c59
Updated docs.
2022-03-29 12:21:09 +01:00
c28504961d
remove references to the mailing list in the manual and replace with forum link, if needed
2022-03-29 07:01:00 -04:00
dcd6bea172
one final fix in constructor of asphere.
2022-03-29 11:22:21 +01:00
27d2fab951
simplify processing for "*" in filenames for embedding timestep by using utility function
2022-03-29 06:06:48 -04:00
da61b6871a
Added in check for ellipsoid in brownian_asphere
2022-03-29 10:46:05 +01:00
db5e4e05a8
fix bug that happens when fix ave/time Nfreq < thermo freq
2022-03-29 15:35:23 +08:00
0bebe6c428
First commit, things not working though.
2022-03-29 07:50:19 +01:00
015257889d
flag compatibility with VTK version 9
2022-03-29 01:03:04 -04:00
b211f97efa
update and improve ADIOS support
...
- modernize code
- remove dead code and unused definitions, enums, and includes
- create default adios2_config.xml file if it doesn't exist
- enable and apply clang-format
- update documentation
2022-03-29 01:01:57 -04:00
333e3b0491
apply clangformat
2022-03-28 22:48:00 -04:00
3ba7b8c24c
add star_subst() utility function that replaces a '*' in a string with a number
2022-03-28 22:47:20 -04:00
82d0a55862
remove merge conflict message
2022-03-28 15:26:20 -06:00
6407745781
update programming style and enable/apply clang-format
2022-03-28 16:49:11 -04:00
a60e1546b2
properly integrate into build system and docs
2022-03-28 16:48:44 -04:00
60e2b84e09
Fuse loops
2022-03-28 14:43:16 -06:00
1a3c6d3dbc
tweak to one MDI doc file
2022-03-28 14:33:17 -06:00
d80fe166d1
Merge branch 'develop' into collected-small-changes
2022-03-28 16:30:01 -04:00
438cba3604
update programming style to latest conventions, enable and apply clang-format
2022-03-28 16:26:55 -04:00
88c075ba90
Tune for HIP
2022-03-28 14:19:50 -06:00
48332c3b18
Rename variable
2022-03-28 14:17:44 -06:00
94645ae720
update of doc pages to match new version of MDI support
2022-03-28 13:56:16 -06:00
63caa8bb44
reorder so that kspace follows improper and comes before compute
2022-03-28 15:12:25 -04:00
120c080fc2
avoid converting a null pointer to a std::string and correct error check
2022-03-28 15:07:23 -04:00
9920b22509
programming style updates
2022-03-28 15:06:55 -04:00
cd8cdc711c
Merge pull request #3189 from CDenniston/develop
...
remove defunct LBtype argument from lb/fluid doc
2022-03-28 14:12:00 -04:00
540cf9b6d7
Merge pull request #3188 from njzjz/kspace_plugin
...
support kspace style plugin
2022-03-28 11:58:40 -04:00
51c41f09bf
recover unit tests for variables
2022-03-28 09:21:25 -04:00
af4afb7e03
modify error/warning message
2022-03-28 21:14:13 +08:00
ebf2b1e706
add doc for compute fep/ta
2022-03-28 20:01:59 +08:00
d7f95da8f3
add extract_setting special function to variable command
2022-03-28 08:00:29 -04:00
4545954385
reformat for wider lines
2022-03-28 07:24:51 -04:00
13228ca29a
add dimension check
2022-03-28 13:34:36 +08:00
c52bffda9c
remove defunct LBtype argument from lb/fluid doc
2022-03-27 11:26:23 -04:00
cf17fd2306
remap ghost atoms, no need to forward_comm()
2022-03-27 21:49:51 +08:00
603136a93b
rename some function & variable, output delta area
2022-03-27 20:52:00 +08:00
7c333b8e07
include bonded eng, cancel neigh build & fix bugs
2022-03-27 20:22:16 +08:00
ff107315cb
need to always extract the path to MPI include directory
2022-03-26 23:20:57 -04:00
980b6cada7
update formatting
2022-03-26 10:55:10 -04:00
36444a1db1
add DOI for 29 September 2021 version
2022-03-26 10:48:45 -04:00
356091e1e0
support kspace plugin
...
I need such feature in the development of deepmd-kit.
2022-03-26 03:39:07 -04:00
2e84700224
delete unused variable "pairflag"
2022-03-26 13:55:22 +08:00
dc668ed0df
update to README instructions
2022-03-25 16:11:17 -06:00
55d3edef2f
doc info in sequence_driver.py
2022-03-25 16:10:43 -06:00
d710d19aef
Enforce pre_exchange() order for (currently) unused update option
2022-03-25 15:56:59 -06:00
4d037376af
include GHub whitespace changes
2022-03-25 15:19:13 -06:00
0c1516b34d
Add another missing change
2022-03-25 14:14:42 -07:00
055fefc542
finished MDI engine and test script debugging
2022-03-25 15:07:38 -06:00
d648247b80
whitespace
2022-03-25 13:03:56 -07:00
d131223161
Restore changes lost in Git shuffle
2022-03-25 12:59:45 -07:00
9f0eb2ea1a
Add note about memory
2022-03-25 12:17:33 -07:00
b14086f3f9
Update docs
2022-03-25 12:12:04 -07:00
a5e22c07c7
Merge branch 'kk_npair_ghost_gpu' of github.com:stanmoore1/lammps into neigh_transpose
2022-03-25 11:49:17 -07:00
01abeda9ef
Merge branch 'develop' of https://github.com/lammps/lammps into kk_npair_ghost_gpu
2022-03-25 12:08:32 -06:00
e2e046c452
add missing host overload to make Clang happy
...
Change-Id: Ib0bd9dec3ecc6bf13b9894b07024172a9810cd77
2022-03-25 12:05:25 -06:00
17b35878ea
Add version of Kokkos Ghost neigh list optimized for GPUs
2022-03-25 12:03:20 -06:00
c3f4dac7dc
Small tweak to comments
2022-03-25 09:45:05 -07:00
6dae6198a2
Add neigh transpose as Kokkos package option
2022-03-25 09:17:39 -07:00
2279b28df2
Update from upstream
2022-03-25 09:00:56 -07:00
8e9b508c88
Merge branch 'develop' of github.com:lammps/lammps into Elastic_stress
2022-03-25 16:01:35 +01:00
274db39aa5
demo of new compute style fep/ta
2022-03-25 22:41:39 +08:00
29ada4e263
Update description header
2022-03-25 11:19:59 +00:00
2ae448d9d0
Add kokkos-sycl.cmake & relevant compiler flags
2022-03-25 11:05:09 +00:00
58f59197ff
silence warnings from coverity scan
2022-03-25 05:30:01 -04:00
5663a9c38b
print current LAMMPS version number in configuration summary
2022-03-24 17:07:45 -04:00
4e180bc237
update URL for downloading old LAMMPS versions
2022-03-24 17:02:07 -04:00
08bdaf8ca7
Merge pull request #3184 from akohlmey/next_patch_release
...
Update version strings for next patch release
2022-03-24 14:27:29 -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
dad8fb8b06
Removing residual files
2022-03-24 11:44:44 -06:00
82f4487d4d
Merge pull request #3185 from akohlmey/collected-small-changes
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Final small changes for patch release
2022-03-24 13:25:01 -04:00
6edaf42b3d
fix temperature initialization bug in KOKKOS nose-hoover code
2022-03-24 11:44:24 -04:00
82c5c622b8
fix temperature initialization bug in KOKKOS nose-hoover code
2022-03-24 11:44:02 -04:00
81d0165c5c
Merge pull request #3181 from jibril-b-coulibaly/new_damp
...
Damping fixes for finite-size particles simulations
2022-03-24 11:08:02 -04:00
79c047487d
fix parallel execution bug for shell command
2022-03-24 07:38:44 -04:00
4278ff8205
update threebody example
2022-03-24 07:32:30 -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
383f0adc94
update version strings for patch release
2022-03-23 19:44:14 -04:00
d8d12ccf1c
Merge pull request #3180 from akohlmey/strtok-parsing-refactor
...
Refactor files to replace parsing with strtok() to use tokenizer classes
2022-03-23 19:40:39 -04:00
6e959b6f43
more robust response to >COORDS command
2022-03-23 17:21:00 -06:00
a3beb063a3
update and simplify parsing of STL mesh using LAMMPS utilities
2022-03-23 18:41:17 -04:00
66f97ef6bc
whitespace
2022-03-23 17:22:46 -04:00
a4018dbb4b
update MDI library to version 1.3.0
2022-03-23 17:18:19 -04:00
92a968a8a9
Resolving merge conflicts
2022-03-23 14:28:27 -06:00
07cec37786
add Note to damping/cundall documentation about fix order. Remove fix order warning from fix viscous/sphere
2022-03-23 14:59:43 -05:00
42dd772455
more work on plugin mode
2022-03-23 13:45:20 -06:00
f95aaf5898
update settings
2022-03-23 15:15:51 -04:00
d785483c4c
update potential file parsing in pair style meam/spline and meam/sw/spline
2022-03-23 15:09:31 -04:00
61f28aea36
add "rewind()" member function to Text and Potential file reader classes
2022-03-23 14:44:50 -04:00
67329b6fff
fix KOKKOS bug
2022-03-23 14:40:17 -04:00
9417e41676
Rename sphere/bpm, remove bond instance, add smooth option
2022-03-23 11:41:27 -06:00
c4425a1b0e
debugging plugin mode
2022-03-23 11:17:51 -06:00
2ab9aa3cdc
dummy commit to trigger resolving github inconsistency
2022-03-23 11:16:54 -04:00
59eca42127
synchronize format handling and fix/compute/variable checking with dump custom
2022-03-23 10:57:52 -04:00
a208f1fc39
minor tweak to one style thermo output for keeping columns straight
2022-03-23 10:48:15 -04:00
ae41996967
add support for determining damping scale factor from atom-style variable
2022-03-23 10:43:26 -04:00
ace6c67697
Copy .h & .cpp from compute_fep for comparison
2022-03-23 22:26:44 +08:00
1fd699d279
enable and apply clang-format
2022-03-23 05:06:15 -04:00
b6e37c828e
move fix viscous/sphere to EXTRA-FIX package
2022-03-23 05:02:32 -04:00
e247c1a4d0
update related commands
2022-03-23 04:57:49 -04:00
4a5f5b9980
Merge remote-tracking branch 'github/develop' into new_damp
2022-03-23 04:47:52 -04:00
23461d4ba8
spelling
2022-03-23 04:47:48 -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
9d500280c9
more tweaks for extep potential file
2022-03-22 22:21:23 -04:00
c18236216b
add MPI_Group_free() support to STUBS
2022-03-22 21:54:36 -04:00
0bd8500da3
whitespace
2022-03-22 21:47:26 -04:00
31f0d5c056
Merge remote-tracking branch 'github/develop' into strtok-parsing-refactor
2022-03-22 21:44:15 -04:00
8ef9eae60a
update potential file parser in pair style extep
2022-03-22 21:43:26 -04:00
080662683d
use tokenizer to read neb initial replica files
2022-03-22 20:54:42 -04:00
3e7de83e6e
Merge pull request #3179 from akohlmey/thermo-refactor-plus-yaml
...
Refactoring of Thermo class and new thermo style yaml
2022-03-22 20:17:25 -04:00
4c13f99b04
convert to use LAMMPS' tokenizer and potential file reader classes
2022-03-22 17:59:53 -04:00
1ee40f8f8f
change to tests
2022-03-22 11:11:43 -06:00
194751e800
add support for full minimizations
2022-03-22 09:32:31 -06:00
eb44b6b1fa
Merge branch 'develop' into mdi-expand
2022-03-22 08:39:24 -06:00
6555c7302d
debugging for series of calcs
2022-03-22 08:38:39 -06:00
d3ba1af89c
rename cundamp to damping/cundall
2022-03-22 09:01:53 -05:00
2e539918c1
slight change in __init__.py to fix *.a bug
2022-03-21 22:55:28 -07:00
862e4ba67a
Added different pytorch modules that allow different handling of element types and proposal for __init__.py bug fix
2022-03-21 22:45:28 -07:00
8954ac4f20
correct/simplify for GPU device specialization
2022-03-21 17:12:43 -04:00
643511294e
create fix for rotational viscous damping on spheres. create fix for Cundall type damping for granular simulations
2022-03-21 15:34:04 -05:00
4c1a6d7ecf
tweak settings for thermo style "one"
2022-03-21 14:44:07 -04:00
6c30bdf082
add missing reaxff files to purge list
2022-03-21 14:35:09 -04:00
d519ca0213
add missing reaxff files to purge list
2022-03-21 14:34:14 -04:00
6f2c09c187
Merge branch 'develop' of github.com:lammps/lammps into Elastic_stress
2022-03-21 10:46:53 +01:00
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
bc86bdf984
use tokenizer in fix phonon
2022-03-20 21:54:58 -04:00
4c95314ea6
must set boxflag *after* checking for rigid fix because we might change the box ourselves
2022-03-20 21:25:26 -04:00
550ae15dff
proper handle partial initialization from infile
2022-03-20 21:12:35 -04:00
83a8f72d83
fix off-by-one bug when writing restart files for rigid bodies
2022-03-20 19:14:13 -04:00
89c7d8f707
replace strtok based file reader with ValueTokernizer
2022-03-20 16:34:41 -04:00
adf4a23f58
refactor and apply clang-format
...
- replace file reader code using TextFileReader and ValueTokenizer
- replace traversing list of fixes with accessor functions
- enable and apply clang-format
- add examples for reading rigid bodies from file
2022-03-20 15:28:31 -04:00
356555418d
remove dead code
2022-03-20 00:41:26 -04:00
45d246b9c5
Merge branch 'develop' into thermo-refactor-plus-yaml
2022-03-19 21:55:18 -04:00
3c54b56cfe
update overlooked date stamp
2022-03-19 21:00:14 -04:00
d539dcd8d4
repair collateral damage to NETCDF package from Thermo class refactor
2022-03-19 20:54:50 -04:00
1b7da77a4a
update some more version change timestamps
2022-03-19 20:20:30 -04:00
294dd2778a
update thermo style yaml docs and examples for reading and parsing
2022-03-19 20:19:52 -04:00
c70b0b39ac
update documentation for modifying LAMMPS to reflect changes to Thermo class
2022-03-19 18:06:56 -04:00
74103b141a
enable and apply clang-format
2022-03-19 18:03:29 -04:00
a4d2062865
reduce redundant code with helper functions and simplify by using std::string
2022-03-19 18:01:12 -04:00
f5ebfbf90b
refactor thermo output processing and add new yaml thermo style
2022-03-19 16:39:09 -04:00
649e8a27b3
Merge pull request #3159 from akohlmey/neigh-request-refactor
...
Refactor neighbor list request code
2022-03-19 00:47:09 -04:00
4399559259
adjust epsilon for unit test on MacOS
2022-03-18 23:37:54 -04:00
ad5235a764
update yaml file for force style unit tests with higher precision numbers
2022-03-18 22:44:50 -04:00
c80a182150
relax epsilon for MSVC++ test
2022-03-18 21:20:44 -04:00
88ac22cd62
silence compiler warnings. avoid uninitialized access.
2022-03-18 20:02:49 -04:00
4f3a9f9b63
Merge branch 'develop' into neigh-request-refactor
2022-03-18 19:23:51 -04:00
3f28768b5e
Merge pull request #3177 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-03-18 19:22:40 -04:00
a96aef73d1
Merge remote-tracking branch 'github/develop' into neigh-request-refactor
2022-03-18 18:28:35 -04:00
3828518e5e
implement suggestions from @athomps
2022-03-18 18:28:20 -04:00
2b2bc64ad9
Merge pull request #3178 from akohlmey/sphinx-theme-update
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Update LAMMPS theme for HTML pages of the manual
2022-03-18 18:09:56 -04:00
68673633f0
silence compiler warnings about unused variables
2022-03-18 18:09:24 -04:00
a7fce6dc39
add harmonic/cut to python example folder. small tweaks to docs and examples
2022-03-18 17:58:30 -04:00
6c6a6b7c64
provide more complex example for using pair style python
2022-03-18 17:07:01 -04:00
30966dfed0
Bugfix from @weinbe2
2022-03-18 14:14:34 -06:00
364ac40724
Merge pull request #3169 from stanmoore1/kk_reduce_mem
...
Reduce memory use in Kokkos package
2022-03-18 14:21:30 -04:00
8fe7b928a7
use newer APIs to get access to fixes and computes
2022-03-18 13:16:18 -04:00
cc2ba3c350
make sure parameters are stored symmetrically
2022-03-18 13:02:34 -04:00
f928cc2335
update github managers.
2022-03-18 11:37:49 -04:00
008c000bfe
update LAMMPS theme for HTML pages from readthedocs theme to version 1.0.0
2022-03-18 07:44:47 -04:00
815718f33a
follow conventions
2022-03-18 06:06:48 -04:00
bc8998c997
correct toycar input example
2022-03-18 06:02:38 -04:00
477d53bcdb
check for sufficient number of arguments in command line
2022-03-18 06:02:38 -04:00
734d867a91
use preprocessor for conditional compilation
2022-03-18 06:02:28 -04:00
626b2c4bab
use utility functions
2022-03-18 05:52:34 -04:00
43b4240503
use sizeof(double) not sizeof(MPI_DOUBLE), bigint instead of long int
...
also use fmt::print() for typesafe output
2022-03-18 05:51:35 -04:00
32612d3f5b
enable and apply clang-format
2022-03-18 00:06:28 -04:00
6d38ce5284
enable and apply clang-format
2022-03-17 23:40:37 -04:00
e12e06198c
enable long md and min runs
2022-03-17 17:58:26 -06:00
85e581eb2a
enable and apply clang-format
2022-03-17 19:44:53 -04:00
58030009da
new math constants: DEG2RAD and RAD2DEG
2022-03-17 19:44:34 -04:00
6e7eedf148
enable and apply clang-format
2022-03-17 18:41:17 -04:00
fb8074d294
renormalize line endings. add .gitattributes to configure them explicitly
2022-03-17 18:21:31 -04:00
ff1a08f148
fixes to CMake build for ML-QUIP package from upstream
2022-03-17 18:07:12 -04:00
fc532ae1a0
list submodules to be updated explicitly for compatibility with CMake 3.16 and later
2022-03-17 16:53:44 -04:00
1e21b8fac1
enable and apply clang-format
2022-03-17 15:37:50 -04:00
57cf2a735a
add support for '-f' option to shell rm built-in command
2022-03-17 15:17:44 -04:00
8ffacb55ca
enable and apply clang-format
2022-03-17 12:20:17 -04:00
982a5719c4
correct mixed up force and energy in pair style harmonic/cut
2022-03-17 12:18:36 -04:00
9dfb099197
change platform::mkdir() to create entire path like "mkdir -p"
...
update the documentation of the shell command to current state
and specifically explain the difference between built-in and
external commands and correct where built in commands were described
as calling external commands.
2022-03-17 11:34:50 -04:00
b7ea33332f
spelling
2022-03-17 11:32:48 -04:00
1fbeba8fa7
remove dead code and silence compiler warnings
2022-03-17 10:12:00 -04:00
cf06f71514
more refactoring of MDI engine
2022-03-16 17:46:01 -06:00
9e91708e27
Merge pull request #3174 from akohlmey/collected-small-changes
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Collected small changes
2022-03-16 16:20:28 -04:00
6d070c7043
more use of modernized APIs
2022-03-16 15:24:42 -04:00
396a95f7af
Merge pull request #12 from weinbe2/neigh_transpose
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Addition of a "smart" transpose routine with scratch memory staging
2022-03-16 12:29:21 -06:00
7e2fef096f
use accessor function to get and process list of fixes
2022-03-16 14:18:09 -04:00
d49c27e362
Added a "smart" transpose routine with scratch memory staging for neighbor table transposes between LR and LL
2022-03-16 14:12:20 -04:00
31bc7b2864
Merge pull request #3170 from akohlmey/auto-load-plugins
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Automatically load LAMMPS plugins if they are in folders listed in LAMMPS_PLUGIN_PATH environment variable
2022-03-16 13:53:14 -04:00
5a53b0fc03
import python3 compatibility changes to tools/python from upstream
2022-03-16 13:24:53 -04:00
4be3da727a
include tools/python in whitespace check
2022-03-16 13:22:39 -04:00
bb4268518b
make python 2 compatible
2022-03-16 12:56:19 -04:00
72425f1874
add '#' to make the list of headers a comment
2022-03-16 12:55:53 -04:00
b774464156
whitespace
2022-03-16 12:55:25 -04:00
ba19090631
Merge pull request #3173 from athomps/snap-inner
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Inner cutoff switching function for SNAP descriptors and potentials
2022-03-16 12:43:23 -04:00
4894263215
Merge pull request #3167 from CDenniston/develop
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Update LATBOLTZ package to new version
2022-03-16 12:22:48 -04:00
e3d4e80407
Merge branch 'develop' into collected-small-changes
2022-03-16 11:55:07 -04:00
0fd02ffd10
Merge pull request #3153 from aliehlen/log-pizza-updates
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Log pizza updates
2022-03-16 11:50:31 -04:00
afc634eef2
Merge branch 'develop' of https://github.com/lammps/lammps into neigh_transpose
2022-03-16 08:44:09 -06:00
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
49b87f9929
enable/apply clang-format, remove redundant code, style fixes
2022-03-16 09:07:38 -04:00
edf7c274b9
Merge branch 'lj_cubic_error' of github.com:olavgal/lammps into collected-small-changes
2022-03-16 09:03:02 -04:00
92bfaeda10
fix bug where it was not possible to use an absolute path for write_coeff
2022-03-16 09:00:56 -04:00
0ac5d8223d
Whitespace
2022-03-16 13:06:32 +01:00
8ac1d5bbc5
Error fixed. Epsilon and sigma must also be symmetric
2022-03-16 13:04:36 +01:00
7215939a89
Streamline documentation
2022-03-16 10:47:56 +00:00
8d341e0714
remove EVAL command
2022-03-15 17:13:15 -06:00
99fa769800
more syncing
2022-03-15 16:15:57 -06:00
2a171cf2a2
sync new and old versions with current LAMMPS
2022-03-15 16:10:54 -06:00
636f00276e
sync with current Modify methods for fix lookup
2022-03-15 14:12:23 -06:00
25d8950f94
Merge branch 'develop' into neigh-request-refactor
2022-03-15 11:39:45 -04:00
8e585620c3
enable and apply clang-format
2022-03-14 17:14:40 -04:00
ec97d859b9
use tokenizer class for parsing
2022-03-14 17:14:01 -04:00
1d1dea56d8
whitespace and programming style fixes
2022-03-14 16:52:58 -04:00
43e486973f
cosmetic changes. remove debug comments and commented out code.
2022-03-14 14:40:38 -04:00
87429366f8
update plugin developer guide
2022-03-14 09:54:31 -04:00
46564c1ee8
recover compilation on windows
2022-03-12 18:43:53 -05:00
0778c12f04
plug memory leaks by freeing MPI data types
2022-03-12 18:06:01 -05:00
ddb35ee455
use utils::logmesg and fmtlib. remove use of sprintf() to temporary buffers
2022-03-12 18:05:05 -05:00
484b7e6d33
must remove and respecify fix lb/fluid around reset_timestep command
2022-03-12 16:16:15 -05:00
fe9b426c7e
cosmetic changes
2022-03-12 16:14:55 -05:00
9931323463
attempt to transparently download the missing data file with curl
2022-03-12 14:03:08 -05:00
293ad3fc03
move lb/fluid pointer initialization to initializer list
2022-03-12 12:03:18 -05:00
4948438265
fix small typesetting issues
2022-03-12 09:53:50 -05:00
a66228b4d2
make sure pointer is null on first use
2022-03-12 09:42:03 -05:00
aca7126cfe
use newer APIs to access list of fixes in Modify class
2022-03-12 09:23:36 -05:00
7e2bb9a065
reformat and spellcheck the documentation
2022-03-12 08:43:17 -05:00
0341599390
fixes were removed from package, remove from the documentation as well
2022-03-12 08:31:00 -05:00
335e7c7bbc
replace use of iostreams and stringstreams with stdio and fmtlib
2022-03-12 08:25:56 -05:00
4c090c5d8e
remove debug comments
2022-03-12 08:24:51 -05:00
84a7596b7c
more closely follow LAMMPS programming style conventions
2022-03-12 08:23:40 -05:00
25b4d8ade1
move static constants to its own header that is only pulled in by files that use them.
2022-03-12 08:21:52 -05:00
b27cbbd1a1
Merge branch 'develop' into CDenniston/develop
2022-03-12 07:28:30 -05:00
aaeb9fe933
Merge branch 'dielectric-updates' of github.com:ndtrung81/lammps into collected-small-changes
2022-03-12 07:26:00 -05:00
b1119d81a9
Minor tweaks
2022-03-11 21:25:44 -07:00
014345a512
Updated a citation
2022-03-11 20:55:59 -07:00
51034c00c0
Completed documentation
2022-03-11 20:40:18 -07:00
b9fd86e7ca
switchinnerflag working for single-element two types SNAP potential
2022-03-11 17:23:38 -07:00
f691805062
More
2022-03-11 16:41:22 -07:00
5216a543ae
More
2022-03-11 15:43:48 -07:00
4d13282120
More
2022-03-11 15:07:18 -07:00
877b764a36
More
2022-03-11 14:38:51 -07:00
8323c4fe45
More progress
2022-03-11 14:14:45 -07:00
a7a66100c6
Updated the doc page of the polarize fixes
2022-03-11 14:13:34 -06:00
3f9cc03fc0
Minor tweaks
2022-03-11 11:39:06 -07:00
9e78818637
Minor tweaks
2022-03-11 11:26:06 -07:00
1a04eabb5e
merge in current develop
2022-03-11 10:01:25 -07:00
8ba4e7e897
tweaks to src files, added examples dir
2022-03-11 09:33:34 -07:00
62c59a5339
document LAMMPS_PLUGIN_PATH environment variable
2022-03-11 10:34:04 -05:00
56658e9c2c
make automatic plugin loads/unloads mostly silent, count/report number of plugins loaded
2022-03-11 10:31:53 -05:00
01bd3d1da0
add functionality to auto-load plugins
2022-03-11 05:52:26 -05:00
45b1213795
silence warnings from coverity scan
2022-03-11 04:29:01 -05:00
e8a550aa22
Reduce memory use in Kokkos package
2022-03-11 00:07:47 -05:00
9b989b1860
Merge pull request #3164 from akohlmey/collected-small-changes
...
Collected small changes
2022-03-10 23:42:04 -05:00
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
3a1921b3ed
correct SHAKE bond stats output and avoid division by zero
2022-03-10 23:01:23 -05:00
ca76ff360f
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 21:17:58 -05:00
11d3b13e31
Added a lot of boilerplate for inner data, not working yet
2022-03-10 18:40:59 -07:00
7343f6e5b8
writing column names is optional
2022-03-10 15:23:21 -06:00
079f7559ea
Merge branch 'develop' of github.com:fujiisoup/lammps into collected-small-changes
2022-03-10 16:01:02 -05:00
fa9683e6d2
Merge remote-tracking branch 'github/develop' into collected-small-changes
2022-03-10 16:00:55 -05:00
adef6bd10c
Added first draft of inner switching functions
2022-03-10 13:58:14 -07:00
0828ae66a0
Fix a typo in the doc
2022-03-11 05:48:34 +09:00
0fcf40c48e
use MathConst::MY_PI more consistently and benefit from it being a constexpr
2022-03-10 14:14:32 -05:00
8e85481afa
use MathConst::MY_PI instead of inferring it from acos(-1).
2022-03-10 14:00:34 -05:00
12b144fd0e
change math const from M_ to MY_ using math_const.h
2022-03-10 12:36:41 -05:00
5bf1ab0e2d
try moving _USE_MATH_DEFINES to cpp file from header for windows compilation
2022-03-10 11:15:25 -05:00
1e4a6dcb41
fix missing #endif in lb/fluid header
2022-03-10 10:37:08 -05:00
c6fe7ed4f4
add _USE_MATH_DEFINES for windows compilation
2022-03-10 10:18:50 -05:00
0a1fa5e040
lb/fluid code cleanup for whitespace, unused vars, windows cmath
2022-03-10 09:53:44 -05:00
c9007501a2
remove cerr iostream reference from lb/fluid
2022-03-10 08:43:54 -05:00
43319120d0
fix qeq/dynamic and qeq/fire need half neighbor list not full
2022-03-10 06:30:10 -05:00
1bba1ca2ae
fix logic bug
2022-03-10 05:44:31 -05:00
61f5bbd633
update logic to avoid stall with neighbor list statistic during final summary
2022-03-10 05:21:53 -05:00
06e7bd8144
follow KOKKOS' advice about CPU binding of threads
2022-03-10 01:18:15 -05:00
abd8a6ee15
remove incorrect comment
2022-03-10 01:17:44 -05:00
10f8a597c7
use proper header for access to Kokkos class.
2022-03-10 01:11:33 -05:00
837b8fb753
bugfix
2022-03-10 01:00:34 -05:00
86b686f159
correct handling of neighflag member variable in KOKKOS styles
2022-03-10 00:52:16 -05:00
799ab965d9
make neighbor list request flags protected and add selected friends
2022-03-09 23:25:26 -05:00
26c0b9cf87
move calculation of number of neighbors to Neighbor class
...
this allows reusing the code in the ImbalanceNeigh class
2022-03-09 23:18:28 -05:00
3ef02edb48
adapt KOKKOS package styles to use new neighbor list request API
2022-03-09 22:43:38 -05:00
9f44221ee3
update neighborlist requests for new API in KSPACE package
2022-03-09 21:20:18 -05:00
2e2bd37883
automatically enable intel neighbor list request property for intel pair styles
2022-03-09 21:19:19 -05:00
9b26726f51
change to clang-format for LATBOLTZ routines
2022-03-09 20:41:28 -05:00
9bbd1df57b
another chunk of neighbor list request updates
2022-03-09 19:49:08 -05:00
c4b23bd7e5
programming style updates use newer/simpler APIs
2022-03-09 19:21:03 -05:00
888db4b0ef
update examples to standard lammps conventions
2022-03-09 18:13:45 -05:00
e8547af049
update neighbor list requests and compute style lookups in machine learning packages
2022-03-09 06:49:07 -05:00
3bb7a247ac
convert some more files to use the new neighbor list request API
2022-03-08 21:29:33 -05:00
cef5076c9a
no need to have a multi-threaded neighbor list in fix peri/neigh
...
I builds just a single neighbor list during setup.
2022-03-08 18:23:46 -05:00
1db981c784
convert a few more styles to the new neighbor request API
2022-03-08 18:20:28 -05:00
3c3912aff2
add deprecated lb/fluid integrator fixes to fix_deprecated
2022-03-08 17:10:22 -05:00
16449c3d11
fix merge conflicts for new version of lb/fluid and minor updates from develop branch on virtual functions and removed fix styles
2022-03-08 16:38:32 -05:00
1249c713f0
Add transpose to neigh list
2022-03-08 14:28:06 -07:00
55f8bf9c51
adapt some more styles to use the new neighbor list request API
2022-03-08 15:27:37 -05:00
fd73d1376a
Merge branch 'develop' into neigh-request-refactor
2022-03-08 13:04:32 -05:00
dfbeedfded
convert more neighbor list requests to the new API
2022-03-08 12:39:05 -05:00
deb694745b
update neighbor list requests with default settings
2022-03-08 06:34:27 -05:00
028c8b5d27
add default arguments for requests with default flags
2022-03-08 06:33:27 -05:00
1296d6d938
update neighbor list request developer notes
2022-03-08 06:32:48 -05:00
3b0a6ac840
add support for requesting SSA neighbor lists and update a few more styles
2022-03-08 06:17:13 -05:00
decdcd0b55
Revert "programming style updates"
...
This reverts commit 5242409ebd
2022-03-08 06:15:11 -05:00
5242409ebd
programming style updates
2022-03-08 05:17:18 -05:00
795f24c3ff
honor NEWTON_ON/OFF request flags
2022-03-08 05:17:18 -05:00
369b8365bf
update QEQ, ASPHERE, and KIM packages to use new neighbor list request API
2022-03-08 05:16:55 -05:00
1aa8b64283
convert GPU package styles to use new neighbor list request API
2022-03-08 04:37:46 -05:00
9742817ba3
Dihedrals analytical results of compute_born_matrix are still wrong but, in some low deformations cases, they are ok. This is a progress...
2022-03-08 10:16:30 +01:00
374917fb6f
tweak platform tests for CPU time to avoid bogus failures on windows
2022-03-07 21:42:02 -05:00
c6b4c418e7
Merge pull request #3161 from athomps/gcmc-relax-mol-mpi-error
...
Relaxed the error check on molecule moves in parallel. Molecule excha…
2022-03-07 20:24:36 -05:00
02f6b4c6e8
whitespace
2022-03-07 19:36:07 -05:00
87613bb106
rename doc file to be more generic and match the examples folder
2022-03-07 15:34:00 -05:00
07059c1362
Merge branch 'develop' into collected-small-changes
2022-03-07 15:29:47 -05:00
b0dae52e2d
Merge pull request #3165 from olavgal/compute_pressure_cartesian_and_spherical
...
Computes for local pressure tensor in Cartesian and spherical coordinates
2022-03-07 15:05:51 -05:00
6edfb49527
update .gitignore for recent additions
2022-03-07 14:37:01 -05:00
bfb9638e6c
correct issue introduced by global pattern replacement
2022-03-07 14:19:29 -05:00
5206d81742
make class name consistent with file name and add backward compatibility
2022-03-07 14:09:43 -05:00
1f3a3bb80b
missing updates
2022-03-07 13:51:16 -05:00
bbcffd4b5a
Merge pull request #3163 from akohlmey/test-compute
...
Add unit tests for computes
2022-03-07 13:49:07 -05:00
8d5a59c0fa
Switched all command and class names from pressure to stress
2022-03-07 11:27:37 -07:00
6c4bc8258c
Merge pull request #3162 from phankl/mesocnt_memory
...
Optimized memory usage for pair style mesocnt
2022-03-07 12:03:58 -05:00
c2b0347b30
Added notes on similarity between these computes
2022-03-07 09:09:29 -07:00
8f10953e92
Small comma error in citation
2022-03-07 10:27:23 +01:00
c8b7fc2144
Added cross-reference to compute pressure/cartesian
2022-03-06 20:19:38 -07:00
6da4db4d7e
Merge branch 'compute_pressure_cartesian_and_spherical' of github.com:olavgal/lammps into compute_pressure_cartesian_and_spherical
2022-03-06 20:11:20 -07:00
e857b923bc
Added representative output to log files
2022-03-06 20:11:10 -07:00
793db836d9
update .gitignore
2022-03-06 19:55:11 -05:00
a2bf40df0a
correct mini-ToC links and add missing entry
2022-03-06 11:45:26 -05:00
aaa51d6fc6
optimizations and avoiding floating point exceptions
2022-03-06 11:04:51 -05:00
2f5f36cff8
move examples to a more appropriate folder. add logfiles
2022-03-06 11:03:57 -05:00
44e3874541
Changed citations
2022-03-06 12:50:25 +01:00
fac3ce4507
example files for pressure/cartesian/cylinder/spherical
2022-03-06 12:43:37 +01:00
005f76a9e6
clang-format
2022-03-06 05:24:29 -05:00
72cbffee7d
fix bug looking up neighbor lists
2022-03-06 05:24:15 -05:00
4781a4c8c6
style update
2022-03-06 04:49:08 -05:00
440e01d243
no longer needed. done by Neighbor class directly.
2022-03-06 04:48:54 -05:00
e9bcde4b58
more openmp neighbor list function to Neighbor class
2022-03-06 04:48:37 -05:00
cc618264a0
allow only one accelerator type enabled for neighbor lists
2022-03-06 04:47:22 -05:00
3f80894857
Merge branch 'develop' into neigh-request-refactor
2022-03-06 04:23:52 -05:00
54e667e491
convert more styles to use new neighbor list request API, apply clang-format
2022-03-05 21:44:45 -05:00
ffb367663d
add more accessor functions
2022-03-05 21:08:25 -05:00
f1d695299e
simplify checking for intel neighbor list requests
2022-03-05 20:31:56 -05:00
8fe78e5fc4
enable and apply clang-format
2022-03-05 20:21:32 -05:00
de4b9a1d20
use new neighbor list request API
2022-03-05 20:20:55 -05:00
21fc072396
enable and apply clang-format
2022-03-05 20:19:24 -05:00
5dbad2354a
use new neighbor list request API
2022-03-05 20:18:40 -05:00
c5c3c335c9
enable clang-format
2022-03-05 20:16:10 -05:00
875560b827
use new neighbor list request API
2022-03-05 20:15:48 -05:00
67a7764086
Initalizing nullptrs, fixing labels, small errors in doc, and sign errors in rot sliding damp
2022-03-05 17:07:02 -07:00
095c9ab9d1
whitespace
2022-03-05 17:08:49 -05:00
83f08ff8ef
small update and correct broken link
2022-03-05 17:07:00 -05:00
8945050423
cosmetic
2022-03-05 16:47:31 -05:00
be4f5288d3
modernize potential file reader in pair style mesocnt
2022-03-05 16:47:06 -05:00
f329711384
Merge branch 'develop' into mesocnt_memory
2022-03-05 15:06:23 -05:00
a9eae51d27
print name of non-existent compute/fix/variable in error message
2022-03-05 14:31:24 -05:00
ece25a95ad
stability improvements: recompute bin width for perfect match, don't test for floating point identity
2022-03-05 13:46:56 -05:00
15fa6049f2
update comments
2022-03-05 12:33:54 -05:00
43ac557a9b
remove unused headers and dead code. reformat a few small items
2022-03-05 12:31:36 -05:00
c24e46c547
don't apply modulus to doubles but integers
2022-03-05 12:30:40 -05:00
9a98817567
reformat doc page and address spelling issues
2022-03-05 11:35:37 -05:00
99d29ea86a
Added kinetic contribution to pressure/cylinder and clang-format on all
2022-03-05 16:30:47 +01:00
089e46a540
Fixed some gramma
2022-03-05 16:29:42 +01:00
4e125ccfc6
Combined pressure profile documentation into one page
2022-03-05 16:22:11 +01:00
f9c02b9735
clarify. improve typesetting
2022-03-05 10:18:00 -05:00
87c96aeeb1
add tests for more compute styles
2022-03-05 10:07:54 -05:00
b3bef9cd34
Merged
2022-03-05 10:30:38 +01:00
9ea0c581ac
Adding kinetic contribution to prssure/cylinder
2022-03-05 10:25:28 +01:00
1ab85f5941
update citation references
2022-03-04 18:16:02 -05:00
8709e26923
Merge pull request #3166 from stanmoore1/reax_tabulate
...
Make it easier to enable tabulation in ReaxFF
2022-03-04 17:37:26 -05:00
c9563d0814
Fixed style changes
2022-03-04 22:30:25 +01:00
f8089bd007
fix cut-n-paste error
2022-03-04 16:08:14 -05:00
789571c4b4
Merge pull request #3158 from arghdos/split_buildlists_half_rebased
...
Split buildlists half kernel into "preview" and "finalize" kernels
2022-03-04 16:06:05 -05:00
5c8f506edf
add unit test input
2022-03-04 16:04:04 -05:00
577eac201b
add sanity check
2022-03-04 16:03:50 -05:00
401180699d
Update docs
2022-03-04 13:10:25 -07:00
1e530dbd19
Changed ref name to avoid duplicate
2022-03-04 20:55:29 +01:00
23580d8ca5
Integrated pressure/cartesian and pressure/spherical
2022-03-04 20:54:33 +01:00
cdeaa83f6d
Make it easier to enable tabulation in ReaxFF
2022-03-04 12:34:51 -07:00
7d8c217657
Anothr tweak of movemode logic
2022-03-04 09:23:51 -07:00
06e9c096ac
Remove unused code
2022-03-04 09:13:43 -07:00
98d2dca83f
Trailing whitespace
2022-03-04 16:58:31 +01:00
6d48ba1577
Trailing whitespace
2022-03-04 16:57:59 +01:00
a7112f173a
Trailing whitespace
2022-03-04 16:56:39 +01:00
9f0607876a
LAMMPS Homepage
2022-03-04 16:49:42 +01:00
47de1234c0
LAMMPS homepage and ø->{\o} in reference
2022-03-04 16:49:03 +01:00
2687228f09
Fixed LAMMPS homepage and changed ø to {\o} it reference
2022-03-04 16:47:16 +01:00
a396ed2b36
Fixed LAMMPS homepage
2022-03-04 16:45:31 +01:00
939171094b
Whitespace
2022-03-04 08:40:22 -07:00
df9a772020
More EVFLAG cleanup
2022-03-04 08:36:27 -07:00
760d85b9c4
Two computes that computes the local mechanical pressure tensor in Cartesian and spherical coordinates
2022-03-04 16:04:18 +01:00
7288828439
defined np1 = ntypes + 1 to shorten allocation commands
2022-03-04 13:48:44 +00:00
8b9be5bf0a
applied clang-format
2022-03-04 12:47:36 +00:00
98f83f9b3a
fix typos and make output section more readable
2022-03-04 06:25:16 -05:00
b94995cf5b
add some TALLY package compute. simplify some code with convenience functions
2022-03-04 06:24:37 -05:00
a70e895e06
updated documentation
2022-03-04 10:37:45 +00:00
550d523c9e
add gyration
2022-03-04 04:41:43 -05:00
73e38014f2
Added explanation of parallel molecule support
2022-03-03 18:21:30 -07:00
91f6805821
Tweaked logic for MC move flags and addedreference output for H2O and CO2 on 4 procs
2022-03-03 18:12:43 -07:00
eaa6fb17af
Relaxed the error check on molecule moves in parallel. Molecule exchange is okay.
2022-03-03 16:47:33 -07:00
f97a2d341c
Clean up evflags
2022-03-03 16:44:53 -07:00
5888ba0514
QEq does not require ghosts in the neighbor list
2022-03-03 16:16:13 -07:00
3bfb03bcb8
test compute com and compute dipole
2022-03-03 17:27:11 -05:00
e4d920d582
add minimal test for testing compute styles that compute global scalars
2022-03-03 17:11:01 -05:00
e5d2555cf2
small tweaks
2022-03-03 10:01:16 -07:00
569147bf11
Revert change of default value for list/blocking
2022-03-03 09:30:16 -07:00
0fbacd4c5d
Add missing optimization to CPU version
2022-03-03 09:02:47 -07:00
9083ff867e
whitespace
2022-03-03 08:48:54 -07:00
ee2b9f28cb
Switch to vector parallelism for half list in QEq
2022-03-03 08:09:25 -07:00
b6b7846c50
Optimization to reduce atomics on CPU
2022-03-03 07:46:35 -07:00
beee3126e0
Recover CPU performance by bifurcating code
2022-03-03 07:21:40 -07:00
22d43d8e05
Change default for list/blocking option
2022-03-03 07:20:53 -07:00
9f8362399d
convert granular pair style and augment docs accordingly
2022-03-03 06:58:54 -05:00
04dbf307d0
remove obsolete TODO item
2022-03-03 06:43:52 -05:00
7120e6354d
add a mini-TOC for faster access to contents as the page is getting longer
2022-03-03 06:43:20 -05:00
13bf72e61c
describe new neighbor list request APIs
2022-03-03 06:42:42 -05:00
b4da01c23a
reduce compiler warnings and need for private variables in OpenMP pragmas
2022-03-02 22:19:28 -05:00
a0996da644
apply new APIs to a few representative cases
2022-03-02 21:31:35 -05:00
d4272815a3
add new APIs for creating and manipulating neighbor list requests
...
also add a few new (delegating) constructors to simplify code
2022-03-02 21:30:16 -05:00
f7514ce358
make friends for access to instance_me member
2022-03-02 19:06:08 -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
0a2a252f08
cleanup
2022-03-02 10:42:41 -07:00
30517fad68
Remove unnecessary atomics/duplication
2022-03-02 10:34:49 -07:00
bac85c4c83
cleanup
2022-03-02 10:04:35 -07:00
083d166885
More cleanup
2022-03-02 09:46:25 -07:00
adefb287c5
whitespace
2022-03-02 09:29:07 -07:00
4ad27034f2
Small tweaks, cleanup
2022-03-02 09:04:13 -07:00
7fb684b802
for 2d systems, rigid bodies always have a moment of inertia and no DOFs need to be subtracted
2022-03-01 21:18:51 -05:00
2a0e66164e
enable and apply clang-format
2022-03-01 21:06:19 -05:00
092720b69a
correctly compute bond count for shake statistics
2022-03-01 20:52:07 -05:00
e79e4c0134
Seperate buildlists half into 'cheap' blocking-based preprocessor, and 'dense' finalizer
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Change-Id: Ic205c1e6f3578c033ec4d8c3c45070fd5b3d7a18
2022-03-01 14:51:40 -05:00
4c57b8f1db
Remove duplicate etypes setting
2022-03-01 19:44:17 +00:00
7cca49b14b
hide pow behind conditional
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Change-Id: I8bb3f7a069207dd0e5a5b980d2a7e3e1a7e22ccb
2022-03-01 12:52:55 -05:00
0edda42eee
Bugfix macro inversion
2022-03-01 17:58:56 +01:00
09e544cb8c
Changed label of compute_angles/dihedrals for better reading. compute_dihedrals is not working ATM. Also implemented some changes from AThompson.
2022-03-01 16:58:14 +01:00
cd9d3ae5d3
Merge branch 'Elastic_stress' of github.com:Bibobu/lammps into Elastic_stress
2022-03-01 11:04:39 +01:00
798975b809
Merge pull request #3155 from akohlmey/collected-small-changes
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Collected small changes
2022-02-28 15:18:27 -05:00
9f315fc2e2
small rewording
2022-02-28 12:17:20 -05:00
763f8f432f
Merge pull request #3156 from stanmoore1/kk_verlet_uvm
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Fix rare bug in Kokkos with CUDA UVM
2022-02-28 12:16:28 -05:00
bd4d1b52f9
Merge branch 'develop' into collected-small-changes
2022-02-27 19:33:04 -05:00
b76a7764fd
use new API to get access to intel fix
2022-02-27 15:19:34 -05:00
0ddefb3754
trigger building an intel style neighbor list so that buffers are allocated
2022-02-27 14:51:17 -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
bc9e45ca5a
use consistent names, avoid memory leaks, fix off-by-1 error in fourier dihedral
2022-02-27 12:24:37 -05:00
7824e43339
Change Update::reset_timestep() API so that rerun can bypass the time depended fix check
2022-02-27 11:35:34 -05:00
e287ef6ff9
Merge pull request #3154 from akohlmey/use-setuptools
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Refactor python/install.py and 'make install-python' to use setuptools and build a binary wheel
2022-02-27 11:32:05 -05:00
750e0435a8
add link to code design page and update/clarify a couple of things
2022-02-27 11:29:20 -05:00
94f97be6e9
link Modify overview paragraph to Code design page
2022-02-27 11:29:19 -05:00
06f4ae0f1f
ignore wheel files
2022-02-27 07:03:02 -05:00
0be14d4ed8
move basename operation from setup.py to install.py
2022-02-27 07:02:39 -05:00
7c11d1675d
fix bug with make install
2022-02-27 06:33:22 -05:00
7fd41bea6a
add some comments to the refactored scripts to explain technical details
2022-02-25 20:10:13 -05:00
27c1ed86fa
Added some self-citations for key contributors
2022-02-25 17:03:45 -07:00
014ad94479
Fix rare bug in Kokkos with CUDA UVM
2022-02-25 16:45:58 -07:00
96fbbc2b1b
Merge branch 'log-pizza-updates' of github.com:aliehlen/lammps into log-pizza-updates
2022-02-25 18:35:08 -05:00
3e01fa49dd
emulate using '-i' command line flag
2022-02-25 18:34:45 -05:00
d26f953a0a
Made the example match the benchmark of Kluge et al.
2022-02-25 15:25:47 -07:00
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
11ba2adbe7
add support for plumed 2.6.6, 2.7.4, and 2.8.0 (default 2.7.4)
2022-02-25 16:34:37 -05:00
1dbff92eeb
spelling
2022-02-25 16:23:48 -05:00
578a7cc54c
document and handle the case of a previous distutils installation.
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in this case 'make install-python' should not continue but instead
it now aborts and asks the user to do a manual uninstall
2022-02-25 16:10:46 -05:00
bb3a5b4057
update docs
2022-02-25 14:13:03 -05:00
511678017e
update inline docs and add -n/--noinstall flag to skipp installation
2022-02-25 13:44:47 -05:00
033045a534
need to check if virtualenv creation failed and exit with a suitable error message
2022-02-25 13:20:34 -05:00
5ba6eb474c
try to appease coverity scan
2022-02-25 12:20:08 -05:00
f0260c3395
restore exception handling with enforce --user install for older pip versions that don't do that automatically
2022-02-25 09:33:26 -05:00
257805d325
make prompt name consistent
2022-02-25 09:32:41 -05:00
6ab247e7f8
no need to create a virtualenv inside a temporal virtualenv
2022-02-25 09:12:01 -05:00
59e2b819e0
need python3-venv package for updated make install-python
2022-02-25 08:44:15 -05:00
ff4cd2a5e9
python2.7 compatibility
2022-02-25 08:43:51 -05:00
4630a5ffb8
must create virtualenv with same python we selected to run install.py
2022-02-25 08:43:38 -05:00
6e74d0a09a
LAMMPS GridComm patch
2022-02-25 08:13:16 +00:00
e2092a5788
first attempt at supporting multi-config builders
2022-02-25 00:52:13 -05:00
4b7731e831
update install.py script to build a wheel and install that
2022-02-25 00:24:16 -05:00
a14a616dc2
make cythonize detection compatible with /bin/dash on ubuntu
2022-02-24 21:26:20 -05:00
fb480f22fc
make cythonize detection compatible with /bin/dash on ubunutu
2022-02-24 21:24:04 -05:00
0680cdcc3c
spelling
2022-02-24 20:43:04 -05:00
44f884316b
when updating ML-IAP due to adding/removing PYTHON we need to delete and re-add cythonize support
2022-02-24 20:42:26 -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
891d3c8296
update setup.py to be compatible with building "pure" and "binary" wheels
2022-02-24 17:04:16 -05:00
4dc5b93c6c
spelling
2022-02-23 16:37:28 -05:00
37ce6cf5f7
Merge branch 'develop' into log-pizza-updates
2022-02-23 16:37:08 -05:00
2d7375798f
more python 3 compatibility
2022-02-23 13:27:33 -05:00
18ced360d3
more python 3 compatibility
2022-02-23 12:30:03 -05:00
58eb331b08
Python 3 compatibility for log commands in tools/python
2022-02-23 10:22:29 -05:00
5594868ef2
retain compatibility with python2
2022-02-23 10:18:02 -05:00
d848e50d0d
Merge pull request #3146 from lammps/programmer-comm-doc
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New developer page for comm functions
2022-02-22 20:13:32 -05:00
b4e42f68b1
Merge pull request #3148 from akohlmey/rename_comm_forw_rev
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Rename forward and reverse communication commands for data in classes
2022-02-22 19:19:56 -05:00
9a1c994a8e
Merge branch 'develop' into rename_comm_forw_rev
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# Conflicts:
# src/KOKKOS/comm_kokkos.cpp
# src/KOKKOS/fix_qeq_reaxff_kokkos.cpp
2022-02-22 16:45:06 -05:00
04ec741f16
Merge pull request #3142 from charlessievers/chem_snap
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SNAP bik flag
2022-02-22 16:29:39 -05:00
07d456c8b2
Merge pull request #3147 from stanmoore1/amd_hip_opt
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Improvements from AMD to KOKKOS Package
2022-02-22 16:06:28 -05:00
95c414e32e
Merge pull request #3139 from akohlmey/collected-small-changes
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Collected small changes
2022-02-22 15:30:31 -05:00
035a16d6d8
remove interactive mode for log plotting
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this doesn't work in linux
2022-02-22 10:51:58 -06:00
7d8f7855d5
add writing column names in logfile
2022-02-22 10:51:58 -06:00
5c297fa4d1
update log pizza.py files to python 3
2022-02-22 10:51:58 -06:00
7ac1bd1180
final tweaks
2022-02-22 09:20:19 -07:00
687a09b8a1
fix errors in pair style harmonic/cut docs
2022-02-22 04:27:12 -05:00
15acfde91e
more updates and corrections
2022-02-21 22:26:01 -05:00
b91788bf71
no need to use default argument
2022-02-21 22:12:26 -05:00
66d7f55a20
apply clang-format
2022-02-21 22:12:13 -05:00
36ecfded81
update according to PR #3148
2022-02-21 21:57:12 -05:00
313d850dd2
Created a Born matrix example for silicon
2022-02-21 19:38:28 -07:00
a3524fc7a1
update atc lib
2022-02-21 21:33:27 -05:00
de4a9f268e
rename reverse communication calls
2022-02-21 21:18:28 -05:00
4c0192cae1
rename forward communication functions for pair, fix, compute, and dump
2022-02-21 21:15:10 -05:00
0988d957f5
Update preset configurations to include release and debug versions of MSVC and Clang only.
2022-02-21 19:09:59 -05:00
7ea26161f7
Merge pull request #3145 from lammps/pair-style-doc-page
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clarify how new pair style command works
2022-02-21 18:22:47 -05:00
ba2a2ddd9f
integrate into manual. fix multiple formal issues. add a few select details.
2022-02-21 18:09:31 -05:00
4d9409dda9
Whitespace
2022-02-21 15:45:03 -07:00
70c149805c
Fix bugs in Kokkos tersoff
2022-02-21 15:29:01 -07:00
0d68aa0c46
rework documentation section on compiling on windows
2022-02-21 17:04:31 -05:00
d1decfe15a
More cleanup
2022-02-21 14:31:50 -07:00
d6664a8e9e
tweak
2022-02-21 14:21:35 -07:00
afbcf5e694
Remove early exit from blocking BuildLists
2022-02-21 14:00:31 -07:00
c2cec53701
Merge branch 'develop' of github.com:lammps/lammps into amd_hip_opt
2022-02-21 13:23:51 -07:00
4a2dc4f14a
Cleanup
2022-02-21 13:11:37 -07:00
e10ebf5236
Fix typos
2022-02-21 12:56:58 -07:00
1268c8c6ad
Update doc page and author contributions
2022-02-21 12:44:53 -07:00
348309582a
new developer page for comm functions
2022-02-21 12:43:35 -07:00
78775a82f4
Merge branch 'develop' into collected-small-changes
2022-02-21 14:26:50 -05:00
850f1a690c
Tweak default
2022-02-21 11:45:07 -07:00
6d790e41fa
Added bik lastcol behavior to documentation
2022-02-21 10:19:37 -08:00
c725550fff
Added in explicit reference column behaviour for bik rows
2022-02-21 10:08:58 -08:00
2a94d7a9a8
Remove HIP_OPT defines in pair_reaxff_kokkos
2022-02-21 11:07:35 -07:00
ed575ee664
clarify how new pair style command works
2022-02-21 10:21:28 -07:00
a9c7d47072
Found parenthesis error in compute_angles(). Now perfect fit with numdiff.
2022-02-21 10:59:37 +01:00
1dae118419
Merged A. Thompson symmetric sheared. Added a bit more explicit comment on virial_addon computation.
2022-02-21 09:40:22 +01:00
67ffef094d
Switch shear strain fields to symmetric
2022-02-20 13:51:14 -07:00
f205567fa6
add born/matrix support to hybrid pair styles
2022-02-20 07:15:11 -05:00
e4027ba98a
update example input files
2022-02-20 06:35:35 -05:00
c1dfd944af
turn some warnings into errors and produce better error messages
2022-02-20 06:07:39 -05:00
60a6747c0e
must propagate and check born_matrix_enable flag
2022-02-20 05:51:51 -05:00
bd48c49c2b
enable and apply clang-format
2022-02-20 05:51:16 -05:00
7d79a7822b
Merge branch 'develop' into Elastic_stress
2022-02-20 05:28:42 -05:00
a3c6d19599
Merged comments modification in EXTRA-COMPUTE/compute_born_matrix from A. Thompson and G. Clavier.
2022-02-20 11:22:20 +01:00
6ee14bfb97
correct formatting of references
2022-02-20 04:26:18 -05:00
c04f4a913f
Thomas-Fermi
2022-02-20 07:47:28 +00:00
bc8d1e0f84
Tweaked one comment
2022-02-19 20:55:37 -07:00
407df3127b
Cleaned up source files
2022-02-19 20:21:02 -07:00
4ca5441cf1
Updated documentation
2022-02-19 19:25:02 -07:00
61377f41ad
Replaced Si.sw with a simlink to potentials dir
2022-02-19 18:01:37 -07:00
f1f2cebf98
Rearranged the directory tree for ELASTIC_T and BORN_MATRIX
2022-02-19 17:59:27 -07:00
c8ae3c45ac
Removed cij_nvt directory and updated RADME
2022-02-19 17:09:39 -07:00
335fa2e742
Addd born/matrix numdiff to example
2022-02-19 17:07:21 -07:00
63a4210391
Fix bug in history
2022-02-19 08:33:47 -07:00
6acf3c8d2a
Merge pull request #3138 from wmbrownIntel/intel_skip_fix
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Bug fix for Intel package skip lists with multiple runs.
2022-02-19 05:55:11 -05:00
3ddcd3308f
Add documentation for bikflag
2022-02-19 00:46:56 -08:00
d619477195
Merge remote-tracking branch 'upstream/develop' into chem_snap
2022-02-19 00:23:30 -08:00
36edecd1e7
Added in ability to keep bispectrum descriptors per atom instead of summed. (Useful for non linear models)
2022-02-19 00:20:43 -08:00
7e876ada13
Merge branch 'develop' into collected-small-changes
2022-02-18 21:49:13 -05:00
86cb37f7ad
Merge pull request #3141 from lammps/developer-doc-tweaks
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tweaks to 2 sub-sections of Developer manual
2022-02-18 21:48:29 -05:00
d88ffcf880
correct file name
2022-02-18 21:24:02 -05:00
bfea3c4589
rename .rst file to match headline
2022-02-18 21:20:35 -05:00
4dad865aea
small tweaks and spelling fixes
2022-02-18 21:19:27 -05:00
49c594be10
add factory function example
2022-02-18 21:19:06 -05:00
78f7e96a3f
grammar tweaks to 2 sub-sections of Developer manual
2022-02-18 16:45:06 -07:00
39f8ccdb42
Fixing an overlooked merge conflict
2022-02-18 15:33:26 -07:00
642b1e25f6
Updating to develop
2022-02-18 13:58:38 -07:00
0ecb9addb2
Fix MPI issues
2022-02-18 10:58:03 -07:00
7087e78138
Cleanup
2022-02-18 10:23:34 -07:00
5a95b35fb3
Adding bondstyle restart and fixing a few labels
2022-02-18 10:22:08 -07:00
adbbad0c2d
silence compiler warnings
2022-02-18 12:13:26 -05:00
c31d79c3a4
add missing override keywords
2022-02-18 12:06:06 -05:00
43f5de4dbf
Give the compiler some help
2022-02-18 09:57:51 -07:00
8fa297e420
update comments about building LAMMPS with visual studio
2022-02-18 11:38:35 -05:00
68dc778d03
update the note based on the suggestion by @athomps
2022-02-18 11:38:05 -05:00
b9f5bb60e9
Fix layout
2022-02-18 08:08:48 -07:00
c68015ca87
Bug fix for Intel package skip lists with multiple runs.
2022-02-18 05:11:34 -05:00
4e03589cee
use symbolic constants and fix out of bound accesses
2022-02-18 05:07:18 -05:00
9151a2e820
address unititialized data warnings from coverity scan
2022-02-18 04:46:30 -05:00
2aff105124
nicer shake stats output
2022-02-18 04:24:27 -05:00
537e3f2539
silence compiler warnings
2022-02-17 23:13:13 -05:00
d14035eb6b
Fix bug
2022-02-17 20:59:36 -07:00
da3c3723bd
add code to print warning if qeq fix is appled to a non-neutral group. document.
2022-02-17 22:51:49 -05:00
0cb45ebd6b
Kokkos QEq refactor
2022-02-17 16:25:02 -07:00
01bbb28418
Merge pull request #3135 from akohlmey/next_patch_release
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Step version strings for the next patch release
2022-02-17 15:05:43 -05:00
7fe194e59e
Merge pull request #3136 from rbberger/collected-small-changes
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Collected small changes
2022-02-17 13:20:51 -05:00
f3e14e7b00
Mark MolPairStyle:soft unstable
2022-02-17 12:58:30 -05:00
7b948e7bb8
Bug fix for Intel package skip lists with multiple runs.
2022-02-17 09:37:01 -08:00
45b92e519d
Merge pull request #3125 from oywg11/ilp-for-tmds
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Anisotropic Interlayer potential for TMDs and Metal Surfaces
2022-02-17 11:42:15 -05:00
d95f0b3cd5
Adjust epsilon in force-style test
2022-02-16 17:43:16 -05:00
793d76c546
Adjust epsilon in force-style tests
2022-02-16 17:40:34 -05:00
12eeaee8a4
Correct bug in PairHybridScaled::single
2022-02-16 13:48:10 -05:00
583c22d6e0
update tools/eam_database from upstream
2022-02-16 11:46:11 -05:00
8b627f92f0
address spelling and achor issues, and integrate into style overview tables
2022-02-16 08:10:29 -05:00
78b123fa4d
apply new convention for virtual functions and disable single() functions (for now)
2022-02-16 06:50:26 -05:00
47bb5f5ccd
use a local std::map with initializer to have variant specific strings
2022-02-16 06:36:17 -05:00
e541f006eb
replace copies of files with symbolic links
2022-02-16 06:34:31 -05:00
08968cbdbf
apply clang-format
2022-02-16 06:14:19 -05:00
32cde04000
Merge branch 'develop' into ilp-for-tmds
2022-02-16 06:04:34 -05:00
6d2f4343d9
Merge pull request #3133 from stanmoore1/kk_error
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Add error if using multiple threads with Kokkos Serial backend
2022-02-15 22:25:04 -05:00
a7939b582a
step version strings for the next patch release
2022-02-15 22:10:06 -05:00
2951eb32a4
Merge pull request #3134 from rbberger/collected-small-changes
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Collected small changes
2022-02-15 22:05:48 -05:00
55703f9027
update class instantiation unit test for kokkos to adapt to thread availability
2022-02-15 21:54:21 -05:00
d4bbb31270
Improve error check
2022-02-15 16:04:23 -07:00
ae72356961
Removed unnecessary declarations in compute_born_matrix numdiff part. Commented virial_addon method.
2022-02-15 23:26:40 +01:00
f53fbf09a6
Fix memory leak in FixBondReact
2022-02-15 15:51:48 -05:00
f3c055e637
Undo change that forces BUILD_SHARED_LIBS=off
2022-02-15 14:53:18 -05:00
d9e06e326a
Merge branch 'develop' of github.com:lammps/lammps into kk_error
2022-02-15 12:11:52 -07:00
3b359a0d81
Merge branch 'develop' of https://github.com/lammps/lammps into amd_hip_opt
2022-02-15 12:08:03 -07:00
c2d59d5d5e
Add error if using multiple threads with Kokkos Serial backend
2022-02-15 11:52:59 -07:00
2f281b3184
Merge branch 'develop' of github.com:lammps/lammps into Elastic_stress
2022-02-15 16:19:03 +01:00
e3222a4bd0
Merge pull request #3126 from Bibobu/EAM_alloy_python_script
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Added Python version of Zhou04_create_v2.f in eam_database
2022-02-14 19:48:51 -05:00
618b3ec94f
Merge pull request #3131 from akohlmey/lammps-cxx-style
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More general LAMMPS code design info for the Programmer guide section of the manual
2022-02-14 18:13:32 -05:00
9a200c9b79
small tweaks
2022-02-14 18:07:29 -05:00
c46dd3675a
add Cr parameters to python database file
2022-02-14 18:06:48 -05:00
b0c0251154
delete unwanted files
2022-02-14 18:06:24 -05:00
c65dbd338b
change create_eam.py so it can be called as a function from another script
2022-02-14 17:44:33 -05:00
702a2dd3f6
Merge pull request #3130 from akohlmey/iwyu-update
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Update list of include statements based on the IWYU utility
2022-02-14 17:25:32 -05:00
5f47ff770c
Merge pull request #3127 from akohlmey/gpu-opencl-updates
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Update compiling OpenCL loader lib
2022-02-14 16:10:53 -05:00
baf443766a
fix a few typos or mistyped words and explain some details better
2022-02-14 16:09:52 -05:00
f84790ba62
add a more specific example to explain how values are rejected and how atoi() fails
2022-02-14 15:52:33 -05:00
8431d72d75
Added a test directory to tools/eam_database
2022-02-14 21:29:51 +01:00
5366621947
Merge pull request #3129 from ndtrung81/sw-hybrid-gpu
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Fixed a bug with sw/gpu neigh no when used with pair hybrid for systems with multiple atom types
2022-02-14 14:21:52 -05:00
f4ce0f0b1c
Merge pull request #3101 from rbberger/python_use_setuptools
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Use setuptools instead of distutils in setup.py
2022-02-14 13:47:46 -05:00
37cd4ba2ea
spelling
2022-02-14 11:55:09 -05:00
1a436c5aa9
fix some broken links
2022-02-14 11:55:04 -05:00
fbf95c2cbc
add notes about file parsing
2022-02-14 11:54:50 -05:00
1a6b627fa0
add section about memory allocations
2022-02-14 11:54:37 -05:00
12f746046f
finalize {fmt} lib info
2022-02-14 08:45:55 -05:00
374a172246
Changed "exclude" keyword to "overlap"
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+ added new error description to header file
+ minor fix in the doc file
2022-02-14 12:46:44 +01:00
3bc91386a0
apply include statement updates suggested by running IWYU
2022-02-13 19:39:15 -05:00
1307371942
update/correct iwyu additional mappings
2022-02-13 18:20:12 -05:00
b42aebc197
silence compiler warnings
2022-02-13 18:19:50 -05:00
83beffbb9f
whitespace
2022-02-13 17:08:18 -05:00
810717bfe5
discuss stdio vs iostreams and fmtlib
2022-02-13 16:01:27 -05:00
1ab5b9d7fd
re-sort list of false poisitives alphabetically with "sort"
2022-02-13 16:01:26 -05:00
1c7e1faeff
add sections on inheritance, compositing, polymorphism
2022-02-13 16:01:14 -05:00
6887a16fa1
start add general code design doc.
2022-02-13 16:00:51 -05:00
193dea6327
Updated the comment to be precise on the case
2022-02-13 14:51:00 -06:00
159f107abd
Corrected the added comment
2022-02-13 11:16:01 -06:00
bae4e45978
Added a comment to the added check while looping over the neighbors of ghost atoms
2022-02-13 09:17:05 -06:00
9d518ee1e2
must ensure that BUILD_SHARED_LIBS retains its original value
2022-02-13 10:00:19 -05:00
55a500cf8a
Fixed bugs with in the kernel sw_three_end kernel
2022-02-13 00:42:26 -06:00
4eedfeb774
detect if LAMMPS library initialization failed and raise an exception
2022-02-12 22:43:18 -05:00
78d149f118
update to download improved loader sources that make installing optional
2022-02-12 13:21:10 -05:00
d85788305d
update manual
2022-02-12 10:37:09 -05:00
4343e8194c
update README file
2022-02-12 10:20:49 -05:00
096ea21dd9
correct potential file output header (must have 3 comment lines)
2022-02-12 10:14:09 -05:00
8808b11d26
must write out 3 lines of comment in fortran code. sync output style with python
2022-02-12 10:04:24 -05:00
2fdadcfeb6
include UNITS: metadata tag
2022-02-12 10:01:20 -05:00
0113346e54
apply some pylint recommendations
2022-02-12 10:01:01 -05:00
3cca41b72e
print help without arguments. clarify help message and argument names text
2022-02-12 09:38:05 -05:00
69d3b1ebf3
output files are now named .eam.alloy
2022-02-12 09:37:23 -05:00
0f5fbf1c42
update citation info format
2022-02-12 09:36:53 -05:00
06d4bb3faf
set date dynamically
2022-02-12 09:33:37 -05:00
e9b11e3673
Added Python version of Zhou04_create_v2.f: create_eam.py and eamDatabase.py in tools/eam_database
2022-02-12 12:42:54 +01:00
563f98b898
Some changes in examples directory, nothing important for now
2022-02-12 12:38:58 +01:00
a77680ac7b
Merge branch 'develop' into python_use_setuptools
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# Conflicts:
# cmake/CMakeLists.txt
2022-02-12 00:37:03 -05:00
99c1b935b5
convert OpenCL loader build from ExternalProject_add to ExternalCMakeProject
2022-02-11 23:49:08 -05:00
eb2fe7d982
correct inconsistent prototypes
2022-02-11 23:37:40 -05:00
75dc7125e6
Update doc of pair sw/mod
2022-02-12 06:12:12 +02:00
e5dec93a1e
Update doc of pair ilp/graphene/hbn
2022-02-12 06:09:29 +02:00
922b240678
Interlayer Potential for TMDs and Metal Surfaces
2022-02-12 06:05:11 +02:00
a5fe8b0581
update OpenCL loader to latest OpenCL spec sources
2022-02-11 22:01:04 -05:00
a17bdf5652
silence compiler warnings and avoid infinite recursion in aspherical pair styles
2022-02-11 21:06:16 -05:00
81587527fe
Merge pull request #3120 from rbberger/collected_small_changes
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Collected small changes
2022-02-11 20:26:10 -05:00
de08307aba
Merge pull request #3124 from akohlmey/hide-factory-symbols
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Reduce number of visible symbols in LAMMPS library by removing factory function templates from class definition
2022-02-11 20:23:52 -05:00
54f975ff52
Merge pull request #3123 from stanmoore1/reax_error
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Remove incorrect error check in ReaxFF
2022-02-11 19:34:53 -05:00
df02598fc1
convert one more factory template
2022-02-11 18:38:36 -05:00
6a0e93a18a
convert more style_creators to use local static functions
2022-02-11 18:29:52 -05:00
5ab9b46b67
enable and apply clang-format
2022-02-11 18:04:46 -05:00
a4244eb7ff
apply simplification suggested by @rbberger
2022-02-11 17:57:30 -05:00
58a4694d92
Remove incorrect error check in ReaxFF
2022-02-11 16:19:00 -05:00
04cff0b47b
remove make factory function templates from class and make them static functions
2022-02-11 16:00:12 -05:00
4df5686709
Merge branch 'amd_hip_opt' of github.com:stanmoore1/lammps into amd_hip_opt
2022-02-11 13:57:19 -07:00
5ba2fc7958
Merge branch 'reax_error' of github.com:stanmoore1/lammps into amd_hip_opt
2022-02-11 13:56:52 -07:00
fbd4d4b9c3
Merge branch 'develop' of github.com:lammps/lammps into amd_hip_opt
2022-02-11 13:56:38 -07:00
a8dbb3a172
Remove incorrect error check in ReaxFF
2022-02-11 13:39:24 -07:00
ea94095bf6
Change email in docs
2022-02-11 12:51:47 -05:00
ecd072a286
address spelling issues
2022-02-11 09:03:59 -05:00
1f6c4089bd
remove some more dead code in CG-DNA package
2022-02-11 07:41:09 -05:00
397889e697
Modifications to virial addon contributions
2022-02-10 19:55:23 -07:00
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
d750ef4890
simplify
2022-02-10 20:39:36 -05:00
c5e6650924
import bugfixes for crashes and memory leaks in MSM kspace style from develop
2022-02-10 20:36:35 -05:00
c32dca2009
avoid failures with "most" presets
2022-02-10 20:11:27 -05:00
10373ea5c9
avoid failures with "most" presets
2022-02-10 20:11:00 -05:00
4ea4bee30c
apply virtual and override keywords consistently
2022-02-10 16:55:35 -05:00
61ff5250ee
add extra communication of special neighbors when using angle constraints
2022-02-10 16:17:56 -05:00
e94854d54f
always initialize arrays with extra grid points for non-periodic to support switching with change_box
2022-02-10 15:57:41 -05:00
9b1a267d85
fix another memory grid deallocation bug. delete before number of levels changes
2022-02-10 15:32:07 -05:00
ab1e68eb42
fix memory access bug with changing box volume/grid
2022-02-10 14:41:25 -05:00
4d5bb08ead
make searching for python interpreter and development version futureproof and more consistent
2022-02-10 14:41:25 -05:00
60d03f34cc
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 14:41:25 -05:00
6366972ef4
remove dead code and reduce compiler warnings
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# Conflicts:
# src/RIGID/fix_rigid_small.cpp
2022-02-10 14:41:09 -05:00
44ded1c1fe
Reorder fields init in IntelBuffer ctor
2022-02-10 14:19:51 -05:00
df00d2225a
Remove unused variable
2022-02-10 14:13:55 -05:00
75f32a60a5
Add missing curly braces
2022-02-10 14:13:43 -05:00
c2ef4425c6
Update doc/utils/check-styles.py
2022-02-10 12:02:23 -05:00
08b16f1f23
Prevent GTest and GMock from being installed
2022-02-10 11:27:32 -05:00
a17a45c761
Fix large number of sign-compare warnings
2022-02-10 11:19:13 -05:00
4f36dad942
Removed the bogus loop in numdiff and manually se the factors in numdiff.
2022-02-10 11:51:03 +01:00
efa5db4c58
ELECTRODE package
2022-02-10 11:33:38 +01:00
439aabc7b1
Merge branch 'develop' of https://github.com/lammps/lammps into amd_hip_opt
2022-02-09 14:26:33 -05:00
ce83ca1efd
Merge pull request #3117 from akohlmey/collected-small-changes
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Collected small changes
2022-02-08 20:21:46 -05:00
861195130c
incorporate suggested changes to github action from @rbberger
2022-02-08 12:08:28 -05:00
4d6fcb3a8b
Merge branch 'develop' of https://github.com/lammps/lammps into Elastic_stress before comiting to pull request
2022-02-08 16:46:23 +01:00
9ed13157eb
Added examples/cij_nvt/in.lj* changes to make Git happy.
2022-02-08 16:42:33 +01:00
9833e5bc66
Hopefully got compute_born_matrix numdiff method working. Also added two BORN_MATRIX examples.
2022-02-08 16:40:52 +01:00
75727ed5af
comment out minimal run test outside of CMake/CTest
2022-02-07 20:52:12 -05:00
8e2581042e
remove unused local variables
2022-02-07 20:30:36 -05:00
78cf0365e6
bugfixes
2022-02-08 02:13:42 +01:00
b01716472b
Merge branch 'develop' into collected-small-changes
2022-02-07 19:59:10 -05:00
b75c306543
Merge pull request #3035 from rbberger/kokkos_unittests
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Add force style tests for Kokkos OpenMP
2022-02-07 19:57:09 -05:00
2445f85dde
Merge branch 'develop' into collected-small-changes
2022-02-07 17:08:03 -05:00
044ada9f2b
update googletest library to current snapshot
2022-02-07 16:46:32 -05:00
e4b5245f4d
Merge pull request #3116 from akohlmey/build-kokkos-staticlib
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Build KOKKOS package updates for Python module and Windows compatibility
2022-02-07 16:36:46 -05:00
35a4c0f501
skip tests that fail with Kokkos+OpenMP
2022-02-07 16:15:32 -05:00
2dfeb96fda
Merge pull request #3115 from rbberger/pylammps_update
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PyLammps update
2022-02-07 15:09:10 -05:00
093c54d8ed
update to use settings from upstream
2022-02-07 14:42:07 -05:00
a7084c8fdb
Merge remote-tracking branch 'origin/develop' into kokkos_unittests
2022-02-07 13:04:59 -05:00
ba89ad546a
Tried to make the fusion with Aidan Thomps modification of compute_born + several headers issues (essentially adding override flag to virtual methods)
2022-02-07 00:12:27 +01:00
b6822a18f7
Merge branch 'Elastic_stress' of github.com:Bibobu/lammps into Elastic_stress
2022-02-06 20:04:51 +01:00
a110b1d475
1) Added born_matrix method to bond_harmonic, angle_cosine_squared and dihedral_nharmonic
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2) Changed compute_born_matrix so it can takes arguments pair bond angle dihedral to output only selected elements. Also moved flags to creator method and added error/warning messages
2022-02-06 20:00:55 +01:00
2548c49876
use fmtlib for formatted output
2022-02-05 17:01:47 -05:00
8209ae9513
fix optional argument parsing bug
2022-02-05 17:01:13 -05:00
59def25eb6
tweak test epsilon for portability
2022-02-05 16:08:43 -05:00
d91c1ff1f0
Merge pull request #3110 from stanmoore1/dump_balance
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Fix issue in new dump balance command
2022-02-05 15:56:17 -05:00
4de02c7f2f
Tweaked input script
2022-02-04 16:28:29 -07:00
a2ff443838
Use utils::flush_buffers() in error.cpp and thermo.cpp
2022-02-04 18:00:47 -05:00
bae6526b5f
Add missing doc entry
2022-02-04 17:55:37 -05:00
50a7d4e7fc
Add utils::flush_buffers()
2022-02-04 17:53:36 -05:00
ea0f31c997
Update SWIG library interface
2022-02-04 17:43:17 -05:00
f45663bfc2
Simplify loop structure to fix issues
2022-02-04 11:45:28 -08:00
0ff3ee0227
Add and use lammps_flush_buffers() in Python interface
2022-02-04 10:42:22 -05:00
293d529ee9
Add lammps_flush_buffers() library function
2022-02-04 10:40:05 -05:00
c0bae49956
simplify with new API and address coverity scan warning
2022-02-04 07:28:59 -05:00
652ff43f64
Got a good match with some Born elements with P != 0
2022-02-03 21:58:25 -07:00
ea0b4f0f33
Got a good match with some Born elements with P != 0
2022-02-03 18:16:21 -07:00
c0ee491f18
protect unconditional "#pragma GCC" with if defined(__GNUC__)
2022-02-03 19:47:52 -05:00
7cd9975e29
Fixed one obvious error in numdiff version, matching analytic quite well for P~=0, need to fix addon term
2022-02-03 17:44:47 -07:00
6edb50b405
Force Python version in GH MSVC test
2022-02-03 18:08:17 -05:00
9bfd6375eb
avoid triggering bogus make file target errors
2022-02-03 18:00:34 -05:00
7d0b4cc131
make portable to cross-compiler
2022-02-03 18:00:12 -05:00
330dd6a7a8
Documentation update for maxtries & exclude
2022-02-03 23:18:51 +01:00
8fbaaffd3e
remove incorrect scope
2022-02-03 17:16:20 -05:00
2137ad04fd
remove non-portable custom (and unused) profiling support code
2022-02-03 17:13:10 -05:00
a56922edc9
include PYTHON package in windows test build
2022-02-03 16:55:26 -05:00
75f389f70c
Enable PyLammps unit test, require NumPy
2022-02-03 16:24:43 -05:00
22efbaf977
Output Capture has to replace FD 1 to work properly in Jupyter
2022-02-03 16:24:43 -05:00
050ce421e9
PyLammps: alternative OutputCapture using tempfiles
2022-02-03 16:24:43 -05:00
f804ea89b9
skip force test requiring cp command
2022-02-03 16:13:07 -05:00
2a7823686d
use introspection to check for Kokkos::OpenMP only when it is enabled
2022-02-03 16:08:00 -05:00
6bfb7a5521
require OpenMP 4 or later for KOKKOS with OpenMP enabled
2022-02-03 16:07:33 -05:00
b06d4a3300
exclude_cutoff to exclude_radius
2022-02-03 21:58:14 +01:00
f550460ecd
Update CMakeSettings.json
2022-02-03 15:44:55 -05:00
36c1db820f
Add command styles to PyLammps auto-completion
2022-02-03 15:44:55 -05:00
41da32d7de
Use modernized LAMMPS Python interface instead of output parsing for Atom properties
2022-02-03 15:44:55 -05:00
3ba85bc68d
replace VLA with explicit new/delete
2022-02-03 15:23:09 -05:00
2627e404b0
Add csforce field to numpy_wrapper detection
2022-02-03 15:14:22 -05:00
c6a17b900e
just call exit() on windows instead forwarding the SEGV signal
2022-02-03 13:31:24 -05:00
b7b7a74c52
when building KOKKOS as part of the LAMMPS build, always build static libs
2022-02-03 12:23:25 -05:00
82ac7c9e12
Merge remote-tracking branch 'origin/develop' into python_use_setuptools
2022-02-02 11:47:13 -05:00
efcb402fdc
Merge pull request #3111 from stanmoore1/kk_compile
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Changes needed to compile LAMMPS with Kokkos upstream
2022-02-02 11:45:55 -05:00
d9c51ca124
Make sure LAMMPS and unit tests use same Python version
2022-02-02 11:44:25 -05:00
172f88a0d5
Merge pull request #3104 from ohenrich/cg-dna
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CG-DNA unit test and performance enhancement
2022-02-01 18:30:13 -05:00
8f07289ed7
Changes needed to compile LAMMPS with latest Kokkos develop
2022-02-01 15:00:40 -07:00
e15ca1eeef
Fix bug in dump balance
2022-02-01 10:23:25 -08:00
fa200f606b
Update from upstream
2022-01-31 20:01:10 -07:00
76c57d54c1
Merge pull request #3102 from akohlmey/mpi-stubs-simplify
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Porting unit tests to run natively on Windows
2022-01-31 21:37:48 -05:00
705bfc10a1
Merge pull request #3100 from rbberger/kokkos_cleanup
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Refactor some declarations in KOKKOS package
2022-01-31 19:35:55 -05:00
1da12feafc
Prepared for implementation of exclude
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- maxtries returned as separate option
- errors for incompatible options (var with single + new)
2022-02-01 00:46:15 +01:00
fad47312e6
Update from upstream
2022-01-31 16:31:46 -07:00
1b6f850d42
Prepared for implementation
2022-02-01 00:17:21 +01:00
91614b64d2
Update from upstream
2022-01-31 15:42:05 -07:00
a6a2492282
Merge pull request #3082 from stanmoore1/reax_count
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Improve PairReaxFFKokkos neigh list algorithm
2022-01-31 17:26:25 -05:00
b2916339a4
Add NeedDup_v and AtomicDup_v helpers to KOKKOS
2022-01-31 13:42:03 -05:00
a124ee4f44
Merge pull request #2233 from charlessievers/OptimizedDynamicalMatrix
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Dynamical_matrix and third_order features+update
2022-01-31 12:57:28 -05:00
dd416f61b5
Rename function to avoid warning
2022-01-31 10:47:56 -07:00
cfd720e1fc
Remove another volatile return type to avoid warning
2022-01-31 09:58:44 -07:00
5d28d06a3c
Fix compiler warning
2022-01-31 09:47:32 -07:00
f537a31c19
Unify comment style
2022-01-31 09:25:25 -07:00
5142d8e968
Merge remote-tracking branch 'origin/develop' into kokkos_cleanup
2022-01-31 11:04:41 -05:00
9a81dc58a1
Merge remote-tracking branch 'origin/develop' into kokkos_unittests
2022-01-31 11:04:18 -05:00
b7c8ab639c
Dummy change
2022-01-30 16:44:35 -07:00
7a14cf765f
Fixed silent error in albe[][]
2022-01-30 16:34:49 -07:00
c09e3c0890
Updated documentation
2022-01-30 16:27:33 -07:00
fb2f7f1b99
Merge branch 'Elastic_stress' of github.com:athomps/lammps into Elastic_stress
2022-01-30 16:19:20 -07:00
d79a96caae
Updated documentation
2022-01-30 16:18:34 -07:00
cc9c578006
Got all the pieces in, now just need to get the right answer
2022-01-30 15:52:16 -07:00
d80ba0d57a
Merge branch 'develop' into mpi-stubs-simplify
2022-01-30 17:19:26 -05:00
7ee7d0c570
apply clang-format
2022-01-30 17:18:40 -05:00
3707b327c0
improve portability of python result value string conversion
2022-01-30 16:52:38 -05:00
a8a76dbbe2
port python module and package tests to be windows compatible. refactor environment processing
2022-01-30 16:48:47 -05:00
2e39971cbc
re-enable python module tests on windows
2022-01-30 16:48:11 -05:00
579ac61b5b
refactor environment variable settings. make windows compatible
2022-01-30 16:47:52 -05:00
fea41d5458
make windows compatible
2022-01-30 16:47:17 -05:00
0f85809acf
Created branch on athomps/lammps repo
2022-01-30 12:37:33 -07:00
af8d1bd768
fix typo
2022-01-30 09:00:39 -05:00
65b198f986
Revert "temporarily switch repo and branch to run on"
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This reverts commit 213259b732
2022-01-30 08:48:52 -05:00
4b22962ec1
roll back MPI target alias change one more time. must wait until CMake 3.11 or later is minimum
2022-01-30 08:47:46 -05:00
f8a4006da7
must promote imported target to global scope in order to be able to alias it
2022-01-30 08:32:21 -05:00
dc0e013297
create alias target MPI::ANY_CXX to be used instead of MPI::MPI_CXX
...
With this alias it is possible to transparently refer to either the
real imported MPI library or to the MPI stub library. this further
reduced the need for if statements related to MPI. Some uses of
MPI::MPI_CXX remain but they are all in branches of the script code
where BUILD_MPI is enabled and thus the imported target will be present.
2022-01-30 07:48:16 -05:00
99cb494594
remove automatic generated tag
2022-01-30 07:08:15 -05:00
b17d8b4494
add building and running unit tests
2022-01-30 05:54:35 -05:00
213259b732
temporarily switch repo and branch to run on
2022-01-30 05:54:21 -05:00
4bb7457d6e
add option to allow skipping tests by setting a no${CMAKE_SYSTEM_NAME} tag
2022-01-30 05:14:57 -05:00
923b0cfc46
allow to override the LAMMPS dll location on windows
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this is to work around the situation that windows
has no equivalent to LD_LIBRARY_PATH (short of augmenting %PATH%,
which is tricky for CMake before 3.20)
2022-01-30 05:13:17 -05:00
a8632d5cb6
always have the lib prefix on the LAMMPS library (windows may drop it on the .dll file)
2022-01-30 05:11:32 -05:00
ebeb29adf6
skip python folder tests for now on windows
2022-01-29 21:34:51 -05:00
6ff157a099
use quoting to avoid issues with blanks and special characters
2022-01-29 21:05:19 -05:00
33be5ff0b4
allow that the include command may have quoted arguments with variables
2022-01-29 21:04:59 -05:00
cc0d91b222
re-add copies of linked files
2022-01-29 21:01:49 -05:00
571821694e
remove links broken on windows
2022-01-29 21:01:35 -05:00
02cadf1b71
port to windows where text file reading may gobble up carriage returns
2022-01-29 20:53:17 -05:00
6c98915a9c
port to windows
2022-01-29 20:52:37 -05:00
0bfc5269dd
fix mismatches causing failures on windows
2022-01-29 20:52:25 -05:00
9014664c13
really fix unit test regexes for windows
2022-01-29 19:07:35 -05:00
c420f804d9
make multi-line regex checks compatible with googletests Windows regex syntax
2022-01-29 18:52:49 -05:00
a1d186b5fa
Merge pull request #3105 from athomps/numdiff-stress
...
Add new numdiff/virial fix style
2022-01-29 18:37:57 -05:00
cd5d1f8a30
reformat
2022-01-29 18:13:01 -05:00
9323a09b39
reduce number of reported memory leaks with google test death tests
2022-01-29 18:12:53 -05:00
c464c40d67
avoid accessing uninitialized data and triggering bogus memcheck output
2022-01-29 18:12:15 -05:00
7b3adb3f1a
must always initialize jtag
2022-01-29 17:09:40 -05:00
c9de8fca1d
silence compiler warnings
2022-01-29 17:07:00 -05:00
75d0a5098f
use -Og for Debug config for better warnings and debug experience
2022-01-29 17:06:30 -05:00
bd4814a51e
don't cache OUTPUT_DIRECTORY variable settings but set them every time
2022-01-29 16:37:40 -05:00
845ab2dd71
On Windows the Regex matcher for '.' does not match '\n'
...
Thus we have to use ContainsRegex instead of MatchesRegex
2022-01-29 16:35:30 -05:00
d62e25decc
don't specify default working directory for tests explicitly
2022-01-29 11:10:23 -05:00
dad72a612a
correct statement (PPPM **does** support triclinic for a while already)
2022-01-29 08:18:08 -05:00
481bcfcd14
spelling
2022-01-29 08:12:28 -05:00
ee98f023b6
enable and apply clang-format
2022-01-29 08:02:59 -05:00
17960c8183
use constexpr instead of const
2022-01-29 07:56:11 -05:00
9427eb800f
add missing "override"
2022-01-29 07:55:58 -05:00
c1185acad7
enable and apply clang-format
2022-01-29 07:52:06 -05:00
d6fa3a08cd
roll back library aliasing changes as that negatively interferes with unit tests
2022-01-28 21:54:32 -05:00
8423ecb211
small tweaks to make things work with the new settings
2022-01-28 21:28:37 -05:00
7978bf671d
use canonical syntax for adding tests
2022-01-28 21:12:13 -05:00
5c0c3df035
make use of CMAKE_(RUNTIME|LIBRARY)_OUTPUT_DIRECTORY
2022-01-28 21:10:30 -05:00
fbecf0051e
Merge remote-tracking branch 'upstream/develop' into numdiff-stress
2022-01-28 18:36:27 -07:00
a9481733a0
Finished debugging, testing, documenting
2022-01-28 18:34:30 -07:00
c28b7c586a
Residual Merge Conflict
2022-01-28 14:59:07 -08:00
6258cf1b9d
Fixed merge conflict
2022-01-28 14:49:13 -08:00
e8ce01079d
whitespace
2022-01-28 17:20:32 -05:00
f6d0be1257
avoid integer overflow due to precedence
2022-01-28 17:08:16 -05:00
96502ae49d
whitespace
2022-01-28 17:07:03 -05:00
1d51f2d151
must not access invalid/uninitialized data
2022-01-28 16:57:58 -05:00
2a3a7c387b
Merge pull request #3103 from tc387/CR-update
...
fixed ewald self-energy update and updated documentation
2022-01-28 16:37:11 -05:00
e5b129fe8d
Grow exponentially to resize less
2022-01-28 13:35:09 -07:00
41c1c64be9
Merged with deveop branch
2022-01-28 20:27:38 +00:00
e76c8bbaa3
spelling
2022-01-28 14:52:31 -05:00
4225c6c288
whitespace
2022-01-28 14:48:34 -05:00
9feec51590
Merge branch 'develop' of https://github.com/lammps/lammps into reax_count
2022-01-28 12:32:37 -07:00
d6a6f64576
Merge pull request #3090 from rbberger/modernize_use_override
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Modernize to C++11: use override
2022-01-28 14:10:45 -05:00
17cb137f3e
Merge branch 'master' into OptimizedDynamicalMatrix
2022-01-28 11:08:31 -08:00
bb89347bac
Fixed kspace issue and added suggested runtime check for intel accelerator
2022-01-28 11:06:29 -08:00
7aa17fbdf7
Merge branch 'develop' of github.com:lammps/lammps into reax_count
2022-01-28 11:58:50 -07:00
d3c45d3389
Removed whitespace
2022-01-28 17:58:00 +00:00
ef96b51a25
Merge branch 'deform-rebuild-rigid' into mpi-stubs-simplify
2022-01-28 05:44:43 -05:00
db4e69bf38
further simplification by making STUBS an interface and alias to MPI::MPI_CXX
2022-01-28 01:00:37 -05:00
ac815fdfba
use improved accessors for fixes
2022-01-27 22:16:43 -05:00
e4fe0a37a1
fixed ewald self-energy update and updated documentation
2022-01-27 16:48:22 -06:00
cd8b674f4b
expand path to include LAMMPS shared lib
2022-01-27 17:46:18 -05:00
0bf941219f
silence compiler warnings
2022-01-27 17:21:50 -05:00
d391ae845b
convert static class members with git info to functions to simplify auto-export on Windows
2022-01-27 17:20:05 -05:00
265588d480
Reduce differences between original pair hybrid and kokkos variant
2022-01-27 16:14:46 -05:00
62ff23abe7
simplify building serial executables by incorporating the STUBS/mpi.o object in LAMMPS library
2022-01-27 15:59:48 -05:00
735d6926a1
Update to KK tersoff styles for consistent nofdotr
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Inspired by f82096c46c
2022-01-27 14:36:45 -05:00
b3647d8e94
Add missing override keywords
2022-01-26 16:16:53 -05:00
a6ef114bfb
Ensure both Python Interpreter and Development header version match
2022-01-26 15:27:36 -05:00
293f4eb0ed
Add Python 3.10 to detection
2022-01-26 15:21:57 -05:00
2ed8e5cf02
Use setuptools instead of distutils in setup.py
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distutils will be removed soon (Python 3.12)
2022-01-26 14:58:28 -05:00
415476983d
Merge branch 'develop' into cg-dna
2022-01-26 19:31:48 +00:00
9b6bb00d07
Added unit test for atom_style oxdna
2022-01-26 19:20:34 +00:00
d51017ff50
Merge pull request #3095 from akohlmey/collect-small-changes
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Collected small changes and fixes
2022-01-26 12:04:44 -05:00
d861dbe8e0
Remove unused variable
2022-01-26 11:37:53 -05:00
71a373cadb
reshuffle Body struct members and add dummy for better alignment
2022-01-26 10:46:19 -05:00
8ca1004c03
cosmetic. align with clang-format
2022-01-26 10:45:46 -05:00
120662c438
correct citation info
2022-01-26 10:45:30 -05:00
cdd23ac9c2
Merge pull request #3097 from stanmoore1/dump_balance
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Add option to balance dump file output
2022-01-25 15:53:38 -05:00
3297ed7c5f
Refactor some declarations in KOKKOS package
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Adds C++11 template helpers to shrink larger declarations.
2022-01-25 14:29:00 -05:00
75a00f4d11
minor cleanup
2022-01-25 08:52:53 -07:00
64dbce26dc
Cannot shrink buf
2022-01-25 08:45:13 -07:00
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
35dbabd471
alternate fix for tag caching issue in INTEL package
2022-01-25 07:39:37 -05:00
0b693e729d
Whitespace
2022-01-24 17:33:36 -07:00
c914fc6baf
Small doc tweak
2022-01-24 16:33:11 -07:00
67af170929
Sorting is not required for balancing
2022-01-24 16:22:55 -07:00
cb9ba8c0a3
Simplify code
2022-01-24 16:05:27 -07:00
a80f7ed11f
Add error message to header file
2022-01-24 15:32:20 -07:00
aeb25b5a37
Tweak docs
2022-01-24 15:28:40 -07:00
1d60e4c463
Add docs
2022-01-24 15:16:49 -07:00
16810b84eb
Add option to balance dump file output
2022-01-24 14:35:27 -07:00
fc13c95c85
tweaks and bugs
2022-01-24 20:55:28 +01:00
86ee1f5a1f
updated create_atoms.h/cpp with accumulated changes
2022-01-24 20:38:51 +01:00
f9a2006d73
reorder includes
2022-01-24 08:44:29 -05:00
88dadd0fff
consistently refer to INTEL package in upper case
2022-01-23 21:12:22 -05:00
cd16556256
add missing break statements.
...
@GenieTim this bug may have tainted your results. you would always get the energy value for any of the dx, dy, dz keywords
2022-01-22 17:13:54 -05:00
81e7583a8d
initialize pointers, use provided constant, reorder include statements
2022-01-22 17:07:12 -05:00
f814dc5ff9
add checks after reading data
2022-01-22 17:06:28 -05:00
458ae4e38a
initialize pointers, remove unused class member
2022-01-22 17:06:13 -05:00
d854e58d00
add sanity check
2022-01-22 16:51:07 -05:00
c93fba5e2d
make certain that offset is always initialized
2022-01-22 16:45:38 -05:00
5142934a26
update to modern matrix representation
2022-01-22 16:38:58 -05:00
900ff39403
make consistent
2022-01-22 16:33:44 -05:00
78ed631877
spelling
2022-01-22 16:30:03 -05:00
fa88dacd7b
integrate into manual and build/source code system. apply conventions
2022-01-22 16:29:48 -05:00
5db5322902
move compute to its designated location
2022-01-22 16:24:07 -05:00
7aed8954a5
Add paragraphs in Modify_style.rst
2022-01-22 11:03:44 -05:00
ef2969dfbf
use override keyword in plugin sources
2022-01-22 10:30:58 -05:00
79a9829e92
Apply override to remaining classes
2022-01-22 09:56:01 -05:00
3e3cd4c94d
Added correct units for pressure, still getting wrong answer
2022-01-21 19:46:54 -07:00
3286fcb13a
Added correct units for pressure, still getting wrong answer
2022-01-21 19:29:23 -07:00
c16caea13b
Fixed bounds error
2022-01-21 19:17:12 -07:00
384b715d8c
First pass at fix numdiff/stress
2022-01-21 18:53:06 -07:00
12d708b97c
Apply override to more classes
2022-01-21 18:24:06 -05:00
44bc766060
Apply override to more classes
2022-01-21 16:58:32 -05:00
06beb28d7d
Apply override to Pair classes
2022-01-21 16:13:49 -05:00
6506be9409
update programming style
2022-01-21 15:56:58 -05:00
ff3f762499
Apply override to Fix classes
2022-01-21 14:45:53 -05:00
f83271aa40
Apply override to Compute classes
2022-01-21 13:23:36 -05:00
0d4bbf60e6
Apply override to Dihedral classes
2022-01-21 12:48:11 -05:00
3ff1902b57
Renamed born method born_matrix in all classes. Changed compute_born to compute_born_matrix. Changed the compute coding to suit the LAMMPS style rules better.
2022-01-21 18:39:16 +01:00
57def1a2d5
output reformatting and refactoring
2022-01-21 11:26:55 -05:00
75d20c40ed
remove threebody tag caching altogether since it is not reliable
2022-01-21 11:26:26 -05:00
3311b1344c
consolidate pair-wise vs pairwise spelling
2022-01-21 10:48:35 -05:00
3a6bd2e698
update comment about pair_write restrictions
2022-01-21 10:47:49 -05:00
67dec40afa
make certain pointers are initialized
2022-01-21 06:55:20 -05:00
9c8431bf87
correct calls to memset()
2022-01-21 06:55:06 -05:00
557e25d6fb
Apply override to Bond classes
2022-01-20 18:00:16 -05:00
4e89488f27
Apply override to Angle classes
2022-01-20 17:53:38 -05:00
d4ec931991
Apply override to FileReader classes
2022-01-20 17:49:23 -05:00
7387643b87
Apply override to Improper classes
2022-01-20 17:36:43 -05:00
5e37f9d5a7
Apply override to KSpace classes
2022-01-20 17:14:33 -05:00
586cf6c3bf
Apply override to Dump classes
2022-01-20 16:58:23 -05:00
e73158bd7e
whitespace/formatting
2022-01-20 16:56:12 -05:00
4104353d7a
plug memory leak
2022-01-20 16:55:59 -05:00
49dca516ea
simplify API of Force::store_style()
2022-01-20 16:48:44 -05:00
7c9b0c1e8e
Apply override to more core classes
2022-01-20 16:43:04 -05:00
5c62dc0986
Apply override to Comm classes
2022-01-20 16:39:36 -05:00
c9776dad6f
Apply override to Command classes
2022-01-20 16:35:59 -05:00
dbe267cb88
join lines, whitespace
2022-01-20 16:04:26 -05:00
0b24c5b498
workaround for segfaults due to NULL pointer dereference with hybrid styles
2022-01-20 16:04:07 -05:00
06cb86dfb9
Apply override to NTopo classes
2022-01-20 15:53:01 -05:00
7aaa85c3a1
Apply override to NBin classes
2022-01-20 15:44:16 -05:00
32a19d982a
Apply override to NStencil classes
2022-01-20 15:37:15 -05:00
222ea31d8d
Remove override = default destructor lines
2022-01-20 15:28:47 -05:00
8531622966
Merge branch 'develop' of https://www.github.com/lammps/lammps into Elastic_stress
2022-01-20 09:53:07 +01:00
f420bce07e
First commit of the Elastic constant computation compute modification
2022-01-20 09:52:24 +01:00
7ee3171d16
Apply override to NPair classes
2022-01-19 21:51:21 -05:00
b45a6d7720
Apply override to AtomVec classes
2022-01-19 17:31:41 -05:00
a0e2a617e0
Merge pull request #3092 from stanmoore1/kk_makefiles
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Small tweaks to Kokkos Files
2022-01-19 16:06:42 -05:00
9d8394fe63
Apply override to text_file_reader.h
2022-01-19 14:45:32 -05:00
c166549c74
Apply override to KOKKOS classes up to this point
2022-01-19 14:26:25 -05:00
b8d4030983
Update more core class destructors
2022-01-19 13:27:08 -05:00
e283bfa1fa
Apply override to Minimize classes
2022-01-19 13:23:28 -05:00
b7dc1d9dd6
Merge pull request #3091 from akohlmey/more-parsing-refactor
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More file parsing refactoring
2022-01-19 12:41:13 -05:00
6e8d9cb532
Port bugfix in Kokkos
2022-01-19 10:27:02 -07:00
0a8cbcef2b
Add -DNDEBUG to Kokkos Makefiles
2022-01-19 10:19:50 -07:00
0a89e5bd24
Remove non-ASCII chars
2022-01-19 10:18:25 -07:00
4f0cde40fd
White no longer exists
2022-01-19 10:16:53 -07:00
4cd5c40374
Merge pull request #3089 from akohlmey/collected-small-changes
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Collected small changes and fixes
2022-01-19 11:44:33 -05:00
7573e60a1e
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-01-19 10:21:12 -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
c85cdb2732
always fall back to using the .so extension if available in the LAMMPS module folder
2022-01-19 10:11:16 -05:00
7676f66674
modernize potential file parsing
2022-01-19 06:29:27 -05:00
f5ad91f9fe
minor tweaks
2022-01-19 06:28:53 -05:00
0595e4d7cd
refactor parsing of pair style list parameter file
2022-01-19 00:24:01 -05:00
c4c3b545b2
modernize fix gle matrix file reading
2022-01-18 19:55:50 -05:00
e22f62f6db
add some metadata for fix gle matrix files
2022-01-18 19:55:30 -05:00
b890b564ca
modernize electron stopping file reader
2022-01-18 16:48:26 -05:00
ef13455d6b
add some metadata tags
2022-01-18 16:48:07 -05:00
0099d2584b
Apply override to Integrator classes
2022-01-18 15:17:04 -05:00
778879a0eb
Apply override to Body classes
2022-01-18 14:56:44 -05:00
1792b3b0cf
Apply override to Reader classes
2022-01-18 14:39:31 -05:00
d19f799585
Apply override to Region classes
2022-01-18 14:31:29 -05:00
576f2266ae
Mark virtual destructors in derived as override
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Following C++ Core Guideline C.128
2022-01-18 14:28:25 -05:00
be7e6d0939
Avoid std::string copies
2022-01-18 13:22:55 -05:00
38bcc493b0
simplify and modernize CMAP file parser
2022-01-18 10:28:40 -05:00
389c35a2d3
use alternate method to create triclinic box for unit test
2022-01-18 09:09:37 -05:00
1c8f427e8a
detect when MSM::setup() is called before proper initialization and error out
2022-01-18 09:09:19 -05:00
29b5c2659c
source code formatting
2022-01-18 09:04:04 -05:00
c1f7685c98
Revert "before changing box settings, it must be initialized at least once"
...
Looking for alternate solution since this change has
too many unwanted side effects.
This reverts commit 2e85233b11
2022-01-18 08:30:54 -05:00
2e85233b11
before changing box settings, it must be initialized at least once
...
otherwise change_box would not really be needed,
but commands like boundary can (still) be used
2022-01-18 07:20:28 -05:00
752552e0f8
remove duplicate code
2022-01-18 06:39:20 -05:00
a02e11040d
whitespace
2022-01-18 06:34:57 -05:00
f0f4a8e6dc
plug some memory leaks in MSM kspace style(s)
2022-01-18 06:01:32 -05:00
241a44f1af
another workaround for rerun
2022-01-18 04:56:47 -05:00
e1d028ec88
Merge pull request #3087 from akohlmey/pair-harmonic
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Add new pair styles harmonic/cut for repulsive-only harmonic interaction
2022-01-17 18:53:35 -05:00
5530927bd4
Merge pull request #3088 from stanmoore1/kk_hip_fixes
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Fix Kokkos HIP compile issues
2022-01-17 18:07:29 -05:00
af231d5447
Fix comments in Makefiles
2022-01-17 08:54:17 -07:00
8b89be6061
Kokkos SNAP tuning for HIP
2022-01-17 08:49:00 -07:00
a93e5baa73
Add Kokkos HIP Makefiles
2022-01-17 08:44:49 -07:00
cb796e8b60
Fix HIP compile issues
2022-01-17 08:21:52 -07:00
dc6e558191
use Tokenizer class to parse bond colors
2022-01-16 20:20:07 -05:00
0eeb3b203c
add tests for molecule command
2022-01-16 16:50:23 -05:00
943fe487b5
update whitespace and argument formats for longer source lines
2022-01-16 15:36:01 -05:00
1e7969c7b9
add new pair styles harmonic/cut and harmonic/cut/omp
2022-01-15 19:34:47 -05:00
aa71ea6c40
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2022-01-14 20:25:05 -05:00
e271a54802
re-enable using rerun after the changes from PR #3052
2022-01-14 20:25:00 -05:00
c17eb14739
Fixing memory leak and wrong label
2022-01-14 15:45:18 -07:00
11cc8a6a59
whitespace
2022-01-14 15:59:05 -05:00
ed702b9309
don't allow exceptions to "escape" a destructor
2022-01-14 15:58:57 -05:00
dcb1ddb282
remove redundant code
2022-01-14 14:55:13 -05:00
2213eb8d3f
use enum with symbolic constants instead of numbers
2022-01-14 14:45:12 -05:00
7afa22f045
check return values for errors
2022-01-14 13:02:15 -05:00
0540b93123
fixed division by zero issue in geometry
2022-01-13 17:15:45 +00:00
524d86605a
Fixing reference in documentation
2022-01-12 10:56:30 -07:00
19abc5d329
Merge branch 'develop' into BPM
2022-01-12 10:52:11 -07:00
b1ed5e5b27
memory optimised with ragged arrays, implemented 3D ragged arrays
2022-01-12 17:02:09 +00:00
698256f4fe
update fedora singularity image to Fedora 35
2022-01-12 08:17:54 -05:00
e0cde6270e
Merge branch 'develop' into kokkos_unittests
2022-01-11 12:59:36 -05:00
5f607fad56
optimised memory management in chain generation
2022-01-11 16:46:50 +00:00
240db21054
silence possible warnings about missing files on "make clean-all"
2022-01-11 11:46:08 -05:00
8aaae8e6ee
Fix count issue
2022-01-07 15:22:53 -07:00
40c140e56e
Improve PairReaxFFKokkos neigh list algorithm
2022-01-07 14:48:07 -07:00
878557dd48
Merge pull request #3079 from akohlmey/next_patch_release
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Step version strings for the next patch release
2022-01-07 11:31:23 -05:00
1f81e2afad
Added duplication of stdout into logfile
2022-01-07 13:45:54 +00:00
11d66f8f1d
Merge branch 'lammps:develop' into cg-dna
2022-01-07 12:45:38 +00:00
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
e3dd2908d9
Step version strings for the next patch release
2022-01-06 19:42:45 -05:00
b300a93b67
Merge pull request #3073 from akohlmey/fmtlib-8.1-update
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Update included fmtlib to version 8.1.1
2022-01-06 19:40:00 -05:00
1f924e9fc1
Merge pull request #3071 from akohlmey/collected-small-changes
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Collected small changes and bug fixes
2022-01-06 19:22:30 -05:00
9c9bc4790b
update to fmtlib-8.1.1
2022-01-06 18:31:15 -05:00
69d6ddccc5
create missing de,df table elements from linear extrapolation
2022-01-05 15:34:30 -05:00
8e0622d523
Merge pull request #3046 from donatas-surblys/centroid-stress-constraint-rigid
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Centroid atomic stress for shake, rattle and rigid/small
2022-01-05 12:36:27 -05:00
3ff2f53ead
add citations to centroid/stress/atom
2022-01-05 18:45:35 +09:00
e5416a9fee
update documentation for new centroid stress for shake and rigid/small
2022-01-05 19:02:25 +09:00
4aba9e9bb6
cosmetic and whitespace changes
2022-01-04 23:08:32 -05:00
40abc0886c
adjust for double precision floating point
2022-01-04 23:02:17 -05:00
d0f203127d
create missing de,df table elements from linear extrapolation
2022-01-04 23:01:38 -05:00
12420181e1
Merge pull request #3072 from akohlmey/refactor-data-file-parsing
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Modernize parsing of topology data sections of data files
2022-01-04 13:21:14 -05:00
8ae68d71dd
Merge pull request #3062 from Luthaf/netcdf-standard
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Follow Amber NetCDF standard more closely
2022-01-04 13:02:50 -05:00
ede7787741
Refactor Atom::data_bodies()
2022-01-04 11:56:56 -05:00
f557bf6e20
implement suggestion by @rbberger
2022-01-04 11:37:32 -05:00
fd3884d705
disable centroid stress for non-small rigid fixes
2022-01-04 18:09:49 +09:00
1225b609d8
disable centroid stress for fix rigid/small/omp
2022-01-04 17:43:32 +09:00
6a73fc0472
refactor reading last line of potential file code to be more efficient
2022-01-03 21:35:26 -05:00
5ae496dcef
backport array dimension bugfix for NETCDF package in simplified form
2022-01-03 19:55:23 -05:00
8439f87b76
make consistent with other reference
2022-01-03 18:26:56 -05:00
de404d1ed8
Merge branch 'update_doc_file' of github.com:jddietz/lammps into collected-small-changes
2022-01-03 18:26:01 -05:00
49412ce0f7
implement workaround windows from https://github.com/fmtlib/fmt/issues/2691
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this also reverts commit c5a7f4c3ac
2022-01-03 18:01:33 -05:00
a9a568aefa
Updated references for pair_nm.rst
2022-01-03 11:50:04 -10:00
7e92809288
Merge pull request #3069 from Vsevak/fix-hip-ffast-math
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Fix HIP Makefile under lib/gpu
2022-01-03 11:37:55 -05:00
b8ed590bde
Merge pull request #3068 from ndtrung81/gpu-lib-makefiles
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Updates to Makefiles under lib/gpu
2022-01-03 10:48:45 -05:00
90726ca088
explain that the computed force in python pair is force/r same as in Pair:single()
2022-01-03 10:12:51 -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
8c95a8db23
Incorporate bugfixes from issue #3074 , a few additional cleanups
2022-01-03 10:11:03 -05:00
c5a7f4c3ac
fmtlib now uses UCRT instead of MSVCRT. add library to avoid linker failure
2022-01-02 15:24:04 -05:00
bb1c12d22b
import fmtlib v8.1.0
2022-01-02 13:42:27 -05:00
9c725d79d6
correct code example for current code
2022-01-01 16:42:28 -05:00
f3c5593c50
correct code example
2022-01-01 16:40:54 -05:00
e5c517c8d8
silence compiler warnings
2022-01-01 00:21:14 -05:00
9efa2369dd
join wrapped strings
2021-12-31 14:34:24 -05:00
c17a183816
do error checking already in read_data code
2021-12-31 14:34:09 -05:00
863de683ee
do not shadow "natoms" class member
2021-12-31 13:43:56 -05:00
6d9764e140
add missing advance of buffer pointer
2021-12-31 00:14:52 -05:00
ca3be99e77
correct function prototypes
2021-12-30 23:48:42 -05:00
e6e9aed385
modernize/correct parsing for Bonus and Bodies sections
2021-12-30 22:58:14 -05:00
8d53cd1e5d
modernize parsing of Velocities section of data files
2021-12-30 19:14:09 -05:00
def1072f0f
port data_atom() changes to KOKKOS
2021-12-30 18:42:15 -05:00
7f2b505df3
apply utils overloads
2021-12-30 11:14:48 -05:00
cf9429dc68
implement overloads so that utils::*numeric() functions can be safely used with std::string()
2021-12-30 11:03:37 -05:00
64d6a2fd1f
modernize parsing of the Atoms section
2021-12-29 20:24:27 -05:00
c97483c46f
modernize parsing of the Masses section in data files
2021-12-29 19:36:18 -05:00
78df5c2258
modernize parsing of Bonds/Angles/Dihedrals/Impropers section of data files
2021-12-29 19:18:42 -05:00
79fbf437a3
correct format string for Error::one()
2021-12-29 16:19:10 -05:00
27a6c63aeb
correct format string for Error::one()
2021-12-29 16:18:48 -05:00
d130aa4289
address segfault issue with fix nve/gpu when group is not "all"
2021-12-29 14:06:52 -05:00
88b42503f9
address segfault issue with fix nve/gpu when group is not "all"
2021-12-29 14:06:22 -05:00
14e5474174
restore obsolete compilation settings similar to parallel makefile
2021-12-27 20:31:42 -05:00
5d8b83a251
backport GPU package build system updates from upstream
2021-12-27 20:30:43 -05:00
053d915fc4
drop -ffast-math for HIP also when compiling with CMake
2021-12-27 20:14:30 -05:00
b781410f92
Delete fast-math flag from Makefile.hip for AMD platforms
2021-12-28 03:11:02 +03:00
47b0c8b33e
whitespace
2021-12-27 11:31:01 -05:00
5594a38bb7
replace explicit Makefile.mpi with symbolic link
2021-12-27 10:47:23 -05:00
3262140b65
more detailed unit tests. do not fail if ncdump is missing.
2021-12-27 10:35:38 -05:00
6357f19260
Added back Makefile.mpi in lib/gpu/ to be consistent with documentation; updated Makefile.*; and removed the unnecessary Makefile.turing
2021-12-27 00:14:04 -06:00
091f6164c8
add minimal unit test for netcdf dumps
2021-12-26 23:22:53 -05:00
30af0cb325
define and use LMP_MAX_VAR_DIMS instead of NC_MAX_VAR_DIMS to avoid stack overflows
2021-12-26 17:15:13 -05:00
84765f4b81
Merge branch 'develop' into netcdf-standard
2021-12-23 16:42:24 -05:00
b39d1993bb
Merge pull request #3052 from lammps/time-dumps2
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Time-dependent dumps for variable timestep (alternate implementation)
2021-12-23 16:34:12 -05:00
6af36075ba
Merge pull request #3064 from rbberger/collected-small-changes
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Collected small changes and fixes
2021-12-23 16:13:35 -05:00
a653ee6b2c
recover failing unit tests and whitespace fixes
2021-12-23 15:22:58 -05:00
7018ba65be
Merge branch 'time-dumps2' of github.com:lammps/lammps into time-dumps2
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# Conflicts:
# src/dump_xyz.cpp
2021-12-23 15:18:56 -05:00
d694b7cc1c
recover compilation
2021-12-23 14:34:49 -05:00
b7dba37e2e
Merge branch 'time-dumps2' of github.com:lammps/lammps into time-dumps2
2021-12-23 14:34:00 -05:00
23f1c9de60
Merge branch 'develop' into time-dumps2
2021-12-23 14:29:04 -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
1185591c76
add missing fclose()
2021-12-23 08:20:47 -05:00
b2adb4df47
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
2021-12-23 08:20:28 -05:00
3748a14582
warn about problems with the MPIIO package
2021-12-23 01:59:45 -05:00
93c7b6928f
remove dead code, silence compiler warnings
2021-12-23 01:32:31 -05:00
3b183bafbb
cosmetic changes (simplify, use constexpr, remove dead code, join wrapped lines)
2021-12-23 01:23:13 -05:00
b53cda778c
Merge branch 'develop' into netcdf-standard
2021-12-22 22:54:30 -05:00
09944f5d7a
Merge pull request #2996 from stanmoore1/compute_phase
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Add compute ave/sphere/atom
2021-12-22 21:16:25 -05:00
3dcfc0dfc6
skip redundant KOKKOS host/device styles info/help lists
2021-12-22 20:13:30 -05:00
8f62cd79f4
add missing list entry
2021-12-22 19:55:06 -05:00
586824be1b
Merge pull request #3021 from stanmoore1/big_dump_sort
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Allow dump sort to work with more than 2 billion atoms
2021-12-22 19:23:39 -05:00
cde7dd34fd
Doc update
2021-12-21 16:46:53 -07:00
2788bc666a
Update .gitignore
2021-12-21 16:44:14 -07:00
9271323cc0
Add dependency
2021-12-21 16:33:14 -07:00
1bbf45784b
Rename and relocate
2021-12-21 16:29:11 -07:00
6a442e1df4
use compute_time() func in xyz output
2021-12-21 14:05:16 -07:00
6f6b384c55
Merge branch 'time-dumps2' of github.com:lammps/lammps into time-dumps2
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# Conflicts:
# src/dump_xyz.cpp
2021-12-21 15:56:19 -05:00
cd6df24e37
Fix a couple issues
2021-12-21 13:45:29 -07:00
2fec3eee6b
Add overflow check to dump_h5md
2021-12-21 13:28:36 -07:00
5932a3f6f9
Merge branch 'develop' of github.com:lammps/lammps into big_dump_sort
2021-12-21 12:58:24 -07:00
cc4d7215f1
simplify. only output absolute time during MD.
2021-12-21 14:37:34 -05:00
cad9f6bf6e
Merge branch 'time-dumps2' of github.com:lammps/lammps into time-dumps2
2021-12-21 12:18:38 -07:00
576e787839
make xyz dumps print out current simulation time
2021-12-21 12:18:26 -07:00
8ed35832f4
Merge branch 'develop' into time-dumps2
2021-12-21 14:16:23 -05:00
e06222099a
Small tweak to docs
2021-12-21 11:51:30 -07:00
192aa7fedb
Merge pull request #3065 from lammps/angle-class2-update
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Angle class2 update and bugfix
2021-12-21 13:46:37 -05:00
c98f7b3e50
Clean up error message text
2021-12-21 11:40:04 -07:00
0576d525ad
simplify and avoid redundant output
2021-12-21 13:39:00 -05:00
364d0be28c
apply clang-format
2021-12-21 13:21:23 -05:00
c780768e91
put contents of netcdf_units into NetCDFUnits namespace
2021-12-21 13:16:23 -05:00
a2ab59b162
Fix cutoff logic
2021-12-21 11:07:03 -07:00
ded48cc031
more optimizations and extend to other dump styles
2021-12-21 10:57:42 -07:00
2533abb266
Add doc page
2021-12-21 10:46:23 -07:00
65204e5df0
Add error checks, tweak input
2021-12-21 10:46:00 -07:00
ecc0205436
reset force test references for Class2 angle styles
2021-12-21 11:28:26 -05:00
6187431399
Fix compile error in angle_class2_kokkos
2021-12-21 08:34:02 -07:00
f72b448544
WIP: cleanup/reorganize
2021-12-21 08:32:51 -07:00
4d31e300c6
change to checking timestep for time dumps at start of each step
2021-12-20 16:39:17 -07:00
f271d2180f
Remove unused variable
2021-12-20 16:05:44 -07:00
8d34fb8e1f
Merge branch 'develop' of https://github.com/lammps/lammps into compute_phase
2021-12-20 14:19:39 -08:00
4bc85f07e3
same changes in OPENMP and KOKKOS versions of angle class2
2021-12-20 14:29:17 -07:00
06c45fbe68
fix compiler errors
2021-12-20 14:26:22 -07:00
6bafa11080
Fix host compile error
2021-12-20 14:08:00 -07:00
36f3c8c899
Merge branch 'develop' of github.com:lammps/lammps into amd_hip_opt
2021-12-20 13:23:51 -07:00
2ee88dab7e
same change for angle class2/p6
2021-12-20 10:35:41 -07:00
97b5651633
minor correction to angle class2
2021-12-20 10:33:05 -07:00
79844a3f34
Tweaks to team_size/vector_length
2021-12-20 09:58:37 -07:00
8dd61144cb
Merge branch 'develop' into kokkos_unittests
2021-12-20 10:54:27 -05:00
f1daa22cdf
Merge branch 'lammps:develop' into cg-dna
2021-12-20 13:13:41 +00:00
461398bc0e
join lines
2021-12-19 17:46:51 -05:00
88f8e41702
PHONON package is now only a soft dependency on KSPACE
2021-12-18 18:22:47 -05:00
3246fd62a7
size_t is unsigned, so can't be negative
2021-12-17 17:10:21 -05:00
a3a6077115
Use sfread and sfgets in reader_native.cpp
2021-12-17 17:03:58 -05:00
1c25c96aaa
netcdf: deduplicate gettings units as strings
2021-12-17 17:13:29 +01:00
f8ee6dc680
netcf: define units for all variable where this is possible
2021-12-17 11:49:25 +01:00
dc9d539b6c
netcdf: fix spatial, cell_spatial and cell_angular variable definitions
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Dimension 0 refered to the frame dimension, but we need the spatial dimension instead
2021-12-17 11:49:25 +01:00
4bf065ed1c
netcdf: use float values for scale factors instead of double
2021-12-17 10:55:54 +01:00
d04f428c1a
netcdf: default to float variable for everything
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The standard convention require all values to be stored as
float, users still have the ability to use double with
`dump_modify <id> double yes`
2021-12-17 10:54:43 +01:00
94aad92b44
Tweaks to optimized SPMV and fused CG solve
2021-12-16 13:55:57 -07:00
90f3b0675e
Cleaned up/reorganized version of optimized Kokkos fix_qeq_reaxff
2021-12-16 13:01:58 -07:00
f7f32642ca
Temporarily revert EAM changes until a more portable/general solution is available
2021-12-16 10:13:00 -07:00
1f1c778225
Remove redundant GPL license
2021-12-15 16:51:53 -07:00
f6f60660c0
Cleanup for EV_FLOAT
2021-12-15 16:42:29 -07:00
2d4f030f11
Merge pull request #3060 from rbberger/binary_dump_reader_bugfix
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Bugfix for binary dump reader heap corruption
2021-12-15 17:20:12 -05:00
b8053e466b
Remove unused header, whitespace
2021-12-15 15:12:55 -07:00
0d238d554c
Cleaned up version of optimized Kokkos Tersoff
2021-12-15 14:45:48 -07:00
884dcbe4fa
Refactor reader_native.cpp
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- Use std::string instead of error-prone char buffers
- Limit reading files to known magic strings DUMPATOM and DUMPCUSTOM
2021-12-15 16:09:50 -05:00
2663087861
Merge branch 'develop' of github.com:lammps/lammps into amd_hip_opt
2021-12-15 13:56:15 -07:00
dccd74d6c4
Merge pull request #11 from arghdos/patched_ff
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Patched ff
2021-12-15 13:46:12 -07:00
902f9dd1fa
Move allocation to correct location
2021-12-15 15:05:59 -05:00
9fbca5111d
fix runtime error from lack of comm->setup()
2021-12-15 11:52:38 -08:00
3748ddb1ae
Merge branch 'lammps:develop' into cg-dna
2021-12-15 09:02:57 +00:00
40c0925cb4
Updated and added third order kokkos
2021-12-14 14:25:49 -08:00
b3fcda3214
Merge pull request #3057 from akohlmey/next_patch_release
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Step version strings for the next patch release
2021-12-14 17:08:29 -05:00
676c5a3666
Merge pull request #3059 from nw13slx/rerun_bin
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[BUGFIX] Wrong block reading in ReaderNative::read_atoms when binary is True and natom > 1024
2021-12-14 16:09:35 -05:00
3efddc4fb6
whitespace
2021-12-14 14:50:38 -05:00
5051055c76
Remove dead code and move nchunk read to read_header
2021-12-14 14:33:17 -05:00
fd18403b0a
Merge pull request #3056 from Ruyk/dpcpp-anon-struct-workaround
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DPC++ Anonymous Struct Workaround
2021-12-14 11:32:52 -05:00
80819f3793
reverse skip_buf with chunk
2021-12-14 11:09:36 -05:00
4be0e0a4e5
Merge branch 'develop' of https://github.com/lammps/lammps into big_dump_sort
2021-12-14 08:00:14 -07:00
26ebf97630
Merge branch 'develop' of https://github.com/lammps/lammps into compute_phase
2021-12-14 07:56:41 -07:00
62cdf7ab2d
update docs
2021-12-14 09:13:05 -05:00
1c38b7633f
generalize and simplify support for accelerated commands with suffixes
2021-12-14 09:06:04 -05:00
dee995f918
consistent author attribution
2021-12-14 09:05:28 -05:00
d6048ba576
added copyright/license header and updated author attribution
2021-12-14 08:41:49 -05:00
5b57d662c3
Merge branch 'develop' into OptimizedDynamicalMatrix
2021-12-14 08:35:58 -05:00
813f756382
Merge branch 'develop' into dpcpp-anon-struct-workaround
2021-12-14 06:59:12 -05:00
91633a4460
make workaround easier to disable and to remove
2021-12-14 06:59:03 -05:00
7c3deaa04b
limit the skip buf to MAXSMALLINT
2021-12-13 23:03:10 -05:00
b1d0dd65ea
simply the while loop and add correct initial m value
2021-12-13 22:57:39 -05:00
d4cec8ebe7
handle block reading in ReaderNative::read_atoms when binary is True
2021-12-13 21:38:16 -05:00
5a39efff19
Merge pull request #3055 from akohlmey/collected-small-changes
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Final changes for next patch release
2021-12-13 21:24:11 -05:00
744e615dbb
Revamping public methods for history, adding support for bond react
2021-12-13 17:35:53 -07:00
ccdb939a40
Merge pull request #3054 from nw13slx/rerun_bin
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Support binary native dump files with read_dump and rerun
2021-12-13 19:22:00 -05:00
a887d880c6
debugged kokkos support to dynamical_matrix command
2021-12-13 14:14:14 -08:00
72420bad3a
Merge pull request #3058 from jtclemm/documentation_edits
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Fixing some references to MISC package in documentation
2021-12-13 16:59:10 -05:00
ff41864cd9
remove redundant deletes
2021-12-13 15:28:27 -05:00
cdc831bb89
Update src/reader_native.cpp
...
Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:30 -08:00
f3543a839e
Update src/reader_native.cpp
...
Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:21 -08:00
3eae7b4200
Update src/reader_native.cpp
...
Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:14 -08:00
af2e295ac2
Update src/reader_native.cpp
...
Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:22:57 -08:00
bb6d581ef8
Update src/reader_native.cpp
...
Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:22:39 -08:00
1e73beca37
Merge pull request #2809 from rbberger/fmt_upgrade
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Upgrades fmtlib to v8.0.1
2021-12-13 15:14:58 -05:00
2b85799729
Updating MISC to EXTRA-X in doc files
2021-12-13 12:27:00 -07:00
94ac1ad4a0
update version strings for the next patch release
2021-12-13 11:56:44 -05:00
9159b37e47
Merge branch 'develop' into fmt_upgrade
2021-12-13 10:03:38 -05:00
d33019d8e4
llvm anonymous struct workaround
2021-12-13 11:08:06 +00:00
94d5c75fdf
small updates for docs and comments
2021-12-12 18:11:33 -05:00
33aea05080
adjust example for changes in when reset_timestep may be used
2021-12-12 10:01:52 -05:00
7db29112d8
replace read_buf to skip_buf in skip function
2021-12-12 00:26:55 -05:00
913b1536d4
whitespace
2021-12-11 21:18:33 -05:00
274b14618f
fold match_fields() back into read_header() function
2021-12-11 21:17:41 -05:00
e23a2bfb55
Merge branch 'rerun_bin' of github.com:nw13slx/lammps into rerun_bin
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# Conflicts:
# src/reader_native_bin.cpp
2021-12-11 21:05:01 -05:00
87501347ad
add minimal unit tests for reading binary dumps
2021-12-11 21:03:32 -05:00
0603dc6323
whitespace
2021-12-11 20:46:24 -05:00
86b696c78c
Merge branch 'develop' into rerun_bin
2021-12-11 20:31:48 -05:00
56fd07d88e
fold native binary reader class in to native reader class
2021-12-11 20:31:44 -05:00
565c8d6589
use fseek to skip bufs
2021-12-11 20:02:32 -05:00
8884acef24
Revert "add to compress read"
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This reverts commit b22c409079
2021-12-11 19:40:21 -05:00
d7bb9b5f30
reverse clang-format on irrelevant lines
2021-12-11 17:49:29 -05:00
b22c409079
add to compress read
2021-12-11 17:44:41 -05:00
626889f534
move the rb mode to the overloaded open_file function
2021-12-11 17:36:29 -05:00
d59458fa37
clean up commands and documentation
2021-12-11 17:24:27 -05:00
8f99d8d1d9
fix skip bugs
2021-12-11 16:41:13 -05:00
6e05aff3bf
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
2021-12-11 15:08:40 -05:00
250a5921a3
move match_field to protected method and format the docstring
2021-12-11 14:25:29 -05:00
2cdafb49a2
remove variable names from func declaration
2021-12-11 14:14:06 -05:00
e9f0351b67
reverse formatting on irrelevant files
2021-12-11 14:10:47 -05:00
eff26ba0b3
add read_buf method and fix bugs in inheritance
2021-12-11 14:02:58 -05:00
b1e7333348
remove wrong compression mode
2021-12-11 12:32:17 -05:00
7ab5d4edd4
add new ReaderNativeBin class
2021-12-11 11:54:21 -05:00
4f34c4374b
Merge pull request #3053 from stanmoore1/kk_desul
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Enable Kokkos Desul atomics in Makefile to match CMake settings
2021-12-11 06:12:50 -05:00
62f5f4d126
Merge remote-tracking branch 'github/develop' into fmt_upgrade
2021-12-10 23:04:58 -05:00
abd3df0c5a
Merge pull request #3040 from akohlmey/collected-small-changes
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Collected small changes and bugfixes
2021-12-10 15:51:13 -05:00
fc64fca3d9
Whitespace
2021-12-10 13:34:38 -07:00
6bd3ddf908
Don't use fetch variant of atomic if not needed
2021-12-10 13:27:57 -07:00
e49b7d0514
Remove atomics for error/warning flags since they are not needed
2021-12-10 13:14:12 -07:00
0ab0e2747c
Update comment
2021-12-10 12:15:10 -07:00
7aeab56eb2
Enable Kokkos Desul atomics in Makefile to match CMake settings
2021-12-10 12:09:32 -07:00
fa8e2ccee8
Merge pull request #2958 from jddietz/nm_split_styles
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nm split styles
2021-12-10 13:42:31 -05:00
668d7805d6
Fixes to doc
2021-12-10 11:34:12 -07:00
5ead32f886
more debugging and features
2021-12-10 11:13:06 -07:00
439853c4a8
Moving store/local to an internal fix
2021-12-10 10:33:52 -07:00
6140503158
update local/density examples to follow conventions more closely
2021-12-10 08:50:58 -05:00
14fc42833f
modernize potential file reader for local/density
2021-12-10 08:45:01 -05:00
e51fd40547
correct names of the pack/unpack routines for forward communication
2021-12-09 18:33:13 -05:00
3fc0ea3e80
correct names of the pack/unpack routines for forward communication
2021-12-09 18:30:54 -05:00
a975d0506a
update examples for pair style local/density
2021-12-09 18:21:32 -05:00
e1e46b5322
Merge pull request #3033 from rbberger/unittest_tags
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Add tags to force-style unit tests
2021-12-09 18:11:08 -05:00
146c6fe5ff
remove check that is no longer needed
2021-12-09 18:08:43 -05:00
0e4e830c79
document "slow" and "unstable" labels for unit tests
2021-12-09 17:02:20 -05:00
0d44c56ccc
use comma consistently
2021-12-09 15:50:57 -05:00
7d48324f51
tweak force test settings
2021-12-09 15:48:24 -05:00
facb49fc27
disallow reset_timestep for time averaging fixes
2021-12-09 15:09:42 -05:00
878dd746db
reduce warnings and improve portability
2021-12-09 13:55:53 -05:00
e2969d09e1
bug fix for fix dt/reset freq of 1
2021-12-09 11:53:47 -07:00
754610b9ee
Merge pull request #3041 from oywg11/modified-sw-potential
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A modified Stillinger-Weber potential for transition metal dichalcogenide
2021-12-09 09:43:49 -05:00
455cb09cf4
Adding compatability with MC fixes, set_array to property/atom, faster update/special/bonds, single methods, and misc small changes
2021-12-08 16:47:42 -07:00
d4149e9139
bug fixes to make a series of test inputs run correctly
2021-12-08 16:44:51 -07:00
62f271658b
correct setting forward/reverse buffer size info
2021-12-08 13:58:12 -05:00
8f0dea91c7
correct setting forward/reverse buffer size info
2021-12-08 13:54:47 -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
a5ee7ca73f
make certain did_mix is initialized
2021-12-08 00:51:04 -05:00
bea273fc3a
correct docs for pair style local/density
2021-12-08 00:22:37 -05:00
40c04a210b
correct handling of data packing for forward and reverse communication
2021-12-08 00:22:36 -05:00
021f6832d5
adjust epsilon for -std=c++14 and add more unstable tags
2021-12-07 17:11:29 -05:00
26492b13d5
logic for dumps every steps and time delta
2021-12-07 13:46:36 -07:00
5cee58a9c8
Merge pull request #3049 from Ruyk/sycl-pinned-host
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Use SYCL pinned host memory from Kokkos.
2021-12-07 14:07:58 -05:00
605d2b7ab2
Use SYCL pinned host memory from Kokkos.
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Depends on this PR from Kokkos:
https://github.com/kokkos/kokkos/pull/4268/
2021-12-07 16:49:27 +00:00
1afdd3c011
new output vars for dumps
2021-12-07 09:16:19 -07:00
a323b00fef
Merge branch 'develop' into unittest_tags
2021-12-07 10:24:46 -05:00
f3eac179e6
Expanding broken bonds documentation, adding support for more create/delete bond commands, misc small edits
2021-12-06 17:27:25 -07:00
ac57c44552
update unit test for renamed bond style
2021-12-06 16:35:20 -05:00
6314290558
clarify docs for bond style fene/nm/split and rename to fene/nm
2021-12-06 16:21:12 -05:00
021a59965e
convert to ASCII
2021-12-06 15:54:34 -05:00
f88009c626
correct comments
2021-12-06 15:50:16 -05:00
fa913c3e5b
clarify r_0 versus sigma
2021-12-06 15:50:09 -05:00
a84c0a43bd
address spelling issues
2021-12-06 15:35:32 -05:00
c48810c545
whitespace
2021-12-06 15:29:23 -05:00
ef186d9628
Updated pair_nm.rst
2021-12-06 15:09:45 -05:00
1238f1b273
correct multiple math typesetting errors, typos, and inconsistencies
2021-12-06 14:10:41 -05:00
274ffe1f48
Consolidate "Jiang" citations
2021-12-06 14:07:36 -05:00
b0305a09e9
whitespace
2021-12-06 13:49:13 -05:00
3d3b153b35
add proper symlink
2021-12-06 13:45:04 -05:00
d7c8cb3e48
fix documentation issues
2021-12-06 05:57:52 +02:00
e36029293a
update documentation and examples
2021-12-04 17:38:29 +02:00
40258f8b9a
Adding Steve's edits in documenation + associated changes in files
2021-12-03 16:12:31 -07:00
8aee8cc427
tweak documentation
2021-12-03 17:20:07 -05:00
8bc1f8b9ea
whitespace
2021-12-03 17:16:54 -05:00
085de6f857
update test and add test using maxdelcs keyword with non-default values
2021-12-03 17:16:46 -05:00
c72771ae1d
align with non-OpenMP version
2021-12-03 17:16:08 -05:00
6b28816c11
must set defaults for (optional) maxdelcs keyword, add consistency check
2021-12-03 17:15:44 -05:00
71edaca36c
update unit test reference
2021-12-03 14:20:23 -05:00
2d6e4d4d79
Merge branch 'develop' into nm_split_styles
2021-12-03 14:18:07 -05:00
405fea44da
convert from CR-LF to consistent line endings
2021-12-03 14:17:31 -05:00
859e0348ea
fixed some issues
2021-12-03 17:45:31 +02:00
1dd4a67771
add keyword for userdefined maxdelcs
2021-12-03 17:32:08 +02:00
262c103aaa
replacing hard-coded values with named constants
2021-12-03 15:46:00 +02:00
9a90803b23
Merge pull request #2984 from lammps/delete-atoms-porosity-group
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Add new group arg for delete_atoms porosity
2021-12-02 16:07:49 -05:00
9307a376aa
Merge pull request #3044 from ellio167/kim-lib-install-py
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Adjustments to lib/kim/Install.py and docs
2021-12-02 15:43:03 -05:00
ef90089d8d
Merge pull request #2867 from ndtrung81/gpu-newton-pair-on
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Enabled newton pair on for gpu pair styles
2021-12-02 15:42:34 -05:00
2ba5aeec31
whitespace
2021-12-02 15:30:53 -05:00
4ecb894d9d
simplify by using new API
2021-12-02 15:27:06 -05:00
637c6bf28a
Merge branch 'develop' into delete-atoms-porosity-group
2021-12-02 15:15:47 -05:00
fc0aa0e844
Merge pull request #3043 from rbberger/container_updates
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Container updates
2021-12-02 14:43:20 -05:00
42df189abd
update .gitignore
2021-12-02 13:49:26 -05:00
2527eb5914
reorganize integration of sw/mod into the sw pair style docs
2021-12-02 12:47:18 -05:00
3dff9cf2c1
update false positives
2021-12-02 12:27:54 -05:00
8847f359ba
integrate sw/mod pair style into documentation
2021-12-02 12:23:01 -05:00
7651be3e02
add force style test
2021-12-02 12:20:33 -05:00
ecd51ba4fe
remove obsolete/redundant files
2021-12-02 12:20:10 -05:00
718a9e2bae
whitespace
2021-12-02 12:13:12 -05:00
c33e6538bb
simplification by deriving pair style sw/mod/omp from sw/omp instead of sw/mod
2021-12-02 12:12:57 -05:00
3bf171d753
move pair sw/mod/omp to correct location
2021-12-02 12:01:05 -05:00
30d3b2c209
merge rst files and add omp style
2021-12-02 15:46:00 +02:00
47f578bcca
Fixup typos
2021-12-01 21:15:28 -06:00
65d31dfeb1
Adjustments to lib/kim/Install.py and docs
2021-12-01 16:49:00 -06:00
ca8dddf002
upgrade of lb/fluid fix
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This includes documentation files in the rst format in the doc/src directory, examples in the examples/PACKAGES/latboltz directory and source files in the src/LATBOLTZ directory.
2021-12-01 14:31:57 -05:00
c03cdfdf60
Add libyaml-cpp dev package
2021-12-01 14:00:08 -05:00
195455faa8
Update GPU and NVIDIA container definitions
2021-12-01 13:48:54 -05:00
01ddfe95f0
prepare fix plumed to be compatible with version 2.8
2021-12-01 13:44:56 -05:00
e75312ddf6
Update ROCm containers to v4.5.0
2021-12-01 13:24:07 -05:00
ff919af3ef
Update container bundled PLUMED to v2.7.3
2021-12-01 11:39:05 -05:00
4d4c04dd7c
include support for building with plumed 2.7.3 and 2.6.5
2021-12-01 10:56:23 -05:00
e0770a2ac0
Add Ubuntu 20.04 OneAPI container definition
2021-12-01 10:41:01 -05:00
3bc36070a9
fix the invoking issue
2021-12-01 04:56:46 +02:00
8589ecd6c1
Merge pull request #3019 from stanmoore1/kk_update_3.5.0
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Update Kokkos library in LAMMPS to v3.5.0
2021-11-30 16:58:38 -05:00
b3d7904120
Update docs
2021-11-30 11:12:30 -07:00
420c1097a9
Update Kokkos CMake file
2021-11-30 11:02:11 -07:00
b2410ee70b
Update Kokkos library in LAMMPS to v3.5.0
2021-11-30 10:57:43 -07:00
c0b827e006
Merge branch 'kk_update_3.5.0' of github.com:stanmoore1/lammps into kk_update_3.5.0
2021-11-30 10:52:51 -07:00
b61fc38711
Merge branch 'develop' of github.com:lammps/lammps into kk_update_3.5.0
2021-11-30 10:52:21 -07:00
4a05628938
bug fixes from Doug Spearot
2021-11-30 08:22:38 -07:00
8556b71949
derived class of sw
2021-11-30 10:14:20 +02:00
7113334f99
Fixing typos in documentation
2021-11-29 16:19:45 -07:00
5fa185bfda
Fixing bug in failing to update values across runs
2021-11-29 14:04:07 -07:00
f1c52ddb5c
make documentation of a few pair styles more consistent with the rest
2021-11-29 15:57:11 -05:00
597054edf3
A modification to SW potential
2021-11-29 16:08:32 +02:00
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
ddf97fa8fc
tweak error messages
2021-11-24 15:34:43 -05:00
2a68c6edba
add (global) restart support to fix charge/regulation
2021-11-24 15:34:30 -05:00
ae0f4dcfc1
generate atom tags for newly created atoms, if tags are enabled. triclinic support.
2021-11-24 15:33:32 -05:00
4d19895a88
Merge branch 'master' into delete-atoms-porosity-group
2021-11-23 16:05:02 -07:00
2c5441257e
Disable tersoff with shift flag tests for kokkos_omp
2021-11-23 15:03:48 -05:00
9517467113
Add missing KOKKOS suffix in PairTersoffZBLKokkos
2021-11-23 14:56:35 -05:00
0b87039fbb
Skip MolPairStyle:hybrid-scaled test for kokkos_omp
2021-11-23 14:28:59 -05:00
2f6bf29adf
Fixup kokkos_omp test for dpd
2021-11-23 14:06:02 -05:00
d365cc7dfc
Add missing destroy_kokkos() calls in pair_lj_gromacs_kokkos.cpp
2021-11-23 13:57:53 -05:00
b603346a0d
Skip kspace-pppm_ad test for kokkos_omp
2021-11-23 13:56:19 -05:00
51c627df76
Add SCOPED_TRACE for better test error messages
2021-11-23 12:22:01 -05:00
073b586eee
Add EXPECT_POSITIONS() and EXPECT_VELOCITIES() test utils
2021-11-23 12:21:27 -05:00
32a53a1ae3
Use EXPECT_FORCES() in more testers
2021-11-23 11:46:33 -05:00
615b7ceca2
Simplify EXPECT_FORCES() utility function
2021-11-23 10:59:40 -05:00
946fd6fb55
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 10:46:22 -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
68360b9335
Add test utility method EXPECT_FORCES()
2021-11-22 16:27:18 -05:00
1a4511bb8d
Merge pull request #3034 from akohlmey/mixing-info
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Provide information about pair_coeff mixing and improve hybrid docs
2021-11-22 16:22:24 -05:00
5c1bb5f13a
Write dump header after sort to fix incorrect atom count for multiproc
2021-11-22 15:52:27 -05:00
62b236a7cd
Use platform::path_join in unittest tree and remove redundant code
2021-11-22 15:34:23 -05:00
3d650a6bf7
Add test utility method EXPECT_STRESS()
2021-11-22 15:24:41 -05:00
ef2e51b344
whitespace fixes
2021-11-22 14:58:41 -05:00
6b605e932b
Merge branch 'develop' into mixing-info
2021-11-22 14:58:19 -05:00
a83329a1a7
Merge pull request #3032 from GenieTim/compute-pair-distance-vector
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Add dx, dy and dz computes to compute bond/local and property/local
2021-11-22 14:50:15 -05:00
bb127603ff
Use platform::unlink in unittests
2021-11-22 14:40:51 -05:00
a6ccdd72ec
Move platform::rmdir docstring to right location
2021-11-22 11:49:09 -05:00
0931da9cad
Cleaned up comments in fix_gpu.cpp
2021-11-20 08:38:13 -06:00
a06c4767a0
Merge branch 'upstream' into gpu-newton-pair-on
2021-11-20 08:30:39 -06:00
f135d8bb4e
Fix issue where direction correction in compute bond/local might not have been correct
2021-11-20 14:34:24 +01:00
a354a763bb
Fix output capture mismatch
2021-11-19 17:14:52 -05:00
79feba1a25
try fix host fused
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Change-Id: If54da165cf0488be39e9c4971bff3edf39d5b067
2021-11-19 17:09:26 -05:00
dcb32dc9f5
Fix no return warnings
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Change-Id: I2ae537d5bfd5258b87bee372896e3ffd030772ab
2021-11-19 16:39:21 -05:00
9eea03aeb7
fix device fused QEQ
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Change-Id: I7ed12d55ca838f9b60cc1292f127067050e8c88b
2021-11-19 16:39:17 -05:00
780cf82bb0
First version of kokkos_omp test variant
2021-11-19 16:23:05 -05:00
2c8c33fb9a
add slow tag to about 60 tests that take about as much time as the 430 others
2021-11-19 15:59:19 -05:00
f8a94a4f10
Minor fixes to align w.r.t upstream
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Change-Id: I4d8bbfe286c986f5bc603041b04f272b3f537476
2021-11-19 15:58:25 -05:00
00cbb633bf
Implement host MPI for fused QEQ
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Change-Id: I3278a72878fb7cdb64a059aaf025c039dc0d71e5
2021-11-19 15:41:37 -05:00
fb379dab15
Fused CG passes 1 & 2 for QEQ solver
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Change-Id: I5fa396d8a2f2713712056a264d2bb05b7321dc1a
2021-11-19 15:41:37 -05:00
2a1823f59d
add a missing CBRT
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Change-Id: I5f70816a2b5ac07ba88511cf3bf14017043b5e76
2021-11-19 15:41:37 -05:00
8e140b4fcd
Use tuned blocking sizes from experiment
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Change-Id: I08a837d9632a45dabd3331108314d3ffc328338c
2021-11-19 15:41:37 -05:00
b2dae36eb9
discuss mixing informational message
2021-11-19 14:36:00 -05:00
3d4b0121cb
improve pair hybrid documentation with respect to mixing
2021-11-19 14:18:55 -05:00
23d40a1d61
report how many pair_coeff settings parameters were generated from mixing
2021-11-19 13:43:32 -05:00
ff2751bf91
Merge pull request #10 from arghdos/fix_missing_hd
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Minor fix for compilation bug
2021-11-19 10:41:26 -07:00
f5a03cb0c6
Minor fix for compilation bug
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Change-Id: I79703cd20b12905855a2b8ec263665dd5be77604
2021-11-19 12:37:23 -05:00
b55ea05f3b
Add some example tags for force style tests
2021-11-19 09:23:47 -05:00
4ac351eba6
Add tags to force-style tests
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Adds an optional "tags" entry in the force style test YAML. This is a
comma-separated list of keywords, which are parsed by CMake and added as labels
for CTest. This allows more fine-grained filtering of tests. Any
newly-generated YAML file automatically adds the "generated" tag.
2021-11-19 09:23:31 -05:00
74577fa584
Fix issue where direction correction in compute pair/local might not have been correct
2021-11-19 08:08:07 +01:00
7f17c55198
Merge branch 'develop' of https://github.com/lammps/lammps into compute_phase
2021-11-18 14:08:01 -08:00
4b6090a8cb
Add direction consistency check to pair/local too
2021-11-18 19:28:51 +01:00
36e4e3e746
Add ddx, dy and dz computes to compute bond/local and property/local
2021-11-18 17:22:32 +01:00
15f1c2d960
Fix inaccurate error message
2021-11-18 08:50:09 -07:00
94b11964f8
Write dump header after sort to fix incorrect atom count for multiproc
2021-11-18 08:32:41 -07:00
5616336d5e
Allow sorting with reorderflag for more than 2 billion atoms
2021-11-18 07:59:45 -07:00
47f3f9d44a
Merge branch 'develop' of github.com:Iximiel/lammps into develop
2021-11-18 14:36:45 +01:00
c918b6fbcc
removed example dump file
2021-11-18 14:36:38 +01:00
8faa750f21
Merge branch 'lammps:develop' into develop
2021-11-18 14:34:12 +01:00
4646671e70
added examples
2021-11-18 14:32:39 +01:00
a759987515
added examples
2021-11-18 14:31:21 +01:00
a5df494176
added examples
2021-11-18 14:30:26 +01:00
b06a70c33c
corrected some errors in the manual
2021-11-18 12:40:10 +01:00
29471bd425
Merge branch 'develop' of github.com:lammps/lammps into big_dump_sort
2021-11-17 14:09:51 -07:00
7544f1bcf8
Fixed comm setup bug and external forces bug, still must look into if package omp needs to set external force flag to zero
2021-11-17 11:48:35 -08:00
229ce0a61b
Merge pull request #3027 from yihengwuKP/fix-reorder-remd
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Fix the indent and ot bugs in reorder_remd_traj.py
2021-11-17 14:11:12 -05:00
377b5b4ab3
Merge pull request #3020 from akohlmey/collected-small-changes
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Collected small changes and fixes
2021-11-17 14:00:13 -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
d178a5ffa3
Extended test script
2021-11-17 13:12:44 +00:00
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
ef30e3bd35
clarifications and corrections for the discussion of the main git branches
2021-11-17 06:58:44 -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
2b480f87f1
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 21:48:33 -05:00
d576b69dbc
plug memory leaks
2021-11-16 21:41:08 -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
d0a4c4467f
replace replicated functionality with shared code in base class
2021-11-16 13:53:52 -05:00
9f4626a62a
correct uninitialized data access bug due to shadowing of a base class member
2021-11-16 10:51:46 -05:00
ed8c86d248
correct uninitialized data access bug due to shadowing of a base class member
2021-11-16 10:46:09 -05:00
1c1cd60baf
Fix the indent and ot bugs in reorder_remd_traj.py
2021-11-15 18:21:17 -06:00
766f975b74
Removed the newton checks in the gpu pair styles; reverted to mixed precision in Makefile.cuda
2021-11-13 07:00:12 -06:00
906e78c198
Merge branch 'gpu-newton-pair-on' of https://github.com/ndtrung81/lammps into gpu-newton-pair-on
2021-11-13 06:39:23 -06:00
65fb78b6d5
Finally updated the nm_split_styles, removed hard-coded r0=2^1/6 cutoff
2021-11-12 14:44:18 -05:00
7a914c84d7
again correction in the documentation
2021-11-12 16:25:48 +01:00
0eb227e7de
working on the documentation
2021-11-12 14:55:48 +01:00
fe5f00bbea
Updating the documentation, now 'make html' do not give errors
2021-11-12 14:37:16 +01:00
bfc34023b1
working on the documentation
2021-11-12 12:01:05 +01:00
cfe08ba55f
working on the manual
2021-11-12 10:32:04 +01:00
c488e912e6
adding the pair_smatb to lammps documentation
2021-11-11 17:01:03 +01:00
80efc8839a
fixed a grammar mistake
2021-11-11 16:36:48 +01:00
bdc4f7fb18
styled the headers
2021-11-11 16:27:09 +01:00
1c0e6578b6
changed some comments
2021-11-11 16:12:26 +01:00
4f4b18ab7e
addig smatb pairs
2021-11-11 16:06:42 +01:00
feac637a2a
Fix compile issues on CPU
2021-11-10 15:31:49 -07:00
7625b9707b
Update to latest upstream develop
2021-11-10 15:14:24 -07:00
f733453f05
Intpos ( #11 )
...
* hbond comm added for rsq_hb
* lrefpos removed, extract scaled for oxDNA1
* Update pair_oxdna_hbond.cpp
* nxyz extract scaled across DNA2/RNA2
* oxDNA2/RNA2 updated to match oxDNA styling from upstream merge
* whitespace corrections
also removed unnecessary local unit vector from oxRNA2_xstk
* whitespace correction in oxdna_coaxstk
2021-11-10 09:25:13 +00:00
3b30fbb218
Merge branch 'lammps:develop' into intpos
2021-11-10 09:13:00 +00:00
367c9dff05
Compilable kokkos dynamical matrix command
2021-11-09 15:21:39 -08:00
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
acb1c8e7f2
Moving update/special/bonds into bond style to ensure correct fix ordering
2021-11-07 17:55:53 -07:00
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
25db8a21bc
account for increased floating point errors when summing numbers to zero
2021-11-07 08:29:16 -05:00
ac6654cf0c
skip MPI tests if they would be oversubscribing the available processors
2021-11-07 08:28:16 -05:00
16c50b3873
whitespace
2021-11-07 08:27:25 -05:00
7c5640c1c9
we may call ->set_molecule() only in MOLECULE mode
2021-11-05 16:27:58 -04:00
49258e9301
add missing assignment
2021-11-05 16:19:19 -04:00
03e3dfa94d
Merge branch 'develop' of https://github.com/lammps/lammps into kk_update_3.5.0
2021-11-05 13:46:50 -04:00
d1403c62c8
update restrictions note for dump_modify
2021-11-05 10:56:54 -04:00
ebb3dcd9ff
Remove error message
2021-11-04 20:20:07 -06:00
07a25144ee
Remove error from dump.h
2021-11-04 20:06:30 -06:00
136c15a8ba
Allow dump sort to work with more than 2 billion atoms
2021-11-04 19:59:48 -06:00
a4ceda9706
Merge pull request #2940 from akohlmey/multi-config-support
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Support multi-config builds with CMake
2021-11-04 15:21:58 -07:00
5e7f2cf54f
Changed tab spacing from 4 to 2, to be in line with lammps standards
2021-11-04 14:33:16 -07:00
18c78e1625
Merge branch 'master' into OptimizedDynamicalMatrix
2021-11-04 14:23:50 -07:00
b3c5f6a4fd
whitespace
2021-11-04 16:48:29 -04:00
935c17f02e
Document multi-configuration build support in CMake
2021-11-04 16:32:21 -04:00
1a940e052e
add support for and apply clang-format to lammps-shell code
2021-11-04 15:55:28 -04:00
aab4f71019
Merge branch 'develop' into multi-config-support
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# Conflicts:
# unittest/force-styles/test_error_stats.cpp
2021-11-04 15:50:49 -04:00
2cd862e4a2
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
2021-11-04 15:24:41 -04:00
8e89c7c654
correct unit description of eta_n0 parameters. fixes #3016
2021-11-04 15:24:41 -04:00
825945f783
mention that dump sorting is limited to less than 2 billion atoms
2021-11-04 15:24:41 -04:00
461a7afc22
remove PYTHON from "most" cmake preset.
...
The PYTHON package cannot be compiled without the python development
support being installed, so it must not be in the "most" preset
2021-11-04 15:24:41 -04:00
3ec3085f39
Merge pull request #3017 from akohlmey/portability-improvements
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Portability improvements
2021-11-04 12:21:11 -07:00
564098e629
Update Kokkos library in LAMMPS to v3.5.0
2021-11-04 12:45:59 -06:00
0909b4da92
Updated dynamical matrix command to work with intel potentials
2021-11-04 11:35:31 -07:00
7c80911f66
whitespace
2021-11-03 15:23:29 -04:00
439f997a10
skip test for file not readable due to permissions on windows
2021-11-03 14:54:38 -04:00
62fc7b6fa0
small tweaks to make replacing the CMakeLists.txt file work as expected
2021-11-03 14:44:16 -04:00
37dfc9e141
simplify by not trying to use fetchcontent but do all steps manually
...
as it turns out, fetchcontent is calling external_project internally at
some point which to avoid is why this function was started in the first place
2021-11-03 14:43:18 -04:00
b7bf60ea53
use the portable platform::unlink() instead of unlink()
2021-11-03 14:26:50 -04:00
b86a3a5d6b
Added missing }
2021-11-03 10:24:22 -07:00
5241f93641
Update third order format
2021-11-03 10:12:17 -07:00
35ff47411b
Merge branch 'multi-config-support' of github.com:akohlmey/lammps into multi-config-support
2021-11-03 12:35:40 -04:00
7f0b2334a5
update plugin loader test
2021-11-03 11:52:32 -04:00
b95e12bb6c
add additional function argument where we can supply our own CMakeLists.txt file
2021-11-03 11:50:39 -04:00
eb3f928f31
tweak epsilon for portability with windows
2021-11-03 10:54:40 -04:00
1ad982aa85
improve portability of unit test code for windows compilers
2021-11-03 10:54:21 -04:00
50f39cd752
implement and use a platform neutral abstraction of unsetenv(3)
2021-11-03 10:53:45 -04:00
e8f6024eae
Fixed more whitespace issues
2021-11-03 11:46:56 +00:00
fc4fdd09ef
Fixed more whitespace issues
2021-11-03 11:44:29 +00:00
a37a113044
Merge branch 'lammps:develop' into intpos
2021-11-03 11:02:01 +00:00
b8970366e0
Fixed whitespace issues
2021-11-03 10:59:04 +00:00
7ba211a727
Update dynamical matrix format
2021-11-02 21:57:55 -07:00
a9c6f943e1
correct test comparisons
2021-11-02 23:07:44 -04:00
6479116419
Merge branch 'develop' into multi-config-support
2021-11-02 16:39:12 -04:00
515ef7bece
Merge pull request #3015 from lammps/dump-image-doc
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Move dump_modify options specific to image/movie to dump image doc page
2021-11-02 13:22:27 -07:00
80579593e0
Merge pull request #3014 from akohlmey/collected_small_changes
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Collected small changes and bugfixes
2021-11-02 13:02:31 -07:00
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
b044a2f88b
switch to https protocol for cloning MathJax
...
https://github.blog/2021-09-01-improving-git-protocol-security-github/
2021-11-02 15:26:45 -04:00
d3af16c1fd
Merge branch 'develop' into collected_small_changes
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# Conflicts:
# src/fix_vector.cpp
2021-11-02 14:41:16 -04:00
71d48bc48a
Merge branch 'cmake_fixes' of https://github.com/pzeiger/lammps into collected_small_changes
2021-11-02 14:36:59 -04:00
91e6586e05
reorder
2021-11-02 14:35:36 -04:00
817e38fe68
change references to git:// protocol for accessing github to https://
2021-11-02 14:33:21 -04:00
278e531c14
fix typo
2021-11-02 14:33:00 -04:00
f5626a2b9d
Few more merge conflicts
2021-11-02 12:29:49 -06:00
175f967051
change references to git:// protocol for accessing github to https://
2021-11-02 14:25:57 -04:00
59c060cc0e
switch to https protocol for cloning MathJax
...
https://github.blog/2021-09-01-improving-git-protocol-security-github/
2021-11-02 14:14:08 -04:00
679132b607
Replacing some needed header files
2021-11-02 12:10:20 -06:00
0439671e86
Merge pull request #3001 from akohlmey/modify-fix-compute-accessors
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Add accessor functions to `Modify` and `Domain` that do not require using class internal data structures
2021-11-02 11:02:01 -07:00
628091c510
add reference instead of replicating headline
2021-11-02 13:33:08 -04:00
21fcdf8c56
Fix bug in Kokkos neighborlist where stencil wasn't updated for occasional list
2021-11-02 13:17:28 -04:00
a58242f24b
couple last tweaks to make the pages easier to navigate
2021-11-02 09:27:27 -06:00
dfc68e3c75
add header for dump_modify command summary
2021-11-02 08:49:34 -04:00
cf968ef286
Intpos ( #10 )
...
* hbond comm added for rsq_hb
* lrefpos removed, extract scaled for oxDNA1
* Update pair_oxdna_hbond.cpp
2021-11-02 09:52:56 +00:00
bb176318fe
Merge branch 'lammps:develop' into intpos
2021-11-02 09:48:24 +00:00
d7f7835069
Fix merge conflicts, minor style fixes
2021-11-01 18:13:06 -06:00
e3c9d7936b
Merge branch 'develop' of github.com:lammps/lammps into coo_opt
2021-11-01 17:00:13 -06:00
7a228eedd2
move dump_modify options specific to image/movie to dump image doc page
2021-11-01 15:16:39 -06:00
f05807f38e
Revert 647380a
2021-11-01 14:34:50 -06:00
3d2a97b4a9
Fix bug in Kokkos neighborlist where stencil wasn't updated for occasional list
2021-11-01 14:07:04 -06:00
7e08525ce3
Merge branch 'master' of https://github.com/lammps/lammps into coo_opt
2021-11-01 12:57:26 -06:00
9caad2be4d
update security statement
2021-11-01 09:59:38 -04:00
d5bfa09faa
modernize argument parsing
2021-11-01 09:19:33 -04:00
0bc9f887ec
fix index error
2021-10-31 19:46:37 -04:00
6b3ddb8a72
fix logic bug
2021-10-31 19:29:12 -04:00
2e72d6b5a5
Merge branch 'develop' into modify-fix-compute-accessors
2021-10-31 18:25:42 -04:00
bbbde3cc15
fix indexing bug
2021-10-31 18:10:32 -04:00
3887b08c1d
update new LAMMPS paper citation info
2021-10-31 18:10:32 -04:00
64764cc7b0
clarify the difference between C++ and Fortran versions of MEAM
2021-10-31 18:10:31 -04:00
4f0f791417
use new API, join loops, modernize
2021-10-31 17:37:43 -04:00
6b400fb4bf
fix indexing bug
2021-10-31 16:19:17 -04:00
c5d6a310d8
Fixed cmake build script for QUIP in cases where MATH_LINKOPTS variable not set
2021-10-29 11:32:03 +02:00
4395530756
bugfix
2021-10-28 23:38:32 -04:00
ac4f2b2a32
use updated APIs
2021-10-28 23:25:04 -04:00
212d699078
implement Domain::get_region_by_id()
2021-10-28 23:24:38 -04:00
b15c02e3cd
Merge pull request #3012 from akohlmey/reserved_data_section_keywords
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Check for reserved data section keywords - update fix processing for data files
2021-10-28 19:52:27 -04:00
ed5c0e74d4
Merge pull request #3011 from stanmoore1/kk_bug
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Revert some changes in 7960a2d
2021-10-28 19:50:27 -04:00
9ae05facb8
Updating file locations to master locations
2021-10-28 16:32:04 -07:00
440a517a5e
update fix rigid + property/atom example to avoid runtime failure
2021-10-28 17:01:12 -04:00
7dbbb9a0e6
refactor fix cmap to use current style and modernized parsing
2021-10-28 16:54:53 -04:00
adf1beea74
add mechanism to check for known data file section names
...
using this mechanism we can reject custom section names that will
conflict with existing section names and thus avoid misleading errors.
apply this also to fix property atom, where the section name is
determined by the fix ID.
in addition, allow to specify NULL as section name, which will use
the fix ID.
2021-10-28 14:23:27 -04:00
e734eb837f
Revert some changes in 7960a2d7d2
2021-10-28 08:39:17 -06:00
d982298ab2
update new LAMMPS paper citation info
2021-10-28 10:09:01 -04:00
608ad0bca0
Merge branch 'lammps:develop' into intpos
2021-10-28 09:48:17 +01:00
c8512249b7
Merge branch 'develop' into modify-fix-compute-accessors
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# Conflicts:
# src/PLUGIN/plugin.cpp
2021-10-27 21:14:05 -04:00
4a048e3f57
Merge pull request #3008 from akohlmey/next_patch_release
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Update version strings for next patch release
2021-10-27 20:19:33 -04:00
f72b532f0f
Merge pull request #3009 from rbberger/collected_small_changes
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Collected small changes
2021-10-27 19:31:22 -04:00
765fd7f763
Use correct sizeof in memset
2021-10-27 17:46:37 -04:00
95d08c6667
update all makefiles to use DYN_LIB variable from master makefile
2021-10-27 17:41:16 -04:00
18a7c15441
forward DYN_LIB variable to Makefile.mpi
2021-10-27 17:21:38 -04:00
9424571ce2
Use correct sizeof in memset
2021-10-27 17:01:03 -04:00
153e77864d
Use LAMMPS_THIRDPARTY_URL variable for EIGEN3_URL
2021-10-27 16:45:08 -04:00
4ea848b4e9
Merge pull request #3002 from akohlmey/more-clang-tidy-refactoring
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Third chunk of semi-automatic refactoring with clang-tidy
2021-10-27 16:38:28 -04:00
2e9cdfa6dc
Merge remote-tracking branch 'origin/develop' into collected_small_changes
2021-10-27 16:38:01 -04:00
51bd05bb77
Make update_downloads.sh detect new URLs and report error
2021-10-27 16:33:21 -04:00
addb087aac
Merge branch 'lammps:develop' into intpos
2021-10-27 21:29:56 +01:00
c9da75ef85
Merge pull request #2968 from yury-lysogorskiy/feature/ml-pace-multispecies
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Add multi-species support to ML-PACE package
2021-10-27 16:04:15 -04:00
a329de81bf
Update source URLs for offline compilation tool
2021-10-27 15:56:28 -04:00
ae3e6e423a
Fix loop level
2021-10-27 13:51:41 -06:00
2ca7dcb853
Use lighter construct than powint
2021-10-27 13:41:29 -06:00
28d86578a3
update version strings for next patch release
2021-10-27 15:26:58 -04:00
da3115be2c
Merge branch 'develop' into more-clang-tidy-refactoring
...
# Conflicts:
# src/MANIFOLD/manifold_thylakoid.cpp
2021-10-27 15:23:57 -04:00
2d52821cf5
Update from develop
2021-10-27 13:14:29 -06:00
bd053d6841
Merge pull request #3004 from akohlmey/collected_small_changes
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Collected small changes and bugfixes for the next patch release
2021-10-27 14:24:37 -04:00
b5e3d69c82
change downloaded archive name to more closely follow the confvention
2021-10-27 14:23:53 -04:00
c0c45be357
bugfix Fedora CMake compilation
2021-10-27 17:19:18 +02:00
9895d8436a
update/clean downloading the ML-PACE/v.2021.10.25.tar.gz
2021-10-27 16:03:44 +02:00
a063209b2b
update URL and filename for offline scripts
2021-10-27 08:31:36 -04:00
c911cd52bb
whitespace
2021-10-27 08:24:07 -04:00
11ee3759df
use consistent formatting
2021-10-27 08:22:18 -04:00
4957c8e382
Merge branch 'develop' into collected_small_changes
2021-10-27 08:20:19 -04:00
cc3349728b
Merge pull request #2997 from stanmoore1/kk_omp_target
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Add preliminary support for Kokkos OpenMPTarget backend
2021-10-27 08:15:45 -04:00
45359847f2
Merge pull request #3007 from masterleinad/avoid_retrict_icpx
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Don't use -restrict for icpx
2021-10-27 08:10:09 -04:00
1247f4d67b
add function to print information about available compressions tools
2021-10-26 20:00:55 -04:00
f0318fb874
try to make changing LMP_INC settings less confusing to inexperienced people
2021-10-26 19:16:13 -04:00
3376f3daa8
Remove unused import
2021-10-26 16:48:57 -04:00
008013ddfb
Explicitly check for None
2021-10-26 15:19:46 -04:00
fe9dfc6095
follow Python style guidelines
2021-10-26 14:17:31 -04:00
3d9e4638a7
Don't use -restrict for icpx
2021-10-26 13:08:03 -04:00
3044923cbf
less ambiguous tests for arguments being not None
2021-10-26 12:12:21 -04:00
f783958e39
add test for create_atoms()
2021-10-26 12:11:28 -04:00
20fec49635
Intpos ( #8 )
...
* use the term 'website' consistently (and not also 'web site')
* update for clang-format
* clarify
* split off the programming/submission style guide to a separate file
* Updates to support ROCm 4.3 in GPU package
* update and reorder the description of the process for submitting contributions
* correct and clarify Python compatibility
* refactor style guide and integrate text from issue
* update contribution guidelines for github
* mention when testing may be added
* integrate file with description of include file conventions
* update github workflow doc
* adapt section about domain decomposition from paper
* use a more compact image
* add communication section
* update man page with missing flags and correct URLs
* improve the load imbalance viz
* add section about neighbor list construction
* break large file into multiple smaller files by section and add toctree
* fix typo
* add section about parallelization in the OPENMP package
* add -skipruin to help message
* add discussion of OpenMP parallelization
* spelling
* add section on PPPM
* use larger version of FFT grid comm image
* minor tweak
* Update compute angle doc page
* Update Singularity definitions to use ROCm 4.3
* Update CUDA container definitions to CUDA 11.4
* Update container definitions to include PLUMED 2.7.2
* Update more definition files
* RHEL8/CentOS8 PowerTools is now powertools
* Add Rocky Linux 8 container definition
* Add omega field to numpy_wrapper detection
* Return None in case of null pointer
* Add more atom fields in numpy_wrapper and correct csforce size
* must not clear force array. will segfault in hybrid atom styles
* update example for dynamically loading LAMMPS with current library API
* update example to use current library interface. No need to use the namespace.
* add note to README files about age of the example
* simplify building shared libs on windows
* detect a few more compilers
* Revert "simplify building shared libs on windows"
This reverts commit fa3429ab02https://matsci.org/t/confusion-about-mixing-and-pair-coeff-section/38317/3
* spelling
* use nullptr
* use symbolic constant
* small optimization
* use cmath header instead of math.h
* use explicit scoping when virtual dispatch is not available.
* cosmetic changes
* simplify/optimize code
* simplify
* Bugfix from Trung for crashes in pppm/gpu without local atoms
* fix typo
* refer to "XXX Coeffs" sections consistently
* small tweaks from static code analysis
* fix small bug
* small tweaks
* simplify and modernize code a little
* use correct data type for MPI calls
* simplify/modernize
* remove dead code
* about 1.5x speedup for pair style comb3 by using MathSpecial::powint()
* small performance optimization for pair style comb
* simplify
* modernize
* simplify
* removed dead code, reformat
* modernize
* use explicit scoping when virtual dispatch is not (yet) available
* reformat for increased readability
* move misplaced #endif and make code more readable
* make sure err_flag is initialized
* modernize
* remove redundant code: all struct members are initialized to defaults in the constructor
* enforce initialization and thus silence compiler warnings
* fix typo
* provide more comprehensive suggestions for GPU neighbor list errors
* add utils::logical() function to complement the *numeric() functions
* Add stable link in docs
* revert modernization change (for now)
* remove unused variable
* include EXTRA-DUMP in "most"
* small tweaks
* simplify
* Add log file printing of KIM search directories in 'kim init'
* use clang-format on kim_init.cpp
* Improve style in response to Axel's suggestions
* initialize all members
* format changes
* simplify. use utils::strdup() more.
* small corrections
* apply fix from balance command to fix balance
* dead code removal
* reformat strings
* implement utils::current_date() convenience function to reduce replicated code
* update list and order of include files from include-what-you-use analysis
* handle changes in GAP repo
* a few remaining updates to include statements
* expand mapping to handle "style_*.h" header files correctly.
* add support for compilation of OpenCL loader on FreeBSD
* more iwyu header updates
* small correction
* fix typo
* a few more (final?) IWYU updates
* expand tests for numeric values
* return int instead of bool to minimize code changes
* fix spelling issues
* some applications of the new function
* fix typo
* Change "offsite" to "external" to correct broken URLs to lammps.org
* improve error message
* insert missing atom-ID
* convert yes/no on/off flags in the package command(s)
* update version strings
* update death tests for change in error message
* correctly specify the destructor function name.
* apply utils::logical() to more commands
* apply utils::logical() in more places
* for consistency with utils::logical()
* only accept lower case to be consistent with the rest of the input
* a few more converted commands and updates for unit tests
* modernize and fix some memory leaks
* adjust for compatibility with C++20 compilers
* do not downgrade C++ standard when adding the KOKKOS package
* undo "risky" C++20 related changes
* mention how to set the path to the fftw3_omp library
* correct paths to downloaded PACE package sources in lib
* Update CMake variable descriptions
* possible workaround for some GPU package neighbor list issue
* final chunk of changes to apply utils::logical()
* update suffix command unit tests
* update citation info with new LAMMPS paper reference and acknowledge it
* update some formulations as suggested by @sjplimp
* add check and suitable error message when fp64 is required but not available
* do not call memset on a null pointer
* fix string formatting bugs in fix npt/cauchy
* must use a soft core potential to avoid a singularity
* in floating point math a*b may be zero even if both a>0 and b>0
* use proper integer type for atom IDs
* Building voro++ lib as part of LAMMPS requires the "patch" program
* silence output from hwloc when launching LAMMPS
* detect double precision support according to OpenCL specs (1.2 and later)
* Fix bug in Kokkos pair_eam_alloy
* calling fwrite() with a null pointer causes undefined behavior. avoid it.
* cosmetic
* apply current include file conventions
* include zstd libs in windows build
* update .gitignore for recent additions
* make check more obvious
* step version strings for stable release
* Adjust for kim-api bug
* cleaner variant of version check, add directory numbering
* hbond comm added for rsq_hb
* rsq_hb removed, exyz added (no MPI comm yet)
* 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.
* add -std=c++11 to a number of machine makefiles for traditional make build
* copy request to mention lammps.org form home page instructions for citing
* be more specific about what the name of the LAMMPS executable can be
also provide a few more examples without a machine suffix
* small tweak
* remove references to USER packages, have package lists alphabetically sorted
"make package-update" or "make pu" must be processed in the special order
because of inter-package dependencies
* make "make package-update" and "make package-overwrite" less verbose
* freeze versions of pip packages for processing the manual of the stable version
this way we avoid surprises in case one of the packages get updated
to an incompatible new version. these are know-to-work versions.
* make sure the one_coeff flag is applied to sub-styles
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.
* Prevent neigh list from copying "unique" stencil/bin
* compiling ML-HDNNP with downloaded n2p2 lib requires the sed command
* detect and error out if BLAS/LAPACK libraries variables are a list
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()
* portability improvement
* must have patch command available to compile ScaFaCoS
* only need Tcl not Tk to compile Tcl swig wrapper
* correctly handle Tcl stub library if available
* add missing keyword
* hbond_pos added, MPI and values ok, Pair time slow.
* make C library example work with strict C compilers
* silence compiler warnings
* make Nevery keyword per-reaction
* recover cross-compilation with mingw64
* reverted wrong approach from last commits
- now intpos flag
- hbond_pos added
- (a/b)xyz WiP
* lrefpos working in serial, MPI wrong
* attempt to merge doubles into n(xyz)[3]
* save
* Update pair_oxdna_hbond.cpp
* hbond now working for MPI, comming lrefpos
* extracting nxyz in excv/bond working
Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com >
Co-authored-by: Richard Berger <richard.berger@temple.edu >
Co-authored-by: Ryan S. Elliott <relliott@umn.edu >
Co-authored-by: Stan Gerald Moore <stamoor@sandia.gov >
Co-authored-by: Giacomo Fiorin <giacomo.fiorin@gmail.com >
Co-authored-by: Jacob Gissinger <jrgiss05@gmail.com >
Co-authored-by: Oliver Henrich <ohenrich@users.noreply.github.com >
2021-10-26 16:45:44 +01:00
2a9a8adfc0
apply clang-format
2021-10-26 06:41:00 -04:00
886d6702c4
remove dead code
2021-10-26 06:38:47 -04:00
5141a80142
remove useless logical
2021-10-26 06:38:35 -04:00
30001f2698
use preprocessor
2021-10-26 06:37:59 -04:00
4551bf4bc0
yaml-cpp-pace: bugfix in CMakeLists.txt
2021-10-26 10:19:11 +02:00
8bf016eaef
use references when looping over fixes from list
2021-10-25 21:41:57 -04:00
52d99700ec
Download and compile modified YAML-cpp 0.6.3 in namespace YAML_PACE
2021-10-25 17:34:08 +02:00
d0416757b7
simplify using new APIs
2021-10-24 18:00:15 -04:00
a782f8f8e0
more specific warning about atoms inability to move
2021-10-24 17:59:30 -04:00
29a44e7065
remove parser_error exception class ambiguity completely
2021-10-23 04:25:20 -04:00
71a24580b8
remove parser_error exception class ambiguity completely
2021-10-23 04:24:54 -04:00
8a9117d511
add configurations for intel compilers
2021-10-22 16:32:16 -04:00
6f14cbf167
Small adjustments for compiling within VS
2021-10-22 16:32:02 -04:00
7abcdc8c4c
use anonymous namespace to manage visibility of multiple copies of parse_error class
2021-10-22 16:16:08 -04:00
47eab736bb
use anonymous namespace to manage visibility of multiple copies of parse_error class
2021-10-22 16:14:06 -04:00
c08093f768
modernize, avoid static buffers, use utility functions, remove debug code
2021-10-22 16:00:01 -04:00
7960a2d7d2
Fix link error with fix_acks2_reaxff_kokkos
2021-10-22 19:13:31 +00:00
b6c610ada2
tweak epsilon for portability to MSVC compilers
2021-10-22 14:12:19 -04:00
89808266dd
remove obsolete file
2021-10-22 13:46:13 -04:00
4edd5238b1
improve putenv() and unsetenv() implementation on windows by using _putenv_s()
2021-10-22 13:21:45 -04:00
0901540fda
Remove deprecated Kokkos code
2021-10-22 16:41:26 +00:00
3cce6b46e2
Fix thread divergence issue when not using CUDA/HIP
2021-10-22 16:20:37 +00:00
7318aa49d8
set define for static linkage to avoid issues linking libyaml on windows
2021-10-22 12:12:20 -04:00
614b751f5f
Add missing brace
2021-10-22 16:09:46 +00:00
228187978d
Merge branch 'develop' of https://github.com/lammps/lammps into kk_omp_target
2021-10-22 16:08:00 +00:00
5c9a4f4be0
implement platform abstraction of unsetenv()
2021-10-22 11:05:32 -04:00
69f5e1feac
Enable testing for Debug configurations in VS
2021-10-22 09:25:44 -05:00
bd9ad288b9
recover compilation of test on windows
2021-10-22 09:13:07 -05:00
d7d1c84b35
only build a custom YAML lib, if not installed
2021-10-22 08:56:00 -04:00
ced96441ef
update hash after change in repo
2021-10-22 08:44:30 -04:00
ad81dd3960
recover original new style library target names through ALIAS library definitions
2021-10-22 08:23:49 -04:00
b57c8bda51
build yaml library using custom CMakeLists.txt file
2021-10-21 23:39:56 -04:00
8d6461ffcd
whitespace
2021-10-21 23:39:14 -04:00
a796d6b824
fix logic bug
2021-10-21 21:04:15 -04:00
7cc5092547
make portable to MSVC++
2021-10-21 21:01:59 -04:00
7d16078cf4
always use .so suffix for plugins
2021-10-21 19:35:48 -04:00
3869e3fce8
adjust for compiling on windows
2021-10-21 19:27:59 -04:00
6ad03498c3
make finding plugins for testing multi-config compatible
2021-10-21 19:22:01 -04:00
e75757007e
always compile position independent code
2021-10-21 19:21:34 -04:00
6e3fcce9e1
move download and extract code into function
2021-10-21 17:35:49 -04:00
d8db9dd3ac
Merge branch 'develop' into multi-config-support
...
# Conflicts:
# cmake/Modules/GTest.cmake
2021-10-21 10:26:31 -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
ede188652b
update a few GPU kernels so they can be compiled on GPUs without double precisions support
2021-10-21 07:33:00 -04:00
a0b25acf35
refactor loops using (auto var : container) syntax
2021-10-20 21:58:31 -04:00
647380a357
Avoid bitshift that gave incorrect results on GPU
2021-10-20 13:21:07 -06:00
85433e8bd1
use true/false instead of 1/0 detected and changed by clang-tidy
2021-10-20 12:41:02 -04:00
682f862f43
apply clang-format
2021-10-20 06:56:54 -04:00
2e362b1f3f
use get_(fix|compute)_by_id() instead of find_(fix|compute)()
2021-10-20 06:56:46 -04:00
8cd4460c62
fix typo
2021-10-19 15:50:19 -04:00
89d70aeabf
work around issue with skipping creation of fix RESPA for whichflag == 0
2021-10-19 15:50:09 -04:00
2857577dda
replace find_region_by_style() with get_region_by_style() with same semantics as find_fix_by_style()
2021-10-19 12:38:00 -04:00
597ee207b1
remove now obsolete find_fix_by_style() and find_compute_by_style() members
2021-10-19 12:37:02 -04:00
3ae0aae018
update remaining uses of find_fix_by_style()
2021-10-19 12:36:31 -04:00
162789ad7f
Merge branch 'develop' into modify-fix-compute-accessors
2021-10-19 12:00:43 -04:00
84666543d1
Merge pull request #2998 from akohlmey/collected_small_changes
...
Collected small changes and bugfixes
2021-10-19 10:33:51 -04:00
2dce8923ee
more direct version of clearing out loaded plugins
2021-10-19 08:28:19 -04:00
1cd0551197
more direct version of clearing out loaded plugins
2021-10-19 08:27:49 -04:00
81a5beb8cc
must not have folders names differing only in case: "MC" versu "mc"
...
This is causing problems on MacOS and Windows with case preserving
but case insensitive file systems.
2021-10-18 18:13:21 -04:00
8d1ba074be
wipe out all loaded plugins before destroying the LAMMPS instance
2021-10-18 18:06:09 -04:00
f9e99f1f4c
wipe out all loaded plugins before destroying the LAMMPS instance
2021-10-18 18:04:04 -04:00
241c816ad3
adapt fix shake and pair style spin
2021-10-18 17:29:25 -04:00
0e369fb9b5
update example to represent recent style changes.
2021-10-18 13:47:29 -04:00
4675a3b560
Only check for GPU double precision support if a GPU is present
2021-10-18 13:44:37 -04:00
5e102e1bfe
ML-PACE.cmake: find_package(yaml-cpp 0.6.3 EXACT QUITE) first, otherwise dowload from github/yaml-cpp tag 0.6.3
2021-10-18 18:43:38 +02:00
87b63f768f
Only check for GPU double precision support if a GPU is present
2021-10-18 12:15:05 -04:00
fc0e6af7dd
fix memory leaks
2021-10-18 07:11:55 -04:00
dd2ff737f1
port mdi/engine command to new fix accessor API
2021-10-18 06:50:28 -04:00
11a4920b30
refactor PERI package pair styles to use new accessors and to increase code sharing
2021-10-18 06:47:01 -04:00
f6fb392c4d
convert some more styles to use the new APIs
2021-10-17 19:19:23 -04:00
26b368848b
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 18:06:29 -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
1e9da5a25b
port dump vtk to correctly support custom per-atom arrays and fix some bugs
2021-10-17 10:58:33 -04:00
6145ef9cd2
fix bugs related to custom per-atom properties in dump style custom
2021-10-17 10:57:16 -04:00
702d861a58
update to use new accessor APIs
2021-10-16 22:31:23 -04:00
064e7fde2f
must not dereference null pointer
2021-10-16 22:30:38 -04:00
f392b089a4
modernize
2021-10-16 21:40:17 -04:00
cfdf9cee5d
modernize
2021-10-16 21:28:18 -04:00
e990a1cf61
remove ambiguity between "double_precision" class member variable and function
2021-10-16 21:07:04 -04:00
8cf030e476
small tweak for mixed precision GPU runs
2021-10-16 07:28:16 -04:00
59d79ce176
update googletest to version 1.11
2021-10-16 07:16:40 -04:00
5b40e4cb38
new accessor APIs for fixes and computes in Modify plus a few applications
2021-10-16 06:00:28 -04:00
ab30ed4ca9
modernize
2021-10-16 05:35:24 -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
83e58eadb7
correct expansion of fix/compute/variable arguments to avoid bogus thermo outpu
2021-10-15 20:23:31 -04:00
6827f71f26
pppm kspace styles also require -DFFT_SINGLE when using GPUs in single precision
2021-10-15 20:23:07 -04:00
47523da16b
allow single precision FFT introspection
2021-10-15 20:03:39 -04:00
222063e5cf
Add preliminary support for Kokkos OpenMPTarget backend
2021-10-15 17:32:37 -06:00
20cd742b4a
whitespace & urls
2021-10-15 15:59:15 -06:00
fa412c13aa
Add compute phase/atom
2021-10-15 15:43:26 -06:00
5f3bf69e30
plug memory leaks
2021-10-15 17:00:46 -04:00
5140d26748
plug memory leaks
2021-10-15 16:59:53 -04:00
01d96fc684
Whitespace
2021-10-15 12:50:46 -06:00
d97e55d54a
Precompute some sqrt factors
2021-10-15 11:53:54 -06:00
23cd143aae
Merge branch 'master' of github.com:lammps/lammps into coo_opt
2021-10-15 10:54:16 -06:00
98cdfa1016
fix bug detected by coverity scan
2021-10-15 09:29:47 -04:00
ef04f6ca69
Merge pull request #2993 from akohlmey/collected_small_changes
...
Collected small changes and fixes
2021-10-14 15:32:42 -04:00
5a90bca49e
Merge pull request #2994 from akohlmey/more-clang-tidy-refactor
...
Second chunk of semi-automatic refactoring with clang-tidy
2021-10-14 13:33:00 -04:00
64268de24b
Merge branch 'master' into collected-small-changes
2021-10-14 13:31:30 -04:00
356dbab587
Merge pull request #2991 from mphowardlab/bugfix-brownian
...
Fix Brownian noise scale factor
2021-10-14 12:23:04 -04:00
cd526ad54c
try to find system libyaml-cpp v.0.6.3 library, otherwise use downloaded one
2021-10-14 15:16:48 +02:00
267bc7ae2d
avoid (unlikely) integer overflows with very large systems
2021-10-14 08:07:43 -04:00
d857685e74
use emplace_back() instead of push_back()
2021-10-14 01:31:48 -04:00
2106075320
use call-by-value with std::move() function
2021-10-14 01:30:18 -04:00
e56cc9be00
use initializer list instead of explicit constructor
2021-10-14 01:12:44 -04:00
27145d2789
catch up on refactoring default destructors that were missed previously
2021-10-14 01:12:04 -04:00
3ad75c40ec
catch up on previous clang-tidy refactor for files that were skipped before
2021-10-13 23:59:43 -04:00
2fba6b44e4
use '= default' when default functions should be used
2021-10-13 23:59:05 -04:00
34d54247b6
Merge branch 'develop' into collected_small_changes
2021-10-13 22:55:21 -04:00
cc416b97f0
Merge pull request #2990 from akohlmey/clang-tidy-refactor
...
First chunk of semi-automated refactoring using clang-tidy
2021-10-13 22:51:25 -04:00
3f3d44bc25
add new files
2021-10-13 22:47:37 -04:00
a1572ce9a5
link with -ldl except on Windows for dlopen/dlclose/dlsym support
2021-10-13 22:47:25 -04:00
f4851e9103
change check for reset image flags to print messages only once per data file
2021-10-13 21:54:18 -04:00
a1fb6902d5
Merge pull request #2992 from lammps/molswap
...
Add a new fix mol/swap command
2021-10-13 21:33:52 -04:00
afad3f42d5
Report only compatible GPU, i.e. no GPU if mixed/double precision is requested by the hardware does not support it
2021-10-13 21:15:16 -04:00
c322064ff3
Merge pull request #2931 from stanmoore1/acks2_release
...
Add ACKS2 charge equilibration method to REAXFF and support for electric fields in qeq/reaxff
2021-10-13 20:27:57 -04:00
c5617dc006
fix spelling and make consistent
2021-10-13 19:25:09 -04:00
660bced187
whitespace, pointer initializer, and permission fixes
2021-10-13 19:17:42 -04:00
69a3b5b215
move common init() code into base class. warn when used with fix efield
2021-10-13 18:54:10 -04:00
a922c91c1a
document restrictions to using ReaxFF charge equilibration with fix efield
2021-10-13 18:53:09 -04:00
06ef216e61
protect against using multiple fix efield instances. improve error messages.
2021-10-13 18:26:09 -04:00
c8dc6c5010
whitespace
2021-10-13 18:25:13 -04:00
547b9850b9
tiny optimization
2021-10-13 18:18:58 -04:00
56ce880b32
update force-style test data with corrected efield strength computation
2021-10-13 18:06:49 -04:00
f206eab338
mv examples/gcmc to mc, add 2 scripts for fix mol/swap
2021-10-13 15:02:33 -06:00
74219585f3
Update log files
2021-10-13 14:03:50 -06:00
5f7e56e1c2
Fix Brownian noise scale factor
2021-10-13 14:51:58 -05:00
9cfb822847
Merge branch 'master' of github.com:lammps/lammps into acks2_release
2021-10-13 13:37:04 -06:00
727a028a6f
Add inputs with field
2021-10-13 13:08:08 -06:00
67673a6055
Fix negative sign in chi_field
2021-10-13 12:30:19 -06:00
552d960b39
Fix double space
2021-10-13 10:43:26 -06:00
87cc67778b
Merge branch 'master' into feature/ml-pace-multispecies
...
# Conflicts:
# src/ML-PACE/pair_pace.cpp
2021-10-13 17:34:29 +02:00
ac8cf33a51
Merge pull request #1 from srmnitc/master
...
Use only itype for scale variable in both forces and energy
2021-10-13 16:53:49 +02:00
1f9ce77c85
Use only itype for scale variable in both forces and energy
2021-10-13 16:34:33 +02:00
d207710b43
lrefpos (nx/y/z) now working in oxdna_hbond. Being comm'ed and MPI working ( #7 )
...
* use the term 'website' consistently (and not also 'web site')
* update for clang-format
* clarify
* split off the programming/submission style guide to a separate file
* Updates to support ROCm 4.3 in GPU package
* update and reorder the description of the process for submitting contributions
* correct and clarify Python compatibility
* refactor style guide and integrate text from issue
* update contribution guidelines for github
* mention when testing may be added
* integrate file with description of include file conventions
* update github workflow doc
* adapt section about domain decomposition from paper
* use a more compact image
* add communication section
* update man page with missing flags and correct URLs
* improve the load imbalance viz
* add section about neighbor list construction
* break large file into multiple smaller files by section and add toctree
* fix typo
* add section about parallelization in the OPENMP package
* add -skipruin to help message
* add discussion of OpenMP parallelization
* spelling
* add section on PPPM
* use larger version of FFT grid comm image
* minor tweak
* Update compute angle doc page
* Update Singularity definitions to use ROCm 4.3
* Update CUDA container definitions to CUDA 11.4
* Update container definitions to include PLUMED 2.7.2
* Update more definition files
* RHEL8/CentOS8 PowerTools is now powertools
* Add Rocky Linux 8 container definition
* Add omega field to numpy_wrapper detection
* Return None in case of null pointer
* Add more atom fields in numpy_wrapper and correct csforce size
* must not clear force array. will segfault in hybrid atom styles
* update example for dynamically loading LAMMPS with current library API
* update example to use current library interface. No need to use the namespace.
* add note to README files about age of the example
* simplify building shared libs on windows
* detect a few more compilers
* Revert "simplify building shared libs on windows"
This reverts commit fa3429ab02https://matsci.org/t/confusion-about-mixing-and-pair-coeff-section/38317/3
* spelling
* use nullptr
* use symbolic constant
* small optimization
* use cmath header instead of math.h
* use explicit scoping when virtual dispatch is not available.
* cosmetic changes
* simplify/optimize code
* simplify
* Bugfix from Trung for crashes in pppm/gpu without local atoms
* fix typo
* refer to "XXX Coeffs" sections consistently
* small tweaks from static code analysis
* fix small bug
* small tweaks
* simplify and modernize code a little
* use correct data type for MPI calls
* simplify/modernize
* remove dead code
* about 1.5x speedup for pair style comb3 by using MathSpecial::powint()
* small performance optimization for pair style comb
* simplify
* modernize
* simplify
* removed dead code, reformat
* modernize
* use explicit scoping when virtual dispatch is not (yet) available
* reformat for increased readability
* move misplaced #endif and make code more readable
* make sure err_flag is initialized
* modernize
* remove redundant code: all struct members are initialized to defaults in the constructor
* enforce initialization and thus silence compiler warnings
* fix typo
* provide more comprehensive suggestions for GPU neighbor list errors
* add utils::logical() function to complement the *numeric() functions
* Add stable link in docs
* revert modernization change (for now)
* remove unused variable
* include EXTRA-DUMP in "most"
* small tweaks
* simplify
* Add log file printing of KIM search directories in 'kim init'
* use clang-format on kim_init.cpp
* Improve style in response to Axel's suggestions
* initialize all members
* format changes
* simplify. use utils::strdup() more.
* small corrections
* apply fix from balance command to fix balance
* dead code removal
* reformat strings
* implement utils::current_date() convenience function to reduce replicated code
* update list and order of include files from include-what-you-use analysis
* handle changes in GAP repo
* a few remaining updates to include statements
* expand mapping to handle "style_*.h" header files correctly.
* add support for compilation of OpenCL loader on FreeBSD
* more iwyu header updates
* small correction
* fix typo
* a few more (final?) IWYU updates
* expand tests for numeric values
* return int instead of bool to minimize code changes
* fix spelling issues
* some applications of the new function
* fix typo
* Change "offsite" to "external" to correct broken URLs to lammps.org
* improve error message
* insert missing atom-ID
* convert yes/no on/off flags in the package command(s)
* update version strings
* update death tests for change in error message
* correctly specify the destructor function name.
* apply utils::logical() to more commands
* apply utils::logical() in more places
* for consistency with utils::logical()
* only accept lower case to be consistent with the rest of the input
* a few more converted commands and updates for unit tests
* modernize and fix some memory leaks
* adjust for compatibility with C++20 compilers
* do not downgrade C++ standard when adding the KOKKOS package
* undo "risky" C++20 related changes
* mention how to set the path to the fftw3_omp library
* correct paths to downloaded PACE package sources in lib
* Update CMake variable descriptions
* possible workaround for some GPU package neighbor list issue
* final chunk of changes to apply utils::logical()
* update suffix command unit tests
* update citation info with new LAMMPS paper reference and acknowledge it
* update some formulations as suggested by @sjplimp
* add check and suitable error message when fp64 is required but not available
* do not call memset on a null pointer
* fix string formatting bugs in fix npt/cauchy
* must use a soft core potential to avoid a singularity
* in floating point math a*b may be zero even if both a>0 and b>0
* use proper integer type for atom IDs
* Building voro++ lib as part of LAMMPS requires the "patch" program
* silence output from hwloc when launching LAMMPS
* detect double precision support according to OpenCL specs (1.2 and later)
* Fix bug in Kokkos pair_eam_alloy
* calling fwrite() with a null pointer causes undefined behavior. avoid it.
* cosmetic
* apply current include file conventions
* include zstd libs in windows build
* update .gitignore for recent additions
* make check more obvious
* step version strings for stable release
* Adjust for kim-api bug
* cleaner variant of version check, add directory numbering
* hbond comm added for rsq_hb
* rsq_hb removed, exyz added (no MPI comm yet)
* 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.
* add -std=c++11 to a number of machine makefiles for traditional make build
* copy request to mention lammps.org form home page instructions for citing
* be more specific about what the name of the LAMMPS executable can be
also provide a few more examples without a machine suffix
* small tweak
* remove references to USER packages, have package lists alphabetically sorted
"make package-update" or "make pu" must be processed in the special order
because of inter-package dependencies
* make "make package-update" and "make package-overwrite" less verbose
* freeze versions of pip packages for processing the manual of the stable version
this way we avoid surprises in case one of the packages get updated
to an incompatible new version. these are know-to-work versions.
* make sure the one_coeff flag is applied to sub-styles
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.
* Prevent neigh list from copying "unique" stencil/bin
* compiling ML-HDNNP with downloaded n2p2 lib requires the sed command
* detect and error out if BLAS/LAPACK libraries variables are a list
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()
* portability improvement
* must have patch command available to compile ScaFaCoS
* only need Tcl not Tk to compile Tcl swig wrapper
* correctly handle Tcl stub library if available
* add missing keyword
* hbond_pos added, MPI and values ok, Pair time slow.
* make C library example work with strict C compilers
* silence compiler warnings
* make Nevery keyword per-reaction
* recover cross-compilation with mingw64
* reverted wrong approach from last commits
- now intpos flag
- hbond_pos added
- (a/b)xyz WiP
* lrefpos working in serial, MPI wrong
* attempt to merge doubles into n(xyz)[3]
* save
* Update pair_oxdna_hbond.cpp
* hbond now working for MPI, comming lrefpos
Co-authored-by: Axel Kohlmeyer <akohlmey@gmail.com >
Co-authored-by: Richard Berger <richard.berger@temple.edu >
Co-authored-by: Ryan S. Elliott <relliott@umn.edu >
Co-authored-by: Stan Gerald Moore <stamoor@sandia.gov >
Co-authored-by: Giacomo Fiorin <giacomo.fiorin@gmail.com >
Co-authored-by: Jacob Gissinger <jrgiss05@gmail.com >
2021-10-13 10:47:41 +01:00
165708adeb
use nullptr in unittest tree
2021-10-12 22:52:50 -04:00
643a7a1acb
replace std::random_shuffle() with std::shuffle() to be compatible with C++17 and beyond
2021-10-12 22:39:30 -04:00
88631372ec
use nullptr instead of NULL or 0 where applicable
2021-10-12 21:47:02 -04:00
dd6f49a753
use 'noexcept' instead of the deprecated 'throw()'
2021-10-12 21:29:33 -04:00
7b6a3c4307
remove redundant void arguments
2021-10-12 21:17:46 -04:00
1002763df3
remove default class members except for the assignment copy constructor
2021-10-12 21:17:00 -04:00
1d1573c5f2
Merge branch 'develop' into multi-config-support
2021-10-12 14:42:32 -04:00
26cd988672
Merge pull request #2989 from rbberger/unittest_bugfixes
...
Avoid file name collisions in dump unit tests
2021-10-12 14:41:25 -04:00
a8f42bd534
tweak to atom/swap doc page
2021-10-12 11:50:04 -06:00
c22dae8d2c
add a new fix
2021-10-12 11:48:26 -06:00
113c53a5da
doc page for new fix mol/swap
2021-10-12 11:45:50 -06:00
0bc6373386
Merge pull request #2983 from akohlmey/collected-small-changes
...
Collected small changes and bugfixes
2021-10-12 13:26:50 -04:00
77d830bf3a
update YAML-CPP library target name to yaml-cpp-pace
2021-10-12 18:15:31 +02:00
a1ff9e35b7
Avoid file name collisions in dump unit tests
2021-10-12 12:15:19 -04:00
0a98ff3c38
add more features to mol/swap, sync with atom/swap
2021-10-12 09:56:51 -06:00
93d6e6dec9
update for new way of using googletest
2021-10-12 11:46:37 -04:00
17316f92c7
Add optimized version of compute_orientorder_atom from Tomas Oppelstrup (LLNL)
2021-10-12 07:50:05 -07:00
2651e4650f
use the new name of the main branch
2021-10-11 23:23:24 -04:00
9cf6b927cb
Merge branch 'master' into collected-small-changes
...
# Conflicts:
# src/REAXFF/fix_reaxff_species.cpp
2021-10-11 21:24:11 -04:00
96a45224de
whitespace
2021-10-11 21:10:14 -04:00
27c9ba465b
avoid duplication of Accelerator package info in additional doc pages
2021-10-11 16:49:59 -06:00
eedd953258
remove debug logic
2021-10-11 16:20:19 -06:00
cb77555fa6
update title in reference to accelerator section
2021-10-11 17:26:24 -04:00
510987dc80
Merge branch 'master' into multi-config-support
...
# Conflicts:
# cmake/Modules/Packages/MSCG.cmake
# examples/plugins/CMakeLists.txt
2021-10-11 17:03:41 -04:00
7bed85ef19
add debug statements
2021-10-11 15:00:20 -06:00
e79930dfb9
add check to prohibit using fix efield component in periodic direction with reaxff
2021-10-11 16:48:38 -04:00
4faca6531a
fix typo
2021-10-11 16:35:54 -04:00
a45dbb6510
no need for static string buffers anymore
2021-10-11 16:35:42 -04:00
1f4c50037b
Merge branch 'master' into acks2_release
2021-10-11 16:13:20 -04:00
a6cde11896
Merge pull request #2985 from stanmoore1/kk_issues
...
Fix issues with Kokkos package
2021-10-11 15:27:58 -04:00
2290ade2f2
ensure that fix efield is initialized before accessing its data.
2021-10-11 15:06:24 -04:00
6d2b32f0b2
move chi field calculation to fix qeq/reaxff
2021-10-11 14:35:23 -04:00
2ea4c71125
Merge pull request #2979 from akohlmey/platform-namespace
...
Implement a "platform" sub-namespace with platform specific functions and wrappers
2021-10-11 13:41:15 -04:00
70cbb72e42
Merge branch 'master' into acks2_release
2021-10-11 09:58:44 -04:00
a3e59082bf
small adjustments and apply clang-format
2021-10-11 08:13:44 -04:00
124f7760d8
Merge branch 'master' into feature/ml-pace-multispecies
2021-10-11 07:30:22 -04:00
0c57267a85
update branch names
2021-10-10 04:44:45 -04:00
eb6b73c752
update documentation to refer to the new branch names (develop, release)
2021-10-10 04:39:16 -04:00
54e2e58aec
update fmtlib to version 8.0.1
2021-10-09 23:57:35 -04:00
cf4e671474
Merge branch 'master' into fmt_upgrade
2021-10-09 23:42:17 -04:00
64b27fa28e
only run windows compilation action on master branch in lammps repo
2021-10-09 20:54:18 -04:00
1bbed2579b
try alternate approach to make MSVC++ happy linking STUBS
2021-10-09 20:32:39 -04:00
c3629b5f01
MS VC++ needs to have STUBS with PUBLIC linkage
2021-10-09 20:27:47 -04:00
5ad7e5a815
correct path to preset file and do two quick runs for checking the binary
2021-10-09 19:55:30 -04:00
2e122ff62b
Add GitHub action compiling LAMMPS with Visual C++
2021-10-09 19:46:52 -04:00
f558a5c06f
update LAMMPS homepage URLs
2021-10-09 11:41:54 -04:00
5739621f5c
make single() function consistent with compute() function
2021-10-09 11:33:02 -04:00
c8c3e8f661
use predefined constant and apply optimization for power function with integer argument
2021-10-09 11:27:35 -04:00
3a4b68a464
modernize code
2021-10-09 11:18:33 -04:00
ed23a3aa69
correct comments
2021-10-09 11:18:16 -04:00
018e37a2e9
add unit tests for bond style fene/nm/split and pair style nm/cut/split
2021-10-09 11:06:18 -04:00
7bdf52eac5
do not shadow members of the BondFENE base class and use the corresponding allocation/deallocation
2021-10-09 11:00:19 -04:00
507c02b9af
must set define to "see" the lammps_open() library function
2021-10-09 10:21:31 -04:00
ba44d6aba2
must set define to "see" the lammps_open() library function
2021-10-09 10:20:47 -04:00
dd6e3c1acc
avoid variable length array and signed vs. unsigned warnings
2021-10-08 20:07:20 -04:00
241e01edba
whitespace
2021-10-08 19:00:30 -04:00
c5205be071
update src/.gitignore
2021-10-08 16:25:55 -04:00
a0fc74f1a9
make class names, include guards and formatting consistent. apply clang-format
2021-10-08 16:25:44 -04:00
3313d3bfa3
make documentation consistent and properly integrate it
2021-10-08 16:24:57 -04:00
fc42992cdf
Merge branch 'master' into nm_split_styles
2021-10-08 15:57:17 -04:00
09bcfc2116
document visual studio support
2021-10-08 15:33:49 -04:00
ae0fa17132
make consistent with include files
2021-10-08 15:33:26 -04:00
83bc70bf05
workaround for classic intel compiler on windows
2021-10-08 15:11:16 -04:00
fb137b26bf
silence compiler warnings
2021-10-08 13:59:17 -04:00
46efae5998
needed for compilation on windows. not really used because of platform::walltime()
2021-10-08 13:58:08 -04:00
6e8da80148
adjustments for intel compilers on windows
2021-10-08 13:57:09 -04:00
cc11fa37b2
whitespace
2021-10-08 11:44:09 -04:00
392ebf7db7
revise automatic seed generation
2021-10-08 11:35:55 -04:00
b7fe47ba48
Fix bugs and compilation issues in KOKKOS
2021-10-08 09:39:53 -04:00
b5061b69be
add warning to fix reaxff/species to explain the impact of large averaging
2021-10-07 20:46:01 -04:00
30c146457a
improve messages
2021-10-07 20:29:01 -04:00
4b86dbd200
add cmake configuration file for visual studio
2021-10-07 17:11:33 -04:00
e12fa57794
A few more tweaks
2021-10-07 17:11:04 -04:00
4fca127ea4
copy MSVC++ compiler hacks to plugin CMakeLists.txt file
2021-10-07 15:59:12 -04:00
d5b3ea263b
awpmd requires blas, mgpt is not portable
2021-10-07 15:45:14 -04:00
5d5cc0ac55
preset with packages that build natively on windows with visual c++
2021-10-07 15:31:26 -04:00
ef8aa4de90
silence warning
2021-10-07 15:29:46 -04:00
3a3f07d91a
use portable logic operators
2021-10-07 15:05:32 -04:00
2b27af1572
fix a few more MSVC issues and reduce warnings
2021-10-07 14:37:37 -04:00
2c7b67203a
recover unit test compile
2021-10-07 13:44:18 -04:00
0f442fddd9
correct use of utils function
2021-10-07 12:40:29 -04:00
6a9bb577cf
rename "zip" functions to "compress" functions. update related docs
2021-10-07 12:38:11 -04:00
4f17082d74
use portable logic operators
2021-10-07 12:23:17 -04:00
3661b8cd50
optimize
2021-10-07 12:22:26 -04:00
a818be585d
use portable functions from platform and utils namespaces
2021-10-07 12:22:16 -04:00
7372211d90
there is no more need to keep a copy of the arguments
...
this also eliminates buffer overflow bugs where the terminating 0 bytes
of copied strings are overwritten causing the fix to fail.
2021-10-07 07:42:13 -04:00
c8ff66e07f
correct file extension for Zstd compressed files
2021-10-07 06:49:49 -04:00
059f450f1b
add uppercase string utility function (for symmetry)
2021-10-07 00:00:33 -04:00
b8d6df6461
add missing platform scope
2021-10-06 20:44:42 -05:00
98d9b675f9
Use portable logical operators
2021-10-06 20:44:27 -05:00
5c34fe4d5d
Replace strcasecmp()
2021-10-06 20:43:56 -05:00
b3ca238a61
silence warning
2021-10-06 17:44:57 -04:00
ef84435b7c
replace non-portable strcasecmp() with comparing two strings converted to lowercase
2021-10-06 17:44:45 -04:00
a9bccee7b2
add utility to convert a string to lowercase
2021-10-06 17:43:41 -04:00
aab3e085a2
silence compiler warning on windows
2021-10-06 16:49:48 -04:00
f643c2b98f
portability changes
2021-10-06 16:34:39 -04:00
50d997526c
a few more MSVC++ tweaks for improved compatibility and fewer warnings
2021-10-06 16:18:21 -04:00
69e600c404
Misc updates and style fixes
2021-10-06 14:13:48 -06:00
4260d31b85
whitespace
2021-10-06 15:57:33 -04:00
7a1cf322e5
more tweaks for Visual C++ compilation and portability
2021-10-06 15:57:26 -04:00
6c7b42a190
small tweaks and fixes for compiling with MSVC++
2021-10-06 15:24:59 -04:00
ec1a55b35b
use platform code for reading/writing of compressed text file via a pipe
2021-10-06 15:04:48 -04:00
a539c317b3
Revert changes to makefile
2021-10-06 11:43:40 -07:00
3d86a0f5f6
Fix two bugs in compute_orientorder_atom_kokkos
2021-10-06 11:15:34 -07:00
891d4c278f
port dump movie to platform namespace
2021-10-06 14:08:45 -04:00
5059bfe32b
add Stan to Modify class as co-codeowner
2021-10-06 12:09:20 -04:00
d9288ae7e9
whitespace
2021-10-06 08:33:02 -07:00
bbfb2d2712
Add missing code to modify_kokkos
2021-10-06 08:27:25 -07:00
4aae11f8fb
port plugin loader to platform namespace
2021-10-06 08:59:56 -04:00
10a8a1b325
add dlerror() call wrapper
2021-10-06 08:59:51 -04:00
7801d112b3
enable building plugins for windows
2021-10-06 07:10:35 -04:00
9fc23a2bda
make use of platform namespace functions
2021-10-06 07:10:04 -04:00
e3cb5a5e25
restore old version of MPI_Wtime(). we're not using it anyway.
2021-10-06 07:09:36 -04:00
81492533e6
recover serial compilation
2021-10-05 23:19:52 -04:00
8b36061db4
replace MPI_Wtime() with platform::walltime()
2021-10-05 22:53:39 -04:00
f17aeebbcd
make compilable on windows
2021-10-05 22:31:39 -04:00
46eaa4888e
simplify using platform function
2021-10-05 22:31:25 -04:00
cc2d23de21
use platform::cputtime()
2021-10-05 22:31:06 -04:00
087c1b3a65
revive skipped code to detect OS revisions
2021-10-05 22:30:45 -04:00
6f2076a9b8
update docs
2021-10-05 22:11:19 -04:00
b2c4f08bbc
use C++11 functionality to determine wall time
2021-10-05 21:52:52 -04:00
fcdabe0002
implement a platform neutral usleep() using C++11
2021-10-05 17:58:27 -04:00
528050aa08
use platform namespace to delete file
2021-10-05 17:57:38 -04:00
0c6707bf0c
Fix compile issue with bond_class2_kokkos and UVM-enabled
2021-10-05 14:49:30 -06:00
e3e82df995
port "embedded" shell commands to use platform functions
2021-10-05 16:36:06 -04:00
5128eb7b43
port read/write_restart to use the platform namespace
2021-10-05 16:35:37 -04:00
af070aa351
add support for seeking to the end of a file
2021-10-05 15:44:58 -04:00
fc5920812f
new group arg for delete_atoms porosity
2021-10-05 13:07:34 -06:00
f0940104f5
first version of new fix mol/swap command
2021-10-05 11:06:32 -06:00
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
340207988c
fix a couple more bugs like in 5246cedda6
2021-10-05 10:36:25 -04:00
741cf9c7d5
remove obsoleted include statements
2021-10-05 07:36:22 -04:00
9f2c5116fa
make lammps and msi2lmp man pages use section 1
2021-10-05 07:35:26 -04:00
0bdc6d47e0
port molfile plugin reader to platform namespace
2021-10-04 22:56:23 -04:00
ee594a879b
make use of platform::putenv()
2021-10-04 22:39:43 -04:00
40f683c1a7
use platform functions to handle piping help output to a pager when on a console
2021-10-04 18:14:21 -04:00
7cdd82dee2
use platform functions for averaging fixes
2021-10-04 18:13:46 -04:00
dd2b5b22d4
fix saed/vtk does not use the overwrite option anywhere
2021-10-04 17:22:58 -04:00
485796f387
Merge branch 'master' into platform-namespace
2021-10-04 15:19:12 -04:00
ab51c1bd3d
Merge pull request #2977 from akohlmey/collected-small-changes
...
Collected small changes
2021-10-04 11:07:03 -07:00
c6a15064b3
Merge pull request #2976 from stanmoore1/update_gitignore
...
Update .gitignore file in /src
2021-10-04 10:10:23 -07:00
6e54295b38
pre-built singularity images have been removed due to lack of interest
2021-10-04 11:34:28 -04:00
9d96e10048
silence compiler warning
2021-10-04 07:32:25 -04:00
c1945b4ec9
Fix misplaced MPI calls bug in pair style drip
2021-10-04 07:12:50 -04:00
dc2453a22b
silence some compiler warnings
2021-10-04 06:56:13 -04:00
5246cedda6
Fix misplaced MPI calls bug in pair style drip
2021-10-04 06:50:38 -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
203b779622
also update eigen download for traditional build
2021-10-02 23:17:08 -04:00
3ca3f6959f
update eigen3 to the latest release and move download to our own server
2021-10-02 22:55:06 -04:00
45ea2b0431
update eigen3 to the latest release and move download to our own server
2021-10-02 22:52:03 -04:00
03f7bf6649
update eigen3 to the latest release and move download to our own server
2021-10-02 22:44:29 -04:00
c341c2c6a9
correct platform call in kim query command
2021-10-02 20:00:53 -04:00
7110e1c15e
small format tweaks
...
- brief description should not end in a dot as it becomes a title line
- add empty line to separate title from body of description
- revert order of file/path separator constants so that the Linux version shows up in doxygen
2021-10-02 18:28:33 -04:00
a6aa3fd3ee
apply clang-format
2021-10-02 18:26:46 -04:00
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
...
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
...
Clarify thermostat doc pages to mention applying the thermostat only to regions of atoms
2021-10-01 12:18:38 -04:00
f7b7bfa406
Avoid assertions in PythonCapabilities check when using external KOKKOS
2021-10-01 12:05:59 -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
...
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
3d2f29c92d
fix memory allocation bug causing memory corruption on 32-bit arches
2021-10-01 01:16:45 -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
277f7a7e51
reduce electric field strength
2021-09-30 08:29:55 -04:00
05d2002db6
add test for using fix acks2/reaxff with fix efield
2021-09-30 07:04:46 -04:00
f2755a8085
simplify
2021-09-30 00:40:30 -04:00
f6cb693d6b
whitespace
2021-09-30 00:40:15 -04:00
1840c51960
fmt::format() is no longer needed for this explicitly
2021-09-30 00:32:34 -04:00
359aa1d805
Merge branch 'master' into acks2_release
2021-09-30 00:26:25 -04:00
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
32049c3484
adopt for new multispecies PACE implementation
2021-09-29 16:04:09 +02:00
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
...
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
...
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
...
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
...
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
...
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
be3468ae07
Trying to fix style error
2021-09-27 16:31:48 -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
d69cb9e847
Changed \n to n \m to m
2021-09-27 14:54:15 -04:00
1e574b3e8a
updated pair_nm doc
2021-09-27 14:12:09 -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
6447bd822c
fixed fene_nm
2021-09-27 11:23:53 -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
b1d65f001e
Merge pull request #2949 from ellio167/kim-print-dirs
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Add log file printing of KIM search directories in 'kim init'
2021-09-26 16:34:15 -04:00
b24079fe33
cleaner variant of version check, add directory numbering
2021-09-26 11:24:03 -04:00
18a3728800
Adjust for kim-api bug
2021-09-26 08:36:02 -05:00
184e5fd779
step version strings for stable release
2021-09-25 23:04:53 -04:00
9da8c932ab
make check more obvious
2021-09-25 21:33:10 -04:00
0534d98987
update .gitignore for recent additions
2021-09-25 15:54:33 -04:00
9df8a12235
include zstd libs in windows build
2021-09-25 15:18:14 -04:00
64cfd90eeb
apply current include file conventions
2021-09-25 13:36:39 -04:00
6f87b1236a
cosmetic
2021-09-25 10:42:52 -04:00
53e773e438
calling fwrite() with a null pointer causes undefined behavior. avoid it.
2021-09-25 10:18:55 -04:00
1435a96d6e
Fix bug in Kokkos pair_eam_alloy
2021-09-25 07:20:24 -06:00
530912a930
detect double precision support according to OpenCL specs (1.2 and later)
2021-09-25 07:20:52 -04:00
24c9bd4cd2
silence output from hwloc when launching LAMMPS
2021-09-24 23:42:33 -04:00
faf9c1532a
issue with EVAL command
2021-09-24 16:26:57 -06:00
0b2a4ec4e7
Building voro++ lib as part of LAMMPS requires the "patch" program
2021-09-24 17:07:59 -04:00
85bc9911b8
use proper integer type for atom IDs
2021-09-24 16:57:06 -04:00
b3a8a7bf6f
in floating point math a*b may be zero even if both a>0 and b>0
2021-09-24 16:43:07 -04:00
4d9cef823d
must use a soft core potential to avoid a singularity
2021-09-24 16:22:44 -04:00
2df1107561
fix string formatting bugs in fix npt/cauchy
2021-09-24 15:52:01 -04:00
973cf017a9
do not call memset on a null pointer
2021-09-24 15:32:59 -04:00
93cc1ae3bb
Removed comments in fene_nm
2021-09-24 14:04:54 -04:00
5229a4e765
Removed comments in fene_nm
2021-09-24 13:41:18 -04:00
0f2bebdb9b
Adding bpm/spring pairstyle, misc small edits
2021-09-24 10:45:46 -06:00
42dca75225
add check and suitable error message when fp64 is required but not available
2021-09-24 12:17:58 -04:00
31f9f17c1b
Merge pull request #2917 from akohlmey/programmer-guide-updates
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Updates to the Programmer guide section of the manual
2021-09-24 11:27:01 -04:00
be17d775e0
more debugging
2021-09-23 15:12:07 -06:00
c855c6f0ab
rename 2 version to regular version
2021-09-23 12:55:28 -06:00
8b69b232a8
rename old version to old in filename
2021-09-23 12:48:43 -06:00
dcfdddf83f
more bug fixes for new MDI classs
2021-09-23 12:39:11 -06:00
a83797091b
Finally added Pair_nm_cut_split and bond_fene_nm_cut_split
2021-09-23 14:05:54 -04:00
46f331095a
update some formulations as suggested by @sjplimp
2021-09-23 13:51:06 -04:00
5b02f704cc
Finally added pair_nm_cut_split fene_nm_cut_split
2021-09-23 13:23:29 -04:00
16ab49cff4
update citation info with new LAMMPS paper reference and acknowledge it
2021-09-23 11:59:43 -04:00
5ef4913ebb
Merge remote-tracking branch 'github/master' into programmer-guide-updates
2021-09-23 11:16:31 -04:00
422cab8878
update suffix command unit tests
2021-09-23 07:30:50 -04:00
f641b1c659
final chunk of changes to apply utils::logical()
2021-09-23 07:30:40 -04:00
17ba0d5804
possible workaround for some GPU package neighbor list issue
2021-09-22 21:47:32 -04:00
7792a4db6b
Merge pull request #2932 from rbberger/container_updates
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Container definition updates
2021-09-22 17:37:50 -04:00
1b1b6298cd
Merge remote-tracking branch 'origin/master' into container_updates
2021-09-22 16:29:42 -04:00
f5fa892ec8
Merge pull request #2916 from rbberger/rocm_updates
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Updates to support ROCm 4.3 in GPU package
2021-09-22 16:23:19 -04:00
407f032a55
Update CMake variable descriptions
2021-09-22 15:14:39 -04:00
9906486578
correct paths to downloaded PACE package sources in lib
2021-09-22 12:40:19 -04:00
e79ae552c8
mention how to set the path to the fftw3_omp library
2021-09-22 12:23:20 -04:00
5142300b2e
undo "risky" C++20 related changes
2021-09-22 12:22:52 -04:00
d89e6f6765
do not downgrade C++ standard when adding the KOKKOS package
2021-09-21 23:52:49 -04:00
ce05ed15c1
adjust for compatibility with C++20 compilers
2021-09-21 23:52:30 -04:00
f2aacca803
modernize and fix some memory leaks
2021-09-21 22:03:38 -04:00
342ca7ff1d
add multi-config build support for MSCG package
2021-09-21 22:02:37 -04:00
914f035475
a few more converted commands and updates for unit tests
2021-09-21 17:23:41 -04:00
cbc5a2933a
tweak epsilon
2021-09-21 15:44:42 -04:00
c9a8319a93
use more relealistic element ratio
2021-09-21 15:02:45 -04:00
0ddf63acc9
update ACKS2 unit test with potential parameters from example
2021-09-21 14:41:37 -04:00
9063466c03
move ACKS2 force field file to potentials folder and add LAMMPS-style metadata
2021-09-21 14:37:37 -04:00
c3d34e8656
only accept lower case to be consistent with the rest of the input
2021-09-21 14:18:23 -04:00
6227396afd
for consistency with utils::logical()
2021-09-21 14:15:23 -04:00
1ba77e1629
apply utils::logical() in more places
2021-09-21 14:15:02 -04:00
41a3eccd1c
apply utils::logical() to more commands
2021-09-21 07:48:50 -04:00
afccf1933f
correctly specify the destructor function name.
2021-09-20 23:40:14 -04:00
fe64649e49
Merge branch 'master' into multi-config-support
2021-09-20 20:42:03 -04:00
6adac6b637
Merge branch 'master' into parse-logical-keyword
2021-09-20 20:41:48 -04:00
8d8c710982
Merge pull request #2942 from akohlmey/next_patch_release
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Step version strings for the next patch release
2021-09-20 20:35:23 -04:00
6e8091470c
update death tests for change in error message
2021-09-20 20:31:13 -04:00
18f0d2e1b5
Adding spring bondstyle
2021-09-20 18:06:10 -06:00
9a2c2b5fe3
Merge pull request #2941 from akohlmey/collected-small-changes
...
Large collection of updates and bugfixes for the stable release
2021-09-20 16:49:00 -04:00
f340e15587
update version strings
2021-09-20 16:26:47 -04:00
100da95e3a
convert yes/no on/off flags in the package command(s)
2021-09-20 16:15:24 -04:00
c39d3057dc
insert missing atom-ID
2021-09-20 16:14:18 -04:00
d79b1b3145
Tweak example and add reference logs
2021-09-20 13:01:57 -06:00
9feab449fb
Add ACKS2 example
2021-09-20 12:23:19 -06:00
b73c9280c9
improve error message
2021-09-20 13:58:48 -04:00
5ff881fb0d
Change "offsite" to "external" to correct broken URLs to lammps.org
2021-09-20 12:05:52 -04:00
22d7ce564a
fix typo
2021-09-20 07:29:10 -04:00
f80259dfae
some applications of the new function
2021-09-19 19:05:40 -04:00
860a93aa8b
fix spelling issues
2021-09-19 18:32:45 -04:00
61c71c6605
return int instead of bool to minimize code changes
2021-09-19 18:07:56 -04:00
bfa2ea1fba
expand tests for numeric values
2021-09-19 16:38:01 -04:00
f80df9ae41
a few more (final?) IWYU updates
2021-09-19 09:41:23 -04:00
4fcf343227
fix typo
2021-09-18 21:59:31 -04:00
3cab58bffe
small correction
2021-09-18 21:34:30 -04:00
12406b90a1
more iwyu header updates
2021-09-18 21:24:01 -04:00
579f08bbbc
add support for compilation of OpenCL loader on FreeBSD
2021-09-18 19:04:08 -04:00
c0a910a6c5
expand mapping to handle "style_*.h" header files correctly.
2021-09-18 16:37:06 -04:00
2b3a09ac88
a few remaining updates to include statements
2021-09-18 16:36:44 -04:00
2382d6c71d
handle changes in GAP repo
2021-09-18 16:36:18 -04:00
bca99f684f
update list and order of include files from include-what-you-use analysis
2021-09-18 14:16:48 -04:00
db76edbade
implement utils::current_date() convenience function to reduce replicated code
2021-09-18 09:05:35 -04:00
8769c0ae98
reformat strings
2021-09-17 22:58:17 -04:00
5a6c1abeed
dead code removal
2021-09-17 22:53:59 -04:00
a46b8688ea
apply fix from balance command to fix balance
2021-09-17 22:52:58 -04:00
cb2de211b2
small corrections
2021-09-17 22:52:13 -04:00
a71b77c06e
simplify. use utils::strdup() more.
2021-09-17 22:51:59 -04:00
385220fd4b
format changes
2021-09-17 22:50:15 -04:00
cd3efc3fa8
initialize all members
2021-09-17 22:45:26 -04:00
029fd56c2a
Improve style in response to Axel's suggestions
2021-09-17 20:17:45 -05:00
eb3e8e19c6
use clang-format on kim_init.cpp
2021-09-17 20:14:37 -05:00
2709e06d25
Add log file printing of KIM search directories in 'kim init'
2021-09-17 19:43:54 -05:00
ffeeb2f977
simplify
2021-09-17 19:54:55 -04:00
e6fb0e3bd8
small tweaks
2021-09-17 16:51:37 -04:00
3046c9ca93
include EXTRA-DUMP in "most"
2021-09-16 23:01:42 -04:00
dc49917412
remove unused variable
2021-09-16 22:58:42 -04:00
5bddddcd7a
revert modernization change (for now)
2021-09-16 22:57:14 -04:00
5c14825d69
Add stable link in docs
2021-09-16 18:13:41 -04:00
cef100991f
add utils::logical() function to complement the *numeric() functions
2021-09-16 17:52:51 -04:00
5bbec337e5
provide more comprehensive suggestions for GPU neighbor list errors
2021-09-16 10:23:44 -04:00
0fcc10b635
fix typo
2021-09-16 10:18:49 -04:00
e82a2a3280
enforce initialization and thus silence compiler warnings
2021-09-16 07:58:21 -04:00
75f2eb604d
remove redundant code: all struct members are initialized to defaults in the constructor
2021-09-16 07:45:33 -04:00
5411075cc6
modernize
2021-09-16 07:44:27 -04:00
90225153d9
make sure err_flag is initialized
2021-09-16 07:33:34 -04:00
00e396c921
move misplaced #endif and make code more readable
2021-09-16 07:33:24 -04:00
353b3a2bb3
reformat for increased readability
2021-09-16 07:25:04 -04:00
dc50db0675
use explicit scoping when virtual dispatch is not (yet) available
2021-09-16 01:01:38 -04:00
1fd25071b9
modernize
2021-09-16 01:01:19 -04:00
ef8a0e5005
removed dead code, reformat
2021-09-16 00:55:30 -04:00
761e519a15
simplify
2021-09-16 00:55:02 -04:00
a47df02f79
modernize
2021-09-16 00:54:46 -04:00
c83ad07740
simplify
2021-09-16 00:27:16 -04:00
2c945f6753
small performance optimization for pair style comb
2021-09-16 00:26:53 -04:00
7aa6241db5
about 1.5x speedup for pair style comb3 by using MathSpecial::powint()
2021-09-16 00:13:28 -04:00
2b6ff442d8
remove dead code
2021-09-16 00:11:53 -04:00
72193bf877
simplify/modernize
2021-09-16 00:11:44 -04:00
707d9f0ad2
use correct data type for MPI calls
2021-09-16 00:11:16 -04:00
94f83c172a
simplify and modernize code a little
2021-09-15 23:15:14 -04:00
272badfa7f
small tweaks
2021-09-15 20:14:06 -04:00
1f1029486a
fix small bug
2021-09-15 20:13:54 -04:00
7196a295a6
small tweaks from static code analysis
2021-09-15 19:50:52 -04:00
fef8f51d80
refer to "XXX Coeffs" sections consistently
2021-09-15 19:20:47 -04:00
8fa5ac28c4
Merge pull request #2939 from rbberger/python_module_fixes
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Python module fixes
2021-09-15 21:47:01 +00:00
fbd0fd7727
fix typo
2021-09-15 17:23:20 -04:00
70b09a809d
Bugfix from Trung for crashes in pppm/gpu without local atoms
2021-09-15 17:23:12 -04:00
36b3ee32a4
simplify
2021-09-15 16:46:33 -04:00
1adbd5f667
Fix remaining issues
2021-09-15 14:32:00 -06:00
3caa066c28
simplify/optimize code
2021-09-15 16:23:07 -04:00
a8220a8502
cosmetic changes
2021-09-15 16:08:53 -04:00
7d92d665e8
use explicit scoping when virtual dispatch is not available.
2021-09-15 16:08:17 -04:00
65d8f7f964
use cmath header instead of math.h
2021-09-15 15:25:58 -04:00
1fdba7280e
small optimization
2021-09-15 15:14:52 -04:00
f01681eae7
use symbolic constant
2021-09-15 15:09:58 -04:00
9c301822fd
use nullptr
2021-09-15 14:57:10 -04:00
eb80102871
spelling
2021-09-15 13:51:31 -04:00
c1fa663dd8
Try to improve the pair style hybrid docs
...
This specifically tries to avoid the ambiguous use of "mixing" and
clarify that similar is still different when pair styles are concerned.
See discussion here: https://matsci.org/t/confusion-about-mixing-and-pair-coeff-section/38317/3
2021-09-15 13:48:47 -04:00
c858703156
Remove unused variables
2021-09-14 20:20:09 -06:00
1b91bfbfa1
spelling
2021-09-14 17:17:46 -04:00
b1ebaa298c
build "fat" cuda binaries only with known toolkits
2021-09-14 17:17:38 -04:00
b4acacf5cb
add minimal example and a unit test input
2021-09-14 16:40:42 -04:00
19bc606a20
fix typo
2021-09-14 16:26:38 -04:00
254dcdf665
include formatting updates for the KOKKOS files as well
2021-09-14 16:23:48 -04:00
86578554bb
apply latest formatting conventions (w/o clang format on the .cpp file)
2021-09-14 15:34:28 -04:00
dfe0e313d5
fully integrate acks2/reaxff fix into documentation build
2021-09-14 15:31:36 -04:00
51cfbaa2ef
Remove tabs
2021-09-14 10:56:03 -06:00
3badb14b5a
Whitespace
2021-09-14 10:49:04 -06:00
65a085c067
Improve docs
2021-09-14 10:45:45 -06:00
2b17796d73
Switch max
2021-09-14 10:23:57 -06:00
f9236fbb33
Remove unused variable
2021-09-14 10:06:51 -06:00
15c7792c33
Fix issues with Kokkos package when ranks have zero atoms
2021-09-14 10:02:29 -06:00
b1092cfa4e
detect C++20 standard
2021-09-14 11:56:43 -04:00
fa3c29dda6
Merge branch 'master' of github.com:lammps/lammps into acks2_release
2021-09-14 08:41:23 -06:00
c8170c3388
fix mingw 32-bit vs 64-bit craziness
2021-09-13 10:14:34 -04:00
80f95e5087
step version strings for next patch release
2021-09-13 07:33:34 -04:00
37894d48c6
Revert "simplify building shared libs on windows"
...
This reverts commit fa3429ab02
2021-09-13 07:24:00 -04:00
ede3762e84
detect a few more compilers
2021-09-13 00:29:04 -04:00
0202b1169a
Minor edits to the error message
2021-09-12 23:08:36 -05:00
fa3429ab02
simplify building shared libs on windows
2021-09-12 22:09:18 -04:00
daa39d680c
simplify
2021-09-11 13:43:25 -04:00
585f35235e
add note to README files about age of the example
2021-09-11 13:31:55 -04:00
8cef98fae7
update example to use current library interface. No need to use the namespace.
2021-09-11 13:31:55 -04:00
bd225e2484
update example for dynamically loading LAMMPS with current library API
2021-09-11 13:31:55 -04:00
c394df5658
simplify and remove unused command. more multi-config adjustments
2021-09-11 07:30:18 -04:00
30558c0cd6
convert plugin compilation to also use add_subdirectory() instead of external project
2021-09-11 07:01:48 -04:00
932b3cabda
add missing include (since we not longer include GTest.cmake)
2021-09-11 06:05:29 -04:00
bf360ad50f
explicitly specify build folder for out-of-source subdirectory
2021-09-11 05:59:50 -04:00
68ddab0341
Report multi-config and adjust paths for python unit tests
2021-09-11 05:36:43 -04:00
84c945f7fb
Use multi-config compatible way to integrate googletest for unit testing
2021-09-11 04:50:04 -04:00
1c21560c70
must not clear force array. will segfault in hybrid atom styles
2021-09-10 20:33:49 -04:00
0029ed106b
more adjustments to MDI engine code
2021-09-10 17:59:19 -06:00
f5f49078ee
Add more atom fields in numpy_wrapper and correct csforce size
2021-09-10 15:40:49 -04:00
7bb863a46c
Return None in case of null pointer
2021-09-10 14:55:17 -04:00
e10d89d8c4
Add omega field to numpy_wrapper detection
2021-09-10 14:55:17 -04:00
02da29513e
Merge branch 'master' into programmer-guide-updates
...
# Conflicts:
# doc/lammps.1
2021-09-09 23:34:46 -04:00
0dd35bdb66
Merge pull request #2935 from akohlmey/python-module-fixes-and-tests
...
Python module fixes and tests
2021-09-09 23:31:16 -04:00
b535e58e16
Merge pull request #2929 from stanmoore1/kk_gridcomm
...
Recover Kokkos compilation
2021-09-09 23:30:41 -04:00
551810d388
Merge pull request #2928 from wouterel/enable-dyngroups-fixbondcreate
...
Enable dynamic groups for fix bond/create
2021-09-09 23:27:55 -04:00
3fd4bd1fcd
Merge branch 'python-module-fixes-and-tests' of github.com:akohlmey/lammps into python-module-fixes-and-tests
2021-09-09 23:05:48 -04:00
6ef8c12457
whitespace
2021-09-09 23:05:30 -04:00
e2b44e89a7
Merge pull request #2927 from akohlmey/docs-update
...
Update documentation for the stable release
2021-09-09 23:03:12 -04:00
d09851e695
Improve MPI support in PyLammps
2021-09-09 21:47:08 -04:00
7b1e951916
add unit test for checking properties parsed from info command output
2021-09-09 21:13:09 -04:00
4eeb90d135
fix PyLammps parser issue with parsing info command output
2021-09-09 21:12:28 -04:00
390f9eff39
Merge branch 'master' into kk_gridcomm
2021-09-09 19:17:55 -04:00
1e26fe2d6f
support for reset_box and create_atom commands
2021-09-09 17:16:33 -06:00
150a695b8c
Merge pull request #2925 from akohlmey/collected-small-changes
...
Collected small changes
2021-09-09 19:03:20 -04:00
a954ddac5a
add missing "private"
2021-09-09 18:03:17 -04:00
5e0c754d04
Fixing style issues
2021-09-09 14:17:39 -06:00
31214de51a
Update name
2021-09-09 12:08:09 -06:00
214725d1ee
Use full precision for 1/3
2021-09-09 09:20:24 -06:00
f9a972220e
Fixing data compression in history, small update to model
2021-09-09 09:00:21 -06:00
f9cd6a384b
Add Rocky Linux 8 container definition
2021-09-09 10:45:30 -04:00
8da122c6a4
RHEL8/CentOS8 PowerTools is now powertools
2021-09-09 10:31:17 -04:00
70cbc5e364
Add external field contribution to OPENMP QEq
2021-09-09 08:30:57 -06:00
ccbd24352e
Remove const to work around GCC 7 compiler bug
2021-09-09 08:03:06 -06:00
4e92c68244
allow skipping fix timestep tests when LAMMPS was compiled for static libs
2021-09-08 23:41:31 -04:00
8c3924352d
only check for meminfo[2] on platforms we know to be supported
2021-09-08 23:02:56 -04:00
4f825db5ab
Add external field contribution to OPENMP QEq
2021-09-08 20:54:42 -06:00
826c4e1cd7
Allow fix acks2 to be backwards compatible with old reax name style
2021-09-08 20:40:57 -06:00
0e72aae0a3
Adding examples and misc bug fixes
2021-09-08 18:39:56 -06:00
6bad470dd5
avoid namespace clash in mini-regex library
2021-09-08 20:39:41 -04:00
bc7dfbed3c
add missing #if
2021-09-08 20:00:39 -04:00
9cdb83a24d
support utils::guesspath() also on Windows
2021-09-08 18:17:14 -04:00
5c1fa54750
Update more definition files
2021-09-08 18:11:40 -04:00
7c5a9841f7
more whitespace
2021-09-08 16:01:45 -06:00
165efcdb07
homepage
2021-09-08 15:50:53 -06:00
ede892c83f
whitespace
2021-09-08 15:45:54 -06:00
d5f70ed347
Update container definitions to include PLUMED 2.7.2
2021-09-08 17:43:12 -04:00
9fb29b165d
Update CUDA container definitions to CUDA 11.4
2021-09-08 17:40:48 -04:00
8b9dd6b0c1
Add ACKS2 charge equilibration method to REAXFF and support for electric fields in QEq
2021-09-08 15:06:23 -06:00
40f861097c
Recover Kokkos compilation
2021-09-08 14:41:51 -06:00
b74a32c1e3
Update Singularity definitions to use ROCm 4.3
2021-09-08 16:07:54 -04:00
b87a48e40b
re-apply clang-format
2021-09-08 15:42:15 -04:00
04748779fd
tweak epsilon for portability to FreeBSD
2021-09-08 15:41:43 -04:00
cfa94dfbaf
add support for utils::guesspath() on macos
2021-09-08 15:14:06 -04:00
22f295ffd8
Prevent buffer overflow in TextFileReader::next_dvector()
2021-09-08 10:52:42 -04:00
ebcf0bd6a1
Enable dyanmic groups for fix bond/create
2021-09-08 11:54:50 +02:00
c1dbc110d9
cosmetic changes for consistency
2021-09-07 19:12:59 -04:00
36eb2e30df
correct URL
2021-09-07 19:12:27 -04:00
a4735628f9
document flags that were missing in the man page and the help message
2021-09-07 19:11:51 -04:00
ad39aa85ab
update style guide and requirements/suggestions for contributions
2021-09-07 19:09:35 -04:00
1ae15cf8b7
Merge branch 'master' into programmer-guide-updates
2021-09-07 19:01:21 -04:00
3562c76a66
Update compute angle doc page
2021-09-07 19:00:22 -04:00
194a42b7a5
use more reasonable install prefix when compiling natively on Windows
2021-09-07 15:05:17 -04:00
a16fd25840
minor tweak
2021-09-07 14:26:19 -04:00
55a802afe3
Merge remote-tracking branch 'github/master' into collected-small-changes
2021-09-07 14:20:53 -04:00
9c50420c14
apply clang-format
2021-09-07 14:20:26 -04:00
19e6a9e0d8
Merge pull request #2924 from ohenrich/cg-dna
...
CG-DNA: Documentation Update
2021-09-07 14:12:07 -04:00
9bc8e0998e
must use Python3 version of imported target
2021-09-07 13:34:07 -04:00
909376b14b
Merge branch 'master' into collected-small-changes
2021-09-07 13:32:21 -04:00
b0fa666de4
Merge pull request #2923 from akohlmey/python-finalize-take2
...
Treat calling Py_Finalize() more like MPI_Finalize() and avoid crashes
2021-09-07 11:57:20 -04:00
e070766915
including lmpwindows.h globally from lmptype.h does more harm than good
...
this addresses some (cross) compilation issues locally.
in the long run, this should be addressed by implementing issue #1884
where platform specific functionality is wrapped into a small library
of generic functions adapted for LAMMPS' needs (like utils:: does for
non-portable convenience functions).
2021-09-07 10:39:16 -04:00
3f83c8397d
windows needs io.h for _isatty()
2021-09-07 10:21:00 -04:00
ea34571da1
avoid 32-bit integer overflow
2021-09-07 01:12:24 -04:00
68c842ca84
workaround for MSVC insanity
2021-09-07 00:59:51 -04:00
b2ee7fa3a3
remove stuff that is incompatible with recent MSVC compilers
2021-09-07 00:59:16 -04:00
f5259f0081
correct non-portable code
2021-09-07 00:58:16 -04:00
9a8a4a111f
include utils::binary_search in docs
2021-09-06 18:16:07 -04:00
29505404bc
add unit test for checking the impact of lammps_python_finalize()
2021-09-06 17:42:18 -04:00
63a2882127
apply clang-format
2021-09-06 17:01:22 -04:00
898f8086db
consolidate binary() member functions of Comm and Balance into utils::binary_search()
2021-09-06 16:58:14 -04:00
31a8940ae8
use larger version of FFT grid comm image
2021-09-06 15:50:02 -04:00
bb8b0ef157
add section on PPPM
2021-09-06 12:23:49 -04:00
c1599ffb3e
spelling
2021-09-06 09:52:32 -04:00
d8ba7a3e9a
add discussion of OpenMP parallelization
2021-09-06 09:52:19 -04:00
bb0188ac1a
Corrected linking errors
2021-09-06 13:29:40 +01:00
57cea77fe9
Updated online docu
2021-09-06 11:38:21 +01:00
b132a7eb3a
Updated docu to new oxdna atom_style
2021-09-06 09:47:46 +01:00
a7696d5f00
add -skipruin to help message
2021-09-05 22:44:37 -04:00
6e17446f38
add section about parallelization in the OPENMP package
2021-09-05 22:42:42 -04:00
6e57f4f08f
fix typo
2021-09-05 22:10:00 -04:00
4fc9753a69
break large file into multiple smaller files by section and add toctree
2021-09-05 21:57:03 -04:00
94f03f169f
add section about neighbor list construction
2021-09-05 21:22:39 -04:00
d3af77a876
improve the load imbalance viz
2021-09-05 17:56:58 -04:00
b34a3cec1e
update man page with missing flags and correct URLs
2021-09-05 12:45:29 -04:00
0c2d8ad210
Merge branch 'master' into programmer-guide-updates
2021-09-05 12:45:15 -04:00
805b15f5c4
apply clang-format
2021-09-04 14:19:51 -04:00
e2d8fd58fa
apply clang-format
2021-09-04 14:01:24 -04:00
0286c3e2be
treat Py_Finalize() more like MPI_Finalize()
...
this is done by
- not automatically calling Py_Finalize() when destructing a python interpreter
- adding wrapper functions so that the call to Py_Finalize() is hidden
and skipped if Python support is no included.
- call the Python::finalize() wrapper in main.cpp (similar to the equivalent Kokkos function)
- add a wrapper of that call to the C library interface
2021-09-04 13:53:51 -04:00
91b0ae798a
make VALUELENGTH constant consistent.
2021-09-04 12:41:52 -04:00
59ef1737c6
add communication section
2021-09-03 22:42:01 -04:00
5be4fb86ea
use a more compact image
2021-09-03 21:05:16 -04:00
801cd647c3
Merge pull request #2919 from akohlmey/collected-small-changes
...
Collected small changes and fixes
2021-09-03 19:03:29 -04:00
6193ebaba7
remove earlier USER-MDI files
2021-09-03 16:01:16 -06:00
481d6128c7
Merge branch 'master' into mdi-expand
2021-09-03 15:51:34 -06:00
a8a97962d2
more changes for AIMD testing
2021-09-03 15:50:17 -06:00
a98ded7722
adapt section about domain decomposition from paper
2021-09-03 16:59:41 -04:00
6290054e52
forgot to update lammps.cpp
2021-09-03 11:37:03 -04:00
f768b701ee
add -skiprun command line flag that sets a timeout so that run and minimizations loops are skipped
2021-09-03 11:21:42 -04:00
75cb6fc51b
added support for LAMMPS as MDI AIMD driver
2021-09-02 17:52:10 -06:00
6cf2aa4fbb
update github workflow doc
2021-09-02 16:29:20 -04:00
0d765a824e
integrate file with description of include file conventions
2021-09-02 15:03:19 -04:00
5851692527
mention when testing may be added
2021-09-02 14:25:10 -04:00
d3447008a1
update contribution guidelines for github
2021-09-02 14:24:57 -04:00
bca9157405
Correct fix bond/swap doc page
2021-09-02 14:10:43 -04:00
ca7bab7e41
refactor style guide and integrate text from issue
2021-09-01 22:16:26 -04:00
72d92ac9e8
correct and clarify Python compatibility
2021-09-01 22:03:12 -04:00
c186b24292
avoid segfaults due to uninitialized data
2021-09-01 21:47:39 -04:00
495f424a67
apply clang-format to pair_lj_cut.cpp so it can serve as example
2021-09-01 20:08:06 -04:00
e6d7a544e2
remove whitespace from comma separated arguments to variable functions
2021-09-01 14:02:35 -04:00
af33724a38
update and reorder the description of the process for submitting contributions
2021-09-01 12:15:52 -04:00
d301c2a71f
Merge branch 'master' into programmer-guide-updates
2021-09-01 10:08:51 -04:00
9085662e2b
Merge pull request #2899 from akohlmey/next_patch_release
...
Step version strings for the next patch release
2021-08-31 19:43:41 -04:00
7943cb2067
Merge branch 'master' into programmer-guide-updates
2021-08-31 18:27:25 -04:00
66008a519b
Merge pull request #2913 from akohlmey/last-minute-fixes
...
Some last minute fixes for the next patch release
2021-08-31 18:24:17 -04:00
8db2d64f11
Updates to support ROCm 4.3 in GPU package
2021-08-31 17:56:01 -04:00
000b4c5fda
integrate fix ttm/grid properly into the documentation
2021-08-31 16:20:21 -04:00
c567f33cc1
apply spelling fixes and update formatting a little
2021-08-31 16:17:03 -04:00
ae2f0ef18d
whitespace
2021-08-31 16:05:11 -04:00
e9ef26c2be
Merge branch 'master' into last-minute-fixes
2021-08-31 16:03:50 -04:00
6448f44fa5
Merge pull request #2914 from rbberger/doc_updates
...
Minor documentation updates
2021-08-31 15:59:34 -04:00
08eb3345af
silence some compiler warnings
2021-08-31 15:11:46 -04:00
6b243845c0
update HIP preset for CMake
2021-08-31 15:11:37 -04:00
b8ed4b28b3
add test for fix adapt with hybrid pair
2021-08-31 14:28:09 -04:00
c66a51bca1
fix bug in fix adapt: reinit must be called for the top-level pair/bond style
2021-08-31 14:23:13 -04:00
888d6fd9b4
small update
2021-08-31 14:20:52 -04:00
191e4671b6
Add section about how to output YAML or JSON
2021-08-31 11:28:13 -04:00
de0aa1e97a
Fixup ttm doc page
2021-08-31 11:28:08 -04:00
8f600f6db7
Merge pull request #2912 from stanmoore1/kk_foward_comm_array
...
Add missing Kokkos sync-to-host to fix false-positive warning
2021-08-31 10:21:31 -04:00
55f20288b1
Merge branch 'master' into mdi-expand
2021-08-30 16:52:49 -06:00
16c063cba5
Fix OPENMP install script properly remove -DLMP_OPENMP from Makefile.packages
2021-08-30 18:39:24 -04:00
c76949e0f0
Merge pull request #2902 from lammps/fix-ttm-grid
...
Add fix ttm/grid and refactor grid communication to make it globally available.
2021-08-30 17:43:39 -04:00
5b42d5f302
Fix compile issue
2021-08-30 15:21:24 -06:00
1703cd4ca2
Whitespace
2021-08-30 14:57:59 -06:00
0e639a2c5b
Add missing Kokkos sync to host
2021-08-30 14:52:26 -06:00
66fc0438a8
Merge branch 'master' into fix-ttm-grid
...
# Conflicts:
# doc/src/pair_snap.rst
2021-08-30 16:37:51 -04:00
328e730c8f
Merge branch 'master' into mdi-expand
2021-08-30 14:31:29 -06:00
25a6c59cea
Merge pull request #2900 from stanmoore1/kk_bugfixes
...
Fix issues in KOKKOS package
2021-08-30 15:28:41 -04:00
00c3c5cf06
Port changes from #2903 to Kokkos
2021-08-30 12:43:07 -06:00
2de482f825
Merge pull request #2911 from akohlmey/fix-gpu-package-issues
...
Fix minor GPU package issues for the stable release
2021-08-30 13:45:23 -04:00
6635b402c6
Merge pull request #2910 from wmbrownIntel/intel-mm-scale-fix
...
Fix (the fix) for _MM_SCALE preprocessor defines for future Intel compilers
2021-08-30 13:10:21 -04:00
22ce955065
Merge pull request #2909 from wmbrownIntel/born_coul_wolf_nofast
...
Override any OpenCL fast math JIT settings for born/coul/wolf{/cs}/gpu…
2021-08-30 11:51:04 -04:00
d9c1a299bf
Merge pull request #2908 from jrgissing/bond-react-fixes
...
Bond/react: memory leak
2021-08-30 11:23:26 -04:00
284ed98fb8
fix spelling error and reformat paragraph
2021-08-29 22:08:49 -04:00
5d03028028
Merge branch 'master' into kk_bugfixes
2021-08-29 22:07:40 -04:00
5257b8d280
split off the programming/submission style guide to a separate file
2021-08-29 22:00:05 -04:00
afc65993d0
clarify
2021-08-29 21:43:13 -04:00
be3348be86
update for clang-format
2021-08-29 21:42:59 -04:00
518b2c24f2
use the term 'website' consistently (and not also 'web site')
2021-08-29 21:42:49 -04:00
664a07a3fe
disallow GPU neighbor list with hybrid pair styles (which has still problems)
2021-08-29 17:57:30 -04:00
39d8b239ff
don't report bogus timings
2021-08-29 17:56:47 -04:00
05eba8e484
move patch release date to august 31st
2021-08-29 16:33:14 -04:00
fb72e00081
Fix (the fix) for _MM_SCALE preprocessor defines for future Intel compilers.
2021-08-28 17:18:05 -07:00
89556f0bcb
Override any OpenCL fast math JIT settings for born/coul/wolf{/cs}/gpu to resolve numerical deviations seen with some OpenCL implementations.
2021-08-28 17:01:58 -07:00
653f6f994f
Merge branch 'lammps:master' into bond-react-fixes
2021-08-28 16:05:59 -04:00
cddac395c6
some more cleanup
2021-08-28 07:52:14 -04:00
993826989c
modernize fix ttm/mod implementation and align with fix ttm
2021-08-28 07:44:06 -04:00
1e37595055
pretty
2021-08-28 07:43:18 -04:00
f49b94e126
update docs. mention support for comments in electron temperature grid files
2021-08-28 07:42:55 -04:00
da1fb924bb
modernize code some more. avoid string pointer magic.
2021-08-28 05:43:39 -04:00
e6a45c1fa7
refactor grid data file reader. support descriptive comment(s) and metadata
2021-08-27 23:23:12 -04:00
90d95466c2
add UNITS: metadata
2021-08-27 23:21:04 -04:00
6be84b72a8
simplify and plug memory leak with file output
2021-08-27 21:10:05 -04:00
c779798f3f
properly disable clang-format processing
2021-08-27 20:34:46 -04:00
59a6c08a43
correct spelling
2021-08-27 20:32:42 -04:00
9c2b96286f
print GPU available info only when GPU package is included
2021-08-27 20:32:22 -04:00
28b6649f0c
whitespace
2021-08-27 20:31:58 -04:00
cf33f0bb96
silence compiler warnings, remove dead code, and do some reformatting
2021-08-27 20:22:29 -04:00
a66f3dfbdd
Merge branch 'master' into fix-ttm-grid
2021-08-27 19:56:42 -04:00
e93ae9ba12
apply clang-format
2021-08-27 19:56:33 -04:00
c513fc8784
update pppm/gpu to use the refactored GridComm class
2021-08-27 19:52:39 -04:00
90f82a8ef1
memory leak
2021-08-27 17:03:11 -04:00
4d1a6cbd73
Merge pull request #2904 from lammps/memory-null
...
force all memory methods to return nullptr if requested size <= 0
2021-08-27 16:59:04 -04:00
3e058b734b
Merge pull request #2887 from jrgissing/bond-react-fixes
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Bond react fixes
2021-08-27 16:58:33 -04:00
cc69431dd3
Merge pull request #2897 from dxhisboy/master
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Correcting non-fdotr Virial tensor computation for interlayer potentials
2021-08-27 16:54:56 -04:00
1795e1530f
Merge pull request #2896 from akohlmey/collected-small-changes
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Collected changes and updates for the next patch release
2021-08-27 15:58:05 -04:00
a58e4fc876
whitespace
2021-08-27 14:59:26 -04:00
4eef3eaac6
Merge branch 'master' into collected-small-changes
2021-08-27 14:58:42 -04:00
4be33df8fb
relax force test epsilon values a little for cross-platform tests
2021-08-27 14:57:31 -04:00
e363b4aeff
Merge pull request #2905 from weinbe2/fea-snap-large-system
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Kokkos SNAP large system optimizations and cleanup
2021-08-27 14:23:37 -04:00
66da0ebada
adjust INTEL pppm files for new GridComm interface
2021-08-27 11:01:27 -06:00
9658d1d983
Bump up the default chunksize in SNAP and update the docs
2021-08-27 12:34:19 -04:00
6ab951fedc
only change functions known to break with zero-length
2021-08-27 10:28:40 -06:00
2387e12464
Merge pull request #2893 from lammps/doc-intro-updates
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Update Intro section of LAMMPS Manual for stable release
2021-08-27 12:09:10 -04:00
d2984d2615
Merge branch 'master' into BPM
2021-08-27 10:04:04 -06:00
0879484827
sync OPENMP package with new GridComm syntax
2021-08-27 09:48:35 -06:00
4089d7757d
error->one to error->all corrections
2021-08-27 11:24:04 -04:00
bb720626e3
Adding files for BPM
2021-08-27 09:22:56 -06:00
89b4cc9498
Remove comment
2021-08-27 11:03:54 -04:00
aa9f337ef5
Small tweak to docs
2021-08-27 10:47:11 -04:00
27cabbf734
Add missing variable
2021-08-27 10:38:47 -04:00
ecba2d8489
Update doc page
2021-08-27 10:33:18 -04:00
1970ede534
Add user-settable threshold for extra parallelism
2021-08-27 10:22:10 -04:00
cfaa3040ed
add a comment explaining the restriction to C and H elements in AIREBO/REBO
2021-08-27 10:02:53 -04:00
7ac2c0c66e
refactor custom constraint
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evaluates per-atom variables once, and correctly communicates values to ghosts
2021-08-26 23:00:15 -04:00
8c96f1a14b
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2021-08-26 22:56:08 -04:00
a686ce33c6
Added less-parallelism-higher-perf paths to recursive polynomial routines. Fixed qSNAP memory coalescing issue. Various modularity improvements.
2021-08-26 22:55:07 -04:00
bbb3f35aa3
"int64_t" is defined in stdint.h; must use "long" in OpenCL kernels instead
2021-08-26 22:46:08 -04:00
fc6b17b82a
improve whitespace handling
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previously, spaces inside of custom 'rxn' functions could cause issues
2021-08-26 22:28:44 -04:00
42a3a7d10f
Merge branch 'master' into collected-small-changes
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# Conflicts:
# src/fix_property_atom.cpp
2021-08-26 21:14:23 -04:00
a587f67423
Merge pull request #2903 from lammps/fix-property-tweak
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Fix property/atom tweak
2021-08-26 20:07:13 -04:00
a519dc3e9a
make DIELECTRIC package use of GridComm compatible with new version
2021-08-26 16:33:39 -06:00
21b017368b
force all memory methods to return nullptr if requested size <= 0
2021-08-26 15:43:12 -06:00
ab8c9851b2
change style to styles to remove override of fix->style string
2021-08-26 15:20:52 -06:00
a85f125ee7
whitespace
2021-08-26 16:58:14 -04:00
892a18c3f6
Merge branch 'master' into fix-ttm-grid
2021-08-26 16:57:19 -04:00
f63d0202be
Rely on auto_sync in verlet setup
2021-08-26 14:54:48 -06:00
6fea5dd316
avoid creating empty per atom position arrays for enforcing pbc for dumps
2021-08-26 16:16:30 -04:00
16d73c86ba
adjust example TTM input scripts
2021-08-26 13:37:00 -06:00
ddbb8f1aa6
Remove unnecessary data tranfer in fix_nve_sphere_kokkos
2021-08-26 13:36:32 -06:00
49b0623d6b
Fix issue with Kokkos granular and pair/only on
2021-08-26 13:26:46 -06:00
62fcaedd33
update example log files
2021-08-26 13:25:46 -06:00
7b3e7d3d3a
allow for command-line setting of initial temp
2021-08-26 11:52:07 -06:00
d38549e05f
Update ancient Kokkos Arch in Makefile.kokkos_cuda_mpi
2021-08-26 11:03:57 -06:00
beffa0d1a1
remove old fix ttm
2021-08-26 10:19:56 -06:00
cbe27096b3
final tweaks
2021-08-26 10:19:22 -06:00
0fb03072b1
restart bug fix in new fix ttm/grid
2021-08-26 10:08:34 -06:00
be98d0bbd9
Fix memory issue in fix_nvt_sllod_kokkos
2021-08-26 09:36:16 -06:00
0e8facdcbb
Makefile.kokkos: fix (standard_in) 1: syntax error (kokkos PR4173)
2021-08-26 08:58:58 -06:00
c1ca58ba82
Merge branch 'master' of github.com:lammps/lammps into kk_bugfixes
2021-08-26 08:21:39 -06:00
7e5782a81b
Fix deallocation issue in pair_lj_charmm_coul_charmm_kokkos
2021-08-26 08:21:16 -06:00
45854bab0c
step version strings for next patch release
2021-08-26 07:46:24 -04:00
0d8c58db02
synchronize DomainOMP::pbc() code with Domain::pbc()
2021-08-26 07:41:57 -04:00
a7f4bbffcf
avoid segfault when trying to apply (strict) pbc or convert to/from fractional coordinates on an MPI rank without atoms
2021-08-26 07:10:47 -04:00
84896fc7d4
add building micelle2d.x
2021-08-26 06:36:27 -04:00
e20d66ac19
avoid module name conflict
2021-08-26 06:36:17 -04:00
49a81d6fba
silence compiler warnings
2021-08-26 06:30:16 -04:00
c7357d5731
Merge remote-tracking branch 'github/master' into collected-small-changes
2021-08-26 05:30:50 -04:00
6fcd4c0e30
Merge remote-tracking branch 'github/master' into doc-intro-updates
2021-08-26 05:29:53 -04:00
e3af1544f1
Merge pull request #2804 from Vsevak/tip4p_fix_types
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Fix atom types handling in the tip4p/gpu kernels
2021-08-26 01:08:19 -04:00
1d33bd1264
whitespace
2021-08-26 01:05:25 -04:00
484f2f4c95
must exclude two more folders from whitespace checking
2021-08-26 01:05:14 -04:00
acf80f5c89
Merge branch 'master' into doc-intro-updates
2021-08-26 01:03:25 -04:00
2845269bdb
use MBytes consistently
2021-08-26 01:00:08 -04:00
0aded3931b
convert to Fortran 2003
2021-08-26 00:37:25 -04:00
4b707b8684
small tweak
2021-08-26 00:35:43 -04:00
f13fe138cc
apply clang-format
2021-08-26 00:35:31 -04:00
9dd1dcab30
remove call to non-portable FDATE() function (a GNU Fortran extension)
2021-08-25 23:56:20 -04:00
61855c5058
apply whitespace checking/fixing also to free-format Fortran files
2021-08-25 23:46:48 -04:00
45e599cb33
modernize Fortran
2021-08-25 23:42:07 -04:00
fe4ec9d1ea
select Fortran 2003 as standard for compiling bundled Fortran code
2021-08-25 23:36:12 -04:00
8468d89ec8
tweak epsilon for passing test on macOS
2021-08-25 23:31:53 -04:00
5361af7082
notes on reducing disk space requirements when building LAMMPS from source
2021-08-25 22:51:21 -04:00
c3083785b7
list some more features
2021-08-25 22:02:51 -04:00
a2d77593bb
fix typo
2021-08-25 22:01:42 -04:00
4846d8283e
convert chain.f to fortran 90+ style free format file chain.f90
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this is to maintain compatibility with some newer fortran compilers
that do not support legacy style fortran by default anymore.
2021-08-25 18:38:08 -04:00
a0dfae9876
more debugging of restarts
2021-08-25 16:28:40 -06:00
abd4a6cfa3
remove calls to Modify::end_of_step() during the full_energy() functions
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the fixes atom/swap, gcmc, widom, and charge_regulation would call
Modify::end_of_step() in order to make certain that all energy contributions
to the total energy are properly tallied. However, this is no longer
true and it causes lots of unexpected problems, since fixes like
fix ave/time, fix store/state, fix print and many more are called at
the wrong time during a timestep and possibly multiple times which can
lead to very unexpected and incorrect results. fix atc and fix colvars
are currently the only fixes that signal that they contribute to the
global energy *and* run during Modify::end_of_step(). However, they
do not perform any actions related to the global energy in those calls.
2021-08-25 16:41:25 -04:00
51d4e91086
Merge pull request #2882 from CTCMS-UQ/SLLOD-Kokkos
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Add Kokkos accelerated styles for shear flow simulations (SLLOD)
2021-08-25 14:44:50 -04:00
ae94a60d4a
more debugging
2021-08-25 12:42:47 -06:00
1c0ac4adb7
correct citation string
2021-08-25 07:57:16 -04:00
cc98f9b1e6
add unit test
2021-08-25 07:42:37 -04:00
ce0f1478cb
correct stress tally to give results consistent with fdotr
2021-08-25 07:42:37 -04:00
b55673f0a6
add unit test
2021-08-25 07:42:37 -04:00
3a8faa8966
correct stress tally
2021-08-25 07:42:37 -04:00
b1e40a05bc
disallow newton pair off
2021-08-25 07:42:37 -04:00
61b9d4a19f
update epsilon
2021-08-25 07:42:37 -04:00
d9579c4ecd
Changed the virial computation method for pair/ilp/graphene/hbn and pair/kolmogorov/crespi/full from fk x rkj to fk x rki
2021-08-25 14:55:28 +08:00
caaea35c64
Merge pull request #2 from akohlmey/SLLOD-Kokkos
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Update pull request to current upstream and resolve merge conflict
2021-08-25 15:29:23 +10:00
0a07f4eae0
spelling issues
2021-08-24 23:48:17 -04:00
c6145e029a
update features list
2021-08-24 23:46:06 -04:00
026d7bd112
update description of development model and release cycles
2021-08-24 23:26:22 -04:00
e4e08972f8
update overview text
2021-08-24 23:02:49 -04:00
a1e0341d8c
detect and update output for OpenMP version 5.1
2021-08-24 23:01:43 -04:00
7ddfa382dc
enable and process pair style table with clang-format
2021-08-24 22:27:11 -04:00
d79c42ac41
improve error messages for incorrect/inconsistent table data
2021-08-24 22:26:59 -04:00
5ba6fee94e
Merge branch 'master' into SLLOD-Kokkos
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# Conflicts:
# src/KOKKOS/compute_temp_kokkos.h
2021-08-24 21:48:03 -04:00
857d0d255d
change OFFSET to correct value
2021-08-24 17:25:53 -06:00
30fc6e3790
consistency between fix TTM variants
2021-08-24 17:17:54 -06:00
ccbf39d2c9
add unit tests using pppm and ewald with a tilted box
2021-08-24 16:00:26 -04:00
dfc03bd107
avoid 32bit integer overflow on 64-bit storage sizes
2021-08-24 15:49:41 -04:00
588f821ac8
add support for text output and restart output
2021-08-24 13:46:29 -06:00
2150fb7413
adjust epsilon for portability
2021-08-24 15:41:42 -04:00
2239130798
randomize bilayer data file positions to make interlayer tests more reliable
2021-08-24 15:41:28 -04:00
eaf5e08542
detect invalid use and silence compiler warnings
2021-08-24 14:27:20 -04:00
25d9d5dfff
Merge pull request #2895 from rbberger/python_coverage_fix
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Use .coveragerc to configure Python coverage reporting
2021-08-24 14:07:23 -04:00
3d34ee5087
Merge branch 'master' into fix-ttm-grid
2021-08-24 11:34:27 -06:00
8dd2428294
Merge pull request #2891 from akohlmey/collected-small-changes
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Collected small changes and bug fixes
2021-08-24 13:34:20 -04:00
0bb26ff296
make fix qeq/reaxff/kk consistent with REAXFF package version
2021-08-24 12:13:06 -04:00
a26da031aa
Use .coveragerc to configure Python coverage reporting
2021-08-24 11:27:30 -04:00
af14e3227d
skip folders/files in lib with downloaded content
2021-08-24 10:32:10 -04:00
1c7cc42846
fix parallel programming bug in interlayer pair styles
2021-08-24 10:28:57 -04:00
862cb43fa9
Enable unittest for GPU lj/cut/tip4p/long
2021-08-24 17:07:51 +03:00
3dc142c0b0
Added fix_nvt_sllod_kokkos and compute_temp_deform_kokkos to Install.sh
2021-08-24 16:23:05 +10:00
d34083dd54
update false positives
2021-08-23 23:25:25 -04:00
4fb67c0cc6
mention pre-C++-11 version as C++-98 version.
2021-08-23 23:25:16 -04:00
d561fe3457
clarify license terms description and reduce redundancy. mention LGPL verison
2021-08-23 23:24:47 -04:00
897dfdfb19
some updates to authors list
2021-08-23 23:24:06 -04:00
e6455c2153
fix spelling errors
2021-08-23 23:12:23 -04:00
3bce886ab7
workaround style checker issue
2021-08-23 22:16:39 -04:00
49c9f4597f
apply clang-format
2021-08-23 21:46:54 -04:00
72679f6127
Merge branch 'master' into collected-small-changes
2021-08-23 21:44:21 -04:00
c84ebd1c93
update docs for build options for development
2021-08-23 21:43:49 -04:00
d72d8fa938
we require python 3.5 or later
2021-08-23 21:43:06 -04:00
1ee1471b56
fix spelling errors
2021-08-23 21:42:48 -04:00
43261c3a4f
Merge pull request #2885 from lammps/grid-adjust
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Grid adjust
2021-08-23 21:39:35 -04:00
7b3755bcf4
remove redundant '// clang-format off' marker
2021-08-23 21:17:04 -04:00
7fe6e95d3a
make clang-format processing verbose to show progress
2021-08-23 21:11:05 -04:00
1bd6e56369
simplify code using utils::strdup()
2021-08-23 21:06:56 -04:00
9a19a814e4
apply clang-format to packages
2021-08-23 21:06:33 -04:00
686f41731f
disable applying clang-format to all "style" classes in the KOKKOS package (for now)
2021-08-23 20:55:41 -04:00
8f71979ba1
update formatting in src folder with clang-format
2021-08-23 20:46:09 -04:00
cb19806020
update ReaxFF reference data due to use of more precise constants in fix qeq/reax
2021-08-23 20:34:44 -04:00
d44edeb32e
make clang-format custom targets in CMake similar to the ones in GNU make
2021-08-23 18:36:44 -04:00
6b6e63f77f
avoid redundant defines
2021-08-23 18:36:07 -04:00
fec77e49bd
add clang-format commands to Makefile
2021-08-23 18:22:12 -04:00
2cfc629388
reformat REAXFF headers with clang-format
2021-08-23 18:21:47 -04:00
86739c46d9
Merge pull request #2889 from jrgissing/property/atom-group-bugfix
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property/atom group bugfix
2021-08-23 18:20:53 -04:00
6bc8da05b9
reformat unittest tree with clang-format
2021-08-23 17:06:30 -04:00
4e715da2f3
Merge branch 'grid-adjust' of github.com:lammps/lammps into grid-adjust
2021-08-23 14:57:12 -06:00
0dea376e1a
restart support for TTM fixes
2021-08-23 14:56:33 -06:00
d640cd6838
Merge pull request #2890 from stanmoore1/kk_deform
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Fix bug with v remap option in Kokkos fix deform
2021-08-23 16:41:23 -04:00
3a3f32d3a8
Merge branch 'master' into tip4p_fix_types
2021-08-23 16:43:55 +03:00
0f8b331d8f
enable check/fix scripts in traditional makefile
2021-08-22 22:47:55 -04:00
0c7cf3cdaa
protect against use with Python 2.x, use full absolute directory path internally
2021-08-22 22:47:09 -04:00
bc91d05857
fix typo
2021-08-22 20:46:58 -04:00
92b5b159e5
replace tabs and remove trailing whitespace in lib folder with updated script
2021-08-22 20:45:24 -04:00
30821b37e5
replace tabs
2021-08-22 20:43:27 -04:00
0c4752b858
add support to check for tabs as whitespace errors including option to fix
2021-08-22 20:43:08 -04:00
607e75f984
remove tabs
2021-08-22 19:42:55 -04:00
8b2e3ad3ee
add unit tests for fix addtorque
2021-08-22 14:27:38 -04:00
bb852f2393
skip some more aliased styles
2021-08-22 14:21:31 -04:00
bb5a11b330
add timestepping unit tests for atom style sphere
2021-08-22 14:16:50 -04:00
bf618b3128
support tests for integrators with dipoles and extended particles
2021-08-22 12:44:02 -04:00
d9538a4745
skip some aliases when checking for missing force style tests
2021-08-22 11:55:37 -04:00
db887b4d7a
add unit test for angle style dipole
2021-08-22 11:49:29 -04:00
433ece22ec
add unit test for dihedral style spherical
2021-08-22 11:28:32 -04:00
9b4317335a
reorder includes
2021-08-22 11:28:04 -04:00
9ce9d36ac5
correct package designations for styles in the EXTRA-MOLECULES package
2021-08-22 11:27:48 -04:00
403ee3a85f
apply clang-format
2021-08-22 11:13:34 -04:00
ce71e45db0
plug memory leak
2021-08-22 11:11:32 -04:00
eeff288541
tweak settings to pass OpenCL GPU tests in mixed precision
2021-08-22 10:50:28 -04:00
dd670bab66
update dipole data file with randomized dipole orientations
2021-08-21 20:50:16 -04:00
46e4e1b60e
add kspace tests with dipoles
2021-08-21 20:45:25 -04:00
1b72cf01a9
add unit test inputs for pair styles with point dipoles
2021-08-21 20:31:18 -04:00
384330aff2
update/correct extract function
2021-08-21 20:31:02 -04:00
1c7bf82930
initialize scale array
2021-08-21 20:30:38 -04:00
4032c6da98
fix restart bug
2021-08-21 20:30:15 -04:00
09b0809d75
add template files for testing dipolar pair styles and kspace styles
2021-08-21 19:18:21 -04:00
3083e6f4cb
make ewald/disp/dipole an alias for ewald/disp for more obvious choices for users
2021-08-21 15:56:46 -04:00
2afa00ae66
pretty
2021-08-21 15:18:54 -04:00
ad5cc694dc
correctly check for and enable/disable dipole and dispersion support
2021-08-21 15:18:44 -04:00
d8f0cec031
updates/bug-fixes to parallel fix ttm/grid
2021-08-20 16:57:20 -06:00
7c61e96f0b
Fix bug with v remap option in Kokkos fix deform
2021-08-20 16:08:06 -06:00
1a81a94dfb
fix up whitespace issues (remove tabs, trailing whitespace)
2021-08-20 15:00:19 -04:00
29fe006e46
fix issue in non-perioidic msm.cpp to allow it to work with any grid partitioning
2021-08-20 12:43:47 -06:00
1eb506002b
Merge pull request #2888 from lammps/sticker-bonds
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Sticker bonds
2021-08-20 14:28:57 -04:00
8735555e00
1 liner fix for PR #2342
2021-08-20 14:17:05 -04:00
fcc6cc628e
fix whitespace
2021-08-20 13:47:24 -04:00
55605167ab
Merge pull request #135 from lammps/master
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rebase
2021-08-20 10:26:57 -04:00
92d9efa1af
Merge branch 'master' into gpu-newton-pair-on
2021-08-19 23:25:49 -05:00
904a2ef910
Reverted the default setting of newton_pair off for FixGPU; newton_pair can be set to be on via command-line options of package gpu
2021-08-19 22:54:06 -05:00
7a8afb6eef
add fragment count to molecule file output
2021-08-19 20:10:26 -04:00
f0a041799f
add original TTM for testing
2021-08-19 16:55:57 -06:00
95bae4d78c
sync with current master
2021-08-19 16:09:41 -06:00
9577db6578
Merge branch 'master' into fix-ttm-grid
2021-08-19 16:00:56 -06:00
3404920e98
Merge pull request #2342 from lammps/fix-property-array
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Enable fix property/atom to create custom arrays
2021-08-19 17:33:55 -04:00
b0197e0607
Merge branch 'master' into grid-adjust
2021-08-19 17:29:51 -04:00
d4de26f6ef
fix whitespace issues
2021-08-19 17:28:48 -04:00
537f0eed8e
Merge pull request #2886 from akohlmey/pair-coul-exclude
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Add a pair style coul/exclude for removing excluded coulomb interactions
2021-08-19 17:25:57 -04:00
f7c8b0c88b
address spellcheck issues
2021-08-19 17:00:46 -04:00
bc6e805c99
fix doc formatting issues
2021-08-19 16:53:03 -04:00
e1c1c663c4
correction to doc page
2021-08-19 14:21:15 -06:00
845cebaab1
Add comment
2021-08-19 14:02:57 -06:00
eebbbe9f73
support a second usage model with fix bond/swap
2021-08-19 14:01:06 -06:00
7d0c052425
Fix deallocation with Kokkos
2021-08-19 14:00:37 -06:00
9470a0eeb6
clarified doc pages for fix property/atom and read_data
2021-08-19 11:34:25 -06:00
8aeaa82909
improve error message
2021-08-19 11:08:04 -04:00
1c67561be8
Merge branch 'fix-property-array' of github.com:lammps/lammps into fix-property-array
2021-08-19 09:00:51 -06:00
7046b75861
remove evil tabs
2021-08-19 10:06:34 -04:00
11b4ae641f
add unit test for pair style coul/exclude
2021-08-19 05:46:12 -04:00
23231118d1
add a couple explanatory comments
2021-08-19 05:29:54 -04:00
093fbfd4b5
add documentation for pair style coul/exclude
2021-08-19 05:25:36 -04:00
8b680d43e5
add pair style coul/exclude for use with kspace style scafacos
2021-08-19 05:00:52 -04:00
7d0cdea282
allow using kspace_style scafacos for molecular systems under certain conditions
2021-08-19 05:00:11 -04:00
4ce71fd767
pretty
2021-08-19 04:23:44 -04:00
89de4eb7c4
make sure that coul/exclude special neighbors are always flagged
2021-08-19 04:23:26 -04:00
3a7a5d13ef
apply clang-format
2021-08-19 04:22:55 -04:00
e149c2fe10
function no longer needs to be public
2021-08-19 04:20:12 -04:00
5c46c6d3a6
update unit test for per-atom arrays and vectors
2021-08-18 22:51:09 -04:00
c53875421b
fix read_data bug
2021-08-18 22:50:42 -04:00
b942c4d122
fix data corruption bug affecting write_data
2021-08-18 22:31:46 -04:00
04b0f98a5f
fix logic bug in utils::expand_args()
2021-08-18 20:26:51 -04:00
d9f3745eff
pretty
2021-08-18 20:26:01 -04:00
546c9a109e
fix uninitialized data bug
2021-08-18 20:25:49 -04:00
5e6079c2fc
Merge branch 'fix-property-array' of github.com:lammps/lammps into fix-property-array
2021-08-18 16:54:02 -06:00
b19a211d70
update code
2021-08-18 18:06:21 -04:00
f6874af7e5
pretty
2021-08-18 18:05:36 -04:00
104fa4624e
correct utils::expand_args()
2021-08-18 18:04:44 -04:00
4e16df9a21
remove prototype for early version of partition_grid method
2021-08-18 15:56:52 -06:00
2119b59d97
code documentation tweaks
2021-08-18 15:49:23 -06:00
1c5bdadcfb
small alteration to code that assigns grid pts to procs
2021-08-18 15:43:54 -06:00
dbfba25e04
Merge pull request #1 from akohlmey/SLLOD-Kokkos
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Update to current upstream, fix a few cosmetic issues, use alternative to str(n)cmp()
2021-08-19 07:29:51 +10:00
cf25a586bd
debugging merged version
2021-08-18 13:07:49 -06:00
de61b3a547
update utils::expand_args
2021-08-18 14:35:27 -04:00
0a99d338f2
update argument parsing
2021-08-18 14:35:02 -04:00
1e37d1ad7f
pretty
2021-08-18 14:34:03 -04:00
40fcfef35b
create_atoms serial build bugfix
2021-08-18 14:17:04 -04:00
355dd5db9b
include 2 use cases in doc page
2021-08-18 11:55:47 -06:00
e08c4abb4b
whitespace fixes
2021-08-18 13:06:00 -04:00
4fed16fe8b
pretty
2021-08-18 13:00:40 -04:00
f9b32f0eef
use ArgInfo class to process references to custom vectors and arrays
2021-08-18 13:00:32 -04:00
300fee0437
add some more checks for typical string matches for references to fixes and alike
2021-08-18 12:59:56 -04:00
c50abed92b
recover compilation
2021-08-18 12:59:31 -04:00
c6819e30cf
simplify
2021-08-18 12:58:39 -04:00
c57da0661d
update package name
2021-08-18 12:49:16 -04:00
6db856fd68
refactor dynamic constraints array
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cannot use memory->* routines with non-primitive types
2021-08-18 11:24:32 -04:00
08e71eee6d
corrections to recent large reformatting PR
2021-08-18 10:30:35 -04:00
f30434659e
Merge branch 'master' into SLLOD-Kokkos
2021-08-18 05:55:34 -04:00
511ac49949
reformat, minor cosmetic changes
2021-08-18 05:53:23 -04:00
ee5273fbb1
Merge pull request #2879 from akohlmey/interlayer-refactor
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Unit tests, bugfixes and file reader refactor for some INTERLAYER pair styles
2021-08-18 04:54:13 -04:00
4876e0cbb6
Changed URLs in the headers to point to the new LAMMPS site.
2021-08-18 17:37:00 +10:00
2e59b5c4de
Fixed whitespace errors and removed some extraneous comments.
2021-08-18 15:23:46 +10:00
b385c85440
Refactored PPPMKokkos::setup_triclinic kernel indexing to be more consistent the rest of the codebase.
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This commit "fixes" the temporary solution using Kokkos::MDRange in commit a98b8bee88.
2021-08-18 15:23:46 +10:00
d7f9f9fead
Updated documentation to include Kokkos accelerated NEMD styles.
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Also tidied up header files and attribution to fit LAMMPS coding style.
2021-08-18 15:23:46 +10:00
8ae9d51466
Fixed memory issues in ComputeTempDeformKokkos.
2021-08-18 15:23:46 +10:00
8945d81be3
Added Kokkos accelerated SLLOD thermostat (nvt/sllod/kk).
2021-08-18 15:23:46 +10:00
e7ba4179a7
Added Kokkos-enabled version of compute temp/deform.
2021-08-18 15:23:46 +10:00
e400e5b6f7
Fixed bug in PPPMKokkos::setup_triclinic for MPI calculations.
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This fix should probably be considered a temporary fix - it relies on a
3-dimensional Kokkos range which seems to be disfavoured in the rest of
LAMMPS' codebase.
2021-08-18 15:23:46 +10:00
cfd9cf625d
Initial draft of Kokkos acclerated PPPM routines for triclinic cells.
2021-08-18 15:23:46 +10:00
a1dd2c7655
move inline functions from header to cpp file
2021-08-17 22:37:47 -04:00
f470964393
apply clang-format
2021-08-17 22:35:05 -04:00
96b563dffc
move common taper functions for interlayer potentials to separate header
2021-08-17 22:34:32 -04:00
bbb8adf656
update kolmogorov/crespi/z and lebedeva/z pair styles to use new file reader and unit conversion
2021-08-17 21:56:17 -04:00
661ec1acc3
fix typo
2021-08-17 21:55:22 -04:00
bb3c4797b3
update some more interlayer potential files
2021-08-17 21:55:12 -04:00
c758d224e0
Merge pull request #2881 from stanmoore1/kk_cmake
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Fix issue when building Kokkos with CMake
2021-08-17 21:12:18 -04:00
62564b0a5c
cmake: only use LMP_KOKKOS define in build interface
2021-08-17 15:52:09 -06:00
58a86412ec
recover compilation
2021-08-17 16:26:59 -04:00
6dafbd2fbe
support metal2real unit conversion
2021-08-17 16:20:00 -04:00
0906e94207
small fixes
2021-08-17 16:13:01 -04:00
e5a194d8d4
sync Kokkos changes with current master
2021-08-17 14:12:47 -06:00
2bf9fa91db
more changes to merge with current master
2021-08-17 14:03:58 -06:00
05bd545cd3
flush tiny stresses to zero to avoid false positives when testing
2021-08-17 15:10:46 -04:00
4f9941e18d
support metal2real unit conversion in pair style drip
2021-08-17 15:05:23 -04:00
6d53cd1986
refactor potential file reader in pair style drip
2021-08-17 14:50:34 -04:00
96280dc185
Merge branch 'master' into fix-property-array
2021-08-17 12:19:27 -06:00
8b8cce4399
add unit test YAML file for DRIP pair style
2021-08-17 14:12:50 -04:00
e6af1eecb8
resolved merge conflicts with master
2021-08-17 11:55:33 -06:00
82871ca515
Merge branch 'master' into interlayer-refactor
2021-08-17 13:25:13 -04:00
527240e941
Merge pull request #2880 from akohlmey/arginfo_update
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Collected bugfixes and small update for ArgInfo class
2021-08-17 13:24:02 -04:00
d321202908
Add change from @junghans
2021-08-17 10:27:50 -06:00
9fa255b3ff
Fix issue when building Kokkos with CMake
2021-08-17 10:09:39 -06:00
18cc43a560
extend ArgInfo class to also accept "i2_name" and "d2_name"
2021-08-17 12:04:58 -04:00
95a2041df3
reformat potential file headers to comply with LAMMPS' conventions
2021-08-17 10:48:51 -04:00
01503535f4
remove unused symlinks
2021-08-17 10:48:09 -04:00
6ccdeafa78
reformat with clang-format
2021-08-17 10:22:42 -04:00
42fadf55cf
fix typos
2021-08-17 10:05:58 -04:00
0dbcb5dd66
replace #define with constrexpr for better compiler error reports on integer constants
2021-08-17 09:42:08 -04:00
f24054f7b3
test utils::fgets_trunc() with buffer size of exactly the length of string
2021-08-17 09:41:19 -04:00
e91185869d
fix bug in utils::fgets_trunc(). closes #2878
2021-08-17 09:38:12 -04:00
a901427ee0
Merge pull request #2876 from akohlmey/address-lgtm-issues
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Address code quality issues flagged by lgtm.com
2021-08-17 08:53:09 -04:00
dad9942bb8
Merge pull request #2869 from akohlmey/modify-add-returns-index
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Have add_fix(), replace_fix() and add_compute() in Modify return class instance and refactor/simplify code
2021-08-16 15:44:16 -04:00
436d200a9a
refactor file reader code
2021-08-16 15:29:43 -04:00
9e559de601
pretty
2021-08-16 15:21:51 -04:00
56a74bbe3d
refactor file reader code
2021-08-16 15:21:38 -04:00
6f46ac57b9
plug small memory leak in pppm/gpu
2021-08-16 13:50:43 -04:00
7b873ffc0b
add unit tests for ilp/graphene/hbn and kolmogorov/crespi/full
2021-08-15 19:07:57 -04:00
832f6499ed
add suppression for OpenMP in newer GCC compilers
2021-08-15 18:39:42 -04:00
7efbdb24cc
fix memory leak
2021-08-15 18:39:21 -04:00
e15c51c7e1
correctly use global cutoff instead of per-type-pair cutoffs
2021-08-15 17:44:22 -04:00
cba8e8237a
avoid memory leak with MPI-IO
2021-08-13 06:25:21 -04:00
eaedd9ad48
fix output issues
2021-08-13 06:24:57 -04:00
9cb8a6205e
apply "no" argument correctly
2021-08-13 06:24:39 -04:00
a765cf373a
update formatting
2021-08-13 06:24:22 -04:00
f08c249d40
don't hide parameter with local variable
2021-08-13 06:23:46 -04:00
1abce8e821
remove dead code
2021-08-13 05:51:05 -04:00
3bfb235070
fix memory leak
2021-08-13 05:50:53 -04:00
3e99e24f41
make calls to virtual functions from constructors explicit
2021-08-13 05:50:44 -04:00
0928c912c0
fix memory leaks and reformat
2021-08-13 05:50:03 -04:00
26c681cf73
update for changes in base class
2021-08-09 16:28:19 -04:00
c8b7b8271d
add missing dependency
2021-08-09 16:28:03 -04:00
1d98388129
Merge branch 'modify-add-returns-index' of github.com:akohlmey/lammps into modify-add-returns-index
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# Conflicts:
# src/GRANULAR/pair_gran_hooke_history.cpp
2021-08-09 16:00:48 -04:00
64d7b73d7c
Update region.rst
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Include a few lines describing the "ellipsoid" option
2021-08-09 07:54:41 +02:00
35aeadfdd4
implementation of a "ellipsoidal" region option
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Based on the code of the region_sphere and the code described in https://www.geometrictools.com/Documentation/DistancePointEllipseEllipsoid.pdf , an option for axis-aligned ellipsoidal regions has been implemented
2021-08-08 17:01:51 +02:00
fe008b93d7
remove obsolete line
2021-08-07 10:33:26 -04:00
42625a82d1
simplify more code for creating fix instances using the improved APIs
2021-08-07 10:09:06 -04:00
68c15ebf04
refactor/simplify code due to changes in Modify
2021-08-07 10:09:06 -04:00
f23b04f9b6
update Eigen3 to support the latest stable release 3.3.9
2021-08-07 10:09:06 -04:00
88604328f5
workaround for PGI compilers
2021-08-07 10:09:06 -04:00
156790df2c
apply changes to modify class
2021-08-07 10:08:58 -04:00
0b30f57812
streamline code by using changes in Modify class
2021-08-07 10:04:49 -04:00
0d9344c9e2
simplify
2021-08-07 10:04:49 -04:00
01f5b7e095
when creating or replacing a fix or compute, return pointer to new instance
2021-08-07 10:04:49 -04:00
e789bf8925
use temporary vector container to avoid explicit delete[]
2021-08-07 10:04:49 -04:00
0123f9290f
update Eigen3 to support the latest stable release 3.3.9
2021-08-06 18:59:56 -04:00
06371629d6
workaround for PGI compilers
2021-08-06 18:44:42 -04:00
c84e7a5040
Merge pull request #2868 from akohlmey/collected-small-changes
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Collected small changes
2021-08-06 18:35:29 -04:00
29bf3acd9e
apply changes to modify class
2021-08-06 18:34:32 -04:00
03f9ef7de9
add unique identifier to the history fix so the gran/*/history styles can be used multiple times with pair style hybrid
2021-08-06 15:34:43 -04:00
e9e6cdca1d
using GPU package is not compatible with fix qeq variants
2021-08-06 14:22:48 -04:00
e29bd3d157
update defines from -DLMP_USER-<PKG> to -DLMP_<PKG> for consistency
2021-08-06 14:07:43 -04:00
93465f98d8
improve error message
2021-08-06 13:55:53 -04:00
aeef6e6773
reformat with clang-format
2021-08-06 13:55:53 -04:00
8baaed5724
use const std::string & instead of const char *. avoid exception in sfree()
2021-08-06 13:55:53 -04:00
a7d05cff09
streamline code by using changes in Modify class
2021-08-06 13:39:02 -04:00
b16bca2f45
simplify
2021-08-06 13:39:02 -04:00
06f6434b38
when creating or replacing a fix or compute, return pointer to new instance
2021-08-06 13:39:02 -04:00
5861577a72
use temporary vector container to avoid explicit delete[]
2021-08-06 13:39:02 -04:00
912a1fc561
Merge pull request #2865 from rbberger/python_update
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Python package update
2021-08-06 13:37:14 -04:00
eece77eecf
Merge pull request #2866 from Colvars/colvars-update
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Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
2021-08-06 11:20:46 -04:00
eb52f7c290
Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
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Also include PDF copy of the manual forgotten in previous PR.
2021-08-06 10:32:37 -04:00
b9fa4e1db2
avoid memory leaks on specifying keywords multiple times
2021-08-06 10:22:31 -04:00
f3a03d6a84
Catch ValueError instead of base exception
2021-08-06 10:21:40 -04:00
0904ffa813
Enabled newton pair on for gpu pair styles
2021-08-06 01:11:31 -05:00
53b94ac94d
Allow fix python/move to load class from __main__
2021-08-05 18:10:19 -04:00
980b817f3f
Allow python pair style to load class from __main__
2021-08-05 18:03:05 -04:00
5045595ad8
Merge pull request #2861 from akohlmey/fix-valgrind-issues
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Address issues flagged by running unit tests with valgrind and sanitizer instrumentation
2021-08-05 16:07:57 -04:00
3fc97e9466
Merge branch 'fix-valgrind-issues' of github.com:akohlmey/lammps into fix-valgrind-issues
2021-08-05 12:20:33 -04:00
5295bb5109
fix refactoring bugs
2021-08-05 12:20:20 -04:00
177e60830e
Merge branch 'master' into fix-valgrind-issues
2021-08-05 12:11:59 -04:00
c23dc22a3e
Merge pull request #2862 from akohlmey/intel-set_ntypes-consistent
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Make ForceConst::set_ntypes() more robust and fix related bug in pair style sw/intel
2021-08-05 11:50:50 -04:00
50c476b6af
Merge pull request #2863 from Colvars/colvars-update
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Update Colvars library to version 2021-08-03
2021-08-05 11:16:51 -04:00
9a60ab0c23
correctly insert atoms/molecules any nfreq timesteps even with multiple run
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this changes the computation of "next_reneighbor" so that it is based
on "nfirst" which is set during the constructor of the class.
This still maintains the property that the first deposit attempt is not
done during setup, but on the next step.
2021-08-04 21:32:10 -04:00
bc6dfdb656
update readme
2021-08-04 17:44:56 -04:00
08a727d510
make some class members temporaries since they don't need to persist
2021-08-04 17:19:23 -04:00
2e7b3081a1
fix bug enumerating output when using python invoke with multiple functions
2021-08-04 17:07:16 -04:00
bb9c0630f8
suppressions for readline function calls from lammps-shell
2021-08-04 17:06:02 -04:00
0ea6406bb9
Merge branch 'fix-valgrind-issues' of github.com:akohlmey/lammps into fix-valgrind-issues
2021-08-04 12:25:12 -04:00
c4442206d4
add special case for heredocs in utils::split_words() to avoid segfaults
2021-08-04 12:03:34 -04:00
7068f3e77b
add a few more test cases for testing utils::split_words()
2021-08-04 12:02:55 -04:00
2a9be42758
Update Colvars to version 2021-08-03
2021-08-03 18:03:18 -04:00
0938bc8999
update docs for hybrid style updates
2021-08-02 21:53:31 -04:00
c1c31c6b04
may not call memmove() on a null pointer, even if 'n' is 0.
2021-08-02 21:35:25 -04:00
04c7e7543e
use friend statement instead of (incorrect) cast to give access to protected class member
2021-08-02 21:34:30 -04:00
37ca6a8e0b
make handling of reference to Memory class in ForceConst class more robust
2021-08-02 15:50:44 -04:00
b7be9415de
fix segfault with pair style sw/intel
2021-08-02 15:49:26 -04:00
53050a0429
add suppressions for FlexiBLAS on Fedora
2021-08-02 15:45:32 -04:00
a3bfcc68ef
add libgomp suppression for newer GCC
2021-08-02 15:45:15 -04:00
848db31a77
reformat with clang-format
2021-08-02 15:25:01 -04:00
8aa39a6c40
make compatible with CLASS2
2021-08-02 15:23:16 -04:00
45858be1b6
avoid uninitialized data access for hybrid styles with OPENMP
2021-08-02 15:22:21 -04:00
50e8d7c36b
Merge pull request #2859 from akohlmey/next_patch_release
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Step version strings for next patch release
2021-07-30 16:40:10 -04:00
29eee29241
Merge pull request #2860 from evoyiatzis/patch-1
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fixing compute gyration/shape indexing bug
2021-07-30 15:45:51 -04:00
db4fcd7537
update package dependency
2021-07-30 15:24:23 -04:00
75214f1eeb
Merge pull request #2857 from akohlmey/update-formatted-output
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Modernize formatted output and string handling in packages
2021-07-30 12:50:25 -04:00
82936b1e4f
fixing indexing bug
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The gyration_tensor[4] element as computed by "compute gyration" corresponds to the xz component of the gyration tensor and the gyration_tensor[5] to the yz component. The code assumed that gyration_tensor[4] corresponds to the yz component and the gyration_tensor[5] to the xz.
2021-07-30 18:14:44 +02:00
f5b82ea3ef
Merge pull request #2856 from akohlmey/collected-small-changes
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Collected small changes and fixes
2021-07-30 11:36:40 -04:00
5f401da462
correct bug in derived CG-DNA FENE bond classes and optimize code
2021-07-30 10:48:15 -04:00
9dc662973e
step version strings for next patch release
2021-07-29 21:18:03 -04:00
d211bbc0d6
expand ArgInfo class unit tests
2021-07-29 20:58:02 -04:00
cb32bb972b
fix bugs in ArgInfo class
2021-07-29 20:57:42 -04:00
6b20da7549
update lammps shell test to use a fix that is always available
2021-07-29 17:48:35 -04:00
4710b7bc9e
modernize and simplify code to find best matching restart file
2021-07-29 17:25:42 -04:00
5cdf55937d
move pair style tracker to a better location
2021-07-29 17:17:06 -04:00
ca2abd22be
remove unused file
2021-07-29 17:08:16 -04:00
a80829bd79
avoid compilation error
2021-07-29 16:14:52 -04:00
a6d66c3518
update .gitignore
2021-07-29 16:07:23 -04:00
33905fd689
fix one more KOKKOS package installation dependency
2021-07-29 16:07:14 -04:00
246b70ae46
update codeowners list
2021-07-29 15:56:21 -04:00
c49a533ad9
reformat, simplify, add reference log files
2021-07-29 15:40:43 -04:00
b108da3e5c
simplify format handling
2021-07-29 15:26:29 -04:00
dcff3d70e0
simplify fix instance creation
2021-07-29 15:18:58 -04:00
520109bda0
simplify
2021-07-29 14:55:22 -04:00
ebe5e6c024
reformat
2021-07-29 14:44:15 -04:00
5b6b6b8767
simplify and use utils functions
2021-07-29 14:33:41 -04:00
b5830b672a
simplify logging code
2021-07-29 14:18:38 -04:00
9cf790a2fe
simplify and use fmtlib
2021-07-29 14:09:49 -04:00
3a968b81ad
update
2021-07-29 13:59:59 -04:00
b4e3795913
fix copy-n-paste error
2021-07-29 13:58:27 -04:00
43b3c97cc0
add unit tests for scafacos kspace solver (skipping p3m)
2021-07-29 13:57:02 -04:00
2a1177fa92
reformat with clang-format
2021-07-29 13:29:56 -04:00
508798ab2b
simplify code, make use of fmtlib and utils
2021-07-29 13:25:06 -04:00
a9271b6d9a
replace temporary char buffer with using fmtlib
2021-07-29 12:36:50 -04:00
211d6636b4
modernize and simplify code to find best matching restart file
2021-07-29 12:09:55 -04:00
5f2b947b99
fix typo
2021-07-29 11:48:24 -04:00
1e48be92aa
avoid segfault
2021-07-28 21:50:20 -04:00
b9ab0eb607
fix broken symbolic links
2021-07-28 21:32:52 -04:00
bf6c982b49
skip using neighbor list load balancing weight when using KOKKOS with GPU
2021-07-28 21:30:06 -04:00
b8d3297659
add missing package dependency
2021-07-28 18:45:09 -04:00
d33863839e
update pair style installation dependencies
2021-07-28 18:37:59 -04:00
294ac76f41
forgot to move pair style beck to EXTRA-PAIR
2021-07-28 18:33:33 -04:00
6fcfbb7793
add missing dependency for conventional build
2021-07-28 18:18:54 -04:00
3a5d3fc541
fix compilation
2021-07-28 18:11:59 -04:00
218467b385
use fabs() instead of abs() on floating point number
2021-07-28 16:17:12 -04:00
9a4bc8eda1
apply citation reminder
2021-07-28 16:16:54 -04:00
f46e1c98f7
removed dead code and make consistent with non-OPENMP version
2021-07-28 16:16:42 -04:00
32be894ae2
silence compiler warnings
2021-07-28 16:16:22 -04:00
d5ba7b2578
Propagate variable rename
2021-07-22 08:10:42 -06:00
6d3a5a6eb9
Port custom changes to atom_kokkos
2021-07-21 17:05:56 -06:00
94ce07b2de
Merge branch 'lammps:master' into tip4p_fix_types
2021-07-21 14:09:39 +03:00
0867299adb
Fixed format error bug in third order tensor print
2021-07-19 11:54:49 -07:00
2a21c4b29f
add sticker-bond support to fix bond/swap
2021-07-02 11:46:25 -06:00
b3fed4d1a9
update regex to match with updated fmtlib
2021-06-24 10:13:52 -04:00
f8ebcff078
changes to mdi_engine
2021-06-22 09:36:40 -06:00
79cbafd3c7
Reapply LAMMPS changes to fmtlib
2021-06-21 11:55:41 -04:00
f7752da97f
Update fmtlib to 8.0.0
2021-06-21 11:50:57 -04:00
d982d153f8
Fix conditions for correct results on other types
2021-06-18 18:26:53 +03:00
8fef6a10dd
Fix atom types handling in the tip4p/gpu kernels
2021-06-18 00:52:23 +03:00
8761ae65a3
Merge branch 'master' into mdi-expand
2021-06-10 09:50:23 -06:00
26127e1fa0
more changes to fix ttm/grid
2021-06-09 15:49:20 -06:00
456b81417d
first version of fix ttm/grid
2021-06-09 09:03:50 -06:00
41d7038c1e
trial versions of new mdi_engine and fix_mdi_engine
2021-05-27 17:24:29 -06:00
3f42e97405
remove old printf workarounds
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Change-Id: I46a66538c886c9961977e0433e900bc91d92c4f2
2021-05-17 13:01:33 -04:00
f44f983b3b
Restore the previous atom/teamsizes for ComputeHFunctor
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Change-Id: I292280efd3d5d0d6a7486c1e9798ef4f632d9df4
2021-05-17 10:11:11 -04:00
abcac33c63
cleanup rebase errors
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Change-Id: Ib8e255fefcb17ff91bc0bfdfcb98e56d3387b9b2
2021-05-17 10:11:06 -04:00
ad1c1637d4
cleanup & the various vector-wise SPMVs
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Change-Id: Id29ec4e1968ddfccf26335a0f41a8652db33b89b
2021-05-14 15:58:54 -04:00
fc2eff64bb
remove hard coded launchbounds / teamsizes for compat. w/ Kokkos LB=256 default
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Change-Id: I7dcd26eee32b3fc049549ae380ffaf85423eed2e
2021-05-14 15:58:53 -04:00
1d6f24f0df
hide additional printf
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Change-Id: I200c85013b9d0163847194ad4b18ac33af65a823
2021-05-14 15:58:53 -04:00
f629de84f9
cleanup printf workarounds
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Change-Id: Id9960f545fa0159d6c38392711b6ac584715d3d9
2021-05-14 15:58:52 -04:00
18466fb05b
legal stuff
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Change-Id: I5ab375285fdea9b20d8174a582aca9e78bf0f8a3
2021-05-14 15:58:52 -04:00
844dea3e1b
temporary fix for EAM
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Change-Id: Ia39bf1b4c3adcbadf0b1bde39d6817f44869946b
2021-05-14 15:58:49 -04:00
dff61617fe
Change LaunchBounds to 64 for TagPairTersoffComputeHalf
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Change-Id: I7fb8871c30acab4fc98654df618af6e786bc6244
2021-05-14 15:56:41 -04:00
926a037cba
thread group dimension adjustment for FixQEqReaxKokkosComputeHFunctor
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Change-Id: I7a62632a2403cdc3491777b090a1cb48d3a7591b
2021-05-14 15:56:41 -04:00
20a4d295e5
Optimized Torsion with blocking, flag needed: HIP_OPT_TORSION_PREVIEW_BLOCKING and HIP_OPT_TORSION_PREVIEW
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Change-Id: I667ded58fc2c8b8253ea655e9fdf9b5cc3f737e4
2021-05-14 15:56:40 -04:00
e3a2eb0713
merging FC_K and DFC calculation, activate with flag HIP_OPT_MERGE_FC_K_DFC
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Change-Id: I68440f02c79f8cc2cc4788dac2447cfa58f0b54a
2021-05-14 15:56:40 -04:00
1856b669be
Apply patch from Stan to fix race in Reax
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Change-Id: I372b5951cf0f5e3343c3c6283f01cf0b8c889a56
2021-05-14 15:56:38 -04:00
56a1cd12e5
fix for multi-GPU failure for reax
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Change-Id: Ia261ff2f1158de2bd6ac2d83a15080f6b6253128
2021-05-14 15:55:54 -04:00
6b568aff7a
adding merged ters_gijk and ters_dgijk, flag AMD_OPT_MERGE_GIJK_DGIJK is required
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Change-Id: I8d9f433ecb38f8bd3cc72d8f2bc1642f753c7270
2021-05-14 15:48:23 -04:00
bb1b269cf8
optimization for Matvec2 and Matvec3, need -DHIP_OPT_SPMV
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Change-Id: Ia40d2f27c38dd0e500cb7f8f02908be8b1f52a63
2021-05-14 15:48:22 -04:00
ce96898331
Add CUDA variants for hip calls
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Change-Id: I5d169ee1563c915c0768675d2ec2e7a1774bc969
2021-05-14 15:48:22 -04:00
c25ccfdb98
adding optimization in tersoff
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Change-Id: I21d2bfe5181b3395430ec4b9949894c61b61587a
2021-05-14 15:48:21 -04:00
9a48ae0c06
optimized pair_eam_kokkos. need more work to avoid large shared memory allocations
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Change-Id: I1c23b0e10fdfa932b17ad764cf5a1d024b43d80a
2021-05-14 15:48:19 -04:00
f732e633ec
Avoid loading data twice if itype==jtype
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Change-Id: I430a761555bdbd93e3ca1b298c962b75b91175aa
2021-05-14 15:36:49 -04:00
4d9c2a97d2
replacing pow(a,1/3) with the cbrt(a) call - optimization is activated using the existing HIP_OPT_USE_LESS_MATH flag
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Change-Id: Ic6670c54f453127e948036e5c9a88154b5af6e68
2021-05-14 15:36:48 -04:00
33346ae961
change teamsize
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Change-Id: Ie7666e8ec8192fced098fe744f318aaf25365f5a
2021-05-14 15:36:48 -04:00
117995c2fc
updated PairReaxBuildListsHalf use -DPairReaxBuildListsHalf_BLOCKING to activate
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Change-Id: I8d1ec5ed9ec7042e9cdc53da825c07d3bc44e2bd
2021-05-14 15:36:47 -04:00
20dc9576d9
updated PairReaxComputeLJCoulomb. use -DPairReaxComputeLJCoulomb_BLOCKING to activate
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Change-Id: Idef8dafc79216368bffbf90547016afca5f32a43
2021-05-14 15:36:47 -04:00
c6efc01a7f
Revised Torsion kernel with -DHIP_PRINTF_WORKAROUND
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Change-Id: Iffee0dfbd507f1a0b873a86a8b1c71ffcb5b344e
2021-05-14 15:36:46 -04:00
397b098ac0
fix memory leak in counter allocs
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Change-Id: Ia45e3e5d1ce92b4fd537a031181bf719a243a8b1
2021-05-14 15:36:46 -04:00
775167ecd9
apply torsion preview to all cases
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Change-Id: Icc619a89fc4af98735c0fbbeb52d655dc60b10fd
2021-05-14 15:36:45 -04:00
b0f638d937
fix bug where preview counters were being used in reduce (but was iterating over inum)
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Change-Id: Ic60f40d5adcc6505ced83c7d5694813e161f73ac
2021-05-14 15:36:44 -04:00
fee6d98201
Catch missing HIP_OPT_TORSION_PREVIEW parts in kernel
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Change-Id: Ib0ed83940bcd870a9531d596422956741e4f735a
2021-05-14 15:36:44 -04:00
dabb120096
fix undefined nnz w/ HIP_OPT_TORSION_PREVIEW off
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Change-Id: Ie11be12a98ba48b9134537b5389b2b9300dc2be8
2021-05-14 15:36:43 -04:00
e2de1c5e8f
Make the torsion preview optional
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- enabled with -DHIP_OPT_TORSION_PREVIEW
- reuse hiphostmalloced' memory when possible
Change-Id: I25fbe7b06cffe1b6047048cd71f78bbf54d73774
2021-05-14 15:36:43 -04:00
de0341121f
test templated workaround for reduce bug
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Change-Id: I858e0446c453b1d194b8c653d388c14aec450c63
2021-05-14 15:36:42 -04:00
44d036f486
fixing a bug in Torsion preview
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Change-Id: I8f119d695f5ea3d9faa27843f87e54d3e0e086e9
2021-05-14 15:35:55 -04:00
3b3ef7e9a5
Minor optimization of tersoff kernel TagPairTersoffComputeShortNeigh
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Change-Id: If70e524b6bf30d3bcdacf732cf3aab897e2843d4
2021-05-14 15:35:54 -04:00
705d314879
revised version of TagPairTersoffComputeHalf; requires defining define USE_COMBINED_JJ_LLOPS_TERSOFF
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Change-Id: I45717fb9af210ef8bedffc2d228b60a7ec0368ef
2021-05-14 15:35:53 -04:00
bcd4ab036c
Implement forward device pack/unpack for fix/qeq/reax
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Change-Id: I690a63f7ef467d3f1b39784ac97cab54ed7fb248
2021-05-14 15:35:51 -04:00
14b388aea9
Revised torsion kernel with preprocessing
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- preprocess the interaction lists to reduce divergence
Change-Id: I842cc424963333308c5aaaeb202c8f41f07a55f5
2021-05-14 15:19:54 -04:00
51b3cb640f
Adding support to reducing number of mat lib. calls (-DHIP_OPT_USE_LESS_MATH)
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Change-Id: I44d140cf1b9421ccb3277b0592d3100b76c6eae9
2021-05-14 15:19:53 -04:00
5b8e138d0f
add more missing launch bounds
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Change-Id: Ifc4c94963b3c1c26455d32598f366af84c73883e
2021-05-14 15:19:53 -04:00
99db66d485
Add launch bounds patches to avoid SWDEV-252521
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Change-Id: I389b5db94c14f1e5bc90c1848bfc0e038774ee19
2021-05-14 15:19:52 -04:00
0423a3e537
Merge branch 'master' into OptimizedDynamicalMatrix
2021-04-27 13:36:34 -07:00
b982542ae6
update indentation to 2 blanks. avoid "hanging else" constructs.
2021-04-21 14:56:26 -04:00
598e82d236
small cosmetic changes
2021-04-21 12:16:43 -04:00
1ee8de42d9
minor cleanups and simplifications using fmtlib
2021-04-21 12:08:37 -04:00
cd236776de
Merge branch 'master' into OptimizedDynamicalMatrix
2021-04-21 11:46:36 -04:00
0fc73c9d67
support for centroid virial stress in rigid/small
2021-04-19 16:18:06 +09:00
b904d256cd
implement keeping track of geometric center in rigid/small
2021-04-20 14:06:53 +09:00
ac7c5592d7
add centroid virial tally function in preparation for rigid/small support
2021-12-06 17:45:49 +09:00
0ed44e0b81
Remove leftover merge conflict string
2021-04-16 18:05:20 -07:00
535384b235
Finish updating to current master
2021-04-16 17:14:55 -07:00
a3e204a99d
Simplified reset_extra_dof
2021-03-17 16:23:04 +10:00
97f90f1146
Cleaned up math for clarity
2021-03-17 15:56:48 +10:00
471cfa8ac3
Fixed inconsistent default extra_dof value
2021-03-17 14:31:17 +10:00
aad0a9a0f3
Updated documentation to reflect changes in compute_temp_profile
2021-03-17 14:14:33 +10:00
b1b7f7a248
Fixed treatment of DoF when streaming velocity not subtracted in some dimensions
2021-03-17 13:59:16 +10:00
5e4dd5321c
Using local dof and tfactor for compute_array to prevent overwrite
2021-03-17 13:38:51 +10:00
c643389ec4
Treat extra_dof as system-wide in compute_array for consistency, and include fix_dof
2021-03-17 11:38:07 +10:00
ab07427339
Corrected default extra_dof
2021-03-17 09:52:05 +10:00
fed47b9ffc
Merged 1/29/2021 master and fixed merge conflicts
2021-01-29 12:33:17 -08:00
b2f96d92df
remove print statement
2021-01-13 10:31:03 -07:00
fc79280548
other USER-DPD uses of dname vs new dvname
2021-01-12 12:37:50 -07:00
6f4d657061
enable pair table/rx for new custom vector syntax
2021-01-12 12:28:06 -07:00
386fe6158a
edits to doc pages, including per-atom variables
2021-01-12 09:07:23 -07:00
bddd26ba6c
additional changes needed to merge with current master
2021-01-11 17:26:00 -07:00
0b14770468
merge with current master
2021-01-11 16:13:33 -07:00
3ff8d8bf41
update centroid/stress/atom compute to correctly handle fixes with CENTROID_AVAIL
2020-12-14 19:41:34 +09:00
8520a71646
centroid stress support in shake (and rattle)
2020-12-14 19:31:38 +09:00
abba1204a8
support for centroid stress in fixes
2021-12-06 17:12:39 +09:00
3a9796d9b3
add flags for centroid stress
2020-12-14 19:29:18 +09:00
64257393b9
remove custom vector usage from USER-DPD:fix_rx.cpp
2020-09-09 10:21:59 -06:00
76725731fd
changes in package files to match new find_custom() syntax
2020-09-08 13:48:41 -06:00
d1442b0538
enable per-atom custom arrays in addition to vectors
2020-09-04 11:33:49 -06:00
e57b391d40
Add threading capability to both commands
2020-07-20 11:35:10 -07:00
5abddfe68d
Fixed nitpicky details, updated output, moved mass out of folded check
2020-07-19 19:12:01 -07:00
9011cfaa96
Added neighbors of neighbors list indexed by tag and return tags.
2020-07-18 02:27:31 -07:00
dd6e5df356
Remove print statement
2020-07-16 14:16:12 -07:00
7133311d2d
Change Allreduce to fit bigint
2020-07-16 14:13:45 -07:00
999dd13924
Draft of force calculation reduction through neighbor lists
2020-07-15 12:45:46 -07:00
4b656b3961
Check if atom is part of group before computing forces
2020-07-14 15:47:14 -07:00
35f3aeb15a
Merge branch 'master' into OptimizedDynamicalMatrix
2020-07-13 19:48:16 -07:00
d368c46ea9
Merge remote-tracking branch 'origin'
2020-07-13 19:46:44 -07:00
57d674cc81
Merge branch 'master' into OptimizedDynamicalMatrix
2020-07-13 19:46:05 -07:00
3a4652613d
Add folded option, change ballistico to eskm, add post force modifications
2020-07-13 19:43:24 -07:00
255cc85b32
Merge branch 'master' of https://github.com/charlessievers/lammps
2019-09-04 16:18:57 -07:00
2e2b1b3687
Initial commit...
2019-05-02 15:17:31 +01:00
65399a6193
Merge branch 'OptimizedDynamicalMatrix' of https://github.com/charlessievers/lammps
2019-02-01 20:51:08 -08:00
